diff --git a/Gradle Project for Netbeans/build.gradle b/Gradle Project for Netbeans/build.gradle
new file mode 100644
index 0000000..b823b75
--- /dev/null
+++ b/Gradle Project for Netbeans/build.gradle
@@ -0,0 +1,80 @@
+plugins {
+ id 'java'
+ id 'application'
+}
+
+group 'de.whs.ibci'
+version '1.0'
+
+defaultTasks 'run'
+
+repositories {
+ mavenCentral()
+}
+
+dependencies {
+ implementation 'org.openscience.cdk:cdk-bundle:2.3'
+ implementation 'org.apache.pdfbox:pdfbox:2.0.17'
+ implementation 'commons-logging:commons-logging:1.2'
+ implementation 'org.apache.xmlgraphics:batik-svggen:1.13'
+ implementation 'org.apache.xmlgraphics:batik-svg-dom:1.13'
+ implementation group: 'org.openjfx', name: 'javafx-base', version: '14', classifier: 'win'
+ implementation group: 'org.openjfx', name: 'javafx-controls', version: '14', classifier: 'win'
+ implementation group: 'org.openjfx', name: 'javafx-swing', version: '14', classifier: 'win'
+ implementation group: 'org.openjfx', name: 'javafx-graphics', version: '14', classifier: 'win'
+ implementation group: 'org.openjfx', name: 'javafx-base', version: '14', classifier: 'mac'
+ implementation group: 'org.openjfx', name: 'javafx-controls', version: '14', classifier: 'mac'
+ implementation group: 'org.openjfx', name: 'javafx-swing', version: '14', classifier: 'mac'
+ implementation group: 'org.openjfx', name: 'javafx-graphics', version: '14', classifier: 'mac'
+ implementation group: 'org.openjfx', name: 'javafx-base', version: '14', classifier: 'linux'
+ implementation group: 'org.openjfx', name: 'javafx-controls', version: '14', classifier: 'linux'
+ implementation group: 'org.openjfx', name: 'javafx-swing', version: '14', classifier: 'linux'
+ implementation group: 'org.openjfx', name: 'javafx-graphics', version: '14', classifier: 'linux'
+ testImplementation 'junit:junit:4.12'
+ testImplementation 'org.openscience.cdk:cdk-bundle:2.3'
+}
+
+java {
+ sourceCompatibility = JavaVersion.VERSION_11
+ targetCompatibility = JavaVersion.VERSION_11
+}
+
+mainClassName = 'de.whs.ibci.msc.main.Main'
+
+application {
+ mainClass = mainClassName
+}
+
+jar {
+ manifest {
+ attributes 'Main-Class': mainClassName
+ }
+}
+
+test {
+ useJUnit()
+ maxHeapSize = '1G'
+}
+
+task resourceCopy(type: Copy, description: "Copy the MSC resources") {
+ from "$projectDir/src/main/java/resources"
+ into "$buildDir/classes/java/main/resources"
+}
+
+compileJava.configure {
+ dependsOn resourceCopy
+}
+
+task fatJar(type: Jar, description: "Creates an executable jar archive that includes all dependencies of the MSC") {
+ manifest {
+ attributes 'Implementation-Title': 'MSC Fat Jar File',
+ 'Implementation-Version': archiveVersion,
+ 'Main-Class': mainClassName
+ }
+ archiveAppendix = "fat"
+ from sourceSets.main.output
+ dependsOn configurations.runtimeClasspath
+ from {
+ configurations.runtimeClasspath.findAll { it.name.endsWith('jar') }.collect { zipTree(it) }
+ }
+}
\ No newline at end of file
diff --git a/Gradle Project for Netbeans/gradle/wrapper/gradle-wrapper.jar b/Gradle Project for Netbeans/gradle/wrapper/gradle-wrapper.jar
new file mode 100644
index 0000000..62d4c05
Binary files /dev/null and b/Gradle Project for Netbeans/gradle/wrapper/gradle-wrapper.jar differ
diff --git a/Gradle Project for Netbeans/gradle/wrapper/gradle-wrapper.properties b/Gradle Project for Netbeans/gradle/wrapper/gradle-wrapper.properties
new file mode 100644
index 0000000..4c5803d
--- /dev/null
+++ b/Gradle Project for Netbeans/gradle/wrapper/gradle-wrapper.properties
@@ -0,0 +1,5 @@
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-6.4-bin.zip
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
diff --git a/Gradle Project for Netbeans/gradlew b/Gradle Project for Netbeans/gradlew
new file mode 100644
index 0000000..fbd7c51
--- /dev/null
+++ b/Gradle Project for Netbeans/gradlew
@@ -0,0 +1,185 @@
+#!/usr/bin/env sh
+
+#
+# Copyright 2015 the original author or authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+##############################################################################
+##
+## Gradle start up script for UN*X
+##
+##############################################################################
+
+# Attempt to set APP_HOME
+# Resolve links: $0 may be a link
+PRG="$0"
+# Need this for relative symlinks.
+while [ -h "$PRG" ] ; do
+ ls=`ls -ld "$PRG"`
+ link=`expr "$ls" : '.*-> \(.*\)$'`
+ if expr "$link" : '/.*' > /dev/null; then
+ PRG="$link"
+ else
+ PRG=`dirname "$PRG"`"/$link"
+ fi
+done
+SAVED="`pwd`"
+cd "`dirname \"$PRG\"`/" >/dev/null
+APP_HOME="`pwd -P`"
+cd "$SAVED" >/dev/null
+
+APP_NAME="Gradle"
+APP_BASE_NAME=`basename "$0"`
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD="maximum"
+
+warn () {
+ echo "$*"
+}
+
+die () {
+ echo
+ echo "$*"
+ echo
+ exit 1
+}
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+nonstop=false
+case "`uname`" in
+ CYGWIN* )
+ cygwin=true
+ ;;
+ Darwin* )
+ darwin=true
+ ;;
+ MINGW* )
+ msys=true
+ ;;
+ NONSTOP* )
+ nonstop=true
+ ;;
+esac
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+ if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+ # IBM's JDK on AIX uses strange locations for the executables
+ JAVACMD="$JAVA_HOME/jre/sh/java"
+ else
+ JAVACMD="$JAVA_HOME/bin/java"
+ fi
+ if [ ! -x "$JAVACMD" ] ; then
+ die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+ fi
+else
+ JAVACMD="java"
+ which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
+ MAX_FD_LIMIT=`ulimit -H -n`
+ if [ $? -eq 0 ] ; then
+ if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
+ MAX_FD="$MAX_FD_LIMIT"
+ fi
+ ulimit -n $MAX_FD
+ if [ $? -ne 0 ] ; then
+ warn "Could not set maximum file descriptor limit: $MAX_FD"
+ fi
+ else
+ warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
+ fi
+fi
+
+# For Darwin, add options to specify how the application appears in the dock
+if $darwin; then
+ GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
+fi
+
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
+ APP_HOME=`cygpath --path --mixed "$APP_HOME"`
+ CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
+
+ JAVACMD=`cygpath --unix "$JAVACMD"`
+
+ # We build the pattern for arguments to be converted via cygpath
+ ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
+ SEP=""
+ for dir in $ROOTDIRSRAW ; do
+ ROOTDIRS="$ROOTDIRS$SEP$dir"
+ SEP="|"
+ done
+ OURCYGPATTERN="(^($ROOTDIRS))"
+ # Add a user-defined pattern to the cygpath arguments
+ if [ "$GRADLE_CYGPATTERN" != "" ] ; then
+ OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
+ fi
+ # Now convert the arguments - kludge to limit ourselves to /bin/sh
+ i=0
+ for arg in "$@" ; do
+ CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
+ CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option
+
+ if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition
+ eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
+ else
+ eval `echo args$i`="\"$arg\""
+ fi
+ i=`expr $i + 1`
+ done
+ case $i in
+ 0) set -- ;;
+ 1) set -- "$args0" ;;
+ 2) set -- "$args0" "$args1" ;;
+ 3) set -- "$args0" "$args1" "$args2" ;;
+ 4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+ 5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+ 6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+ 7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+ 8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+ 9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+ esac
+fi
+
+# Escape application args
+save () {
+ for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
+ echo " "
+}
+APP_ARGS=`save "$@"`
+
+# Collect all arguments for the java command, following the shell quoting and substitution rules
+eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+
+exec "$JAVACMD" "$@"
diff --git a/Gradle Project for Netbeans/gradlew.bat b/Gradle Project for Netbeans/gradlew.bat
new file mode 100644
index 0000000..5093609
--- /dev/null
+++ b/Gradle Project for Netbeans/gradlew.bat
@@ -0,0 +1,104 @@
+@rem
+@rem Copyright 2015 the original author or authors.
+@rem
+@rem Licensed under the Apache License, Version 2.0 (the "License");
+@rem you may not use this file except in compliance with the License.
+@rem You may obtain a copy of the License at
+@rem
+@rem https://www.apache.org/licenses/LICENSE-2.0
+@rem
+@rem Unless required by applicable law or agreed to in writing, software
+@rem distributed under the License is distributed on an "AS IS" BASIS,
+@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+@rem See the License for the specific language governing permissions and
+@rem limitations under the License.
+@rem
+
+@if "%DEBUG%" == "" @echo off
+@rem ##########################################################################
+@rem
+@rem Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+set DIRNAME=%~dp0
+if "%DIRNAME%" == "" set DIRNAME=.
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Resolve any "." and ".." in APP_HOME to make it shorter.
+for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if "%ERRORLEVEL%" == "0" goto init
+
+echo.
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto init
+
+echo.
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:init
+@rem Get command-line arguments, handling Windows variants
+
+if not "%OS%" == "Windows_NT" goto win9xME_args
+
+:win9xME_args
+@rem Slurp the command line arguments.
+set CMD_LINE_ARGS=
+set _SKIP=2
+
+:win9xME_args_slurp
+if "x%~1" == "x" goto execute
+
+set CMD_LINE_ARGS=%*
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+
+:end
+@rem End local scope for the variables with windows NT shell
+if "%ERRORLEVEL%"=="0" goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
+exit /b 1
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega
diff --git a/Gradle Project for Netbeans/settings.gradle b/Gradle Project for Netbeans/settings.gradle
new file mode 100644
index 0000000..63cd06f
--- /dev/null
+++ b/Gradle Project for Netbeans/settings.gradle
@@ -0,0 +1,10 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ *
+ * The settings file is used to specify which projects to include in your build.
+ *
+ * Detailed information about configuring a multi-project build in Gradle can be found
+ * in the user manual at https://docs.gradle.org/6.4/userguide/multi_project_builds.html
+ */
+
+rootProject.name = 'MoleculeSetComparator'
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/control/ApplicationController.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/control/ApplicationController.java
new file mode 100644
index 0000000..b56775a
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/control/ApplicationController.java
@@ -0,0 +1,815 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.control;
+
+import de.whs.ibci.msc.model.JobTaskManager;
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.utility.MSCConstants;
+import de.whs.ibci.msc.model.HistogramDataManager;
+import de.whs.ibci.msc.model.ComparisonFeature;
+import de.whs.ibci.msc.model.ComparisonResult;
+import de.whs.ibci.msc.model.HistogramData;
+import de.whs.ibci.msc.utility.GuiUtilities;
+import de.whs.ibci.msc.view.MainView;
+import de.whs.ibci.msc.view.PreferencesConfigurationDialog;
+import java.awt.Desktop;
+import java.awt.Toolkit;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.util.Iterator;
+import java.util.Optional;
+import java.util.Queue;
+import java.util.Set;
+import java.util.concurrent.ConcurrentLinkedQueue;
+import java.util.logging.Level;
+import java.util.zip.GZIPInputStream;
+import java.util.zip.GZIPOutputStream;
+import javafx.application.Application;
+import javafx.application.Platform;
+import javafx.concurrent.Task;
+import javafx.event.ActionEvent;
+import javafx.event.Event;
+import javafx.scene.Cursor;
+import javafx.scene.control.Alert;
+import javafx.scene.control.Button;
+import javafx.scene.control.ButtonBar;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.TextFormatter;
+import javafx.scene.input.KeyCode;
+import javafx.scene.input.KeyCodeCombination;
+import javafx.scene.input.KeyCombination;
+import javafx.scene.input.KeyEvent;
+import javafx.stage.DirectoryChooser;
+import javafx.stage.Stage;
+import javafx.stage.WindowEvent;
+
+/**
+ * Entry point and main controller of this JavaFX application. Handles events
+ * for the menu-bar and general controls. Controls the creation and deletion of
+ * JobControllers
+ *
+ * @author Jan-Mathis Hein
+ */
+public class ApplicationController extends Application implements PropertyChangeListener {
+
+ //
+ /**
+ * True if the input for the number of parallel threads given by the user in
+ * the PreferencesConfigurationDialog is valid, false otherwise
+ */
+ private boolean isValidNumberOfParallelThreads;
+
+ /**
+ * True if the input for the default number of bins given by the user in
+ * the PreferencesConfigurationDialog is valid, false otherwise
+ */
+ private boolean isValidDefaultNumberOfBins;
+
+ /**
+ * True if the input for the maximal number of molecule pairs to save given
+ * by the user in the PreferencesConfigurationDialog is valid, false otherwise
+ */
+ private boolean isValidMaximalNumberOfMoleculePairsToSave;
+
+ /**
+ * DirectoryChooser that is used to choose the default directory for
+ * different file choosers
+ */
+ private final DirectoryChooser defaultDirectoryChooser = new DirectoryChooser();
+
+ /**
+ * Directory from where the last output file was loaded or directory where
+ * the last output file was saved
+ */
+ private File lastOutputDirectoryParent;
+
+ /**
+ * DirectoryChooser that is used to choose the directory for job saving and
+ * loading
+ */
+ private final DirectoryChooser outputDirectoryChooser = new DirectoryChooser();
+
+ /**
+ * Number of JobControllers created in this session of the application
+ */
+ private int numberOfCreatedJobControllers = 0;
+
+ /**
+ * The JobController which is currently active and shown
+ */
+ private JobController activeJobController;
+
+ /**
+ * Queue of currently opened JobControllers
+ */
+ private final Queue jobControllerList = new ConcurrentLinkedQueue<>();
+
+ /**
+ * Main window of this application. This variable must be effectively final
+ */
+ private MainView view;
+
+ /**
+ * Dialog in which some preferences can be configured by the user
+ */
+ private PreferencesConfigurationDialog preferencesConfigurationDialog;
+ //
+ //
+ //
+ /**
+ * The entry point for this JavaFX application. Starts and intializes the
+ * graphical user interface. Checks the screen size, the java version,
+ * whether this is the only currently running instance and whether the
+ * preferneces can be loaded. Sets up the file choosers and handles menu-bar
+ * and general controls events.
+ *
+ * NOTE: This method is called on the JavaFX Application Thread.
+ *
+ * @param primaryStage the primary stage for this application, onto which
+ * the application scene is set
+ */
+ @Override
+ public void start(Stage primaryStage) {
+ try {
+ //
+ String tmpJavaVersion = System.getProperty("java.version");
+ if (tmpJavaVersion.compareTo(MSCConstants.JAVA_VERSION) < 0) {
+ GeneralUtilities.showErrorDialog(null, String.format(
+ GeneralUtilities.getUIText("ErrorDescription.WrongVersion.text"),
+ tmpJavaVersion, MSCConstants.JAVA_VERSION),
+ "ApplicationController.start()"
+ );
+ System.exit(-1);
+ }
+ if (!MSCConstants.MSC_FILES_DIRECTORY.isDirectory()) {
+ MSCConstants.MSC_FILES_DIRECTORY.mkdirs();
+ }
+ if (!GeneralUtilities.isSingleInstance()) {
+ GeneralUtilities.showErrorDialog(
+ null,
+ GeneralUtilities.getUIText("ErrorDescription.NotSingleInstance.text") + " \n" + MSCConstants.MSC_FILES_DIRECTORY.getPath(),
+ "ApplicationController.start()"
+ );
+ System.exit(-1);
+ }
+ if (Toolkit.getDefaultToolkit().getScreenSize().height < MSCConstants.MINIMAL_MAIN_WINDOW_HEIGHT ||
+ Toolkit.getDefaultToolkit().getScreenSize().height < MSCConstants.MINIMAL_MOLECULE_DISPLAYER_HEIGHT ||
+ Toolkit.getDefaultToolkit().getScreenSize().width < MSCConstants.MINIMAL_MAIN_WINDOW_WIDTH ||
+ Toolkit.getDefaultToolkit().getScreenSize().width < MSCConstants.MINIMAL_MOLECULE_DISPLAYER_WIDTH) {
+ GeneralUtilities.showErrorDialog(null, GeneralUtilities.getUIText("ErrorDescription.ScreenTooSmall.text"), "ApplicationController.start()");
+ System.exit(-1);
+ }
+ // Do this after checking for single instance or
+ // otherwise an additional log-file will be created
+ GeneralUtilities.initializeLogger();
+ try {
+ // Check if the preferences are available
+ UserPreferences.getInstance();
+ } catch (SecurityException | IllegalStateException ex) {
+ GeneralUtilities.showErrorDialog(null, GeneralUtilities.getUIText("ErrorDescription.CanNotInstantiatePreferences.text"), "ApplicationController.start()");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ System.exit(-1);
+ }
+ //
+ //
+ GeneralUtilities.logMessage(Level.INFO, "", "", GeneralUtilities.getUIText("Logging.ApplicationStart.text"));
+ this.view = new MainView(primaryStage);
+ this.view.getPrimaryStage().setMinHeight(MSCConstants.MINIMAL_MAIN_WINDOW_HEIGHT);
+ this.view.getPrimaryStage().setMinWidth(MSCConstants.MINIMAL_MAIN_WINDOW_WIDTH);
+ this.view.getPrimaryStage().setHeight(MSCConstants.MINIMAL_MAIN_WINDOW_HEIGHT);
+ this.view.getPrimaryStage().setWidth(MSCConstants.MINIMAL_MAIN_WINDOW_WIDTH);
+ this.view.getPrimaryStage().show();
+ //
+ //
+ this.preferencesConfigurationDialog = new PreferencesConfigurationDialog(this.view.getPrimaryStage(), GeneralUtilities.getUIText("PreferencesConfigurationDialog.title.text"));
+ this.preferencesConfigurationDialog.getNumberOfParallelThreadsField().setTextFormatter(new TextFormatter<>((TextFormatter.Change tmpChange) -> {
+ if (!tmpChange.getControlNewText().matches("\\d*")) {
+ tmpChange.setText("");
+ }
+ try {
+ if (Integer.parseInt(tmpChange.getControlNewText()) == 0) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ this.isValidNumberOfParallelThreads = false;
+ }
+ tmpChange.getControl().setStyle("-fx-background-color: white;");
+ this.isValidNumberOfParallelThreads = true;
+ } catch (NumberFormatException ex) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ this.isValidNumberOfParallelThreads = false;
+ }
+ return tmpChange;
+ }));
+ this.preferencesConfigurationDialog.getDefaultNumberOfBinsField().setTextFormatter(new TextFormatter<>((TextFormatter.Change tmpChange) -> {
+ if (!tmpChange.getControlNewText().matches("\\d*")) {
+ tmpChange.setText("");
+ }
+ try {
+ if (Integer.parseInt(tmpChange.getControlNewText()) == 0) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ this.isValidDefaultNumberOfBins = false;
+ }
+ tmpChange.getControl().setStyle("-fx-background-color: white;");
+ this.isValidDefaultNumberOfBins = true;
+ } catch (NumberFormatException ex) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ this.isValidDefaultNumberOfBins = false;
+ }
+ return tmpChange;
+ }));
+ this.preferencesConfigurationDialog.getMaximalNumberOfMoleculePairsToSaveField().setTextFormatter(new TextFormatter<>((TextFormatter.Change tmpChange) -> {
+ if (!tmpChange.getControlNewText().matches("\\d*")) {
+ tmpChange.setText("");
+ }
+ try {
+ Integer.parseInt(tmpChange.getControlNewText());
+ tmpChange.getControl().setStyle("-fx-background-color: white;");
+ this.isValidMaximalNumberOfMoleculePairsToSave = true;
+ } catch (NumberFormatException ex) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ this.isValidMaximalNumberOfMoleculePairsToSave = false;
+ }
+ return tmpChange;
+ }));
+ //
+ //
+ //
+ this.view.getPrimaryStage().setOnCloseRequest((WindowEvent e) -> {
+ Optional tmpResult = GeneralUtilities.showConfirmationDialog(
+ this.view.getPrimaryStage(), GeneralUtilities.getUIText("ConfirmationDialog.ClosingApplicationContent.text"),
+ GeneralUtilities.getUIText("ConfirmationDialog.ClosingTitle.text"),
+ GeneralUtilities.getUIText("ConfirmationDialog.ClosingApplicationHeader.text")
+ );
+ if (tmpResult.isPresent() && tmpResult.get().getButtonData() == ButtonBar.ButtonData.APPLY) {
+ Platform.exit();
+ } else {
+ e.consume();
+ }
+ });
+ this.view.getCenterButton().setOnAction((ActionEvent e) -> {
+ this.view.getPrimaryStage().centerOnScreen();
+ });
+ this.view.getMinButton().setOnAction((ActionEvent e) -> {
+ this.view.getPrimaryStage().setMaximized(false);
+ this.view.getPrimaryStage().setHeight(MSCConstants.MINIMAL_MAIN_WINDOW_HEIGHT);
+ this.view.getPrimaryStage().setWidth(MSCConstants.MINIMAL_MAIN_WINDOW_WIDTH);
+ });
+ this.view.getMaxButton().setOnAction((ActionEvent e) -> {
+ this.view.getPrimaryStage().setMaximized(true);
+ });
+ //
+ //
+ this.view.getSaveJobMenuItem().setOnAction((ActionEvent e) -> {
+ if (this.activeJobController == null || this.activeJobController.getHistogramDataManager() == null) {
+ GeneralUtilities.showInfoDialog(this.view.getPrimaryStage(), GeneralUtilities.getUIText("InfoDescription.SavingNotPossible.text"));
+ return;
+ }
+ if (!UserPreferences.getInstance().getOutputDir().isEmpty() && new File(UserPreferences.getInstance().getOutputDir()).isDirectory()) {
+ this.outputDirectoryChooser.setInitialDirectory(new File(UserPreferences.getInstance().getOutputDir()));
+ } else {
+ this.outputDirectoryChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ if (this.lastOutputDirectoryParent != null && this.lastOutputDirectoryParent.isDirectory()) {
+ this.outputDirectoryChooser.setInitialDirectory(this.lastOutputDirectoryParent);
+ }
+ this.outputDirectoryChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.SaveOutput.text"));
+ final File tmpDirectory = this.outputDirectoryChooser.showDialog(this.view.getPrimaryStage());
+ if (tmpDirectory == null) {
+ return;
+ }
+ if (tmpDirectory.isDirectory()) {
+ if (tmpDirectory.list() != null && tmpDirectory.list().length != 0) {
+ Optional tmpResult = GeneralUtilities.showConfirmationDialog(
+ this.view.getPrimaryStage(), GeneralUtilities.getUIText("ConfirmationDialog.DirectoryAlreadyExistsContent.text"),
+ GeneralUtilities.getUIText("ConfirmationDialog.SelectionTitle.text"),
+ GeneralUtilities.getUIText("ConfirmationDialog.DirectoryAlreadyExistsHeader.text")
+ );
+ if (tmpResult.isPresent() && tmpResult.get().getButtonData() == ButtonBar.ButtonData.APPLY) {
+ new File(tmpDirectory.getAbsolutePath() + File.separator + "output.ser").delete();
+ new File(tmpDirectory.getAbsolutePath() + File.separator + "README.txt").delete();
+ new File(tmpDirectory.getAbsolutePath() + File.separator + "moleculeSet1.txt").delete();
+ new File(tmpDirectory.getAbsolutePath() + File.separator + "moleculeSet2.txt").delete();
+ } else {
+ return;
+ }
+ }
+ } else {
+ if (!tmpDirectory.mkdirs()) {
+ GeneralUtilities.showErrorDialog(this.view.getPrimaryStage(), GeneralUtilities.getUIText("ErrorDescription.CanNotCreateDirectory.text"), "ApplicationController.view.getSaveJobMenuItem().setOnAction()");
+ }
+ }
+ this.lastOutputDirectoryParent = tmpDirectory.getParentFile();
+ final JobController tmpJobController = this.activeJobController;
+ final HistogramDataManager tmpHistogramDataManager = tmpJobController.getHistogramDataManager();
+ Task tmpTask = new Task() {
+
+ @Override
+ protected Void call() throws Exception {
+ File tmpFirstMoleculeSetFile = new File(tmpDirectory.getAbsolutePath() + File.separator + MSCConstants.MOLECULE_SET_1_FILE);
+ File tmpSecondMoleculeSetFile = new File(tmpDirectory.getAbsolutePath() + File.separator + MSCConstants.MOLECULE_SET_2_FILE);
+ File tmpOutputFile = new File(tmpDirectory.getAbsolutePath() + File.separator + MSCConstants.OUTPUT_FILE_NAME);
+ File tmpInfoFile = new File(tmpDirectory.getAbsolutePath() + File.separator + MSCConstants.INFO_FILE_NAME);
+ try (
+ ObjectOutputStream tmpObjectOutputStream = new ObjectOutputStream(new GZIPOutputStream(new FileOutputStream(tmpOutputFile), 64 * 1024));
+ BufferedWriter tmpInfoFileWritter = new BufferedWriter(new FileWriter(tmpInfoFile));
+ BufferedWriter tmpFirstMoleculeSetFileWritter = new BufferedWriter(new FileWriter(tmpFirstMoleculeSetFile));
+ BufferedWriter tmpSecondMoleculeSetFileWritter = new BufferedWriter(new FileWriter(tmpSecondMoleculeSetFile));
+ ) {
+ //
+ synchronized (tmpHistogramDataManager) {
+ tmpObjectOutputStream.writeObject(tmpHistogramDataManager);
+ }
+ //
+ //
+ tmpInfoFileWritter.write(String.format(
+ GeneralUtilities.getUIText("SavingJob.InfoFile.text"),
+ tmpFirstMoleculeSetFile.getName(), tmpSecondMoleculeSetFile.getName(), tmpOutputFile.getName()
+ ));
+ //
+ //
+ Iterator tmpIterator = tmpHistogramDataManager.getNativeDataList().iterator();
+ ComparisonResult tmpComparisonResult;
+ int tmpCounter = 0;
+ while (tmpIterator.hasNext() && tmpCounter < UserPreferences.getInstance().getMaximalNumberOfMoleculePairsToSave()) {
+ tmpComparisonResult = tmpIterator.next();
+ tmpFirstMoleculeSetFileWritter.write(tmpComparisonResult.getMolecule1().trim());
+ tmpFirstMoleculeSetFileWritter.newLine();
+ tmpSecondMoleculeSetFileWritter.write(tmpComparisonResult.getMolecule2().trim());
+ tmpSecondMoleculeSetFileWritter.newLine();
+ tmpCounter++;
+ }
+ //
+ tmpJobController.setOutputIsSaved(true);
+ } catch (IOException ex) {
+ Platform.runLater(() -> {
+ ApplicationController.this.view.getScene().setCursor(Cursor.DEFAULT);
+ GeneralUtilities.showErrorDialog(ApplicationController.this.view.getPrimaryStage(), ex.toString(), "ApplicationController.view.getSaveJobMenuItem().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ });
+ } finally {
+ Platform.runLater(() -> {
+ ApplicationController.this.view.getScene().setCursor(Cursor.DEFAULT);
+ });
+ }
+ return null;
+ }
+
+ };
+ Thread tmpBackgroundThread = new Thread(tmpTask);
+ this.view.getScene().setCursor(Cursor.WAIT);
+ tmpBackgroundThread.start();
+ });
+ this.view.getLoadJobOutputMenuItem().setOnAction((ActionEvent e) -> {
+ if (!UserPreferences.getInstance().getOutputDir().isEmpty() && new File(UserPreferences.getInstance().getOutputDir()).isDirectory()) {
+ this.outputDirectoryChooser.setInitialDirectory(new File(UserPreferences.getInstance().getOutputDir()));
+ } else {
+ this.outputDirectoryChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ if (this.lastOutputDirectoryParent != null && this.lastOutputDirectoryParent.isDirectory()) {
+ this.outputDirectoryChooser.setInitialDirectory(this.lastOutputDirectoryParent);
+ }
+ this.outputDirectoryChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.LoadOutput.text"));
+ File tmpDirectory = this.outputDirectoryChooser.showDialog(this.view.getPrimaryStage());
+ if (tmpDirectory == null) {
+ return;
+ }
+ if (!tmpDirectory.isDirectory()) {
+ GeneralUtilities.showInfoDialog(this.view.getPrimaryStage(), GeneralUtilities.getUIText("InfoDescription.FileNotReadable.text"));
+ return;
+ }
+ this.lastOutputDirectoryParent = tmpDirectory.getParentFile();
+ Task tmpTask = new Task() {
+
+ @Override
+ protected Void call() throws Exception {
+ File tmpFirstMoleculeSetFile = new File(tmpDirectory.getAbsolutePath() + File.separator + MSCConstants.MOLECULE_SET_1_FILE);
+ File tmpSecondMoleculeSetFile = new File(tmpDirectory.getAbsolutePath() + File.separator + MSCConstants.MOLECULE_SET_2_FILE);
+ File tmpOutputFile = new File(tmpDirectory.getAbsolutePath() + File.separator + MSCConstants.OUTPUT_FILE_NAME);
+ try (
+ ObjectInputStream tmpObjectInputStream = new ObjectInputStream(new GZIPInputStream(new FileInputStream(tmpOutputFile), 64 * 1024));
+ BufferedReader tmpFirstMoleculeSetFileReader = new BufferedReader(new FileReader(tmpFirstMoleculeSetFile));
+ BufferedReader tmpSecondMoleculeSetFileReader = new BufferedReader(new FileReader(tmpSecondMoleculeSetFile));
+ ) {
+ //
+ HistogramDataManager tmpHistogramDataManager = (HistogramDataManager) tmpObjectInputStream.readObject();
+ //
+ //
+ Iterator tmpIterator = tmpHistogramDataManager.getNativeDataList().iterator();
+ ComparisonResult tmpComparisonResult;
+ String tmpLine1 = null;
+ String tmpLine2 = null;
+ while (
+ (tmpLine1 = tmpFirstMoleculeSetFileReader.readLine()) != null &&
+ (tmpLine2 = tmpSecondMoleculeSetFileReader.readLine()) != null &&
+ tmpIterator.hasNext()
+ ) {
+ tmpComparisonResult = tmpIterator.next();
+ tmpComparisonResult.setMolecule1(tmpLine1);
+ tmpComparisonResult.setMolecule2(tmpLine2);
+ }
+ //
+ //
+ tmpHistogramDataManager.getComparisonFeatureSet().forEach((ComparisonFeature tmpComparisonFeature) -> {
+ HistogramData tmpHistogramData = tmpHistogramDataManager.getHistogramData(tmpComparisonFeature);
+ double tmpLowerFrequencyBound = tmpHistogramData.getLowerFrequencyBound();
+ double tmpUpperFrequencyBound = tmpHistogramData.getUpperFrequencyBound();
+ // Resets the frequency bounds
+ tmpHistogramData.call();
+ // Set the pre-reset frequency bounds
+ tmpHistogramData.setLowerFrequencyBound(tmpLowerFrequencyBound);
+ tmpHistogramData.setUpperFrequencyBound(tmpUpperFrequencyBound);
+ });
+ //
+ Platform.runLater(() -> {
+ ApplicationController.this.createNewJobController(true, tmpHistogramDataManager);
+ ApplicationController.this.view.getScene().setCursor(Cursor.DEFAULT);
+ });
+ } catch (IOException | ClassNotFoundException | IllegalArgumentException ex) {
+ Platform.runLater(() -> {
+ ApplicationController.this.view.getScene().setCursor(Cursor.DEFAULT);
+ GeneralUtilities.showErrorDialog(ApplicationController.this.view.getPrimaryStage(), ex.toString(), "ApplicationController.view.getLoadJobOutputMenuItem().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ });
+ }
+ return null;
+ }
+
+ };
+ Thread tmpBackgroundThread = new Thread(tmpTask);
+ this.view.getScene().setCursor(Cursor.WAIT);
+ tmpBackgroundThread.start();
+ });
+ this.view.getNewJobMenuItem().setOnAction((ActionEvent e) -> {
+ this.createNewJobController(false, null);
+ });
+ this.view.getDefaultInputDirectoryMenuItem().setOnAction((ActionEvent e) -> {
+ try {
+ this.defaultDirectoryChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.DefaultInputDirectory.text"));
+ if (!UserPreferences.getInstance().getInputDir().isEmpty() && new File(UserPreferences.getInstance().getInputDir()).isDirectory()) {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(UserPreferences.getInstance().getInputDir()));
+ } else {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ File tmpFile = this.defaultDirectoryChooser.showDialog(this.view.getPrimaryStage());
+ if (tmpFile != null && tmpFile.isDirectory()) {
+ UserPreferences.getInstance().setInputDir(tmpFile.getAbsolutePath());
+ UserPreferences.savePreferences();
+ }
+ } catch (Exception ex) {
+ GeneralUtilities.showErrorDialog(this.view.getPrimaryStage(), ex.toString(), "ApplicationController.view.getInputDirectoryMenuItem().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ this.view.getDefaultOutputDirectoryMenuItem().setOnAction((ActionEvent e) -> {
+ try {
+ this.defaultDirectoryChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.DefaultOutputDirectory.text"));
+ if (!UserPreferences.getInstance().getOutputDir().isEmpty() && new File(UserPreferences.getInstance().getOutputDir()).isDirectory()) {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(UserPreferences.getInstance().getOutputDir()));
+ } else {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ File tmpFile = this.defaultDirectoryChooser.showDialog(this.view.getPrimaryStage());
+ if (tmpFile != null && tmpFile.isDirectory()) {
+ UserPreferences.getInstance().setOutputDir(tmpFile.getAbsolutePath());
+ UserPreferences.savePreferences();
+ }
+ } catch (Exception ex) {
+ GeneralUtilities.showErrorDialog(this.view.getPrimaryStage(), ex.toString(), "ApplicationController.view.getOutputDirectoryMenuItem().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ this.view.getDefaultImageDirectoryMenutItem().setOnAction((ActionEvent e) -> {
+ try {
+ this.defaultDirectoryChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.DefaultImageDirectory.text"));
+ if (!UserPreferences.getInstance().getImageDir().isEmpty() && new File(UserPreferences.getInstance().getImageDir()).isDirectory()) {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(UserPreferences.getInstance().getImageDir()));
+ } else {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ File tmpFile = this.defaultDirectoryChooser.showDialog(this.view.getPrimaryStage());
+ if (tmpFile != null && tmpFile.isDirectory()) {
+ UserPreferences.getInstance().setImageDir(tmpFile.getAbsolutePath());
+ UserPreferences.savePreferences();
+ }
+ } catch (Exception ex) {
+ GeneralUtilities.showErrorDialog(this.view.getPrimaryStage(), ex.toString(), "ApplicationController.view.getImageDirectoryMenuItem().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ this.view.getDefaultMoleculeListDirectoryMenuItem().setOnAction((ActionEvent e) -> {
+ try {
+ this.defaultDirectoryChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.DefaultMoleculeListDirectory.text"));
+ if (!UserPreferences.getInstance().getMoleculeListDir().isEmpty() && new File(UserPreferences.getInstance().getMoleculeListDir()).isDirectory()) {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(UserPreferences.getInstance().getMoleculeListDir()));
+ } else {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ File tmpFile = this.defaultDirectoryChooser.showDialog(this.view.getPrimaryStage());
+ if (tmpFile != null && tmpFile.isDirectory()) {
+ UserPreferences.getInstance().setMoleculeListDir(tmpFile.getAbsolutePath());
+ UserPreferences.savePreferences();
+ }
+ } catch (Exception ex) {
+ GeneralUtilities.showErrorDialog(this.view.getPrimaryStage(), ex.toString(), "ApplicationController.view.getMoleculeListDirectoryMenuItem().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ this.view.getDefaultSummaryReportDirectoryMenuItem().setOnAction((ActionEvent e) -> {
+ try {
+ this.defaultDirectoryChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.DefaultSummaryReportDirectory.text"));
+ if (!UserPreferences.getInstance().getSummaryReportDir().isEmpty() && new File(UserPreferences.getInstance().getSummaryReportDir()).isDirectory()) {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(UserPreferences.getInstance().getSummaryReportDir()));
+ } else {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ File tmpFile = this.defaultDirectoryChooser.showDialog(this.view.getPrimaryStage());
+ if (tmpFile != null && tmpFile.isDirectory()) {
+ UserPreferences.getInstance().setSummaryReportDir(tmpFile.getAbsolutePath());
+ UserPreferences.savePreferences();
+ }
+ } catch (Exception ex) {
+ GeneralUtilities.showErrorDialog(this.view.getPrimaryStage(), ex.toString(), "ApplicationController.view.getDefaultSummaryReportDirectoryMenuItem().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ this.view.getOtherPreferencesMenuItem().setOnAction((ActionEvent e) -> {
+ this.preferencesConfigurationDialog.getNumberOfParallelThreadsField().setText(Integer.toString(UserPreferences.getInstance().getNumberOfParallelThreads()));
+ this.preferencesConfigurationDialog.getDefaultNumberOfBinsField().setText(Integer.toString(UserPreferences.getInstance().getDefaultNumberOfBins()));
+ this.preferencesConfigurationDialog.getMaximalNumberOfMoleculePairsToSaveField().setText(Integer.toString(UserPreferences.getInstance().getMaximalNumberOfMoleculePairsToSave()));
+ this.preferencesConfigurationDialog.getImageQualitySlider().setValue(UserPreferences.getInstance().getImageQuality());
+ this.preferencesConfigurationDialog.showAndWait();
+ });
+ this.view.getBrowseLogMenuItem().setOnAction((ActionEvent e) -> {
+ File tmpLogFile = GeneralUtilities.getLogFile();
+ if (!Desktop.isDesktopSupported()) {
+ GeneralUtilities.showInfoDialog(this.view.getPrimaryStage(), GeneralUtilities.getUIText("InfoDescription.DesktopNotSupported.text"));
+ return;
+ }
+ if (!tmpLogFile.canRead()) {
+ GeneralUtilities.showInfoDialog(this.view.getPrimaryStage(), GeneralUtilities.getUIText("InfoDescription.LogFileNotReadable.text"));
+ return;
+ }
+ try {
+ Desktop.getDesktop().open(tmpLogFile);
+ } catch (IOException ex) {
+ GeneralUtilities.showErrorDialog(this.view.getPrimaryStage(), ex.toString(), "ApplicationController.view.getBrowseLogMenuItem().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ this.view.getResetLogMenuItem().setOnAction((ActionEvent e) -> {
+ // Also deletes the log file and then resets the handlers
+ GeneralUtilities.closeAndRemoveHandlersFromLogger(true);
+ GeneralUtilities.logMessage(Level.INFO, "", "", GeneralUtilities.getUIText("Logging.NewLoggingSession.text"));
+ });
+ this.view.getAboutMenuItem().setOnAction((ActionEvent e) -> {
+ Alert tmpAboutDialog = new Alert(Alert.AlertType.INFORMATION, "", ButtonType.OK);
+ tmpAboutDialog.initOwner(this.view.getPrimaryStage());
+ tmpAboutDialog.setTitle(GeneralUtilities.getUIText("InfoDialog.AboutTitle.text"));
+ tmpAboutDialog.setHeaderText(null);
+ tmpAboutDialog.getDialogPane().setContentText(String.format(GeneralUtilities.getUIText("InfoDescription.About.text"), MSCConstants.MSC_VERSION));
+ Button tmpButton = (Button) tmpAboutDialog.getDialogPane().lookupButton(ButtonType.OK);
+ GuiUtilities.setMinMaxPrefSize(tmpButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ tmpAboutDialog.showAndWait();
+ });
+ //
+ //
+ this.preferencesConfigurationDialog.getCancelButton().setOnAction((ActionEvent e) -> {
+ this.preferencesConfigurationDialog.hide();
+ });
+ this.preferencesConfigurationDialog.getApplyButton().setOnAction((ActionEvent e) -> {
+ if (this.isValidNumberOfParallelThreads) {
+ UserPreferences.getInstance().setNumberOfParallelThreads(Integer.parseInt(this.preferencesConfigurationDialog.getNumberOfParallelThreadsField().getText()));
+ UserPreferences.savePreferences();
+ this.jobControllerList.stream().filter((JobController tmpJobController) -> tmpJobController.getJobTaskManager() != null).forEach((JobController tmpJobController) -> {
+ tmpJobController.getJobTaskManager().setNumberOfParallelThreads(UserPreferences.getInstance().getNumberOfParallelThreads());
+ });
+ }
+ if (this.isValidDefaultNumberOfBins) {
+ UserPreferences.getInstance().setDefaultNumberOfBins(Integer.parseInt(this.preferencesConfigurationDialog.getDefaultNumberOfBinsField().getText()));
+ UserPreferences.savePreferences();
+ this.jobControllerList.stream().filter((JobController tmpJobController) -> tmpJobController.getJobTaskManager() != null).forEach((JobController tmpJobController) -> {
+ tmpJobController.getJobTaskManager().setDefaultNumberOfBins(UserPreferences.getInstance().getDefaultNumberOfBins());
+ });
+ }
+ if (this.isValidMaximalNumberOfMoleculePairsToSave) {
+ UserPreferences.getInstance().setMaximalNumberOfMoleculePairsToSave(Integer.parseInt(this.preferencesConfigurationDialog.getMaximalNumberOfMoleculePairsToSaveField().getText()));
+ UserPreferences.savePreferences();
+ }
+ UserPreferences.getInstance().setImageQuality(this.preferencesConfigurationDialog.getImageQualitySlider().getValue());
+ UserPreferences.savePreferences();
+ this.preferencesConfigurationDialog.hide();
+ });
+ this.preferencesConfigurationDialog.getDialogPane().addEventFilter(KeyEvent.KEY_PRESSED, (KeyEvent tmpEvent) -> {
+ KeyCombination tmpKeyCombination = new KeyCodeCombination(KeyCode.ENTER);
+ if (tmpKeyCombination.match(tmpEvent)) {
+ this.preferencesConfigurationDialog.getApplyButton().fire();
+ }
+ });
+ this.preferencesConfigurationDialog.getResetButton().setOnAction((ActionEvent e) -> {
+ this.preferencesConfigurationDialog.getNumberOfParallelThreadsField().setText(Integer.toString(UserPreferences.getInstance().getNumberOfParallelThreads()));
+ this.preferencesConfigurationDialog.getDefaultNumberOfBinsField().setText(Integer.toString(UserPreferences.getInstance().getDefaultNumberOfBins()));
+ this.preferencesConfigurationDialog.getMaximalNumberOfMoleculePairsToSaveField().setText(Integer.toString(UserPreferences.getInstance().getMaximalNumberOfMoleculePairsToSave()));
+ this.preferencesConfigurationDialog.getImageQualitySlider().setValue(UserPreferences.getInstance().getImageQuality());
+ });
+ //
+ //
+ } catch (Exception ex) {
+ GeneralUtilities.showErrorDialog(null, ex.toString(), "ApplicationController.start()");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ }
+
+ /**
+ * Handle PropertyChangeEvents that are coming from the JobControllers and
+ * update the GUI accordingly
+ *
+ * @param evt PropertyChangeEvent that was fired by one of the
+ * JobControllers
+ */
+ @Override
+ public void propertyChange(PropertyChangeEvent evt) {
+ try {
+ if (evt.getSource() instanceof JobController) {
+ JobController tmpJobController = (JobController) evt.getSource();
+ switch (evt.getPropertyName()) {
+ case "Created charts successfully":
+ this.view.getTabPane().getTabs().add(tmpJobController.getOutputTab());
+ this.view.getCenterPane().setStyle("-fx-background-color: rgb(200, 200, 200);");
+ this.view.getTabPane().getSelectionModel().select(tmpJobController.getOutputTab());
+ this.view.getTabPane().getTabs().remove(tmpJobController.getInputTab());
+ break;
+ case "Want to close InputTab":
+ if (tmpJobController.getJobTaskManager().isWorking()) {
+ Optional tmpResult = GeneralUtilities.showConfirmationDialog(
+ this.view.getPrimaryStage(), GeneralUtilities.getUIText("ConfirmationDialog.ClosingInputTabContent.text"),
+ GeneralUtilities.getUIText("ConfirmationDialog.ClosingTitle.text"),
+ GeneralUtilities.getUIText("ConfirmationDialog.ClosingInputTabHeader.text")
+ );
+ if (tmpResult.isPresent() && tmpResult.get().getButtonData() == ButtonBar.ButtonData.APPLY) {
+ this.closeJobController(tmpJobController);
+ // The Tab hasn't been closed yet
+ if (this.view.getTabPane().getTabs().size() <= 1) {
+ this.view.getCenterPane().setStyle("-fx-background-color: rgb(220, 220, 220);");
+ }
+ this.activeJobController = null;
+ } else {
+ // Destroy the closing event
+ if (evt.getNewValue() instanceof Event) {
+ Event tmpEvent = (Event) evt.getNewValue();
+ tmpEvent.consume();
+ }
+ }
+ } else {
+ this.closeJobController(tmpJobController);
+ // The Tab hasn't been closed yet
+ if (this.view.getTabPane().getTabs().size() <= 1) {
+ this.view.getCenterPane().setStyle("-fx-background-color: rgb(220, 220, 220);");
+ }
+ this.activeJobController = null;
+ }
+ break;
+ case "Want to close OutputTab":
+ if (!tmpJobController.outputIsSaved()) {
+ Optional tmpResult = GeneralUtilities.showConfirmationDialog(
+ this.view.getPrimaryStage(), GeneralUtilities.getUIText("ConfirmationDialog.ClosingOutputTabContent.text"),
+ GeneralUtilities.getUIText("ConfirmationDialog.ClosingTitle.text"),
+ GeneralUtilities.getUIText("ConfirmationDialog.ClosingOutputTabHeader.text")
+ );
+ if (tmpResult.isPresent() && tmpResult.get().getButtonData() == ButtonBar.ButtonData.APPLY) {
+ this.closeJobController(tmpJobController);
+ // The Tab hasn't been closed yet
+ if (this.view.getTabPane().getTabs().size() <= 1) {
+ this.view.getCenterPane().setStyle("-fx-background-color: rgb(220, 220, 220);");
+ }
+ this.activeJobController = null;
+ } else {
+ // Destroy the closing event
+ if (evt.getNewValue() instanceof Event) {
+ Event tmpEvent = (Event) evt.getNewValue();
+ tmpEvent.consume();
+ }
+ }
+ } else {
+ this.closeJobController(tmpJobController);
+ // The Tab hasn't been closed yet
+ if (this.view.getTabPane().getTabs().size() <= 1) {
+ this.view.getCenterPane().setStyle("-fx-background-color: rgb(220, 220, 220);");
+ }
+ this.activeJobController = null;
+ }
+ break;
+ case "JobController selected":
+ this.activeJobController = tmpJobController;
+ break;
+ default:
+ GeneralUtilities.logMessage(
+ Level.INFO, "ApplicationController", "propertyChange()",
+ String.format(GeneralUtilities.getUIText("Logging.UnexptectedPropertyChange.text"), evt.getPropertyName())
+ );
+ break;
+ }
+ }
+ } catch (Exception ex) {
+ GeneralUtilities.showErrorDialog(this.view.getPrimaryStage(), ex.toString(), "ApplicationController.propertyChange()");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ }
+
+ /**
+ * This is called whenever this JavaFX Application is closed and it closes
+ * all open JobControllers
+ */
+ @Override
+ public void stop() {
+ this.jobControllerList.forEach((tmpJobController) -> {
+ this.closeJobController(tmpJobController);
+ });
+ this.activeJobController = null;
+ GeneralUtilities.logMessage(Level.INFO, "", "", GeneralUtilities.getUIText("Logging.ApplicationClosed.text"));
+ // Closes the log file
+ GeneralUtilities.closeAndRemoveHandlersFromLogger(false);
+ }
+ //
+ //
+ //
+ /**
+ * Close the given JobController and its JobTaskManager
+ *
+ * @param tmpJobController the JobController that will be closed
+ */
+ private void closeJobController(JobController tmpJobController) {
+ tmpJobController.removePropertyChangeListener(this);
+ JobTaskManager tmpJobTaskManager = tmpJobController.getJobTaskManager();
+ if (tmpJobTaskManager != null) {
+ tmpJobTaskManager.cancelWorkingProcess();
+ }
+ this.jobControllerList.remove(tmpJobController);
+ }
+
+ /**
+ * Create a new JobController, add it to the JobController list and
+ * handle some related things
+ */
+ private synchronized void createNewJobController(boolean tmpIsLoaded, HistogramDataManager tmpHistogramDataManager) {
+ this.numberOfCreatedJobControllers++;
+ try {
+ JobController tmpController = new JobController(
+ this.view, tmpIsLoaded, Integer.toString(this.numberOfCreatedJobControllers)
+ );
+ tmpController.addPropertyChangeListener(this);
+ this.jobControllerList.add(tmpController);
+ if (tmpIsLoaded) {
+ tmpController.setHistogramDataManager(tmpHistogramDataManager);
+ // Set this first to avoid NullPointerExcpetions
+ tmpController.setCurrentlyChosenComparisonFeature(tmpHistogramDataManager.getComparisonFeatureSet().iterator().next());
+ tmpController.getOutputTab().setBinLabelChoiceBoxItems(Set.of(BinLabelType.values()));
+ tmpController.getOutputTab().setChartChoiceBoxItems(tmpController.getHistogramDataManager().getComparisonFeatureSet());
+ tmpController.getOutputTab().getBinLabelChoiceBox().setValue(BinLabelType.MAX);
+ tmpController.getOutputTab().getChartChoiceBox().setValue(tmpController.getHistogramDataManager().getComparisonFeatureSet().iterator().next());
+ tmpController.getOutputTab().getInfoLabel().setText(String.format(
+ GeneralUtilities.getUIText("OutputTab.infoLabel.text"),
+ tmpController.getJobNumber(),
+ tmpController.getHistogramDataManager().getNumberOfComparedPairs(),
+ tmpHistogramDataManager.getInputFile1(), tmpHistogramDataManager.getInputFile2()
+ ));
+ this.view.getTabPane().getTabs().add(tmpController.getOutputTab());
+ this.view.getCenterPane().setStyle("-fx-background-color: rgb(200, 200, 200);");
+ this.view.getTabPane().getSelectionModel().select(tmpController.getOutputTab());
+ } else {
+ this.view.getTabPane().getTabs().add(tmpController.getInputTab());
+ this.view.getCenterPane().setStyle("-fx-background-color: rgb(200, 200, 200);");
+ this.view.getTabPane().getSelectionModel().select(tmpController.getInputTab());
+ }
+ } catch (IllegalArgumentException ex) {
+ this.numberOfCreatedJobControllers--;
+ GeneralUtilities.showErrorDialog(this.view.getPrimaryStage(), ex.toString(), "ApplicationController.createNewJobController()");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/control/BinLabelType.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/control/BinLabelType.java
new file mode 100644
index 0000000..42c9b1b
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/control/BinLabelType.java
@@ -0,0 +1,61 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.control;
+
+/**
+ * Defines different types of bin labels
+ *
+ * @author Jan-Mathis Hein
+ */
+public enum BinLabelType {
+
+ //
+ MIN ("Lower bin border"), MAX ("Upper bin border"), MEAN ("Mean of both borders"), INTERVAL ("Interval");
+ //
+ //
+ //
+ /**
+ * A more precise description for the BinLabelType
+ */
+ private final String description;
+ //
+ //
+ //
+ /**
+ * Initialize the instance variables
+ *
+ * @param tmpDescription a more precise description for the BinLabelType
+ */
+ private BinLabelType(String tmpDescription) {
+ this.description = tmpDescription;
+ }
+ //
+ //
+ //
+ /**
+ * Get a more precise description for the BinLabelType
+ *
+ * @return a more precise description for the BinLabelType
+ */
+ @Override
+ public String toString() {
+ return this.description;
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/control/JobController.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/control/JobController.java
new file mode 100644
index 0000000..5c5f9e1
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/control/JobController.java
@@ -0,0 +1,1759 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.control;
+
+import de.whs.ibci.msc.model.ComparisonResult;
+import de.whs.ibci.msc.model.JobTaskManager;
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.model.MSCInputException;
+import de.whs.ibci.msc.view.ChartConfigurationDialog;
+import de.whs.ibci.msc.view.InputTab;
+import de.whs.ibci.msc.view.MainView;
+import de.whs.ibci.msc.view.OutputTab;
+import de.whs.ibci.msc.model.HistogramDataManager;
+import de.whs.ibci.msc.model.InputType;
+import de.whs.ibci.msc.model.ComparisonFeature;
+import de.whs.ibci.msc.model.HistogramData;
+import de.whs.ibci.msc.utility.ResultFormattingUtility;
+import de.whs.ibci.msc.view.BinBorderConfigurationBox;
+import de.whs.ibci.msc.view.BinBorderConfigurationDialog;
+import java.awt.Graphics2D;
+import java.awt.geom.AffineTransform;
+import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.nio.file.Files;
+import java.text.DecimalFormat;
+import java.util.Date;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.ListIterator;
+import java.util.Optional;
+import java.util.Set;
+import java.util.logging.Level;
+import javafx.application.Platform;
+import javafx.beans.value.ChangeListener;
+import javafx.beans.value.ObservableValue;
+import javafx.concurrent.Task;
+import javafx.embed.swing.SwingFXUtils;
+import javafx.event.ActionEvent;
+import javafx.event.Event;
+import javafx.event.EventHandler;
+import javafx.geometry.Insets;
+import javafx.geometry.Pos;
+import javafx.scene.Cursor;
+import javafx.scene.Scene;
+import javafx.scene.SnapshotParameters;
+import javafx.scene.chart.BarChart;
+import javafx.scene.chart.CategoryAxis;
+import javafx.scene.chart.NumberAxis;
+import javafx.scene.chart.XYChart;
+import javafx.scene.control.Button;
+import javafx.scene.control.ButtonBar;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.CheckBox;
+import javafx.scene.control.Label;
+import javafx.scene.control.TextFormatter;
+import javafx.scene.input.KeyCode;
+import javafx.scene.input.KeyCodeCombination;
+import javafx.scene.input.KeyCombination;
+import javafx.scene.input.KeyEvent;
+import javafx.scene.input.MouseEvent;
+import javafx.scene.layout.Region;
+import javafx.scene.layout.StackPane;
+import javafx.scene.layout.VBox;
+import javafx.scene.paint.Color;
+import javafx.scene.paint.Paint;
+import javafx.scene.transform.Transform;
+import javafx.stage.FileChooser;
+import javafx.stage.Stage;
+import javax.imageio.ImageIO;
+import org.apache.batik.dom.GenericDOMImplementation;
+import org.apache.batik.svggen.SVGGraphics2D;
+import org.apache.pdfbox.pdmodel.PDDocument;
+import org.apache.pdfbox.pdmodel.PDPage;
+import org.apache.pdfbox.pdmodel.PDPageContentStream;
+import org.apache.pdfbox.pdmodel.common.PDRectangle;
+import org.apache.pdfbox.pdmodel.graphics.image.LosslessFactory;
+import org.apache.pdfbox.pdmodel.graphics.image.PDImageXObject;
+import org.w3c.dom.DOMException;
+import org.w3c.dom.DOMImplementation;
+import org.w3c.dom.Document;
+
+/**
+ * Manages the ChartConfigurationDialog, the In and OutputTab as well as
+ * related events. Also directly communicates with the JobTaskManager and
+ * converts the resulting HistogramData objects in to charts.
+ *
+ * @author Jan-Mathis Hein
+ */
+public class JobController implements PropertyChangeListener{
+
+ //
+ /**
+ * Directory from where the last input file of any job was loaded
+ */
+ private static File lastInputFileDirectory;
+
+ /**
+ * Directory where the last chart file of any job was saved
+ */
+ private static File lastChartFileDirectory;
+
+ /**
+ * Directory where the last summary report of any job was saved
+ */
+ private static File lastSummaryReportDirectory;
+ //
+ //
+ //
+ /**
+ * A dialog that enables the user to specifically set the bin borders
+ */
+ private BinBorderConfigurationDialog binBorderConfigurationDialog;
+
+ /**
+ * False if there are changes that are not saved, true otherwise
+ */
+ private boolean outputIsSaved;
+
+ /**
+ * True if the input for the lower bin border given by the user in the
+ * ChartConfigurationDialog is valid, false: Otherwise
+ */
+ private boolean isValidLowerBinBorder;
+
+ /**
+ * True if the input for the upper bin border given by the user in the
+ * ChartConfigurationDialog is valid, false otherwise
+ */
+ private boolean isValidUpperBinBorder;
+
+ /**
+ * True if the input for the lower frequency bound given by the user in
+ * the ChartConfigurationDialog is valid, false: Otherwise
+ */
+ private boolean isValidLowerFrequencyBound;
+
+ /**
+ * True if the input for the upper frequency bound given by the user in
+ * the ChartConfigurationDialog is valid, false: Otherwise
+ */
+ private boolean isValidUpperFrequencyBound;
+
+ /**
+ * The BinLabelType that is currently chosen
+ */
+ private BinLabelType currentlyChosenBinLabelType = BinLabelType.MAX;
+
+ /**
+ * A dialog that enables the user to configure the chart
+ */
+ private ChartConfigurationDialog chartConfigurationDialog;
+
+ /**
+ * The ComparisonFeature that is currently chosen
+ */
+ private ComparisonFeature currentlyChosenComparisonFeature;
+
+ /**
+ * An EventHandler that handles the action of the user clicking any
+ * "Add"-button in the binBorderConfigurationDialog
+ */
+ private final EventHandler binBorderConfigurationDialogAddHandler;
+
+ /**
+ * An EventHandler that handles the action of the user clicking any
+ * "Remove"-button in the binBorderConfigurationDialog
+ */
+ private final EventHandler binBorderConfigurationDialogRemoveHandler;
+
+ /**
+ * A FileChooser that is used to choose files for loading and saving
+ */
+ private final FileChooser fileChooser = new FileChooser();
+
+ /**
+ * The InputTab that allows the user to enter his input
+ */
+ private InputTab inputTab;
+
+ /**
+ * The JobTaskManager that manages the task that is specified by the
+ * InputTab
+ */
+ private final JobTaskManager jobTaskManager;
+
+ /**
+ * Manages the data of the histograms for all ComparisonFeatures
+ */
+ private HistogramDataManager histogramDataManager;
+
+ /**
+ * List of BinBorderConfigurationBoxes for the BinBorderConfigurationDialog.
+ * Each box is for the configuration of one bin border
+ */
+ private final LinkedList binBorderConfigurationBoxList = new LinkedList<>();
+
+ /**
+ * The time difference, in milliseconds, between the time of the start of
+ * the job and midnight, January 1, 1970 UTC
+ */
+ private long calculationStartTime;
+
+ /**
+ * The OutputTab that displays the results of the task execution
+ */
+ private OutputTab outputTab;
+
+ /**
+ * PropertyChangeSupport that manages the firing of PropertyChangeEvents and
+ * the adding and removing of PropertyChangeListeners
+ */
+ private final PropertyChangeSupport propertyChangeSupport;
+
+ /**
+ * The chart that is currently shown. If the chart creation failed, this
+ * will be an error label
+ */
+ private Region currentlyShownChart;
+
+ /**
+ * The scene on which the In and OutputTab will be displayed
+ */
+ private final Scene scene;
+
+ /**
+ * A number that identifies this job in the current application session. It
+ * indicates the order in which different jobs have been opened or created
+ */
+ private String jobNumber;
+
+ /**
+ * The stage onto which the In and OutputTab will be projected
+ */
+ private final Stage applicationStage;
+ //
+ //
+ //
+ /**
+ * Initialize the instance variables, set TextFormatters for the
+ * ChartConfigurationDialog, add event handlers for the In and OutputTab and
+ * the ChartConfigurationDialog and set up the tab that will be shown
+ *
+ * @param tmpView main view of the application
+ * @param tmpIsLoaded true if the job is loaded, false otherwise
+ * @param tmpJobNumber identifies this job in this application session
+ */
+ public JobController (
+ MainView tmpView, boolean tmpIsLoaded, String tmpJobNumber
+ ) throws IllegalArgumentException {
+ //
+ if (tmpView == null) {
+ throw new IllegalArgumentException("tmpView is null");
+ }
+ if (tmpJobNumber == null || tmpJobNumber.matches("\\W*\\w*\\D+\\W*\\w*")) {
+ throw new IllegalArgumentException("tmpJobNumber is invalid");
+ }
+ //
+ //
+ this.applicationStage = tmpView.getPrimaryStage();
+ this.scene = tmpView.getScene();
+ this.jobNumber = tmpJobNumber;
+ if (!tmpIsLoaded) {
+ this.inputTab = new InputTab(this.jobNumber);
+ this.jobTaskManager = new JobTaskManager(
+ UserPreferences.getInstance().getNumberOfParallelThreads(),
+ UserPreferences.getInstance().getDefaultNumberOfBins()
+ );
+ this.jobTaskManager.addPropertyChangeListener(this);
+ } else {
+ this.jobTaskManager = null;
+ }
+ this.outputIsSaved = tmpIsLoaded;
+ this.outputTab = new OutputTab(this.jobNumber);
+ this.chartConfigurationDialog = new ChartConfigurationDialog(this.applicationStage, String.format(GeneralUtilities.getUIText("ChartConfigurationDialog.Title.text"), this.jobNumber));
+ this.propertyChangeSupport = new PropertyChangeSupport(this);
+ this.binBorderConfigurationDialog = new BinBorderConfigurationDialog(this.applicationStage, GeneralUtilities.getUIText("BinBorderConfigurationDialog.Title.text"));
+ this.binBorderConfigurationDialogRemoveHandler = (ActionEvent tmpEvent) -> {
+ Button tmpButton = (Button) tmpEvent.getSource();
+ int tmpIndex = JobController.this.binBorderConfigurationBoxList.indexOf(tmpButton.getParent());
+ JobController.this.binBorderConfigurationBoxList.remove(tmpIndex);
+ ListIterator tmpIterator = JobController.this.binBorderConfigurationBoxList.listIterator(tmpIndex);
+ while (tmpIterator.hasNext()) {
+ int tmpNextIndex = tmpIterator.nextIndex();
+ tmpIterator.next().getLabel().setText(Integer.toString(tmpNextIndex + 1));
+ }
+ if (JobController.this.binBorderConfigurationBoxList.size() <= 2) {
+ JobController.this.binBorderConfigurationBoxList.forEach((tmpBox1) -> {
+ // Removing is disabled if there are only two bin borders
+ tmpBox1.getRemoveButton().setDisable(true);
+ });
+ } else {
+ JobController.this.binBorderConfigurationBoxList.forEach((tmpBox1) -> {
+ // Removing is enabled if there are more than two bin borders
+ tmpBox1.getRemoveButton().setDisable(false);
+ });
+ }
+ JobController.this.binBorderConfigurationDialog.getBinBorderConfigurationBoxesBox().getChildren().setAll(JobController.this.binBorderConfigurationBoxList);
+ // Remove the insets because they were only a bug fix that is no longer necessary, because the ScrollPane has been resized
+ JobController.this.binBorderConfigurationDialog.getBinBorderConfigurationBoxesBox().setPadding(Insets.EMPTY);
+ };
+ this.binBorderConfigurationDialogAddHandler = new EventHandler() {
+
+ @Override
+ public void handle(ActionEvent tmpEvent) {
+ Button tmpButton = (Button) tmpEvent.getSource();
+ int tmpIndex = JobController.this.binBorderConfigurationBoxList.indexOf(tmpButton.getParent());
+ BinBorderConfigurationBox tmpBox = new BinBorderConfigurationBox("", Integer.toString(tmpIndex + 2));
+ tmpBox.getAddButton().setOnAction(this);
+ tmpBox.getRemoveButton().setOnAction(JobController.this.binBorderConfigurationDialogRemoveHandler);
+ tmpBox.getTextField().setTextFormatter(GeneralUtilities.getSignedDecimalNumberTextFormatter());
+ JobController.this.binBorderConfigurationBoxList.add(tmpIndex + 1, tmpBox);
+ ListIterator tmpIterator = JobController.this.binBorderConfigurationBoxList.listIterator(tmpIndex + 2);
+ while (tmpIterator.hasNext()) {
+ int tmpNextIndex = tmpIterator.nextIndex();
+ tmpIterator.next().getLabel().setText(Integer.toString(tmpNextIndex + 1));
+ }
+ if (JobController.this.binBorderConfigurationBoxList.size() <= 2) {
+ JobController.this.binBorderConfigurationBoxList.forEach((tmpBox1) -> {
+ // Removing is disabled if there are only two bin borders
+ tmpBox1.getRemoveButton().setDisable(true);
+ });
+ } else {
+ JobController.this.binBorderConfigurationBoxList.forEach((tmpBox1) -> {
+ // Removing is enabled if there are more than two bin borders
+ tmpBox1.getRemoveButton().setDisable(false);
+ });
+ }
+ JobController.this.binBorderConfigurationDialog.getBinBorderConfigurationBoxesBox().getChildren().setAll(JobController.this.binBorderConfigurationBoxList);
+ // Remove the insets because they were only a bug fix that is no longer necessary, because the ScrollPane has been resized
+ JobController.this.binBorderConfigurationDialog.getBinBorderConfigurationBoxesBox().setPadding(Insets.EMPTY);
+ }
+
+ };
+ //
+ //
+ this.outputTab.getNumberOfBinsTextField().setTextFormatter(GeneralUtilities.getUnsignedIntegerTextFormatter());
+ this.chartConfigurationDialog.getLowerBinBorderInputField().setTextFormatter(new TextFormatter<>((TextFormatter.Change tmpChange) -> {
+ if (!tmpChange.getControlNewText().matches("[-\\+]?\\d*\\.?\\d*E?\\d*")) {
+ tmpChange.setText("");
+ }
+ try {
+ Double.parseDouble(tmpChange.getControlNewText());
+ tmpChange.getControl().setStyle("-fx-background-color: white;");
+ this.isValidLowerBinBorder = true;
+ } catch (NumberFormatException ex) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ this.isValidLowerBinBorder = false;
+ }
+ return tmpChange;
+ }));
+ this.chartConfigurationDialog.getUpperBinBorderInputField().setTextFormatter(new TextFormatter<>((TextFormatter.Change tmpChange) -> {
+ if (!tmpChange.getControlNewText().matches("[-\\+]?\\d*\\.?\\d*E?\\d*")) {
+ tmpChange.setText("");
+ }
+ try {
+ Double.parseDouble(tmpChange.getControlNewText());
+ tmpChange.getControl().setStyle("-fx-background-color: white;");
+ this.isValidUpperBinBorder = true;
+ } catch (NumberFormatException ex) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ this.isValidUpperBinBorder = false;
+ }
+ return tmpChange;
+ }));
+ this.chartConfigurationDialog.getLowerFrequencyBoundInputField().setTextFormatter(new TextFormatter<>((TextFormatter.Change tmpChange) -> {
+ if (!tmpChange.getControlNewText().matches("\\d*\\.?\\d*E?\\d*")) {
+ tmpChange.setText("");
+ }
+ try {
+ Double.parseDouble(tmpChange.getControlNewText());
+ tmpChange.getControl().setStyle("-fx-background-color: white;");
+ this.isValidLowerFrequencyBound = true;
+ } catch (NumberFormatException ex) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ this.isValidLowerFrequencyBound = false;
+ }
+ return tmpChange;
+ }));
+ this.chartConfigurationDialog.getUpperFrequencyBoundInputField().setTextFormatter(new TextFormatter<>((TextFormatter.Change tmpChange) -> {
+ if (!tmpChange.getControlNewText().matches("\\d*\\.?\\d*E?\\d*")) {
+ tmpChange.setText("");
+ }
+ try {
+ Double.parseDouble(tmpChange.getControlNewText());
+ tmpChange.getControl().setStyle("-fx-background-color: white;");
+ this.isValidUpperFrequencyBound = true;
+ } catch (NumberFormatException ex) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ this.isValidUpperFrequencyBound = false;
+ }
+ return tmpChange;
+ }));
+ //
+ //
+ //
+ if (!tmpIsLoaded) {
+ //
+ this.inputTab.setOnCloseRequest((Event e) -> {
+ this.propertyChangeSupport.firePropertyChange("Want to close InputTab", null, e);
+ });
+ this.inputTab.setOnSelectionChanged((Event e) -> {
+ this.propertyChangeSupport.firePropertyChange("JobController selected", false, this.inputTab.isSelected());
+ });
+ //
+ //
+ this.inputTab.getChooseFile1Button().setOnAction((ActionEvent e) -> {
+ try {
+ this.fileChooser.getExtensionFilters().clear();
+ this.fileChooser.getExtensionFilters().addAll(
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.All.text"), "*.*"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.Text.text"), "*.txt")
+ );
+ if (!UserPreferences.getInstance().getInputDir().isEmpty() && new File(UserPreferences.getInstance().getInputDir()).isDirectory()) {
+ this.fileChooser.setInitialDirectory(new File(UserPreferences.getInstance().getInputDir()));
+ } else {
+ this.fileChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ synchronized (JobController.class) {
+ if (JobController.lastInputFileDirectory != null && JobController.lastInputFileDirectory.isDirectory()) {
+ this.fileChooser.setInitialDirectory(JobController.lastInputFileDirectory);
+ }
+ }
+ this.fileChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.MoleculeFile.text"));
+ File tmpFile = this.fileChooser.showOpenDialog(this.applicationStage);
+ if (tmpFile != null && tmpFile.canRead()) {
+ this.inputTab.getInputFile1Label().setText(GeneralUtilities.getUIText("InputTab.inputFile1Label.text") + " " + tmpFile.getName());
+ this.jobTaskManager.setInputFile1(tmpFile);
+ this.inputTab.getJobInfoLabel().setText(GeneralUtilities.getUIText("InfoDescription.InputFile1.text"));
+ synchronized (JobController.class) {
+ JobController.lastInputFileDirectory = tmpFile.getParentFile();
+ }
+ }
+ for (CheckBox tmpCheckBox : this.inputTab.getComparisonFeatureCheckBoxes()) {
+ if (tmpCheckBox.isSelected() && this.jobTaskManager.canReadInput()) {
+ this.inputTab.getJobStartButton().setDisable(false);
+ return;
+ }
+ }
+ this.inputTab.getJobStartButton().setDisable(true);
+ } catch (IllegalArgumentException ex) {
+ GeneralUtilities.showErrorDialog(this.applicationStage, ex.toString(), "JobController.inputTab.getChooseFile1Button().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ this.inputTab.getChooseFile2Button().setOnAction((ActionEvent e) -> {
+ try {
+ this.fileChooser.getExtensionFilters().clear();
+ this.fileChooser.getExtensionFilters().addAll(
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.All.text"), "*.*"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.Text.text"), "*.txt")
+ );
+ if (!UserPreferences.getInstance().getInputDir().isEmpty() && new File(UserPreferences.getInstance().getInputDir()).isDirectory()) {
+ this.fileChooser.setInitialDirectory(new File(UserPreferences.getInstance().getInputDir()));
+ } else {
+ this.fileChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ synchronized (JobController.class) {
+ if (JobController.lastInputFileDirectory != null && JobController.lastInputFileDirectory.isDirectory()) {
+ this.fileChooser.setInitialDirectory(JobController.lastInputFileDirectory);
+ }
+ }
+ this.fileChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.MoleculeFile.text"));
+ File tmpFile = this.fileChooser.showOpenDialog(this.applicationStage);
+ if (tmpFile != null && tmpFile.canRead()) {
+ this.inputTab.getInputFile2Label().setText(GeneralUtilities.getUIText("InputTab.inputFile2Label.text") + " " + tmpFile.getName());
+ this.jobTaskManager.setInputFile2(tmpFile);
+ this.inputTab.getJobInfoLabel().setText(GeneralUtilities.getUIText("InfoDescription.InputFile2.text"));
+ synchronized (JobController.class) {
+ JobController.lastInputFileDirectory = tmpFile.getParentFile();
+ }
+ }
+ for (CheckBox tmpCheckBox : this.inputTab.getComparisonFeatureCheckBoxes()) {
+ if (tmpCheckBox.isSelected() && this.jobTaskManager.canReadInput()) {
+ this.inputTab.getJobStartButton().setDisable(false);
+ return;
+ }
+ }
+ this.inputTab.getJobStartButton().setDisable(true);
+ } catch (IllegalArgumentException ex) {
+ GeneralUtilities.showErrorDialog(this.applicationStage, ex.toString(), "JobController.inputTab.getChooseFile2Button().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ this.inputTab.getInputType1ChoiceBox().setOnAction((ActionEvent e) -> {
+ InputType tmpType = this.inputTab.getInputType1ChoiceBox().getValue();
+ if (tmpType != null) {
+ this.jobTaskManager.setInputType1(tmpType);
+ }
+ this.inputTab.getJobStartButton().setDisable(!this.jobTaskManager.canReadInput());
+ });
+ this.inputTab.getInputType2ChoiceBox().setOnAction((ActionEvent e) -> {
+ InputType tmpType = this.inputTab.getInputType2ChoiceBox().getValue();
+ if (tmpType != null) {
+ this.jobTaskManager.setInputType2(tmpType);
+ }
+ this.inputTab.getJobStartButton().setDisable(!this.jobTaskManager.canReadInput());
+ });
+ //
+ //
+ this.inputTab.getSelectAllComparisonFeaturesButton().setOnAction((ActionEvent e) -> {
+ for (CheckBox tmpCheckBox : this.inputTab.getComparisonFeatureCheckBoxes()) {
+ tmpCheckBox.setSelected(true);
+ }
+ for (CheckBox tmpCheckBox : this.inputTab.getSelectAllCheckBoxes()) {
+ tmpCheckBox.setSelected(true);
+ }
+ });
+ this.inputTab.getReverseComparisonFeatureSelectionButton().setOnAction((ActionEvent e) -> {
+ for (CheckBox tmpCheckBox : this.inputTab.getComparisonFeatureCheckBoxes()) {
+ tmpCheckBox.setSelected(!tmpCheckBox.isSelected());
+ }
+ });
+ for (CheckBox tmpCheckBox1 : this.inputTab.getComparisonFeatureCheckBoxes()) {
+ tmpCheckBox1.selectedProperty().addListener((ObservableValue tmpObservableValue, Boolean tmpOldValue, Boolean tmpNewValue) -> {
+ int tmpInt = 0;
+ for (CheckBox tmpCheckBox2 : this.inputTab.getComparisonFeatureCheckBoxes()) {
+ if (tmpCheckBox2.isSelected()) {
+ tmpInt++;
+ }
+ }
+ if (tmpInt == 0) {
+ this.inputTab.getJobInfoLabel().setText(GeneralUtilities.getUIText("InfoDescription.noFeaturesSelected.text"));
+ this.inputTab.getJobStartButton().setDisable(true);
+ } else {
+ this.inputTab.getJobInfoLabel().setText(String.format(GeneralUtilities.getUIText("InfoDescription.xFeaturesSelected.text"), tmpInt));
+ if (this.jobTaskManager.canReadInput()) {
+ this.inputTab.getJobStartButton().setDisable(false);
+ } else {
+ this.inputTab.getJobStartButton().setDisable(true);
+ }
+ }
+
+ });
+ }
+ ListIterator tmpCheckBoxIterator = this.inputTab.getSelectAllCheckBoxes().listIterator();
+ Iterator tmpVBoxIterator = this.inputTab.getCheckBoxesBoxes().iterator();
+ while (tmpCheckBoxIterator.hasNext() && tmpVBoxIterator.hasNext()) {
+ tmpCheckBoxIterator.next().setOnAction(new EventHandler() {
+
+ private final VBox box = tmpVBoxIterator.next();
+
+ private final CheckBox checkBox = tmpCheckBoxIterator.previous();
+
+ {
+ tmpCheckBoxIterator.next();
+ }
+
+ @Override
+ public void handle(ActionEvent e) {
+ boolean tmpIsChecked = this.checkBox.isSelected();
+ this.box.getChildren().stream().map((tmpNode) -> (CheckBox) tmpNode).forEach((tmpCheckBox) -> {
+ tmpCheckBox.setSelected(tmpIsChecked);
+ });
+ }
+ });
+ }
+ //
+ //
+ this.inputTab.getJobStartButton().setOnAction((ActionEvent e) -> {
+ //
+ if (this.jobTaskManager.isWorking()) {
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.JobStillWorking.text"));
+ this.inputTab.getJobStartButton().setDisable(true);
+ return;
+ }
+ if (!this.jobTaskManager.canReadInput()) {
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.InputConfigurationNotReadable.text"));
+ this.inputTab.getJobStartButton().setDisable(true);
+ return;
+ }
+ //
+ boolean[] tmpChoosenComparisonFeatures = new boolean[this.inputTab.getComparisonFeatureCheckBoxes().length];
+ for (int i = 0; i < tmpChoosenComparisonFeatures.length; i++) {
+ tmpChoosenComparisonFeatures[i] = this.inputTab.getComparisonFeatureCheckBoxes()[i].isSelected();
+ }
+ try {
+ // Checks if at least one ComparisonFeature is chosen
+ this.jobTaskManager.setComparisonFeatures(tmpChoosenComparisonFeatures);
+ } catch (MSCInputException | IllegalArgumentException ex) {
+ GeneralUtilities.showInfoDialog(this.applicationStage, ex.toString());
+ return;
+ }
+ this.inputTab.getJobStartButton().setVisible(false);
+ this.inputTab.getJobCancelButton().setVisible(true);
+ this.inputTab.getChooseFile1Button().setDisable(true);
+ this.inputTab.getChooseFile2Button().setDisable(true);
+ this.inputTab.getInputType1ChoiceBox().setDisable(true);
+ this.inputTab.getInputType2ChoiceBox().setDisable(true);
+ this.inputTab.getInputFile1Label().setDisable(true);
+ this.inputTab.getInputFile2Label().setDisable(true);
+ this.inputTab.getJobCancelButton().setDisable(false);
+ this.inputTab.getReverseComparisonFeatureSelectionButton().setDisable(true);
+ for (CheckBox tmpCheckBox : this.inputTab.getSelectAllCheckBoxes()) {
+ tmpCheckBox.setDisable(true);
+ }
+ this.inputTab.getSelectAllComparisonFeaturesButton().setDisable(true);
+ for (CheckBox tmpCheckBox : this.inputTab.getComparisonFeatureCheckBoxes()) {
+ tmpCheckBox.setDisable(true);
+ }
+ this.inputTab.getJobProgressBar().setVisible(true);
+ this.inputTab.getJobProgressBar().setProgress(0);
+ this.inputTab.getJobInfoLabel().setText(GeneralUtilities.getUIText("InfoDescription.JobStarted.text"));
+ try {
+ Task tmpTask = new Task() {
+ @Override
+ protected Void call() throws Exception {
+ JobController.this.jobTaskManager.startTasks();
+ return null;
+ }
+ };
+ Thread tmpBackgroundThread = new Thread(tmpTask);
+ this.calculationStartTime = System.currentTimeMillis();
+ tmpBackgroundThread.start();
+ } catch (Exception ex) {
+ GeneralUtilities.logException(Level.SEVERE, ex);
+ GeneralUtilities.showErrorDialog(this.applicationStage, ex.toString(), "JobController.inputTab.getJobStartButton().setOnAction($lambda)");
+ this.jobTaskManager.cancelWorkingProcess();
+ this.inputTab.getJobStartButton().setVisible(true);
+ this.inputTab.getJobCancelButton().setVisible(false);
+ this.inputTab.getChooseFile1Button().setDisable(false);
+ this.inputTab.getChooseFile2Button().setDisable(false);
+ this.inputTab.getInputType1ChoiceBox().setDisable(false);
+ this.inputTab.getInputType2ChoiceBox().setDisable(false);
+ this.inputTab.getInputFile1Label().setDisable(false);
+ this.inputTab.getInputFile2Label().setDisable(false);
+ this.inputTab.getReverseComparisonFeatureSelectionButton().setDisable(false);
+ for (CheckBox tmpCheckBox : this.inputTab.getSelectAllCheckBoxes()) {
+ tmpCheckBox.setDisable(false);
+ }
+ this.inputTab.getSelectAllComparisonFeaturesButton().setDisable(false);
+ for (CheckBox tmpCheckBox : this.inputTab.getComparisonFeatureCheckBoxes()) {
+ tmpCheckBox.setDisable(false);
+ }
+ this.inputTab.getJobProgressBar().setVisible(false);
+ this.inputTab.getJobProgressBar().setProgress(0);
+ this.inputTab.getJobInfoLabel().setText(GeneralUtilities.getUIText("InfoDescription.StartingJobFailed.text"));
+ }
+ });
+ this.inputTab.getJobCancelButton().setOnAction((ActionEvent e) -> {
+ this.jobTaskManager.cancelWorkingProcess();
+ this.inputTab.getJobStartButton().setVisible(true);
+ this.inputTab.getJobCancelButton().setVisible(false);
+ this.inputTab.getChooseFile1Button().setDisable(false);
+ this.inputTab.getChooseFile2Button().setDisable(false);
+ this.inputTab.getInputType1ChoiceBox().setDisable(false);
+ this.inputTab.getInputType2ChoiceBox().setDisable(false);
+ this.inputTab.getInputFile1Label().setDisable(false);
+ this.inputTab.getInputFile2Label().setDisable(false);
+ this.inputTab.getReverseComparisonFeatureSelectionButton().setDisable(false);
+ for (CheckBox tmpCheckBox : this.inputTab.getSelectAllCheckBoxes()) {
+ tmpCheckBox.setDisable(false);
+ }
+ this.inputTab.getSelectAllComparisonFeaturesButton().setDisable(false);
+ for (CheckBox tmpCheckBox : this.inputTab.getComparisonFeatureCheckBoxes()) {
+ tmpCheckBox.setDisable(false);
+ }
+ this.inputTab.getJobProgressBar().setVisible(false);
+ this.inputTab.getJobProgressBar().setProgress(0);
+ synchronized (this) {
+ // Guarantees that the label is set correctly
+ Platform.runLater(() -> {
+ this.inputTab.getJobInfoLabel().setText(GeneralUtilities.getUIText("InfoDescription.JobCanceled.text"));
+ });
+ }
+ });
+ //
+ }
+ //
+ //
+ //
+ this.outputTab.setOnCloseRequest((Event e) -> {
+ this.propertyChangeSupport.firePropertyChange("Want to close OutputTab", null, e);
+ });
+ this.outputTab.setOnSelectionChanged((Event e) -> {
+ this.propertyChangeSupport.firePropertyChange("JobController selected", false, this.outputTab.isSelected());
+ });
+ //
+ //
+ this.outputTab.getSummaryReportButton().setOnAction((ActionEvent e) -> {
+ try {
+ this.fileChooser.getExtensionFilters().clear();
+ this.fileChooser.getExtensionFilters().addAll(
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.All.text"), "*.*"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.Text.text"), "*.txt")
+ );
+ if (!UserPreferences.getInstance().getSummaryReportDir().isEmpty() && new File(UserPreferences.getInstance().getSummaryReportDir()).isDirectory()) {
+ this.fileChooser.setInitialDirectory(new File(UserPreferences.getInstance().getSummaryReportDir()));
+ } else {
+ this.fileChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ synchronized (JobController.class) {
+ if (JobController.lastSummaryReportDirectory != null && JobController.lastSummaryReportDirectory.isDirectory()) {
+ this.fileChooser.setInitialDirectory(JobController.lastSummaryReportDirectory);
+ }
+ }
+ this.fileChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.SaveSummaryReport.text"));
+ final File tmpFile = this.fileChooser.showSaveDialog(this.applicationStage);
+ if (tmpFile == null) {
+ return;
+ }
+ boolean tmpIsNewFile = tmpFile.createNewFile();
+ if (!tmpFile.canWrite()) {
+ if (tmpIsNewFile) {
+ Files.delete(tmpFile.toPath());
+ }
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.FileNotWritable.text"));
+ return;
+ }
+ synchronized (JobController.class) {
+ JobController.lastSummaryReportDirectory = tmpFile.getParentFile();
+ }
+ String tmpFormat = tmpFile.getAbsolutePath().substring(tmpFile.getAbsolutePath().lastIndexOf(".")).toLowerCase();
+ switch (tmpFormat) {
+ case ".txt":
+ try (BufferedWriter tmpBufferedWriter = new BufferedWriter(new FileWriter(tmpFile))) {
+ for (String tmpString : ResultFormattingUtility.getResultSummaryReportHeader()) {
+ tmpBufferedWriter.write(tmpString);
+ tmpBufferedWriter.newLine();
+ }
+ for (String tmpString : ResultFormattingUtility.getGeneralInfoBlock(
+ new Date(this.histogramDataManager.getCalculationFinishTime()),
+ (this.histogramDataManager.getCalculationFinishTime() - this.histogramDataManager.getCalculationStartTime()) / 1000,
+ this.histogramDataManager.getNumberOfComparedPairs(), this.histogramDataManager.getInputFile1(), this.histogramDataManager.getInputFile2()
+ )) {
+ tmpBufferedWriter.write(tmpString);
+ tmpBufferedWriter.newLine();
+ }
+ for (ComparisonFeature tmpComparisonFeature : this.histogramDataManager.getComparisonFeatureSet()) {
+ for (String tmpString : ResultFormattingUtility.getVerticalHistogramBlock(this.histogramDataManager.getHistogramData(tmpComparisonFeature))) {
+ tmpBufferedWriter.write(tmpString);
+ tmpBufferedWriter.newLine();
+ }
+ }
+ }
+ break;
+ default:
+ GeneralUtilities.showInfoDialog(JobController.this.applicationStage, GeneralUtilities.getUIText("InfoDescription.FileFormatNotSupported.text"));
+ break;
+ }
+ } catch (IOException ex) {
+ GeneralUtilities.showErrorDialog(this.applicationStage, ex.toString(), "JobController.outputTab.getSummaryReportButton().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ //
+ //
+ this.outputTab.getImageButton().setOnAction((ActionEvent e) -> {
+ try {
+ this.fileChooser.getExtensionFilters().clear();
+ this.fileChooser.getExtensionFilters().addAll(
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.All.text"), "*.*"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.pdf.text"), "*.pdf"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.png.text"), "*.png"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.jpeg.text"), "*.jpeg"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.svg.text"), "*.svg")
+ );
+ if (!UserPreferences.getInstance().getImageDir().isEmpty() && new File(UserPreferences.getInstance().getImageDir()).isDirectory()) {
+ this.fileChooser.setInitialDirectory(new File(UserPreferences.getInstance().getImageDir()));
+ } else {
+ this.fileChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ synchronized (JobController.class) {
+ if (JobController.lastChartFileDirectory != null && JobController.lastChartFileDirectory.isDirectory()) {
+ this.fileChooser.setInitialDirectory(JobController.lastChartFileDirectory);
+ }
+ }
+ this.fileChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.SaveChart.text"));
+ final File tmpFile = this.fileChooser.showSaveDialog(this.applicationStage);
+ if (tmpFile == null) {
+ return;
+ }
+ boolean tmpIsNewFile = tmpFile.createNewFile();
+ if (!tmpFile.canWrite()) {
+ if (tmpIsNewFile) {
+ Files.delete(tmpFile.toPath());
+ }
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.FileNotWritable.text"));
+ return;
+ }
+ synchronized (JobController.class) {
+ JobController.lastChartFileDirectory = tmpFile.getParentFile();
+ }
+ SnapshotParameters tmpSnapshotParameters = new SnapshotParameters();
+ // IMPORTANT: Setting tmpScalingFactor too low will cause the program to throw an exception
+ final float tmpScalingFactor = (float) ((-0.91) * UserPreferences.getInstance().getImageQuality() + 1);
+ tmpSnapshotParameters.setTransform(Transform.scale(1 / tmpScalingFactor, 1 / tmpScalingFactor));
+ final BufferedImage tmpBufferedImage = SwingFXUtils.fromFXImage(this.currentlyShownChart.snapshot(tmpSnapshotParameters, null), null);
+ final String tmpFormat = tmpFile.getAbsolutePath().substring(tmpFile.getAbsolutePath().lastIndexOf(".")).toLowerCase();
+ Task tmpTask = new Task() {
+ @Override
+ protected Void call() throws Exception {
+ try {
+ switch (tmpFormat) {
+ case ".png":
+ ImageIO.write(tmpBufferedImage, "PNG", tmpFile);
+ break;
+ case ".jpg":
+ case ".jpeg":
+ BufferedImage tmpImage = new BufferedImage(tmpBufferedImage.getWidth(), tmpBufferedImage.getHeight(), BufferedImage.TYPE_INT_RGB);
+ // Change the color model of the BufferedImage for the jpeg format
+ Graphics2D tmpGraphics2D = tmpImage.createGraphics();
+ tmpGraphics2D.drawImage(tmpBufferedImage, 0, 0, null);
+ tmpGraphics2D.dispose();
+ ImageIO.write(tmpImage, "JPG", tmpFile);
+ break;
+ case ".svg":
+ DOMImplementation domImpl = GenericDOMImplementation.getDOMImplementation();
+ Document document = domImpl.createDocument("http://www.w3.org/2000/svg", "svg", null);
+ SVGGraphics2D tmpSvgGenerator = new SVGGraphics2D(document);
+ tmpSvgGenerator.drawImage(tmpBufferedImage, AffineTransform.getScaleInstance(tmpScalingFactor, tmpScalingFactor), null);
+ try (BufferedWriter tmpWriter = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(tmpFile)))) {
+ tmpSvgGenerator.stream(tmpWriter);
+ }
+ break;
+ case ".pdf":
+ try (PDDocument tmpDocument = new PDDocument()) {
+ PDPage tmpPage = new PDPage();
+ tmpDocument.addPage(tmpPage);
+ PDImageXObject tmpPDImage = LosslessFactory.createFromImage(tmpDocument, tmpBufferedImage);
+ try (PDPageContentStream tmpStream = new PDPageContentStream(tmpDocument, tmpPage)) {
+ float tmpWidth = tmpBufferedImage.getWidth() * tmpScalingFactor;
+ float tmpHeight = tmpBufferedImage.getHeight() * tmpScalingFactor;
+ tmpPage.setMediaBox(new PDRectangle(tmpWidth, tmpHeight));
+ tmpStream.drawImage(tmpPDImage, 0, 0, tmpWidth, tmpHeight);
+ }
+ tmpDocument.save(tmpFile);
+ }
+ break;
+ default:
+ Platform.runLater(() -> {
+ GeneralUtilities.showInfoDialog(JobController.this.applicationStage, GeneralUtilities.getUIText("InfoDescription.FileFormatNotSupported.text"));
+ });
+ }
+ } catch (IOException | DOMException ex) {
+ Platform.runLater(() -> {
+ JobController.this.scene.setCursor(Cursor.DEFAULT);
+ GeneralUtilities.showErrorDialog(JobController.this.applicationStage, ex.toString(), "JobController.outputTab.getSaveButton().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ });
+ } finally {
+ Platform.runLater(() -> {
+ JobController.this.scene.setCursor(Cursor.DEFAULT);
+ });
+ }
+ return null;
+ }
+ };
+ Thread tmpBackgroundThread = new Thread(tmpTask);
+ this.scene.setCursor(Cursor.WAIT);
+ tmpBackgroundThread.start();
+ } catch (StringIndexOutOfBoundsException ex) {
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.FileFormatNotSupported.text"));
+ } catch (Exception ex) {
+ GeneralUtilities.showErrorDialog(this.applicationStage, ex.toString(), "JobController.outputTab.getSaveButton().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ //
+ //
+ this.outputTab.getRelativeFrequenciesCheckBox().setOnAction((ActionEvent e) -> {
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ tmpHistogramData.setUseRelativeFrequencies(this.outputTab.getRelativeFrequenciesCheckBox().isSelected());
+ this.outputTab.getFrequency1Slider().setMin(0.0);
+ this.outputTab.getFrequency1Slider().setMax(tmpHistogramData.getMaxFrequency());
+ this.outputTab.getFrequency2Slider().setMin(0.0);
+ this.outputTab.getFrequency2Slider().setMax(tmpHistogramData.getMaxFrequency());
+ double tmpTickUnit;
+ tmpTickUnit = (tmpHistogramData.getMaxFrequency() - 0.0) / 10;
+ if (tmpTickUnit > 0) {
+ this.outputTab.getFrequency1Slider().setMajorTickUnit(tmpTickUnit);
+ this.outputTab.getFrequency2Slider().setMajorTickUnit(tmpTickUnit);
+ }
+ this.updateOutputTab();
+ });
+ //
+ //
+ this.outputTab.getChartChoiceBox().setOnAction((ActionEvent e) -> {
+ ComparisonFeature tmpComparisonFeature = this.outputTab.getChartChoiceBox().getValue();
+ //
+ if (!this.histogramDataManager.getComparisonFeatureSet().contains(tmpComparisonFeature)) {
+ GeneralUtilities.showErrorDialog(this.applicationStage, GeneralUtilities.getUIText("ErrorDescription.InvalidComparisonFeatureSelection.text"), "JobController.outputTab.getChartChoiceBox().setOnAction($lambda)");
+ GeneralUtilities.logMessage(Level.WARNING, "JobController", "Constructor()", GeneralUtilities.getUIText("Logging.InvalidComparisonFeatureSelection.text"));
+ return;
+ }
+ //
+ this.currentlyChosenComparisonFeature = tmpComparisonFeature;
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ //
+ double tmpMin = Double.isNaN(this.currentlyChosenComparisonFeature.getMinimalValue()) ? tmpHistogramData.getMinComparisonFeatureValue() : this.currentlyChosenComparisonFeature.getMinimalValue();
+ double tmpMax = Double.isNaN(this.currentlyChosenComparisonFeature.getMaximalValue()) ? tmpHistogramData.getMaxComparisonFeatureValue() : this.currentlyChosenComparisonFeature.getMaximalValue();
+ this.outputTab.getBinBorder1Slider().setMin(tmpMin);
+ this.outputTab.getBinBorder1Slider().setMax(tmpMax);
+ this.outputTab.getBinBorder2Slider().setMin(tmpMin);
+ this.outputTab.getBinBorder2Slider().setMax(tmpMax);
+ double tmpTickUnit1;
+ tmpTickUnit1 = (tmpMax - tmpMin) / 10;
+ if (tmpTickUnit1 > 0) {
+ this.outputTab.getBinBorder1Slider().setMajorTickUnit(tmpTickUnit1);
+ this.outputTab.getBinBorder2Slider().setMajorTickUnit(tmpTickUnit1);
+ }
+ this.outputTab.getFrequency1Slider().setMin(0.0);
+ this.outputTab.getFrequency1Slider().setMax(tmpHistogramData.getMaxFrequency());
+ this.outputTab.getFrequency2Slider().setMin(0.0);
+ this.outputTab.getFrequency2Slider().setMax(tmpHistogramData.getMaxFrequency());
+ double tmpTickUnit2;
+ tmpTickUnit2 = (tmpHistogramData.getMaxFrequency() - 0.0) / 10;
+ if (tmpTickUnit2 > 0) {
+ this.outputTab.getFrequency1Slider().setMajorTickUnit(tmpTickUnit2);
+ this.outputTab.getFrequency2Slider().setMajorTickUnit(tmpTickUnit2);
+ }
+ //
+ this.updateOutputTab();
+ if (this.currentlyShownChart instanceof BarChart) {
+ this.outputTab.getBinBorder1Slider().setDisable(!(tmpTickUnit1 > 0));
+ this.outputTab.getBinBorder2Slider().setDisable(!(tmpTickUnit1 > 0));
+ this.outputTab.getFrequency1Slider().setDisable(!(tmpTickUnit2 > 0));
+ this.outputTab.getFrequency2Slider().setDisable(!(tmpTickUnit2 > 0));
+ }
+ });
+ //
+ //
+ this.outputTab.getNumberOfBinsTextField().addEventFilter(KeyEvent.KEY_PRESSED, (KeyEvent tmpEvent) -> {
+ KeyCombination tmpKeyCombination = new KeyCodeCombination(KeyCode.ENTER);
+ if (tmpKeyCombination.match(tmpEvent)) {
+ int tmpNumberOfBins;
+ try {
+ tmpNumberOfBins = Integer.parseInt(this.outputTab.getNumberOfBinsTextField().getText());
+ } catch (NumberFormatException ex) {
+ // This happens if the text field is empty or the input is too large
+ if (!this.outputTab.getNumberOfBinsTextField().getText().isEmpty()) {
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.NumberInputTooHigh.text"));
+ }
+ return;
+ }
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ if (tmpNumberOfBins >= 500) {
+ // Confirm, because binning could take a while
+ Optional tmpResult = GeneralUtilities.showConfirmationDialog(
+ this.applicationStage, GeneralUtilities.getUIText("ConfirmationDialog.ManyBinsContent.text"),
+ GeneralUtilities.getUIText("ConfirmationDialog.SelectionTitle.text"),
+ String.format(GeneralUtilities.getUIText("ConfirmationDialog.ManyBinsHeader.text"), tmpNumberOfBins)
+ );
+ if (tmpResult.isPresent() && tmpResult.get().getButtonData() == ButtonBar.ButtonData.APPLY) {
+ tmpHistogramData.setNumberOfBins(tmpNumberOfBins);
+ this.outputIsSaved = false;
+ } else {
+ return;
+ }
+ } else {
+ tmpHistogramData.setNumberOfBins(tmpNumberOfBins);
+ this.outputIsSaved = false;
+ }
+ // Resets the frequency bounds
+ tmpHistogramData.call();
+ // Update the reseted frequency bounds
+ this.updateOutputTab();
+ }
+ });
+ //
+ //
+ this.outputTab.getBinBorder1Slider().setOnMouseReleased((MouseEvent e) -> {
+ double tmpBinBorder1 = this.outputTab.getBinBorder1Slider().getValue();
+ double tmpBinBorder2 = this.outputTab.getBinBorder2Slider().getValue();
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ tmpHistogramData.setUpperBinBorder(tmpBinBorder1 > tmpBinBorder2 ? tmpBinBorder1 : tmpBinBorder2);
+ tmpHistogramData.setLowerBinBorder(tmpBinBorder1 < tmpBinBorder2 ? tmpBinBorder1 : tmpBinBorder2);
+ double tmpFrequency1SliderValue = this.outputTab.getFrequency1Slider().getValue();
+ double tmpFrequency2SliderValue = this.outputTab.getFrequency2Slider().getValue();
+ // Resets the frequency bounds
+ tmpHistogramData.call();
+ // Set the pre-reset frequency bounds
+ tmpHistogramData.setUpperFrequencyBound(tmpFrequency1SliderValue);
+ tmpHistogramData.setLowerFrequencyBound(tmpFrequency2SliderValue);
+ this.updateOutputTab();
+ this.outputIsSaved = false;
+ });
+ this.outputTab.getBinBorder2Slider().setOnMouseReleased((MouseEvent e) -> {
+ double tmpBinBorder1 = this.outputTab.getBinBorder1Slider().getValue();
+ double tmpBinBorder2 = this.outputTab.getBinBorder2Slider().getValue();
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ tmpHistogramData.setUpperBinBorder(tmpBinBorder1 > tmpBinBorder2 ? tmpBinBorder1 : tmpBinBorder2);
+ tmpHistogramData.setLowerBinBorder(tmpBinBorder1 < tmpBinBorder2 ? tmpBinBorder1 : tmpBinBorder2);
+ double tmpFrequency1SliderValue = this.outputTab.getFrequency1Slider().getValue();
+ double tmpFrequency2SliderValue = this.outputTab.getFrequency2Slider().getValue();
+ // Resets the frequency bounds
+ tmpHistogramData.call();
+ // Set the pre-reset frequency bounds
+ tmpHistogramData.setUpperFrequencyBound(tmpFrequency1SliderValue);
+ tmpHistogramData.setLowerFrequencyBound(tmpFrequency2SliderValue);
+ this.updateOutputTab();
+ this.outputIsSaved = false;
+ });
+ //
+ //
+ this.outputTab.getFrequency1Slider().setOnMouseReleased((MouseEvent e) -> {
+ double tmpFrequencyBound1 = this.outputTab.getFrequency1Slider().getValue();
+ double tmpFrequencyBound2 = this.outputTab.getFrequency2Slider().getValue();
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ tmpHistogramData.setUpperFrequencyBound(
+ tmpFrequencyBound1 > tmpFrequencyBound2 ? tmpFrequencyBound1 : tmpFrequencyBound2
+ );
+ tmpHistogramData.setLowerFrequencyBound(
+ tmpFrequencyBound1 < tmpFrequencyBound2 ? tmpFrequencyBound1 : tmpFrequencyBound2
+ );
+ this.updateOutputTab();
+ this.outputIsSaved = false;
+ });
+ this.outputTab.getFrequency2Slider().setOnMouseReleased((MouseEvent e) -> {
+ double tmpFrequencyBound1 = this.outputTab.getFrequency1Slider().getValue();
+ double tmpFrequencyBound2 = this.outputTab.getFrequency2Slider().getValue();
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ tmpHistogramData.setUpperFrequencyBound(
+ tmpFrequencyBound1 > tmpFrequencyBound2 ? tmpFrequencyBound1 : tmpFrequencyBound2
+ );
+ tmpHistogramData.setLowerFrequencyBound(
+ tmpFrequencyBound1 < tmpFrequencyBound2 ? tmpFrequencyBound1 : tmpFrequencyBound2
+ );
+ this.updateOutputTab();
+ this.outputIsSaved = false;
+ });
+ //
+ //
+ this.outputTab.getBarLabelCheckBox().setOnAction((ActionEvent e) -> {
+ this.updateOutputTab();
+ });
+ //
+ //
+ this.outputTab.getBinLabelChoiceBox().setOnAction((ActionEvent e) -> {
+ this.currentlyChosenBinLabelType = this.outputTab.getBinLabelChoiceBox().getValue();
+ this.updateOutputTab();
+ });
+ //
+ //
+ this.outputTab.getDefaultButton().setOnAction((ActionEvent e) -> {
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ tmpHistogramData.setNumberOfBins(UserPreferences.getInstance().getDefaultNumberOfBins());
+ tmpHistogramData.setUseRelativeFrequencies(false);
+ tmpHistogramData.setLowerBinBorder(tmpHistogramData.getMinComparisonFeatureValue());
+ tmpHistogramData.setUpperBinBorder(tmpHistogramData.getMaxComparisonFeatureValue());
+ // Resets the frequency bounds
+ tmpHistogramData.call();
+ this.updateOutputTab();
+ });
+ //
+ //
+ this.outputTab.getChartConfigurationButton().setOnAction((ActionEvent e) -> {
+ //
+ if (this.currentlyChosenComparisonFeature == null) {
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.NoComparisonFeatureChosen.text"));
+ return;
+ }
+ //
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ this.chartConfigurationDialog.getLowerBinBorderInputField().setText(Double.toString(tmpHistogramData.getLowerBinBorder()));
+ this.chartConfigurationDialog.getUpperBinBorderInputField().setText(Double.toString(tmpHistogramData.getUpperBinBorder()));
+ this.chartConfigurationDialog.getLowerFrequencyBoundInputField().setText(Double.toString(tmpHistogramData.getLowerFrequencyBound()));
+ this.chartConfigurationDialog.getUpperFrequencyBoundInputField().setText(Double.toString(tmpHistogramData.getUpperFrequencyBound()));
+ this.chartConfigurationDialog.setHeaderText(String.format(GeneralUtilities.getUIText("ChartConfigurationDialog.Header.text"), this.currentlyChosenComparisonFeature.toString()));
+ this.chartConfigurationDialog.showAndWait();
+ });
+ //
+ //
+ this.outputTab.getBinBorderConfigurationButton().setOnAction((ActionEvent e) -> {
+ BinBorderConfigurationBox tmpBox;
+ this.binBorderConfigurationBoxList.clear();
+ int tmpIndex = 0;
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ for (double tmpDouble : tmpHistogramData.getBinBorders()) {
+ tmpBox = new BinBorderConfigurationBox(Double.toString(tmpDouble), Integer.toString(++tmpIndex));
+ tmpBox.getAddButton().setOnAction(this.binBorderConfigurationDialogAddHandler);
+ tmpBox.getRemoveButton().setOnAction(this.binBorderConfigurationDialogRemoveHandler);
+ tmpBox.getTextField().setTextFormatter(GeneralUtilities.getSignedDecimalNumberTextFormatter());
+ this.binBorderConfigurationBoxList.add(tmpBox);
+ // Removing is disabled if there are only two bin borders
+ tmpBox.getRemoveButton().setDisable(tmpHistogramData.getBinBorders().length <= 2);
+ }
+ this.binBorderConfigurationDialog.getBinBorderConfigurationBoxesBox().getChildren().setAll(this.binBorderConfigurationBoxList);
+ this.binBorderConfigurationDialog.showAndWait();
+ });
+ //
+ //
+ //
+ this.binBorderConfigurationDialog.getCancelButton().setOnAction((ActionEvent e) -> {
+ this.binBorderConfigurationDialog.hide();
+ });
+ this.binBorderConfigurationDialog.getApplyButton().setOnAction((ActionEvent e) -> {
+ ListIterator tmpIterator = this.binBorderConfigurationBoxList.listIterator();
+ while (tmpIterator.hasNext()) {
+ BinBorderConfigurationBox tmpBox = tmpIterator.next();
+ // Remove all BinConfigurationBoxs with invalid textfields
+ if (tmpBox.getTextField().getText() != null) {
+ try {
+ Double.parseDouble(tmpBox.getTextField().getText());
+ } catch (NumberFormatException ex) {
+ tmpIterator.remove();
+ }
+ } else {
+ tmpIterator.remove();
+ }
+ }
+ if (this.binBorderConfigurationBoxList.size() <= 1) {
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.InvalidBinBorders.text"));
+ return;
+ }
+ double[] tmpBinBorders = new double[this.binBorderConfigurationBoxList.size()];
+ int tmpIndex = 0;
+ for (BinBorderConfigurationBox tmpBox : this.binBorderConfigurationBoxList) {
+ tmpBinBorders[tmpIndex] = Double.parseDouble(tmpBox.getTextField().getText());
+ if (tmpIndex != 0 && tmpBinBorders[tmpIndex] <= tmpBinBorders[tmpIndex - 1]) {
+ // Every bin border has to be greater than the previous bin border
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.InvalidBinBorders.text"));
+ return;
+ }
+ tmpIndex++;
+ }
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ // Important: Do this first or else the new borders will not be used
+ tmpHistogramData.setNumberOfBins(tmpBinBorders.length - 1);
+ tmpHistogramData.setSpecificBinBorders(tmpBinBorders);
+ this.outputIsSaved = false;
+ // Resets the frequency bounds
+ tmpHistogramData.call();
+ // Update the reseted frequency bounds
+ this.updateOutputTab();
+ this.binBorderConfigurationDialog.hide();
+ });
+ this.binBorderConfigurationDialog.getDialogPane().addEventFilter(KeyEvent.KEY_PRESSED, (KeyEvent tmpEvent) -> {
+ KeyCombination tmpKeyCombination = new KeyCodeCombination(KeyCode.ENTER);
+ if (tmpKeyCombination.match(tmpEvent)) {
+ this.binBorderConfigurationDialog.getApplyButton().fire();
+ }
+ });
+ this.binBorderConfigurationDialog.getResetButton().setOnAction((ActionEvent e) -> {
+ BinBorderConfigurationBox tmpBox;
+ this.binBorderConfigurationBoxList.clear();
+ int tmpIndex = 0;
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ for (double tmpDouble : tmpHistogramData.getBinBorders()) {
+ tmpBox = new BinBorderConfigurationBox(Double.toString(tmpDouble), Integer.toString(++tmpIndex));
+ tmpBox.getAddButton().setOnAction(this.binBorderConfigurationDialogAddHandler);
+ tmpBox.getRemoveButton().setOnAction(this.binBorderConfigurationDialogRemoveHandler);
+ tmpBox.getTextField().setTextFormatter(GeneralUtilities.getSignedDecimalNumberTextFormatter());
+ this.binBorderConfigurationBoxList.add(tmpBox);
+ // Removing is disabled if there are only two bin borders
+ tmpBox.getRemoveButton().setDisable(tmpHistogramData.getBinBorders().length <= 2);
+ }
+ this.binBorderConfigurationDialog.getBinBorderConfigurationBoxesBox().getChildren().setAll(this.binBorderConfigurationBoxList);
+ });
+ this.chartConfigurationDialog.getCancelButton().setOnAction((ActionEvent e) -> {
+ this.chartConfigurationDialog.hide();
+ });
+ this.chartConfigurationDialog.getApplyButton().setOnAction((ActionEvent e) -> {
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ if (this.isValidLowerBinBorder) {
+ tmpHistogramData.setLowerBinBorder(Double.parseDouble(this.chartConfigurationDialog.getLowerBinBorderInputField().getText()));
+ this.outputIsSaved = false;
+ }
+ if (this.isValidUpperBinBorder) {
+ tmpHistogramData.setUpperBinBorder(Double.parseDouble(this.chartConfigurationDialog.getUpperBinBorderInputField().getText()));
+ this.outputIsSaved = false;
+ }
+ // Resets the frequency bounds
+ tmpHistogramData.call();
+ // Set the new frequency bounds AFTER the binning
+ if (this.isValidLowerFrequencyBound) {
+ double tmpDouble = Double.parseDouble(this.chartConfigurationDialog.getLowerFrequencyBoundInputField().getText());
+ if (tmpHistogramData.isUseRelativeFrequencies() && tmpDouble > 1.5) {
+ GeneralUtilities.showInfoDialog(
+ this.applicationStage, String.format(GeneralUtilities.getUIText("InfoDescription.RelativeFrequencyTooHigh.text"), tmpDouble)
+ );
+ } else {
+ tmpHistogramData.setLowerFrequencyBound(tmpDouble);
+ this.outputIsSaved = false;
+ }
+ }
+ if (this.isValidUpperFrequencyBound) {
+ double tmpDouble = Double.parseDouble(this.chartConfigurationDialog.getUpperFrequencyBoundInputField().getText());
+ if (tmpHistogramData.isUseRelativeFrequencies() && tmpDouble > 1.5) {
+ GeneralUtilities.showInfoDialog(
+ this.applicationStage, String.format(GeneralUtilities.getUIText("InfoDescription.RelativeFrequencyTooHigh.text"), tmpDouble)
+ );
+ } else {
+ tmpHistogramData.setUpperFrequencyBound(tmpDouble);
+ this.outputIsSaved = false;
+ }
+ }
+ this.updateOutputTab();
+ this.chartConfigurationDialog.hide();
+ });
+ this.chartConfigurationDialog.getDialogPane().addEventFilter(KeyEvent.KEY_PRESSED, (KeyEvent tmpEvent) -> {
+ KeyCombination tmpKeyCombination = new KeyCodeCombination(KeyCode.ENTER);
+ if (tmpKeyCombination.match(tmpEvent)) {
+ this.chartConfigurationDialog.getApplyButton().fire();
+ }
+ });
+ this.chartConfigurationDialog.getResetButton().setOnAction((ActionEvent e) -> {
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ this.chartConfigurationDialog.getLowerBinBorderInputField().setText(Double.toString(this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature).getLowerBinBorder()));
+ this.chartConfigurationDialog.getUpperBinBorderInputField().setText(Double.toString(tmpHistogramData.getUpperBinBorder()));
+ this.chartConfigurationDialog.getLowerFrequencyBoundInputField().setText(Double.toString(tmpHistogramData.getLowerFrequencyBound()));
+ this.chartConfigurationDialog.getUpperFrequencyBoundInputField().setText(Double.toString(tmpHistogramData.getUpperFrequencyBound()));
+ });
+ this.chartConfigurationDialog.getDefaultButton().setOnAction((ActionEvent e) -> {
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ this.chartConfigurationDialog.getLowerBinBorderInputField().setText(Double.toString(tmpHistogramData.getMinComparisonFeatureValue()));
+ this.chartConfigurationDialog.getUpperBinBorderInputField().setText(Double.toString(tmpHistogramData.getMaxComparisonFeatureValue()));
+ this.chartConfigurationDialog.getLowerFrequencyBoundInputField().setText(Double.toString(0.0));
+ this.chartConfigurationDialog.getUpperFrequencyBoundInputField().setText(Double.toString(tmpHistogramData.getMaxFrequency()));
+ });
+ //
+ //
+ //
+ if (!tmpIsLoaded) {
+ this.inputTab.getButtonsTitledPane().setExpanded(true);
+ this.inputTab.getInputType1ChoiceBox().setValue(InputType.SMILES);
+ this.inputTab.getInputType2ChoiceBox().setValue(InputType.SMILES);
+ this.inputTab.getJobStartButton().setDisable(true);
+ this.inputTab.getJobCancelButton().setDisable(true);
+ this.inputTab.getJobProgressBar().setVisible(false);
+ this.inputTab.getJobInfoLabel().setText(GeneralUtilities.getUIText("InfoDescription.NewJob.text"));
+ }
+ //
+ }
+ //
+ //
+ //
+ //
+ //
+ /**
+ * True if the output of this JobController is saved, false otherwise
+ *
+ * @return true if the output of this JobController is saved,
+ * false otherwise
+ */
+ public boolean outputIsSaved() {
+ return this.outputIsSaved;
+ }
+
+ /**
+ * Get the InputTab of this JobController
+ *
+ * @return the InputTab
+ */
+ public InputTab getInputTab() {
+ return this.inputTab;
+ }
+
+ /**
+ * Get the JobTaskManager of this JobController or null if this
+ * JobController was loaded
+ *
+ * @return the JobTaskManager
+ */
+ public JobTaskManager getJobTaskManager() {
+ return this.jobTaskManager;
+ }
+
+ /**
+ * Get the HistogramDataManager
+ *
+ * @return the HistogramDataManager
+ */
+ public HistogramDataManager getHistogramDataManager() {
+ return this.histogramDataManager;
+ }
+
+ /**
+ * Get the ComparisonFeature that is currently selected in the OutputTab
+ *
+ * @return the currently selected ComparisonFeature
+ */
+ public ComparisonFeature getCurrentlyChosenComparisonFeature() {
+ return this.currentlyChosenComparisonFeature;
+ }
+
+ /**
+ * Get the OutputTab of this JobController
+ *
+ * @return the OutputTab
+ */
+ public OutputTab getOutputTab() {
+ return this.outputTab;
+ }
+
+ /**
+ * Get the number that identifies this JobController in the current
+ * application session
+ *
+ * @return the number of this JobController
+ */
+ public String getJobNumber() {
+ return this.jobNumber;
+ }
+ //
+ //
+ /**
+ * Set the HistogramDataManager
+ *
+ * @param tmpHistogramDataManager a HistogramDataManager
+ */
+ public void setHistogramDataManager(HistogramDataManager tmpHistogramDataManager) {
+ this.histogramDataManager = tmpHistogramDataManager;
+ }
+
+ /**
+ * Set whether the result of this JobController is saved or not
+ *
+ * @param tmpOutputIsSaved true if the output is saved, false otherwise
+ */
+ public void setOutputIsSaved(boolean tmpOutputIsSaved) {
+ this.outputIsSaved = tmpOutputIsSaved;
+ }
+
+ /**
+ * Set a value for the currentlyChosenComparisonFeature
+ *
+ * @param tmpCurrentlyChosenComparisonFeature the value to be set
+ */
+ public void setCurrentlyChosenComparisonFeature(ComparisonFeature tmpCurrentlyChosenComparisonFeature) {
+ this.currentlyChosenComparisonFeature = tmpCurrentlyChosenComparisonFeature;
+ }
+ //
+ //
+ //
+ /**
+ * Adds a PropertyChangeListener that listens for changes fired from this
+ * JobController
+ *
+ * @param tmpListener a listener to be added
+ */
+ public void addPropertyChangeListener(PropertyChangeListener tmpListener) {
+ this.propertyChangeSupport.addPropertyChangeListener(tmpListener);
+ }
+
+ /**
+ * Removes a PropertyChangeListener
+ *
+ * @param tmpListener a listener to be removed
+ */
+ public void removePropertyChangeListener(PropertyChangeListener tmpListener) {
+ this.propertyChangeSupport.removePropertyChangeListener(tmpListener);
+ }
+
+ /**
+ * Handle all PropertyChangeEvents that reach this JobController.
+ *
+ * @param evt a PropertyChangeEvent that reached this JobController
+ */
+ @Override
+ public void propertyChange(PropertyChangeEvent evt) {
+ try {
+ if (evt.getSource() instanceof JobTaskManager) {
+ switch (evt.getPropertyName()) {
+ case "Exception":
+ this.jobTaskManager.cancelWorkingProcess();
+ Exception tmpException = (Exception) evt.getNewValue();
+ String tmpOrigin = (String) evt.getOldValue();
+ Platform.runLater(() -> {
+ GeneralUtilities.showErrorDialog(this.applicationStage, tmpException.toString(), tmpOrigin);
+ GeneralUtilities.logException(Level.WARNING, tmpException);
+ });
+ break;
+ case "ParseAndCompareTasks progress":
+ synchronized (this) {
+ if (this.jobTaskManager.isWorking()) {
+ double tmpProgressValue = (double) evt.getNewValue();
+ Platform.runLater(() -> {
+ // The JavaFX Application can be only updated from the JavaFX Application Thread.
+ // NOTE: Applications should avoid flooding JavaFX with too many pending Runnables. Otherwise, the application may become unresponsive.
+ this.inputTab.getJobProgressBar().setProgress(tmpProgressValue);
+ this.inputTab.getJobInfoLabel().setText(
+ String.format(GeneralUtilities.getUIText("InfoDescription.ReadingInputProgress.text"), (int) (tmpProgressValue * 100))
+ );
+ });
+ }
+ }
+ break;
+ case "ParseAndCompareTasks finished":
+ synchronized (this) {
+ if (this.jobTaskManager.isWorking()) {
+ this.jobTaskManager.cancelWorkingProcess();
+ this.histogramDataManager = this.jobTaskManager.getHistogramDataManager();
+ this.histogramDataManager.setCalculationStartTime(this.calculationStartTime);
+ this.histogramDataManager.setCalculationFinishTime(System.currentTimeMillis());
+ Platform.runLater(() -> {
+ this.inputTab.getJobStartButton().setVisible(true);
+ this.inputTab.getJobCancelButton().setVisible(false);
+ this.inputTab.getJobProgressBar().setVisible(false);
+ this.inputTab.getJobInfoLabel().setText(GeneralUtilities.getUIText("InfoDescription.FinishedJob.text"));
+ // Set this first to avoid NullPointerExcpetions
+ this.currentlyChosenComparisonFeature = this.histogramDataManager.getComparisonFeatureSet().iterator().next();
+ this.outputTab.setBinLabelChoiceBoxItems(Set.of(BinLabelType.values()));
+ this.outputTab.setChartChoiceBoxItems(this.histogramDataManager.getComparisonFeatureSet());
+ this.outputTab.getBinLabelChoiceBox().setValue(this.currentlyChosenBinLabelType);
+ this.outputTab.getChartChoiceBox().setValue(this.currentlyChosenComparisonFeature);
+ this.outputTab.getInfoLabel().setText(String.format(
+ GeneralUtilities.getUIText("OutputTab.infoLabel.text"), this.jobNumber,
+ this.histogramDataManager.getNumberOfComparedPairs(), this.histogramDataManager.getInputFile1(),
+ this.histogramDataManager.getInputFile2()
+ ));
+ // Displays OutputTab and closes InputTab
+ this.propertyChangeSupport.firePropertyChange("Created charts successfully", false, true);
+ });
+ }
+ }
+ break;
+ case "Unpaired inputs":
+ Platform.runLater(() -> {
+ GeneralUtilities.showInfoDialog(this.applicationStage, String.format(
+ GeneralUtilities.getUIText("InfoDescription.UnpairedStrings.text"),
+ evt.getNewValue()
+ ));
+ });
+ break;
+ default:
+ GeneralUtilities.logMessage(
+ Level.INFO, "JobController", "propertyChange()",
+ String.format(GeneralUtilities.getUIText("Logging.UnexptectedPropertyChange.text"), evt.getPropertyName())
+ );
+ break;
+ }
+ }
+ } catch (Exception ex) {
+ Platform.runLater(() -> {
+ GeneralUtilities.showErrorDialog(this.applicationStage, ex.toString(), "JobController.propertyChange()");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ });
+ }
+ }
+ //
+ //
+ /**
+ * Create a BarChart from the given HistogramData. Also add a mouse click
+ * listener to every bar.
+ *
+ * @param tmpHistogramData the HistogramData from which the chart will be
+ * created
+ * @param tmpBinLabelType specifies the type of labeling used for the bins
+ * @return the created BarChart or an error label if something went wrong
+ */
+ public Region createChart(HistogramData tmpHistogramData, BinLabelType tmpBinLabelType) {
+ try {
+ //
+ CategoryAxis tmpXAxis = new CategoryAxis();
+ tmpXAxis.setLabel(GeneralUtilities.getUIText("OutputTab.xAxisLabel.text"));
+ tmpXAxis.setTickLabelFill(Color.color(0.2, 0.2, 0.2));
+ final NumberAxis tmpYAxis = new NumberAxis();
+ tmpYAxis.setLabel(GeneralUtilities.getUIText("OutputTab.yAxisLabel.text"));
+ tmpYAxis.setTickLabelFill(Color.color(0.2, 0.2, 0.2));
+ tmpYAxis.setAutoRanging(false);
+ BarChart tmpChart = new BarChart<>(tmpXAxis, tmpYAxis);
+ tmpChart.setBarGap(0.0);
+ tmpChart.setLegendVisible(false);
+ //
+ //
+ tmpYAxis.heightProperty().addListener(new ChangeListener() {
+
+ /**
+ * True if the last resize of the chart pane was done
+ * automatically, false otherwise
+ */
+ private boolean lastResizeWasAutomatic1 = false;
+
+ /**
+ * True if the last resize of the application stage was done
+ * automatically, false otherwise
+ */
+ private boolean lastResizeWasAutomatic2 = false;
+
+ @Override
+ public void changed(ObservableValue tmpObservableValue, Number tmpOldAxisHeight, Number tmpNewAxisHeight) {
+ double tmpUpperBound = tmpHistogramData.getUpperFrequencyBound();
+ double tmpLowerBound = tmpHistogramData.getLowerFrequencyBound();
+ double tmpBoundDifference = tmpUpperBound - tmpLowerBound;
+ double tmpTickSpacing = 25.0;
+ int tmpMaxTickNumber = (int) ((double) tmpNewAxisHeight / tmpTickSpacing);
+ double[] tmpTickUnits = {1, 2.5, 5};
+ double tmpResultTickUnit = -1;
+ if (JobController.this.outputTab.getRelativeFrequenciesCheckBox().isSelected()) {
+ double[] tmpFactors = {0.0000001, 0.000001, 0.00001, 0.0001, 0.001, 0.01, 0.1};
+ outerLoop:
+ for (double tmpFactor : tmpFactors) {
+ for (double tmpTickUnit : tmpTickUnits) {
+ if (tmpMaxTickNumber * tmpFactor * tmpTickUnit >= tmpBoundDifference) {
+ tmpResultTickUnit = tmpFactor * tmpTickUnit;
+ break outerLoop;
+ }
+ }
+ }
+ tmpResultTickUnit = tmpResultTickUnit == -1 ? 0.0000001 : tmpResultTickUnit;
+ tmpYAxis.setMinorTickVisible(true);
+ } else {
+ long[] tmpFactors = {1L, 10L, 100L, 1000L, 10000L, 100000L, 1000000L, 10000000L, 100000000L, 1000000000L, 10000000000L, 100000000000L, 1000000000000L, 10000000000000L, 100000000000000L};
+ outerLoop:
+ for (long tmpFactor : tmpFactors) {
+ for (double tmpTickUnit : tmpTickUnits) {
+ if (tmpMaxTickNumber * tmpFactor * tmpTickUnit >= tmpBoundDifference) {
+ tmpResultTickUnit = tmpFactor * tmpTickUnit;
+ break outerLoop;
+ }
+ }
+ }
+ tmpResultTickUnit = tmpResultTickUnit == -1 ? 1000000000000000L : tmpResultTickUnit;
+ tmpYAxis.setMinorTickVisible(tmpResultTickUnit >= 5);
+ }
+ tmpYAxis.setTickUnit(tmpResultTickUnit);
+ tmpYAxis.setLowerBound(tmpLowerBound);
+ tmpYAxis.setUpperBound((((int) (tmpUpperBound * 1.02 / tmpResultTickUnit)) + 1) * tmpResultTickUnit);
+ //
+ // If a chart has just been created the layout of the y-axis may be incorrect.
+ // This section tries to resize the y-axis and later undo the resize in an attempt to thus correct the layout of the y-axis
+ if ((double) tmpOldAxisHeight == 0.0 && JobController.this.applicationStage.isMaximized() && !JobController.this.histogramDataManager.getHistogramData(currentlyChosenComparisonFeature).isUseRelativeFrequencies()) {
+ JobController.this.outputTab.getChartPane().setMaxHeight(JobController.this.outputTab.getChartPane().getHeight() - 10);
+ this.lastResizeWasAutomatic1 = true;
+ } else if (this.lastResizeWasAutomatic1) {
+ JobController.this.outputTab.getChartPane().setMaxHeight(Double.MAX_VALUE);
+ JobController.this.outputTab.getChartPane().autosize();
+ this.lastResizeWasAutomatic1 = false;
+ } else if ((double) tmpOldAxisHeight == 0.0 || this.lastResizeWasAutomatic2) {
+ JobController.this.applicationStage.setHeight(JobController.this.applicationStage.getHeight() + (this.lastResizeWasAutomatic2 ? -5.8 : 5));
+ this.lastResizeWasAutomatic2 = !this.lastResizeWasAutomatic2;
+ }
+ //
+ }
+ });
+ //
+ double[] tmpFrequencyData = tmpHistogramData.getFrequencies();
+ List> tmpDataList = new LinkedList<>();
+ for (int i = tmpFrequencyData.length - 1; i >= 0; i--) {
+ //
+ double tmpFrequency = tmpFrequencyData[i];
+ String tmpCategory;
+ int tmpPrecision = tmpHistogramData.getComparisonFeauture().isContinuous() ? 3 : 2;
+ switch (tmpBinLabelType) {
+ case MIN:
+ tmpCategory = tmpHistogramData.getComparisonFeauture().isContinuous() ?
+ String.format("%." + tmpPrecision + "f", tmpHistogramData.getBinBorders()[i]) :
+ String.format("%d", (int) Math.ceil(tmpHistogramData.getBinBorders()[i]));
+ // Check for and eliminate duplicate categories
+ outerLoop:
+ while (true) {
+ for (XYChart.Data tmpData : tmpDataList) {
+ if (Double.parseDouble(tmpData.getXValue()) == Double.parseDouble((tmpCategory))) {
+ tmpCategory = String.format("%." + (++tmpPrecision) + "f", tmpHistogramData.getBinBorders()[i]);
+ continue outerLoop;
+ }
+ }
+ break;
+ }
+ break;
+ case MAX:
+ tmpCategory = tmpHistogramData.getComparisonFeauture().isContinuous() ?
+ String.format("%." + tmpPrecision + "f", tmpHistogramData.getBinBorders()[i + 1]) :
+ String.format("%d", (int) Math.ceil(tmpHistogramData.getBinBorders()[i + 1]));
+ // Check for and eliminate duplicate categories
+ outerLoop:
+ while (true) {
+ for (XYChart.Data tmpData : tmpDataList) {
+ if (Double.parseDouble(tmpData.getXValue()) == Double.parseDouble((tmpCategory))) {
+ tmpCategory = String.format("%." + (++tmpPrecision) + "f", tmpHistogramData.getBinBorders()[i + 1]);
+ continue outerLoop;
+ }
+ }
+ break;
+ }
+ break;
+ case MEAN:
+ tmpPrecision = tmpHistogramData.getComparisonFeauture().isContinuous() ? 3 : 1;
+ tmpCategory = String.format("%." + tmpPrecision + "f", (tmpHistogramData.getBinBorders()[i] + tmpHistogramData.getBinBorders()[i + 1]) / 2.0);
+ // Check for and eliminate duplicate categories
+ outerLoop:
+ while (true) {
+ for (XYChart.Data tmpData : tmpDataList) {
+ if (Double.parseDouble(tmpData.getXValue()) == Double.parseDouble((tmpCategory))) {
+ tmpCategory = String.format("%." + (++tmpPrecision) + "f", (tmpHistogramData.getBinBorders()[i] + tmpHistogramData.getBinBorders()[i + 1]) / 2.0);
+ continue outerLoop;
+ }
+ }
+ break;
+ }
+ break;
+ case INTERVAL:
+ if (i == tmpFrequencyData.length - 1 && tmpHistogramData.getComparisonFeauture().isContinuous()) {
+ tmpCategory = String.format(
+ "[%." + tmpPrecision + "f - %." + tmpPrecision + "f]",
+ tmpHistogramData.getBinBorders()[i], tmpHistogramData.getBinBorders()[i + 1]
+ );
+ } else if (i == tmpFrequencyData.length - 1) {
+ tmpCategory = String.format(
+ "[%d - %d]",
+ (int) Math.ceil(tmpHistogramData.getBinBorders()[i]), (int) Math.ceil(tmpHistogramData.getBinBorders()[i + 1])
+ );
+ } else if (tmpHistogramData.getComparisonFeauture().isContinuous()) {
+ tmpCategory = String.format(
+ "[%." + tmpPrecision + "f - %." + tmpPrecision + "f)",
+ tmpHistogramData.getBinBorders()[i], tmpHistogramData.getBinBorders()[i + 1]
+ );
+ } else {
+ tmpCategory = String.format(
+ "[%d - %d)",
+ (int) Math.ceil(tmpHistogramData.getBinBorders()[i]), (int) Math.ceil(tmpHistogramData.getBinBorders()[i + 1])
+ );
+ }
+ // Check for and eliminate duplicate categories
+ outerLoop:
+ while (true) {
+ for (XYChart.Data tmpData : tmpDataList) {
+ if (tmpData.getXValue().equals(tmpCategory)) {
+ tmpCategory = String.format(
+ "[%." + (++tmpPrecision) + "f - %." + (++tmpPrecision) + "f)",
+ tmpHistogramData.getBinBorders()[i], tmpHistogramData.getBinBorders()[i + 1]
+ );
+ continue outerLoop;
+ }
+ }
+ break;
+ }
+ break;
+ default:
+ tmpCategory = "";
+ }
+ XYChart.Data tmpData = new XYChart.Data<>(tmpCategory, tmpFrequency);
+ tmpDataList.add(tmpData);
+ //
+ //
+ StackPane tmpMouseClickListener = new StackPane();
+ tmpMouseClickListener.setAlignment(Pos.TOP_CENTER);
+ //
+ if (this.outputTab.getBarLabelCheckBox().isSelected()) {
+ Label tmpBarLabel = tmpHistogramData.isUseRelativeFrequencies() ? new Label(new DecimalFormat("0.000").format(tmpFrequency)) : new Label(new DecimalFormat("###").format(tmpFrequency));
+ tmpMouseClickListener.getChildren().add(tmpBarLabel);
+ tmpYAxis.heightProperty().addListener((ObservableValue tmpObservableValue, Number tmpOldAxisHeight, Number tmpNewAxisHeight) -> {
+ double tmpMouseClickListenerHeight = tmpMouseClickListener.boundsInParentProperty().getValue().getHeight();
+ if (tmpMouseClickListenerHeight >= (double) tmpNewAxisHeight) {
+ tmpBarLabel.setTranslateY((tmpMouseClickListenerHeight + 5) - (double) tmpNewAxisHeight);
+ tmpBarLabel.setTextFill(Paint.valueOf("White"));
+ } else {
+ tmpBarLabel.setTranslateY(-20);
+ tmpBarLabel.setTextFill(Paint.valueOf("Black"));
+ }
+ });
+ }
+ //
+ List tmpComparisonResultList = tmpHistogramData.getBin(i);
+ int tmpBinNumber = i + 1;
+ // The list may be empty even though the bin is not
+ if (!tmpComparisonResultList.isEmpty()) {
+ tmpMouseClickListener.setOnMouseClicked((MouseEvent e) -> {
+ MoleculePairDisplayerController tmpController = new MoleculePairDisplayerController(
+ tmpComparisonResultList, this.applicationStage, this.fileChooser,
+ tmpBinNumber, tmpHistogramData.getComparisonFeauture(), tmpFrequency,
+ tmpHistogramData.getBinBorders()[tmpBinNumber - 1], tmpHistogramData.getBinBorders()[tmpBinNumber]
+ );
+ });
+ tmpMouseClickListener.setOnMouseEntered((MouseEvent e) -> {
+ this.scene.setCursor(Cursor.HAND);
+ });
+ tmpMouseClickListener.setOnMouseExited((MouseEvent e) -> {
+ this.scene.setCursor(Cursor.DEFAULT);
+ });
+ } else {
+ tmpMouseClickListener.setOnMouseClicked((MouseEvent e) -> {
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.NoMoleculesPairs.text"));
+ });
+ }
+ tmpData.setNode(tmpMouseClickListener);
+ //
+ }
+ //
+ XYChart.Series tmpSeries = new XYChart.Series<>();
+ ListIterator> tmpIterator = tmpDataList.listIterator(tmpDataList.size());
+ while (tmpIterator.hasPrevious()) {
+ tmpSeries.getData().add(tmpIterator.previous());
+ }
+ tmpChart.getData().add(tmpSeries);
+ //
+ return tmpChart;
+ } catch (Exception ex) {
+ GeneralUtilities.showErrorDialog(
+ this.applicationStage,
+ String.format(GeneralUtilities.getUIText("ErrorDescription.ChartCreationFailed.text"), tmpHistogramData.getComparisonFeauture().toString()),
+ "JobController.createChart()"
+ );
+ GeneralUtilities.logException(Level.WARNING, ex);
+ return new Label(String.format(GeneralUtilities.getUIText("InfoDescription.ChartPlaceHolder.text"), tmpHistogramData.getComparisonFeauture().toString()));
+ }
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Update the outputTab. Set the new chart and the states of some controls
+ */
+ private void updateOutputTab() {
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ this.outputTab.getFrequency1Slider().setValue(tmpHistogramData.getUpperFrequencyBound());
+ this.outputTab.getFrequency2Slider().setValue(tmpHistogramData.getLowerFrequencyBound());
+ this.outputTab.getBinBorder1Slider().setValue(tmpHistogramData.getUpperBinBorder());
+ this.outputTab.getBinBorder2Slider().setValue(tmpHistogramData.getLowerBinBorder());
+ this.outputTab.getNumberOfBinsTextField().setText(Integer.toString(tmpHistogramData.getNumberOfBins()));
+ this.outputTab.getRelativeFrequenciesCheckBox().setSelected(tmpHistogramData.isUseRelativeFrequencies());
+ this.currentlyShownChart = this.createChart(tmpHistogramData, this.currentlyChosenBinLabelType);
+ this.outputTab.setComparisonFeatureChart(this.currentlyShownChart);
+ if (this.currentlyShownChart instanceof Label) {
+ this.outputTab.getImageButton().setDisable(true);
+ this.outputTab.getSummaryReportButton().setDisable(true);
+ this.outputTab.getBinLabelChoiceBox().setDisable(true);
+ this.outputTab.getChartConfigurationButton().setDisable(true);
+ this.outputTab.getDefaultButton().setDisable(true);
+ this.outputTab.getBinBorderConfigurationButton().setDisable(true);
+ this.outputTab.getRelativeFrequenciesCheckBox().setDisable(true);
+ this.outputTab.getNumberOfBinsTextField().setDisable(true);
+ this.outputTab.getBinBorder1Slider().setDisable(true);
+ this.outputTab.getBinBorder2Slider().setDisable(true);
+ this.outputTab.getFrequency1Slider().setDisable(true);
+ this.outputTab.getFrequency2Slider().setDisable(true);
+ } else if (this.currentlyShownChart instanceof BarChart) {
+ this.outputTab.getImageButton().setDisable(false);
+ this.outputTab.getSummaryReportButton().setDisable(false);
+ this.outputTab.getBinLabelChoiceBox().setDisable(false);
+ this.outputTab.getChartConfigurationButton().setDisable(false);
+ this.outputTab.getDefaultButton().setDisable(false);
+ this.outputTab.getBinBorderConfigurationButton().setDisable(false);
+ this.outputTab.getRelativeFrequenciesCheckBox().setDisable(false);
+ this.outputTab.getNumberOfBinsTextField().setDisable(false);
+ this.outputTab.getBinBorder1Slider().setDisable(false);
+ this.outputTab.getBinBorder2Slider().setDisable(false);
+ this.outputTab.getFrequency1Slider().setDisable(false);
+ this.outputTab.getFrequency2Slider().setDisable(false);
+ }
+ }
+ //
+
+}
\ No newline at end of file
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/control/MoleculePairDisplayerController.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/control/MoleculePairDisplayerController.java
new file mode 100644
index 0000000..377863a
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/control/MoleculePairDisplayerController.java
@@ -0,0 +1,723 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.control;
+
+import de.whs.ibci.msc.model.ComparisonUtility;
+import de.whs.ibci.msc.model.ComparisonFeature;
+import de.whs.ibci.msc.model.ComparisonResult;
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.utility.GuiUtilities;
+import de.whs.ibci.msc.utility.MSCConstants;
+import de.whs.ibci.msc.view.MoleculePairDisplayerStage;
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.geom.AffineTransform;
+import java.awt.image.BufferedImage;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.nio.file.Files;
+import java.text.DecimalFormat;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
+import java.util.ListIterator;
+import java.util.logging.Level;
+import javafx.application.Platform;
+import javafx.beans.value.ObservableValue;
+import javafx.concurrent.Task;
+import javafx.embed.swing.SwingFXUtils;
+import javafx.scene.Cursor;
+import javafx.scene.control.CheckBox;
+import javafx.scene.control.Control;
+import javafx.scene.control.Labeled;
+import javafx.scene.input.KeyCode;
+import javafx.scene.input.KeyCodeCombination;
+import javafx.scene.input.KeyCombination;
+import javafx.scene.input.KeyEvent;
+import javafx.stage.FileChooser;
+import javafx.stage.Modality;
+import javafx.stage.Window;
+import javax.imageio.ImageIO;
+import org.apache.batik.dom.GenericDOMImplementation;
+import org.apache.batik.svggen.SVGGraphics2D;
+import org.apache.pdfbox.pdmodel.PDDocument;
+import org.apache.pdfbox.pdmodel.PDPage;
+import org.apache.pdfbox.pdmodel.PDPageContentStream;
+import org.apache.pdfbox.pdmodel.common.PDRectangle;
+import org.apache.pdfbox.pdmodel.graphics.image.LosslessFactory;
+import org.apache.pdfbox.pdmodel.graphics.image.PDImageXObject;
+import org.openscience.cdk.depict.DepictionGenerator;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
+import org.openscience.cdk.smiles.SmilesParser;
+import org.w3c.dom.DOMException;
+import org.w3c.dom.DOMImplementation;
+import org.w3c.dom.Document;
+
+/**
+ * Controller for a MoleculePairDisplayerStage that handles related events. This
+ * is used to display a list of molecule pairs
+ *
+ * @author Jan-Mathis Hein
+ */
+public class MoleculePairDisplayerController {
+
+ //
+ /**
+ * If true the MoleculePairDisplayerStage will be maximized,
+ * if false it will not
+ */
+ private static boolean isMaximized = false;
+
+ /**
+ * The MoleculePairDisplayerStage's initial width
+ */
+ private static double stageWidth = Double.NaN;
+
+ /**
+ * The MoleculePairDisplayerStage's initial height
+ */
+ private static double stageHeight = Double.NaN;
+
+ /**
+ * The MoleculePairDisplayerStage's initial X position
+ */
+ private static double stageXPosition = Double.NaN;
+
+ /**
+ * The MoleculePairDisplayerStage's initial Y position
+ */
+ private static double stageYPosition = Double.NaN;
+
+ /**
+ * Directory where the last molecule list file of any
+ * MoleculePairDisplayerController was saved
+ */
+ private static File lastMoleculeListFileDirectory;
+
+ /**
+ * Directory where the last molecule image file of any
+ * MoleculePairDisplayerController was saved
+ */
+ private static File lastMoleculeImageFileDirectory;
+ //
+ //
+ //
+ /**
+ * True if the last move of the comparisonResultListIterator was forward,
+ * false otherwise
+ */
+ private boolean wasLastIteratorStepForward;
+
+ /**
+ * The ComparisonFeature which was used for the comparison of the molecule
+ * pairs
+ */
+ private ComparisonFeature comparisonFeature;
+
+ /**
+ * The ComparisonResult that is currently displayed
+ */
+ private ComparisonResult currentComparisonResult;
+
+ /**
+ * Formats numerical input to fit the given pattern
+ */
+ private final DecimalFormat formatter = new DecimalFormat("###.##");
+
+ /**
+ * The lower border of the bin from which the molecule pairs will be
+ * displayed
+ */
+ private final double lowerBorder;
+
+ /**
+ * The upper border of the bin from which the molecule pairs will be
+ * displayed
+ */
+ private final double upperBorder;
+
+ /**
+ * The frequency-value of the bin from which the molecule pairs will be
+ * displayed
+ */
+ private final double frequencyValue;
+
+ /**
+ * Depicts molecules contained in IAtomContainers as BufferedImages
+ */
+ private DepictionGenerator depictionGenerator;
+
+ /**
+ * FileChooser to choose a location where images and lists of molecules will
+ * be saved
+ */
+ private FileChooser fileChooser;
+
+ /**
+ * List of ComparisonResults which contain the molecule pairs
+ * that will be displayed
+ */
+ private final List comparisonResultList;
+
+ /**
+ * Iterator for iterating through the comparisonResultList
+ */
+ private ListIterator comparisonResultListIterator;
+
+ /**
+ * MoleculePairDisplayerStage that is being controlled
+ */
+ private MoleculePairDisplayerStage moleculePairDisplayerStage;
+
+ /**
+ * Object that takes a SMILES string as input and parses it to the
+ * corresponding IAtomContainer
+ */
+ private final SmilesParser smilesParser = new SmilesParser(SilentChemObjectBuilder.getInstance());
+ //
+ //
+ //
+ /**
+ * Initialize instance variables, add event handlers, set up and show the
+ * MoleculePairDisplayerStage
+ *
+ * @param tmpMoleculePairList list of ComparisonResults which contain
+ * molecule pairs
+ * @param tmpOwner specifies the owner window of the
+ * MoleculePairDisplayerStage
+ * @param tmpFileChooser a FileChooser to choose a file where the molecule
+ * pair list will be saved
+ * @param tmpBinNumber specifies the number of the bin from which the
+ * molecule pairs will be displayed
+ * @param tmpComparisonFeature the ComparisonFeature which was used for the
+ * comparison of the molecule pairs
+ * @param tmpFrequencyValue the frequency-value of the bin from which the
+ * molecule pairs will be displayed
+ * @param tmpLowerBorder the lower border of the bin from which the
+ * molecule pairs will be displayed
+ * @param tmpUpperBorder the upper border of the bin from which the
+ * molecule pairs will be displayed
+ * @throws IllegalArgumentException if the tmpMoleculePairList is empty or
+ * null
+ */
+ public MoleculePairDisplayerController(
+ List tmpMoleculePairList, Window tmpOwner,
+ FileChooser tmpFileChooser, int tmpBinNumber, ComparisonFeature tmpComparisonFeature, double tmpFrequencyValue,
+ double tmpLowerBorder, double tmpUpperBorder
+ ) throws IllegalArgumentException {
+ //
+ if (tmpMoleculePairList == null || tmpMoleculePairList.isEmpty()) {
+ throw new IllegalArgumentException("Invalid moleculePairList");
+ }
+ //
+ //
+ this.comparisonResultList = tmpMoleculePairList;
+ this.comparisonResultListIterator = this.comparisonResultList.listIterator();
+ this.currentComparisonResult = this.comparisonResultListIterator.next();
+ this.wasLastIteratorStepForward = true;
+ this.moleculePairDisplayerStage = new MoleculePairDisplayerStage();
+ this.moleculePairDisplayerStage.setTitle(String.format(GeneralUtilities.getUIText("MoleculePairDisplayerStage.title.text"), tmpBinNumber));
+ this.moleculePairDisplayerStage.initOwner(tmpOwner);
+ this.moleculePairDisplayerStage.initModality(Modality.APPLICATION_MODAL);
+ this.fileChooser = tmpFileChooser;
+ this.comparisonFeature = tmpComparisonFeature;
+ this.frequencyValue = tmpFrequencyValue;
+ this.lowerBorder = tmpLowerBorder;
+ this.upperBorder = tmpUpperBorder;
+ this.depictionGenerator = new DepictionGenerator().withAtomColors().withSize(200, 200).withFillToFit().withBackgroundColor(Color.WHITE).withMargin(10);
+ //
+ //
+ this.updateDisplay();
+ //
+ //
+ this.moleculePairDisplayerStage.getNextButton().setOnAction((ActionEvent) -> {
+ if (!this.wasLastIteratorStepForward) {
+ // Iterator has to move one step further because of change of direction
+ this.comparisonResultListIterator.next();
+ }
+ this.currentComparisonResult = this.comparisonResultListIterator.next();
+ this.wasLastIteratorStepForward = true;
+ this.updateDisplay();
+ });
+ this.moleculePairDisplayerStage.getLastButton().setOnAction((ActionEvent) -> {
+ boolean tmpHadNext = this.comparisonResultListIterator.hasNext();
+ while (this.comparisonResultListIterator.hasNext()) {
+ this.currentComparisonResult = this.comparisonResultListIterator.next();
+ }
+ if (tmpHadNext) {
+ this.wasLastIteratorStepForward = true;
+ } else {
+ return;
+ }
+ this.updateDisplay();
+ });
+ this.moleculePairDisplayerStage.getPreviousButton().setOnAction((ActionEvent) -> {
+ if (this.wasLastIteratorStepForward) {
+ // Iterator has to move one step further because of change of direction
+ this.comparisonResultListIterator.previous();
+ }
+ this.currentComparisonResult = this.comparisonResultListIterator.previous();
+ this.wasLastIteratorStepForward = false;
+ this.updateDisplay();
+ });
+ this.moleculePairDisplayerStage.getFirstButton().setOnAction((ActionEvent) -> {
+ boolean tmpHadPrevious = this.comparisonResultListIterator.hasPrevious();
+ while (this.comparisonResultListIterator.hasPrevious()) {
+ this.currentComparisonResult = this.comparisonResultListIterator.previous();
+ }
+ if (tmpHadPrevious) {
+ this.wasLastIteratorStepForward = false;
+ } else {
+ return;
+ }
+ this.updateDisplay();
+ });
+ this.moleculePairDisplayerStage.getPositionTextField().addEventFilter(KeyEvent.KEY_PRESSED, (KeyEvent tmpEvent) -> {
+ KeyCombination tmpKeyCombination = new KeyCodeCombination(KeyCode.ENTER);
+ if (tmpKeyCombination.match(tmpEvent)) {
+ int tmpDesiredIndex;
+ try {
+ tmpDesiredIndex = Integer.parseInt(this.moleculePairDisplayerStage.getPositionTextField().getText());
+ } catch (NumberFormatException ex) {
+ // This happens if the text field is empty or the input is too large
+ if (!this.moleculePairDisplayerStage.getPositionTextField().getText().isEmpty()) {
+ GeneralUtilities.showInfoDialog(this.moleculePairDisplayerStage, GeneralUtilities.getUIText("InfoDescription.NumberInputTooHigh.text"));
+ }
+ return;
+ }
+ int tmpCurrentIndex = this.wasLastIteratorStepForward ? this.comparisonResultListIterator.nextIndex() : this.comparisonResultListIterator.nextIndex() + 1;
+ if (tmpDesiredIndex < tmpCurrentIndex && this.comparisonResultListIterator.hasPrevious()) {
+ if (this.wasLastIteratorStepForward) {
+ // Iterator has to move one step further because of change of direction
+ this.comparisonResultListIterator.previous();
+ }
+ do {
+ this.currentComparisonResult = this.comparisonResultListIterator.previous();
+ tmpCurrentIndex--;
+ } while (tmpDesiredIndex != tmpCurrentIndex && this.comparisonResultListIterator.hasPrevious());
+ this.wasLastIteratorStepForward = false;
+ } else if (tmpDesiredIndex > tmpCurrentIndex && this.comparisonResultListIterator.hasNext()) {
+ if (!this.wasLastIteratorStepForward) {
+ // Iterator has to move one step further because of change of direction
+ this.comparisonResultListIterator.next();
+ }
+ do {
+ this.currentComparisonResult = this.comparisonResultListIterator.next();
+ tmpCurrentIndex++;
+ } while (tmpDesiredIndex != tmpCurrentIndex && this.comparisonResultListIterator.hasNext());
+ this.wasLastIteratorStepForward = true;
+ } else {
+ return;
+ }
+ this.updateDisplay();
+ }
+ });
+ this.moleculePairDisplayerStage.getSaveLeftListButton().setOnAction((ActionEvent) -> {
+ this.saveMoleculeList(true);
+ });
+ this.moleculePairDisplayerStage.getSaveRightListButton().setOnAction((ActionEvent) -> {
+ this.saveMoleculeList(false);
+ });
+ this.moleculePairDisplayerStage.getSaveLeftImageButton().setOnAction((ActionEvent) -> {
+ this.saveMoleculeImage(true);
+ });
+ this.moleculePairDisplayerStage.getSaveRightImageButton().setOnAction((ActionEvent) -> {
+ this.saveMoleculeImage(false);
+ });
+ for (int i = 0; i < this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls().length; i++) {
+ Control[] tmpControlArray = this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls()[i];
+ int tmpIndex = i;
+ ((CheckBox) tmpControlArray[0]).selectedProperty().addListener((ObservableValue tmpObservableValue, Boolean tmpOldValue, Boolean tmpNewValue) -> {
+ try {
+ if (tmpNewValue) {
+ boolean[] tmpCalculateFeature = new boolean[this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls().length];
+ Arrays.fill(tmpCalculateFeature, false);
+ tmpCalculateFeature[tmpIndex] = true;
+ double[][] tmpCalculations = ComparisonUtility.compareMoleculePair(
+ tmpCalculateFeature, this.currentComparisonResult.getMolecule1(), this.currentComparisonResult.getMolecule2()
+ );
+ // This can be NaN if there aren't two seperate values for each molecule
+ if (!Double.isNaN(tmpCalculations[tmpIndex][0])) {
+ if (tmpCalculations[tmpIndex][1] < 0) {
+ ((Labeled) tmpControlArray[1]).setText(
+ "| " + this.formatter.format(tmpCalculations[tmpIndex][0])
+ + " - (" + this.formatter.format(tmpCalculations[tmpIndex][1])
+ + ") | = " + this.formatter.format(tmpCalculations[tmpIndex][2])
+ );
+ } else {
+ ((Labeled) tmpControlArray[1]).setText(
+ "| " + this.formatter.format(tmpCalculations[tmpIndex][0])
+ + " - " + this.formatter.format(tmpCalculations[tmpIndex][1])
+ + " | = " + this.formatter.format(tmpCalculations[tmpIndex][2])
+ );
+ }
+ } else {
+ ((Labeled) tmpControlArray[1]).setText(this.formatter.format(tmpCalculations[tmpIndex][2]));
+ }
+ } else {
+ ((Labeled) tmpControlArray[1]).setText("");
+ }
+ } catch (CDKException CDKException) {
+ ((Labeled) tmpControlArray[1]).setText("");
+ }
+ });
+ }
+ //
+ //
+ this.moleculePairDisplayerStage.getScene().addEventFilter(KeyEvent.KEY_PRESSED, (KeyEvent tmpEvent) -> {
+ KeyCombination tmpKeyCombination = new KeyCodeCombination(KeyCode.LEFT);
+ if (!this.moleculePairDisplayerStage.getPreviousButton().isDisabled() && tmpKeyCombination.match(tmpEvent)) {
+ this.moleculePairDisplayerStage.getPreviousButton().fire();
+ tmpEvent.consume();
+ }
+ tmpKeyCombination = new KeyCodeCombination(KeyCode.RIGHT);
+ if (!this.moleculePairDisplayerStage.getNextButton().isDisabled() && tmpKeyCombination.match(tmpEvent)) {
+ this.moleculePairDisplayerStage.getNextButton().fire();
+ tmpEvent.consume();
+ }
+ });
+ //
+ //
+ this.moleculePairDisplayerStage.getPositionTextField().setTextFormatter(GeneralUtilities.getUnsignedIntegerTextFormatter());
+ //
+ //
+ this.moleculePairDisplayerStage.setMinWidth(MSCConstants.MINIMAL_MOLECULE_DISPLAYER_WIDTH);
+ this.moleculePairDisplayerStage.setWidth(
+ Double.isNaN(MoleculePairDisplayerController.stageWidth) ?
+ MSCConstants.MINIMAL_MOLECULE_DISPLAYER_WIDTH :
+ MoleculePairDisplayerController.stageWidth
+ );
+ this.moleculePairDisplayerStage.setMinHeight(MSCConstants.MINIMAL_MOLECULE_DISPLAYER_HEIGHT);
+ this.moleculePairDisplayerStage.setHeight(
+ Double.isNaN(MoleculePairDisplayerController.stageHeight) ?
+ MSCConstants.MINIMAL_MOLECULE_DISPLAYER_HEIGHT :
+ MoleculePairDisplayerController.stageHeight
+ );
+ if (!Double.isNaN(MoleculePairDisplayerController.stageXPosition)) {
+ this.moleculePairDisplayerStage.setX(MoleculePairDisplayerController.stageXPosition);
+ }
+ if (!Double.isNaN(MoleculePairDisplayerController.stageXPosition)) {
+ this.moleculePairDisplayerStage.setY(MoleculePairDisplayerController.stageYPosition);
+ }
+ this.moleculePairDisplayerStage.setMaximized(MoleculePairDisplayerController.isMaximized);
+ this.moleculePairDisplayerStage.showAndWait();
+ MoleculePairDisplayerController.stageWidth = this.moleculePairDisplayerStage.getWidth();
+ MoleculePairDisplayerController.stageHeight = this.moleculePairDisplayerStage.getHeight();
+ MoleculePairDisplayerController.stageXPosition = this.moleculePairDisplayerStage.getX();
+ MoleculePairDisplayerController.stageYPosition = this.moleculePairDisplayerStage.getY();
+ MoleculePairDisplayerController.isMaximized = this.moleculePairDisplayerStage.isMaximized();
+ //
+ }
+ //
+ //
+ //
+ /**
+ * Save one of the molecule images in a file that the user chooses.
+ *
+ * @param tmpSaveLeft if true the image of the left molecule will be saved,
+ * if false the image of the right molecule will be saved
+ */
+ private void saveMoleculeImage(boolean tmpSaveLeft) {
+ try {
+ this.fileChooser.getExtensionFilters().clear();
+ this.fileChooser.getExtensionFilters().addAll(
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.All.text"), "*.*"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.pdf.text"), "*.pdf"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.png.text"), "*.png"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.jpeg.text"), "*.jpeg"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.svg.text"), "*.svg")
+ );
+ if (!UserPreferences.getInstance().getImageDir().isEmpty() && new File(UserPreferences.getInstance().getImageDir()).isDirectory()) {
+ this.fileChooser.setInitialDirectory(new File(UserPreferences.getInstance().getImageDir()));
+ } else {
+ this.fileChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ synchronized (MoleculePairDisplayerController.class) {
+ if (MoleculePairDisplayerController.lastMoleculeImageFileDirectory != null && MoleculePairDisplayerController.lastMoleculeImageFileDirectory.isDirectory()) {
+ this.fileChooser.setInitialDirectory(MoleculePairDisplayerController.lastMoleculeImageFileDirectory);
+ }
+ }
+ this.fileChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.MoleculeList.text"));
+ final File tmpFile = this.fileChooser.showSaveDialog(this.moleculePairDisplayerStage);
+ if (tmpFile == null) {
+ return;
+ }
+ boolean tmpIsNewFile = tmpFile.createNewFile();
+ if (!tmpFile.canWrite()) {
+ if (tmpIsNewFile) {
+ Files.delete(tmpFile.toPath());
+ }
+ return;
+ }
+ synchronized (MoleculePairDisplayerController.class) {
+ MoleculePairDisplayerController.lastMoleculeImageFileDirectory = tmpFile.getParentFile();
+ }
+ BufferedImage tmpBufferedImage;
+ // IMPORTANT: Setting tmpSideLength too high will cause the program to throw an exception
+ double tmpSideLength = 9800 * UserPreferences.getInstance().getImageQuality() + 200;
+ DepictionGenerator tmpDepictionGenerator = new DepictionGenerator().withAtomColors().withSize(tmpSideLength, tmpSideLength).withFillToFit().withBackgroundColor(Color.WHITE).withMargin(tmpSideLength / 20);
+ if (tmpSaveLeft) {
+ tmpBufferedImage = tmpDepictionGenerator.depict(this.smilesParser.parseSmiles(this.currentComparisonResult.getMolecule1())).toImg();
+ } else {
+ tmpBufferedImage = tmpDepictionGenerator.depict(this.smilesParser.parseSmiles(this.currentComparisonResult.getMolecule2())).toImg();
+ }
+ final String tmpFormat = tmpFile.getAbsolutePath().substring(tmpFile.getAbsolutePath().lastIndexOf(".")).toLowerCase();
+ Task tmpTask = new Task() {
+ @Override
+ protected Void call() throws Exception {
+ try {
+ switch (tmpFormat) {
+ case ".png":
+ ImageIO.write(tmpBufferedImage, "PNG", tmpFile);
+ break;
+ case ".jpg":
+ case ".jpeg":
+ BufferedImage tmpImage = new BufferedImage(tmpBufferedImage.getWidth(), tmpBufferedImage.getHeight(), BufferedImage.TYPE_INT_RGB);
+ // Change the color model of the BufferedImage for the jpeg format
+ Graphics2D tmpGraphics2D = tmpImage.createGraphics();
+ tmpGraphics2D.drawImage(tmpBufferedImage, 0, 0, null);
+ tmpGraphics2D.dispose();
+ ImageIO.write(tmpImage, "JPG", tmpFile);
+ break;
+ case ".svg":
+ DOMImplementation domImpl = GenericDOMImplementation.getDOMImplementation();
+ Document document = domImpl.createDocument("http://www.w3.org/2000/svg", "svg", null);
+ SVGGraphics2D tmpSvgGenerator = new SVGGraphics2D(document);
+ tmpSvgGenerator.drawImage(tmpBufferedImage, AffineTransform.getScaleInstance(100 / tmpSideLength, 100 / tmpSideLength), null);
+ try (BufferedWriter tmpWriter = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(tmpFile)))) {
+ tmpSvgGenerator.stream(tmpWriter);
+ }
+ break;
+ case ".pdf":
+ try (PDDocument tmpDocument = new PDDocument()) {
+ PDPage tmpPage = new PDPage();
+ tmpDocument.addPage(tmpPage);
+ PDImageXObject tmpPDImage = LosslessFactory.createFromImage(tmpDocument, tmpBufferedImage);
+ try (PDPageContentStream tmpStream = new PDPageContentStream(tmpDocument, tmpPage)) {
+ float tmpWidth = tmpBufferedImage.getWidth();
+ float tmpHeight = tmpBufferedImage.getHeight();
+ tmpPage.setMediaBox(new PDRectangle(tmpWidth, tmpHeight));
+ tmpStream.drawImage(tmpPDImage, 0, 0, tmpWidth, tmpHeight);
+ }
+ tmpDocument.save(tmpFile);
+ }
+ break;
+ default:
+ Platform.runLater(() -> {
+ GeneralUtilities.showInfoDialog(MoleculePairDisplayerController.this.moleculePairDisplayerStage, GeneralUtilities.getUIText("InfoDescription.FileFormatNotSupported.text"));
+ });
+ }
+ } catch (IOException | DOMException ex) {
+ Platform.runLater(() -> {
+ MoleculePairDisplayerController.this.moleculePairDisplayerStage.getScene().setCursor(Cursor.DEFAULT);
+ GeneralUtilities.showErrorDialog(MoleculePairDisplayerController.this.moleculePairDisplayerStage, ex.toString(), "MoleculePairDisplayerController.saveMoleculeImage()");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ });
+ } finally {
+ Platform.runLater(() -> {
+ MoleculePairDisplayerController.this.moleculePairDisplayerStage.getScene().setCursor(Cursor.DEFAULT);
+ });
+ }
+ return null;
+ }
+ };
+ Thread tmpBackgroundThread = new Thread(tmpTask);
+ this.moleculePairDisplayerStage.getScene().setCursor(Cursor.WAIT);
+ tmpBackgroundThread.start();
+ } catch (StringIndexOutOfBoundsException ex) {
+ GeneralUtilities.showInfoDialog(this.moleculePairDisplayerStage, GeneralUtilities.getUIText("InfoDescription.FileFormatNotSupported.text"));
+ } catch (IOException | CDKException ex) {
+ GeneralUtilities.showErrorDialog(
+ this.moleculePairDisplayerStage, ex.toString(),
+ "MoleculePairDisplayerController.saveMoleculeImage()"
+ );
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ }
+
+ /**
+ * Save either the left or the right list of molecules in a file that the
+ * user chooses.
+ *
+ * @param tmpSaveLeft if true the left list of molecules will be saved,
+ * if false the right list of molecules will be saved
+ */
+ private void saveMoleculeList(boolean tmpSaveLeft) {
+ try {
+ this.fileChooser.getExtensionFilters().clear();
+ this.fileChooser.getExtensionFilters().addAll(
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.All.text"), "*.*"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.Text.text"), "*.txt")
+ );
+ if (!UserPreferences.getInstance().getMoleculeListDir().isEmpty() && new File(UserPreferences.getInstance().getMoleculeListDir()).isDirectory()) {
+ this.fileChooser.setInitialDirectory(new File(UserPreferences.getInstance().getMoleculeListDir()));
+ } else {
+ this.fileChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ synchronized (MoleculePairDisplayerController.class) {
+ if (MoleculePairDisplayerController.lastMoleculeListFileDirectory != null && MoleculePairDisplayerController.lastMoleculeListFileDirectory.isDirectory()) {
+ this.fileChooser.setInitialDirectory(MoleculePairDisplayerController.lastMoleculeListFileDirectory);
+ }
+ }
+ this.fileChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.MoleculeList.text"));
+ final File tmpFile = this.fileChooser.showSaveDialog(this.moleculePairDisplayerStage);
+ if (tmpFile == null) {
+ return;
+ }
+ boolean tmpIsNewFile = tmpFile.createNewFile();
+ if (!tmpFile.canWrite()) {
+ if (tmpIsNewFile) {
+ Files.delete(tmpFile.toPath());
+ }
+ return;
+ }
+ synchronized (MoleculePairDisplayerController.class) {
+ MoleculePairDisplayerController.lastMoleculeListFileDirectory = tmpFile.getParentFile();
+ }
+ Task tmpTask = new Task() {
+ @Override
+ protected Void call() throws Exception {
+ try (BufferedWriter tmpMoleculeWriter = new BufferedWriter(new FileWriter(tmpFile))) {
+ Iterator tmpIterator = MoleculePairDisplayerController.this.comparisonResultList.iterator();
+ while (tmpIterator.hasNext()) {
+ ComparisonResult tmpResult = tmpIterator.next();
+ tmpMoleculeWriter.write(tmpSaveLeft ? tmpResult.getMolecule1().strip() : tmpResult.getMolecule2().strip());
+ tmpMoleculeWriter.newLine();
+ }
+ } catch (IOException ex) {
+ Platform.runLater(() -> {
+ MoleculePairDisplayerController.this.moleculePairDisplayerStage.getScene().setCursor(Cursor.DEFAULT);
+ });
+ try {
+ Files.delete(tmpFile.toPath());
+ } catch (IOException tmpEx) {
+ }
+ Platform.runLater(() -> {
+ GeneralUtilities.showErrorDialog(
+ MoleculePairDisplayerController.this.moleculePairDisplayerStage, ex.toString(),
+ "MoleculePairDisplayerController.saveMoleculeList()"
+ );
+ GeneralUtilities.logException(Level.WARNING, ex);
+ });
+ } finally {
+ Platform.runLater(() -> {
+ MoleculePairDisplayerController.this.moleculePairDisplayerStage.getScene().setCursor(Cursor.DEFAULT);
+ });
+ }
+ return null;
+ }
+ };
+ Thread tmpBackgroundThread = new Thread(tmpTask);
+ this.moleculePairDisplayerStage.getScene().setCursor(Cursor.WAIT);
+ tmpBackgroundThread.start();
+ } catch (IOException ex) {
+ GeneralUtilities.showErrorDialog(
+ this.moleculePairDisplayerStage, ex.toString(),
+ "MoleculePairDisplayerController.saveMoleculeList()"
+ );
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ }
+
+ /**
+ * Update the MoleculePairDisplayerStage
+ */
+ private void updateDisplay() {
+ DecimalFormat tmpFormat = new DecimalFormat("#.####");
+ try {
+ BufferedImage tmpBufferedImage;
+ tmpBufferedImage = this.depictionGenerator.depict(this.smilesParser.parseSmiles(this.currentComparisonResult.getMolecule1())).toImg();
+ this.moleculePairDisplayerStage.getLeftMoleculeImageView().setImage(SwingFXUtils.toFXImage(tmpBufferedImage, null));
+ tmpBufferedImage = this.depictionGenerator.depict(this.smilesParser.parseSmiles(this.currentComparisonResult.getMolecule2())).toImg();
+ this.moleculePairDisplayerStage.getRightMoleculeImageView().setImage(SwingFXUtils.toFXImage(tmpBufferedImage, null));
+ this.moleculePairDisplayerStage.getInfoLabel().setText(String.format(
+ GeneralUtilities.getUIText("MoleculePairDisplayerStage.infoLabel.text"),
+ this.comparisonFeature, this.comparisonResultList.size(),
+ tmpFormat.format(this.frequencyValue),
+ tmpFormat.format(this.lowerBorder), tmpFormat.format(this.upperBorder),
+ this.currentComparisonResult.getMolecule1().strip(), this.currentComparisonResult.getMolecule2().strip(),
+ this.currentComparisonResult.getSimilarities()[this.comparisonFeature.getFeatureNumber()]
+ ));
+ this.moleculePairDisplayerStage.getPositionTextField().setText(Integer.toString(
+ this.wasLastIteratorStepForward ?
+ this.comparisonResultListIterator.nextIndex() :
+ this.comparisonResultListIterator.nextIndex() + 1)
+ );
+ } catch (CDKException ex) {
+ this.moleculePairDisplayerStage.getRightMoleculeImageView().setImage(GuiUtilities.WHITE_SQUARE);
+ this.moleculePairDisplayerStage.getLeftMoleculeImageView().setImage(GuiUtilities.WHITE_SQUARE);
+ this.moleculePairDisplayerStage.getInfoLabel().setText(String.format(
+ GeneralUtilities.getUIText("MoleculePairDisplayerStage.infoLabel.text"),
+ this.comparisonFeature, this.comparisonResultList.size(),
+ tmpFormat.format(this.frequencyValue),
+ tmpFormat.format(this.lowerBorder), tmpFormat.format(this.upperBorder),
+ "", "", ""
+ ));
+ this.moleculePairDisplayerStage.getPositionTextField().setText("");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ try {
+ boolean[] tmpCalculateFeature = new boolean[this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls().length];
+ for (int i = 0; i < this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls().length; i++) {
+ tmpCalculateFeature[i] = ((CheckBox) this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls()[i][0]).isSelected();
+ }
+ double[][] tmpCalculations = ComparisonUtility.compareMoleculePair(
+ tmpCalculateFeature, this.currentComparisonResult.getMolecule1(), this.currentComparisonResult.getMolecule2()
+ );
+ for (int i = 0; i < this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls().length; i++) {
+ if (tmpCalculateFeature[i]) {
+ // This can be NaN if there aren't two seperate values for each molecule
+ if (!Double.isNaN(tmpCalculations[i][0])) {
+ if (tmpCalculations[i][1] < 0) {
+ ((Labeled) this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls()[i][1]).setText(
+ "| " + this.formatter.format(tmpCalculations[i][0]) +
+ " - (" + this.formatter.format(tmpCalculations[i][1]) +
+ ") | = " + this.formatter.format(tmpCalculations[i][2])
+ );
+ } else {
+ ((Labeled) this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls()[i][1]).setText(
+ "| " + this.formatter.format(tmpCalculations[i][0]) +
+ " - " + this.formatter.format(tmpCalculations[i][1]) +
+ " | = " + this.formatter.format(tmpCalculations[i][2])
+ );
+ }
+ } else {
+ ((Labeled) this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls()[i][1]).setText(this.formatter.format(tmpCalculations[i][2]));
+ }
+ } else {
+ ((Labeled) this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls()[i][1]).setText("");
+ }
+ }
+ } catch (CDKException ex) {
+ for (Control[] additionalComparisonFeatureControl : this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls()) {
+ ((Labeled) additionalComparisonFeatureControl[1]).setText("");
+ }
+ }
+ this.moleculePairDisplayerStage.getNextButton().setDisable(!this.comparisonResultListIterator.hasNext());
+ this.moleculePairDisplayerStage.getLastButton().setDisable(!this.comparisonResultListIterator.hasNext());
+ this.moleculePairDisplayerStage.getPreviousButton().setDisable(!this.comparisonResultListIterator.hasPrevious());
+ this.moleculePairDisplayerStage.getFirstButton().setDisable(!this.comparisonResultListIterator.hasPrevious());
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/control/UserPreferences.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/control/UserPreferences.java
new file mode 100644
index 0000000..df80605
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/control/UserPreferences.java
@@ -0,0 +1,334 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.control;
+
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.utility.MSCConstants;
+import java.beans.XMLDecoder;
+import java.beans.XMLEncoder;
+import java.io.BufferedInputStream;
+import java.io.BufferedOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.logging.Level;
+
+/**
+ * Handles, loads and permanently saves preferences of the user.
+ *
+ * @author Jan-Mathis Hein
+ */
+public class UserPreferences {
+
+ //
+ /**
+ * Instance of this class. Other instances should not exist
+ */
+ private static UserPreferences instance;
+
+ /**
+ * File where the user preferences will be saved
+ */
+ private static final File USER_PREFERENCE_FILE = new File(MSCConstants.MSC_FILES_DIRECTORY.getAbsolutePath() + File.separator + "UserPreferences.xml");
+ //
+ //
+ //
+ static {
+ if (UserPreferences.USER_PREFERENCE_FILE.canRead()) {
+ try {
+ try (XMLDecoder tmpDecoder = new XMLDecoder(new BufferedInputStream(new FileInputStream(UserPreferences.USER_PREFERENCE_FILE)))) {
+ UserPreferences.instance = (UserPreferences) tmpDecoder.readObject();
+ }
+ } catch (Exception ex) {
+ GeneralUtilities.logMessage(Level.INFO, "", "", GeneralUtilities.getUIText("Logging.PreferencesLoadingNotPossible.text"));
+ GeneralUtilities.logException(Level.WARNING, ex);
+ // Sets default values
+ UserPreferences.instance = new UserPreferences();
+ }
+ } else {
+ // Sets default values
+ UserPreferences.instance = new UserPreferences();
+ }
+ }
+ //
+ //
+ //
+ /**
+ * The preference for the input directory
+ */
+ private String inputDir = "";
+
+ /**
+ * The preference for the output directory
+ */
+ private String outputDir = "";
+
+ /**
+ * The preference for the image directory
+ */
+ private String imageDir = "";
+
+ /**
+ * The preference for the molecule list directory
+ */
+ private String moleculeListDir = "";
+
+ /**
+ * The preference for the summary report directory
+ */
+ private String summaryReportDir = "";
+
+ /**
+ * The preference for the number of parallel threads
+ */
+ private int numberOfParallelThreads = 1;
+
+ /**
+ * The preference for the default number of bins
+ */
+ private int defaultNumberOfBins = 10;
+
+ /**
+ * The preference for the maximal number of molecule pairs to be saved when
+ * saving a job
+ */
+ private int maximalNumberOfMoleculePairsToSave = 1000;
+
+ /**
+ * The preference for the quality of images. 0.0 corresponds to a low
+ * quality and 1.0 to a high quality.
+ * NOTE: The value can't be higher than 1 or lower than 0
+ */
+ private double imageQuality = 0.5;
+ //
+ //
+ //
+ /**
+ * Public empty constructor that does nothing. Should only be invoked in
+ * this class and by the XMLDecoder
+ */
+ public UserPreferences() {
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Get an instance. Other instances should not exist
+ *
+ * @return an instance
+ */
+ public static UserPreferences getInstance() {
+ return UserPreferences.instance;
+ }
+
+ /**
+ * Get the preference for the input directory
+ *
+ * @return the preference for the input directory
+ */
+ public String getInputDir() {
+ return this.inputDir;
+ }
+
+ /**
+ * Get the preference for the output directory
+ *
+ * @return the preference for the output directory
+ */
+ public String getOutputDir() {
+ return this.outputDir;
+ }
+
+ /**
+ * Get the preference for the image directory
+ *
+ * @return the preference for the image directory
+ */
+ public String getImageDir() {
+ return this.imageDir;
+ }
+
+ /**
+ * Get the preference for the molecule list directory
+ *
+ * @return the preference for the molecule list directory
+ */
+ public String getMoleculeListDir() {
+ return this.moleculeListDir;
+ }
+
+ /**
+ * Get the preference for the summary report directory
+ *
+ * @return the preference for the summary report directory
+ */
+ public String getSummaryReportDir() {
+ return this.summaryReportDir;
+ }
+
+ /**
+ * Get the preference for the number of parallel threads
+ *
+ * @return the preference for the number of parallel threads
+ */
+ public int getNumberOfParallelThreads() {
+ return this.numberOfParallelThreads;
+ }
+
+ /**
+ * Get the preference for the default number of bins
+ *
+ * @return the preference for the default number of bins
+ */
+ public int getDefaultNumberOfBins() {
+ return this.defaultNumberOfBins;
+ }
+
+ /**
+ * Get the preference for the maximal number of molecule pairs to be saved
+ *
+ * @return the preference for the maximal number of molecule pairs to be
+ * saved
+ */
+ public int getMaximalNumberOfMoleculePairsToSave() {
+ return this.maximalNumberOfMoleculePairsToSave;
+ }
+
+ /**
+ * Get the preference for the quality of images. 0.0 corresponds to a low
+ * quality and 1.0 to a high quality
+ *
+ * @return a value between 0.0 and 1.0 that represents the
+ * imageQuality preference
+ */
+ public double getImageQuality() {
+ return this.imageQuality;
+ }
+ //
+ //
+ /**
+ * Set the preference for the input directory
+ *
+ * @param tmpInputDir the input directory
+ */
+ public void setInputDir(String tmpInputDir) {
+ this.inputDir = tmpInputDir;
+ }
+
+ /**
+ * Set the preference for the output directory
+ *
+ * @param tmpOutputDir the output directory
+ */
+ public void setOutputDir(String tmpOutputDir) {
+ this.outputDir = tmpOutputDir;
+ }
+
+ /**
+ * Set the preference for the image directory
+ *
+ * @param tmpImageDir the image directory
+ */
+ public void setImageDir(String tmpImageDir) {
+ this.imageDir = tmpImageDir;
+ }
+
+ /**
+ * Set the preference for the molecule list directory
+ *
+ * @param tmpMoleculeListDir the molecule list directory
+ */
+ public void setMoleculeListDir(String tmpMoleculeListDir) {
+ this.moleculeListDir = tmpMoleculeListDir;
+ }
+
+ /**
+ * Set the preference for the summary report directory
+ *
+ * @param tmpSummaryReportDir the summary report directory
+ */
+ public void setSummaryReportDir(String tmpSummaryReportDir) {
+ this.summaryReportDir = tmpSummaryReportDir;
+ }
+
+ /**
+ * Set the preference for the number of parallel threads
+ *
+ * @param tmpNumberOfParallelThreads the number of parallel threads
+ */
+ public void setNumberOfParallelThreads(int tmpNumberOfParallelThreads) {
+ this.numberOfParallelThreads = tmpNumberOfParallelThreads;
+ }
+
+ /**
+ * Set the preference for the dafault number of bins
+ *
+ * @param tmpDefaultNumberOfBins the deafult number of bins
+ */
+ public void setDefaultNumberOfBins(int tmpDefaultNumberOfBins) {
+ this.defaultNumberOfBins = tmpDefaultNumberOfBins;
+ }
+
+ /**
+ * Set the preference for the maximal number of molecule pairs to be saved
+ *
+ * @param tmpMaximalNumberOfMoleculePairsToSave the maximal number of
+ * molecule pairs to be saved
+ */
+ public void setMaximalNumberOfMoleculePairsToSave(int tmpMaximalNumberOfMoleculePairsToSave) {
+ this.maximalNumberOfMoleculePairsToSave = tmpMaximalNumberOfMoleculePairsToSave;
+ }
+
+ /**
+ * Set the preference for the quality of images. 0.0 corresponds to a low
+ * quality and 1.0 to a high quality. If the value is higher than 1.0 or
+ * lower than 0.0, 1.0 or 0.0 is used instead
+ *
+ * @param tmpImageQuality the new value for the imageQuality preference
+ */
+ public void setImageQuality(double tmpImageQuality) {
+ if (tmpImageQuality < 0.0) {
+ tmpImageQuality = 0.0;
+ } else if (tmpImageQuality > 1.0) {
+ tmpImageQuality = 1.0;
+ }
+ this.imageQuality = tmpImageQuality;
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Permanently save the preferences as an XML file
+ */
+ public static synchronized void savePreferences() {
+ try {
+ UserPreferences.USER_PREFERENCE_FILE.createNewFile();
+ try (XMLEncoder tmpEncoder = new XMLEncoder(new BufferedOutputStream(new FileOutputStream(UserPreferences.USER_PREFERENCE_FILE)))) {
+ tmpEncoder.writeObject(UserPreferences.getInstance());
+ }
+ } catch (IOException ex) {
+ GeneralUtilities.logMessage(Level.INFO, "", "", GeneralUtilities.getUIText("Logging.PreferencesSavingNotPossible.text"));
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/main/Main.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/main/Main.java
new file mode 100644
index 0000000..a9d4dec
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/main/Main.java
@@ -0,0 +1,47 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.main;
+
+import de.whs.ibci.msc.control.ApplicationController;
+import java.util.Locale;
+import java.util.Properties;
+import javafx.application.Application;
+
+/**
+ * Main class of the application
+ *
+ * @author Jan-Mathis Hein
+ */
+public class Main {
+
+ //
+ /**
+ * Set the default locale and some properties and start the application
+ *
+ * @param args the command line arguments
+ */
+ public static void main(String[] args) {
+ Properties tmpProperties = new Properties(System.getProperties());
+ tmpProperties.setProperty("CdkUseLegacyAtomContainer", "f");
+ System.setProperties(tmpProperties);
+ Locale.setDefault(Locale.US);
+ Application.launch(ApplicationController.class, args);
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/ComparisonFeature.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/ComparisonFeature.java
new file mode 100644
index 0000000..98e7b5d
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/ComparisonFeature.java
@@ -0,0 +1,244 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+/**
+ * Defines different features that can be used to compare molecules
+ *
+ * @author Jan-Mathis Hein
+ */
+public enum ComparisonFeature {
+
+ //
+ TANIMOTO_BASIC_FINGERPRINTER ("Basic fingerprint", true, 0.0, 1.0, "The Tanimoto coefficient with the basic CDK fingerprint"),
+ TANIMOTO_LINGO_FINGERPRINTER ("LINGO fingerprint", true, 0.0, 1.0, "The Tanimoto coefficient with the LINGO fingerprint"),
+ TANIMOTO_EXTENDED_FINGERPRINTER ("Extended fingerprint", true, 0.0, 1.0, "The Tanimoto coefficient with the extended CDK fingerprint"),
+ TANIMOTO_ESTATE_FINGERPRINTER ("E-State fingerprint", true, 0.0, 1.0, "The Tanimoto coefficient with the E-State fingerprint"),
+ TANIMOTO_PUBCHEM_FINGERPRINTER ("PubChem fingerprint", true, 0.0, 1.0, "The Tanimoto coefficient with the pubchem fingerprint"),
+ TANIMOTO_SHORTEST_PATH_FINGERPRINTER ("Shortest path fingerprint", true, 0.0, 1.0, "The Tanimoto coefficient with the shortest path fingerprint"),
+ TANIMOTO_SUBSTRUCTURE_FINGERPRINTER ("Substructure fingerprint", true, 0.0, 1.0, "The Tanimoto coefficient with default substructure fingerprint"),
+ ATOM_COUNT ("Atom count", false, 0.0, Double.NaN, "The difference of the counts of all atoms"),
+ CARBON_COUNT ("C count", false, 0.0, Double.NaN, "The difference of the counts of all carbon atoms"),
+ OXYGEN_COUNT ("O count", false, 0.0, Double.NaN, "The difference of the counts of all oyxgen atoms"),
+ SULFUR_COUNT ("S count", false, 0.0, Double.NaN, "The difference of the counts of all sulfur atoms"),
+ NITROGEN_COUNT ("N count", false, 0.0, Double.NaN, "The difference of the counts of all nitrogen atoms"),
+ PHOSPHOR_COUNT ("P count", false, 0.0, Double.NaN, "The difference of the counts of all phosphor atoms"),
+ MOLECULAR_WEIGHT ("Molecular weight", true, 0.0, Double.NaN, "The difference of molecular weights"),
+ MANNHOLD_LOGP ("Mannhold LogP", true, Double.NaN, Double.NaN, "The difference of Mannhold LogP values"),
+ APOL ("Atomic polarizability", true, Double.NaN, Double.NaN, "The difference of atomic polarizabilites"),
+ ACIDIC_GROUP_COUNT ("Acidic group count", false, 0.0, Double.NaN, "The difference of the acidic group counts"),
+ AROMATIC_ATOM_COUNT ("Aromatic atom count", false, 0.0, Double.NaN, "The difference of the counts of all aromatic atoms"),
+ BASIC_GROUP_COUNT ("Basic group count", false, 0.0, Double.NaN, "The difference of basic group counts"),
+ BOND_COUNT ("Bond count", false, 0.0, Double.NaN, "The difference of counts of all bonds"),
+ AROMATIC_BOND_COUNT ("Aromatic bond count", false, 0.0, Double.NaN, "The difference of counts of all aromatic bonds"),
+ SINGLE_BOND_COUNT ("Single bond count", false, 0.0, Double.NaN, "The difference of counts of all single bonds"),
+ DOUBLE_BOND_COUNT ("Double bond count", false, 0.0, Double.NaN, "The difference of counts of all double bonds"),
+ TRIPLE_BOND_COUNT ("Triple bond count", false, 0.0, Double.NaN, "The difference of counts of all triple bonds"),
+ QUADRUPLE_BOND_COUNT ("Quadruple bond count", false, 0.0, Double.NaN, "The difference of counts of all quadruple bonds"),
+ ALL_SMALL_RINGS_COUNT ("Small rings count", false, 0.0, Double.NaN, "The difference of the counts of all rings with a size of 9 or smaller"),
+ AROMATIC_RINGS_COUNT ("Aromatic rings count", false, 0.0, Double.NaN, "The difference of the counts of all aromatic rings with a size of 9 or smaller"),
+ SIZE_3_RINGS_COUNT ("Size 3 rings count", false, 0.0, Double.NaN, "The difference of the counts of all rings with size 3"),
+ SIZE_4_RINGS_COUNT ("Size 4 rings count", false, 0.0, Double.NaN, "The difference of the counts of all rings with size 4"),
+ SIZE_5_RINGS_COUNT ("Size 5 rings count", false, 0.0, Double.NaN, "The difference of the counts of all rings with size 5"),
+ SIZE_6_RINGS_COUNT ("Size 6 rings count", false, 0.0, Double.NaN, "The difference of the counts of all rings with size 6"),
+ SIZE_7_RINGS_COUNT ("Size 7 rings count", false, 0.0, Double.NaN, "The difference of the counts of all rings with size 7"),
+ SIZE_8_RINGS_COUNT ("Size 8 rings count", false, 0.0, Double.NaN, "The difference of the counts of all rings with size 8"),
+ SIZE_9_RINGS_COUNT ("Size 9 rings count", false, 0.0, Double.NaN, "The difference of the counts of all rings with size 9"),
+ ALL_RINGS_COUNT ("All rings count", false, 0.0, Double.NaN, "The difference of the counts of all rings (no size limitation"),
+ ATS_CHARGE1 ("ATS charge", true, Double.NaN, Double.NaN, "The difference of the autocorrelations of a topological structure, where the weights are equal to the charges"),
+ ATS_MASS1 ("ATS mass", true, Double.NaN, Double.NaN, "The difference of the autocorrelations of a topological structure, where the weights are equal to the masses"),
+ ATS_POLARIZABILITY1 ("ATS polarizability", true, Double.NaN, Double.NaN, "The difference of the autocorrelations of a topological structure, where the weights are equal to the polarizabilities"),
+ BPOL ("Bond polarizabilities", true, Double.NaN, Double.NaN, "The difference of the bond polarizabilites"),
+ C1SP1_COUNT ("C1SP1 count", false, 0.0, Double.NaN, "The difference of the counts of sp1 hybridized carbons bound to 1 other carbon"),
+ C2SP1_COUNT ("C2SP1 count", false, 0.0, Double.NaN, "The difference of the counts of sp1 hybridized carbons bound to 2 other carbons"),
+ C1SP2_COUNT ("C1SP2 count", false, 0.0, Double.NaN, "The difference of the counts of sp2 hybridized carbons bound to 1 other carbon"),
+ C2SP2_COUNT ("C2SP2 count", false, 0.0, Double.NaN, "The difference of the counts of sp2 hybridized carbons bound to 2 other carbons"),
+ C3SP2_COUNT ("C3SP2 count", false, 0.0, Double.NaN, "The difference of the counts of sp2 hybridized carbons bound to 3 other carbons"),
+ C1SP3_COUNT ("C1SP3 count", false, 0.0, Double.NaN, "The difference of the counts of sp3 hybridized carbons bound to 1 other carbon"),
+ C2SP3_COUNT ("C2SP3 count", false, 0.0, Double.NaN, "The difference of the counts of sp3 hybridized carbons bound to 2 other carbons"),
+ C3SP3_COUNT ("C3SP3 count", false, 0.0, Double.NaN, "The difference of the counts of sp3 hybridized carbons bound to 3 other carbons"),
+ C4SP3_COUNT ("C4SP3 count", false, 0.0, Double.NaN, "The difference of the counts of sp3 hybridized carbons bound to 4 other carbons"),
+ ECCENTRIC_CONNECTIVITY_INDEX ("Eccentric connectivity", false, Double.NaN, Double.NaN, "The difference of the eccentric conectivity indices"),
+ FMF ("Fraction of MF", true, 0.0, 1.0, "The difference of the fractions of the number of heavy atoms in the molecular framework to the total number of heavy atoms"),
+ FCSP3 ("Fraction of SP3 carbons", true, 0.0, 1.0, "The difference of the fractions of the number of sp3 hybridized carbons to the total number of carbons"),
+ FPSA ("Fractional PSA", true, 0.0, 1.0, "The difference of the polar surface areas expressed as a ratio to the molecular size"),
+ FRAGMENT_COMPLEXITY ("Fragment complexity", true, Double.NaN, Double.NaN, "The difference of the values of the FragmentComplexityDescriptor of the CDK"),
+ H_BOND_ACCEPTOR_COUNT ("H-bond acceptor count", false, 0.0, Double.NaN, "The difference of the counts of H-bond acceptors"),
+ H_BOND_DONOR_COUNT ("H-bond donor count", false, 0.0, Double.NaN, "The difference of the counts of H-bond donors"),
+ JP_LOGP ("JPLogP", true, Double.NaN, Double.NaN, "The difference of the JPLogP values"),
+ KAPPA_SHAPE_INDEX_1 ("1. kappa shape index", true, Double.NaN, Double.NaN, "The difference of the first kappa shape indices"),
+ KAPPA_SHAPE_INDEX_2 ("2. kappa shape index", true, Double.NaN, Double.NaN, "The difference of the second kappa shape indices"),
+ KAPPA_SHAPE_INDEX_3 ("3. kappa shape index", true, Double.NaN, Double.NaN, "The difference of the third kappa shape indices"),
+ LARGEST_CHAIN ("Largest chain", false, 0.0, Double.NaN, "The difference of the lengths of the longest chains"),
+ LARGEST_PI_SYSTEM ("Largest pi system", false, 0.0, Double.NaN, "The difference of the sizes of the largest pi-systems"),
+ LONGEST_ALIPHATIC_CHAIN ("Longest aliphatic chain", false, 0.0, Double.NaN, "The difference of the lengths of the longest aliphatic chains"),
+ PETITJEAN_NUMBER ("Petitjean number", true, Double.NaN, Double.NaN, "The difference of the Petitjean numbers"),
+ PETITJEAN_SHAPE_INDEX ("Petitjean shape index", true, Double.NaN, Double.NaN, "The difference of the topological Petitjean shape indices"),
+ ROTATABLE_BOND_COUNT ("Rotatable bond count", false, 0.0, Double.NaN, "The difference of the counts of rotatable bonds"),
+ SPIRO_ATOM_COUNT ("Spiro atom count", false, 0.0, Double.NaN, "The difference of the coutns of spiro-atoms"),
+ TPSA ("Topolgical PSA", true, 0.0, Double.NaN, "The difference of the topological polar surface areas"),
+ VABC ("VdW volume (using VABC)", true, 0.0, Double.NaN, "The difference of the Van der Waals volumes calculated using VABC method"),
+ V_ADJ_MA ("Vertex adjacency", true, Double.NaN, Double.NaN, "The difference of the vertex adjacency numbers"),
+ WEIGHTED_PATH_1 ("Weighted path descriptor", true, Double.NaN, Double.NaN, "The difference of the values of the weighted path descriptor which characterizes molecular branching"),
+ WIENER_PATH ("Wiener path number", true, Double.NaN, Double.NaN, "The difference of the Wiener path numbers"),
+ WIENER_POLARITY ("Wiener polarity number", true, Double.NaN, Double.NaN, "The difference of the Wiener polarity numbers"),
+ X_LOGP ("XLogP", true, Double.NaN, Double.NaN, "The difference of the XLogP values"),
+ ZAGREB_INDEX ("Zagreb index", false, Double.NaN, Double.NaN, "The difference of the Zagreb indices"),
+ A_LOGP ("Ghose-Crippen LogP", true, Double.NaN, Double.NaN, "The difference of the ALogP values (Ghose-Crippen LogKow)"),
+ A_LOGP_2 ("Ghose-Crippen LogP 2", true, Double.NaN, Double.NaN, "The difference of the ALogP2 values (Ghose-Crippen LogKow)"),
+ MOLAR_REFRACTIVITY ("Molar refractivity", true, Double.NaN, Double.NaN, "The difference of the molar refractivities"),
+ EQUALITY ("Equality", false, 0.0, 1.0, "Returns 1 if the unique SMILES are the same, else returns 0");
+ //
+ //
+ //
+ /**
+ * If true this ComparisonFeature has continuous values, if false it has
+ * discrete values
+ */
+ private final boolean isContinuous;
+
+ /**
+ * The minimal value this ComparisonFeature can take on or NaN if no such
+ * value is defined
+ */
+ private final double minimalValue;
+
+ /**
+ * The maximal value this ComparisonFeature can take on or NaN if no such
+ * value is defined
+ */
+ private final double maximalValue;
+
+ /**
+ * A number that uniquely corresponds to a ComparisonFeature
+ */
+ private final int featureNumber;
+
+ /**
+ * The value for the featureNumber of the next ComparisonFeature
+ */
+ private static int nextFeatureNumber = 0;
+
+ /**
+ * A more userfriendly name for the ComparisonFeature
+ */
+ private final String name;
+
+ /**
+ * A detailed description for the ComparisonFeature
+ */
+ private final String detailedDescription;
+ //
+ //
+ //
+ /**
+ * Initialize the instance variables
+ *
+ * @param tmpName specifies a more userfriendly name for the
+ * ComparisonFeature
+ * @param tmpIsContinuous if true this ComparisonFeature has continuous
+ * values, if false it has discrete values
+ * @param tmpMinValue the minimal value this ComparisonFeature can take on
+ * or NaN if no such value is defined
+ * @param tmpMaxValue the minimal value this ComparisonFeature can take on
+ * or NaN if no such value is defined
+ * @param tmpDescription a detailed description for the ComparisonFeature
+ */
+ private ComparisonFeature(String tmpName, boolean tmpIsContinuous, double tmpMinValue, double tmpMaxValue, String tmpDescription) {
+ this.featureNumber = ComparisonFeature.getNextFeatureNumber();
+ this.isContinuous = tmpIsContinuous;
+ this.name = tmpName;
+ this.minimalValue = tmpMinValue;
+ this.maximalValue = tmpMaxValue;
+ this.detailedDescription = tmpDescription;
+ }
+ //
+ //
+ //
+ /**
+ * If true this ComparisonFeature has continuous values, if false it has
+ * discrete values
+ *
+ * @return true if this ComparisonFeature has continuous values,
+ * false if it has discrete values
+ */
+ public boolean isContinuous() {
+ return this.isContinuous;
+ }
+
+ /**
+ * Get the minimal value this ComparisonFeature can take on or NaN if no
+ * such value is defined
+ *
+ * @return the minimal value this ComparisonFeature can take on or NaN if no
+ * such value is defined
+ */
+ public double getMinimalValue() {
+ return this.minimalValue;
+ }
+
+ /**
+ * Get the maximal value this ComparisonFeature can take on or NaN if no
+ * such value is defined
+ *
+ * @return the maximal value this ComparisonFeature can take on or NaN if no
+ * such value is defined
+ */
+ public double getMaximalValue() {
+ return this.maximalValue;
+ }
+
+ /**
+ * Get the feature number corresponding to the ComparisonFeature
+ *
+ * @return the feature number
+ */
+ public int getFeatureNumber() {
+ return this.featureNumber;
+ }
+
+ /**
+ * Get the value for the next featureNumber an increment nextFeatureNumber
+ * by one
+ *
+ * @return the value for the next featureNumber
+ */
+ private static int getNextFeatureNumber() {
+ return ComparisonFeature.nextFeatureNumber++;
+ }
+
+ /**
+ * Get a detailed description for the ComparisonFeature
+ *
+ * @return a detailed description for the ComparisonFeature
+ */
+ public String getDetailedDescription() {
+ return this.detailedDescription;
+ }
+
+ /**
+ * Return a string representation of the ComparisonFeature
+ *
+ * @return a string representation of the ComparisonFeature
+ */
+ @Override
+ public String toString() {
+ return this.name;
+ }
+ //
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/ComparisonResult.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/ComparisonResult.java
new file mode 100644
index 0000000..4560144
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/ComparisonResult.java
@@ -0,0 +1,169 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+/**
+ * Represents the result of a molecule pair comparison. Also stores the two
+ * compared molecules as SMILES.
+ *
+ * @author Jan-Mathis Hein
+ */
+public class ComparisonResult {
+
+ //
+ /**
+ * Array with the different comparison results. The index corresponds to the
+ * number of the ComparisonFeature. If the computation of a comparison
+ * failed, Double.NaN is put instead
+ */
+ private final double[] similarities;
+
+ /**
+ * SMILES encoding of the first compared molecule
+ */
+ private String molecule1;
+
+ /**
+ * SMILES encoding of the second compared molecule
+ */
+ private String molecule2;
+
+ /**
+ * Unique identifier for this object
+ */
+ private final int identifier;
+
+ /**
+ * Reason why the comparison may have failed
+ */
+ private final String reasonOfFailure;
+ //
+ //
+ //
+ /**
+ * Initialize the instance variables
+ *
+ * @param tmpSimilarities the comparsion results in array form
+ * @param tmpMolecule1 SMILES encoding of the first compared molecule,
+ * should never be null
+ * @param tmpMolecule2 SMILES encoding of the second compared molecule,
+ * should never be null
+ * @param tmpIdentifier specifies an unique identifier for this object
+ */
+ public ComparisonResult(double[] tmpSimilarities, String tmpMolecule1, String tmpMolecule2, int tmpIdentifier) {
+ this.similarities = tmpSimilarities;
+ this.molecule1 = tmpMolecule1;
+ this.molecule2 = tmpMolecule2;
+ this.identifier = tmpIdentifier;
+ this.reasonOfFailure = "";
+ }
+
+ /**
+ * Initialize the instance variables
+ *
+ * @param tmpString reason why the comparison failed
+ * @param tmpIdentifier specifies an unique identifier for this object
+ */
+ public ComparisonResult(String tmpString, int tmpIdentifier) {
+ this.similarities = null;
+ this.molecule1 = "";
+ this.molecule2 = "";
+ this.reasonOfFailure = tmpString;
+ this.identifier = tmpIdentifier;
+ }
+ //
+ //
+ //
+ /**
+ * Get the comparison results. The index corresponds to the number of the
+ * ComparisonFeature. If the computation of a comparison failed, Double.NaN
+ * is put instead
+ *
+ * @return the comparison results
+ */
+ public double[] getSimilarities() {
+ return this.similarities;
+ }
+
+ /**
+ * Get the SMILES encoding of the first compared molecule
+ *
+ * @return the first molecule
+ */
+ public String getMolecule1() {
+ return this.molecule1;
+ }
+
+ /**
+ * Get the SMILES encoding of the second compared molecule
+ *
+ * @return the second molecule
+ */
+ public String getMolecule2() {
+ return this.molecule2;
+ }
+
+ /**
+ * Get the unique identifier of this object
+ *
+ * @return the unique identifier of this object
+ */
+ public int getIdentifier() {
+ return this.identifier;
+ }
+
+ /**
+ * Get the reason why the comparison failed
+ *
+ * @return the reason why the comparison failed
+ */
+ public String getReasonOfFailure() {
+ return this.reasonOfFailure;
+ }
+
+ /**
+ * True if for both molecules a SMILES encoding is available,
+ * false otherwise
+ *
+ * @return true if for both molecules a SMILES encoding is available,
+ * false otherwise
+ */
+ public boolean hasMoleculePair() {
+ return !this.molecule1.isBlank()&& !this.molecule2.isBlank();
+ }
+
+ /**
+ * Set the first molecule
+ *
+ * @param tmpMolecule specifies the molecule to set
+ */
+ public void setMolecule1(String tmpMolecule) {
+ this.molecule1 = tmpMolecule;
+ }
+
+ /**
+ * Set the second molecule
+ *
+ * @param tmpMolecule specifies the molecule to set
+ */
+ public void setMolecule2(String tmpMolecule) {
+ this.molecule2 = tmpMolecule;
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/ComparisonUtility.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/ComparisonUtility.java
new file mode 100644
index 0000000..7a7f72c
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/ComparisonUtility.java
@@ -0,0 +1,938 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.aromaticity.Aromaticity;
+import org.openscience.cdk.aromaticity.ElectronDonation;
+import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.fingerprint.*;
+import org.openscience.cdk.graph.Cycles;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IAtomType;
+import org.openscience.cdk.qsar.IMolecularDescriptor;
+import org.openscience.cdk.qsar.descriptors.molecular.*;
+import org.openscience.cdk.ringsearch.AllRingsFinder;
+import org.openscience.cdk.ringsearch.RingSearch;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
+import org.openscience.cdk.similarity.Tanimoto;
+import org.openscience.cdk.smiles.SmiFlavor;
+import org.openscience.cdk.smiles.SmilesGenerator;
+import org.openscience.cdk.smiles.SmilesParser;
+import org.openscience.cdk.tools.CDKHydrogenAdder;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
+import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
+
+/**
+ * This abstract class provides utility methods for the comparison of
+ * molecule pairs
+ *
+ * @author Jan-Mathis Hein
+ */
+public abstract class ComparisonUtility {
+
+ //
+ /**
+ * A molecular descriptor that calculates the number of acidic groups
+ */
+ private static final AcidicGroupCountDescriptor ACIDIC_GROUP_COUNT_DESCRIPTOR = new AcidicGroupCountDescriptor();
+
+ /**
+ * Calculates the total number of rings in a molecule
+ */
+ private static final AllRingsFinder ALL_RINGS_FINDER = new AllRingsFinder();
+
+ /**
+ * A molecular descriptor that calculates the number of aromatic atoms
+ */
+ private static final AromaticAtomsCountDescriptor AROMATIC_ATOMS_COUNTS_DESCRIPTOR = new AromaticAtomsCountDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the number of aromatic bonds
+ */
+ private static final AromaticBondsCountDescriptor AROMATIC_BONDS_COUNT_DESCRIPTOR = new AromaticBondsCountDescriptor();
+
+ /**
+ * Used to set the aromaticity flags of atoms in molecules
+ */
+ private static final Aromaticity AROMATICITY = new Aromaticity(ElectronDonation.cdk(), Cycles.or(Cycles.all(), Cycles.cdkAromaticSet()));
+
+ /**
+ * A molecular descriptor that calculates the number of atoms
+ */
+ private static final AtomCountDescriptor ATOM_COUNT_DESCRIPTOR = new AtomCountDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the atomic polarizability
+ */
+ private static final APolDescriptor A_POL_DESCRIPTOR = new APolDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the autocorrelation of a
+ * topological structure, where the weight is equal to the charges.
+ */
+ private static final AutocorrelationDescriptorCharge AUTOCORRELATION_DESCRIPTOR_CHARGE = new AutocorrelationDescriptorCharge();
+
+ /**
+ * A molecular descriptor that calculates the autocorrelation of a
+ * topological structure, where the weight is equal to the mass.
+ */
+ private static final AutocorrelationDescriptorMass AUTOCORRELATION_DESCRIPTOR_MASS = new AutocorrelationDescriptorMass();
+
+ /**
+ * A molecular descriptor that calculates the autocorrelation of a
+ * topological structure, where the weight is equal to the polarizability.
+ */
+ private static final AutocorrelationDescriptorPolarizability AUTOCORRELATION_DESCRIPTOR_POLARIZABILITY = new AutocorrelationDescriptorPolarizability();
+
+ /**
+ * A molecular descriptor that calculates the number of basic groups
+ */
+ private static final BasicGroupCountDescriptor BASCIS_GROUP_COUNT_DESCRIPTOR = new BasicGroupCountDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the number of bonds
+ */
+ private static final BondCountDescriptor BOND_COUNT_DESCRIPTOR = new BondCountDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the bond polarizability
+ */
+ private static final BPolDescriptor B_POL_DESCRIPTOR = new BPolDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the number of different carbon
+ * types
+ */
+ private static final CarbonTypesDescriptor CARBON_TYPES_DESCRIPTOR = new CarbonTypesDescriptor();
+
+ /**
+ * Matches atom types to atoms
+ */
+ private static final CDKAtomTypeMatcher CDK_ATOM_TYPE_MATCHER = CDKAtomTypeMatcher.getInstance(DefaultChemObjectBuilder.getInstance());
+
+ /**
+ * Adds implicit hydrogens to a molecule
+ */
+ private static final CDKHydrogenAdder CDK_HYDROGEN_ADDER = CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance());
+
+ /**
+ * A molecular descriptor that calculates the eccentric connectivity
+ */
+ private static final EccentricConnectivityIndexDescriptor ECCENTRIC_CONNECTIVITY_DESCRIPTOR = new EccentricConnectivityIndexDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the fraction of the molecular
+ * framework
+ */
+ private static final FMFDescriptor FMF_DESCRIPTOR = new FMFDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the fraction of CSP3 atoms
+ */
+ private static final FractionalCSP3Descriptor FRACTIONAL_CSP3_DESCRIPTOR = new FractionalCSP3Descriptor();
+
+ /**
+ * A molecular descriptor that calculates the fraction of the PSA
+ */
+ private static final FractionalPSADescriptor FRACTIONAL_PSA_DESCRIPTOR = new FractionalPSADescriptor();
+
+ /**
+ * A molecular descriptor that calculates the fragment complexity
+ */
+ private static final FragmentComplexityDescriptor FRAGMENT_COMPLEXITY_DESCRIPTOR = new FragmentComplexityDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the number of H-bond acceptors
+ */
+ private static final HBondAcceptorCountDescriptor HBOND_ACCEPTOR_COUNT_DESCRIPTOR = new HBondAcceptorCountDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the number of H-bond donors
+ */
+ private static final HBondDonorCountDescriptor HBOND_DONOR_COUNT_DESCRIPTOR = new HBondDonorCountDescriptor();
+
+ /**
+ * Generates a basic fingerprint for a molecule
+ */
+ private static final IFingerprinter BASIC_FINGERPRINTER = new Fingerprinter();
+
+ /**
+ * Generates a LINGO fingerprint for a molecule
+ */
+ private static final IFingerprinter LINGO_FINGERPRINTER = new LingoFingerprinter();
+
+ /**
+ * Generates an extended fingerprint for a molecule
+ */
+ private static final IFingerprinter EXTENDED_FINGERPRINTER = new ExtendedFingerprinter();
+
+ /**
+ * Generates a E-State fingerprint for a molecule
+ */
+ private static final IFingerprinter ESTATE_FINGERPRINTER = new EStateFingerprinter();
+
+ /**
+ * Generates a PubChem fingerprint for a molecule
+ */
+ private static final IFingerprinter PUBCHEM_FINGERPRINTER = new PubchemFingerprinter(DefaultChemObjectBuilder.getInstance());
+
+ /**
+ * Generates a shortest path fingerprint for a molecule
+ */
+ private static final IFingerprinter SHORTEST_PATH_FINGERPRINTER = new ShortestPathFingerprinter();
+
+ /**
+ * Generates a fingerprint for a molecule based on a given substructure set
+ */
+ private static final IFingerprinter SUBSTRUCTURE_FINGERPRINTER = new SubstructureFingerprinter();
+
+ /**
+ * A molecular descriptor that calculates the JP-logP value
+ */
+ private static final JPlogPDescriptor JP_LOGP_DESCRIPTOR = new JPlogPDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the kappa shape indices
+ */
+ private static final KappaShapeIndicesDescriptor KAPPA_SHAPE_INDICES_DESCRIPTOR = new KappaShapeIndicesDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the length of the largest chain
+ */
+ private static final LargestChainDescriptor LARGEST_CHAIN_DESCRIPTOR = new LargestChainDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the size of the largest pi system
+ */
+ private static final LargestPiSystemDescriptor LARGEST_PI_SYSTEM_DESCRIPTOR = new LargestPiSystemDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the lenght of the longest
+ * aliphatic chain
+ */
+ private static final LongestAliphaticChainDescriptor LONGEST_ALIPHATIC_CHAIN_DESCRIPTOR = new LongestAliphaticChainDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the Mannhold-logP value
+ */
+ private static final MannholdLogPDescriptor MANNHOLD_LOG_P_DESCRIPTOR = new MannholdLogPDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the Petitjean number
+ */
+ private static final PetitjeanNumberDescriptor PETITJEAN_NUMBER_DESCRIPTOR = new PetitjeanNumberDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the Petitjean shape index
+ */
+ private static final PetitjeanShapeIndexDescriptor PETITJEAN_SHAPE_INDEX_DESCRIPTOR = new PetitjeanShapeIndexDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the number of rotatable bonds
+ */
+ private static final RotatableBondsCountDescriptor ROTATABLE_BOND_COUNT = new RotatableBondsCountDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the number of small rings
+ */
+ private static final SmallRingDescriptor SMALL_RING_DESCRIPTOR = new SmallRingDescriptor();
+
+ /**
+ * Generates unique and canoncical SMILES
+ */
+ private static final SmilesGenerator SMILES_GENERATOR = new SmilesGenerator(SmiFlavor.Unique);
+
+ /**
+ * Parses SMILES to IAtomContainers
+ */
+ private static final SmilesParser SMILES_PARSER = new SmilesParser(SilentChemObjectBuilder.getInstance());
+
+ /**
+ * A molecular descriptor that calculates the number of spiro atoms
+ */
+ private static final SpiroAtomCountDescriptor SPIRO_ATOM_COUNT_DESCRIPTOR = new SpiroAtomCountDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the TPSA
+ */
+ private static final TPSADescriptor TPSA_DESCRIPTOR = new TPSADescriptor();
+
+ /**
+ * A molecular descriptor that calculates the VdW volume
+ */
+ private static final VABCDescriptor VABC_DESCRIPTOR = new VABCDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the vertex adjacency
+ */
+ private static final VAdjMaDescriptor V_ADJ_MA_DESCRIPTOR = new VAdjMaDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the molecular weight
+ */
+ private static final WeightDescriptor WEIGHT_DESCRIPTOR = new WeightDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the weighted path
+ */
+ private static final WeightedPathDescriptor WEIGHTER_PATH_DESCRIPTOR = new WeightedPathDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the Wiener numbers
+ */
+ private static final WienerNumbersDescriptor WIENER_NUMBERS_DESCRIPTOR = new WienerNumbersDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the X-logP value
+ */
+ private static final XLogPDescriptor X_LOGP_DESCRIPTOR = new XLogPDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the Zagreb index
+ */
+ private static final ZagrebIndexDescriptor ZAGREB_INDEY_DESCRIPTOR = new ZagrebIndexDescriptor();
+ //
+ //
+ //
+ static {
+ ComparisonUtility.ACIDIC_GROUP_COUNT_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ AllRingsFinder.usingThreshold(AllRingsFinder.Threshold.PubChem_99);
+ ComparisonUtility.A_POL_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.AROMATIC_ATOMS_COUNTS_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.AROMATIC_BONDS_COUNT_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.AUTOCORRELATION_DESCRIPTOR_CHARGE.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.AUTOCORRELATION_DESCRIPTOR_MASS.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.AUTOCORRELATION_DESCRIPTOR_POLARIZABILITY.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.BASCIS_GROUP_COUNT_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.B_POL_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.CARBON_TYPES_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.ECCENTRIC_CONNECTIVITY_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.FMF_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.FRACTIONAL_CSP3_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.FRAGMENT_COMPLEXITY_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.HBOND_ACCEPTOR_COUNT_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.HBOND_DONOR_COUNT_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.JP_LOGP_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.KAPPA_SHAPE_INDICES_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.LARGEST_CHAIN_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.LARGEST_PI_SYSTEM_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.LONGEST_ALIPHATIC_CHAIN_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.MANNHOLD_LOG_P_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.PETITJEAN_NUMBER_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.PETITJEAN_SHAPE_INDEX_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.ROTATABLE_BOND_COUNT.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.SMALL_RING_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.SPIRO_ATOM_COUNT_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.TPSA_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.VABC_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.V_ADJ_MA_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.WEIGHT_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.WEIGHTER_PATH_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.WIENER_NUMBERS_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.X_LOGP_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.ZAGREB_INDEY_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ }
+ //
+ //
+ //
+ /**
+ * Compare the given molecule based on the specified ComparisonFeatures and
+ * return an array containing the individual values
+ * (if available, else return NaN) and the resulting similarity for every
+ * ComparisonFeature
+ *
+ * @param tmpCalculateFeature specifies the ComparisonFeatures which will be
+ * calculated
+ * @param tmpSmiles1 the first molecule in SMILES form
+ * @param tmpSmiles2 the second molecule in SMILES form
+ * @return an array where each element is an array of the form
+ * {firstComparisonFeatureValue, secondComparisonFeatureValue,
+ * resultingSimilarity}. The index of the element corresponds to the
+ * featureNumber of the corresponding ComparisonFeature. If there are no
+ * individual values available for the molecules, NaN is returned instead.
+ * @throws org.openscience.cdk.exception.CDKException if there is something
+ * wrong with the molecules
+ */
+ public static synchronized double[][] compareMoleculePair(boolean[] tmpCalculateFeature, String tmpSmiles1, String tmpSmiles2) throws CDKException {
+ double[][] tmpResult = new double[tmpCalculateFeature.length][3];
+ //
+ IAtomContainer tmpMolecule1 = ComparisonUtility.SMILES_PARSER.parseSmiles(tmpSmiles1);
+ IAtomContainer tmpMolecule2 = ComparisonUtility.SMILES_PARSER.parseSmiles(tmpSmiles2);
+ RingSearch tmpRingSearch = new RingSearch(tmpMolecule1);
+ for (IAtom tmpAtom : tmpMolecule1.atoms()) {
+ tmpAtom.setIsInRing(tmpRingSearch.cyclic(tmpAtom));
+ IAtomType tmpType = ComparisonUtility.CDK_ATOM_TYPE_MATCHER.findMatchingAtomType(tmpMolecule1, tmpAtom);
+ AtomTypeManipulator.configure(tmpAtom, tmpType);
+ }
+ ComparisonUtility.CDK_HYDROGEN_ADDER.addImplicitHydrogens(tmpMolecule1);
+ AtomContainerManipulator.convertImplicitToExplicitHydrogens(tmpMolecule1);
+ // Set aromaticity flags
+ ComparisonUtility.AROMATICITY.apply(tmpMolecule1);
+ tmpRingSearch = new RingSearch(tmpMolecule2);
+ for (IAtom tmpAtom : tmpMolecule2.atoms()) {
+ tmpAtom.setIsInRing(tmpRingSearch.cyclic(tmpAtom));
+ IAtomType tmpType = ComparisonUtility.CDK_ATOM_TYPE_MATCHER.findMatchingAtomType(tmpMolecule2, tmpAtom);
+ AtomTypeManipulator.configure(tmpAtom, tmpType);
+ }
+ ComparisonUtility.CDK_HYDROGEN_ADDER.addImplicitHydrogens(tmpMolecule2);
+ AtomContainerManipulator.convertImplicitToExplicitHydrogens(tmpMolecule2);
+ // Set aromaticity flags
+ ComparisonUtility.AROMATICITY.apply(tmpMolecule2);
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.ACIDIC_GROUP_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.ACIDIC_GROUP_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ACIDIC_GROUP_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.ALL_RINGS_COUNT.getFeatureNumber()]) {
+ try {
+ int tmpRingCount1 = ComparisonUtility.ALL_RINGS_FINDER.findAllRings(tmpMolecule1).getAtomContainerCount();
+ int tmpRingCount2 = ComparisonUtility.ALL_RINGS_FINDER.findAllRings(tmpMolecule2).getAtomContainerCount();
+ tmpResult[ComparisonFeature.ALL_RINGS_COUNT.getFeatureNumber()] = new double[] {tmpRingCount1, tmpRingCount2, Math.abs(tmpRingCount1 - tmpRingCount2)};
+ } catch (CDKException CDKException) {
+ tmpResult[ComparisonFeature.ALL_RINGS_COUNT.getFeatureNumber()] = new double[] {Double.NaN, Double.NaN, Double.NaN};
+ }
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.A_LOGP.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.A_LOGP_2.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.MOLAR_REFRACTIVITY.getFeatureNumber()]) {
+ ALOGPDescriptor tmpALOGPDescriptor = new ALOGPDescriptor();
+ tmpALOGPDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpALOGPDescriptor.calculate(tmpMolecule1).getValue().toString().split(",");
+ String[] tmpArray2 = tmpALOGPDescriptor.calculate(tmpMolecule2).getValue().toString().split(",");
+ // Ghose-Grippen logP
+ if (tmpCalculateFeature[ComparisonFeature.A_LOGP.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.A_LOGP.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[0]), Double.parseDouble(tmpArray2[0]), Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]))};
+ }
+ // Ghose-Grippen logP 2
+ if (tmpCalculateFeature[ComparisonFeature.A_LOGP_2.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.A_LOGP_2.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[1]), Double.parseDouble(tmpArray2[1]), Math.abs(Double.parseDouble(tmpArray1[1]) - Double.parseDouble(tmpArray2[1]))};
+ }
+ // Molar refractivity
+ if (tmpCalculateFeature[ComparisonFeature.MOLAR_REFRACTIVITY.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.MOLAR_REFRACTIVITY.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[2]), Double.parseDouble(tmpArray2[2]), Math.abs(Double.parseDouble(tmpArray1[2]) - Double.parseDouble(tmpArray2[2]))};
+ }
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.APOL.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.APOL.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.A_POL_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.AROMATIC_ATOM_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.AROMATIC_ATOMS_COUNTS_DESCRIPTOR.setParameters(new Object[] {true});
+ tmpResult[ComparisonFeature.AROMATIC_ATOM_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.AROMATIC_ATOMS_COUNTS_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.AROMATIC_BOND_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.AROMATIC_BONDS_COUNT_DESCRIPTOR.setParameters(new Object[] {true});
+ tmpResult[ComparisonFeature.AROMATIC_BOND_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.AROMATIC_BONDS_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ // Atom count
+ if (tmpCalculateFeature[ComparisonFeature.ATOM_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR.setParameters(new Object[] {"*"});
+ tmpResult[ComparisonFeature.ATOM_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Carbon count
+ if (tmpCalculateFeature[ComparisonFeature.CARBON_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR.setParameters(new Object[] {"C"});
+ tmpResult[ComparisonFeature.CARBON_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Oxygen count
+ if (tmpCalculateFeature[ComparisonFeature.OXYGEN_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR.setParameters(new Object[] {"O"});
+ tmpResult[ComparisonFeature.OXYGEN_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Sulfur count
+ if (tmpCalculateFeature[ComparisonFeature.SULFUR_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR.setParameters(new Object[] {"S"});
+ tmpResult[ComparisonFeature.SULFUR_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Nitrogen count
+ if (tmpCalculateFeature[ComparisonFeature.NITROGEN_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR.setParameters(new Object[] {"N"});
+ tmpResult[ComparisonFeature.NITROGEN_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Phosphor count
+ if (tmpCalculateFeature[ComparisonFeature.PHOSPHOR_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR.setParameters(new Object[] {"P"});
+ tmpResult[ComparisonFeature.PHOSPHOR_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.ATS_CHARGE1.getFeatureNumber()]) {
+ String[] tmpArray1 = ComparisonUtility.AUTOCORRELATION_DESCRIPTOR_CHARGE.calculate(tmpMolecule1).getValue().toString().split(",");
+ String[] tmpArray2 = ComparisonUtility.AUTOCORRELATION_DESCRIPTOR_CHARGE.calculate(tmpMolecule2).getValue().toString().split(",");
+ tmpResult[ComparisonFeature.ATS_CHARGE1.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[0]), Double.parseDouble(tmpArray2[0]), Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]))};
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.ATS_MASS1.getFeatureNumber()]) {
+ String[] tmpArray1 = ComparisonUtility.AUTOCORRELATION_DESCRIPTOR_MASS.calculate(tmpMolecule1).getValue().toString().split(",");
+ String[] tmpArray2 = ComparisonUtility.AUTOCORRELATION_DESCRIPTOR_MASS.calculate(tmpMolecule2).getValue().toString().split(",");
+ tmpResult[ComparisonFeature.ATS_MASS1.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[0]), Double.parseDouble(tmpArray2[0]), Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]))};
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.ATS_POLARIZABILITY1.getFeatureNumber()]) {
+ String[] tmpArray1 = ComparisonUtility.AUTOCORRELATION_DESCRIPTOR_POLARIZABILITY.calculate(tmpMolecule1).getValue().toString().split(",");
+ String[] tmpArray2 = ComparisonUtility.AUTOCORRELATION_DESCRIPTOR_POLARIZABILITY.calculate(tmpMolecule2).getValue().toString().split(",");
+ tmpResult[ComparisonFeature.ATS_POLARIZABILITY1.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[0]), Double.parseDouble(tmpArray2[0]), Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]))};
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.BASIC_GROUP_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.BASIC_GROUP_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.BASCIS_GROUP_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ // Bond count
+ if (tmpCalculateFeature[ComparisonFeature.BOND_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR.setParameters(new Object[] {""});
+ tmpResult[ComparisonFeature.BOND_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Single bond count
+ if (tmpCalculateFeature[ComparisonFeature.SINGLE_BOND_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR.setParameters(new Object[] {"s"});
+ tmpResult[ComparisonFeature.SINGLE_BOND_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Double bond count
+ if (tmpCalculateFeature[ComparisonFeature.DOUBLE_BOND_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR.setParameters(new Object[] {"d"});
+ tmpResult[ComparisonFeature.DOUBLE_BOND_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Triple bond count
+ if (tmpCalculateFeature[ComparisonFeature.TRIPLE_BOND_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR.setParameters(new Object[] {"t"});
+ tmpResult[ComparisonFeature.TRIPLE_BOND_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Quadruple bond count
+ if (tmpCalculateFeature[ComparisonFeature.QUADRUPLE_BOND_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR.setParameters(new Object[] {"q"});
+ tmpResult[ComparisonFeature.QUADRUPLE_BOND_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.BPOL.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.BPOL.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.B_POL_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.C1SP1_COUNT.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.C2SP1_COUNT.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.C1SP2_COUNT.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.C2SP2_COUNT.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.C3SP2_COUNT.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.C1SP3_COUNT.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.C2SP3_COUNT.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.C3SP3_COUNT.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.C4SP3_COUNT.getFeatureNumber()]) {
+ String[] tmpArray1 = ComparisonUtility.CARBON_TYPES_DESCRIPTOR.calculate(tmpMolecule1).getValue().toString().split(",");
+ String[] tmpArray2 = ComparisonUtility.CARBON_TYPES_DESCRIPTOR.calculate(tmpMolecule2).getValue().toString().split(",");
+ // C1SP1 count
+ if (tmpCalculateFeature[ComparisonFeature.C1SP1_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.C1SP1_COUNT.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[0]), Double.parseDouble(tmpArray2[0]), Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]))};
+ }
+ // C2SP1 count
+ if (tmpCalculateFeature[ComparisonFeature.C2SP1_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.C2SP1_COUNT.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[1]), Double.parseDouble(tmpArray2[1]), Math.abs(Double.parseDouble(tmpArray1[1]) - Double.parseDouble(tmpArray2[1]))};
+ }
+ // C1SP2 count
+ if (tmpCalculateFeature[ComparisonFeature.C1SP2_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.C1SP2_COUNT.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[2]), Double.parseDouble(tmpArray2[2]), Math.abs(Double.parseDouble(tmpArray1[2]) - Double.parseDouble(tmpArray2[2]))};
+ }
+ // C2SP2 count
+ if (tmpCalculateFeature[ComparisonFeature.C2SP2_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.C2SP2_COUNT.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[3]), Double.parseDouble(tmpArray2[3]), Math.abs(Double.parseDouble(tmpArray1[3]) - Double.parseDouble(tmpArray2[3]))};
+ }
+ // C3SP2 count
+ if (tmpCalculateFeature[ComparisonFeature.C3SP2_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.C3SP2_COUNT.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[4]), Double.parseDouble(tmpArray2[4]), Math.abs(Double.parseDouble(tmpArray1[4]) - Double.parseDouble(tmpArray2[4]))};
+ }
+ // C1SP3 count
+ if (tmpCalculateFeature[ComparisonFeature.C1SP3_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.C1SP3_COUNT.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[5]), Double.parseDouble(tmpArray2[5]), Math.abs(Double.parseDouble(tmpArray1[5]) - Double.parseDouble(tmpArray2[5]))};
+ }
+ // C2SP3 count
+ if (tmpCalculateFeature[ComparisonFeature.C2SP3_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.C2SP3_COUNT.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[6]), Double.parseDouble(tmpArray2[6]), Math.abs(Double.parseDouble(tmpArray1[6]) - Double.parseDouble(tmpArray2[6]))};
+ }
+ // C3SP3 count
+ if (tmpCalculateFeature[ComparisonFeature.C3SP3_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.C3SP3_COUNT.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[7]), Double.parseDouble(tmpArray2[7]), Math.abs(Double.parseDouble(tmpArray1[7]) - Double.parseDouble(tmpArray2[7]))};
+ }
+ // C4SP3 count
+ if (tmpCalculateFeature[ComparisonFeature.C4SP3_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.C4SP3_COUNT.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[8]), Double.parseDouble(tmpArray2[8]), Math.abs(Double.parseDouble(tmpArray1[8]) - Double.parseDouble(tmpArray2[8]))};
+ }
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.EQUALITY.getFeatureNumber()]) {
+ String tmpUniqueSmiles1 = ComparisonUtility.SMILES_GENERATOR.create(tmpMolecule1);
+ String tmpUniqueSmiles2 = ComparisonUtility.SMILES_GENERATOR.create(tmpMolecule2);
+ tmpResult[ComparisonFeature.EQUALITY.getFeatureNumber()] = new double[] {Double.NaN, Double.NaN, tmpUniqueSmiles1.equals(tmpUniqueSmiles2) ? 1 : 0};
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.ECCENTRIC_CONNECTIVITY_INDEX.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.ECCENTRIC_CONNECTIVITY_INDEX.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ECCENTRIC_CONNECTIVITY_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.FMF.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.FMF.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.FMF_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.FCSP3.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.FCSP3.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.FRACTIONAL_CSP3_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.FPSA.getFeatureNumber()]) {
+ ComparisonUtility.FRACTIONAL_PSA_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpResult[ComparisonFeature.FPSA.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.FRACTIONAL_PSA_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.FRAGMENT_COMPLEXITY.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.FRAGMENT_COMPLEXITY.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.FRAGMENT_COMPLEXITY_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.H_BOND_ACCEPTOR_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.HBOND_ACCEPTOR_COUNT_DESCRIPTOR.setParameters(new Object[] {true});
+ tmpResult[ComparisonFeature.H_BOND_ACCEPTOR_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.HBOND_ACCEPTOR_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.H_BOND_DONOR_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.H_BOND_DONOR_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.HBOND_DONOR_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.JP_LOGP.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.JP_LOGP.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.JP_LOGP_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_1.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_2.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_3.getFeatureNumber()]) {
+ String[] tmpArray1 = ComparisonUtility.KAPPA_SHAPE_INDICES_DESCRIPTOR.calculate(tmpMolecule1).getValue().toString().split(",");
+ String[] tmpArray2 = ComparisonUtility.KAPPA_SHAPE_INDICES_DESCRIPTOR.calculate(tmpMolecule2).getValue().toString().split(",");
+ // First kappa shape index
+ if (tmpCalculateFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_1.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.KAPPA_SHAPE_INDEX_1.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[0]), Double.parseDouble(tmpArray2[0]), Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]))};
+ }
+ // Second kappa shape index
+ if (tmpCalculateFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_2.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.KAPPA_SHAPE_INDEX_2.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[1]), Double.parseDouble(tmpArray2[1]), Math.abs(Double.parseDouble(tmpArray1[1]) - Double.parseDouble(tmpArray2[1]))};
+ }
+ // Third kappa shape index
+ if (tmpCalculateFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_3.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.KAPPA_SHAPE_INDEX_3.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[2]), Double.parseDouble(tmpArray2[2]), Math.abs(Double.parseDouble(tmpArray1[2]) - Double.parseDouble(tmpArray2[2]))};
+ }
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.LARGEST_CHAIN.getFeatureNumber()]) {
+ // Doesn't need to check for rings because that is done in the preproccesing
+ ComparisonUtility.LARGEST_CHAIN_DESCRIPTOR.setParameters(new Object[] {false, false});
+ tmpResult[ComparisonFeature.LARGEST_CHAIN.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.LARGEST_CHAIN_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.LARGEST_PI_SYSTEM.getFeatureNumber()]) {
+ // Doesn't need to check for aromaticity because that is done in the preproccesing
+ ComparisonUtility.LARGEST_PI_SYSTEM_DESCRIPTOR.setParameters(new Object[] {false});
+ tmpResult[ComparisonFeature.LARGEST_PI_SYSTEM.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.LARGEST_PI_SYSTEM_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.LONGEST_ALIPHATIC_CHAIN.getFeatureNumber()]) {
+ // Doesn't need to check for rings because that is done in the preproccesing
+ ComparisonUtility.LONGEST_ALIPHATIC_CHAIN_DESCRIPTOR.setParameters(new Object[] {false});
+ tmpResult[ComparisonFeature.LONGEST_ALIPHATIC_CHAIN.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.LONGEST_ALIPHATIC_CHAIN_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.MANNHOLD_LOGP.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.MANNHOLD_LOGP.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.MANNHOLD_LOG_P_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.PETITJEAN_NUMBER.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.PETITJEAN_NUMBER.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.PETITJEAN_NUMBER_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.PETITJEAN_SHAPE_INDEX.getFeatureNumber()]) {
+ String[] tmpArray1 = ComparisonUtility.PETITJEAN_SHAPE_INDEX_DESCRIPTOR.calculate(tmpMolecule1).getValue().toString().split(",");
+ String[] tmpArray2 = ComparisonUtility.PETITJEAN_SHAPE_INDEX_DESCRIPTOR.calculate(tmpMolecule2).getValue().toString().split(",");
+ tmpResult[ComparisonFeature.PETITJEAN_SHAPE_INDEX.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[0]), Double.parseDouble(tmpArray2[0]), Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]))};
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.ROTATABLE_BOND_COUNT.getFeatureNumber()]) {
+ // Don't include terminal bonds and don't exclude amide bonds
+ ComparisonUtility.ROTATABLE_BOND_COUNT.setParameters(new Object[] {false, false});
+ tmpResult[ComparisonFeature.ROTATABLE_BOND_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ROTATABLE_BOND_COUNT, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.ALL_SMALL_RINGS_COUNT.getFeatureNumber()]) {
+ int tmpRingCount1 = Integer.parseInt(ComparisonUtility.SMALL_RING_DESCRIPTOR.calculate(tmpMolecule1).getValue().toString().split(",")[0]);
+ int tmpRingCount2 = Integer.parseInt(ComparisonUtility.SMALL_RING_DESCRIPTOR.calculate(tmpMolecule2).getValue().toString().split(",")[0]);
+ tmpResult[ComparisonFeature.ALL_SMALL_RINGS_COUNT.getFeatureNumber()] = new double[] {tmpRingCount1, tmpRingCount2, Math.abs(tmpRingCount1 - tmpRingCount2)};
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.SPIRO_ATOM_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.SPIRO_ATOM_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.SPIRO_ATOM_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ // Basic fingerprint
+ if (tmpCalculateFeature[ComparisonFeature.TANIMOTO_BASIC_FINGERPRINTER.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.TANIMOTO_BASIC_FINGERPRINTER.getFeatureNumber()] = calculateTanimotoCoefficient(
+ ComparisonUtility.BASIC_FINGERPRINTER, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // LINGO fingerprint
+ if (tmpCalculateFeature[ComparisonFeature.TANIMOTO_LINGO_FINGERPRINTER.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.TANIMOTO_LINGO_FINGERPRINTER.getFeatureNumber()] = calculateTanimotoCoefficient(
+ ComparisonUtility.LINGO_FINGERPRINTER, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Extended fingerprint
+ if (tmpCalculateFeature[ComparisonFeature.TANIMOTO_EXTENDED_FINGERPRINTER.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.TANIMOTO_EXTENDED_FINGERPRINTER.getFeatureNumber()] = calculateTanimotoCoefficient(
+ ComparisonUtility.EXTENDED_FINGERPRINTER, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // E-State fingerprint
+ if (tmpCalculateFeature[ComparisonFeature.TANIMOTO_ESTATE_FINGERPRINTER.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.TANIMOTO_ESTATE_FINGERPRINTER.getFeatureNumber()] = calculateTanimotoCoefficient(
+ ComparisonUtility.ESTATE_FINGERPRINTER, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // PubChem fingerprint
+ if (tmpCalculateFeature[ComparisonFeature.TANIMOTO_PUBCHEM_FINGERPRINTER.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.TANIMOTO_PUBCHEM_FINGERPRINTER.getFeatureNumber()] = calculateTanimotoCoefficient(
+ ComparisonUtility.PUBCHEM_FINGERPRINTER, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Shortest path fingerprint
+ if (tmpCalculateFeature[ComparisonFeature.TANIMOTO_SHORTEST_PATH_FINGERPRINTER.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.TANIMOTO_SHORTEST_PATH_FINGERPRINTER.getFeatureNumber()] = calculateTanimotoCoefficient(
+ ComparisonUtility.SHORTEST_PATH_FINGERPRINTER, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Substructure fingerprint
+ if (tmpCalculateFeature[ComparisonFeature.TANIMOTO_SUBSTRUCTURE_FINGERPRINTER.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.TANIMOTO_SUBSTRUCTURE_FINGERPRINTER.getFeatureNumber()] = calculateTanimotoCoefficient(
+ ComparisonUtility.SUBSTRUCTURE_FINGERPRINTER, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.TPSA.getFeatureNumber()]) {
+ // Doesn't need to check for aromaticity because that is done in the preproccesing
+ ComparisonUtility.TPSA_DESCRIPTOR.setParameters(new Object[] {false});
+ tmpResult[ComparisonFeature.TPSA.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.TPSA_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.VABC.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.VABC.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.VABC_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.V_ADJ_MA.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.V_ADJ_MA.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.V_ADJ_MA_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.MOLECULAR_WEIGHT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.MOLECULAR_WEIGHT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.WEIGHT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.WEIGHTED_PATH_1.getFeatureNumber()]) {
+ String[] tmpArray1 = ComparisonUtility.WEIGHTER_PATH_DESCRIPTOR.calculate(tmpMolecule1).getValue().toString().split(",");
+ String[] tmpArray2 = ComparisonUtility.WEIGHTER_PATH_DESCRIPTOR.calculate(tmpMolecule2).getValue().toString().split(",");
+ tmpResult[ComparisonFeature.WEIGHTED_PATH_1.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[0]), Double.parseDouble(tmpArray2[0]), Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]))};
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.WIENER_PATH.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.WIENER_POLARITY.getFeatureNumber()]) {
+ String[] tmpArray1 = ComparisonUtility.WIENER_NUMBERS_DESCRIPTOR.calculate(tmpMolecule1).getValue().toString().split(",");
+ String[] tmpArray2 = ComparisonUtility.WIENER_NUMBERS_DESCRIPTOR.calculate(tmpMolecule2).getValue().toString().split(",");
+ // Wiener path number
+ if (tmpCalculateFeature[ComparisonFeature.WIENER_PATH.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.WIENER_PATH.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[0]), Double.parseDouble(tmpArray2[0]), Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]))};
+ }
+ // Wiener polarity number
+ if (tmpCalculateFeature[ComparisonFeature.WIENER_POLARITY.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.WIENER_POLARITY.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[1]), Double.parseDouble(tmpArray2[1]), Math.abs(Double.parseDouble(tmpArray1[1]) - Double.parseDouble(tmpArray2[1]))};
+ }
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.X_LOGP.getFeatureNumber()]) {
+ // Aromaticity is already checked in preprocessing; use the salicyl acid correction factor
+ ComparisonUtility.X_LOGP_DESCRIPTOR.setParameters(new Object[] {false, true});
+ tmpResult[ComparisonFeature.X_LOGP.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.X_LOGP_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.ZAGREB_INDEX.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.ZAGREB_INDEX.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ZAGREB_INDEY_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ return tmpResult;
+ }
+ //
+ //
+ //
+ /**
+ * Calculate the individual descriptor values and their difference of the
+ * two given molecules and the given descriptor
+ *
+ * @param tmpDescriptor specifies the descriptor
+ * @param tmpMolecule1 the first molecule
+ * @param tmpMolecule2 the second molecule
+ * @return an array of the form
+ * {firstDescriptorValue, secondDescriptorValue, difference}
+ */
+ private static double[] calculateDescriptorDifference(IMolecularDescriptor tmpDescriptor, IAtomContainer tmpMolecule1, IAtomContainer tmpMolecule2) {
+ double tmpResult1 = Double.parseDouble(tmpDescriptor.calculate(tmpMolecule1).getValue().toString());
+ double tmpResult2 = Double.parseDouble(tmpDescriptor.calculate(tmpMolecule2).getValue().toString());
+ return new double[] {tmpResult1, tmpResult2, Math.abs(tmpResult1 - tmpResult2)};
+ };
+
+ /**
+ * Calculate the Tanimoto coefficient for the two given molecules with
+ * the given fingerprint
+ *
+ * @param tmpFingerprinter specifies the fingerprint
+ * @param tmpMolecule1 the first molecule
+ * @param tmpMolecule2 the second molecule
+ * @return an array of the form {NaN, NaN, Tanimoto coefficient}
+ */
+ private static double[] calculateTanimotoCoefficient(IFingerprinter tmpFingerprinter, IAtomContainer tmpMolecule1, IAtomContainer tmpMolecule2) {
+ try {
+ return new double[] {Double.NaN, Double.NaN, Tanimoto.calculate(tmpFingerprinter.getBitFingerprint(tmpMolecule1), tmpFingerprinter.getBitFingerprint(tmpMolecule2))};
+ } catch (CDKException ex) {
+ return new double[] {Double.NaN, Double.NaN, Double.NaN};
+ }
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/HistogramData.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/HistogramData.java
new file mode 100644
index 0000000..7bfb872
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/HistogramData.java
@@ -0,0 +1,603 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+import java.io.IOException;
+import java.io.ObjectStreamException;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.concurrent.Callable;
+
+/**
+ * Handles the frequency data, the bin borders and the bins list for one
+ * particular ComparisonFeature which is represented by its corresponding number
+ *
+ * @author Jan-Mathis Hein
+ */
+public class HistogramData implements Callable, Serializable {
+
+ //
+ /**
+ * A serial version UID to check whether loaded data is compatible
+ */
+ private static final long serialVersionUID = 5L;
+ //
+ //
+ //
+ /**
+ * If true the specifically set bin borders will be used, if false the bin
+ * borders are calculated automatically
+ */
+ private boolean useSpecificBinBorders;
+
+ /**
+ * If true all returning frequencies will be relative ones and all
+ * inputted frequencies will be regarded as relative ones;
+ * if false all returning frequencies will be absolute ones and all
+ * inputted frequencies will be regarded as absolute ones
+ */
+ private boolean useRelativeFrequencies;
+
+ /**
+ * Maximal value of all comparison results
+ */
+ private double maxComparisonFeatureValue;
+
+ /**
+ * Minimal value of all comparison results
+ */
+ private double minComparisonFeatureValue;
+
+ /**
+ * The average value off all comparison results
+ */
+ private transient double averageComparisonFeatureValue;
+
+ /**
+ * The lower border of the first bin
+ */
+ private double lowerBinBorder;
+
+ /**
+ * The upper border of the last bin
+ */
+ private double upperBinBorder;
+
+ /**
+ * The lower boundary for frequency values. Is set to NaN if the data is
+ * binned
+ */
+ private double lowerFrequencyBound;
+
+ /**
+ * The upper boundary for frequency values. Is set to NaN if the data is
+ * binned
+ */
+ private double upperFrequencyBound;
+
+ /**
+ * The current maximal frequency value of any bin
+ */
+ private double currentMaxFrequencyValue;
+
+ /**
+ * Borders of the bins
+ */
+ private double[] binBorders;
+
+ /**
+ * Number which represents a ComparisonFeature
+ */
+ private int comparisonFeatureNumber;
+
+ /**
+ * Number of bins into which the comparison results will be devided.
+ * This will always be positive
+ */
+ private int numberOfBins;
+
+ /**
+ * The number of invalid similarity values
+ */
+ private int numberOfInvalidComparisonFeatureValues;
+
+ /**
+ * This frequency data. The value at each index represents the frequency of
+ * ComparisonResults in the corresponding bin.
+ */
+ private transient int[] frequencies;
+
+ /**
+ * List of all the ComparisonResults (the native data) that belong to the
+ * data set
+ */
+ private transient List nativeDataList;
+
+ /**
+ * List of lists where each list corresponds to a bin and contains
+ * a sample of molecule pairs whos comparison result belongs to this bin
+ */
+ private transient List> binsList;
+ //
+ //
+ //
+ /**
+ * Initialize some instance variables
+ *
+ * @param tmpComparisonFeatureNumber specifies the ComparisonFeature to which
+ * this HistogramData belongs
+ * @param tmpList reference to the native data
+ */
+ public HistogramData(int tmpComparisonFeatureNumber, List tmpList) {
+ this.comparisonFeatureNumber = tmpComparisonFeatureNumber;
+ this.nativeDataList = tmpList;
+ this.lowerBinBorder = Double.NaN;
+ this.upperBinBorder = Double.NaN;
+ this.lowerFrequencyBound = Double.NaN;
+ this.upperFrequencyBound = Double.NaN;
+ this.currentMaxFrequencyValue = 0.0;
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Calculate the bin borders and the corresponding frequency data. Also
+ * reset upperFrequencyBound and lowerFrequencyBound to NaN
+ */
+ @Override
+ public Void call() {
+ this.lowerFrequencyBound = Double.NaN;
+ this.upperFrequencyBound = Double.NaN;
+ int tmpNumberOfBins;
+ //
+ if (!this.useSpecificBinBorders) {
+ double tmpLowestBinBorder = Double.isNaN(this.lowerBinBorder) ? this.minComparisonFeatureValue : this.lowerBinBorder;
+ double tmpHighestBinBorder = Double.isNaN(this.upperBinBorder) ? this.maxComparisonFeatureValue : this.upperBinBorder;
+ double tmpBinSize = (tmpHighestBinBorder - tmpLowestBinBorder) / this.numberOfBins;
+ if (tmpBinSize < 0) {
+ // If binSize is negative, reasonable values are inferred
+ tmpBinSize = Math.abs(tmpBinSize);
+ this.lowerBinBorder = tmpHighestBinBorder;
+ this.upperBinBorder = tmpLowestBinBorder;
+ tmpLowestBinBorder = this.lowerBinBorder;
+ tmpHighestBinBorder = this.upperBinBorder;
+ }
+ if (tmpBinSize == 0) {
+ tmpNumberOfBins = 1;
+ } else {
+ tmpNumberOfBins= this.numberOfBins;
+ }
+ this.binBorders = new double[tmpNumberOfBins + 1];
+ for (int i = 0; i < tmpNumberOfBins; i++) {
+ this.binBorders[i] = tmpLowestBinBorder + (tmpBinSize * i);
+ }
+ this.binBorders[tmpNumberOfBins] = tmpHighestBinBorder;
+ } else {
+ tmpNumberOfBins = this.numberOfBins;
+ }
+ //
+ this.binsList = new ArrayList<>(tmpNumberOfBins);
+ for (int i = 0; i < tmpNumberOfBins; i++) {
+ this.binsList.add(i, new LinkedList<>());
+ }
+ this.frequencies = new int[tmpNumberOfBins];
+ Arrays.fill(this.frequencies, 0);
+ Iterator tmpIterator = this.nativeDataList.iterator();
+ ComparisonResult tmpResult;
+ double tmpValue;
+ this.averageComparisonFeatureValue = 0.0;
+ this.numberOfInvalidComparisonFeatureValues = 0;
+ iteratorLoop:
+ while (tmpIterator.hasNext()) {
+ tmpResult = tmpIterator.next();
+ tmpValue = tmpResult.getSimilarities()[this.comparisonFeatureNumber];
+ if (Double.isNaN(tmpValue)) {
+ this.numberOfInvalidComparisonFeatureValues++;
+ continue;
+ }
+ this.averageComparisonFeatureValue += tmpValue;
+ for (int i = 1; i < this.binBorders.length; i++) {
+ // Lower bound included, upper bound excluded
+ if (tmpValue < this.binBorders[i] && tmpValue >= this.binBorders[i - 1]) {
+ this.frequencies[i - 1]++;
+ if (tmpResult.hasMoleculePair()) {
+ List tmpBin = this.binsList.get(i - 1);
+ tmpBin.add(tmpResult);
+ }
+ continue iteratorLoop;
+ }
+ }
+ // If tmpValue exactly matches the highest bin border it contributes to the last bin
+ if (tmpValue == this.binBorders[tmpNumberOfBins]) {
+ this.frequencies[tmpNumberOfBins - 1]++;
+ if (tmpResult.hasMoleculePair()) {
+ List tmpBin = this.binsList.get(tmpNumberOfBins - 1);
+ tmpBin.add(tmpResult);
+ }
+ }
+ }
+ this.averageComparisonFeatureValue /= (this.nativeDataList.size() - this.numberOfInvalidComparisonFeatureValues);
+ this.currentMaxFrequencyValue = this.frequencies[0];
+ for (int tmpInt : this.frequencies) {
+ this.currentMaxFrequencyValue = this.currentMaxFrequencyValue >= tmpInt ? this.currentMaxFrequencyValue : tmpInt;
+ }
+ return null;
+ }
+ //
+ //
+ /**
+ * If true all returning frequencies will be relative ones and all
+ * inputted frequencies will be regarded as relative ones;
+ * if false all returning frequencies will be absolute ones and all
+ * inputted frequencies will be regarded as absolute ones
+ *
+ * @return true if all returning frequencies will be relative ones and all
+ * inputted frequencies will be regarded as relative ones;
+ * return false if all returning frequencies will be absolute ones and all
+ * inputted frequencies will be regarded as absolute ones
+ */
+ public boolean isUseRelativeFrequencies() {
+ return this.useRelativeFrequencies;
+ }
+
+ /**
+ * Get a copy of the bin borders.
+ *
+ * @return a copy of the bin borders
+ */
+ public double[] getBinBorders() {
+ return Arrays.copyOf(this.binBorders, this.binBorders.length);
+ }
+
+ /**
+ * Get the maximal ComparisonFeature value
+ *
+ * @return the maximal ComparisonFeature value
+ */
+ public double getMaxComparisonFeatureValue() {
+ return this.maxComparisonFeatureValue;
+ }
+
+ /**
+ * Get the minimal ComparisonFeature value
+ *
+ * @return the minmal ComparisonFeature value
+ */
+ public double getMinComparisonFeatureValue() {
+ return this.minComparisonFeatureValue;
+ }
+
+ /**
+ * Get the average ComparisonFeature value
+ *
+ * @return the average ComparisonFeature value
+ */
+ public double getAverageComparisonFeatureValue() {
+ return this.averageComparisonFeatureValue;
+ }
+
+ /**
+ * Get the value that will be or is the lowest bin border
+ *
+ * @return the lowest bin border
+ */
+ public double getLowerBinBorder() {
+ return Double.isNaN(this.lowerBinBorder) ? this.minComparisonFeatureValue : this.lowerBinBorder;
+ }
+
+ /**
+ * Get the value that will be or is the highest bin border
+ *
+ * @return the highest bin border
+ */
+ public double getUpperBinBorder() {
+ return Double.isNaN(this.upperBinBorder) ? this.maxComparisonFeatureValue : this.upperBinBorder;
+ }
+
+ /**
+ * Get the lower bound for the frequency values
+ *
+ * @return the lower bound for the frequency values
+ */
+ public double getLowerFrequencyBound() {
+ if (this.useRelativeFrequencies) {
+ return Double.isNaN(this.lowerFrequencyBound) ?
+ (0.0 / (this.nativeDataList.size() - this.numberOfInvalidComparisonFeatureValues)) :
+ (this.lowerFrequencyBound / (this.nativeDataList.size() - this.numberOfInvalidComparisonFeatureValues));
+ } else {
+ return Double.isNaN(this.lowerFrequencyBound) ? 0.0 : this.lowerFrequencyBound;
+ }
+ }
+
+ /**
+ * Get the upper bound for the frequency values
+ *
+ * @return the upper bound for the frequency values
+ */
+ public double getUpperFrequencyBound() {
+ if (this.useRelativeFrequencies) {
+ return Double.isNaN(this.upperFrequencyBound) ?
+ (this.currentMaxFrequencyValue / (this.nativeDataList.size() - this.numberOfInvalidComparisonFeatureValues)) :
+ (this.upperFrequencyBound / (this.nativeDataList.size() - this.numberOfInvalidComparisonFeatureValues));
+ } else {
+ return Double.isNaN(this.upperFrequencyBound) ? this.currentMaxFrequencyValue : this.upperFrequencyBound;
+ }
+ }
+
+ /**
+ * Get the maximal possible frequency value
+ *
+ * @return the maximal possible frequency value
+ */
+ public double getMaxFrequency() {
+ if (this.useRelativeFrequencies) {
+ return 1;
+ } else {
+ return (this.nativeDataList.size() - this.numberOfInvalidComparisonFeatureValues);
+ }
+ }
+
+ /**
+ * Get the number of bins
+ *
+ * @return the number of bins
+ */
+ public int getNumberOfBins() {
+ return this.numberOfBins;
+ }
+
+ /**
+ * Get the frequencies as an array where each index corresponds to a bin
+ *
+ * @return the frequencies
+ */
+ public double[] getFrequencies() {
+ double tmpScaling = 1.0;
+ if (this.useRelativeFrequencies) {
+ tmpScaling = (this.nativeDataList.size() - this.numberOfInvalidComparisonFeatureValues);
+ }
+ double[] tmpResult = new double[this.frequencies.length];
+ for (int i = 0; i < tmpResult.length; i++) {
+ tmpResult[i] = (this.frequencies[i] / tmpScaling);
+ }
+ return tmpResult;
+ }
+
+ /**
+ * Get the bin specified by the index as a list that contains
+ * associated ComparisonResults.
+ * NOTE: If this HistogramData is loaded, this list can be empty even
+ * though the frequency of the bin is not zero
+ *
+ * @param tmpBinIndex specifies the bin
+ * @return the specified bin as a list of IAtomContainer arrays
+ */
+ public List getBin(int tmpBinIndex) {
+ return this.binsList.get(tmpBinIndex);
+ }
+
+ /**
+ * Get the number corresponding to the ComparisonFeature of this
+ * HistogramData
+ *
+ * @return the number corresponding to the ComparisonFeature
+ */
+ public int getComparisonFeautureNumber() {
+ return this.comparisonFeatureNumber;
+ }
+
+ /**
+ * Get the ComparisonFeature of this HistogramData
+ *
+ * @return the ComparisonFeature of this HistogramData
+ */
+ public ComparisonFeature getComparisonFeauture() {
+ return ComparisonFeature.values()[this.comparisonFeatureNumber];
+ }
+ //
+ //
+ /**
+ * Set the useRelativeFrequencies flag. If this flag is true all
+ * returning and inputted frequencies will be realtive ones, if false all
+ * returning and inputted frequencies will be absolute ones
+ *
+ * @param tmpUseRelativeFrequencies the value to which the flag will
+ * be set
+ */
+ public synchronized void setUseRelativeFrequencies(boolean tmpUseRelativeFrequencies) {
+ this.useRelativeFrequencies = tmpUseRelativeFrequencies;
+ }
+
+ /**
+ * Set the lower bin border
+ *
+ * @param tmpBorder specifies the new value of the lower bin border
+ */
+ public synchronized void setLowerBinBorder(double tmpBorder) {
+ this.lowerBinBorder = tmpBorder;
+ this.useSpecificBinBorders = false;
+ }
+
+ /**
+ * Set the upper bin border
+ *
+ * @param tmpBorder specifies the new value of the upper bin border
+ */
+ public synchronized void setUpperBinBorder(double tmpBorder) {
+ this.upperBinBorder = tmpBorder;
+ this.useSpecificBinBorders = false;
+ }
+
+ /**
+ * Set the number of bins. If the given value is smaller than one,
+ * one is used instead.
+ *
+ * @param tmpNumberOfBins specifies the new number of bins
+ */
+ public synchronized void setNumberOfBins(int tmpNumberOfBins) {
+ this.numberOfBins = tmpNumberOfBins > 1 ? tmpNumberOfBins : 1;
+ this.useSpecificBinBorders = false;
+ }
+
+ /**
+ * Set the lower frequency bound. If the resulting frequency bounds
+ * would be irrational, reasonable values are inferred. If the given
+ * bound is not a number the method returns without doing anything
+ *
+ * @param tmpLowerBound specifies the new value of the lower frequency bound
+ */
+ public synchronized void setLowerFrequencyBound(double tmpLowerBound) {
+ if (Double.isNaN(tmpLowerBound)) {
+ return;
+ }
+ if (this.useRelativeFrequencies) {
+ tmpLowerBound *= (this.nativeDataList.size() - this.numberOfInvalidComparisonFeatureValues);
+ }
+ double tmpUpperBound = this.upperFrequencyBound;
+ if (tmpLowerBound > tmpUpperBound) {
+ this.lowerFrequencyBound = tmpUpperBound;
+ this.upperFrequencyBound = tmpLowerBound;
+ } else {
+ this.lowerFrequencyBound = tmpLowerBound;
+ this.upperFrequencyBound = tmpUpperBound;
+ }
+ }
+
+ /**
+ * Set the upper frequency bound. If the resulting frequency bounds
+ * would be irrational, reasonable values are inferred. If the given
+ * bound is not a number the method returns without doing anything
+ *
+ * @param tmpUpperBound specifies the new value of the upper frequency bound
+ */
+ public synchronized void setUpperFrequencyBound(double tmpUpperBound) {
+ if (Double.isNaN(tmpUpperBound)) {
+ return;
+ }
+ if (this.useRelativeFrequencies) {
+ tmpUpperBound *= (this.nativeDataList.size() - this.numberOfInvalidComparisonFeatureValues);
+ }
+ double tmpLowerBound = this.lowerFrequencyBound;
+ if (tmpLowerBound > tmpUpperBound) {
+ this.lowerFrequencyBound = tmpUpperBound;
+ this.upperFrequencyBound = tmpLowerBound;
+ } else {
+ this.lowerFrequencyBound = tmpLowerBound;
+ this.upperFrequencyBound = tmpUpperBound;
+ }
+ }
+
+ /**
+ * Set the maximal ComparisonFeature value
+ *
+ * @param tmpValue specifies the value to set
+ */
+ public void setMaxComparisonFeatureValue(double tmpValue) {
+ this.maxComparisonFeatureValue = tmpValue;
+ }
+
+ /**
+ * Set the minimal ComparisonFeature value
+ *
+ * @param tmpValue specifies the value to set
+ */
+ public void setMinComparisonFeatureValue(double tmpValue) {
+ this.minComparisonFeatureValue = tmpValue;
+ }
+
+ /**
+ * Set the native data list
+ *
+ * @param tmpList the native data list to be set
+ */
+ public void setNativeDataList(List tmpList) {
+ this.nativeDataList = tmpList;
+ }
+
+ /**
+ * Set the bin borders
+ *
+ * @param tmpBinBorders the bin borders to be set
+ */
+ public void setSpecificBinBorders(double[] tmpBinBorders) {
+ this.binBorders = Arrays.copyOf(tmpBinBorders, tmpBinBorders.length);
+ this.useSpecificBinBorders = true;
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Write the state of this object to the given ObjectOutputStream
+ *
+ * @param tmpObjectOutputStream the ObjectOutputStream to which information
+ * will be written
+ * @throws IOException if an I/O error occurs
+ */
+ private synchronized void writeObject(java.io.ObjectOutputStream tmpObjectOutputStream) throws IOException {
+ tmpObjectOutputStream.writeBoolean(this.useRelativeFrequencies);
+ tmpObjectOutputStream.writeBoolean(this.useSpecificBinBorders);
+ tmpObjectOutputStream.writeDouble(this.lowerBinBorder);
+ tmpObjectOutputStream.writeDouble(this.lowerFrequencyBound);
+ tmpObjectOutputStream.writeDouble(this.maxComparisonFeatureValue);
+ tmpObjectOutputStream.writeDouble(this.minComparisonFeatureValue);
+ tmpObjectOutputStream.writeDouble(this.upperBinBorder);
+ tmpObjectOutputStream.writeDouble(this.upperFrequencyBound);
+ tmpObjectOutputStream.writeDouble(this.currentMaxFrequencyValue);
+ tmpObjectOutputStream.writeInt(this.comparisonFeatureNumber);
+ tmpObjectOutputStream.writeInt(this.numberOfBins);
+ tmpObjectOutputStream.writeObject(this.binBorders);
+ }
+
+ /**
+ * Read the state of an object from the given ObjectInputStream
+ *
+ * @param tmpObjectInputStream ObjectInputStream from which to read
+ * @throws IOException if an I/O error occurs
+ * @throws ClassNotFoundException Class of a serialized object cannot be
+ * found
+ */
+ private void readObject(java.io.ObjectInputStream tmpObjectInputStream) throws IOException, ClassNotFoundException {
+ this.useRelativeFrequencies = tmpObjectInputStream.readBoolean();
+ this.useSpecificBinBorders = tmpObjectInputStream.readBoolean();
+ this.lowerBinBorder = tmpObjectInputStream.readDouble();
+ this.lowerFrequencyBound = tmpObjectInputStream.readDouble();
+ this.maxComparisonFeatureValue = tmpObjectInputStream.readDouble();
+ this.minComparisonFeatureValue = tmpObjectInputStream.readDouble();
+ this.upperBinBorder = tmpObjectInputStream.readDouble();
+ this.upperFrequencyBound = tmpObjectInputStream.readDouble();
+ this.currentMaxFrequencyValue = tmpObjectInputStream.readDouble();
+ this.comparisonFeatureNumber = tmpObjectInputStream.readInt();
+ this.numberOfBins = tmpObjectInputStream.readInt();
+ this.binBorders = (double[]) tmpObjectInputStream.readObject();
+ }
+
+ /**
+ * This method is not implemented
+ */
+ private void readObjectNoData() {
+ throw new RuntimeException("Method \"readObjectNoData\" is not implemented");
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/HistogramDataManager.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/HistogramDataManager.java
new file mode 100644
index 0000000..978d378
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/HistogramDataManager.java
@@ -0,0 +1,335 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.ObjectStreamException;
+import java.io.Serializable;
+import java.util.EnumMap;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+/**
+ * Stores and manages the histogram data for multiple ComparisonFeatures.
+ * Also handles the saving and loading of the histogram data
+ *
+ * @author Jan-Mathis Hein
+ */
+public class HistogramDataManager implements Serializable {
+
+ //
+ /**
+ * A serial version UID to check whether loaded data is compatible
+ */
+ private static final long serialVersionUID = 5L;
+ //
+ //
+ //
+ /**
+ * List of all the ComparisonResults (the native data) that belong to the
+ * data set
+ */
+ private transient List nativeDataList;
+
+ /**
+ * Maps all the HistogramData objects to their corresponding
+ * ComparisonFeature
+ */
+ private transient Map comparisonFeatureToDataMap;
+
+ /**
+ * The time difference, in milliseconds, between the data's calculation
+ * start time and midnight, January 1, 1970 UTC
+ */
+ private long calculationStartTime;
+
+ /**
+ * The time difference, in milliseconds, between the data's calculation
+ * finish time and midnight, January 1, 1970 UTC
+ */
+ private long calculationFinishTime;
+
+ /**
+ * Name of the first input file which was used for the comparison
+ */
+ private String inputFile1;
+
+ /**
+ * Name of the second input file which was used for the comparison
+ */
+ private String inputFile2;
+ //
+ //
+ //
+ /**
+ * Initialize the instance variables and add the first ComparisonResult to
+ * the data set
+ *
+ * @param tmpConsideredComparisonFeaturesList list of ComparisonFeatures for
+ * which histogram data will be stored
+ * @param tmpNumberOfInitialBins initial number of bins
+ * @param tmpFirstResult first ComparisonResult for the data set
+ * @param tmpInputFile1 the name of the first input file
+ * @param tmpInputFile2 the name of the second input file
+ */
+ public HistogramDataManager(
+ List tmpConsideredComparisonFeaturesList, int tmpNumberOfInitialBins,
+ ComparisonResult tmpFirstResult, String tmpInputFile1, String tmpInputFile2
+ ) throws IllegalArgumentException {
+ //
+ if (tmpConsideredComparisonFeaturesList == null || tmpFirstResult == null) {
+ throw new IllegalArgumentException("An argument is null");
+ }
+ //
+ this.comparisonFeatureToDataMap = new EnumMap<>(ComparisonFeature.class);
+ this.nativeDataList = new LinkedList<>();
+ this.nativeDataList.add(tmpFirstResult);
+ tmpConsideredComparisonFeaturesList.forEach((ComparisonFeature tmpComparisonFeature) -> {
+ this.comparisonFeatureToDataMap.putIfAbsent(tmpComparisonFeature, new HistogramData(tmpComparisonFeature.getFeatureNumber(), this.nativeDataList));
+ });
+ this.comparisonFeatureToDataMap.values().forEach((HistogramData tmpHistogramData) -> {
+ tmpHistogramData.setMinComparisonFeatureValue(tmpFirstResult.getSimilarities()[tmpHistogramData.getComparisonFeautureNumber()]);
+ tmpHistogramData.setMaxComparisonFeatureValue(tmpFirstResult.getSimilarities()[tmpHistogramData.getComparisonFeautureNumber()]);
+ tmpHistogramData.setNumberOfBins(tmpNumberOfInitialBins < 1 ? 1 : tmpNumberOfInitialBins);
+ });
+ this.inputFile1 = tmpInputFile1;
+ this.inputFile2 = tmpInputFile2;
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Add a new ComparisonResult to the data set
+ *
+ * @param tmpResult ComparisonResult to be added
+ */
+ public synchronized void addDatum(ComparisonResult tmpResult) {
+ //
+ if (tmpResult == null) {
+ return;
+ }
+ //
+ this.comparisonFeatureToDataMap.values().forEach((HistogramData tmpData) -> {
+ if (Double.isNaN(tmpResult.getSimilarities()[tmpData.getComparisonFeautureNumber()])) {
+ return;
+ }
+ tmpData.setMinComparisonFeatureValue(
+ tmpData.getMinComparisonFeatureValue() < tmpResult.getSimilarities()[tmpData.getComparisonFeautureNumber()] ?
+ tmpData.getMinComparisonFeatureValue() : tmpResult.getSimilarities()[tmpData.getComparisonFeautureNumber()]
+ );
+ tmpData.setMaxComparisonFeatureValue(
+ tmpData.getMaxComparisonFeatureValue() > tmpResult.getSimilarities()[tmpData.getComparisonFeautureNumber()] ?
+ tmpData.getMaxComparisonFeatureValue() : tmpResult.getSimilarities()[tmpData.getComparisonFeautureNumber()]
+ );
+ });
+ this.nativeDataList.add(tmpResult);
+ }
+ //
+ public synchronized ByteArrayOutputStream getObjectAsByteStream() throws IOException {
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+
+ baos.write(toBytes(this.inputFile1.length()));
+ baos.write(this.inputFile1.getBytes());
+ baos.write(toBytes(this.inputFile2.length()));
+ baos.write(this.inputFile2.getBytes());
+
+ return baos;
+ }
+ private byte[] toBytes(int i) {
+ byte[] result = new byte[4];
+
+ result[0] = (byte) (i >> 24);
+ result[1] = (byte) (i >> 16);
+ result[2] = (byte) (i >> 8);
+ result[3] = (byte) (i /*>> 0*/);
+
+ return result;
+ }
+ //
+ /**
+ * Get the number of data that were added to the data set
+ *
+ * @return number of added data
+ */
+ public int getNumberOfComparedPairs() {
+ return this.nativeDataList.size();
+ }
+
+ /**
+ * Get the set of ComparisonFeatures for which histogram data is available
+ *
+ * @return the set of ComparisonFeatures for which histogram data is
+ * available
+ */
+ public Set getComparisonFeatureSet() {
+ return this.comparisonFeatureToDataMap.keySet();
+ }
+
+ /**
+ * Get the HistogramData object corresponding to the given ComparisonFeature
+ *
+ * @param tmpComparisonFeature specifies which HistogramData object
+ * to return
+ * @return the HistogramData object corresponding to the given
+ * ComparisonFeature
+ */
+ public HistogramData getHistogramData(ComparisonFeature tmpComparisonFeature) {
+ return this.comparisonFeatureToDataMap.get(tmpComparisonFeature);
+ }
+
+ /**
+ * Get the list of all the ComparisonResults (the native data) that belong
+ * to the data set
+ *
+ * @return a list of ComparisonResults
+ */
+ public List getNativeDataList() {
+ return this.nativeDataList;
+ }
+
+ /**
+ * Get the name of the first input file
+ *
+ * @return the name of the first input file
+ */
+ public String getInputFile1() {
+ return this.inputFile1;
+ }
+
+ /**
+ * Get the name of the second input file
+ *
+ * @return the name of the second input file
+ */
+ public String getInputFile2() {
+ return this.inputFile2;
+ }
+
+ /**
+ * Get the time difference, in milliseconds, between the data's calculation
+ * start time and midnight, January 1, 1970 UTC
+ *
+ * @return the calculationStartTime in milliseconds
+ */
+ public long getCalculationStartTime() {
+ return this.calculationStartTime;
+ }
+
+ /**
+ * Get the time difference, in milliseconds, between the data's calculation
+ * finish time and midnight, January 1, 1970 UTC
+ *
+ * @return the calculationFinishTime in milliseconds
+ */
+ public long getCalculationFinishTime() {
+ return this.calculationFinishTime;
+ }
+
+ /**
+ * Set the time difference, in milliseconds, between the data's calculation
+ * start time and midnight, January 1, 1970 UTC
+ *
+ * @param tmpStartTime the difference to be set in milliseconds
+ */
+ public void setCalculationStartTime(long tmpStartTime) {
+ this.calculationStartTime = tmpStartTime;
+ }
+
+ /**
+ * Set the time difference, in milliseconds, between the data's calculation
+ * finish time and midnight, January 1, 1970 UTC
+ *
+ * @param tmpFinishTime the difference to be set in milliseconds
+ */
+ public void setCalculationFinishTime(long tmpFinishTime) {
+ this.calculationFinishTime = tmpFinishTime;
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Write the important contents of this HistogramDataManager to an
+ * ObjectOutputStream so this HistogramDataManager can be loaded at
+ * a later point in time. Important contents are the HistogramData
+ * objects, the previously calculated similarities and the origirnal input
+ * files
+ *
+ * @param tmpObjectOutputStream ObjectOutputStream to which the contents
+ * will be written
+ * @throws IOException any exception thrown by the underlying OutputStream
+ */
+ private synchronized void writeObject(java.io.ObjectOutputStream tmpObjectOutputStream) throws IOException {
+ tmpObjectOutputStream.writeObject(this.comparisonFeatureToDataMap.values().toArray(new HistogramData[this.comparisonFeatureToDataMap.values().size()]));
+ Iterator tmpIterator = this.nativeDataList.iterator();
+ double[][] tmpSimilaritiesArray = new double[this.nativeDataList.size()][this.nativeDataList.get(0).getSimilarities().length];
+ int tmpCounter = 0;
+ while (tmpIterator.hasNext()) {
+ tmpSimilaritiesArray[tmpCounter] = tmpIterator.next().getSimilarities();
+ tmpCounter++;
+ }
+ tmpObjectOutputStream.writeObject(tmpSimilaritiesArray);
+ tmpObjectOutputStream.writeUTF(this.inputFile1);
+ tmpObjectOutputStream.writeUTF(this.inputFile2);
+ tmpObjectOutputStream.writeLong(this.calculationStartTime);
+ tmpObjectOutputStream.writeLong(this.calculationFinishTime);
+ }
+
+ /**
+ * Read the contents of the given ObjectInputStream and use them to recreate
+ * the corresponding HistogramDataManager.
+ *
+ * @param tmpObjectInputStream ObjectInputStream from which the contents
+ * will be read
+ * @throws IOException any of the usual Input/Output related exceptions
+ * @throws ClassNotFoundException Class of a serialized object cannot be
+ * found
+ */
+ private void readObject(java.io.ObjectInputStream tmpObjectInputStream) throws IOException, ClassNotFoundException {
+ HistogramData[] tmpDataAray = (HistogramData[]) tmpObjectInputStream.readObject();
+ this.nativeDataList = new LinkedList<>();
+ this.comparisonFeatureToDataMap = new EnumMap<>(ComparisonFeature.class);
+ for (HistogramData tmpData : tmpDataAray) {
+ // Set nativeDataList because it transient in HistogramData
+ tmpData.setNativeDataList(this.nativeDataList);
+ this.comparisonFeatureToDataMap.putIfAbsent(ComparisonFeature.values()[tmpData.getComparisonFeautureNumber()], tmpData);
+ }
+ double[][] tmpSimilaritiesArray = (double[][]) tmpObjectInputStream.readObject();
+ for (int i = 0; i < tmpSimilaritiesArray.length; i++) {
+ this.nativeDataList.add(new ComparisonResult(tmpSimilaritiesArray[i], "", "", i));
+ }
+ this.inputFile1 = tmpObjectInputStream.readUTF();
+ this.inputFile2 = tmpObjectInputStream.readUTF();
+ this.calculationStartTime = tmpObjectInputStream.readLong();
+ this.calculationFinishTime = tmpObjectInputStream.readLong();
+ }
+
+ /**
+ * This method is not implemented
+ */
+ private void readObjectNoData() {
+ throw new RuntimeException("Method \"readObjectNoData\" is not implemented");
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/InputType.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/InputType.java
new file mode 100644
index 0000000..8987a06
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/InputType.java
@@ -0,0 +1,32 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+/**
+ * Defines different supported data types for the molecule set input
+ *
+ * @author Jan-Mathis Hein
+ */
+public enum InputType {
+
+ //
+ SMILES,
+ SDF;
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/JobTaskManager.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/JobTaskManager.java
new file mode 100644
index 0000000..86706b6
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/JobTaskManager.java
@@ -0,0 +1,680 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.Reader;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.concurrent.ConcurrentLinkedQueue;
+import java.util.Queue;
+import java.util.concurrent.Executors;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.ThreadLocalRandom;
+
+/**
+ * Manages the cancelation and execution of the ParseAndCompareTasks. This class
+ * also communicates its progress and handles the task's inputs.
+ *
+ * @author Jan-Mathis Hein
+ */
+public class JobTaskManager implements PropertyChangeListener{
+
+ //
+ /**
+ * True if this TaskManager is initializing task, executing tasks or
+ * processing the results of tasks, false otherwise. Is also used for
+ * cancelation
+ */
+ private boolean isStillWorking;
+
+ /**
+ * True if a valid first input type has been set, false otherwise
+ */
+ private boolean hasValidInputType1;
+
+ /**
+ * True if a valid second input type has been set, false otherwise
+ */
+ private boolean hasValidInputType2;
+
+ /**
+ * True if a valid first input file has been chosen, false otherwise
+ */
+ private boolean hasValidInputFile1;
+
+ /**
+ * True if a valid second input file has been chosen, false otherwise
+ */
+ private boolean hasValidInputFile2;
+
+ /**
+ * True if the HistogramDataManager has been created, false otherwise
+ */
+ private boolean hasCreatedHistogramDataManager;
+
+ /**
+ * An array that defines which features will be considered for
+ * the comparison. The index corresponds to the number of the feature
+ */
+ private boolean[] considerFeature;
+
+ /**
+ * Highest task progress value reached so far
+ */
+ private double highestProgressValue;
+
+ /**
+ * Number of created ParseAndCompareTasks
+ */
+ private double numberOfParseAndCompareTasks;
+
+ /**
+ * ExecutorService that handles threads and the execution of the tasks
+ */
+ private ExecutorService executorService;
+
+ /**
+ * First input file which contains a string encoding of the molecule set
+ */
+ private File inputFile1;
+
+ /**
+ * Second input file which contains a string encoding of the molecule set
+ */
+ private File inputFile2;
+
+ /**
+ * Manages the histogram data for each ComparisonFeature
+ */
+ private HistogramDataManager histogramDataManager;
+
+ /**
+ * Type of input of the first input file
+ */
+ private InputType inputType1;
+
+ /**
+ * Type of input of the second input file
+ */
+ private InputType inputType2;
+
+ /**
+ * Number of threads that can be used concurrently by the ExecutorService
+ */
+ private int numberOfParallelThreads;
+
+ /**
+ * Default number of bins in a histogram
+ */
+ private int defaultNumberOfBins;
+
+ /**
+ * Number of inputs that one set has as a surplus
+ */
+ private int numberOfUnpairedInputs;
+
+ /**
+ * List of features that are considered for the comparison. Is never null
+ */
+ private final List consideredFeaturesList = new LinkedList<>();
+
+ /**
+ * PropertyChangeSupport that manages the firing of PropertyChangeEvents and
+ * the adding and removing of PropertyChangeListeners
+ */
+ private final PropertyChangeSupport propertyChangeSupport;
+
+ /**
+ * Queue of ComparisonResults of ParseAndCompareTasks that finished
+ * successfully. Is never null
+ */
+ private final Queue comparisonResultsQueue = new ConcurrentLinkedQueue<>();
+
+ /**
+ * Queue of ComparisonResults of ParseAndCompareTask that did not finish
+ * successfully. Is never null
+ */
+ private final Queue failedComparisonsQueue = new ConcurrentLinkedQueue<>();
+
+ /**
+ * Queue of ParseAndCompareTasks that were initialized but not
+ * submitted for execution yet. Is never null
+ */
+ private final Queue remainingParseAndCompareTasksQueue = new ConcurrentLinkedQueue<>();
+
+ /**
+ * Queue of ParseAndCompareTasks that have been submitted for
+ * execution. Is never null
+ */
+ private final Queue submittedParseAndCompareTasksQueue = new ConcurrentLinkedQueue<>();
+ //
+ //
+ //
+ /**
+ * Initialize the instance variables
+ *
+ * @param tmpNumberOfParallelThreads number of threads that will be used in
+ * parallel
+ * @param tmpDefaultNumberOfBins default number of bins used for histograms
+ */
+ public JobTaskManager(int tmpNumberOfParallelThreads, int tmpDefaultNumberOfBins) {
+ this.hasCreatedHistogramDataManager = false;
+ this.isStillWorking = false;
+ this.hasValidInputType1 = false;
+ this.hasValidInputType2 = false;
+ this.hasValidInputFile1 = false;
+ this.hasValidInputFile2 = false;
+ this.propertyChangeSupport = new PropertyChangeSupport(this);
+ this.numberOfParallelThreads = tmpNumberOfParallelThreads;
+ this.defaultNumberOfBins = tmpDefaultNumberOfBins;
+ }
+ //
+ //
+ //
+ //
+ /**
+ * True if this JobTaskManager is initializing tasks, executing tasks or
+ * processing the results of tasks AND was not canceled, false otherwise
+ *
+ * @return true if this JobTaskManager is initializing tasks, executing
+ * tasks or processing the results of tasks AND was not canceled,
+ * false otherwise
+ */
+ public boolean isWorking() {
+ return this.isStillWorking;
+ }
+
+ /**
+ * Cancel the working process of this JobTaskManager i.e. the
+ * initialization, execution or result processing of tasks. The
+ * ExecutorService will be shutdown and disposed of. After cancelation the
+ * JobTaskManager can be reused.
+ */
+ public void cancelWorkingProcess() {
+ this.isStillWorking = false;
+ synchronized (this) {
+ int tmpNumberOfSubmittedTasks = this.submittedParseAndCompareTasksQueue.size();
+ for (int i = 0; i < tmpNumberOfSubmittedTasks; i++) {
+ try {
+ ParseAndCompareTask tmpTask = this.submittedParseAndCompareTasksQueue.poll();
+ tmpTask.cancel();
+ tmpTask.removePropertyChangeListener(this);
+ } catch (NullPointerException ex) {
+ // This can happen if the task finishes and in the process removes itself from the queue
+ }
+ }
+ this.remainingParseAndCompareTasksQueue.clear();
+ this.comparisonResultsQueue.clear();
+ this.failedComparisonsQueue.clear();
+ if (this.executorService != null) {
+ this.executorService.shutdown();
+ this.executorService = null;
+ }
+ }
+ }
+
+ /**
+ * Initialize the tasks and start their execution
+ *
+ * @throws IOException if there is something wrong with the input files
+ * @throws MSCInputException if the input is not sufficient
+ */
+ public synchronized void startTasks() throws IOException, MSCInputException {
+ //
+ if (!(this.hasValidInputFile1 && this.hasValidInputFile2)) {
+ throw new MSCInputException("Can't read these files");
+ }
+ if (this.consideredFeaturesList.isEmpty()) {
+ throw new MSCInputException("There are no features to compare");
+ }
+ if (!(this.hasValidInputType1 && this.hasValidInputType2)) {
+ throw new MSCInputException("The input types are invalid");
+ }
+ //
+ try (Reader tmpReader1 = new BufferedReader(new FileReader(this.inputFile1));
+ Reader tmpReader2 = new BufferedReader(new FileReader(this.inputFile2));) {
+ // Clears all queues
+ this.cancelWorkingProcess();
+ this.executorService = Executors.newFixedThreadPool(this.numberOfParallelThreads);
+ this.isStillWorking = true;
+ this.hasCreatedHistogramDataManager = false;
+ this.highestProgressValue = 0;
+ this.numberOfParseAndCompareTasks = 0;
+ this.numberOfUnpairedInputs = 0;
+ int tmpIdentifier = 0;
+ // Byte value of the new line character
+ int tmpSeperator = 10;
+ boolean tmpReachedEOF1, tmpReachedEOF2;
+ String tmpMolecule1, tmpMolecule2;
+ Object[] tmpArray1, tmpArray2;
+ outerLoop:
+ while (true) {
+ //
+ switch (this.inputType1) {
+ case SMILES:
+ tmpArray1 = this.readCharactersUntilSeperator(tmpReader1, tmpSeperator);
+ tmpMolecule1 = (String) tmpArray1[0];
+ tmpReachedEOF1 = (boolean) tmpArray1[1];
+ break;
+ case SDF:
+ tmpArray1 = this.readCharactersUntil$$$$(tmpReader1);
+ tmpMolecule1 = (String) tmpArray1[0];
+ tmpReachedEOF1 = (boolean) tmpArray1[1];
+ break;
+ default:
+ throw new MSCInputException("The first input type is invalid");
+ }
+ switch (this.inputType2) {
+ case SMILES:
+ tmpArray2 = this.readCharactersUntilSeperator(tmpReader2, tmpSeperator);
+ tmpMolecule2 = (String) tmpArray2[0];
+ tmpReachedEOF2 = (boolean) tmpArray2[1];
+ break;
+ case SDF:
+ tmpArray2 = this.readCharactersUntil$$$$(tmpReader2);
+ tmpMolecule2 = (String) tmpArray2[0];
+ tmpReachedEOF2 = (boolean) tmpArray2[1];
+ break;
+ default:
+ throw new MSCInputException("The second input type is invalid");
+ }
+ //
+ if (!tmpMolecule1.isEmpty() && !tmpMolecule2.isEmpty()) {
+ ParseAndCompareTask tmpTask = new ParseAndCompareTask(tmpMolecule1, tmpMolecule2, this.inputType1, this.inputType2, this.considerFeature, tmpIdentifier++);
+ tmpTask.addPropertyChangeListener(this);
+ this.remainingParseAndCompareTasksQueue.add(tmpTask);
+ this.numberOfParseAndCompareTasks++;
+ } else if (tmpMolecule1.isEmpty() ^ tmpMolecule2.isEmpty()) {
+ this.numberOfUnpairedInputs++;
+ }
+ if (!this.isStillWorking) {
+ return;
+ }
+ if (tmpReachedEOF1 && tmpReachedEOF2) {
+ break;
+ }
+ }
+ this.propertyChangeSupport.firePropertyChange("Unpaired inputs", 0, this.numberOfUnpairedInputs);
+ if (this.isStillWorking) {
+ for (int i = 0; i < this.numberOfParallelThreads; i++) {
+ ParseAndCompareTask tmpNextTask;
+ if ((tmpNextTask = this.remainingParseAndCompareTasksQueue.poll()) != null) {
+ this.submittedParseAndCompareTasksQueue.add(tmpNextTask);
+ this.executorService.submit(tmpNextTask);
+ }
+ }
+ }
+ } catch (Exception ex) {
+ throw ex;
+ }
+ }
+ //
+ //
+ /**
+ * Add a PropertyChangeListener that listens for changes fired from this
+ * JobTaskManager
+ *
+ * @param tmpListener a listener to be added
+ */
+ public void addPropertyChangeListener(PropertyChangeListener tmpListener) {
+ this.propertyChangeSupport.addPropertyChangeListener(tmpListener);
+ }
+
+ /**
+ * Remove a PropertyChangeListener
+ *
+ * @param tmpListener a listener to be removed
+ */
+ public void removePropertyChangeListener(PropertyChangeListener tmpListener) {
+ this.propertyChangeSupport.removePropertyChangeListener(tmpListener);
+ }
+
+ /**
+ * Handle all PropertyChangeEvents that reach this JobTaskManager.
+ *
+ * @param evt PropertyChangeEvent that reached this JobTaskManager
+ */
+ @Override
+ public void propertyChange(PropertyChangeEvent evt) {
+ try {
+ if (evt.getSource() instanceof ParseAndCompareTask) {
+ ParseAndCompareTask tmpTask = (ParseAndCompareTask) evt.getSource();
+ if (!tmpTask.isFinished()) {
+ return;
+ }
+ switch1:
+ switch (evt.getPropertyName()) {
+ case "Task completed":
+ if ((boolean) evt.getNewValue()) {
+ this.comparisonResultsQueue.add(tmpTask.getResult());
+ } else {
+ this.failedComparisonsQueue.add(tmpTask.getResult());
+ }
+ tmpTask.removePropertyChangeListener(this);
+ this.submittedParseAndCompareTasksQueue.remove(tmpTask);
+ double tmpProgress = tmpTask.getIdentifier() / this.numberOfParseAndCompareTasks;
+ if (tmpProgress > this.highestProgressValue && ThreadLocalRandom.current().nextInt(0, 100) < 5) {
+ this.highestProgressValue = tmpProgress;
+ this.propertyChangeSupport.firePropertyChange("ParseAndCompareTasks progress", 0.0, tmpProgress);
+ }
+ synchronized (this) {
+ if (this.isStillWorking && !this.remainingParseAndCompareTasksQueue.isEmpty()) {
+ ParseAndCompareTask tmpNextTask;
+ if ((tmpNextTask = this.remainingParseAndCompareTasksQueue.poll()) != null) {
+ this.submittedParseAndCompareTasksQueue.add(tmpNextTask);
+ this.executorService.submit(tmpNextTask);
+ }
+ } else if (this.remainingParseAndCompareTasksQueue.isEmpty() && this.submittedParseAndCompareTasksQueue.isEmpty() &&
+ this.isStillWorking && !this.hasCreatedHistogramDataManager) {
+ Iterator tmpIterator = this.comparisonResultsQueue.iterator();
+ if (!tmpIterator.hasNext()) {
+ throw new MSCInputException("At least one result is required");
+ }
+ ComparisonResult tmpResult = tmpIterator.next();
+ this.histogramDataManager = new HistogramDataManager(
+ this.consideredFeaturesList, this.defaultNumberOfBins, tmpResult,
+ this.inputFile1.getName(), this.inputFile2.getName()
+ );
+ while(tmpIterator.hasNext()) {
+ if (!this.isStillWorking) {
+ this.comparisonResultsQueue.clear();
+ this.failedComparisonsQueue.clear();
+ this.histogramDataManager = null;
+ break switch1;
+ }
+ tmpResult = tmpIterator.next();
+ this.histogramDataManager.addDatum(tmpResult);
+ }
+ for (ComparisonFeature tmpComparisonFeature : this.consideredFeaturesList) {
+ if (!this.isStillWorking) {
+ this.comparisonResultsQueue.clear();
+ this.failedComparisonsQueue.clear();
+ this.histogramDataManager = null;
+ break switch1;
+ }
+ this.histogramDataManager.getHistogramData(tmpComparisonFeature).call();
+ }
+ this.comparisonResultsQueue.clear();
+ this.hasCreatedHistogramDataManager = true;
+ this.propertyChangeSupport.firePropertyChange("ParseAndCompareTasks finished", false, true);
+ this.isStillWorking = false;
+ }
+ }
+ break;
+ default:
+ this.propertyChangeSupport.firePropertyChange("Exception", "JobTaskManager.propertyChange()", new RuntimeException("Unexpected PropertyChange:" + evt.getPropertyName()));
+ break;
+ }
+ }
+ } catch (Exception ex) {
+ this.propertyChangeSupport.firePropertyChange("Exception", "JobTaskManager.propertyChange(): " + evt.getPropertyName(), ex);
+ }
+ }
+ //
+ //
+ //
+ /**
+ * Get the HistogramDataManager that manages the histogram data for each
+ * ComparisonFeature
+ *
+ * @return the HistogramDataManager that manages the histogram data for each
+ * ComparisonFeature or null if the task execution has not been
+ * finished successfully
+ */
+ public synchronized HistogramDataManager getHistogramDataManager() {
+ return this.hasCreatedHistogramDataManager ? this.histogramDataManager : null;
+ }
+ //
+ //
+ /**
+ * Set the ComparisonFeatures which will be considered during the
+ * comparison.
+ *
+ * @param tmpConsideredFeatures specifies which ComparisonFeatures
+ * will be considered
+ * @throws MSCInputException if no ComparisonFeatures are being considered
+ */
+ public synchronized void setComparisonFeatures(boolean[] tmpConsideredFeatures) throws MSCInputException, IllegalArgumentException {
+ //
+ if (tmpConsideredFeatures == null || tmpConsideredFeatures.length < 1) {
+ throw new IllegalArgumentException("tmpConsideredFeatures is invalid");
+ }
+ //
+ this.considerFeature = tmpConsideredFeatures;
+ this.consideredFeaturesList.clear();
+ for (int i = 0; i < this.considerFeature.length; i++) {
+ if (this.considerFeature[i]) {
+ this.consideredFeaturesList.add(ComparisonFeature.values()[i]);
+ }
+ }
+ if (this.consideredFeaturesList.size() < 1 || this.consideredFeaturesList.isEmpty()) {
+ throw new MSCInputException("There are no features for the comparison");
+ }
+ }
+
+ /**
+ * Set the first input file
+ *
+ * @param tmpFile the input file
+ */
+ public synchronized void setInputFile1(File tmpFile) throws IllegalArgumentException {
+ //
+ if (tmpFile == null) {
+ throw new IllegalArgumentException("tmpFile is null");
+ }
+ //
+ this.inputFile1 = tmpFile;
+ this.hasValidInputFile1 = this.inputFile1.canRead();
+ }
+
+ /**
+ * Set the second input file
+ *
+ * @param tmpFile the input file
+ */
+ public synchronized void setInputFile2(File tmpFile) throws IllegalArgumentException {
+ //
+ if (tmpFile == null) {
+ throw new IllegalArgumentException("tmpFile is null");
+ }
+ //
+ this.inputFile2 = tmpFile;
+ this.hasValidInputFile2 = this.inputFile2.canRead();
+ }
+
+ /**
+ * Set the first input type
+ *
+ * @param tmpInputType the input type
+ */
+ public synchronized void setInputType1(InputType tmpInputType) {
+ this.inputType1 = tmpInputType;
+ this.hasValidInputType1 = this.inputType1 == InputType.SMILES || this.inputType1 == InputType.SDF;
+ }
+
+ /**
+ * Set the second input type
+ *
+ * @param tmpInputType the input type
+ */
+ public synchronized void setInputType2(InputType tmpInputType) {
+ this.inputType2 = tmpInputType;
+ this.hasValidInputType2 = this.inputType2 == InputType.SMILES || this.inputType2 == InputType.SDF;
+ }
+
+ /**
+ * Set the number of parallel threads to be used by the executor service and
+ * initialize a new executor service
+ *
+ * @param tmpNumberOfParallelThreads specifies the number of parallel
+ * threads
+ */
+ public synchronized void setNumberOfParallelThreads(int tmpNumberOfParallelThreads) {
+ this.numberOfParallelThreads = tmpNumberOfParallelThreads;
+ if (this.executorService != null) {
+ this.executorService.shutdown();
+ this.executorService = Executors.newFixedThreadPool(this.numberOfParallelThreads);
+ }
+ }
+
+ /**
+ * Set the default number of bins used for histograms
+ *
+ * @param tmpDefaultNumberOfBins specifies the default number of bins used
+ * for histograms
+ */
+ public void setDefaultNumberOfBins(int tmpDefaultNumberOfBins) {
+ this.defaultNumberOfBins = tmpDefaultNumberOfBins;
+ }
+ //
+ //
+ //
+ /**
+ * True if input file configuration can be read, false otherwise
+ *
+ * @return true if input file configuration can be read, false otherwise
+ */
+ public boolean canReadInput() {
+ return this.hasValidInputType1 && this.hasValidInputType2 && this.hasValidInputFile1 && this.hasValidInputFile2;
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Finalize this object by stopping the working process, shuting down the
+ * ExecutorService and calling Object.finalize()
+ */
+ @Override
+ @SuppressWarnings("deprecation")
+ protected void finalize() throws Throwable {
+ this.cancelWorkingProcess();
+ super.finalize();
+ }
+ //
+ //
+ //
+ /**
+ * Read characters from the stream of the given reader until the given
+ * seperator is read. Concatenate all read characters to a String. Return
+ * the String and true if the end of the stream has been reached and false
+ * otherwise
+ *
+ * @param tmpReader the reader from whos stream the characters will be read
+ * @param tmpSeperator specifies the seperator as its byte value
+ * @return an Object array where the first element is the concatenated
+ * String and the second element is a Boolean that is true if the end of
+ * the stream has been reached and false otherwise
+ * @throws IOException
+ */
+ private Object[] readCharactersUntilSeperator(Reader tmpReader, int tmpSeperator) throws IOException {
+ String tmpMolecule = "";
+ Boolean tmpReachedEndOfStream = false;
+ int tmpByte;
+ while (true) {
+ tmpByte = tmpReader.read();
+ if (tmpByte == tmpSeperator) {
+ break;
+ } else if (tmpByte == -1) {
+ tmpReachedEndOfStream = true;
+ break;
+ } else {
+ tmpMolecule += (char) tmpByte;
+ }
+ }
+ return new Object[]{tmpMolecule, tmpReachedEndOfStream};
+ }
+
+ /**
+ * Read characters from the stream of the given reader until '$$$$' is read.
+ * Concatenate all read characters to a String. Return the String and true
+ * if the end of the stream has been reached and false otherwise
+ *
+ * @param tmpReader the reader from whos stream the characters will be read
+ * @return an Object array where the first element is the concatenated
+ * String and the second element is a Boolean that is true if the end of
+ * the stream has been reached and false otherwise
+ * @throws IOException
+ */
+ private Object[] readCharactersUntil$$$$(Reader tmpReader) throws IOException {
+ String tmpMolecule = "";
+ Boolean tmpReachedEndOfStream = false;
+ int tmpByte;
+ int tmp$Counter = 0;
+ loop:
+ while (true) {
+ tmpByte = tmpReader.read();
+ outerSwitch:
+ switch (tmpByte) {
+ case -1:
+ tmpReachedEndOfStream = true;
+ break loop;
+ case 36:
+ tmpMolecule += (char) tmpByte;
+ tmp$Counter++;
+ while (true) {
+ tmpByte = tmpReader.read();
+ switch (tmpByte) {
+ case -1:
+ tmpReachedEndOfStream = true;
+ break loop;
+ case 36:
+ tmpMolecule += (char) tmpByte;
+ tmp$Counter++;
+ break;
+ case 10:
+ tmpMolecule += (char) tmpByte;
+ if (tmp$Counter == 4) {
+ tmp$Counter = 0;
+ break loop;
+ }
+ tmp$Counter = 0;
+ break outerSwitch;
+ // Characters that are allowed to follow '$$$$' like \r
+ case 13:
+ tmpMolecule += (char) tmpByte;
+ if (tmp$Counter != 4) {
+ tmp$Counter = 0;
+ break outerSwitch;
+ }
+ break;
+ default:
+ tmpMolecule += (char) tmpByte;
+ tmp$Counter = 0;
+ break outerSwitch;
+ }
+ }
+ default:
+ tmpMolecule += (char) tmpByte;
+ tmp$Counter = 0;
+ break;
+ }
+ }
+ return new Object[]{tmpMolecule, tmpReachedEndOfStream};
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/MSCInputException.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/MSCInputException.java
new file mode 100644
index 0000000..9c41e57
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/MSCInputException.java
@@ -0,0 +1,73 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+/**
+ * An Exception that is thrown whenever the Molecule Set Comparator application
+ * received unexpected input with which it can't continue operating
+ *
+ * @author Jan-Mathis Hein
+ */
+public class MSCInputException extends Exception {
+
+ //
+ /**
+ * A serial version UID to check whether the loaded data is compatible
+ */
+ private static final long serialVersionUID = 1L;
+ //
+ //
+ //
+ /**
+ * A message that furhter describes the exception
+ */
+ private String message;
+ //
+ //
+ //
+ /**
+ * Create an Exception without a message
+ */
+ public MSCInputException() {
+ super();
+ }
+
+ /**
+ * Create an Exception with the specified message
+ *
+ * @param tmpMessage specifies the message
+ */
+ public MSCInputException(String tmpMessage) {
+ super(tmpMessage);
+ this.message = tmpMessage;
+ }
+ //
+ //
+ //
+ /**
+ * Return a string representation of the MSCInputException
+ *
+ * @return a string representation of the MSCInputException
+ */
+ @Override
+ public String toString() {
+ return "InsufficientDataException: " + this.message;
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/ParseAndCompareTask.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/ParseAndCompareTask.java
new file mode 100644
index 0000000..3d47182
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/model/ParseAndCompareTask.java
@@ -0,0 +1,1390 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.util.concurrent.Callable;
+import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.aromaticity.Aromaticity;
+import org.openscience.cdk.aromaticity.ElectronDonation;
+import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.fingerprint.*;
+import org.openscience.cdk.graph.Cycles;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IAtomType;
+import org.openscience.cdk.io.SMILESWriter;
+import org.openscience.cdk.io.iterator.IIteratingChemObjectReader;
+import org.openscience.cdk.io.iterator.IteratingSDFReader;
+import org.openscience.cdk.qsar.descriptors.molecular.*;
+import org.openscience.cdk.ringsearch.AllRingsFinder;
+import org.openscience.cdk.ringsearch.RingSearch;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
+import org.openscience.cdk.similarity.Tanimoto;
+import org.openscience.cdk.smiles.SmiFlavor;
+import org.openscience.cdk.smiles.SmilesGenerator;
+import org.openscience.cdk.smiles.SmilesParser;
+import org.openscience.cdk.tools.CDKHydrogenAdder;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
+import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
+
+/**
+ * A task that parses a pair of string encodings to a molecule pair and compares
+ * the pair on the basis of specified ComparisonFeatures.
+ *
+ * @author Jan-Mathis Hein
+ */
+public class ParseAndCompareTask implements Callable {
+
+ //
+ /**
+ * True if this task has finished in any way, false otherwise
+ */
+ private boolean isFinished;
+
+ /**
+ * True if this task has been started, false otherwise
+ */
+ private boolean isStarted;
+
+ /**
+ * True if this task has been cancelled, false otherwise
+ */
+ private boolean isCancelled;
+
+ /**
+ * An array that defines on the basis of which ComparisonFeatures the
+ * comparison will be made. The index corresponds to the number of the
+ * ComparisonFeature
+ */
+ private final boolean[] consideredComparisonFeature;
+
+ /**
+ * The result of the comparison
+ */
+ private ComparisonResult result;
+
+ /**
+ * InputType of the first molecule
+ */
+ private final InputType type1;
+
+ /**
+ * InputType of the second molecule
+ */
+ private final InputType type2;
+
+ /**
+ * Number that identifies this task
+ */
+ private final int identifier;
+
+ /**
+ * PropertyChangeSupport that manages the firing of PropertyChangeEvents and
+ * the adding and removing of PropertyChangeListeners
+ */
+ private final PropertyChangeSupport propertyChangeSupport;
+
+ /**
+ * String encoding of the first molecule
+ */
+ private String molecule1;
+
+ /**
+ * String encoding of the second molecule
+ */
+ private String molecule2;
+ //
+ //
+ //
+ /**
+ * Initialize the instance variables
+ *
+ * @param tmpInput1 specifies the first input string
+ * @param tmpInput2 specifies the second input string
+ * @param tmpType1 specifies the first input type
+ * @param tmpType2 specifies the first input type
+ * @param tmpConsiderFeature specifies on the basis of which
+ * ComparisonFeatures the comparison will be made
+ * @param tmpIdentifier unique identifier for this task
+ */
+ public ParseAndCompareTask(String tmpInput1, String tmpInput2, InputType tmpType1, InputType tmpType2, boolean[] tmpConsiderFeature, int tmpIdentifier) {
+ this.isStarted = false;
+ this.isFinished = false;
+ this.isCancelled = false;
+ this.molecule1 = tmpInput1;
+ this.molecule2 = tmpInput2;
+ this.type1 = tmpType1;
+ this.type2 = tmpType2;
+ this.consideredComparisonFeature = tmpConsiderFeature;
+ this.identifier = tmpIdentifier;
+ this.propertyChangeSupport = new PropertyChangeSupport(this);
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Parse the input strings to molecules and compare them on the basis of the
+ * specified ComparisonFeatures
+ *
+ * @return null
+ */
+ @Override
+ public Void call() {
+ try {
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ this.isStarted = true;
+ double[] tmpSimilarities = new double[this.consideredComparisonFeature.length];
+ IAtomContainer[] tmpMoleculePair = new IAtomContainer[2];
+ SmilesParser tmpSmilesParser = new SmilesParser(SilentChemObjectBuilder.getInstance());
+ IIteratingChemObjectReader tmpSdfParser = new IteratingSDFReader(new StringReader(""), DefaultChemObjectBuilder.getInstance());
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ switch (this.type1) {
+ case SMILES:
+ tmpMoleculePair[0] = tmpSmilesParser.parseSmiles(this.molecule1);
+ break;
+ case SDF:
+ tmpSdfParser.setReader(new StringReader(this.molecule1));
+ tmpMoleculePair[0] = tmpSdfParser.next();
+ break;
+ default:
+ break;
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ switch (this.type2) {
+ case SMILES:
+ tmpMoleculePair[1] = tmpSmilesParser.parseSmiles(this.molecule2);
+ break;
+ case SDF:
+ tmpSdfParser.setReader(new StringReader(this.molecule2));
+ tmpMoleculePair[1] = tmpSdfParser.next();
+ break;
+ default:
+ break;
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ CDKAtomTypeMatcher tmpCDKAtomTypeMatcher = CDKAtomTypeMatcher.getInstance(DefaultChemObjectBuilder.getInstance());
+ CDKHydrogenAdder tmpCDKHydrogenAdder = CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance());
+ Aromaticity tmpAromaticity = new Aromaticity(ElectronDonation.cdk(), Cycles.or(Cycles.all(), Cycles.cdkAromaticSet()));
+ RingSearch tmpRingSearch;
+ for (IAtomContainer tmpMolecule : tmpMoleculePair) {
+ tmpRingSearch = new RingSearch(tmpMolecule);
+ for (IAtom tmpAtom : tmpMolecule.atoms()) {
+ tmpAtom.setIsInRing(tmpRingSearch.cyclic(tmpAtom));
+ IAtomType tmpType = tmpCDKAtomTypeMatcher.findMatchingAtomType(tmpMolecule, tmpAtom);
+ AtomTypeManipulator.configure(tmpAtom, tmpType);
+ }
+ tmpCDKHydrogenAdder.addImplicitHydrogens(tmpMolecule);
+ AtomContainerManipulator.convertImplicitToExplicitHydrogens(tmpMolecule);
+ // Sets aromaticity flags
+ tmpAromaticity.apply(tmpMolecule);
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.ACIDIC_GROUP_COUNT.getFeatureNumber()]) {
+ AcidicGroupCountDescriptor tmpAcidicGroupCountDescriptor = new AcidicGroupCountDescriptor();
+ tmpAcidicGroupCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.ACIDIC_GROUP_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAcidicGroupCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAcidicGroupCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.ALL_RINGS_COUNT.getFeatureNumber()]) {
+ try {
+ AllRingsFinder.usingThreshold(AllRingsFinder.Threshold.PubChem_99);
+ AllRingsFinder tmpAllRingsFinder = new AllRingsFinder();
+ int tmpAllRingsCount1 = tmpAllRingsFinder.findAllRings(tmpMoleculePair[0]).getAtomContainerCount();
+ int tmpAllRingsCount2 = tmpAllRingsFinder.findAllRings(tmpMoleculePair[1]).getAtomContainerCount();
+ tmpSimilarities[ComparisonFeature.ALL_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpAllRingsCount1 - tmpAllRingsCount2);
+ } catch (CDKException CDKException) {
+ tmpSimilarities[ComparisonFeature.ALL_RINGS_COUNT.getFeatureNumber()] = Double.NaN;
+ }
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.A_LOGP.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.A_LOGP_2.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.MOLAR_REFRACTIVITY.getFeatureNumber()]) {
+ ALOGPDescriptor tmpALOGPDescriptor = new ALOGPDescriptor();
+ tmpALOGPDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpALOGPDescriptor.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpALOGPDescriptor.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ // Ghose-Grippen logP
+ if (this.consideredComparisonFeature[ComparisonFeature.A_LOGP.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.A_LOGP.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]));
+ }
+ // Ghose-Grippen logP 2
+ if (this.consideredComparisonFeature[ComparisonFeature.A_LOGP_2.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.A_LOGP_2.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[1]) - Double.parseDouble(tmpArray2[1]));
+ }
+ // Molar refractivity
+ if (this.consideredComparisonFeature[ComparisonFeature.MOLAR_REFRACTIVITY.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.MOLAR_REFRACTIVITY.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[2]) - Double.parseDouble(tmpArray2[2]));
+ }
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.APOL.getFeatureNumber()]) {
+ APolDescriptor tmpAPolDescriptor = new APolDescriptor();
+ tmpAPolDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.APOL.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAPolDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAPolDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.AROMATIC_ATOM_COUNT.getFeatureNumber()]) {
+ AromaticAtomsCountDescriptor tmpAromaticAtomsCountDescriptor = new AromaticAtomsCountDescriptor();
+ tmpAromaticAtomsCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpAromaticAtomsCountDescriptor.setParameters(new Object[] {true});
+ tmpSimilarities[ComparisonFeature.AROMATIC_ATOM_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAromaticAtomsCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAromaticAtomsCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.AROMATIC_BOND_COUNT.getFeatureNumber()]) {
+ AromaticBondsCountDescriptor tmpAromaticBondsCountDescriptor = new AromaticBondsCountDescriptor();
+ tmpAromaticBondsCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpAromaticBondsCountDescriptor.setParameters(new Object[] {true});
+ tmpSimilarities[ComparisonFeature.AROMATIC_BOND_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAromaticBondsCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAromaticBondsCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ AtomCountDescriptor tmpAtomCountDescriptor = new AtomCountDescriptor();
+ tmpAtomCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ // Atom count
+ if (this.consideredComparisonFeature[ComparisonFeature.ATOM_COUNT.getFeatureNumber()]) {
+ tmpAtomCountDescriptor.setParameters(new Object[] {"*"});
+ tmpSimilarities[ComparisonFeature.ATOM_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ // Carbon count
+ if (this.consideredComparisonFeature[ComparisonFeature.CARBON_COUNT.getFeatureNumber()]) {
+ tmpAtomCountDescriptor.setParameters(new Object[] {"C"});
+ tmpSimilarities[ComparisonFeature.CARBON_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ // Oxygen count
+ if (this.consideredComparisonFeature[ComparisonFeature.OXYGEN_COUNT.getFeatureNumber()]) {
+ tmpAtomCountDescriptor.setParameters(new Object[] {"O"});
+ tmpSimilarities[ComparisonFeature.OXYGEN_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ // Sulfur count
+ if (this.consideredComparisonFeature[ComparisonFeature.SULFUR_COUNT.getFeatureNumber()]) {
+ tmpAtomCountDescriptor.setParameters(new Object[] {"S"});
+ tmpSimilarities[ComparisonFeature.SULFUR_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ // Nitrogen count
+ if (this.consideredComparisonFeature[ComparisonFeature.NITROGEN_COUNT.getFeatureNumber()]) {
+ tmpAtomCountDescriptor.setParameters(new Object[] {"N"});
+ tmpSimilarities[ComparisonFeature.NITROGEN_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ // Phosphor count
+ if (this.consideredComparisonFeature[ComparisonFeature.PHOSPHOR_COUNT.getFeatureNumber()]) {
+ tmpAtomCountDescriptor.setParameters(new Object[] {"P"});
+ tmpSimilarities[ComparisonFeature.PHOSPHOR_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.ATS_CHARGE1.getFeatureNumber()]) {
+ AutocorrelationDescriptorCharge tmpAutocorrelationDescriptorCharge = new AutocorrelationDescriptorCharge();
+ tmpAutocorrelationDescriptorCharge.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpAutocorrelationDescriptorCharge.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpAutocorrelationDescriptorCharge.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ tmpSimilarities[ComparisonFeature.ATS_CHARGE1.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]));
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.ATS_MASS1.getFeatureNumber()]) {
+ AutocorrelationDescriptorMass tmpAutocorrelationDescriptorMass = new AutocorrelationDescriptorMass();
+ tmpAutocorrelationDescriptorMass.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpAutocorrelationDescriptorMass.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpAutocorrelationDescriptorMass.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ tmpSimilarities[ComparisonFeature.ATS_MASS1.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]));
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.ATS_POLARIZABILITY1.getFeatureNumber()]) {
+ AutocorrelationDescriptorPolarizability tmpAutocorrelationDescriptorPolarizability = new AutocorrelationDescriptorPolarizability();
+ tmpAutocorrelationDescriptorPolarizability.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpAutocorrelationDescriptorPolarizability.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpAutocorrelationDescriptorPolarizability.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ tmpSimilarities[ComparisonFeature.ATS_POLARIZABILITY1.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]));
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.BASIC_GROUP_COUNT.getFeatureNumber()]) {
+ BasicGroupCountDescriptor tmpBasicGroupCountDescriptor = new BasicGroupCountDescriptor();
+ tmpBasicGroupCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.BASIC_GROUP_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpBasicGroupCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpBasicGroupCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ BondCountDescriptor tmpBondCountDescriptor = new BondCountDescriptor();
+ tmpBondCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ // Bond count
+ if (this.consideredComparisonFeature[ComparisonFeature.BOND_COUNT.getFeatureNumber()]) {
+ tmpBondCountDescriptor.setParameters(new Object[] {""});
+ tmpSimilarities[ComparisonFeature.BOND_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ // Single bond count
+ if (this.consideredComparisonFeature[ComparisonFeature.SINGLE_BOND_COUNT.getFeatureNumber()]) {
+ tmpBondCountDescriptor.setParameters(new Object[] {"s"});
+ tmpSimilarities[ComparisonFeature.SINGLE_BOND_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ // Double bond count
+ if (this.consideredComparisonFeature[ComparisonFeature.DOUBLE_BOND_COUNT.getFeatureNumber()]) {
+ tmpBondCountDescriptor.setParameters(new Object[] {"d"});
+ tmpSimilarities[ComparisonFeature.DOUBLE_BOND_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ // Triple bond count
+ if (this.consideredComparisonFeature[ComparisonFeature.TRIPLE_BOND_COUNT.getFeatureNumber()]) {
+ tmpBondCountDescriptor.setParameters(new Object[] {"t"});
+ tmpSimilarities[ComparisonFeature.TRIPLE_BOND_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ // Quadruple bond count
+ if (this.consideredComparisonFeature[ComparisonFeature.QUADRUPLE_BOND_COUNT.getFeatureNumber()]) {
+ tmpBondCountDescriptor.setParameters(new Object[] {"q"});
+ tmpSimilarities[ComparisonFeature.QUADRUPLE_BOND_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.BPOL.getFeatureNumber()]) {
+ BPolDescriptor tmpBPolDescriptor = new BPolDescriptor();
+ tmpBPolDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.BPOL.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpBPolDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpBPolDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.C1SP1_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.C2SP1_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.C1SP2_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.C2SP2_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.C3SP2_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.C1SP3_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.C2SP3_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.C3SP3_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.C4SP3_COUNT.getFeatureNumber()]) {
+ CarbonTypesDescriptor tmpCarbonTypesDescriptor = new CarbonTypesDescriptor();
+ tmpCarbonTypesDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpCarbonTypesDescriptor.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpCarbonTypesDescriptor.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ // C1SP1 count
+ if (this.consideredComparisonFeature[ComparisonFeature.C1SP1_COUNT.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.C1SP1_COUNT.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]));
+ }
+ // C2SP1 count
+ if (this.consideredComparisonFeature[ComparisonFeature.C2SP1_COUNT.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.C2SP1_COUNT.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[1]) - Double.parseDouble(tmpArray2[1]));
+ }
+ // C1SP2 count
+ if (this.consideredComparisonFeature[ComparisonFeature.C1SP2_COUNT.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.C1SP2_COUNT.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[2]) - Double.parseDouble(tmpArray2[2]));
+ }
+ // C2SP2 count
+ if (this.consideredComparisonFeature[ComparisonFeature.C2SP2_COUNT.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.C2SP2_COUNT.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[3]) - Double.parseDouble(tmpArray2[3]));
+ }
+ // C3SP2 count
+ if (this.consideredComparisonFeature[ComparisonFeature.C3SP2_COUNT.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.C3SP2_COUNT.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[4]) - Double.parseDouble(tmpArray2[4]));
+ }
+ // C1SP3 count
+ if (this.consideredComparisonFeature[ComparisonFeature.C1SP3_COUNT.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.C1SP3_COUNT.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[5]) - Double.parseDouble(tmpArray2[5]));
+ }
+ // C2SP3 count
+ if (this.consideredComparisonFeature[ComparisonFeature.C2SP3_COUNT.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.C2SP3_COUNT.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[6]) - Double.parseDouble(tmpArray2[6]));
+ }
+ // C3SP3 count
+ if (this.consideredComparisonFeature[ComparisonFeature.C3SP3_COUNT.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.C3SP3_COUNT.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[7]) - Double.parseDouble(tmpArray2[7]));
+ }
+ // C4SP3 count
+ if (this.consideredComparisonFeature[ComparisonFeature.C4SP3_COUNT.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.C4SP3_COUNT.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[8]) - Double.parseDouble(tmpArray2[8]));
+ }
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.EQUALITY.getFeatureNumber()]) {
+ SmilesGenerator tmpSmilesGenerator = new SmilesGenerator(SmiFlavor.Unique);
+ String tmpUniqueSmiles1 = tmpSmilesGenerator.create(tmpMoleculePair[0]);
+ String tmpUniqueSmiles2 = tmpSmilesGenerator.create(tmpMoleculePair[1]);
+ tmpSimilarities[ComparisonFeature.EQUALITY.getFeatureNumber()] = tmpUniqueSmiles1.equals(tmpUniqueSmiles2) ? 1 : 0;
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.ECCENTRIC_CONNECTIVITY_INDEX.getFeatureNumber()]) {
+ EccentricConnectivityIndexDescriptor tmpEccentricConnectivityIndexDescriptor = new EccentricConnectivityIndexDescriptor();
+ tmpEccentricConnectivityIndexDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.ECCENTRIC_CONNECTIVITY_INDEX.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpEccentricConnectivityIndexDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpEccentricConnectivityIndexDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.FMF.getFeatureNumber()]) {
+ FMFDescriptor tmpFMFDescriptor = new FMFDescriptor();
+ tmpFMFDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.FMF.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpFMFDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpFMFDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.FCSP3.getFeatureNumber()]) {
+ FractionalCSP3Descriptor tmpFractionalCSP3Descriptor = new FractionalCSP3Descriptor();
+ tmpFractionalCSP3Descriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.FCSP3.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpFractionalCSP3Descriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpFractionalCSP3Descriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.FPSA.getFeatureNumber()]) {
+ FractionalPSADescriptor tmpFractionalPSADescriptor = new FractionalPSADescriptor();
+ tmpFractionalPSADescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.FPSA.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpFractionalPSADescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpFractionalPSADescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.FRAGMENT_COMPLEXITY.getFeatureNumber()]) {
+ FragmentComplexityDescriptor tmpFragmentComplexityDescriptor = new FragmentComplexityDescriptor();
+ tmpFragmentComplexityDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.FRAGMENT_COMPLEXITY.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpFragmentComplexityDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpFragmentComplexityDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.H_BOND_ACCEPTOR_COUNT.getFeatureNumber()]) {
+ HBondAcceptorCountDescriptor tmpHBondAcceptorCountDescriptor = new HBondAcceptorCountDescriptor();
+ tmpHBondAcceptorCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpHBondAcceptorCountDescriptor.setParameters(new Object[] {true});
+ tmpSimilarities[ComparisonFeature.H_BOND_ACCEPTOR_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpHBondAcceptorCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpHBondAcceptorCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.H_BOND_DONOR_COUNT.getFeatureNumber()]) {
+ HBondDonorCountDescriptor tmpHBondDonorCountDescriptor = new HBondDonorCountDescriptor();
+ tmpHBondDonorCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.H_BOND_DONOR_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpHBondDonorCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpHBondDonorCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.JP_LOGP.getFeatureNumber()]) {
+ JPlogPDescriptor tmpJPlogPDescriptor = new JPlogPDescriptor();
+ tmpJPlogPDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.JP_LOGP.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpJPlogPDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpJPlogPDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_1.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_2.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_3.getFeatureNumber()]) {
+ KappaShapeIndicesDescriptor tmpKappaShapeIndicesDescriptor = new KappaShapeIndicesDescriptor();
+ tmpKappaShapeIndicesDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpKappaShapeIndicesDescriptor.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpKappaShapeIndicesDescriptor.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ // First kappa shape index
+ if (this.consideredComparisonFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_1.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.KAPPA_SHAPE_INDEX_1.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]));
+ }
+ // Second kappa shape index
+ if (this.consideredComparisonFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_2.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.KAPPA_SHAPE_INDEX_2.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[1]) - Double.parseDouble(tmpArray2[1]));
+ }
+ // Third kappa shape index
+ if (this.consideredComparisonFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_3.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.KAPPA_SHAPE_INDEX_3.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[2]) - Double.parseDouble(tmpArray2[2]));
+ }
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.LARGEST_CHAIN.getFeatureNumber()]) {
+ LargestChainDescriptor tmpLargestChainDescriptor = new LargestChainDescriptor();
+ tmpLargestChainDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ // Doesn't need to check for rings because that is done in the preproccesing
+ tmpLargestChainDescriptor.setParameters(new Object[] {false, false});
+ tmpSimilarities[ComparisonFeature.LARGEST_CHAIN.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpLargestChainDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpLargestChainDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.LARGEST_PI_SYSTEM.getFeatureNumber()]) {
+ LargestPiSystemDescriptor tmpLargestPiSystemDescriptor = new LargestPiSystemDescriptor();
+ tmpLargestPiSystemDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ // Doesn't need to check for aromaticity because that is done in the preproccesing
+ tmpLargestPiSystemDescriptor.setParameters(new Object[] {false});
+ tmpSimilarities[ComparisonFeature.LARGEST_PI_SYSTEM.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpLargestPiSystemDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpLargestPiSystemDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.LONGEST_ALIPHATIC_CHAIN.getFeatureNumber()]) {
+ LongestAliphaticChainDescriptor tmpLongestAliphaticChainDescriptor = new LongestAliphaticChainDescriptor();
+ tmpLongestAliphaticChainDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ // Doesn't need to check for rings because that is done in the preproccesing
+ tmpLongestAliphaticChainDescriptor.setParameters(new Object[] {false});
+ tmpSimilarities[ComparisonFeature.LONGEST_ALIPHATIC_CHAIN.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpLongestAliphaticChainDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpLongestAliphaticChainDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.MANNHOLD_LOGP.getFeatureNumber()]) {
+ MannholdLogPDescriptor tmpMannholdLogPDescriptor = new MannholdLogPDescriptor();
+ tmpMannholdLogPDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.MANNHOLD_LOGP.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpMannholdLogPDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpMannholdLogPDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.PETITJEAN_NUMBER.getFeatureNumber()]) {
+ PetitjeanNumberDescriptor tmpPetitjeanNumberDescriptor = new PetitjeanNumberDescriptor();
+ tmpPetitjeanNumberDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.PETITJEAN_NUMBER.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpPetitjeanNumberDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpPetitjeanNumberDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.PETITJEAN_SHAPE_INDEX.getFeatureNumber()]) {
+ PetitjeanShapeIndexDescriptor tmpPetitjeanShapeIndexDescriptor = new PetitjeanShapeIndexDescriptor();
+ tmpPetitjeanShapeIndexDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpPetitjeanShapeIndexDescriptor.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpPetitjeanShapeIndexDescriptor.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ tmpSimilarities[ComparisonFeature.PETITJEAN_SHAPE_INDEX.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]));
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.ROTATABLE_BOND_COUNT.getFeatureNumber()]) {
+ RotatableBondsCountDescriptor tmpRotatableBondsCountDescriptor = new RotatableBondsCountDescriptor();
+ tmpRotatableBondsCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ // Don't include terminal bonds and don't exclude amide bonds
+ tmpRotatableBondsCountDescriptor.setParameters(new Object[] {false, false});
+ tmpSimilarities[ComparisonFeature.ROTATABLE_BOND_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpRotatableBondsCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpRotatableBondsCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.ALL_SMALL_RINGS_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.AROMATIC_RINGS_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.SIZE_3_RINGS_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.SIZE_4_RINGS_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.SIZE_5_RINGS_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.SIZE_6_RINGS_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.SIZE_7_RINGS_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.SIZE_8_RINGS_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.SIZE_9_RINGS_COUNT.getFeatureNumber()]) {
+ SmallRingDescriptor tmpSmallRingDescriptor = new SmallRingDescriptor();
+ tmpSmallRingDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ double tmpRingCount1, tmpRingCount2;
+ String[] tmpArray1 = tmpSmallRingDescriptor.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpSmallRingDescriptor.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ //All small rings count
+ if (this.consideredComparisonFeature[ComparisonFeature.ALL_SMALL_RINGS_COUNT.getFeatureNumber()]) {
+ tmpRingCount1 = Double.parseDouble(tmpArray1[0]);
+ tmpRingCount2 = Double.parseDouble(tmpArray2[0]);
+ tmpSimilarities[ComparisonFeature.ALL_SMALL_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpRingCount1 - tmpRingCount2);
+ }
+ //Aromatic rings count
+ if (this.consideredComparisonFeature[ComparisonFeature.AROMATIC_RINGS_COUNT.getFeatureNumber()]) {
+ tmpRingCount1 = Double.parseDouble(tmpArray1[1]);
+ tmpRingCount2 = Double.parseDouble(tmpArray2[1]);
+ tmpSimilarities[ComparisonFeature.AROMATIC_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpRingCount1 - tmpRingCount2);
+ }
+ //Size 3 rings count
+ if (this.consideredComparisonFeature[ComparisonFeature.SIZE_3_RINGS_COUNT.getFeatureNumber()]) {
+ tmpRingCount1 = Double.parseDouble(tmpArray1[4]);
+ tmpRingCount2 = Double.parseDouble(tmpArray2[4]);
+ tmpSimilarities[ComparisonFeature.SIZE_3_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpRingCount1 - tmpRingCount2);
+ }
+ //Size 4 rings count
+ if (this.consideredComparisonFeature[ComparisonFeature.SIZE_4_RINGS_COUNT.getFeatureNumber()]) {
+ tmpRingCount1 = Double.parseDouble(tmpArray1[5]);
+ tmpRingCount2 = Double.parseDouble(tmpArray2[5]);
+ tmpSimilarities[ComparisonFeature.SIZE_4_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpRingCount1 - tmpRingCount2);
+ }
+ //Size 5 rings count
+ if (this.consideredComparisonFeature[ComparisonFeature.SIZE_5_RINGS_COUNT.getFeatureNumber()]) {
+ tmpRingCount1 = Double.parseDouble(tmpArray1[6]);
+ tmpRingCount2 = Double.parseDouble(tmpArray2[6]);
+ tmpSimilarities[ComparisonFeature.SIZE_5_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpRingCount1 - tmpRingCount2);
+ }
+ //Size 6 rings count
+ if (this.consideredComparisonFeature[ComparisonFeature.SIZE_6_RINGS_COUNT.getFeatureNumber()]) {
+ tmpRingCount1 = Double.parseDouble(tmpArray1[7]);
+ tmpRingCount2 = Double.parseDouble(tmpArray2[7]);
+ tmpSimilarities[ComparisonFeature.SIZE_6_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpRingCount1 - tmpRingCount2);
+ }
+ //Size 7 rings count
+ if (this.consideredComparisonFeature[ComparisonFeature.SIZE_7_RINGS_COUNT.getFeatureNumber()]) {
+ tmpRingCount1 = Double.parseDouble(tmpArray1[8]);
+ tmpRingCount2 = Double.parseDouble(tmpArray2[8]);
+ tmpSimilarities[ComparisonFeature.SIZE_7_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpRingCount1 - tmpRingCount2);
+ }
+ //Size 8 rings count
+ if (this.consideredComparisonFeature[ComparisonFeature.SIZE_8_RINGS_COUNT.getFeatureNumber()]) {
+ tmpRingCount1 = Double.parseDouble(tmpArray1[9]);
+ tmpRingCount2 = Double.parseDouble(tmpArray2[9]);
+ tmpSimilarities[ComparisonFeature.SIZE_8_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpRingCount1 - tmpRingCount2);
+ }
+ //Size 9 rings count
+ if (this.consideredComparisonFeature[ComparisonFeature.SIZE_9_RINGS_COUNT.getFeatureNumber()]) {
+ tmpRingCount1 = Double.parseDouble(tmpArray1[10]);
+ tmpRingCount2 = Double.parseDouble(tmpArray2[10]);
+ tmpSimilarities[ComparisonFeature.SIZE_9_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpRingCount1 - tmpRingCount2);
+ }
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.SPIRO_ATOM_COUNT.getFeatureNumber()]) {
+ SpiroAtomCountDescriptor tmpSpiroAtomCountDescriptor = new SpiroAtomCountDescriptor();
+ tmpSpiroAtomCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.SPIRO_ATOM_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpSpiroAtomCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpSpiroAtomCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ // Basic
+ IFingerprinter tmpFingerprinter;
+ if (this.consideredComparisonFeature[ComparisonFeature.TANIMOTO_BASIC_FINGERPRINTER.getFeatureNumber()]) {
+ tmpFingerprinter = new Fingerprinter();
+ tmpSimilarities[ComparisonFeature.TANIMOTO_BASIC_FINGERPRINTER.getFeatureNumber()] = Tanimoto.calculate(
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[0]),
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[1])
+ );
+ }
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ // LINGO
+ if (this.consideredComparisonFeature[ComparisonFeature.TANIMOTO_LINGO_FINGERPRINTER.getFeatureNumber()]) {
+ tmpFingerprinter = new LingoFingerprinter();
+ tmpSimilarities[ComparisonFeature.TANIMOTO_LINGO_FINGERPRINTER.getFeatureNumber()] = Tanimoto.calculate(
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[0]),
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[1])
+ );
+ }
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ // Extended
+ if (this.consideredComparisonFeature[ComparisonFeature.TANIMOTO_EXTENDED_FINGERPRINTER.getFeatureNumber()]) {
+ tmpFingerprinter = new ExtendedFingerprinter();
+ tmpSimilarities[ComparisonFeature.TANIMOTO_EXTENDED_FINGERPRINTER.getFeatureNumber()] = Tanimoto.calculate(
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[0]),
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[1])
+ );
+ }
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ // E-State
+ if (this.consideredComparisonFeature[ComparisonFeature.TANIMOTO_ESTATE_FINGERPRINTER.getFeatureNumber()]) {
+ tmpFingerprinter = new EStateFingerprinter();
+ tmpSimilarities[ComparisonFeature.TANIMOTO_ESTATE_FINGERPRINTER.getFeatureNumber()] = Tanimoto.calculate(
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[0]),
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[1])
+ );
+ }
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ // PubChem
+ if (this.consideredComparisonFeature[ComparisonFeature.TANIMOTO_PUBCHEM_FINGERPRINTER.getFeatureNumber()]) {
+ tmpFingerprinter = new PubchemFingerprinter(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.TANIMOTO_PUBCHEM_FINGERPRINTER.getFeatureNumber()] = Tanimoto.calculate(
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[0]),
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[1])
+ );
+ }
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ // Shortest path
+ if (this.consideredComparisonFeature[ComparisonFeature.TANIMOTO_SHORTEST_PATH_FINGERPRINTER.getFeatureNumber()]) {
+ tmpFingerprinter = new ShortestPathFingerprinter();
+ tmpSimilarities[ComparisonFeature.TANIMOTO_SHORTEST_PATH_FINGERPRINTER.getFeatureNumber()] = Tanimoto.calculate(
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[0]),
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[1])
+ );
+ }
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ // Substructure
+ if (this.consideredComparisonFeature[ComparisonFeature.TANIMOTO_SUBSTRUCTURE_FINGERPRINTER.getFeatureNumber()]) {
+ tmpFingerprinter = new SubstructureFingerprinter();
+ tmpSimilarities[ComparisonFeature.TANIMOTO_SUBSTRUCTURE_FINGERPRINTER.getFeatureNumber()] = Tanimoto.calculate(
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[0]),
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[1])
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.TPSA.getFeatureNumber()]) {
+ TPSADescriptor tmpTPSADescriptor = new TPSADescriptor();
+ tmpTPSADescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ // Doesn't need to check for aromaticity because that is done in the preproccesing
+ tmpTPSADescriptor.setParameters(new Object[] {false});
+ tmpSimilarities[ComparisonFeature.TPSA.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpTPSADescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpTPSADescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.VABC.getFeatureNumber()]) {
+ VABCDescriptor tmpVABCDescriptor = new VABCDescriptor();
+ tmpVABCDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.VABC.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpVABCDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpVABCDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.V_ADJ_MA.getFeatureNumber()]) {
+ VAdjMaDescriptor tmpVAdjMaDescriptor = new VAdjMaDescriptor();
+ tmpVAdjMaDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.V_ADJ_MA.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpVAdjMaDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpVAdjMaDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.MOLECULAR_WEIGHT.getFeatureNumber()]) {
+ WeightDescriptor tmpWeightDescriptor = new WeightDescriptor();
+ tmpWeightDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ // Calculate the weight of all atoms
+ tmpWeightDescriptor.setParameters(new Object[] {"*"});
+ tmpSimilarities[ComparisonFeature.MOLECULAR_WEIGHT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpWeightDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpWeightDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.WEIGHTED_PATH_1.getFeatureNumber()]) {
+ WeightedPathDescriptor tmpWeightedPathDescriptor = new WeightedPathDescriptor();
+ tmpWeightedPathDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpWeightedPathDescriptor.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpWeightedPathDescriptor.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ tmpSimilarities[ComparisonFeature.WEIGHTED_PATH_1.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]));
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.WIENER_PATH.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.WIENER_POLARITY.getFeatureNumber()]) {
+ WienerNumbersDescriptor tmpWienerNumbersDescriptor = new WienerNumbersDescriptor();
+ tmpWienerNumbersDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpWienerNumbersDescriptor.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpWienerNumbersDescriptor.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ // Wiener path number
+ if (this.consideredComparisonFeature[ComparisonFeature.WIENER_PATH.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.WIENER_PATH.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]));
+ }
+ // Wiener polarity number
+ if (this.consideredComparisonFeature[ComparisonFeature.WIENER_POLARITY.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.WIENER_POLARITY.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[1]) - Double.parseDouble(tmpArray2[1]));
+ }
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.X_LOGP.getFeatureNumber()]) {
+ XLogPDescriptor tmpXLogPDescriptor = new XLogPDescriptor();
+ tmpXLogPDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ // Aromaticity is already checked in preprocessing; use the salicyl acid correction factor
+ tmpXLogPDescriptor.setParameters(new Object[] {false, true});
+ tmpSimilarities[ComparisonFeature.X_LOGP.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpXLogPDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpXLogPDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.ZAGREB_INDEX.getFeatureNumber()]) {
+ ZagrebIndexDescriptor tmpZagrebIndexDescriptor = new ZagrebIndexDescriptor();
+ tmpZagrebIndexDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.ZAGREB_INDEX.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpZagrebIndexDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpZagrebIndexDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.type1 != InputType.SMILES) {
+ StringWriter tmpWriter = new StringWriter();
+ SMILESWriter tmpSmilesWriter = new SMILESWriter(tmpWriter);
+ tmpSmilesWriter.writeAtomContainer(tmpMoleculePair[0]);
+ this.molecule1 = tmpWriter.toString();
+ }
+ if (this.type2 != InputType.SMILES) {
+ StringWriter tmpWriter = new StringWriter();
+ SMILESWriter tmpSmilesWriter = new SMILESWriter(tmpWriter);
+ tmpSmilesWriter.writeAtomContainer(tmpMoleculePair[1]);
+ this.molecule2 = tmpWriter.toString();
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ this.result = new ComparisonResult(tmpSimilarities, this.molecule1, this.molecule2, this.identifier);
+ this.isFinished = true;
+ this.propertyChangeSupport.firePropertyChange("Task completed", false, true);
+ return null;
+ } catch (Exception ex) {
+ this.result = new ComparisonResult(ex.toString(), this.identifier);
+ this.isFinished = true;
+ this.propertyChangeSupport.firePropertyChange("Task completed", true, false);
+ return null;
+ }
+ }
+
+ /**
+ * Cancel the execution of this task
+ */
+ public void cancel(){
+ this.isCancelled = true;
+ }
+
+ /**
+ * True if this task finished its execution in any way, false otherwise
+ *
+ * @return true if this task finished its execution in any way,
+ * false otherwise
+ */
+ public boolean isFinished() {
+ return this.isFinished;
+ }
+
+ /**
+ * True if this task is still working, false otherwise
+ *
+ * @return true if this task is still working, false otherwise
+ */
+ public boolean isWorking() {
+ return this.isStarted && !this.isFinished;
+ }
+
+ /**
+ * True is this task has been started, false otherwise
+ *
+ * @return true is this task has been started, false otherwise
+ */
+ public boolean isStarted() {
+ return this.isStarted;
+ }
+ //
+ //
+ /**
+ * Get the result of the execution of this task
+ *
+ * @return the result of the execution of this task
+ */
+ public ComparisonResult getResult() {
+ return this.result;
+ }
+
+ /**
+ * Get the identifier of this task
+ *
+ * @return the identifier of this task
+ */
+ public int getIdentifier() {
+ return this.identifier;
+ }
+ //
+ //
+ /**
+ * Add a PropertyChangeListener that listens for changes from this
+ * CompareAtomContainerPairTask
+ *
+ * @param tmpListener a listener to be added
+ */
+ public void addPropertyChangeListener(PropertyChangeListener tmpListener) {
+ this.propertyChangeSupport.addPropertyChangeListener(tmpListener);
+ }
+
+ /**
+ * Remove a PropertyChangeListener
+ *
+ * @param tmpListener a listener to be removed
+ */
+ public void removePropertyChangeListener(PropertyChangeListener tmpListener) {
+ this.propertyChangeSupport.removePropertyChangeListener(tmpListener);
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Cancel the execution of this task and call Object.finialize()
+ */
+ @Override
+ @SuppressWarnings("deprecation")
+ protected void finalize() throws Throwable {
+ this.cancel();
+ super.finalize();
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/utility/GeneralUtilities.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/utility/GeneralUtilities.java
new file mode 100644
index 0000000..e550d96
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/utility/GeneralUtilities.java
@@ -0,0 +1,375 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.utility;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.RandomAccessFile;
+import java.io.StringWriter;
+import java.nio.channels.FileChannel;
+import java.nio.channels.FileLock;
+import java.util.Date;
+import java.util.MissingResourceException;
+import java.util.Optional;
+import java.util.ResourceBundle;
+import java.util.logging.FileHandler;
+import java.util.logging.Formatter;
+import java.util.logging.Handler;
+import java.util.logging.Level;
+import java.util.logging.LogRecord;
+import java.util.logging.Logger;
+import javafx.scene.control.Alert;
+import javafx.scene.control.Button;
+import javafx.scene.control.ButtonBar;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.TextFormatter;
+import javafx.stage.Window;
+
+/**
+ * This class provides utility methods for the MSC application. The methods in
+ * this class are used for logging, to show various dialogs, to get Strings from
+ * property files and for checking whether only a single instance of the
+ * application is running
+ *
+ * @author Jan-Mathis Hein
+ */
+public final class GeneralUtilities {
+
+ //
+ /**
+ * Resource bundle for the user interface texts
+ */
+ private static final ResourceBundle RESOURCE_BUNDLE = ResourceBundle.getBundle("resources/UIText");
+
+ /**
+ * A logger that documents exceptions and information about the execution of
+ * the application
+ */
+ private static final Logger LOGGER = Logger.getLogger(GeneralUtilities.class.getName());
+
+ /**
+ * File used to check whether only a single instance of the application is
+ * running
+ */
+ private static File singleInstanceFile;
+
+ /**
+ * FileChannel used to attempt to acquire an exclusive lock on the
+ * singleInstanceFile
+ */
+ private static FileChannel fileChannel;
+
+ /**
+ * A token representing a lock on the singleInstanceFile
+ */
+ private static FileLock fileLock;
+ //
+ //
+ //
+ //
+ /**
+ * Return false if the calling application is not the only currently running
+ * instance or if an error occurs, true otherwise
+ *
+ * @return false if the calling application is not the only currently
+ * running instance or if an error occurs, true otherwise
+ */
+ public static boolean isSingleInstance() {
+ try {
+ GeneralUtilities.singleInstanceFile = new File(MSCConstants.MSC_FILES_DIRECTORY.getAbsolutePath() + File.separator + "MSC_SingleInstance.lck");
+ if (GeneralUtilities.singleInstanceFile.exists()) {
+ GeneralUtilities.singleInstanceFile.delete();
+ }
+ GeneralUtilities.fileChannel = new RandomAccessFile(GeneralUtilities.singleInstanceFile, "rw").getChannel();
+ GeneralUtilities.fileLock = GeneralUtilities.fileChannel.tryLock();
+ if (GeneralUtilities.fileLock == null) {
+ GeneralUtilities.fileChannel.close();
+ return false;
+ }
+ Thread tmpThread = new Thread(() -> {
+ try {
+ if (GeneralUtilities.fileLock != null) {
+ GeneralUtilities.fileLock.release();
+ GeneralUtilities.fileChannel.close();
+ GeneralUtilities.singleInstanceFile.delete();
+ }
+ } catch (IOException ex) {
+ // Can't log this because the log-handlers were already removed
+ ex.printStackTrace();
+ }
+ });
+ Runtime.getRuntime().addShutdownHook(tmpThread);
+ return true;
+ } catch (IOException ex) {
+ return false;
+ }
+ }
+ //
+ //
+ /**
+ * Initialize the logger by setting the level, adding the handlers and
+ * creating the log-file.
+ */
+ public static synchronized void initializeLogger() {
+ GeneralUtilities.LOGGER.setLevel(Level.INFO);
+ GeneralUtilities.addNewHandlersToLogger();
+ }
+
+ /**
+ * Write information about the excpetion to the log-file
+ *
+ * @param tmpLevel the severity of the exception
+ * @param tmpException the exception that has been thrown and that will be
+ * logged
+ * @return false if the logging failed and true otherwise
+ */
+ public static synchronized boolean logException(Level tmpLevel, Exception tmpException) {
+ //
+ if (tmpException == null || tmpLevel == null) {
+ return false;
+ }
+ if (GeneralUtilities.LOGGER.getHandlers().length == 0 || GeneralUtilities.LOGGER.getHandlers()[0] == null) {
+ if(!GeneralUtilities.addNewHandlersToLogger()) {
+ return false;
+ }
+ }
+ //
+ StringWriter tmpStringWriter = new StringWriter();
+ tmpException.printStackTrace(new PrintWriter(tmpStringWriter));
+ LogRecord tmpLogRecord = new LogRecord(tmpLevel, tmpStringWriter.toString());
+ Handler tmpFileHandler = GeneralUtilities.LOGGER.getHandlers()[0];
+ tmpFileHandler.setFormatter(new Formatter() {
+ @Override
+ public String format(LogRecord tmpLogRecord) {
+ return tmpLogRecord.getThreadID() + ": " + new Date(tmpLogRecord.getMillis()) + ": " + tmpLogRecord.getMessage() + "\n";
+ }
+ });
+ tmpFileHandler.publish(tmpLogRecord);
+ return true;
+ }
+
+ /**
+ * Write a given message to the log-file
+ *
+ * @param tmpLevel the importance of the message
+ * @param tmpSourceClass the class from where the message originated
+ * @param tmpSourceMethod the method from where the message originated
+ * @param tmpMessage the message that will be logged
+ * @return false if the logging failed and true otherwise
+ */
+ public static synchronized boolean logMessage(Level tmpLevel, String tmpSourceClass, String tmpSourceMethod, String tmpMessage) {
+ //
+ if (tmpLevel == null || tmpSourceClass == null || tmpSourceMethod == null || tmpMessage == null) {
+ return false;
+ }
+ if (GeneralUtilities.LOGGER.getHandlers().length == 0 || GeneralUtilities.LOGGER.getHandlers()[0] == null) {
+ if(!GeneralUtilities.addNewHandlersToLogger()) {
+ return false;
+ }
+ }
+ //
+ LogRecord tmpLogRecord = new LogRecord(tmpLevel, tmpMessage);
+ tmpLogRecord.setSourceClassName(tmpSourceClass);
+ tmpLogRecord.setSourceMethodName(tmpSourceMethod);
+ Handler tmpFileHandler = GeneralUtilities.LOGGER.getHandlers()[0];
+ tmpFileHandler.setFormatter(new Formatter() {
+ @Override
+ public String format(LogRecord tmpLogRecord) {
+ return tmpLogRecord.getThreadID() + ": " + tmpLogRecord.getSourceClassName() +
+ ": " + tmpLogRecord.getSourceMethodName() + ": " + new Date(tmpLogRecord.getMillis()) +
+ ": " + tmpLogRecord.getLevel().toString() + ": " + tmpLogRecord.getMessage() + "\n";
+ }
+ });
+ tmpFileHandler.publish(tmpLogRecord);
+ return true;
+ }
+
+ /**
+ * Get an abstract representation of the log-file
+ *
+ * @return an abstract representation of the log-file
+ */
+ public static synchronized File getLogFile() {
+ return new File(MSCConstants.MSC_FILES_DIRECTORY.getAbsolutePath() + File.separator + "MSC_LOG.log");
+ }
+
+ /**
+ * Close and remove all the handlers from the logger. Optionaly you
+ * can reset the log-file and logger by deleting and reconstructing the
+ * log-file and adding new handlers to the logger.
+ *
+ * @param tmpResetLogFile if true, the log-file and logger will be reset
+ * otherwise not
+ * @return true if everything went as intended
+ */
+ public static synchronized boolean closeAndRemoveHandlersFromLogger(boolean tmpResetLogFile) {
+ for (Handler tmpFileHandler : GeneralUtilities.LOGGER.getHandlers()) {
+ tmpFileHandler.flush();
+ tmpFileHandler.close();
+ GeneralUtilities.LOGGER.removeHandler(tmpFileHandler);
+ }
+ if (tmpResetLogFile) {
+ GeneralUtilities.getLogFile().delete();
+ // Creates a new file
+ return(GeneralUtilities.addNewHandlersToLogger());
+ }
+ return true;
+ }
+ //
+ //
+ /**
+ * Show an error dialog with the specified information.
+ *
+ * @param tmpOwner specifies the owner window of this dialog
+ * @param tmpContentText a text that describes the error
+ * @param tmpOrigin origin of the error
+ */
+ public static void showErrorDialog(Window tmpOwner, String tmpContentText , String tmpOrigin) {
+ Alert tmpErrorDialog = new Alert(Alert.AlertType.ERROR, tmpContentText, ButtonType.OK);
+ tmpErrorDialog.initOwner(tmpOwner);
+ tmpErrorDialog.setTitle(GeneralUtilities.getUIText("ErrorAlertDialog.Title.text"));
+ tmpErrorDialog.getDialogPane().setHeaderText(String.format(GeneralUtilities.getUIText("ErrorAlertDialog.Header.text"), tmpOrigin));
+ Button tmpButton = (Button) tmpErrorDialog.getDialogPane().lookupButton(ButtonType.OK);
+ GuiUtilities.setMinMaxPrefSize(tmpButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ tmpErrorDialog.showAndWait();
+ }
+
+ /**
+ * Show an info dialog with the specified information
+ *
+ * @param tmpOwner specifies the owner window of this dialog
+ * @param tmpInfoText the information that will be displayes
+ */
+ public static void showInfoDialog(Window tmpOwner, String tmpInfoText) {
+ Alert tmpInfoDialog = new Alert(Alert.AlertType.INFORMATION, "", ButtonType.OK);
+ tmpInfoDialog.initOwner(tmpOwner);
+ tmpInfoDialog.setTitle(GeneralUtilities.getUIText("InfoDialog.Title.text"));
+ tmpInfoDialog.getDialogPane().setHeaderText(tmpInfoText);
+ Button tmpButton = (Button) tmpInfoDialog.getDialogPane().lookupButton(ButtonType.OK);
+ GuiUtilities.setMinMaxPrefSize(tmpButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ tmpInfoDialog.showAndWait();
+ }
+
+ /**
+ * Show a confirmation dialog with the specified information
+ *
+ * @param tmpOwner specifies the owner window of this dialog
+ * @param tmpContentText specifies the content area's text
+ * @param tmpTitle the title of the dialog
+ * @param tmpHeaderText specifies the header's text
+ * @return the ButtonType the user chose (APPLY or CANCEL)
+ */
+ public static Optional showConfirmationDialog(Window tmpOwner, String tmpContentText, String tmpTitle, String tmpHeaderText) {
+ ButtonType tmpYesButtonType = new ButtonType(GeneralUtilities.getUIText("ConfirmationDialog.Yes.text"), ButtonBar.ButtonData.APPLY);
+ ButtonType tmpNoButtonType = new ButtonType(GeneralUtilities.getUIText("ConfirmationDialog.No.text"), ButtonBar.ButtonData.CANCEL_CLOSE);
+ Alert tmpConfirmationDialog = new Alert(Alert.AlertType.CONFIRMATION, tmpContentText, tmpYesButtonType, tmpNoButtonType);
+ tmpConfirmationDialog.initOwner(tmpOwner);
+ tmpConfirmationDialog.setTitle(tmpTitle);
+ tmpConfirmationDialog.getDialogPane().setHeaderText(tmpHeaderText);
+ Button tmpButton = (Button) tmpConfirmationDialog.getDialogPane().lookupButton(tmpYesButtonType);
+ GuiUtilities.setMinMaxPrefSize(tmpButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ tmpButton = (Button) tmpConfirmationDialog.getDialogPane().lookupButton(tmpNoButtonType);
+ GuiUtilities.setMinMaxPrefSize(tmpButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ return tmpConfirmationDialog.showAndWait();
+ }
+ //
+ //
+ /**
+ * Get the text specified by the key from the resource bundle
+ *
+ * @param tmpKey specifies the text which to get
+ * @return the retrieved text or an exception message if the retrieval was
+ * not possible
+ */
+ public static String getUIText(String tmpKey) {
+ try {
+ return RESOURCE_BUNDLE.getString(tmpKey).trim();
+ } catch (MissingResourceException ex) {
+ return "Key '" + tmpKey + "' not found.";
+ }
+ }
+ //
+ //
+ /**
+ * Get a TextFormatter that formats all input so that the resulting
+ * text will always represent an unsigned whole number
+ *
+ * @return a TextFormatter that formats all input so that the resulting
+ * text will always represent an unsigned whole number
+ */
+ public static TextFormatter getUnsignedIntegerTextFormatter() {
+ return new TextFormatter<>((TextFormatter.Change tmpChange) -> {
+ if (!tmpChange.getControlNewText().matches("\\d*")) {
+ tmpChange.setText("");
+ }
+ try {
+ Integer.parseInt(tmpChange.getControlNewText());
+ tmpChange.getControl().setStyle("-fx-background-color: white;");
+ } catch (NumberFormatException ex) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ }
+ return tmpChange;
+ });
+ }
+
+ /**
+ * Get a TextFormatter that formats all input so that the resulting
+ * text will always represent a signed decimal number.
+ *
+ * @return a TextFormatter that formats all input so that the resulting
+ * text will always represent a signed decimal number
+ */
+ public static TextFormatter getSignedDecimalNumberTextFormatter() {
+ return new TextFormatter<>((TextFormatter.Change tmpChange) -> {
+ if (!tmpChange.getControlNewText().matches("[-\\+]?\\d*\\.?\\d*E?\\d*")) {
+ tmpChange.setText("");
+ }
+ try {
+ Double.parseDouble(tmpChange.getControlNewText());
+ tmpChange.getControl().setStyle("-fx-background-color: white;");
+ } catch (NumberFormatException ex) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ }
+ return tmpChange;
+ });
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Add new handlers to the logger and create a new log-file
+ *
+ * @return true if all new handlers have been added
+ */
+ private static synchronized boolean addNewHandlersToLogger() {
+ try {
+ GeneralUtilities.getLogFile().createNewFile();
+ // Appends to already exisiting file
+ FileHandler tmpFileHandler = new FileHandler(GeneralUtilities.getLogFile().getAbsolutePath(), true);
+ GeneralUtilities.LOGGER.addHandler(tmpFileHandler);
+ return true;
+ } catch (IOException | SecurityException ex) {
+ ex.printStackTrace();
+ return false;
+ }
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/utility/GuiUtilities.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/utility/GuiUtilities.java
new file mode 100644
index 0000000..9e64579
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/utility/GuiUtilities.java
@@ -0,0 +1,185 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.utility;
+
+import java.awt.Graphics2D;
+import java.awt.image.BufferedImage;
+import javafx.embed.swing.SwingFXUtils;
+import javafx.geometry.Insets;
+import javafx.scene.image.Image;
+import javafx.scene.layout.Border;
+import javafx.scene.layout.BorderStroke;
+import javafx.scene.layout.BorderStrokeStyle;
+import javafx.scene.layout.BorderWidths;
+import javafx.scene.layout.CornerRadii;
+import javafx.scene.layout.Region;
+import javafx.scene.paint.Color;
+import javafx.scene.paint.Paint;
+
+/**
+ * Defines some constants and utility methods for a graphical user interface.
+ * This class can't be instantiated
+ *
+ * @author Jan-Mathis Hein
+ */
+public final class GuiUtilities {
+
+ //
+ /**
+ * Standard horizontal gap between controls that are located in the same
+ * region
+ */
+ public static final double HORIZONTAL_GAP_BETWEEN_CONTROLS = 10;
+
+ /**
+ * Standard vertical gap between controls that are located in the same
+ * region
+ */
+ public static final double VERTICAL_GAP_BETWEEN_CONTROLS = 10;
+
+ /**
+ * Standard insets that are used to isolate different regions from
+ * each other
+ */
+ public static final Insets STANDARD_INSETS = new Insets(10);
+
+ /**
+ * An image of a white square with a dimension of 200 x 200
+ */
+ public static final Image WHITE_SQUARE;
+
+ /**
+ * A border that lets a region appear as if it is lowered
+ */
+ public static final Border LOWERED_BORDER = new Border(new BorderStroke(
+ Color.color(0.4, 0.4, 0.4), Color.color(0.99, 0.99, 0.99),
+ Color.color(0.99, 0.99, 0.99), Color.color(0.4, 0.4, 0.4),
+ BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ BorderStrokeStyle.SOLID, new CornerRadii(0), new BorderWidths(2), new Insets(0)
+ ));
+
+ /**
+ * A border that lets a region appear as if it is raised
+ */
+ public static final Border RAISED_BORDER = new Border(new BorderStroke(
+ Color.color(0.99, 0.99, 0.99), Color.color(0.4, 0.4, 0.4),
+ Color.color(0.4, 0.4, 0.4), Color.color(0.99, 0.99, 0.99),
+ BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ BorderStrokeStyle.SOLID, new CornerRadii(0), new BorderWidths(2), new Insets(0)
+ ));
+
+ /**
+ * A thin red border
+ */
+ public static final Border RED_BORDER = new Border(new BorderStroke(
+ Paint.valueOf("Red"), Paint.valueOf("Red"), Paint.valueOf("Red"),
+ Paint.valueOf("Red"), BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ new CornerRadii(0), new BorderWidths(2), new Insets(0)
+ ));
+
+ /**
+ * A thin green border
+ */
+ public static final Border GREEN_BORDER = new Border(new BorderStroke(
+ Paint.valueOf("Green"), Paint.valueOf("Green"), Paint.valueOf("Green"),
+ Paint.valueOf("Green"), BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ new CornerRadii(0), new BorderWidths(2), new Insets(0)
+ ));
+
+ /**
+ * A thin black border
+ */
+ public static final Border BLACK_BORDER = new Border(new BorderStroke(
+ Paint.valueOf("Black"), Paint.valueOf("Black"), Paint.valueOf("Black"),
+ Paint.valueOf("Black"), BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ new CornerRadii(0), new BorderWidths(2), new Insets(0)
+ ));
+
+ /**
+ * The standard width of a button
+ */
+ public static final double BUTTON_WIDTH = 100;
+
+ /**
+ * The standard width of a textfield
+ */
+ public static final double TEXT_FIELD_WIDTH = 160;
+
+ /**
+ * The standard width of a small button
+ */
+ public static final double SMALL_BUTTON_WIDTH = 75.2;
+
+ /**
+ * The standard height of a button
+ */
+ public static final double BUTTON_HEIGHT = 25;
+ //
+ //
+ //
+ static {
+ BufferedImage tmpImage = new BufferedImage(200, 200, BufferedImage.TYPE_INT_RGB);
+ Graphics2D tmpGraphics2D = tmpImage.createGraphics();
+ tmpGraphics2D.setColor(java.awt.Color.WHITE);
+ tmpGraphics2D.fillRect(0, 0, tmpImage.getWidth(), tmpImage.getHeight());
+ WHITE_SQUARE = SwingFXUtils.toFXImage(tmpImage, null);
+ }
+ //
+ //
+ //
+ /**
+ * Set the maximal, minimal and prefered size of a specified region
+ *
+ * @param tmpRegion specifies the region
+ * @param tmpWidth specifies the height
+ * @param tmpHeight specifies the width
+ */
+ public static void setMinMaxPrefSize(Region tmpRegion, double tmpWidth, double tmpHeight) {
+ GuiUtilities.setMinMaxPrefWidth(tmpRegion, tmpWidth);
+ GuiUtilities.setMinMaxPrefHeight(tmpRegion, tmpHeight);
+ }
+
+ /**
+ * Set the maximal, minimal and prefered width of a specified region
+ *
+ * @param tmpRegion specifies the region
+ * @param tmpWidth specifies the width
+ */
+ public static void setMinMaxPrefWidth(Region tmpRegion, double tmpWidth) {
+ tmpRegion.setMinWidth(tmpWidth);
+ tmpRegion.setMaxWidth(tmpWidth);
+ tmpRegion.setPrefWidth(tmpWidth);
+ }
+
+ /**
+ * Set the maximal, minimal and prefered height of a specified region
+ *
+ * @param tmpRegion specifies the region
+ * @param tmpHeight specifies the height
+ */
+ public static void setMinMaxPrefHeight(Region tmpRegion, double tmpHeight) {
+ tmpRegion.setMinHeight(tmpHeight);
+ tmpRegion.setMaxHeight(tmpHeight);
+ tmpRegion.setPrefHeight(tmpHeight);
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/utility/MSCConstants.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/utility/MSCConstants.java
new file mode 100644
index 0000000..863834f
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/utility/MSCConstants.java
@@ -0,0 +1,87 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.utility;
+
+import java.io.File;
+
+/**
+ * Defines some constants for the MSC application.
+ * This class can't be instantiated
+ *
+ * @author Jan-Mathis Hein
+ */
+public final class MSCConstants {
+
+ //
+ /**
+ * The main window's minimal width
+ */
+ public final static double MINIMAL_MAIN_WINDOW_WIDTH = 514.0;
+
+ /**
+ * The main window's minimal height
+ */
+ public final static double MINIMAL_MAIN_WINDOW_HEIGHT = 686.0;
+
+ /**
+ * The MoleculePairDisplayerStage's minimal width
+ */
+ public final static double MINIMAL_MOLECULE_DISPLAYER_WIDTH = 859.0;
+
+ /**
+ * The MoleculePairDisplayerStage's minimal height
+ */
+ public final static double MINIMAL_MOLECULE_DISPLAYER_HEIGHT = 444.0;
+
+ /**
+ * Directory where important MSC files will be saved
+ */
+ public static final File MSC_FILES_DIRECTORY = new File(System.getProperty("user.dir") + File.separator + "MSC_Files");
+
+ /**
+ * A String representing the current version of the MSC
+ */
+ public final static String MSC_VERSION = "1.0";
+
+ /**
+ * Minimal java version needed to run the application.
+ */
+ public final static String JAVA_VERSION = "11";
+
+ /**
+ * String representing the name of an info file
+ */
+ public final static String INFO_FILE_NAME = "README.txt";
+
+ /**
+ * String representing the name of an output file
+ */
+ public final static String OUTPUT_FILE_NAME = "jobOutput.mosc";
+
+ /**
+ * String representing the name of an molecule set 1 file
+ */
+ public final static String MOLECULE_SET_1_FILE = "moleculeSet1.txt";
+
+ /**
+ * String representing the name of an molecule set 2 file
+ */
+ public final static String MOLECULE_SET_2_FILE = "moleculeSet2.txt";
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/utility/ResultFormattingUtility.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/utility/ResultFormattingUtility.java
new file mode 100644
index 0000000..24e11c1
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/utility/ResultFormattingUtility.java
@@ -0,0 +1,259 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.utility;
+
+import de.whs.ibci.msc.model.HistogramData;
+import java.text.DecimalFormat;
+import java.util.Date;
+
+/**
+ * Utility class that provides methods to convert job results into formatted
+ * texts
+ *
+ * @author Jan-Mathis Hein
+ */
+public abstract class ResultFormattingUtility {
+
+ //
+ /**
+ * Get the header for a result summary report
+ *
+ * @return an array that contains the individual lines of text
+ */
+ public static String[] getResultSummaryReportHeader() {
+ String[] tmpLines = new String[6];
+ tmpLines[0] = "Molecule Set Comparator";
+ tmpLines[1] = "Version: " + MSCConstants.MSC_VERSION;
+ tmpLines[2] = "Covered under the GNU GPLv3, copyright Jan-Mahis Hein";
+ tmpLines[3] = "";
+ tmpLines[4] = "Result summary report";
+ tmpLines[5] = "";
+ //tmpLines[5] = "Job ID:";
+ return tmpLines;
+ }
+
+ /**
+ * Get the general information block for a job
+ *
+ * @param tmpDateOfCompletion specifies the date of completion of the job
+ * @param tmpComputingTime specifies the computing time of the job
+ * @param tmpNumberOfPairs specifies the number of pairs of the job
+ * @param tmpInputFile1 specifies the job's first input file
+ * @param tmpInputFile2 specifies the job's second input file
+ * @return an array that contains the individual lines of text
+ */
+ public static String[] getGeneralInfoBlock(Date tmpDateOfCompletion, double tmpComputingTime, int tmpNumberOfPairs, String tmpInputFile1, String tmpInputFile2) {
+ String[] tmpLines = new String[9];
+ tmpLines[0] = "Date of completion: " + tmpDateOfCompletion.toString();
+ tmpLines[1] = "Computing time: " + Double.toString(tmpComputingTime) + " (Seconds)";
+ tmpLines[2] = "";
+ tmpLines[3] = "Number of pairs: " + Integer.toString(tmpNumberOfPairs);
+ tmpLines[4] = "";
+ tmpLines[5] = "Input set files:";
+ tmpLines[6] = tmpInputFile1;
+ tmpLines[7] = tmpInputFile2;
+ tmpLines[8] = "";
+ return tmpLines;
+ }
+
+ /**
+ * Get a text representation of an HistogramData object in vertical form.
+ * This representation contains a table with the frequencies and the min,
+ * max and average ComparisonFeature values
+ *
+ * @param tmpHistogramData contains the histogram data
+ * @return an array that contains the individual lines of text
+ */
+ public static String[] getVerticalHistogramBlock(HistogramData tmpHistogramData) {
+ //
+ String[] tmpLines = new String[(tmpHistogramData.getBinBorders().length * 2) + 8];
+ String tmpSpace;
+ //
+ //
+ String[] tmpBinBorders = new String[tmpHistogramData.getBinBorders().length];
+ DecimalFormat tmpBinBorderFormatter = new DecimalFormat("##0.00000");
+ int tmpMaxLength = 0;
+ if (tmpHistogramData.getComparisonFeauture().isContinuous()) {
+ for (int i = 0; i < tmpBinBorders.length; i++) {
+ tmpBinBorders[i] = tmpBinBorderFormatter.format(tmpHistogramData.getBinBorders()[i]);
+ tmpMaxLength = tmpBinBorders[i].length() > tmpMaxLength ? tmpBinBorders[i].length() : tmpMaxLength;
+ }
+ } else {
+ for (int i = 0; i < tmpBinBorders.length; i++) {
+ if (i < (tmpBinBorders.length - 1)) {
+ tmpBinBorders[i] = Integer.toString((int) Math.ceil(tmpHistogramData.getBinBorders()[i]));
+ } else {
+ tmpBinBorders[i] = Integer.toString((int) Math.ceil(tmpHistogramData.getBinBorders()[i] + 1));
+ }
+ tmpMaxLength = tmpBinBorders[i].length() > tmpMaxLength ? tmpBinBorders[i].length() : tmpMaxLength;
+ }
+ }
+ //
+ tmpLines[0] = tmpHistogramData.getComparisonFeauture().toString() + ":";
+ tmpLines[1] = "";
+ //
+ tmpLines[2] = "bin borders | frequency of pairs";
+ int tmpLinePosition = tmpLines[2].indexOf("|");
+ if ((tmpLinePosition - 2) < tmpMaxLength) {
+ tmpLinePosition = tmpMaxLength + 2;
+ }
+ tmpSpace = "";
+ while (tmpLines[2].indexOf("|") < tmpLinePosition) {
+ tmpSpace += " ";
+ tmpLines[2] = "bin borders " + tmpSpace + "| frequency of pairs";
+ }
+ //
+ //
+ tmpLines[3] = "";
+ while (tmpLines[3].length() < tmpLines[2].length()) {
+ tmpLines[3] += "-";
+ }
+ //
+ //
+ for (int i = 0; i < tmpBinBorders.length; i++) {
+ tmpSpace = "";
+ while ((tmpSpace.length() + tmpBinBorders[i].length() + 2) < tmpLinePosition) {
+ tmpSpace += " ";
+ }
+ tmpLines[4 + (i * 2)] = tmpSpace + tmpBinBorders[i] + " |";
+ }
+ //
+ //
+ int tmpInt;
+ DecimalFormat tmpFrequencyFormatter = tmpHistogramData.isUseRelativeFrequencies() ? new DecimalFormat("##0.00000") : new DecimalFormat("###");
+ int tmpMaxPrePointLength = 0;
+ String[] tmpFrequencies = new String[tmpHistogramData.getFrequencies().length];
+ for (int i = 0; i < tmpFrequencies.length; i++) {
+ tmpFrequencies[i] = tmpFrequencyFormatter.format(tmpHistogramData.getFrequencies()[i]);
+ tmpInt = tmpFrequencies[i].indexOf('.') == -1 ? tmpFrequencies[i].length() : tmpFrequencies[i].indexOf('.');
+ tmpMaxPrePointLength = tmpInt > tmpMaxPrePointLength ? tmpInt : tmpMaxPrePointLength;
+ }
+ //
+ //
+ String[] tmpArray;
+ for (int i = 0; i < tmpHistogramData.getFrequencies().length; i++) {
+ tmpArray = tmpFrequencies[i].split("\\.");
+ tmpSpace = "";
+ while (tmpSpace.length() < tmpLinePosition) {
+ tmpSpace += " ";
+ }
+ tmpLines[5 + (i * 2)] = tmpSpace + "| ";
+ tmpSpace = "";
+ while (tmpSpace.length() < (tmpMaxPrePointLength - tmpArray[0].length())) {
+ tmpSpace += " ";
+ }
+ tmpLines[5 + (i * 2)] += tmpSpace + tmpFrequencies[i] + (tmpHistogramData.isUseRelativeFrequencies() ? "%" : "");
+ }
+ //
+ tmpLines[3 + (tmpHistogramData.getBinBorders().length * 2)] = "";
+ tmpLines[4 + (tmpHistogramData.getBinBorders().length * 2)] = "min: " + Double.toString(tmpHistogramData.getMinComparisonFeatureValue());
+ tmpLines[5 + (tmpHistogramData.getBinBorders().length * 2)] = "max: " + Double.toString(tmpHistogramData.getMaxComparisonFeatureValue());
+ tmpLines[6 + (tmpHistogramData.getBinBorders().length * 2)] = "average: " + Double.toString(tmpHistogramData.getAverageComparisonFeatureValue());
+ tmpLines[7 + (tmpHistogramData.getBinBorders().length * 2)] = "";
+ return tmpLines;
+ }
+
+ /**
+ * Get a text representation of an HistogramData object in horizontal form.
+ * This representation contains a table with the frequencies and the min,
+ * max and average ComparisonFeature values
+ *
+ * @param tmpHistogramData contains the histogram data
+ * @return an array that contains the individual lines of text
+ */
+ public static String[] getHorizontalHistogramBlock(HistogramData tmpHistogramData) {
+ //
+ String[] tmpStringArray;
+ String[] tmpLines = new String[5];
+ String tmpSpaceBetweenNumbers = " ";
+ String tmpString;
+ String tmpSpace;
+ String tmpPattern = "####0.0####";
+ DecimalFormat tmpFormatter = new DecimalFormat(tmpPattern);
+ int tmpMaxPrePointLength = 0;
+ int tmpMaxPostPointLength = 0;
+ int tmpMaxFrequencyLength = 0;
+ int tmpNumberOfLeadingSpaces;
+ //
+ //
+ for (double tmpBinBorder : tmpHistogramData.getBinBorders()) {
+ tmpStringArray = tmpFormatter.format(tmpBinBorder).split("\\.");
+ tmpMaxPrePointLength = tmpStringArray[0].length() > tmpMaxPrePointLength ? tmpStringArray[0].length() : tmpMaxPrePointLength;
+ tmpMaxPostPointLength = tmpStringArray[1].length() > tmpMaxPostPointLength ? tmpStringArray[1].length() : tmpMaxPostPointLength;
+ }
+ for (double tmpFrequency : tmpHistogramData.getFrequencies()) {
+ tmpString = Double.toString(tmpFrequency);
+ tmpMaxFrequencyLength = tmpString.length() > tmpMaxFrequencyLength ? tmpString.length() : tmpMaxFrequencyLength;
+ }
+ while ((tmpMaxPostPointLength + tmpSpaceBetweenNumbers.length() + tmpMaxPrePointLength) < tmpMaxFrequencyLength + 2) {
+ tmpSpaceBetweenNumbers += " ";
+ }
+ while ((tmpMaxPostPointLength + tmpSpaceBetweenNumbers.length() + tmpMaxPrePointLength) > tmpMaxFrequencyLength + 2) {
+ tmpMaxFrequencyLength++;
+ }
+ //
+ //
+ tmpLines[0] = tmpHistogramData.getComparisonFeauture().toString() + ":";
+ tmpLines[1] = "";
+ //
+ //
+ for (double tmpBorder : tmpHistogramData.getBinBorders()) {
+ tmpString = tmpFormatter.format(tmpBorder);
+ while (tmpString.split("\\.")[0].length() < tmpMaxPrePointLength) {
+ tmpString = " " + tmpString;
+ }
+ while (tmpString.split("\\.")[1].length() < tmpMaxPostPointLength) {
+ tmpString += " ";
+ }
+ tmpLines[2] += tmpString + tmpSpaceBetweenNumbers;
+ }
+ tmpLines[2] = tmpLines[2].trim();
+ //
+ //
+ char[] tmpArray = new char[tmpLines[2].split("\\.")[0].length()];
+ for (int i = 0; i < tmpArray.length; i++) {
+ tmpArray[i] = ' ';
+ }
+ tmpLines[3] += new String(tmpArray);
+ for (double tmpFrequencyValue : tmpHistogramData.getFrequencies()) {
+ tmpString = Double.toString(tmpFrequencyValue);
+ tmpLines[3] += "| ";
+ if (tmpString.length() < tmpMaxFrequencyLength) {
+ tmpNumberOfLeadingSpaces = (tmpMaxFrequencyLength - tmpString.length()) / 2;
+ tmpNumberOfLeadingSpaces += (tmpMaxFrequencyLength - tmpString.length()) % 2;
+ tmpSpace = "";
+ while (tmpSpace.length() != tmpNumberOfLeadingSpaces) {
+ tmpSpace += " ";
+ }
+ tmpString = tmpSpace + tmpString;
+ tmpSpace = "";
+ while (tmpSpace.length() != (tmpMaxFrequencyLength - tmpString.length())) {
+ tmpSpace += " ";
+ }
+ tmpString += tmpSpace;
+ }
+ tmpLines[3] += tmpString + " ";
+ }
+ tmpLines[3] += "|";
+ tmpLines[4] = "";
+ //
+ return tmpLines;
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/BinBorderConfigurationBox.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/BinBorderConfigurationBox.java
new file mode 100644
index 0000000..fa92c42
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/BinBorderConfigurationBox.java
@@ -0,0 +1,104 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.view;
+
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.utility.GuiUtilities;
+import javafx.scene.control.Button;
+import javafx.scene.control.Label;
+import javafx.scene.control.TextField;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.HBox;
+
+/**
+ * Box for the configuration of a single bin border
+ *
+ * @author Jan-Mathis Hein
+ */
+public class BinBorderConfigurationBox extends HBox {
+
+ //
+ private final Label label;
+
+ private final TextField textField;
+
+ private final Button removeButton, addButton;
+ //
+ //
+ //
+ /**
+ * Initializes the instance variables
+ *
+ * @param tmpTextFieldValue initial value for the textField
+ * @param tmpLabelText specifies the text for the label
+ */
+ public BinBorderConfigurationBox(String tmpTextFieldValue, String tmpLabelText) {
+ super(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.label = new Label(tmpLabelText);
+ GuiUtilities.setMinMaxPrefSize(this.label, 20, GuiUtilities.BUTTON_HEIGHT);
+ this.textField = new TextField(tmpTextFieldValue);
+ GuiUtilities.setMinMaxPrefSize(this.textField, 150, GuiUtilities.BUTTON_HEIGHT);
+ this.removeButton = new Button(GeneralUtilities.getUIText("BinBorderConfigurationBox.removeButton.text"));
+ this.removeButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("BinBorderConfigurationBox.removeButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.removeButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.addButton = new Button(GeneralUtilities.getUIText("BinBorderConfigurationBox.addButton.text"));
+ this.addButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("BinBorderConfigurationBox.addButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.addButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.getChildren().addAll(this.label, this.textField, this.removeButton, this.addButton);
+ }
+ //
+ //
+ //
+ /**
+ * Get the textField
+ *
+ * @return the textField
+ */
+ public TextField getTextField() {
+ return this.textField;
+ }
+
+ /**
+ * Get the label
+ *
+ * @return the label
+ */
+ public Label getLabel() {
+ return this.label;
+ }
+
+ /**
+ * Get the removeButton
+ *
+ * @return the removeButton
+ */
+ public Button getRemoveButton() {
+ return this.removeButton;
+ }
+
+ /**
+ * Get the addButton
+ *
+ * @return the addButton
+ */
+ public Button getAddButton() {
+ return this.addButton;
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/BinBorderConfigurationDialog.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/BinBorderConfigurationDialog.java
new file mode 100644
index 0000000..a1ff84d
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/BinBorderConfigurationDialog.java
@@ -0,0 +1,108 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.view;
+
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.utility.GuiUtilities;
+import javafx.geometry.Insets;
+import javafx.geometry.Pos;
+import javafx.scene.control.Button;
+import javafx.scene.control.ScrollPane;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.GridPane;
+import javafx.scene.layout.HBox;
+import javafx.scene.layout.VBox;
+import javafx.stage.Window;
+
+/**
+ * A configuration-dialog in which the user can specify any number of bin
+ * borders with specifically set values.
+ *
+ * @author Jan-Mathis Hein
+ */
+public class BinBorderConfigurationDialog extends ConfigurationDialog {
+
+ //
+ private final Button resetButton;
+
+ private final ScrollPane scrollPane;
+
+ private final VBox binBorderConfigurationBoxesBox;
+
+ private final HBox controlsBox;
+
+ private final GridPane inputPane;
+ //
+ //
+ //
+ /**
+ * Create the Dialog with all its controls and handle their layout and size
+ *
+ * @param tmpOwner specifies the window that owns the ConfigurationDialog
+ * @param tmpTitle specifies the title of the ConfigurationDialog
+ */
+ public BinBorderConfigurationDialog(Window tmpOwner, String tmpTitle) {
+ super(tmpOwner, tmpTitle);
+ this.inputPane = new GridPane();
+ this.inputPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.inputPane.setBorder(GuiUtilities.RAISED_BORDER);
+ this.inputPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.scrollPane = new ScrollPane();
+ this.scrollPane.setVbarPolicy(ScrollPane.ScrollBarPolicy.ALWAYS);
+ this.scrollPane.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER);
+ this.scrollPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.binBorderConfigurationBoxesBox = new VBox(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ // This fixes a bug where the ScrollPane cuts off its content at the bottom
+ this.binBorderConfigurationBoxesBox.setPadding(new Insets(0, 0, 10, 0));
+ this.scrollPane.setContent(this.binBorderConfigurationBoxesBox);
+ this.inputPane.add(this.scrollPane, 0, 0);
+ this.controlsBox = new HBox(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.controlsBox.setAlignment(Pos.CENTER_RIGHT);
+ this.resetButton = new Button(GeneralUtilities.getUIText("BinBorderConfigurationDialog.resetButton.text"));
+ this.resetButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("BinBorderConfigurationDialog.resetButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.resetButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.controlsBox.getChildren().add(this.resetButton);
+ this.inputPane.add(this.controlsBox, 0, 1);
+ this.getContentPane().getChildren().add(this.inputPane);
+ this.setHeaderText(GeneralUtilities.getUIText("BinBorderConfigurationDialog.Header.text"));
+ GuiUtilities.setMinMaxPrefHeight(this.getDialogPane(), 500);
+ }
+ //
+ //
+ //
+ /**
+ * Get the resetButton
+ *
+ * @return the resetButton
+ */
+ public Button getResetButton() {
+ return this.resetButton;
+ }
+
+
+ /**
+ * Get the binBorderConfigurationBoxesBox
+ *
+ * @return the binBorderConfigurationBoxesBox
+ */
+ public VBox getBinBorderConfigurationBoxesBox() {
+ return this.binBorderConfigurationBoxesBox;
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/ChartConfigurationDialog.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/ChartConfigurationDialog.java
new file mode 100644
index 0000000..3b31f00
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/ChartConfigurationDialog.java
@@ -0,0 +1,166 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.view;
+
+import de.whs.ibci.msc.utility.GuiUtilities;
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import javafx.geometry.Insets;
+import javafx.geometry.Pos;
+import javafx.scene.control.Button;
+import javafx.scene.control.Label;
+import javafx.scene.control.TextField;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.GridPane;
+import javafx.scene.layout.HBox;
+import javafx.stage.Window;
+
+/**
+ * A configuration-dialog in which the user can specify the upper and lower bin
+ * borders as well as the upper and lower frequency bounds of a chart.
+ *
+ * @author Jan-Mathis Hein
+ */
+public class ChartConfigurationDialog extends ConfigurationDialog {
+
+ //
+ private final GridPane inputPane;
+
+ private final Label lowerBinBorderLabel, upperBinBorderLabel, lowerFrequencyBoundLabel, upperFrequencyBoundLabel;
+
+ private final TextField lowerBinBorderInputField, upperBinBorderInputField, lowerFrequencyBoundInputField, upperFrequencyBoundInputField;
+
+ private final Button resetButton, defaultButton;
+
+ private final HBox buttonBox;
+ //
+ //
+ //
+ /**
+ * Create the Dialog with all its controls and handle their layout and size
+ *
+ * @param tmpOwner specifies the window that owns the ConfigurationDialog
+ * @param tmpTitle specifies the title of the ConfigurationDialog
+ */
+ public ChartConfigurationDialog(Window tmpOwner, String tmpTitle) {
+ super(tmpOwner, tmpTitle);
+ this.inputPane = new GridPane();
+ this.inputPane.setBorder(GuiUtilities.RAISED_BORDER);
+ this.inputPane.setPadding(new Insets(10, 10, 10, 10));
+ this.inputPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.inputPane.setHgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.lowerBinBorderInputField = new TextField();
+ this.lowerBinBorderInputField.setTooltip(new Tooltip(GeneralUtilities.getUIText("ChartConfigurationDialog.lowerBinBorderInputField.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.lowerBinBorderInputField, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.lowerBinBorderLabel = new Label(GeneralUtilities.getUIText("ChartConfigurationDialog.lowerBinBorderLabel.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.lowerBinBorderLabel, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.lowerBinBorderInputField, 1, 0);
+ this.inputPane.add(this.lowerBinBorderLabel, 0, 0);
+ this.upperBinBorderInputField = new TextField();
+ this.upperBinBorderInputField.setTooltip(new Tooltip(GeneralUtilities.getUIText("ChartConfigurationDialog.upperBinBorderInputField.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.upperBinBorderInputField, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.upperBinBorderLabel = new Label(GeneralUtilities.getUIText("ChartConfigurationDialog.upperBinBorderLabel.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.upperBinBorderLabel, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.upperBinBorderInputField, 1, 1);
+ this.inputPane.add(this.upperBinBorderLabel, 0, 1);
+ this.lowerFrequencyBoundInputField = new TextField();
+ this.lowerFrequencyBoundInputField.setTooltip(new Tooltip(GeneralUtilities.getUIText("ChartConfigurationDialog.lowerFrequencyBoundInputField.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.lowerFrequencyBoundInputField, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.lowerFrequencyBoundLabel = new Label(GeneralUtilities.getUIText("ChartConfigurationDialog.lowerFrequencyBoundLabel.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.lowerFrequencyBoundLabel, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(lowerFrequencyBoundInputField, 1, 2);
+ this.inputPane.add(lowerFrequencyBoundLabel, 0, 2);
+ this.upperFrequencyBoundInputField = new TextField();
+ this.upperFrequencyBoundInputField.setTooltip(new Tooltip(GeneralUtilities.getUIText("ChartConfigurationDialog.upperFrequencyBoundInputField.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.upperFrequencyBoundInputField, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.upperFrequencyBoundLabel = new Label(GeneralUtilities.getUIText("ChartConfigurationDialog.upperFrequencyBoundLabel.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.upperFrequencyBoundLabel, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(upperFrequencyBoundInputField, 1, 3);
+ this.inputPane.add(upperFrequencyBoundLabel, 0, 3);
+ this.buttonBox = new HBox(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.buttonBox.setAlignment(Pos.CENTER_RIGHT);
+ this.defaultButton = new Button(GeneralUtilities.getUIText("ChartConfigurationDialog.defaultButton.text"));
+ this.defaultButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("ChartConfigurationDialog.defaultButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.defaultButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.buttonBox.getChildren().add(this.defaultButton);
+ this.resetButton = new Button(GeneralUtilities.getUIText("ChartConfigurationDialog.resetButton.text"));
+ this.resetButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("ChartConfigurationDialog.resetButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.resetButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.buttonBox.getChildren().add(this.resetButton);
+ this.inputPane.add(this.buttonBox, 1, 4);
+ this.getContentPane().getChildren().add(this.inputPane);
+ GuiUtilities.setMinMaxPrefHeight(this.getDialogPane(), 304);
+ }
+ //
+ //
+ //
+ /**
+ * Get the lowerBinBorderInputField
+ *
+ * @return the lowerBinBorderInputField
+ */
+ public TextField getLowerBinBorderInputField() {
+ return this.lowerBinBorderInputField;
+ }
+
+ /**
+ * Get the upperBinBorderInputField
+ *
+ * @return the upperBinBorderInputField
+ */
+ public TextField getUpperBinBorderInputField() {
+ return this.upperBinBorderInputField;
+ }
+
+ /**
+ * Get the lowerFrequencyBoundInputField
+ *
+ * @return the lowerFrequencyBoundInputField
+ */
+ public TextField getLowerFrequencyBoundInputField() {
+ return this.lowerFrequencyBoundInputField;
+ }
+
+ /**
+ * Get the upperFrequencyBoundInputField
+ *
+ * @return the upperFrequencyBoundInputField
+ */
+ public TextField getUpperFrequencyBoundInputField() {
+ return this.upperFrequencyBoundInputField;
+ }
+
+ /**
+ * Get the resetButton
+ *
+ * @return the resetButton
+ */
+ public Button getResetButton() {
+ return this.resetButton;
+ }
+
+ /**
+ * Get the defaultButton
+ *
+ * @return the defaultButton
+ */
+ public Button getDefaultButton() {
+ return this.defaultButton;
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/ConfigurationDialog.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/ConfigurationDialog.java
new file mode 100644
index 0000000..7efd1de
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/ConfigurationDialog.java
@@ -0,0 +1,113 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.view;
+
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.utility.GuiUtilities;
+import javafx.geometry.Insets;
+import javafx.scene.control.Button;
+import javafx.scene.control.ButtonBar;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.Dialog;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.Border;
+import javafx.scene.layout.BorderStroke;
+import javafx.scene.layout.BorderStrokeStyle;
+import javafx.scene.layout.BorderWidths;
+import javafx.scene.layout.CornerRadii;
+import javafx.scene.layout.StackPane;
+import javafx.scene.paint.Color;
+import javafx.stage.Window;
+
+/**
+ * A base framework for a Dialog for configuration purposes
+ *
+ * @author Jan-Mathis Hein
+ */
+public abstract class ConfigurationDialog extends Dialog {
+
+ //
+ private final Button applyButton, cancelButton;
+
+ private final StackPane contentPane;
+ //
+ //
+ //
+ /**
+ * Create the Dialog with all its controls and handle their layout and size
+ *
+ * @param tmpOwner specifies the window that owns the Dialog
+ * @param tmpTitle specifies the title of the Dialog
+ */
+ public ConfigurationDialog(Window tmpOwner, String tmpTitle) {
+ super();
+ this.initOwner(tmpOwner);
+ this.setTitle(tmpTitle);
+ this.setHeaderText(GeneralUtilities.getUIText("ConfigurationDialog.Header.text"));
+ ButtonType tmpApplyButtonType = new ButtonType(GeneralUtilities.getUIText("ConfigurationDialog.applyButtonType.text"), ButtonBar.ButtonData.APPLY);
+ ButtonType tmpCancelButtonType = new ButtonType(GeneralUtilities.getUIText("ConfigurationDialog.cancelButtonType.text"), ButtonBar.ButtonData.CANCEL_CLOSE);
+ this.getDialogPane().getButtonTypes().addAll(tmpApplyButtonType, tmpCancelButtonType);
+ this.applyButton = (Button) this.getDialogPane().lookupButton(tmpApplyButtonType);
+ GuiUtilities.setMinMaxPrefSize(this.applyButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.applyButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("ConfigurationDialog.applyButton.tooltipText")));
+ this.cancelButton = (Button) this.getDialogPane().lookupButton(tmpCancelButtonType);
+ GuiUtilities.setMinMaxPrefSize(this.cancelButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.cancelButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("ConfigurationDialog.cancelButton.tooltipText")));
+ this.contentPane = new StackPane();
+ this.contentPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.contentPane.setBorder(new Border(new BorderStroke(
+ Color.WHITE, Color.WHITE, Color.color(0.1, 0.1, 0.1),
+ Color.WHITE, BorderStrokeStyle.NONE, BorderStrokeStyle.NONE,
+ BorderStrokeStyle.SOLID, BorderStrokeStyle.NONE,
+ new CornerRadii(0), new BorderWidths(0, 0, 2, 0), new Insets(0)
+ )));
+ this.getDialogPane().setContent(this.contentPane);
+
+ }
+ //
+ //
+ //
+ /**
+ * Get the cancelButton
+ *
+ * @return the cancelButton
+ */
+ public final Button getCancelButton() {
+ return this.cancelButton;
+ }
+
+ /**
+ * Get the applyButton
+ *
+ * @return the applyButton
+ */
+ public final Button getApplyButton() {
+ return this.applyButton;
+ }
+
+ /**
+ * Get the contentPane
+ *
+ * @return the contentPane
+ */
+ public final StackPane getContentPane() {
+ return this.contentPane;
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/InputTab.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/InputTab.java
new file mode 100644
index 0000000..af0e79d
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/InputTab.java
@@ -0,0 +1,561 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.view;
+
+import de.whs.ibci.msc.utility.GuiUtilities;
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.model.InputType;
+import de.whs.ibci.msc.model.ComparisonFeature;
+import java.util.Arrays;
+import java.util.LinkedList;
+import java.util.List;
+import javafx.collections.FXCollections;
+import javafx.collections.ObservableList;
+import javafx.geometry.HPos;
+import javafx.geometry.Insets;
+import javafx.geometry.Pos;
+import javafx.geometry.VPos;
+import javafx.scene.control.Button;
+import javafx.scene.control.CheckBox;
+import javafx.scene.control.ChoiceBox;
+import javafx.scene.control.Label;
+import javafx.scene.control.ProgressBar;
+import javafx.scene.control.ScrollPane;
+import javafx.scene.control.Tab;
+import javafx.scene.control.TitledPane;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.AnchorPane;
+import javafx.scene.layout.ColumnConstraints;
+import javafx.scene.layout.GridPane;
+import javafx.scene.layout.HBox;
+import javafx.scene.layout.Priority;
+import javafx.scene.layout.RowConstraints;
+import javafx.scene.layout.StackPane;
+import javafx.scene.layout.VBox;
+
+/**
+ * A Tab in which the user can specify his input for a job
+ *
+ * @author Jan-Mathis Hein
+ */
+public class InputTab extends Tab {
+
+ //
+ private final ChoiceBox inputType1ChoiceBox, inputType2ChoiceBox;
+
+ private final Button chooseFile1Button, chooseFile2Button, jobStartButton,
+ reverseComparisonFeatureSelectionButton, jobCancelButton, selectAllComparisonFeaturesButton;
+
+ private final StackPane startCancelPane;
+
+ private final ProgressBar jobProgressBar;
+
+ private final Label inputFile1Label, inputFile2Label, jobInfoLabel;
+
+ private final ScrollPane scrollPane;
+
+ private final GridPane mainPane, inputFilesPane;
+
+ private final HBox startProgressCancelBox;
+
+ private final VBox tanimotoCheckBoxesBox, atomCountsCheckBoxesBox, bondCountsCheckBoxesBox, functionalGroupCountsCheckBoxesBox,
+ logPValuesCheckBoxesBox, autocorrelationCheckBoxesBox, electronicDescriptorsCheckBoxesBox, miscellaneousCheckBoxesBox,
+ comparisonFeatureSelectionBox;
+
+ private final AnchorPane comparisonFeaturePane, comparisonFeatureButtonsPane, infoStartProgressCancelPane;
+
+ private final CheckBox[] comparisonFeatureCheckBoxes;
+
+ private final CheckBox selectAllTanimotoCheckBox, selectAllAtomCountsCheckBox, selectAllMiscellaneousCheckBox,
+ selectAllBondCountsCheckBox, selectAllFunctionalGroupCountsCheckBox, selectAllLogPValuesCheckBox,
+ selectAllAutocorrelationCheckBox, selectAllElectronicDescriptorsCheckBox;
+
+ private final TitledPane buttonsTitledPane, tanimotoTitledPane, atomCountsTitledPane,
+ miscellaneousTitledPane, bondCountsTitledPane, functionalGroupCountsTitledPane, logPValuesTitledPane,
+ autocorrelationTitledPane, electronicDescriptorsTitledPane;
+ //
+ //
+ //
+ /**
+ * Create the Tab with all its controls and handle their layout and size
+ *
+ * @param tmpJobNumber specifies the title of the Tab
+ */
+ public InputTab(String tmpJobNumber) {
+ super(GeneralUtilities.getUIText("InputTab.title.text") + tmpJobNumber);
+ this.setClosable(true);
+ this.mainPane = new GridPane();
+ this.mainPane.setHgap(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.mainPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.mainPane.getColumnConstraints().addAll(
+ new ColumnConstraints(),
+ new ColumnConstraints(234.0, 234.0, Double.MAX_VALUE, Priority.ALWAYS, HPos.LEFT, true)
+ );
+ this.mainPane.getRowConstraints().addAll(
+ new RowConstraints(142.4, 142.4, Double.MAX_VALUE, Priority.ALWAYS, VPos.CENTER, true),
+ new RowConstraints()
+ );
+ // The 12 is intentional
+ this.mainPane.setPadding(new Insets(10, 10, 12, 10));
+ //
+ this.inputFilesPane = new GridPane();
+ this.inputFilesPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.inputFilesPane.setHgap(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.inputFilesPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.inputFilesPane.setBorder(GuiUtilities.RAISED_BORDER);
+ ObservableList inputTypeCollection = FXCollections.observableArrayList(new LinkedList<>(Arrays.asList(InputType.values())));
+ this.inputType1ChoiceBox = new ChoiceBox<>(inputTypeCollection);
+ this.inputType1ChoiceBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.inputType1ChoiceBox.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.inputType1ChoiceBox, GuiUtilities.BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.inputType2ChoiceBox = new ChoiceBox<>(inputTypeCollection);
+ this.inputType2ChoiceBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.inputType2ChoiceBox.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.inputType2ChoiceBox, GuiUtilities.BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.chooseFile1Button = new Button(GeneralUtilities.getUIText("InputTab.chooseFile1Button.text"));
+ this.chooseFile1Button.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.chooseFile1Button.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.chooseFile1Button, GuiUtilities.BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.chooseFile2Button = new Button(GeneralUtilities.getUIText("InputTab.chooseFile2Button.text"));
+ this.chooseFile2Button.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.chooseFile2Button.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.chooseFile2Button, GuiUtilities.BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.inputFile1Label = new Label(GeneralUtilities.getUIText("InputTab.inputFile1Label.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.inputFile1Label, GuiUtilities.BUTTON_WIDTH * 2 + GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.inputFile2Label = new Label(GeneralUtilities.getUIText("InputTab.inputFile2Label.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.inputFile2Label, GuiUtilities.BUTTON_WIDTH * 2 + GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.inputFilesPane.add(this.inputType1ChoiceBox, 0, 0);
+ this.inputFilesPane.add(this.chooseFile1Button, 1, 0);
+ this.inputFilesPane.add(this.inputFile1Label, 0, 1, 2, 1);
+ this.inputFilesPane.add(this.inputType2ChoiceBox, 0, 2);
+ this.inputFilesPane.add(this.chooseFile2Button, 1, 2);
+ this.inputFilesPane.add(this.inputFile2Label, 0, 3, 2, 1);
+ this.mainPane.add(this.inputFilesPane, 0, 0);
+ //
+ //
+ this.comparisonFeaturePane = new AnchorPane();
+ this.comparisonFeaturePane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.comparisonFeaturePane.setBorder(GuiUtilities.RAISED_BORDER);
+ this.scrollPane = new ScrollPane();
+ this.scrollPane.setVbarPolicy(ScrollPane.ScrollBarPolicy.ALWAYS);
+ // The content node is resized to fit the width of the scrollpane
+ this.scrollPane.setFitToWidth(true);
+ this.comparisonFeatureSelectionBox = new VBox();
+ this.comparisonFeatureSelectionBox.setStyle("-fx-background-color: rgb(200, 200, 200);");
+ this.buttonsTitledPane = new TitledPane();
+ this.buttonsTitledPane.setText(GeneralUtilities.getUIText("InputTab.comparisonFeatureButtonsTitlePane.text"));
+ this.buttonsTitledPane.setAnimated(false);
+ this.buttonsTitledPane.setExpanded(false);
+ this.comparisonFeatureButtonsPane = new AnchorPane();
+ this.comparisonFeatureButtonsPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.selectAllComparisonFeaturesButton = new Button(GeneralUtilities.getUIText("InputTab.selectAllComparisonFeaturesButton.text"));
+ this.selectAllComparisonFeaturesButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.selectAllComparisonFeaturesButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.selectAllComparisonFeaturesButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ AnchorPane.setLeftAnchor(this.selectAllComparisonFeaturesButton, 0.0);
+ AnchorPane.setTopAnchor(this.selectAllComparisonFeaturesButton, 0.0);
+ this.reverseComparisonFeatureSelectionButton = new Button(GeneralUtilities.getUIText("InputTab.reverseComparisonFeatureSelectionButton.text"));
+ this.reverseComparisonFeatureSelectionButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.reverseComparisonFeatureSelectionButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.reverseComparisonFeatureSelectionButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ AnchorPane.setRightAnchor(this.reverseComparisonFeatureSelectionButton, 0.0);
+ AnchorPane.setTopAnchor(this.reverseComparisonFeatureSelectionButton, 0.0);
+ this.comparisonFeatureButtonsPane.getChildren().setAll(this.selectAllComparisonFeaturesButton, this.reverseComparisonFeatureSelectionButton);
+ this.buttonsTitledPane.setContent(this.comparisonFeatureButtonsPane);
+ this.comparisonFeatureSelectionBox.getChildren().add(this.buttonsTitledPane);
+ //
+ this.tanimotoTitledPane = new TitledPane();
+ this.tanimotoTitledPane.setText(GeneralUtilities.getUIText("InputTab.tanimotoTitledPane.text"));
+ this.tanimotoTitledPane.setAnimated(false);
+ this.tanimotoTitledPane.setExpanded(false);
+ this.atomCountsTitledPane = new TitledPane();
+ this.atomCountsTitledPane.setText(GeneralUtilities.getUIText("InputTab.atomCountsTitledPane.text"));
+ this.atomCountsTitledPane.setAnimated(false);
+ this.atomCountsTitledPane.setExpanded(false);
+ this.bondCountsTitledPane = new TitledPane();
+ this.bondCountsTitledPane.setText(GeneralUtilities.getUIText("InputTab.bondCountsTitledPane.text"));
+ this.bondCountsTitledPane.setAnimated(false);
+ this.bondCountsTitledPane.setExpanded(false);
+ this.functionalGroupCountsTitledPane = new TitledPane();
+ this.functionalGroupCountsTitledPane.setText(GeneralUtilities.getUIText("InputTab.functionalGroupCountsTitledPane.text"));
+ this.functionalGroupCountsTitledPane.setAnimated(false);
+ this.functionalGroupCountsTitledPane.setExpanded(false);
+ this.logPValuesTitledPane = new TitledPane();
+ this.logPValuesTitledPane.setText(GeneralUtilities.getUIText("InputTab.logPValuesTitledPane.text"));
+ this.logPValuesTitledPane.setAnimated(false);
+ this.logPValuesTitledPane.setExpanded(false);
+ this.autocorrelationTitledPane = new TitledPane();
+ this.autocorrelationTitledPane.setText(GeneralUtilities.getUIText("InputTab.autocorrelationTitledPane.text"));
+ this.autocorrelationTitledPane.setAnimated(false);
+ this.autocorrelationTitledPane.setExpanded(false);
+ this.electronicDescriptorsTitledPane = new TitledPane();
+ this.electronicDescriptorsTitledPane.setText(GeneralUtilities.getUIText("InputTab.electricsDescriptorsTitledPane.text"));
+ this.electronicDescriptorsTitledPane.setAnimated(false);
+ this.electronicDescriptorsTitledPane.setExpanded(false);
+ this.miscellaneousTitledPane = new TitledPane();
+ this.miscellaneousTitledPane.setText(GeneralUtilities.getUIText("InputTab.miscellaneousTitledPane.text"));
+ this.miscellaneousTitledPane.setAnimated(false);
+ this.miscellaneousTitledPane.setExpanded(false);
+ //
+ //
+ this.tanimotoCheckBoxesBox = new VBox();
+ this.tanimotoCheckBoxesBox.setSpacing(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.tanimotoCheckBoxesBox.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.selectAllTanimotoCheckBox = new CheckBox(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.text"));
+ this.selectAllTanimotoCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.tooltipText")));
+ this.tanimotoCheckBoxesBox.getChildren().add(this.selectAllTanimotoCheckBox);
+ this.atomCountsCheckBoxesBox = new VBox();
+ this.atomCountsCheckBoxesBox.setSpacing(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.atomCountsCheckBoxesBox.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.selectAllAtomCountsCheckBox = new CheckBox(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.text"));
+ this.selectAllAtomCountsCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.tooltipText")));
+ this.atomCountsCheckBoxesBox.getChildren().add(this.selectAllAtomCountsCheckBox);
+ this.bondCountsCheckBoxesBox = new VBox();
+ this.bondCountsCheckBoxesBox.setSpacing(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.bondCountsCheckBoxesBox.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.selectAllBondCountsCheckBox = new CheckBox(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.text"));
+ this.selectAllBondCountsCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.tooltipText")));
+ this.bondCountsCheckBoxesBox.getChildren().add(this.selectAllBondCountsCheckBox);
+ this.functionalGroupCountsCheckBoxesBox = new VBox();
+ this.functionalGroupCountsCheckBoxesBox.setSpacing(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.functionalGroupCountsCheckBoxesBox.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.selectAllFunctionalGroupCountsCheckBox = new CheckBox(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.text"));
+ this.selectAllFunctionalGroupCountsCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.tooltipText")));
+ this.functionalGroupCountsCheckBoxesBox.getChildren().add(this.selectAllFunctionalGroupCountsCheckBox);
+ this.logPValuesCheckBoxesBox = new VBox();
+ this.logPValuesCheckBoxesBox .setSpacing(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.logPValuesCheckBoxesBox .setPadding(GuiUtilities.STANDARD_INSETS);
+ this.selectAllLogPValuesCheckBox = new CheckBox(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.text"));
+ this.selectAllLogPValuesCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.tooltipText")));
+ this.logPValuesCheckBoxesBox.getChildren().add(this.selectAllLogPValuesCheckBox);
+ this.autocorrelationCheckBoxesBox = new VBox();
+ this.autocorrelationCheckBoxesBox .setSpacing(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.autocorrelationCheckBoxesBox .setPadding(GuiUtilities.STANDARD_INSETS);
+ this.selectAllAutocorrelationCheckBox = new CheckBox(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.text"));
+ this.selectAllAutocorrelationCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.tooltipText")));
+ this.autocorrelationCheckBoxesBox.getChildren().add(this.selectAllAutocorrelationCheckBox);
+ this.electronicDescriptorsCheckBoxesBox = new VBox();
+ this.electronicDescriptorsCheckBoxesBox .setSpacing(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.electronicDescriptorsCheckBoxesBox .setPadding(GuiUtilities.STANDARD_INSETS);
+ this.selectAllElectronicDescriptorsCheckBox = new CheckBox(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.text"));
+ this.selectAllElectronicDescriptorsCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.tooltipText")));
+ this.electronicDescriptorsCheckBoxesBox.getChildren().add(this.selectAllElectronicDescriptorsCheckBox);
+ this.miscellaneousCheckBoxesBox = new VBox();
+ this.miscellaneousCheckBoxesBox.setSpacing(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.miscellaneousCheckBoxesBox.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.selectAllMiscellaneousCheckBox = new CheckBox(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.text"));
+ this.selectAllMiscellaneousCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.tooltipText")));
+ this.miscellaneousCheckBoxesBox.getChildren().add(this.selectAllMiscellaneousCheckBox);
+ //
+ //
+ this.comparisonFeatureCheckBoxes = new CheckBox[ComparisonFeature.values().length];
+ CheckBox tmpCheckBox;
+ for (int i = 0; i < this.comparisonFeatureCheckBoxes.length; i++) {
+ tmpCheckBox = new CheckBox(ComparisonFeature.values()[i].toString());
+ tmpCheckBox.setTooltip(new Tooltip(ComparisonFeature.values()[i].getDetailedDescription()));
+ if (i == ComparisonFeature.TANIMOTO_BASIC_FINGERPRINTER.getFeatureNumber() ||
+ i == ComparisonFeature.TANIMOTO_LINGO_FINGERPRINTER.getFeatureNumber() ||
+ i == ComparisonFeature.TANIMOTO_EXTENDED_FINGERPRINTER.getFeatureNumber() ||
+ i == ComparisonFeature.TANIMOTO_ESTATE_FINGERPRINTER.getFeatureNumber() ||
+ i == ComparisonFeature.TANIMOTO_PUBCHEM_FINGERPRINTER.getFeatureNumber() ||
+ i == ComparisonFeature.TANIMOTO_SHORTEST_PATH_FINGERPRINTER.getFeatureNumber() ||
+ i == ComparisonFeature.TANIMOTO_SUBSTRUCTURE_FINGERPRINTER.getFeatureNumber()) {
+ this.tanimotoCheckBoxesBox.getChildren().add(tmpCheckBox);
+ } else if (i == ComparisonFeature.ATOM_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.CARBON_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.NITROGEN_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.OXYGEN_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.PHOSPHOR_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SULFUR_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.AROMATIC_ATOM_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.C1SP1_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.C1SP2_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.C1SP3_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.C2SP1_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.C2SP2_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.C2SP3_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.C3SP2_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.C3SP3_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.C4SP3_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SPIRO_ATOM_COUNT.getFeatureNumber()) {
+ this.atomCountsCheckBoxesBox.getChildren().add(tmpCheckBox);
+ } else if (i == ComparisonFeature.BOND_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SINGLE_BOND_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.DOUBLE_BOND_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.TRIPLE_BOND_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.QUADRUPLE_BOND_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.AROMATIC_BOND_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.ROTATABLE_BOND_COUNT.getFeatureNumber()) {
+ this.bondCountsCheckBoxesBox.getChildren().add(tmpCheckBox);
+ } else if (i == ComparisonFeature.ACIDIC_GROUP_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.BASIC_GROUP_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.H_BOND_ACCEPTOR_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.H_BOND_DONOR_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SIZE_3_RINGS_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SIZE_4_RINGS_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SIZE_5_RINGS_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SIZE_6_RINGS_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SIZE_7_RINGS_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SIZE_8_RINGS_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SIZE_9_RINGS_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.AROMATIC_RINGS_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.ALL_RINGS_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.ALL_SMALL_RINGS_COUNT.getFeatureNumber()) {
+ this.functionalGroupCountsCheckBoxesBox.getChildren().add(tmpCheckBox);
+ } else if (i == ComparisonFeature.A_LOGP.getFeatureNumber() ||
+ i == ComparisonFeature.A_LOGP_2.getFeatureNumber() ||
+ i == ComparisonFeature.X_LOGP.getFeatureNumber() ||
+ i == ComparisonFeature.MANNHOLD_LOGP.getFeatureNumber() ||
+ i == ComparisonFeature.JP_LOGP.getFeatureNumber()) {
+ this.logPValuesCheckBoxesBox.getChildren().add(tmpCheckBox);
+ } else if (i == ComparisonFeature.ATS_CHARGE1.getFeatureNumber() ||
+ i == ComparisonFeature.ATS_MASS1.getFeatureNumber() ||
+ i == ComparisonFeature.ATS_POLARIZABILITY1.getFeatureNumber()) {
+ this.autocorrelationCheckBoxesBox.getChildren().add(tmpCheckBox);
+ } else if (i == ComparisonFeature.APOL.getFeatureNumber() ||
+ i == ComparisonFeature.BPOL.getFeatureNumber() ||
+ i == ComparisonFeature.FPSA.getFeatureNumber() ||
+ i == ComparisonFeature.TPSA.getFeatureNumber() ||
+ i == ComparisonFeature.MOLAR_REFRACTIVITY.getFeatureNumber()) {
+ this.electronicDescriptorsCheckBoxesBox.getChildren().add(tmpCheckBox);
+ } else {
+ this.miscellaneousCheckBoxesBox.getChildren().add(tmpCheckBox);
+ }
+ this.comparisonFeatureCheckBoxes[i] = tmpCheckBox;
+ }
+ //
+ this.tanimotoTitledPane.setContent(this.tanimotoCheckBoxesBox);
+ this.atomCountsTitledPane.setContent(this.atomCountsCheckBoxesBox);
+ this.bondCountsTitledPane.setContent(this.bondCountsCheckBoxesBox);
+ this.functionalGroupCountsTitledPane.setContent(this.functionalGroupCountsCheckBoxesBox);
+ this.logPValuesTitledPane.setContent(this.logPValuesCheckBoxesBox);
+ this.autocorrelationTitledPane.setContent(this.autocorrelationCheckBoxesBox);
+ this.electronicDescriptorsTitledPane.setContent(this.electronicDescriptorsCheckBoxesBox);
+ this.miscellaneousTitledPane.setContent(this.miscellaneousCheckBoxesBox);
+ this.comparisonFeatureSelectionBox.getChildren().add(this.tanimotoTitledPane);
+ this.comparisonFeatureSelectionBox.getChildren().add(this.atomCountsTitledPane);
+ this.comparisonFeatureSelectionBox.getChildren().add(this.bondCountsTitledPane);
+ this.comparisonFeatureSelectionBox.getChildren().add(this.functionalGroupCountsTitledPane);
+ this.comparisonFeatureSelectionBox.getChildren().add(this.logPValuesTitledPane);
+ this.comparisonFeatureSelectionBox.getChildren().add(this.autocorrelationTitledPane);
+ this.comparisonFeatureSelectionBox.getChildren().add(this.electronicDescriptorsTitledPane);
+ this.comparisonFeatureSelectionBox.getChildren().add(this.miscellaneousTitledPane);
+ this.scrollPane.setContent(this.comparisonFeatureSelectionBox);
+ AnchorPane.setLeftAnchor(this.scrollPane, 0.0);
+ AnchorPane.setTopAnchor(this.scrollPane, 0.0);
+ AnchorPane.setRightAnchor(this.scrollPane, 0.0);
+ AnchorPane.setBottomAnchor(this.scrollPane, 0.0);
+ this.comparisonFeaturePane.getChildren().add(this.scrollPane);
+ this.mainPane.add(this.comparisonFeaturePane, 1, 0);
+ //
+ //
+ this.infoStartProgressCancelPane = new AnchorPane();
+ this.infoStartProgressCancelPane.setBorder(GuiUtilities.RAISED_BORDER);
+ this.infoStartProgressCancelPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.jobInfoLabel = new Label("");
+ AnchorPane.setLeftAnchor(this.jobInfoLabel, 0.0);
+ AnchorPane.setTopAnchor(this.jobInfoLabel, 0.0);
+ AnchorPane.setBottomAnchor(this.jobInfoLabel, 0.0);
+ this.infoStartProgressCancelPane.getChildren().add(this.jobInfoLabel);
+ this.startProgressCancelBox = new HBox(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.startProgressCancelBox.setAlignment(Pos.CENTER);
+ AnchorPane.setRightAnchor(this.startProgressCancelBox, 0.0);
+ AnchorPane.setBottomAnchor(this.startProgressCancelBox, 0.0);
+ AnchorPane.setTopAnchor(this.startProgressCancelBox, 0.0);
+ this.jobProgressBar = new ProgressBar(0);
+ GuiUtilities.setMinMaxPrefWidth(this.jobProgressBar, GuiUtilities.BUTTON_WIDTH);
+ this.startProgressCancelBox.getChildren().add(this.jobProgressBar);
+ this.startCancelPane = new StackPane();
+ this.jobCancelButton = new Button(GeneralUtilities.getUIText("InputTab.jobCancelButton.text"));
+ this.jobCancelButton.setVisible(false);
+ this.jobCancelButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.jobCancelButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.jobCancelButton, GuiUtilities.BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.startCancelPane.getChildren().add(this.jobCancelButton);
+ this.jobStartButton = new Button(GeneralUtilities.getUIText("InputTab.jobStartButton.text"));
+ this.jobStartButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.jobStartButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.jobStartButton, GuiUtilities.BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.startCancelPane.getChildren().add(this.jobStartButton);
+ this.startProgressCancelBox.getChildren().add(this.startCancelPane);
+ this.infoStartProgressCancelPane.getChildren().add(this.startProgressCancelBox);
+ this.mainPane.add(this.infoStartProgressCancelPane, 0, 1, 2, 1);
+ //
+ this.setContent(this.mainPane);
+ }
+ //
+ //
+ //
+ /**
+ * Get the reverseComparisonFeatureSelectionButton
+ *
+ * @return the reverseComparisonFeatureSelectionButton
+ */
+ public Button getReverseComparisonFeatureSelectionButton() {
+ return this.reverseComparisonFeatureSelectionButton;
+ }
+
+ /**
+ * Get the selectAllComparisonFeaturesButton
+ *
+ * @return the selectAllComparisonFeaturesButton
+ */
+ public Button getSelectAllComparisonFeaturesButton() {
+ return this.selectAllComparisonFeaturesButton;
+ }
+
+ /**
+ * Get the buttonsTitledPane
+ *
+ * @return the buttonsTitledPane
+ */
+ public TitledPane getButtonsTitledPane() {
+ return this.buttonsTitledPane;
+ }
+
+ /**
+ * Get a list containing all xxxCheckBoxesBox boxes. Order corresponds
+ * to the one of getSelectAllCheckBoxes()
+ *
+ * @return a list containing all xxxCheckBoxesBox boxes
+ */
+ public List getCheckBoxesBoxes() {
+ LinkedList tmpList = new LinkedList<>();
+ tmpList.add(this.atomCountsCheckBoxesBox);
+ tmpList.add(this.autocorrelationCheckBoxesBox);
+ tmpList.add(this.bondCountsCheckBoxesBox);
+ tmpList.add(this.electronicDescriptorsCheckBoxesBox);
+ tmpList.add(this.functionalGroupCountsCheckBoxesBox);
+ tmpList.add(this.logPValuesCheckBoxesBox);
+ tmpList.add(this.miscellaneousCheckBoxesBox);
+ tmpList.add(this.tanimotoCheckBoxesBox);
+ return tmpList;
+ }
+
+ /**
+ * Get a list containing all selectAllXxxCheckBox check boxes. Order
+ * corresponds to the one of getCheckBoxesBoxes()
+ *
+ * @return a list containing all selectAllXxxCheckBox check boxes
+ */
+ public List getSelectAllCheckBoxes() {
+ LinkedList tmpList = new LinkedList<>();
+ tmpList.add(this.selectAllAtomCountsCheckBox);
+ tmpList.add(this.selectAllAutocorrelationCheckBox);
+ tmpList.add(this.selectAllBondCountsCheckBox);
+ tmpList.add(this.selectAllElectronicDescriptorsCheckBox);
+ tmpList.add(this.selectAllFunctionalGroupCountsCheckBox);
+ tmpList.add(this.selectAllLogPValuesCheckBox);
+ tmpList.add(this.selectAllMiscellaneousCheckBox);
+ tmpList.add(this.selectAllTanimotoCheckBox);
+ return tmpList;
+ }
+
+ /**
+ * Get the comparisonFeatureCheckBoxes
+ *
+ * @return the comparisonFeatureCheckBoxes
+ */
+ public CheckBox[] getComparisonFeatureCheckBoxes() {
+ return this.comparisonFeatureCheckBoxes;
+ }
+
+ /**
+ * Get the chooseFile1Button
+ *
+ * @return the chooseFile1Button
+ */
+ public Button getChooseFile1Button() {
+ return this.chooseFile1Button;
+ }
+
+ /**
+ * Get the compareSetsButton
+ *
+ * @return the compareSetsButton
+ */
+ public Button getJobStartButton() {
+ return this.jobStartButton;
+ }
+
+ /**
+ * Get the inputFile1Label
+ *
+ * @return the inputFile1Label
+ */
+ public Label getInputFile1Label() {
+ return this.inputFile1Label;
+ }
+
+ /**
+ * Get the inputFile2Label
+ *
+ * @return the inputFile2Label
+ */
+ public Label getInputFile2Label() {
+ return this.inputFile2Label;
+ }
+
+ /**
+ * Get the chooseFile2Button
+ *
+ * @return the chooseFile2Button
+ */
+ public Button getChooseFile2Button() {
+ return chooseFile2Button;
+ }
+
+ /**
+ * Get the inputType1ChoiceBox
+ *
+ * @return the inputType1ChoiceBox
+ */
+ public ChoiceBox getInputType1ChoiceBox() {
+ return this.inputType1ChoiceBox;
+ }
+
+ /**
+ * Get the inputType2ChoiceBox
+ *
+ * @return the inputType2ChoiceBox
+ */
+ public ChoiceBox getInputType2ChoiceBox() {
+ return this.inputType2ChoiceBox;
+ }
+
+ /**
+ * Get the jobCancelButton
+ *
+ * @return the jobCancelButton
+ */
+ public Button getJobCancelButton() {
+ return this.jobCancelButton;
+ }
+
+ /**
+ * Get the jobProgressBar
+ *
+ * @return the jobProgressBar
+ */
+ public ProgressBar getJobProgressBar() {
+ return this.jobProgressBar;
+ }
+
+ /**
+ * Get the jobInfoLabel
+ *
+ * @return the jobInfoLabel
+ */
+ public Label getJobInfoLabel() {
+ return this.jobInfoLabel;
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/MainView.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/MainView.java
new file mode 100644
index 0000000..24e2bf6
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/MainView.java
@@ -0,0 +1,335 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.view;
+
+import de.whs.ibci.msc.utility.GuiUtilities;
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.utility.MSCConstants;
+import javafx.geometry.Insets;
+import javafx.scene.control.Button;
+import javafx.scene.control.Menu;
+import javafx.scene.control.MenuBar;
+import javafx.scene.control.MenuItem;
+import javafx.scene.control.TabPane;
+import javafx.scene.layout.BorderPane;
+import javafx.scene.layout.HBox;
+import javafx.scene.Scene;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.Border;
+import javafx.scene.layout.BorderStroke;
+import javafx.scene.layout.BorderStrokeStyle;
+import javafx.scene.layout.BorderWidths;
+import javafx.scene.layout.CornerRadii;
+import javafx.scene.layout.StackPane;
+import javafx.scene.paint.Color;
+import javafx.stage.Stage;
+
+/**
+ * The MainView holds the main application window which contains a MenuBar,
+ * the TabPane in which the In and OutputTabs will be displayed and
+ * some Controls
+ *
+ * @author Jan-Mathis Hein
+ */
+public class MainView {
+
+ //
+ private final Button centerButton, minButton, maxButton;
+
+ private final MenuBar menuBar;
+
+ private final Menu preferencesMenu, logMenu, helpMenu, jobMenu, directoryMenu;
+
+ private final MenuItem saveJobMenuItem, otherPreferencesMenuItem, newJobMenuItem,
+ loadJobOutputMenuItem, defaultInputDirectoryMenuItem, defaultOutputDirectoryMenuItem,
+ defaultImageDirectoryMenutItem, defaultMoleculeListDirectoryMenuItem, browseLogMenuItem,
+ resetLogMenuItem, aboutMenuItem, defaultSummaryReportDirectoryMenuItem;
+
+ private final Stage primaryStage;
+
+ private final Scene scene;
+
+ private final BorderPane mainPane;
+
+ private final TabPane tabPane;
+
+ private final HBox windowControlsBox;
+
+ private final StackPane centerPane;
+ //
+ //
+ //
+ /**
+ * Set up the main window with all its controls and
+ * handle their layout and size
+ *
+ * @param tmpPrimaryStage the main application window or more specifically
+ * the primary stage of the application
+ */
+ public MainView(Stage tmpPrimaryStage) {
+ this.primaryStage = tmpPrimaryStage;
+ this.primaryStage.setTitle(GeneralUtilities.getUIText("MainView.title.text") + " " + MSCConstants.MSC_VERSION);
+ this.mainPane = new BorderPane();
+ //
+ this.menuBar = new MenuBar();
+ this.jobMenu = new Menu(GeneralUtilities.getUIText("MainView.jobMenu.text"));
+ this.jobMenu.setStyle("-fx-background-color: rgb(180, 180, 180);-fx-border-color: rgb(150, 150, 150);");
+ this.newJobMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.newJobMenuItem.text"));
+ this.jobMenu.getItems().add(this.newJobMenuItem);
+ this.saveJobMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.saveJobMenuItem.text"));
+ this.jobMenu.getItems().add(this.saveJobMenuItem);
+ this.loadJobOutputMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.loadJobOutputMenuItem.text"));
+ this.jobMenu.getItems().add(this.loadJobOutputMenuItem);
+ this.menuBar.getMenus().add(this.jobMenu);
+ this.preferencesMenu = new Menu(GeneralUtilities.getUIText("MainView.preferencesMenu.text"));
+ this.preferencesMenu.setStyle("-fx-background-color: rgb(180, 180, 180);-fx-border-color: rgb(150, 150, 150);");
+ this.directoryMenu = new Menu(GeneralUtilities.getUIText("MainView.directoryMenu.text"));
+ this.defaultInputDirectoryMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.inputDirectoryMenuItem.text"));
+ this.defaultOutputDirectoryMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.outputDirectoryMenuItem.text"));
+ this.defaultImageDirectoryMenutItem = new MenuItem(GeneralUtilities.getUIText("MainView.imageDirectoryMenuItem.text"));
+ this.defaultMoleculeListDirectoryMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.moleculeListDirectoryMenuItem.text"));
+ this.defaultSummaryReportDirectoryMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.summaryReportDirectoryMenuItem.text"));
+ this.directoryMenu.getItems().addAll(
+ this.defaultInputDirectoryMenuItem, this.defaultOutputDirectoryMenuItem,
+ this.defaultImageDirectoryMenutItem, this.defaultMoleculeListDirectoryMenuItem,
+ this.defaultSummaryReportDirectoryMenuItem
+ );
+ this.preferencesMenu.getItems().add(this.directoryMenu);
+ this.otherPreferencesMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.otherPreferencesMenuItem.text"));
+ this.preferencesMenu.getItems().add(this.otherPreferencesMenuItem);
+ this.menuBar.getMenus().add(this.preferencesMenu);
+ this.helpMenu = new Menu(GeneralUtilities.getUIText("MainView.helpMenu.text"));
+ this.helpMenu.setStyle("-fx-background-color: rgb(180, 180, 180);-fx-border-color: rgb(150, 150, 150);");
+ this.logMenu = new Menu(GeneralUtilities.getUIText("MainView.logMenu.text"));
+ this.browseLogMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.browseLogMenuItem.text"));
+ this.resetLogMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.resetLogMenuItem.text"));
+ this.logMenu.getItems().addAll(this.browseLogMenuItem, this.resetLogMenuItem);
+ this.helpMenu.getItems().add(this.logMenu);
+ this.aboutMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.aboutMenuItem.text"));
+ this.helpMenu.getItems().add(this.aboutMenuItem);
+ this.menuBar.getMenus().add(this.helpMenu);
+ this.mainPane.setTop(this.menuBar);
+ //
+ //
+ this.centerPane = new StackPane();
+ this.centerPane.setStyle("-fx-background-color: rgb(220, 220, 220);");
+ this.tabPane = new TabPane();
+ this.centerPane.getChildren().add(this.tabPane);
+ this.mainPane.setCenter(this.centerPane);
+ //
+ //
+ this.windowControlsBox = new HBox(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.windowControlsBox.setBorder(new Border(new BorderStroke(
+ Color.color(0.1, 0.1, 0.1), Color.WHITE, Color.WHITE,
+ Color.WHITE, BorderStrokeStyle.SOLID, BorderStrokeStyle.NONE,
+ BorderStrokeStyle.NONE, BorderStrokeStyle.NONE,
+ new CornerRadii(0), new BorderWidths(2, 0, 0, 0), new Insets(0)
+ )));
+ this.windowControlsBox.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.maxButton = new Button(GeneralUtilities.getUIText("MainView.maxButton.text"));
+ GuiUtilities.setMinMaxPrefSize(this.maxButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.maxButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MainView.maxButton.tooltipText")));
+ this.minButton = new Button(GeneralUtilities.getUIText("MainView.minButton.text"));
+ GuiUtilities.setMinMaxPrefSize(this.minButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.minButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MainView.minButton.tooltipText")));
+ this.centerButton = new Button(GeneralUtilities.getUIText("MainView.centerButton.text"));
+ GuiUtilities.setMinMaxPrefSize(this.centerButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.centerButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MainView.centerButton.tooltipText")));
+ this.windowControlsBox.getChildren().addAll(this.maxButton, this.minButton, this.centerButton);
+ this.mainPane.setBottom(this.windowControlsBox);
+ //
+ this.scene = new Scene(this.mainPane);
+ this.scene.getStylesheets().add("resources/MainStyle.css");
+ this.primaryStage.setScene(this.scene);
+ }
+ //
+ //
+ //
+ /**
+ * Get the browseLogMenuItem
+ *
+ * @return the browseLogMenuItem
+ */
+ public MenuItem getBrowseLogMenuItem() {
+ return this.browseLogMenuItem;
+ }
+
+ /**
+ * Get the resetLogMenuItem
+ *
+ * @return the resetLogMenuItem
+ */
+ public MenuItem getResetLogMenuItem() {
+ return this.resetLogMenuItem;
+ }
+
+ /**
+ * Get the otherPreferencesMenuItem
+ *
+ * @return the otherPreferencesMenuItem
+ */
+ public MenuItem getOtherPreferencesMenuItem() {
+ return this.otherPreferencesMenuItem;
+ }
+
+ /**
+ * Get the defaultOutputDirectoryMenuItem
+ *
+ * @return the defaultOutputDirectoryMenuItem
+ */
+ public MenuItem getDefaultOutputDirectoryMenuItem() {
+ return this.defaultOutputDirectoryMenuItem;
+ }
+
+ /**
+ * Get the defaultImageDirectoryMenutItem
+ *
+ * @return the defaultImageDirectoryMenutItem
+ */
+ public MenuItem getDefaultImageDirectoryMenutItem() {
+ return this.defaultImageDirectoryMenutItem;
+ }
+
+ /**
+ * Get the defaultMoleculeListDirectoryMenuItem
+ *
+ * @return the defaultMoleculeListDirectoryMenuItem
+ */
+ public MenuItem getDefaultMoleculeListDirectoryMenuItem() {
+ return this.defaultMoleculeListDirectoryMenuItem;
+ }
+
+ /**
+ * Get the defaultSummaryReportDirectoryMenuItem
+ *
+ * @return the defaultSummaryReportDirectoryMenuItem
+ */
+ public MenuItem getDefaultSummaryReportDirectoryMenuItem() {
+ return this.defaultSummaryReportDirectoryMenuItem;
+ }
+
+ /**
+ * Get the newJobMenuItem
+ *
+ * @return the newJobMenuItem
+ */
+ public MenuItem getNewJobMenuItem() {
+ return this.newJobMenuItem;
+ }
+
+ /**
+ * Get the loadJobOutputMenuItem
+ *
+ * @return the loadJobOutputMenuItem
+ */
+ public MenuItem getLoadJobOutputMenuItem() {
+ return this.loadJobOutputMenuItem;
+ }
+
+ /**
+ * Get the defaultInputDirectoryMenuItem
+ *
+ * @return the defaultInputDirectoryMenuItem
+ */
+ public MenuItem getDefaultInputDirectoryMenuItem() {
+ return this.defaultInputDirectoryMenuItem;
+ }
+
+ /**
+ * Get the saveJobMenuItem
+ *
+ * @return the saveJobMenuItem
+ */
+ public MenuItem getSaveJobMenuItem() {
+ return this.saveJobMenuItem;
+ }
+
+ /**
+ * Get the aboutMenuItem
+ *
+ * @return the aboutMenuItem
+ */
+ public MenuItem getAboutMenuItem() {
+ return this.aboutMenuItem;
+ }
+
+ /**
+ * Get the centerButton
+ *
+ * @return the centerButton
+ */
+ public Button getCenterButton() {
+ return this.centerButton;
+ }
+
+ /**
+ * Get the minButton
+ *
+ * @return the minButton
+ */
+ public Button getMinButton() {
+ return this.minButton;
+ }
+
+ /**
+ * Get the maxButton
+ *
+ * @return the maxButton
+ */
+ public Button getMaxButton() {
+ return this.maxButton;
+ }
+
+ /**
+ * Get the primaryStage
+ *
+ * @return the primaryStage
+ */
+ public Stage getPrimaryStage() {
+ return this.primaryStage;
+ }
+
+ /**
+ * Get the scene
+ *
+ * @return the scene
+ */
+ public Scene getScene() {
+ return this.scene;
+ }
+
+ /**
+ * Get the centerPane
+ *
+ * @return the centerPane
+ */
+ public StackPane getCenterPane() {
+ return this.centerPane;
+ }
+
+ /**
+ * Get the tabPane
+ *
+ * @return the tabPane
+ */
+ public TabPane getTabPane() {
+ return this.tabPane;
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/MoleculePairDisplayerStage.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/MoleculePairDisplayerStage.java
new file mode 100644
index 0000000..174f082
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/MoleculePairDisplayerStage.java
@@ -0,0 +1,355 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.view;
+
+import de.whs.ibci.msc.model.ComparisonFeature;
+import de.whs.ibci.msc.utility.GuiUtilities;
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import javafx.geometry.HPos;
+import javafx.geometry.Insets;
+import javafx.geometry.Pos;
+import javafx.geometry.VPos;
+import javafx.scene.Scene;
+import javafx.scene.control.Button;
+import javafx.scene.control.CheckBox;
+import javafx.scene.control.Control;
+import javafx.scene.control.Label;
+import javafx.scene.control.ScrollPane;
+import javafx.scene.control.TextField;
+import javafx.scene.control.Tooltip;
+import javafx.scene.image.ImageView;
+import javafx.scene.layout.Border;
+import javafx.scene.layout.BorderStroke;
+import javafx.scene.layout.BorderStrokeStyle;
+import javafx.scene.layout.BorderWidths;
+import javafx.scene.layout.ColumnConstraints;
+import javafx.scene.layout.CornerRadii;
+import javafx.scene.layout.FlowPane;
+import javafx.scene.layout.GridPane;
+import javafx.scene.layout.HBox;
+import javafx.scene.layout.Priority;
+import javafx.scene.layout.RowConstraints;
+import javafx.scene.layout.StackPane;
+import javafx.scene.layout.VBox;
+import javafx.scene.paint.Paint;
+import javafx.stage.Stage;
+
+/**
+ * A window or more specifically a Stage on which a collection of molecule pairs
+ * can be displayed.
+ *
+ * @author Jan-Mathis Hein
+ */
+public class MoleculePairDisplayerStage extends Stage {
+
+ //
+ private final Button saveLeftListButton, saveRightListButton, saveLeftImageButton, saveRightImageButton, nextButton, previousButton, lastButton, firstButton;
+
+ private final Scene scene;
+
+ private final TextField positionTextField;
+
+ private final ImageView leftMoleculeImageView, rightMoleculeImageView;
+
+ private final Label infoLabel;
+
+ private final HBox moleculePairBox, positionControlsBox, otherControlsBox;
+
+ private final VBox controlsBox;
+
+ private final GridPane mainPane, infoPane, savingControlsPane;
+
+ private final FlowPane additionalComparisonFeatureControlsPane;
+
+ private final ScrollPane additionalComparisonFeaturesScrollPane;
+
+ private final StackPane leftMoleculePane, rightMoleculePane;
+
+ private final Control[][] additionalComparisonFeatureControls;
+ //
+ //
+ //
+ /**
+ * Creates the stage with all its controls and handle their layout and size
+ */
+ public MoleculePairDisplayerStage() {
+ super();
+ this.mainPane = new GridPane();
+ this.mainPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.mainPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.mainPane.setHgap(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.mainPane.getColumnConstraints().addAll(
+ new ColumnConstraints(60, 100, Double.MAX_VALUE, Priority.ALWAYS, HPos.LEFT, true),
+ new ColumnConstraints()
+ );
+ this.mainPane.getRowConstraints().addAll(
+ new RowConstraints(),
+ new RowConstraints(49.6, 49.6, Double.MAX_VALUE, Priority.ALWAYS, VPos.TOP, true)
+ );
+ this.moleculePairBox = new HBox();
+ this.moleculePairBox.setBorder(GuiUtilities.RAISED_BORDER);
+ this.leftMoleculePane = new StackPane();
+ this.leftMoleculePane.setBorder(new Border(new BorderStroke(
+ Paint.valueOf("Black"), Paint.valueOf("Black"), Paint.valueOf("Black"),
+ Paint.valueOf("Black"), BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ new CornerRadii(0), new BorderWidths(2, 1, 2, 2), new Insets(10, 0, 10, 10)
+ )));
+ this.leftMoleculeImageView = new ImageView();
+ this.leftMoleculeImageView.setPreserveRatio(true);
+ this.leftMoleculePane.getChildren().add(this.leftMoleculeImageView);
+ this.rightMoleculePane = new StackPane();
+ this.rightMoleculePane.setBorder(new Border(new BorderStroke(
+ Paint.valueOf("Black"), Paint.valueOf("Black"), Paint.valueOf("Black"),
+ Paint.valueOf("Black"), BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ new CornerRadii(0), new BorderWidths(2, 2, 2, 1), new Insets(10, 10, 10, 0)
+ )));
+ this.rightMoleculeImageView = new ImageView();
+ this.rightMoleculeImageView.setPreserveRatio(true);
+ this.rightMoleculePane.getChildren().add(this.rightMoleculeImageView);
+ this.moleculePairBox.getChildren().addAll(this.leftMoleculePane, this.rightMoleculePane);
+ this.mainPane.add(this.moleculePairBox, 1, 0, 1, 1);
+ this.infoPane = new GridPane();
+ this.infoPane.setBorder(GuiUtilities.RAISED_BORDER);
+ this.infoPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.infoPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.infoPane.setMaxWidth(Double.MAX_VALUE);
+ this.infoPane.getRowConstraints().addAll(
+ new RowConstraints(),
+ new RowConstraints(20, 20, Double.MAX_VALUE, Priority.ALWAYS, VPos.TOP, true)
+ );
+ this.infoPane.getColumnConstraints().addAll(
+ new ColumnConstraints(40, 80, Double.MAX_VALUE, Priority.ALWAYS, HPos.LEFT, true)
+ );
+ this.infoLabel = new Label();
+ this.infoLabel.setWrapText(true);
+ this.infoLabel.setAlignment(Pos.TOP_LEFT);
+ this.infoLabel.setMaxSize(Double.MAX_VALUE, Double.MAX_VALUE);
+ this.infoPane.add(this.infoLabel, 0, 0);
+ this.additionalComparisonFeaturesScrollPane = new ScrollPane();
+ this.additionalComparisonFeaturesScrollPane.setFitToWidth(true);
+ this.additionalComparisonFeaturesScrollPane.setVbarPolicy(ScrollPane.ScrollBarPolicy.ALWAYS);
+ this.additionalComparisonFeaturesScrollPane.setHbarPolicy(ScrollPane.ScrollBarPolicy.AS_NEEDED);
+ this.additionalComparisonFeaturesScrollPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.additionalComparisonFeatureControlsPane = new FlowPane();
+ this.additionalComparisonFeatureControlsPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.additionalComparisonFeatureControlsPane.setHgap(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.additionalComparisonFeatureControls = new Control[ComparisonFeature.values().length][2];
+ CheckBox tmpCheckBox;
+ Label tmpLabel;
+ HBox tmpBox;
+ for (int i = 0; i < this.additionalComparisonFeatureControls.length; i++) {
+ tmpBox = new HBox(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ GuiUtilities.setMinMaxPrefWidth(tmpBox, 320);
+ tmpCheckBox = new CheckBox(ComparisonFeature.values()[i].toString());
+ tmpCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.additionalComparisonFeatureCheckBox.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(tmpCheckBox, 160);
+ this.additionalComparisonFeatureControls[i][0] = tmpCheckBox;
+ tmpBox.getChildren().add(tmpCheckBox);
+ tmpLabel = new Label("");
+ this.additionalComparisonFeatureControls[i][1] = tmpLabel;
+ tmpBox.getChildren().add(tmpLabel);
+ this.additionalComparisonFeatureControlsPane.getChildren().add(tmpBox);
+ }
+ this.additionalComparisonFeaturesScrollPane.setContent(this.additionalComparisonFeatureControlsPane);
+ this.infoPane.add(this.additionalComparisonFeaturesScrollPane, 0, 1);
+ this.mainPane.add(this.infoPane, 0, 0, 1, 2);
+ this.controlsBox = new VBox(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.controlsBox.setBorder(GuiUtilities.RAISED_BORDER);
+ this.controlsBox.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.positionControlsBox = new HBox(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.positionControlsBox.setAlignment(Pos.TOP_CENTER);
+ this.firstButton = new Button(GeneralUtilities.getUIText("MoleculePairDisplayerStage.firstButton.text"));
+ this.firstButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.firstButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.firstButton, 30, GuiUtilities.BUTTON_HEIGHT);
+ this.previousButton = new Button(GeneralUtilities.getUIText("MoleculePairDisplayerStage.previousButton.text"));
+ this.previousButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.previousButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.previousButton, 30, GuiUtilities.BUTTON_HEIGHT);
+ this.positionTextField = new TextField();
+ this.positionTextField.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.positionTextField.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.positionTextField, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.nextButton = new Button(GeneralUtilities.getUIText("MoleculePairDisplayerStage.nextButton.text"));
+ this.nextButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.nextButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.nextButton, 30, GuiUtilities.BUTTON_HEIGHT);
+ this.lastButton = new Button(GeneralUtilities.getUIText("MoleculePairDisplayerStage.lastButton.text"));
+ this.lastButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.lastButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.lastButton, 30, GuiUtilities.BUTTON_HEIGHT);
+ this.positionControlsBox.getChildren().addAll(this.firstButton, this.previousButton, this.positionTextField, this.nextButton, this.lastButton);
+ this.controlsBox.getChildren().addAll(this.positionControlsBox);
+ this.otherControlsBox = new HBox(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.savingControlsPane = new GridPane();
+ this.savingControlsPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.savingControlsPane.setHgap(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.savingControlsPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.savingControlsPane.setBorder(GuiUtilities.LOWERED_BORDER);
+ this.saveLeftListButton = new Button(GeneralUtilities.getUIText("MoleculePairDisplayerStage.saveLeftListButton.text"));
+ this.saveLeftListButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.saveLeftListButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.saveLeftListButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.savingControlsPane.add(this.saveLeftListButton, 0, 0);
+ this.saveRightListButton = new Button(GeneralUtilities.getUIText("MoleculePairDisplayerStage.saveRightListButton.text"));
+ this.saveRightListButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.saveRightListButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.saveRightListButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.savingControlsPane.add(this.saveRightListButton, 0, 1);
+ this.saveLeftImageButton = new Button(GeneralUtilities.getUIText("MoleculePairDisplayerStage.saveLeftImageButton.text"));
+ this.saveLeftImageButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.saveLeftImageButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.saveLeftImageButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.savingControlsPane.add(this.saveLeftImageButton, 1, 0);
+ this.saveRightImageButton = new Button(GeneralUtilities.getUIText("MoleculePairDisplayerStage.saveRightImageButton.text"));
+ this.saveRightImageButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.saveRightImageButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.saveRightImageButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.savingControlsPane.add(this.saveRightImageButton, 1, 1);
+ this.otherControlsBox.getChildren().add(this.savingControlsPane);
+ this.controlsBox.getChildren().add(this.otherControlsBox);
+ this.mainPane.add(this.controlsBox, 1, 1, 1, 1);
+ this.scene = new Scene(this.mainPane);
+ this.scene.getStylesheets().add("resources/MainStyle.css");
+ this.setScene(this.scene);
+ }
+ //
+ //
+ //
+ /**
+ * Get the nextButton
+ *
+ * @return the nextButton
+ */
+ public Button getNextButton() {
+ return this.nextButton;
+ }
+
+ /**
+ * Get the previousButton
+ *
+ * @return the previousButton
+ */
+ public Button getPreviousButton() {
+ return this.previousButton;
+ }
+
+ /**
+ * Get the saveLeftListButton
+ *
+ * @return the saveLeftListButton
+ */
+ public Button getSaveLeftListButton() {
+ return this.saveLeftListButton;
+ }
+
+ /**
+ * Get the saveRightListButton
+ *
+ * @return the saveRightListButton
+ */
+ public Button getSaveRightListButton() {
+ return this.saveRightListButton;
+ }
+
+ /**
+ * Get the saveLeftImageButton
+ *
+ * @return the saveLeftImageButton
+ */
+ public Button getSaveLeftImageButton() {
+ return this.saveLeftImageButton;
+ }
+
+ /**
+ * Get the saveRightImageButton
+ *
+ * @return the saveRightImageButton
+ */
+ public Button getSaveRightImageButton() {
+ return this.saveRightImageButton;
+ }
+
+ /**
+ * Get the lastButton
+ *
+ * @return the lastButton
+ */
+ public Button getLastButton() {
+ return this.lastButton;
+ }
+
+ /**
+ * Get the firstButton
+ *
+ * @return the firstButton
+ */
+ public Button getFirstButton() {
+ return this.firstButton;
+ }
+
+ /**
+ * Get the infoPane
+ *
+ * @return the infoPane
+ */
+ public GridPane getInfoPane() {
+ return this.infoPane;
+ }
+
+ /**
+ * Get the leftMoleculeImageView
+ *
+ * @return the leftMoleculeImageView
+ */
+ public ImageView getLeftMoleculeImageView() {
+ return this.leftMoleculeImageView;
+ }
+
+ /**
+ * Get the rightMoleculeImageView
+ *
+ * @return the rightMoleculeImageView
+ */
+ public ImageView getRightMoleculeImageView() {
+ return this.rightMoleculeImageView;
+ }
+
+ /**
+ * Get the infoLabel
+ *
+ * @return the infoLabel
+ */
+ public Label getInfoLabel() {
+ return infoLabel;
+ }
+
+ /**
+ * Get the positionTextField
+ *
+ * @return the positionTextField
+ */
+ public TextField getPositionTextField() {
+ return this.positionTextField;
+ }
+
+ /**
+ * Get the additionalComparisonFeatureControls array where each element is
+ * an array of the form {checkbox, label}
+ *
+ * @return the additionalComparisonFeatureControls array
+ */
+ public Control[][] getAdditionalComparisonFeatureControls() {
+ return this.additionalComparisonFeatureControls;
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/OutputTab.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/OutputTab.java
new file mode 100644
index 0000000..536708e
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/OutputTab.java
@@ -0,0 +1,383 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.view;
+
+import de.whs.ibci.msc.control.BinLabelType;
+import de.whs.ibci.msc.control.JobController;
+import de.whs.ibci.msc.utility.GuiUtilities;
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.model.ComparisonFeature;
+import java.util.Set;
+import javafx.collections.FXCollections;
+import javafx.geometry.Insets;
+import javafx.geometry.Orientation;
+import javafx.geometry.Pos;
+import javafx.scene.control.Button;
+import javafx.scene.control.CheckBox;
+import javafx.scene.control.ChoiceBox;
+import javafx.scene.control.Label;
+import javafx.scene.control.Slider;
+import javafx.scene.control.Tab;
+import javafx.scene.control.TextField;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.AnchorPane;
+import javafx.scene.layout.GridPane;
+import javafx.scene.layout.HBox;
+import javafx.scene.layout.Region;
+import javafx.scene.layout.VBox;
+
+/**
+ * A Tab in which a job's output is displayed and that contains some controls
+ * with which the user can interact with the output
+ *
+ * @author Jan-Mathis Hein
+ */
+public class OutputTab extends Tab {
+
+ //
+ private final HBox contentPane;
+
+ private final VBox binBorderSlidersBox, frequencySlidersBox, binBorderBox, frequencyBox;
+
+ private final AnchorPane chartPane;
+
+ private final Label infoLabel, binBorderSlidersLabel, frequencySlidersLabel, numberOfBinsLabel;
+
+ private final GridPane controlsPane, chartConfigurationPane;
+
+ private final ChoiceBox chartChoiceBox;
+
+ private final TextField numberOfBinsTextField;
+
+ private final ChoiceBox binLabelChoiceBox;
+
+ private final Button imageButton, chartConfigurationButton, defaultButton, binBorderConfigurationButton, summaryReportButton;
+
+ private final Slider binBorder1Slider, binBorder2Slider, frequency1Slider, frequency2Slider;
+
+ private final CheckBox relativeFrequenciesCheckBox, barLabelCheckBox;
+ //
+ //
+ //
+ /**
+ * Create the Tab with all its controls and handle their layout and size
+ *
+ * @param tmpJobNumber the job's identifier number
+ */
+ public OutputTab(String tmpJobNumber) {
+ super(GeneralUtilities.getUIText("OutputTab.title.text") + tmpJobNumber);
+ this.setClosable(true);
+ this.contentPane = new HBox(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ // The 11 is intentional
+ this.contentPane.setPadding(new Insets(10, 10, 11, 10));
+ this.controlsPane = new GridPane();
+ this.controlsPane.setHgap(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.controlsPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.controlsPane.setBorder(GuiUtilities.RAISED_BORDER);
+ this.controlsPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.infoLabel = new Label("");
+ this.infoLabel.setWrapText(true);
+ this.infoLabel.setAlignment(Pos.TOP_LEFT);
+ this.controlsPane.add(this.infoLabel, 0, 0, 2, 1);
+ this.summaryReportButton = new Button(GeneralUtilities.getUIText("OutputTab.summaryReportButton.text"));
+ this.summaryReportButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.summaryReportButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.summaryReportButton, GuiUtilities.BUTTON_WIDTH);
+ this.controlsPane.add(this.summaryReportButton, 0, 1, 1, 1);
+ this.barLabelCheckBox = new CheckBox(GeneralUtilities.getUIText("OutputTab.barLabelCheckBox.text"));
+ this.barLabelCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.barLabelCheckBox.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.barLabelCheckBox, GuiUtilities.BUTTON_WIDTH);
+ this.controlsPane.add(this.barLabelCheckBox, 1, 1, 1, 1);
+ this.chartChoiceBox = new ChoiceBox<>();
+ this.chartChoiceBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.chartChoiceBox.tooltipText")));
+ this.chartChoiceBox.setMaxWidth(Double.MAX_VALUE);
+ this.controlsPane.add(this.chartChoiceBox, 0, 2, 2, 1);
+ this.binLabelChoiceBox = new ChoiceBox<>();
+ this.binLabelChoiceBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.binLabelChoiceBox.tooltipText")));
+ this.binLabelChoiceBox.setMaxWidth(Double.MAX_VALUE);
+ this.controlsPane.add(this.binLabelChoiceBox, 0, 3, 2, 1);
+ this.chartConfigurationPane = new GridPane();
+ this.chartConfigurationPane.setHgap(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.chartConfigurationPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.chartConfigurationPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.chartConfigurationPane.setBorder(GuiUtilities.LOWERED_BORDER);
+ this.chartConfigurationButton = new Button(GeneralUtilities.getUIText("OutputTab.configureButton.text"));
+ this.chartConfigurationButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.configureButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.chartConfigurationButton, GuiUtilities.BUTTON_WIDTH);
+ this.chartConfigurationPane.add(this.chartConfigurationButton, 0, 0, 1, 1);
+ this.defaultButton = new Button(GeneralUtilities.getUIText("ChartConfigurationDialog.defaultButton.text"));
+ this.defaultButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("ChartConfigurationDialog.defaultButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.defaultButton, GuiUtilities.BUTTON_WIDTH);
+ this.chartConfigurationPane.add(this.defaultButton, 1, 0, 1, 1);
+ this.binBorderConfigurationButton = new Button(GeneralUtilities.getUIText("OutputTab.binBorderConfigurationButton.text"));
+ this.binBorderConfigurationButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.binBorderConfigurationButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.binBorderConfigurationButton, GuiUtilities.BUTTON_WIDTH);
+ this.chartConfigurationPane.add(this.binBorderConfigurationButton, 0, 1, 1, 1);
+ this.relativeFrequenciesCheckBox = new CheckBox(GeneralUtilities.getUIText("OutputTab.relativeFrequenciesCheckBox.text"));
+ this.relativeFrequenciesCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.relativeFrequenciesCheckBox.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.relativeFrequenciesCheckBox, GuiUtilities.BUTTON_WIDTH);
+ this.chartConfigurationPane.add(this.relativeFrequenciesCheckBox, 1, 1, 1, 1);
+ this.numberOfBinsLabel = new Label(GeneralUtilities.getUIText("OutputTab.numberOfBinsLabel.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.numberOfBinsLabel, GuiUtilities.BUTTON_WIDTH);
+ this.chartConfigurationPane.add(this.numberOfBinsLabel, 0, 2, 1, 1);
+ this.numberOfBinsTextField = new TextField();
+ this.numberOfBinsTextField.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.numberOfBinsTextField.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.numberOfBinsTextField, GuiUtilities.BUTTON_WIDTH);
+ this.chartConfigurationPane.add(this.numberOfBinsTextField, 1, 2, 1, 1);
+ this.binBorderBox = new VBox(-5);
+ this.binBorderSlidersLabel = new Label(GeneralUtilities.getUIText("OutputTab.binBorderSlidersLabel.text"));
+ this.binBorderBox.getChildren().add(this.binBorderSlidersLabel);
+ this.binBorderSlidersBox = new VBox(-10);
+ this.binBorder1Slider = new Slider();
+ this.binBorder1Slider.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.binBorderSlider.tooltipText")));
+ this.binBorder1Slider.setOrientation(Orientation.HORIZONTAL);
+ GuiUtilities.setMinMaxPrefHeight(this.binBorder1Slider, 50);
+ this.binBorder1Slider.setShowTickMarks(true);
+ this.binBorder1Slider.setShowTickLabels(true);
+ this.binBorderSlidersBox.getChildren().add(this.binBorder1Slider);
+ this.binBorder2Slider = new Slider();
+ this.binBorder2Slider.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.binBorderSlider.tooltipText")));
+ this.binBorder2Slider.setOrientation(Orientation.HORIZONTAL);
+ GuiUtilities.setMinMaxPrefHeight(this.binBorder2Slider, 20);
+ this.binBorder2Slider.setShowTickMarks(false);
+ this.binBorder2Slider.setShowTickLabels(false);
+ this.binBorderSlidersBox.getChildren().add(this.binBorder2Slider);
+ this.binBorderBox.getChildren().add(this.binBorderSlidersBox);
+ this.chartConfigurationPane.add(this.binBorderBox, 0, 3, 2, 1);
+ this.frequencyBox = new VBox(-5);
+ this.frequencySlidersLabel = new Label(GeneralUtilities.getUIText("OutputTab.frequencySlidersLabel.text"));
+ this.frequencyBox.getChildren().add(this.frequencySlidersLabel);
+ this.frequencySlidersBox = new VBox(-10);
+ this.frequency1Slider = new Slider();
+ this.frequency1Slider.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.frequencySlider.tooltipText")));
+ this.frequency1Slider.setOrientation(Orientation.HORIZONTAL);
+ GuiUtilities.setMinMaxPrefHeight(this.frequency1Slider, 50);
+ this.frequency1Slider.setShowTickMarks(true);
+ this.frequency1Slider.setShowTickLabels(true);
+ this.frequencySlidersBox.getChildren().add(this.frequency1Slider);
+ this.frequency2Slider = new Slider();
+ this.frequency2Slider.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.frequencySlider.tooltipText")));
+ this.frequency2Slider.setOrientation(Orientation.HORIZONTAL);
+ GuiUtilities.setMinMaxPrefHeight(this.frequency2Slider, 20);
+ this.frequency2Slider.setShowTickMarks(false);
+ this.frequency2Slider.setShowTickLabels(false);
+ this.frequencySlidersBox.getChildren().add(this.frequency2Slider);
+ this.frequencyBox.getChildren().add(this.frequencySlidersBox);
+ this.chartConfigurationPane.add(this.frequencyBox, 0, 4, 2, 1);
+ this.controlsPane.add(this.chartConfigurationPane, 0, 4, 2, 1);
+ this.contentPane.getChildren().add(this.controlsPane);
+ this.chartPane = new AnchorPane();
+ this.chartPane.setBorder(GuiUtilities.RAISED_BORDER);
+ this.chartPane.setPrefWidth(999999);
+ this.imageButton = new Button(GeneralUtilities.getUIText("OutputTab.saveButton.text"));
+ this.imageButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.saveButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.imageButton, GuiUtilities.BUTTON_WIDTH);
+ AnchorPane.setRightAnchor(this.imageButton, 10.0);
+ AnchorPane.setTopAnchor(this.imageButton, 10.0);
+ this.chartPane.getChildren().add(this.imageButton);
+ this.contentPane.getChildren().add(this.chartPane);
+ this.setContent(this.contentPane);
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Get the chartChoiceBox
+ *
+ * @return the chartChoiceBox
+ */
+ public ChoiceBox getChartChoiceBox() {
+ return this.chartChoiceBox;
+ }
+
+ /**
+ * Get the binLabelChoiceBox
+ *
+ * @return the binLabelChoiceBox
+ */
+ public ChoiceBox getBinLabelChoiceBox() {
+ return this.binLabelChoiceBox;
+ }
+
+ /**
+ * Get the numberOfBinsTextField
+ *
+ * @return the numberOfBinsTextField
+ */
+ public TextField getNumberOfBinsTextField() {
+ return this.numberOfBinsTextField;
+ }
+
+ /**
+ * Get the chartConfigurationButton
+ *
+ * @return the chartConfigurationButton
+ */
+ public Button getChartConfigurationButton() {
+ return this.chartConfigurationButton;
+ }
+
+ /**
+ * Get the imageButton
+ *
+ * @return the imageButton
+ */
+ public Button getImageButton() {
+ return this.imageButton;
+ }
+
+ /**
+ * Get the summaryReportButton
+ *
+ * @return the summaryReportButton
+ */
+ public Button getSummaryReportButton() {
+ return this.summaryReportButton;
+ }
+
+ /**
+ * Get the defaultButton
+ *
+ * @return the defaultButton
+ */
+ public Button getDefaultButton() {
+ return this.defaultButton;
+ }
+
+ /**
+ * Get the binBorderConfigurationButton
+ *
+ * @return the binBorderConfigurationButton
+ */
+ public Button getBinBorderConfigurationButton() {
+ return this.binBorderConfigurationButton;
+ }
+
+ /**
+ * Get the relativeFrequenciesCheckBox
+ *
+ * @return the relativeFrequenciesCheckBox
+ */
+ public CheckBox getRelativeFrequenciesCheckBox() {
+ return this.relativeFrequenciesCheckBox;
+ }
+
+ /**
+ * Get the barLabelCheckBox
+ *
+ * @return the barLabelCheckBox
+ */
+ public CheckBox getBarLabelCheckBox() {
+ return this.barLabelCheckBox;
+ }
+
+ /**
+ * Get the infoLabel
+ *
+ * @return the infoLabel
+ */
+ public Label getInfoLabel() {
+ return this.infoLabel;
+ }
+
+ /**
+ * Get the frequency1Slider
+ *
+ * @return the frequency1Slider
+ */
+ public Slider getFrequency1Slider() {
+ return this.frequency1Slider;
+ }
+
+ /**
+ * Get the frequency2Slider
+ *
+ * @return the frequency2Slider
+ */
+ public Slider getFrequency2Slider() {
+ return this.frequency2Slider;
+ }
+
+ /**
+ * Get the binBorder1Slider
+ *
+ * @return the binBorder1Slider
+ */
+ public Slider getBinBorder1Slider() {
+ return this.binBorder1Slider;
+ }
+
+ /**
+ * Get the binBorder2Slider
+ *
+ * @return the binBorder2Slider
+ */
+ public Slider getBinBorder2Slider() {
+ return this.binBorder2Slider;
+ }
+
+ /**
+ * Get the chartPane
+ *
+ * @return the chartPane
+ */
+ public AnchorPane getChartPane() {
+ return this.chartPane;
+ }
+ //
+ //
+ /**
+ * Set the set of ComparisonFeatures that will be the items of the
+ * chartChoiceBox
+ *
+ * @param tmpComparisonFeatureSet specifies the set of ComparisonFeatures
+ */
+ public void setChartChoiceBoxItems(Set tmpComparisonFeatureSet) {
+ this.chartChoiceBox.setItems(FXCollections.observableArrayList(tmpComparisonFeatureSet));
+ }
+
+ /**
+ * Set the set of BinLabelTypes that will be the items of the
+ * binLabelChoiceBox
+ *
+ * @param tmpBinLabelTypeSet specifies the set of BinLabelTypes
+ */
+ public void setBinLabelChoiceBoxItems(Set tmpBinLabelTypeSet) {
+ this.binLabelChoiceBox.setItems(FXCollections.observableArrayList(tmpBinLabelTypeSet));
+ }
+
+ /**
+ * Set a region that will be displayed in the chartPane
+ *
+ * @param tmpRegion specifies the region
+ */
+ public void setComparisonFeatureChart(Region tmpRegion){
+ this.chartPane.getChildren().clear();
+ AnchorPane.setRightAnchor(this.imageButton, 10.0);
+ AnchorPane.setTopAnchor(this.imageButton, 10.0);
+ this.chartPane.getChildren().add(this.imageButton);
+ AnchorPane.setLeftAnchor(tmpRegion, 0.0);
+ AnchorPane.setTopAnchor(tmpRegion, 38.0);
+ // Alignes the chart with the button
+ AnchorPane.setRightAnchor(tmpRegion, 3.0);
+ AnchorPane.setBottomAnchor(tmpRegion, 0.0);
+ this.chartPane.getChildren().add(tmpRegion);
+ }
+ //
+ //
+}
diff --git a/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/PreferencesConfigurationDialog.java b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/PreferencesConfigurationDialog.java
new file mode 100644
index 0000000..981ddcc
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/de/whs/ibci/msc/view/PreferencesConfigurationDialog.java
@@ -0,0 +1,161 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.view;
+
+import de.whs.ibci.msc.utility.GuiUtilities;
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import javafx.geometry.Orientation;
+import javafx.geometry.Pos;
+import javafx.scene.control.Button;
+import javafx.scene.control.Label;
+import javafx.scene.control.Slider;
+import javafx.scene.control.TextField;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.GridPane;
+import javafx.scene.layout.HBox;
+import javafx.stage.Window;
+
+/**
+ * A Dialog in which the user can configure some of the application's
+ * preferences
+ *
+ * @author Jan-Mathis Hein
+ */
+public class PreferencesConfigurationDialog extends ConfigurationDialog {
+
+ //
+ private final GridPane inputPane;
+
+ private final Label numberOfParallelThreadsLabel, defaultNumberOfBinsLabel, maximalNumberOfMoleculePairsToSaveLabel, imageQualityLabel;
+
+ private final TextField numberOfParallelThreadsField, defaultNumberOfBinsField, maximalNumberOfMoleculePairsToSaveField;
+
+ private final Button resetButton;
+
+ private final Slider imageQualitySlider;
+
+ private final HBox resetButtonBox;
+ //
+ //
+ //
+ /**
+ * Create the Dialog with all its controls and handle their layout and size
+ *
+ * @param tmpOwner specifies the window that owns the Dialog
+ * @param tmpTitle specifies the title of the Dialog
+ */
+ public PreferencesConfigurationDialog(Window tmpOwner, String tmpTitle) {
+ super(tmpOwner, tmpTitle);
+ this.inputPane = new GridPane();
+ this.inputPane.setBorder(GuiUtilities.RAISED_BORDER);
+ this.inputPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.inputPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.inputPane.setHgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.numberOfParallelThreadsLabel = new Label(GeneralUtilities.getUIText("PreferencesConfigurationDialog.numberOfParallelThreadsLabel.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.numberOfParallelThreadsLabel, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.numberOfParallelThreadsLabel, 0, 0);
+ this.numberOfParallelThreadsField = new TextField();
+ this.numberOfParallelThreadsField.setTooltip(new Tooltip(GeneralUtilities.getUIText("PreferencesConfigurationDialog.numberOfParallelThreadsField.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.numberOfParallelThreadsField, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.numberOfParallelThreadsField, 1, 0);
+ this.defaultNumberOfBinsLabel = new Label(GeneralUtilities.getUIText("PreferencesConfigurationDialog.defaultNumberOfBinsLabel.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.defaultNumberOfBinsLabel, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.defaultNumberOfBinsLabel, 0, 1);
+ this.defaultNumberOfBinsField = new TextField();
+ this.defaultNumberOfBinsField.setTooltip(new Tooltip(GeneralUtilities.getUIText("PreferencesConfigurationDialog.defaultNumberOfBinsField.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.defaultNumberOfBinsField, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.defaultNumberOfBinsField, 1, 1);
+ this.maximalNumberOfMoleculePairsToSaveLabel = new Label(GeneralUtilities.getUIText("PreferencesConfigurationDialog.maximalNumberOfMoleculePairsToSaveLabel.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.maximalNumberOfMoleculePairsToSaveLabel, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.maximalNumberOfMoleculePairsToSaveLabel, 0, 2);
+ this.maximalNumberOfMoleculePairsToSaveField = new TextField();
+ this.maximalNumberOfMoleculePairsToSaveField.setTooltip(new Tooltip(GeneralUtilities.getUIText("PreferencesConfigurationDialog.maximalNumberOfMoleculePairsToSaveField.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.maximalNumberOfMoleculePairsToSaveField, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.maximalNumberOfMoleculePairsToSaveField, 1, 2);
+ this.imageQualityLabel = new Label(GeneralUtilities.getUIText("PreferencesConfigurationDialog.imageQualityLabel.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.imageQualityLabel, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.imageQualityLabel, 0, 3);
+ this.imageQualitySlider = new Slider(0.0, 1.0, 0.5);
+ this.imageQualitySlider.setMajorTickUnit(0.25);
+ this.imageQualitySlider.setOrientation(Orientation.HORIZONTAL);
+ this.imageQualitySlider.setShowTickLabels(true);
+ this.imageQualitySlider.setShowTickMarks(true);
+ this.imageQualitySlider.setTooltip(new Tooltip(GeneralUtilities.getUIText("PreferencesConfigurationDialog.imageQualitySlider.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.imageQualitySlider, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.imageQualitySlider, 1, 3);
+ this.resetButtonBox = new HBox();
+ this.resetButtonBox.setAlignment(Pos.CENTER_RIGHT);
+ this.resetButton = new Button(GeneralUtilities.getUIText("PreferencesConfigurationDialog.resetButton.text"));
+ this.resetButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("PreferencesConfigurationDialog.resetButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.resetButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.resetButtonBox.getChildren().add(this.resetButton);
+ this.inputPane.add(this.resetButtonBox, 1, 4);
+ this.getContentPane().getChildren().add(this.inputPane);
+ this.setHeaderText(GeneralUtilities.getUIText("PreferencesConfigurationDialog.Header.text"));
+ GuiUtilities.setMinMaxPrefHeight(this.getDialogPane(), 317.0);
+ }
+ //
+ //
+ //
+ /**
+ * Get the numberOfParallelThreadsField
+ *
+ * @return the numberOfParallelThreadsField
+ */
+ public TextField getNumberOfParallelThreadsField() {
+ return this.numberOfParallelThreadsField;
+ }
+
+ /**
+ * Get the defaultNumberOfBinsField
+ *
+ * @return the defaultNumberOfBinsField
+ */
+ public TextField getDefaultNumberOfBinsField() {
+ return this.defaultNumberOfBinsField;
+ }
+
+ /**
+ * Get the maximalNumberOfMoleculePairsToSaveField
+ *
+ * @return the maximalNumberOfMoleculePairsToSaveField
+ */
+ public TextField getMaximalNumberOfMoleculePairsToSaveField() {
+ return this.maximalNumberOfMoleculePairsToSaveField;
+ }
+
+ /**
+ * Get the resetButton
+ *
+ * @return the resetButton
+ */
+ public Button getResetButton() {
+ return this.resetButton;
+ }
+
+ /**
+ * Get the imageQualitySlider
+ *
+ * @return the imageQualitySlider
+ */
+ public Slider getImageQualitySlider() {
+ return this.imageQualitySlider;
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/main/java/resources/MainStyle.css b/Gradle Project for Netbeans/src/main/java/resources/MainStyle.css
new file mode 100644
index 0000000..3ef12ad
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/resources/MainStyle.css
@@ -0,0 +1,70 @@
+/*
+ Created on : 09.11.2019, 12:42:54
+ Author : Jan-Mathis Hein
+*/
+
+.axis {
+ -fx-tick-label-fill: rgb(50, 50, 50);
+ -fx-start-margin: 4;
+ -fx-end-margin: 4;
+ -fx-tick-label-gap: 5;
+ -fx-tick-length: 6;
+ -fx-minor-tick-length: 3;
+ -fx-tick-mark-visible: true;
+}
+
+.axis-minor-tick-mark {
+ -fx-stroke: rgb(50, 50, 50);
+ -fx-stroke-width: 1;
+ -fx-opacity: 0.5;
+}
+
+.axis-tick-mark {
+ -fx-stroke: rgb(50, 50, 50);
+ -fx-stroke-width: 1;
+ -fx-opacity: 0.5;
+}
+
+.chart {
+ -fx-padding: 0px;
+ -fx-vertical-grid-lines-visible: false;
+ -fx-category-gap: 8;
+}
+
+.chart-bar {
+ -fx-background-color: rgb(50, 50, 170);
+}
+
+.chart-content {
+ -fx-padding: 10px;
+}
+
+.dialog-pane:header .header-panel {
+ -fx-background-color: rgb(220, 220, 220);
+}
+
+.menu-bar {
+ -fx-background-color: rgb(160, 160, 160);
+}
+
+.root {
+ default-color: rgb(200, 200, 200);
+ -fx-background-color: default-color;
+ -fx-base-color: default-color;
+}
+
+.tab {
+ -fx-background-color: rgb(160, 160, 160);
+}
+
+.tab:selected {
+ -fx-background-color: rgb(140, 140, 140);
+}
+
+.tab-header-background {
+ -fx-background-color: rgb(220, 220, 220);
+}
+
+.tab-label {
+ -fx-text-fill: rgb(250, 250, 250);
+}
\ No newline at end of file
diff --git a/Gradle Project for Netbeans/src/main/java/resources/UIText.properties b/Gradle Project for Netbeans/src/main/java/resources/UIText.properties
new file mode 100644
index 0000000..6145291
--- /dev/null
+++ b/Gradle Project for Netbeans/src/main/java/resources/UIText.properties
@@ -0,0 +1,239 @@
+BinBorderConfigurationBox.addButton.text=Add
+BinBorderConfigurationBox.addButton.tooltipText=Add a new BinBorderConfigurationBox under this one
+BinBorderConfigurationBox.removeButton.text=Remove
+BinBorderConfigurationBox.removeButton.tooltipText=Remove this BinBorderConfigurationBox
+
+BinBorderConfigurationDialog.Title.text=Bin border configuration
+BinBorderConfigurationDialog.Header.text=Specify the bin borders
+BinBorderConfigurationDialog.resetButton.text=Reset
+BinBorderConfigurationDialog.resetButton.tooltipText=Reset the bin borders to their original number and to their original values (state at the time of the opening of this dialog)
+
+ChartConfigurationDialog.lowerBinBorderLabel.text=Lower binning border
+ChartConfigurationDialog.upperBinBorderLabel.text=Upper binning border
+ChartConfigurationDialog.lowerFrequencyBoundLabel.text=Lower frequency bound
+ChartConfigurationDialog.upperFrequencyBoundLabel.text=Upper frequency bound
+ChartConfigurationDialog.resetButton.text=Reset
+ChartConfigurationDialog.resetButton.tooltipText=Reset all configurations to their initial state (state at the time of the opening of this dialog)
+ChartConfigurationDialog.defaultButton.text=Default
+ChartConfigurationDialog.defaultButton.tooltipText=Reset all configurations to their default state (state at the time of the creation of the chart)
+ChartConfigurationDialog.Title.text=Output%s: Chart configuration
+ChartConfigurationDialog.Header.text=Configure the %s-chart
+ChartConfigurationDialog.lowerBinBorderInputField.tooltipText=Set the lower border of the first bin
+ChartConfigurationDialog.upperBinBorderInputField.tooltipText=Set the upper border of the last bin
+ChartConfigurationDialog.lowerFrequencyBoundInputField.tooltipText=Set the lower bound for the frequency range that will be displayed
+ChartConfigurationDialog.upperFrequencyBoundInputField.tooltipText=Set the upper bound for the frequency range that will be displayed
+
+ConfigurationDialog.Header.text=Configure
+ConfigurationDialog.applyButtonType.text=Apply
+ConfigurationDialog.applyButton.tooltipText=Apply all valid configurations
+ConfigurationDialog.cancelButtonType.text=Cancel
+ConfigurationDialog.cancelButton.tooltipText=Close this dialog and apply no configurations
+
+ConfirmationDialog.ClosingTitle.text=Confirm closing
+ConfirmationDialog.SelectionTitle.text=Confirm selection
+ConfirmationDialog.ClosingApplicationHeader.text=You are about to close the application
+ConfirmationDialog.ClosingApplicationContent.text=Do you really want to close the application?
+ConfirmationDialog.ClosingInputTabHeader.text=This job is still working
+ConfirmationDialog.ClosingInputTabContent.text=Do you still want to close this input tab?
+ConfirmationDialog.ClosingOutputTabHeader.text=This job is not saved
+ConfirmationDialog.ClosingOutputTabContent.text=Do you still want to close this output tab?
+ConfirmationDialog.ManyBinsHeader.text=The given number of bins is %s. Therefore the binning could take a while
+ConfirmationDialog.ManyBinsContent.text=Do you still want to use this amount of bins?
+ConfirmationDialog.DirectoryAlreadyExistsHeader.text=The selected directory already contains some files. These may be overwritten
+ConfirmationDialog.DirectoryAlreadyExistsContent.text=Do you still want to use this directory?
+ConfirmationDialog.Yes.text=Yes
+ConfirmationDialog.No.text=No
+
+ErrorAlertDialog.Header.text=An error has occured while calling: %s
+ErrorAlertDialog.Title.text=Warning: Exception
+
+ErrorDescription.WrongVersion.text=Found version: %s%nNecessary version: %s
+ErrorDescription.ScreenTooSmall.text=The screen size is too small for this application
+ErrorDescription.CanNotInstantiatePreferences.text=Preferences could not be instantiated
+ErrorDescription.InvalidComparisonFeatureSelection.text=Invalid ComparisonFeature selection. Please select something else
+ErrorDescription.InvalidBinLabelTypeSelection.text=Invalid bin label type selection. Please select something else
+ErrorDescription.NoDataForComparisonFeature.text=No data for the given ComparisonFeature is accessible
+ErrorDescription.ChartCreationFailed.text=Could not create the %s chart
+ErrorDescription.NotSingleInstance.text=Another MSC application seems to be already running.\nIf this not the case try to delete the MSC_SingleInstance.lck\nfile in the directory:
+ErrorDescription.CanNotCreateDirectory.text=The given directory does not exist and can't be created
+
+FileChooserTitle.SaveChart.text=Select a file where to save the chart as an image
+FileChooserTitle.SaveOutput.text=Select a folder where the output files will be saved
+FileChooserTitle.LoadOutput.text=Select a folder from where the output files will be loaded
+FileChooserTitle.DefaultInputDirectory.text=Select a default input directory
+FileChooserTitle.DefaultOutputDirectory.text=Select a default output directory
+FileChooserTitle.DefaultImageDirectory.text=Select a default image directory
+FileChooserTitle.DefaultMoleculeListDirectory.text=Select a default molecule list directory
+FileChooserTitle.DefaultSummaryReportDirectory.text=Select a default summary report directory
+FileChooserTitle.MoleculeFile.text=Select a file that contains a molecule set
+FileChooserTitle.MoleculeList.text=Select a file where to save the molecule list
+FileChooserTitle.SaveSummaryReport.text=Select a file where to save the summary report
+
+FileExtensionFilter.All.text=All
+FileExtensionFilter.Text.text=Text
+FileExtensionFilter.pdf.text=PDF
+FileExtensionFilter.png.text=PNG
+FileExtensionFilter.jpeg.text=JPEG
+FileExtensionFilter.svg.text=SVG
+FileExtensionFilter.xml.text=XML
+
+InfoDescription.SavingNotPossible.text=Saving the input is not possible
+InfoDescription.FileNotWritable.text=Writing to this file is not possible
+InfoDescription.FileNotReadable.text=Reading from this file is not possible
+InfoDescription.DesktopNotSupported.text=Desktop is not supported, log file can't be shown
+InfoDescription.LogFileNotReadable.text=Log file can't be read
+InfoDescription.ReadingInputCanceled.text=Reading input was canceled
+InfoDescription.ReadingInputFailed.text=Reading the input failed
+InfoDescription.NoComparisonFeatureChosen.text=Please choose a ComparisonFeature first
+InfoDescription.ChartPlaceHolder.text=Could not create the chart for%n the ComparisonFeature %s.%nThis is just a placeholder
+InfoDescription.UnpairedStrings.text=One input file contains %s more input string(s) than the other
+InfoDescription.NoMoleculesPairs.text=There were no molecule pairs loaded for this bin
+InfoDescription.FileFormatNotSupported.text=The chosen file format is not supported
+InfoDescription.InputConfigurationNotReadable.text=Can't read this input configuration. Please try again
+InfoDescription.JobStillWorking.text=This job is still working
+InfoDescription.About.text=MSC Version %s%n%nDeveloped and managed by Jan-Mathis Hein%n%nMany thanks to Kohulan Rajan, Christoph%nSteinbeck, Achim Zielesny and the communities%nthat created the open libraries%n%nThe MSC is published under the GNU GPL V3%n%nThe source code is available at GitHub%n(https://github.com/zielesny/MSC)
+InfoDescription.JobStarted.text=The job has been started
+InfoDescription.StartingJobFailed.text=Starting the job failed
+InfoDescription.JobFinished.text=The job has been finished
+InfoDescription.NewJob.text=A new job has been created
+InfoDescription.JobCanceled.text=The job has been canceled
+InfoDescription.ReadingInputProgress.text=Comparing molecules: %d%%
+InfoDescription.InputFile1.text=The first input file has been chosen
+InfoDescription.InputFile2.text=The second input file has been chosen
+InfoDescription.xFeaturesSelected.text=%d comparison features are selected
+InfoDescription.noFeaturesSelected.text=No comparison features are selected
+InfoDescription.InvalidBinBorders.text=The given bin borders are invalid and can't be applied
+InfoDescription.RelativeFrequencyTooHigh.text=The given relative frequency of %f is too high and will not be used
+InfoDescription.NumberInputTooHigh.text=The given numeric input is too high and can't be parsed and will thus not be used
+
+InfoDialog.Title.text=Information
+InfoDialog.AboutTitle.text=Application information
+
+InputTab.title.text=Input
+InputTab.selectAllComparisonFeaturesButton.text=All
+InputTab.selectAllComparisonFeaturesButton.tooltipText=Select all ComparisonFeatures
+InputTab.reverseComparisonFeatureSelectionButton.text=Reverse
+InputTab.reverseComparisonFeatureSelectionButton.tooltipText=Reverse all selections
+InputTab.selectAllCheckBox.text=Select all
+InputTab.selectAllCheckBox.tooltipText=Select/Deselect all check boxes of this section
+InputTab.jobStartButton.text=Start
+InputTab.jobStartButton.tooltipText=Start the reading and comparing of the two molecule sets
+InputTab.chooseFile1Button.text=Choose File
+InputTab.chooseFile1Button.tooltipText=Choose the file that contains the first molecule set
+InputTab.inputType1ChoiceBox.tooltipText=Select the encoding used for the first molecule set
+InputTab.inputType2ChoiceBox.tooltipText=Select the encoding used for the second molecule set
+InputTab.chooseFile2Button.text=Choose File
+InputTab.chooseFile2Button.tooltipText=Choose the file that contains the second molecule set
+InputTab.inputFile1Label.text=Filename:
+InputTab.inputFile2Label.text=Filename:
+InputTab.jobCancelButton.text=Cancel
+InputTab.jobCancelButton.tooltipText=Cancel the currently ongoing process
+InputTab.comparisonFeatureButtonsTitlePane.text=General
+InputTab.tanimotoTitledPane.text=Tanimoto
+InputTab.atomCountsTitledPane.text=Atom counts
+InputTab.bondCountsTitledPane.text=Bond counts
+InputTab.functionalGroupCountsTitledPane.text=Group counts
+InputTab.logPValuesTitledPane.text=LogP values
+InputTab.autocorrelationTitledPane.text=Autocorrelation
+InputTab.electricsDescriptorsTitledPane.text=Electronic descriptors
+InputTab.chiIndicesTitledPane.text=Chi indices
+InputTab.miscellaneousTitledPane.text=Miscellaneous
+
+Logging.ApplicationStart.text=The application has been started
+Logging.NewLoggingSession.text=A new logging session has been started
+Logging.UnexptectedPropertyChange.text=Unexpected PropertyChange: %s
+Logging.CompareBeforeReadingInput.text=Tried to compare sets before reading them
+Logging.InvalidComparisonFeatureSelection.text=An invalid ComparisonFeature has been chosen
+Logging.InvalidBinLabelTypeSelection.text=An invalid bin label type has been chosen
+Logging.PreferencesSavingNotPossible.text=The user preferences could not be saved
+Logging.PreferencesLoadingNotPossible.text=The user preferences could not be loaded
+Logging.ApplicationClosed.text=The application has been closed
+
+MainView.title.text=Molecule Set Comparator
+MainView.fileMenu.text=File
+MainView.saveJobMenuItem.text=Save
+MainView.loadJobOutputMenuItem.text=Load
+MainView.newJobMenuItem.text=New
+MainView.preferencesMenu.text=Preferences
+MainView.inputDirectoryMenuItem.text=Input directory
+MainView.outputDirectoryMenuItem.text=Output directory
+MainView.imageDirectoryMenuItem.text=Image directory
+MainView.moleculeListDirectoryMenuItem.text=Molecule list directory
+MainView.summaryReportDirectoryMenuItem.text=Summary report directory
+MainView.otherPreferencesMenuItem.text=Others
+MainView.logMenu.text=Logging
+MainView.browseLogMenuItem.text=Browse
+MainView.resetLogMenuItem.text=Reset
+MainView.maxButton.text=Large
+MainView.maxButton.tooltipText=Maximize the application window
+MainView.minButton.text=Small
+MainView.minButton.tooltipText=Minimize the application window
+MainView.centerButton.text=Center
+MainView.centerButton.tooltipText=Put the application window in the center of the screen
+MainView.jobMenu.text=Job
+MainView.directoryMenu.text=Directories
+MainView.helpMenu.text=Help
+MainView.aboutMenuItem.text=About
+
+MoleculePairDisplayerStage.title.text=Molecule pairs of bin %s
+MoleculePairDisplayerStage.saveLeftListButton.text=L list
+MoleculePairDisplayerStage.saveLeftListButton.tooltipText=Save the left list of molecules
+MoleculePairDisplayerStage.saveRightListButton.text=R list
+MoleculePairDisplayerStage.saveRightListButton.tooltipText=Save the right list of molecules
+MoleculePairDisplayerStage.saveLeftImageButton.text=L image
+MoleculePairDisplayerStage.saveLeftImageButton.tooltipText=Save the molecule image on the left
+MoleculePairDisplayerStage.saveRightImageButton.text=R image
+MoleculePairDisplayerStage.saveRightImageButton.tooltipText=Save the molecule image on the right
+MoleculePairDisplayerStage.highlightDifferencesCheckBox.text=Highlight
+MoleculePairDisplayerStage.highlightDifferencesCheckBox.tooltipText=Graphically highlight the molecule pair's differences
+MoleculePairDisplayerStage.firstButton.text=|<
+MoleculePairDisplayerStage.firstButton.tooltipText=Go to the first molecule pair
+MoleculePairDisplayerStage.previousButton.text=<
+MoleculePairDisplayerStage.previousButton.tooltipText=Go to the previous molecule pair
+MoleculePairDisplayerStage.nextButton.text=>
+MoleculePairDisplayerStage.nextButton.tooltipText=Go to the next molecule pair
+MoleculePairDisplayerStage.lastButton.text=>|
+MoleculePairDisplayerStage.lastButton.tooltipText=Go to the last molecule pair
+MoleculePairDisplayerStage.positionTextField.tooltipText=Press enter to go the specified molecule pair
+MoleculePairDisplayerStage.additionalComparisonFeatureCheckBox.tooltipText=Calculate and display the similarity of the currently shown molecule pair based on this ComparisonFeature
+MoleculePairDisplayerStage.infoLabel.text=Used ComparisonFeature: %s%nNumber of displayed pairs: %d%nFrequency value of this bin: %s%nLower bin border: %s%nUpper bin border: %s%nSMILES of the first molecule: %s%nSMILES of the second molecule: %s%nComparison result: %f
+
+OutputTab.title.text=Output
+OutputTab.summaryReportButton.text=Summarize
+OutputTab.summaryReportButton.tooltipText=Create and save a short summary report for this job result
+OutputTab.saveButton.text=Image
+OutputTab.saveButton.tooltipText=Save this chart as an image
+OutputTab.configureButton.text=Configure
+OutputTab.configureButton.tooltipText=Open the configuration dialog for charts
+OutputTab.binBorderConfigurationButton.text=Bin borders
+OutputTab.binBorderConfigurationButton.tooltipText=Open a dialog with which all bin borders can explicity be specified
+OutputTab.infoLabel.text=Chart: %s%nNumber of pairs: %d%nInput files: %n%s, %n%s
+OutputTab.xAxisLabel.text=Bins
+OutputTab.yAxisLabel.text=Frequency
+OutputTab.numberOfBinsLabel.text=Number of bins:
+OutputTab.binBorderSlidersLabel.text=Upper and lower bin border:
+OutputTab.frequencySlidersLabel.text=Frequency range:
+OutputTab.chartChoiceBox.tooltipText=Select a ComparisonFeature whose chart will be displayed
+OutputTab.binLabelChoiceBox.tooltipText=Select a bin label type which will be used to label the bins in the chart
+OutputTab.binBorderSlider.tooltipText=Move the slider to change the lower and upper bin border of the first and last bin respectively
+OutputTab.frequencySlider.tooltipText=Move the slider to change the displayed range of the y axis
+OutputTab.numberOfBinsTextField.tooltipText=Set the number of bins for this histogram
+OutputTab.relativeFrequenciesCheckBox.text=Rel. Freq.
+OutputTab.relativeFrequenciesCheckBox.tooltipText=If this is selected all returned and inputted frequencies will be given in relative terms, otherwise in absolute terms
+OutputTab.barLabelCheckBox.text=Bar labels
+OutputTab.barLabelCheckBox.tooltipText=If this is selected all bars will be labeled with their respective y-value
+
+PreferencesConfigurationDialog.title.text=Other preferences
+PreferencesConfigurationDialog.Header.text=Configure the preferences
+PreferencesConfigurationDialog.numberOfParallelThreadsLabel.text=Parallel threads
+PreferencesConfigurationDialog.defaultNumberOfBinsLabel.text=Number of bins
+PreferencesConfigurationDialog.maximalNumberOfMoleculePairsToSaveLabel.text=Pairs to save
+PreferencesConfigurationDialog.imageQualityLabel.text=Image quality
+PreferencesConfigurationDialog.resetButton.text=Reset
+PreferencesConfigurationDialog.resetButton.tooltipText=Reset all preferences to their initial state (state at the time of the opening of this dialog)
+PreferencesConfigurationDialog.numberOfParallelThreadsField.tooltipText=Set the number of threads that will be used concurrently for calculations
+PreferencesConfigurationDialog.defaultNumberOfBinsField.tooltipText=Set the default number of bins a histogram will have
+PreferencesConfigurationDialog.maximalNumberOfMoleculePairsToSaveField.tooltipText=Set the number of molecule pairs that will be saved when a job is being saved
+PreferencesConfigurationDialog.imageQualitySlider.tooltipText=Set the image quality preference where 0 and 1 represent low and high quality respectively
+
+SavingJob.InfoFile.text=The files \"%s\", \"%s\" and \"%s\" should not be %nrenamed or removed. This whole folder can be %nmoved anywhere and can also be renamed. %nEvery saved job has to have its own folder
\ No newline at end of file
diff --git a/Gradle Project for Netbeans/src/test/java/de/whs/ibci/msc/model/GeneralTestSuite.java b/Gradle Project for Netbeans/src/test/java/de/whs/ibci/msc/model/GeneralTestSuite.java
new file mode 100644
index 0000000..73ea621
--- /dev/null
+++ b/Gradle Project for Netbeans/src/test/java/de/whs/ibci/msc/model/GeneralTestSuite.java
@@ -0,0 +1,34 @@
+/*
+ * Copyright (C) 2019 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+
+/**
+ * Test suite that combines all test classes
+ *
+ * @author Jan-Mathis Hein
+ */
+@RunWith(Suite.class)
+@Suite.SuiteClasses({
+ de.whs.ibci.msc.model.ParseAndCompareTaskTest.class,
+ de.whs.ibci.msc.model.HistogramDataManagerTest.class
+})
+public class GeneralTestSuite {
+
+}
diff --git a/Gradle Project for Netbeans/src/test/java/de/whs/ibci/msc/model/HistogramDataManagerTest.java b/Gradle Project for Netbeans/src/test/java/de/whs/ibci/msc/model/HistogramDataManagerTest.java
new file mode 100644
index 0000000..965a057
--- /dev/null
+++ b/Gradle Project for Netbeans/src/test/java/de/whs/ibci/msc/model/HistogramDataManagerTest.java
@@ -0,0 +1,179 @@
+/*
+ * Copyright (C) 2019 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+import de.whs.ibci.msc.utility.MSCConstants;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.util.Collections;
+import org.junit.Test;
+import static org.junit.Assert.*;
+
+/**
+ * Test class of the HistogramDataManager class
+ *
+ * @author Jan-Mathis Hein
+ */
+public class HistogramDataManagerTest {
+
+ //
+ /**
+ * The tolerance used when two double values are compared. Every deviation
+ * that is smaller than this is still accepted as equal
+ */
+ private static final double TOLERANCE = 0.00001;
+
+ /**
+ * The histogram's expected bin borders
+ */
+ private static final double[] EXPECTED_BIN_BORDERS = {0, 0.8, 1.6, 2.4, 3.2, 4};
+
+ /**
+ * A HistogramDataManager instance on which the tests are done
+ */
+ private HistogramDataManager histogramDataManager;
+
+ /**
+ * The number of pairs that were added to the HistogramDataManager
+ */
+ private final int numberOfPairs;
+
+ /**
+ * The histogram's expected frequency data
+ */
+ private static final int[] EXPECTED_FREQUENCY_DATA = {1, 0, 0, 6, 1};
+
+ /**
+ * The ComparisonFeature that is used in this test
+ */
+ private static final ComparisonFeature MOLECULAR_DESCRIPTOR = ComparisonFeature.ATOM_COUNT;
+ //
+ //
+ //
+ /**
+ * Initialize a HistogramDataManager and add some comparison results to it
+ *
+ * @throws java.lang.Exception
+ */
+ public HistogramDataManagerTest() throws Exception {
+ String[][] tmpInputPairs = {
+ {"CC\n", "CC\n"}, {"C\n", "CC\n"}, {"C\n", "CC\n"}, {"C\n", "CC\n"},
+ {"C\n", "CC\n"}, {"C\n", "CC\n"}, {"C\n", "CC\n"}
+ };
+ int tmpIdentifier = 0;
+ final boolean[] tmpCompareAspects = new boolean[ComparisonFeature.values().length];
+ tmpCompareAspects[HistogramDataManagerTest.MOLECULAR_DESCRIPTOR.getFeatureNumber()] = true;
+ ParseAndCompareTask tmpTask = new ParseAndCompareTask("CC\n", "OO\n", InputType.SMILES, InputType.SMILES, tmpCompareAspects, tmpIdentifier++);
+ tmpTask.call();
+ this.histogramDataManager = new HistogramDataManager(
+ Collections.singletonList(HistogramDataManagerTest.MOLECULAR_DESCRIPTOR),
+ HistogramDataManagerTest.EXPECTED_BIN_BORDERS.length - 1, tmpTask.getResult(),
+ "", ""
+ );
+ for (String[] tmpPair : tmpInputPairs) {
+ tmpTask = new ParseAndCompareTask(tmpPair[0], tmpPair[1], InputType.SMILES, InputType.SMILES, tmpCompareAspects, tmpIdentifier++);
+ tmpTask.call();
+ this.histogramDataManager.addDatum(tmpTask.getResult());
+ }
+ this.numberOfPairs = tmpIdentifier;
+ }
+ //
+ //
+ //
+ /**
+ * Test of binData method, of class HistogramDataManager. Also assert that
+ * the borders, the number of added data and the histogram data are as
+ * expected
+ */
+ @Test
+ public void testBinDataAndCheckResults() {
+ this.histogramDataManager.getHistogramData(HistogramDataManagerTest.MOLECULAR_DESCRIPTOR).call();
+ assertEquals("Test number of added data", this.numberOfPairs, this.histogramDataManager.getNumberOfComparedPairs());
+ for (int i = 0; i < HistogramDataManagerTest.EXPECTED_BIN_BORDERS.length; i++) {
+ assertEquals(
+ "Test bin border " + Integer.toString(i),
+ HistogramDataManagerTest.EXPECTED_BIN_BORDERS[i],
+ this.histogramDataManager.getHistogramData(HistogramDataManagerTest.MOLECULAR_DESCRIPTOR).getBinBorders()[i], TOLERANCE
+ );
+ }
+ for (int i = 0; i < HistogramDataManagerTest.EXPECTED_FREQUENCY_DATA.length; i++) {
+ assertEquals(
+ HistogramDataManagerTest.EXPECTED_FREQUENCY_DATA[i],
+ this.histogramDataManager.getHistogramData(HistogramDataManagerTest.MOLECULAR_DESCRIPTOR).getFrequencies()[i],
+ HistogramDataManagerTest.TOLERANCE
+ );
+ }
+ }
+
+ /**
+ * Test of the writeObject and readObject methods or rather the
+ * serialization and deserialization, of class HistogramDataManager. Also
+ * assert that the borders and the histogram data are as expected.
+ * NOTE: Created files and directories will normaly be deleted upon
+ * completion
+ *
+ * @throws IOException
+ * @throws ClassNotFoundException
+ */
+ @Test
+ public void testSerializationAndDeserialization() throws IOException, ClassNotFoundException {
+ File tmpTemporaryFile = new File(System.getProperty("user.dir") + File.separator + MSCConstants.OUTPUT_FILE_NAME);
+ try {
+ tmpTemporaryFile.createNewFile();
+ assertTrue("Test if file is readable", tmpTemporaryFile.canRead());
+ assertTrue("Test if file is writable", tmpTemporaryFile.canWrite());
+ try (
+ FileOutputStream tmpFileOutputStream = new FileOutputStream(tmpTemporaryFile);
+ ObjectOutputStream tmpObjectOutputStream = new ObjectOutputStream(tmpFileOutputStream)
+ ) {
+ tmpObjectOutputStream.writeObject(this.histogramDataManager);
+ }
+ this.histogramDataManager = null;
+ try (
+ FileInputStream tmpFileInputStream = new FileInputStream(tmpTemporaryFile);
+ ObjectInputStream tmpOutputStream = new ObjectInputStream(tmpFileInputStream)
+ ) {
+ this.histogramDataManager = (HistogramDataManager) tmpOutputStream.readObject();
+ }
+ this.histogramDataManager.getComparisonFeatureSet().forEach((ComparisonFeature tmpComparisonFeature) -> {
+ this.histogramDataManager.getHistogramData(tmpComparisonFeature).call();
+ });
+ for (int i = 0; i < HistogramDataManagerTest.EXPECTED_BIN_BORDERS.length; i++) {
+ assertEquals(
+ "Test bin border " + Integer.toString(i),
+ HistogramDataManagerTest.EXPECTED_BIN_BORDERS[i],
+ this.histogramDataManager.getHistogramData(HistogramDataManagerTest.MOLECULAR_DESCRIPTOR).getBinBorders()[i], TOLERANCE
+ );
+ }
+ for (int i = 0; i < HistogramDataManagerTest.EXPECTED_FREQUENCY_DATA.length; i++) {
+ assertEquals(
+ HistogramDataManagerTest.EXPECTED_FREQUENCY_DATA[i],
+ this.histogramDataManager.getHistogramData(HistogramDataManagerTest.MOLECULAR_DESCRIPTOR).getFrequencies()[i],
+ HistogramDataManagerTest.TOLERANCE
+ );
+ }
+ } finally {
+ tmpTemporaryFile.delete();
+ }
+ }
+ //
+
+}
diff --git a/Gradle Project for Netbeans/src/test/java/de/whs/ibci/msc/model/ParseAndCompareTaskTest.java b/Gradle Project for Netbeans/src/test/java/de/whs/ibci/msc/model/ParseAndCompareTaskTest.java
new file mode 100644
index 0000000..90589e9
--- /dev/null
+++ b/Gradle Project for Netbeans/src/test/java/de/whs/ibci/msc/model/ParseAndCompareTaskTest.java
@@ -0,0 +1,145 @@
+/*
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+import java.util.Arrays;
+import java.util.Collection;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameter;
+import org.junit.runners.Parameterized.Parameters;
+
+/**
+ * Test class of the ParseAndCompareTask class
+ *
+ * @author Jan-Mathis Hein
+ */
+@RunWith(Parameterized.class)
+public class ParseAndCompareTaskTest {
+
+ //
+ /**
+ * The tolerance used when two double values are compared. Every deviation
+ * that is smaller than this is still accepted as equal
+ */
+ private static final double TOLERANCE = 0.00001;
+ //
+ //
+ //
+ /**
+ * The first input molecule
+ */
+ @Parameter(0)
+ public String molecule1;
+
+ /**
+ * The second input molecule
+ */
+ @Parameter(1)
+ public String molecule2;
+
+ /**
+ * The first input type
+ */
+ @Parameter(2)
+ public InputType inputType1;
+
+ /**
+ * The second input type
+ */
+ @Parameter(3)
+ public InputType inputType2;
+
+ /**
+ * Defines which descriptors will be used for the molecule comparison
+ */
+ @Parameter(4)
+ public boolean[] useDescriptors;
+
+ /**
+ * The the expected results of the comparison
+ */
+ @Parameter(5)
+ public Double[] expectedResults;
+ //
+ //
+ //
+ /**
+ * Create the parameter sets that contain the inputs and the expected
+ * outputs that will be used for testing
+ *
+ * @return a collection where each item is an array that contains a
+ * parameter set
+ * @throws java.lang.Exception
+ */
+ @Parameters
+ public static Collection createParameterSets() throws Exception {
+ //
+ String tmpMolecule1 = "COC(N)CP\n";
+ String tmpMolecule2 = "COC(O)CS\n";
+ InputType tmpInputType1 = InputType.SMILES;
+ InputType tmpInputType2 = InputType.SMILES;
+ boolean[] tmpCompareAspects = new boolean[ComparisonFeature.values().length];
+ Double[] tmpExpectedResults = new Double[ComparisonFeature.values().length];
+ // If a result is not set, that descriptor will not be used
+ tmpExpectedResults[ComparisonFeature.TANIMOTO_BASIC_FINGERPRINTER.getFeatureNumber()] = 0.277777;
+ tmpExpectedResults[ComparisonFeature.ATOM_COUNT.getFeatureNumber()] = 2.0;
+ tmpExpectedResults[ComparisonFeature.CARBON_COUNT.getFeatureNumber()] = 0.0;
+ tmpExpectedResults[ComparisonFeature.OXYGEN_COUNT.getFeatureNumber()] = 1.0;
+ tmpExpectedResults[ComparisonFeature.SULFUR_COUNT.getFeatureNumber()] = 1.0;
+ tmpExpectedResults[ComparisonFeature.NITROGEN_COUNT.getFeatureNumber()] = 1.0;
+ tmpExpectedResults[ComparisonFeature.PHOSPHOR_COUNT.getFeatureNumber()] = 1.0;
+ tmpExpectedResults[ComparisonFeature.MOLECULAR_WEIGHT.getFeatureNumber()] = 1.069143575;
+ for (int i = 0; i < tmpExpectedResults.length; i++) {
+ tmpCompareAspects[i] = tmpExpectedResults[i] != null;
+ }
+ //
+ Object[][] tmpData = {
+ {tmpMolecule1, tmpMolecule2, tmpInputType1, tmpInputType2, tmpCompareAspects, tmpExpectedResults}
+ };
+ return Arrays.asList(tmpData);
+ }
+
+ /**
+ * Test of call method, of class ParseAndCompareTask. Also assert that the
+ * results and state of the task are as expected
+ */
+ @Test
+ public void testCall() throws Exception {
+ ParseAndCompareTask tmpTask = new ParseAndCompareTask(this.molecule1, this.molecule2, this.inputType1, this.inputType2, this.useDescriptors, 0);
+ tmpTask.call();
+ assertFalse("Test if this is working", tmpTask.isWorking());
+ assertTrue("Test if this is finished", tmpTask.isFinished());
+ assertTrue("Test if this was started", tmpTask.isStarted());
+ ComparisonResult tmpResult = tmpTask.getResult();
+ assertEquals("Test for exceptions that occured during comparing", tmpResult.getReasonOfFailure(), "");
+ Arrays.stream(ComparisonFeature.values()).filter((ComparisonFeature descriptor) -> this.useDescriptors[descriptor.getFeatureNumber()]).forEach((ComparisonFeature descriptor) -> {
+ assertEquals(
+ "Test " + descriptor.toString(),
+ tmpTask.getResult().getSimilarities()[descriptor.getFeatureNumber()],
+ this.expectedResults[descriptor.getFeatureNumber()],
+ ParseAndCompareTaskTest.TOLERANCE
+ );
+ });
+ }
+ //
+
+}
diff --git a/README.md b/README.md
index 1204b14..9a1151d 100644
--- a/README.md
+++ b/README.md
@@ -1,2 +1,29 @@
-# MSC
-Molecule Set Comparator (MSC)
+# Molecule Set Comparator (MSC)
+The open rich-client Molecule Set Comparator (MSC) application enables a versatile and fast comparison of large molecule sets with a unique inter-set molecule-to-molecule mapping obtained e.g. by machine learning approaches. The molecule-to-molecule comparison is based on chemical descriptors obtained with the Chemistry Development Kit (CDK), such as Tanimoto similarities, atom/bond/ring counts or physicochemical properties like logP. The results are presented graphically and summarized by interactive histograms that can be exported in publication quality.
+
+MSC is currently under scientific review - more information will be available soon.
+
+
+
+## Contents of subfolders
+
+- ***Tutorial*** - short introductory PDF document for MSC usage
+
+- ***src*** - all Java source files and resources
+
+- ***lib*** - open libraries used by MSC
+
+- ***installation*** - contains installation folder *MSC_1.0* to be copied to a local machine for MSC execution. Note, that an additional JDK download is necessary (see instructions in text file *JDK download info.txt* in subdirectory *jdk-11.0.2*)
+
+- ***Gradle Project for Netbeans*** - Gradle project for Netbeans IDE (JDK 11 or higher)
+ - To compile MSC, execute command *gradlew compileJava*
+ - To test MSC, execute *gradlew test*
+ - To create a JAR file of MSC, execute *gradlew jar*
+ - To create an executable "fat" JAR file for MSC, execute *gradlew fatJar*
+ - To create the MSC javadoc, execute *gradlew javadoc*
+ - To run MSC, execute *gradlew run*
+ - To delete the project build directory, execute *gradlew clean*
+
+
+## Notes
+- MSC is not modularized due to its non-modularized library dependencies.
\ No newline at end of file
diff --git a/Tutorial/MSC_1.0_Tutorial.pdf b/Tutorial/MSC_1.0_Tutorial.pdf
new file mode 100644
index 0000000..e1989fd
Binary files /dev/null and b/Tutorial/MSC_1.0_Tutorial.pdf differ
diff --git a/installation/MSC_1.0/Licenses/ApacheLicensev2.0.txt b/installation/MSC_1.0/Licenses/ApacheLicensev2.0.txt
new file mode 100644
index 0000000..4947287
--- /dev/null
+++ b/installation/MSC_1.0/Licenses/ApacheLicensev2.0.txt
@@ -0,0 +1,177 @@
+
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
+
+ "License" shall mean the terms and conditions for use, reproduction,
+ and distribution as defined by Sections 1 through 9 of this document.
+
+ "Licensor" shall mean the copyright owner or entity authorized by
+ the copyright owner that is granting the License.
+
+ "Legal Entity" shall mean the union of the acting entity and all
+ other entities that control, are controlled by, or are under common
+ control with that entity. For the purposes of this definition,
+ "control" means (i) the power, direct or indirect, to cause the
+ direction or management of such entity, whether by contract or
+ otherwise, or (ii) ownership of fifty percent (50%) or more of the
+ outstanding shares, or (iii) beneficial ownership of such entity.
+
+ "You" (or "Your") shall mean an individual or Legal Entity
+ exercising permissions granted by this License.
+
+ "Source" form shall mean the preferred form for making modifications,
+ including but not limited to software source code, documentation
+ source, and configuration files.
+
+ "Object" form shall mean any form resulting from mechanical
+ transformation or translation of a Source form, including but
+ not limited to compiled object code, generated documentation,
+ and conversions to other media types.
+
+ "Work" shall mean the work of authorship, whether in Source or
+ Object form, made available under the License, as indicated by a
+ copyright notice that is included in or attached to the work
+ (an example is provided in the Appendix below).
+
+ "Derivative Works" shall mean any work, whether in Source or Object
+ form, that is based on (or derived from) the Work and for which the
+ editorial revisions, annotations, elaborations, or other modifications
+ represent, as a whole, an original work of authorship. For the purposes
+ of this License, Derivative Works shall not include works that remain
+ separable from, or merely link (or bind by name) to the interfaces of,
+ the Work and Derivative Works thereof.
+
+ "Contribution" shall mean any work of authorship, including
+ the original version of the Work and any modifications or additions
+ to that Work or Derivative Works thereof, that is intentionally
+ submitted to Licensor for inclusion in the Work by the copyright owner
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+ to the Licensor or its representatives, including but not limited to
+ communication on electronic mailing lists, source code control systems,
+ and issue tracking systems that are managed by, or on behalf of, the
+ Licensor for the purpose of discussing and improving the Work, but
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+
+ "Contributor" shall mean Licensor and any individual or Legal Entity
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+
+ 2. Grant of Copyright License. Subject to the terms and conditions of
+ this License, each Contributor hereby grants to You a perpetual,
+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable
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+
+ 3. Grant of Patent License. Subject to the terms and conditions of
+ this License, each Contributor hereby grants to You a perpetual,
+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+ (except as stated in this section) patent license to make, have made,
+ use, offer to sell, sell, import, and otherwise transfer the Work,
+ where such license applies only to those patent claims licensable
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+ Contribution(s) alone or by combination of their Contribution(s)
+ with the Work to which such Contribution(s) was submitted. If You
+ institute patent litigation against any entity (including a
+ cross-claim or counterclaim in a lawsuit) alleging that the Work
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+ 4. Redistribution. You may reproduce and distribute copies of the
+ Work or Derivative Works thereof in any medium, with or without
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+ meet the following conditions:
+
+ (a) You must give any other recipients of the Work or
+ Derivative Works a copy of this License; and
+
+ (b) You must cause any modified files to carry prominent notices
+ stating that You changed the files; and
+
+ (c) You must retain, in the Source form of any Derivative Works
+ that You distribute, all copyright, patent, trademark, and
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+ excluding those notices that do not pertain to any part of
+ the Derivative Works; and
+
+ (d) If the Work includes a "NOTICE" text file as part of its
+ distribution, then any Derivative Works that You distribute must
+ include a readable copy of the attribution notices contained
+ within such NOTICE file, excluding those notices that do not
+ pertain to any part of the Derivative Works, in at least one
+ of the following places: within a NOTICE text file distributed
+ as part of the Derivative Works; within the Source form or
+ documentation, if provided along with the Derivative Works; or,
+ within a display generated by the Derivative Works, if and
+ wherever such third-party notices normally appear. The contents
+ of the NOTICE file are for informational purposes only and
+ do not modify the License. You may add Your own attribution
+ notices within Derivative Works that You distribute, alongside
+ or as an addendum to the NOTICE text from the Work, provided
+ that such additional attribution notices cannot be construed
+ as modifying the License.
+
+ You may add Your own copyright statement to Your modifications and
+ may provide additional or different license terms and conditions
+ for use, reproduction, or distribution of Your modifications, or
+ for any such Derivative Works as a whole, provided Your use,
+ reproduction, and distribution of the Work otherwise complies with
+ the conditions stated in this License.
+
+ 5. Submission of Contributions. Unless You explicitly state otherwise,
+ any Contribution intentionally submitted for inclusion in the Work
+ by You to the Licensor shall be under the terms and conditions of
+ this License, without any additional terms or conditions.
+ Notwithstanding the above, nothing herein shall supersede or modify
+ the terms of any separate license agreement you may have executed
+ with Licensor regarding such Contributions.
+
+ 6. Trademarks. This License does not grant permission to use the trade
+ names, trademarks, service marks, or product names of the Licensor,
+ except as required for reasonable and customary use in describing the
+ origin of the Work and reproducing the content of the NOTICE file.
+
+ 7. Disclaimer of Warranty. Unless required by applicable law or
+ agreed to in writing, Licensor provides the Work (and each
+ Contributor provides its Contributions) on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ implied, including, without limitation, any warranties or conditions
+ of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+ PARTICULAR PURPOSE. You are solely responsible for determining the
+ appropriateness of using or redistributing the Work and assume any
+ risks associated with Your exercise of permissions under this License.
+
+ 8. Limitation of Liability. In no event and under no legal theory,
+ whether in tort (including negligence), contract, or otherwise,
+ unless required by applicable law (such as deliberate and grossly
+ negligent acts) or agreed to in writing, shall any Contributor be
+ liable to You for damages, including any direct, indirect, special,
+ incidental, or consequential damages of any character arising as a
+ result of this License or out of the use or inability to use the
+ Work (including but not limited to damages for loss of goodwill,
+ work stoppage, computer failure or malfunction, or any and all
+ other commercial damages or losses), even if such Contributor
+ has been advised of the possibility of such damages.
+
+ 9. Accepting Warranty or Additional Liability. While redistributing
+ the Work or Derivative Works thereof, You may choose to offer,
+ and charge a fee for, acceptance of support, warranty, indemnity,
+ or other liability obligations and/or rights consistent with this
+ License. However, in accepting such obligations, You may act only
+ on Your own behalf and on Your sole responsibility, not on behalf
+ of any other Contributor, and only if You agree to indemnify,
+ defend, and hold each Contributor harmless for any liability
+ incurred by, or claims asserted against, such Contributor by reason
+ of your accepting any such warranty or additional liability.
+
+ END OF TERMS AND CONDITIONS
\ No newline at end of file
diff --git a/installation/MSC_1.0/Licenses/GPLv2.txt b/installation/MSC_1.0/Licenses/GPLv2.txt
new file mode 100644
index 0000000..533c344
--- /dev/null
+++ b/installation/MSC_1.0/Licenses/GPLv2.txt
@@ -0,0 +1,262 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
+by others will not reflect on the original authors' reputations.
+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
+everyone's free use or not licensed at all.
+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
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+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
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+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the source
+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
\ No newline at end of file
diff --git a/installation/MSC_1.0/Licenses/GPLv3.txt b/installation/MSC_1.0/Licenses/GPLv3.txt
new file mode 100644
index 0000000..31a1019
--- /dev/null
+++ b/installation/MSC_1.0/Licenses/GPLv3.txt
@@ -0,0 +1,611 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc.
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ TERMS AND CONDITIONS
+
+ 0. Definitions.
+
+ "This License" refers to version 3 of the GNU General Public License.
+
+ "Copyright" also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+
+ "The Program" refers to any copyrightable work licensed under this
+License. Each licensee is addressed as "you". "Licensees" and
+"recipients" may be individuals or organizations.
+
+ To "modify" a work means to copy from or adapt all or part of the work
+in a fashion requiring copyright permission, other than the making of an
+exact copy. The resulting work is called a "modified version" of the
+earlier work or a work "based on" the earlier work.
+
+ A "covered work" means either the unmodified Program or a work based
+on the Program.
+
+ To "propagate" a work means to do anything with it that, without
+permission, would make you directly or secondarily liable for
+infringement under applicable copyright law, except executing it on a
+computer or modifying a private copy. Propagation includes copying,
+distribution (with or without modification), making available to the
+public, and in some countries other activities as well.
+
+ To "convey" a work means any kind of propagation that enables other
+parties to make or receive copies. Mere interaction with a user through
+a computer network, with no transfer of a copy, is not conveying.
+
+ An interactive user interface displays "Appropriate Legal Notices"
+to the extent that it includes a convenient and prominently visible
+feature that (1) displays an appropriate copyright notice, and (2)
+tells the user that there is no warranty for the work (except to the
+extent that warranties are provided), that licensees may convey the
+work under this License, and how to view a copy of this License. If
+the interface presents a list of user commands or options, such as a
+menu, a prominent item in the list meets this criterion.
+
+ 1. Source Code.
+
+ The "source code" for a work means the preferred form of the work
+for making modifications to it. "Object code" means any non-source
+form of a work.
+
+ A "Standard Interface" means an interface that either is an official
+standard defined by a recognized standards body, or, in the case of
+interfaces specified for a particular programming language, one that
+is widely used among developers working in that language.
+
+ The "System Libraries" of an executable work include anything, other
+than the work as a whole, that (a) is included in the normal form of
+packaging a Major Component, but which is not part of that Major
+Component, and (b) serves only to enable use of the work with that
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+"Major Component", in this context, means a major essential component
+(kernel, window system, and so on) of the specific operating system
+(if any) on which the executable work runs, or a compiler used to
+produce the work, or an object code interpreter used to run it.
+
+ The "Corresponding Source" for a work in object code form means all
+the source code needed to generate, install, and (for an executable
+work) run the object code and to modify the work, including scripts to
+control those activities. However, it does not include the work's
+System Libraries, or general-purpose tools or generally available free
+programs which are used unmodified in performing those activities but
+which are not part of the work. For example, Corresponding Source
+includes interface definition files associated with source files for
+the work, and the source code for shared libraries and dynamically
+linked subprograms that the work is specifically designed to require,
+such as by intimate data communication or control flow between those
+subprograms and other parts of the work.
+
+ The Corresponding Source need not include anything that users
+can regenerate automatically from other parts of the Corresponding
+Source.
+
+ The Corresponding Source for a work in source code form is that
+same work.
+
+ 2. Basic Permissions.
+
+ All rights granted under this License are granted for the term of
+copyright on the Program, and are irrevocable provided the stated
+conditions are met. This License explicitly affirms your unlimited
+permission to run the unmodified Program. The output from running a
+covered work is covered by this License only if the output, given its
+content, constitutes a covered work. This License acknowledges your
+rights of fair use or other equivalent, as provided by copyright law.
+
+ You may make, run and propagate covered works that you do not
+convey, without conditions so long as your license otherwise remains
+in force. You may convey covered works to others for the sole purpose
+of having them make modifications exclusively for you, or provide you
+with facilities for running those works, provided that you comply with
+the terms of this License in conveying all material for which you do
+not control copyright. Those thus making or running the covered works
+for you must do so exclusively on your behalf, under your direction
+and control, on terms that prohibit them from making any copies of
+your copyrighted material outside their relationship with you.
+
+ Conveying under any other circumstances is permitted solely under
+the conditions stated below. Sublicensing is not allowed; section 10
+makes it unnecessary.
+
+ 3. Protecting Users' Legal Rights From Anti-Circumvention Law.
+
+ No covered work shall be deemed part of an effective technological
+measure under any applicable law fulfilling obligations under article
+11 of the WIPO copyright treaty adopted on 20 December 1996, or
+similar laws prohibiting or restricting circumvention of such
+measures.
+
+ When you convey a covered work, you waive any legal power to forbid
+circumvention of technological measures to the extent such circumvention
+is effected by exercising rights under this License with respect to
+the covered work, and you disclaim any intention to limit operation or
+modification of the work as a means of enforcing, against the work's
+users, your or third parties' legal rights to forbid circumvention of
+technological measures.
+
+ 4. Conveying Verbatim Copies.
+
+ You may convey verbatim copies of the Program's source code as you
+receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice;
+keep intact all notices stating that this License and any
+non-permissive terms added in accord with section 7 apply to the code;
+keep intact all notices of the absence of any warranty; and give all
+recipients a copy of this License along with the Program.
+
+ You may charge any price or no price for each copy that you convey,
+and you may offer support or warranty protection for a fee.
+
+ 5. Conveying Modified Source Versions.
+
+ You may convey a work based on the Program, or the modifications to
+produce it from the Program, in the form of source code under the
+terms of section 4, provided that you also meet all of these conditions:
+
+ a) The work must carry prominent notices stating that you modified
+ it, and giving a relevant date.
+
+ b) The work must carry prominent notices stating that it is
+ released under this License and any conditions added under section
+ 7. This requirement modifies the requirement in section 4 to
+ "keep intact all notices".
+
+ c) You must license the entire work, as a whole, under this
+ License to anyone who comes into possession of a copy. This
+ License will therefore apply, along with any applicable section 7
+ additional terms, to the whole of the work, and all its parts,
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+unpacking, reading or copying.
+
+ 7. Additional Terms.
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+ "Additional permissions" are terms that supplement the terms of this
+License by making exceptions from one or more of its conditions.
+Additional permissions that are applicable to the entire Program shall
+be treated as though they were included in this License, to the extent
+that they are valid under applicable law. If additional permissions
+apply only to part of the Program, that part may be used separately
+under those permissions, but the entire Program remains governed by
+this License without regard to the additional permissions.
+
+ When you convey a copy of a covered work, you may at your option
+remove any additional permissions from that copy, or from any part of
+it. (Additional permissions may be written to require their own
+removal in certain cases when you modify the work.) You may place
+additional permissions on material, added by you to a covered work,
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+
+ Notwithstanding any other provision of this License, for material you
+add to a covered work, you may (if authorized by the copyright holders of
+that material) supplement the terms of this License with terms:
+
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+ author attributions in that material or in the Appropriate Legal
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+ All other non-permissive additional terms are considered "further
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+received it, or any part of it, contains a notice stating that it is
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+ Additional terms, permissive or non-permissive, may be stated in the
+form of a separately written license, or stated as exceptions;
+the above requirements apply either way.
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+ 8. Termination.
+
+ You may not propagate or modify a covered work except as expressly
+provided under this License. Any attempt otherwise to propagate or
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+this License (including any patent licenses granted under the third
+paragraph of section 11).
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+your receipt of the notice.
+
+ Termination of your rights under this section does not terminate the
+licenses of parties who have received copies or rights from you under
+this License. If your rights have been terminated and not permanently
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+
+ 9. Acceptance Not Required for Having Copies.
+
+ You are not required to accept this License in order to receive or
+run a copy of the Program. Ancillary propagation of a covered work
+occurring solely as a consequence of using peer-to-peer transmission
+to receive a copy likewise does not require acceptance. However,
+nothing other than this License grants you permission to propagate or
+modify any covered work. These actions infringe copyright if you do
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+covered work, you indicate your acceptance of this License to do so.
+
+ 10. Automatic Licensing of Downstream Recipients.
+
+ Each time you convey a covered work, the recipient automatically
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+propagate that work, subject to this License. You are not responsible
+for enforcing compliance by third parties with this License.
+
+ An "entity transaction" is a transaction transferring control of an
+organization, or substantially all assets of one, or subdividing an
+organization, or merging organizations. If propagation of a covered
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+
+ You may not impose any further restrictions on the exercise of the
+rights granted or affirmed under this License. For example, you may
+not impose a license fee, royalty, or other charge for exercise of
+rights granted under this License, and you may not initiate litigation
+(including a cross-claim or counterclaim in a lawsuit) alleging that
+any patent claim is infringed by making, using, selling, offering for
+sale, or importing the Program or any portion of it.
+
+ 11. Patents.
+
+ A "contributor" is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based. The
+work thus licensed is called the contributor's "contributor version".
+
+ A contributor's "essential patent claims" are all patent claims
+owned or controlled by the contributor, whether already acquired or
+hereafter acquired, that would be infringed by some manner, permitted
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+but do not include claims that would be infringed only as a
+consequence of further modification of the contributor version. For
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+patent sublicenses in a manner consistent with the requirements of
+this License.
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+patent license under the contributor's essential patent claims, to
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+agreement or commitment, however denominated, not to enforce a patent
+(such as an express permission to practice a patent or covenant not to
+sue for patent infringement). To "grant" such a patent license to a
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+patent against the party.
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+and the Corresponding Source of the work is not available for anyone
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+available, or (2) arrange to deprive yourself of the benefit of the
+patent license for this particular work, or (3) arrange, in a manner
+consistent with the requirements of this License, to extend the patent
+license to downstream recipients. "Knowingly relying" means you have
+actual knowledge that, but for the patent license, your conveying the
+covered work in a country, or your recipient's use of the covered work
+in a country, would infringe one or more identifiable patents in that
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+
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+arrangement, you convey, or propagate by procuring conveyance of, a
+covered work, and grant a patent license to some of the parties
+receiving the covered work authorizing them to use, propagate, modify
+or convey a specific copy of the covered work, then the patent license
+you grant is automatically extended to all recipients of the covered
+work and works based on it.
+
+ A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License. You may not convey a covered
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+in the business of distributing software, under which you make payment
+to the third party based on the extent of your activity of conveying
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+parties who would receive the covered work from you, a discriminatory
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+for and in connection with specific products or compilations that
+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+
+ Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+ 12. No Surrender of Others' Freedom.
+
+ If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all. For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+ 13. Use with the GNU Affero General Public License.
+
+ Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
+combined work, and to convey the resulting work. The terms of this
+License will continue to apply to the part which is the covered work,
+but the special requirements of the GNU Affero General Public License,
+section 13, concerning interaction through a network will apply to the
+combination as such.
+
+ 14. Revised Versions of this License.
+
+ The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
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+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+
+ Copyright (C)
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see .
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ Copyright (C)
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+.
\ No newline at end of file
diff --git a/installation/MSC_1.0/MSC_16GB_Linux.sh b/installation/MSC_1.0/MSC_16GB_Linux.sh
new file mode 100644
index 0000000..2ea433a
--- /dev/null
+++ b/installation/MSC_1.0/MSC_16GB_Linux.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+chmod -R a+rwx .
+./jdk-11.0.2/bin/java -Xmx16g -jar ./lib/MoleculeSetComparator-fat-1.0.jar
+exit
diff --git a/installation/MSC_1.0/MSC_16GB_Mac.sh b/installation/MSC_1.0/MSC_16GB_Mac.sh
new file mode 100644
index 0000000..c6ddc8f
--- /dev/null
+++ b/installation/MSC_1.0/MSC_16GB_Mac.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+chmod -R 777 .
+./jdk-11.0.2/Contents/Home/bin/java -Xmx16g -jar ./Libraries/MoleculeSetComparator-fat-1.0.jar
+exit
diff --git a/installation/MSC_1.0/MSC_16GB_Windows.bat b/installation/MSC_1.0/MSC_16GB_Windows.bat
new file mode 100644
index 0000000..d0ba8bc
--- /dev/null
+++ b/installation/MSC_1.0/MSC_16GB_Windows.bat
@@ -0,0 +1,4 @@
+if not DEFINED IS_MINIMIZED set IS_MINIMIZED=1 && start "" /min "%~dpnx0" %* && exit
+@echo off
+.\jdk-11.0.2\bin\java -Xmx16g -jar .\lib\MoleculeSetComparator-fat-1.0.jar
+exit
diff --git a/installation/MSC_1.0/MSC_1GB_Linux.sh b/installation/MSC_1.0/MSC_1GB_Linux.sh
new file mode 100644
index 0000000..3a55c1b
--- /dev/null
+++ b/installation/MSC_1.0/MSC_1GB_Linux.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+chmod -R a+rwx .
+./jdk-11.0.2/bin/java -Xmx1g -jar ./lib/MoleculeSetComparator-fat-1.0.jar
+exit
diff --git a/installation/MSC_1.0/MSC_1GB_Mac.sh b/installation/MSC_1.0/MSC_1GB_Mac.sh
new file mode 100644
index 0000000..2998db9
--- /dev/null
+++ b/installation/MSC_1.0/MSC_1GB_Mac.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+chmod -R 777 .
+./jdk-11.0.2/Contents/Home/bin/java -Xmx1g -jar ./Libraries/MoleculeSetComparator-fat-1.0.jar
+exit
diff --git a/installation/MSC_1.0/MSC_1GB_Windows.bat b/installation/MSC_1.0/MSC_1GB_Windows.bat
new file mode 100644
index 0000000..aa7faec
--- /dev/null
+++ b/installation/MSC_1.0/MSC_1GB_Windows.bat
@@ -0,0 +1,4 @@
+if not DEFINED IS_MINIMIZED set IS_MINIMIZED=1 && start "" /min "%~dpnx0" %* && exit
+@echo off
+.\jdk-11.0.2\bin\java -Xmx1g -jar .\lib\MoleculeSetComparator-fat-1.0.jar
+exit
diff --git a/installation/MSC_1.0/MSC_2GB_Linux.sh b/installation/MSC_1.0/MSC_2GB_Linux.sh
new file mode 100644
index 0000000..4744dd4
--- /dev/null
+++ b/installation/MSC_1.0/MSC_2GB_Linux.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+chmod -R a+rwx .
+./jdk-11.0.2/bin/java -Xmx2g -jar ./lib/MoleculeSetComparator-fat-1.0.jar
+exit
diff --git a/installation/MSC_1.0/MSC_2GB_Mac.sh b/installation/MSC_1.0/MSC_2GB_Mac.sh
new file mode 100644
index 0000000..a7292fc
--- /dev/null
+++ b/installation/MSC_1.0/MSC_2GB_Mac.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+chmod -R 777 .
+./jdk-11.0.2/Contents/Home/bin/java -Xmx2g -jar ./Libraries/MoleculeSetComparator-fat-1.0.jar
+exit
diff --git a/installation/MSC_1.0/MSC_2GB_Windows.bat b/installation/MSC_1.0/MSC_2GB_Windows.bat
new file mode 100644
index 0000000..81fd65c
--- /dev/null
+++ b/installation/MSC_1.0/MSC_2GB_Windows.bat
@@ -0,0 +1,4 @@
+if not DEFINED IS_MINIMIZED set IS_MINIMIZED=1 && start "" /min "%~dpnx0" %* && exit
+@echo off
+.\jdk-11.0.2\bin\java -Xmx2g -jar .\lib\MoleculeSetComparator-fat-1.0.jar
+exit
diff --git a/installation/MSC_1.0/MSC_32GB_Linux.sh b/installation/MSC_1.0/MSC_32GB_Linux.sh
new file mode 100644
index 0000000..0366ada
--- /dev/null
+++ b/installation/MSC_1.0/MSC_32GB_Linux.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+chmod -R a+rwx .
+./jdk-11.0.2/bin/java -Xmx32g -jar ./lib/MoleculeSetComparator-fat-1.0.jar
+exit
diff --git a/installation/MSC_1.0/MSC_32GB_Mac.sh b/installation/MSC_1.0/MSC_32GB_Mac.sh
new file mode 100644
index 0000000..c4f71f9
--- /dev/null
+++ b/installation/MSC_1.0/MSC_32GB_Mac.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+chmod -R 777 .
+./jdk-11.0.2/Contents/Home/bin/java -Xmx32g -jar ./Libraries/MoleculeSetComparator-fat-1.0.jar
+exit
diff --git a/installation/MSC_1.0/MSC_32GB_Windows.bat b/installation/MSC_1.0/MSC_32GB_Windows.bat
new file mode 100644
index 0000000..589e175
--- /dev/null
+++ b/installation/MSC_1.0/MSC_32GB_Windows.bat
@@ -0,0 +1,4 @@
+if not DEFINED IS_MINIMIZED set IS_MINIMIZED=1 && start "" /min "%~dpnx0" %* && exit
+@echo off
+.\jdk-11.0.2\bin\java -Xmx32g -jar .\lib\MoleculeSetComparator-fat-1.0.jar
+exit
diff --git a/installation/MSC_1.0/MSC_4GB_Linux.sh b/installation/MSC_1.0/MSC_4GB_Linux.sh
new file mode 100644
index 0000000..dde1c2b
--- /dev/null
+++ b/installation/MSC_1.0/MSC_4GB_Linux.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+chmod -R a+rwx .
+./jdk-11.0.2/bin/java -Xmx4g -jar ./lib/MoleculeSetComparator-fat-1.0.jar
+exit
diff --git a/installation/MSC_1.0/MSC_4GB_Mac.sh b/installation/MSC_1.0/MSC_4GB_Mac.sh
new file mode 100644
index 0000000..2d1d2ea
--- /dev/null
+++ b/installation/MSC_1.0/MSC_4GB_Mac.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+chmod -R 777 .
+./jdk-11.0.2/Contents/Home/bin/java -Xmx4g -jar ./Libraries/MoleculeSetComparator-fat-1.0.jar
+exit
diff --git a/installation/MSC_1.0/MSC_4GB_Windows.bat b/installation/MSC_1.0/MSC_4GB_Windows.bat
new file mode 100644
index 0000000..4c7a136
--- /dev/null
+++ b/installation/MSC_1.0/MSC_4GB_Windows.bat
@@ -0,0 +1,4 @@
+if not DEFINED IS_MINIMIZED set IS_MINIMIZED=1 && start "" /min "%~dpnx0" %* && exit
+@echo off
+.\jdk-11.0.2\bin\java -Xmx4g -jar .\lib\MoleculeSetComparator-fat-1.0.jar
+exit
diff --git a/installation/MSC_1.0/MSC_8GB_Linux.sh b/installation/MSC_1.0/MSC_8GB_Linux.sh
new file mode 100644
index 0000000..6511a13
--- /dev/null
+++ b/installation/MSC_1.0/MSC_8GB_Linux.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+chmod -R a+rwx .
+./jdk-11.0.2/bin/java -Xmx8g -jar ./lib/MoleculeSetComparator-fat-1.0.jar
+exit
diff --git a/installation/MSC_1.0/MSC_8GB_Mac.sh b/installation/MSC_1.0/MSC_8GB_Mac.sh
new file mode 100644
index 0000000..42a491a
--- /dev/null
+++ b/installation/MSC_1.0/MSC_8GB_Mac.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+chmod -R 777 .
+./jdk-11.0.2/Contents/Home/bin/java -Xmx8g -jar ./Libraries/MoleculeSetComparator-fat-1.0.jar
+exit
diff --git a/installation/MSC_1.0/MSC_8GB_Windows.bat b/installation/MSC_1.0/MSC_8GB_Windows.bat
new file mode 100644
index 0000000..115b4d2
--- /dev/null
+++ b/installation/MSC_1.0/MSC_8GB_Windows.bat
@@ -0,0 +1,4 @@
+if not DEFINED IS_MINIMIZED set IS_MINIMIZED=1 && start "" /min "%~dpnx0" %* && exit
+@echo off
+.\jdk-11.0.2\bin\java -Xmx8g -jar .\lib\MoleculeSetComparator-fat-1.0.jar
+exit
diff --git a/installation/MSC_1.0/README.txt b/installation/MSC_1.0/README.txt
new file mode 100644
index 0000000..26c2242
--- /dev/null
+++ b/installation/MSC_1.0/README.txt
@@ -0,0 +1,12 @@
+You need to download OpenJDK Version 11.0.2 from http://jdk.java.net/archive/ :
+See instructions in "JDK download info.txt" in subfolder "jdk-11.0.2"
+
+You can start MSC by executing one of the "MSC_?GB_" files, where should
+be your operating system and ? specifies the number of gigabytes of RAM that is
+allocated for the JVM.
+
+If you want to start MSC with a different RAM specification, you have to edit one of the
+existing "MSC_?GB_" files (or a copy of them). In the third row, modify option
+"-Xmx?g" where ? specifies the amount of RAM you want to allocate for the JVM in gigabytes.
+
+A short and comprehensive introduction to MSC is provided in the "Tutorial" folder.
diff --git a/installation/MSC_1.0/TestSets/testSet1.txt b/installation/MSC_1.0/TestSets/testSet1.txt
new file mode 100644
index 0000000..5dad163
--- /dev/null
+++ b/installation/MSC_1.0/TestSets/testSet1.txt
@@ -0,0 +1,50000 @@
+O(CC(=O)NC1=CON=C1)C2C(=CC=CC=2)C#N
+OC(=O)C1CC(NC(=O)CCNC)CCC1
+BrCC2=CC=C(COC1=C(Br)C=C(Br)C=C1Br)C=C2
+O=C(NC1NCCC1)CCC
+S1C=C(OC(=O)N)C=C1
+OC(=O)CC2N=C1N=CC=CC1=CN=2
+ClC1SN=NC=1CNC2=CC(NC(=O)C)=C(F)C=C2F
+FC3=CC=C(C1C(C2N(C(C1)CC2)C)C(=O)N)C=C3
+OC(CN1C(CCCC1)CC)CN
+S2C(C(=O)NC1CC1)=CC=C2N
+O=C(NC1C(CN(C)C)=CC=CC=1)C2N=CNC=2C(O)=O
+O=C1CCC(C(CCCC)=C1)C=CCC
+S1C=C(N=C1)C(=O)NCC(N)CC
+S(C1=CC=C(OC)C=C1)C3=NN2N=NN=C2C=C3
+O=C(NCCCCN(C)C)C1NCCC1
+O1N=C(N=C1C(C(=O)CC)C)C2N=CC=CN=2
+S2C(NN=CC1CCCCC1)=NC3C2=CC=CC=3
+ClC1=C(OCC=O)C(Cl)=CC(=C1)C
+ClC3C(=C(N1CCC2C(C1)=CC=CC=2)C=CC=3)C=O
+O1CCC(C(NC)C(C)C)C2C1=CC=CC=2
+BrC1=CC(=C(OCC(F)(F)F)C=C1)C=CC(O)=O
+ClC2=NN=C(NC(=O)C(OC)C1=CC=CC=C1)C=C2
+O(C1CC(O)C1)C2=CC=C(OC)C=C2
+BrC2=C(F)C=C(OC1N=C(C=CC=1)CO)C=C2
+O1CCN(CC1)C2=C(CNC(C)C)C=NC=C2
+O=C(NC(CC)(C)C)C(NCC1CC1)C
+BrC3C=C(CN1CC2=C(C1=O)C(O)=CC=C2)C=CC=3
+FC2=C(C(N)CC1N=CC=CC=1)C=C(F)C=C2
+OCCCCCN1N=CC2C1=CC=CC=2
+NC(C(C)C)CCC1=CC2C(N=C1)=CC=CC=2
+BrC1N=NN(C=1C#N)C
+C(C1=C(CC=CC1)CC)(C)(C)C
+O(CC(NC1=CC=NC=C1)CCC)C
+P(O)(O)(=O)C=CCCCCCCCCCC
+O=C(N1CCCC1)CN2C(C3C(C2=O)=CC=CC=3)=C
+O(CCNC(=O)CCCCC)CCN
+O=C2NC1N=CC(=CC=1CC2)C=CC(=O)C
+FC(F)C1NC=C(O)C(=O)C=1
+O=C2N(C1(CCCC1)C)C(=O)NC2=O
+ClC2=CC(OCC1OC=CC=1C(=O)NN)=C(C=C2)C
+O(C1CN=CC1=O)C
+ClC(C1=CC(Cl)=C(OC)C=C1)C(=O)N(C)C
+FC(F)(F)COCC(=O)N1CC(OCC1)CC
+N1(N=NN=C1C2C(N)=CC=CC=2)CC
+O=C(N1C(CCC1)C(=O)NC)C2NC3C(C=2)=CC=CC=3
+S(CC1N=CNC=1C)CCNC(=NCCN)N
+O=C(NC1CCCCCC1)CN2CCCC2=O
+OC(=O)C2=CN(C(C1=CC=CC=C1)C)C=C2
+BrC2C=C(OCCCC(=O)NC1C(Cl)=CC=CC=1)C=CC=2
+O=C(NC)CCNC1=CC=C(N(C)C)C=C1
+O(C(NCCCC(OC)=O)=CC(=O)C)C
+FC(F)(F)CN(C1CC1)C(=O)C2=NC(NN)=CC=C2
+O=C(NC2N=C(NC1=NC=NC(CC)=C1)C=CC=2)C
+BrC1=NC=C(N=C1)CCC2N(S(=O)(=O)C)CCCC2
+FC(F)(F)C2=CC(NC(=O)CCNCC1OC=CC=1)=CC=C2
+FC(F)(F)CCN(CC(NCC)(C1CC1)C#N)C
+FC1C=C(C(N)CN)C=CC=1O
+BrC3=CC=C(N2CC(NCC1N=CC=CC=1)CC2)C=C3
+O(CC(N)CO)C1=CC(=C(C=C1)C)C
+S(SC1=NC=CC(=C1)C)C2=NC=CC(=C2)C
+ClC1=CC(C(NCC)C)=C(OCCO)C=C1
+S(=O)(=O)(C(C(CC)C)C(O)=O)C(F)(F)F
+N1CC(C=CC=1C2=CC=CC=C2)C=C
+S(CCNC(CC)CC)C
+BrC1=C(Cl)C(=C(O)C=C1)C#N
+NC(C1CC1)CC2=NC=CN3C2=NN=C3
+BrC2=C(OCC1CCOCC1)C(Br)=CC(N)=C2
+O2C(=C(C(NC(=O)C1C(=NC=NC=1)N)C)C=C2C)C
+OCC1=CN(N=C1)CC2=CC=C(CC)C=C2
+FC2N=C(N(CC1=CC=C(OCC)C=C1)C)C=CC=2
+N(C1CC1)(CCC)C2=NC=C(C=C2)C#N
+ClC2C=C(N1CC(CC1)CN)C=CC=2
+O2C1C=C(CC(N)(C)C)C=CC=1C(=C2)C
+O(CC(NC1=CC=C(C=C1)CC(=O)N)CC)C
+S2C1=C(CCNC1)C=C2C(OCC)=O
+OC1C2=C(NC1=O)C=C(N(CCCC)CCO)C=C2
+O=C(NCC1NC(=O)CC1)C2(CCNC2)C
+ClC1=C(NC(=O)CS(=O)CCC)C=C(C=C1)C(O)=O
+SCC(N)C(=O)N(CC(=O)NCC(O)=O)C(=O)C
+FCC1CC(N(C1=O)C)C2ON=C(C=2)C
+OC(C1CC1)(CN(C(C)C)C)CN
+O=C(NC(C)C)C2=CN(CC1=CC=NC=C1)C(=O)C=C2
+S2C(C(NCC(CC)C)C1=CC=CC=C1)=CC=C2
+OCC(C(=O)N(C)C)C(=O)C
+S(C2=CC1=C(CCCC1=O)C=C2)C(=O)N(C)C
+S2C(C(NC1CCN(C1)C)CCC)=CC=C2
+O=C(CCC(=O)C)CC(=O)C1=CC=CC=C1
+O=C(NCC2=CC1=C(N(C(=C1)C)C)C=C2)CCC
+BrC1=CC=C(C(NC(=O)C(SC)C)C(OC)=O)C=C1
+S=C1N(C(C)C(OC)=O)C(=NN1)C2=CC=CC=C2
+O=C(N1C(CCCC1)C(=O)N)CC
+ClC2=CC=C(C(NC(C1=C(F)C=CC=C1F)C)CC)C=C2
+FC(F)(F)CCNCC1N(N=CN=1)CCC
+FC2=C(C1=CC(F)=C(O)C=C1)C(F)=CC=C2
+BrCC2=C1N=C(OC1=CC=C2)C
+BrCC(CN1N=CC(=O)C2C1=CC=CC=2)CC
+S(=O)(=O)(N1CCS(=O)CC1)C(CC)C#N
+FC3=C(C1NCCC(C1)C2=C(NC=C2)C)C(F)=CC=C3
+FC1N=CC=CC=1C(=O)COCC2=CC=CC=C2
+NC(C1CC(CC1)C)C2C=C(C=NC=2N)C
+FC1C=C(C(=O)N(C(C)C)CCO)C=CC=1C
+BrC2C=C(NC(=O)CNC(CC1CC1)C)C=CC=2
+FC(F)(F)C2C=C(C(N1CCOCC1)C(O)=O)C=CC=2
+O(C1CCNC1)C2N=C(C=CC=2C(=O)N)C
+OC(=O)C1=C3N(C(=C1)C2NN=CC=2)C=CC=C3
+O(CC1(N)CCCCCC1)C2=NC=CN3C2=NN=C3
+FC2=CC(C1=CC(=C(CC)C=C1)CC)=CC(F)=C2
+S(=O)(=O)(CCCC(O)C1C(=CC=CC=1)C)C
+S1(=O)C(CC=CC1)C(OC)=O
+O1C(CN(CC1)C(=O)NC(C)C=C)(CC)C
+O(C(=O)C2C=C(C1=C(C=CC=C1O)C=O)C=CC=2)CC
+OC(=O)C(C(C)C=CC)C(C)C=CC
+O=C(NC(CC)(CN)C)C1C(C1)C
+ClC1=NC(SCC)=C(C=C1)C(OC)=O
+S1C(CC(=O)NC(CCCCCC)C)=CC=C1
+S1C2C(OCC1)=C(C=CC=2C)C
+N2C=C(C=C1CCC(CC1)C)C=CC=2
+C1(C(CCCC1)CCC)CCC
+S2(=O)(=O)CC(OC1=C(N=CC=C1)C(O)=O)C(O)C2
+OC(C1C2=C(N(C=1)C)C=CC(=C2)CCC)=CC(=O)C
+BrC1CC(CCC1=O)C2=C(Cl)C=C(F)C=C2
+P(O)(O)(=O)COCCN2C1=NC(=NC(=C1N=C2)CN)N
+O(C1CCC(C(C)(C)C)CC1)C(=O)NN
+BrCC1(CCCCC1)CN2N=CC(=C2)C
+O(O)C(=N)C
+ClC1OC(C(N)C(C)C)=CC=1
+OCCN(C1CCCC1)C2=NN=C(C=C2)C
+ClC1=NSS(=O)(=O)C=C1
+O(C2=C1CCCC(=O)NC1=C(N=O)C=C2)C
+S(=O)(=O)(CC(OCC)OCC)C1=CC=C(C=C1)C
+BrC1C=CC(=NC=1)C(=NOC)C2=CC=C(C=C2)C
+FC2=C(C(NC)C1=CC(=C(F)C=C1)C)C=CC(F)=C2
+FC2=CC=C(C1OC(=NC=1)CN)C=C2
+N(C(CC(C)(C)C)(C)C)=CC(C#N)C#N
+ClC2=CC1N=C(NCCN(C)C)C=C(C=1C=C2)C
+S(CC(=O)NC2C=C1OC3C(C1=CC=2OC)=CC=CC=3)C
+O(C1(CC1)C(=O)N(OC)C)C
+OC(C(=O)NCCCCC(O)=O)C1=CC=CC=C1
+ClC1=CC=C(C=C1)C(=S)OCSC#N
+O(CC(=O)NCC#CC1C(=CC=CC=1)C(=O)NC)CC
+O=C1NC(C(=N1)N)(C)C
+IC1=C(N=C(N=C1N)C2SC=C(Br)C=2)C3CC3
+O1C(CCC(C1OC)C)(C(OC)OC)C
+S2C1CC(CCC=1N=C2C(O)C)(C)C
+O(C1N=CC=CC=1C2C=CC(=NC=2)C#N)C
+S(C1CCCC1=O)C2SC=NN=2
+S1N=C(N=C1N)C3=CC=C(OC2=CC=C(F)C=C2)C=C3
+S=C=NC1=CC=C(N(CC(OC(C)(C)C)=O)C)C=C1
+O=C1N(C(CC1)C#C)C(=O)C
+O=C(NC(=C(C)C)C(NC(=O)C)=CC)C
+O(C(C)(C)C)C(=O)C(O)(CN)C(O)=O
+S3C(C(=O)N2C(C1N(CCC1)C)CCC2)=CC=C3
+S(N1C(=O)CCC1=O)C(=O)C(C)C(=O)C
+FCCCOC(CC(N)C(O)=O)C(=O)N
+P1(=O)(N(N=C(C1)C)C(=O)C)C
+O=C(N1CC(CC1)CO)C2CN(C(=O)C2)C
+O(C1C=C(CNCC=C)C=CC=1OCC)CC
+FC2=C(NC1=CC=C(OC)C=C1)C=C(C=C2)C
+S(CC(=O)NCC1CCOC1)C2C=C(OC)C=CC=2
+S2CC(OC(=O)C1C(C1C=C(C)C)(C)C)CC2
+ClC4=NC=NC3C2C(=CC(N1CCCC1)=NC=2SC=34)C
+O=C1C3C4C2C(C1CC(C2)C3)C=CC4
+O(C1=C(C(OC)=C(OC)C=C1)C(O)=O)COC
+O(C2C=C(C1N=CC=CC=1C(C)C)C=CC=2OC)C
+IC2=CC=C(NC(C1C(=CC=CC=1)C(F)(F)F)C)C=C2
+FC1=CN(N=C1)CC#N
+BrC2N=C(N1CC(O)CC1)C=CC=2
+ClC(=NSN1C(CCCC1(C)C)(C)C)C#N
+N(C1C(CC(CC1)C)C)CC2N(C=CN=2)C
+N(CNC1N=CC=CN=1)C2N=CC=CN=2
+N(CC1C2CC(C1)CC2)CC3NC=NC=3
+OC1(CCN(CC1)CC#C)C2=CC=CC=C2
+O1C(C(OCC)C(O)C(O)C1OCC)CO
+OC(=O)C(NC1=CN(N=C1)CCN(CC)CC)C
+C1(=C(C(=CC(=CC(=C1C)C)C)C)C)C
+OC(=O)C1N(CCCC1)C(=O)NC2C=CC(OC)=NC=2
+ClC1=NC=C(C(=C1)C)C2=CC=NC=C2
+S(C1C=C(C=CC=1)C)CC(O)=O
+FC(F)(F)C2C=C(N1CCOCC1)C=C(C=2C(=O)N)C
+ClC2=CC=C(N=C1SC(CC(=O)N1C)C(O)=O)C=C2
+FC1=CC=C(CC(CC(OC)=O)C(OC)=O)C=C1
+N(CCNN=CC)CC
+OC(=O)CC1N(CCCC1)CC2C(=CC=CC=2)C
+FC2=CC1C(CCCC)=CCC=1C=C2
+BrC3C(C=CCC2C=C1OCCC1=CC=2O)=CC=CC=3
+N#CCCC1=CC(=CC=C1)C#N
+O(C(=O)C2=CC1N=NN(C=1C=C2)C(=O)N)C
+O(C(=O)C1C(C1)C)CC(=O)NC2=CC=C(OCC)C=C2
+S2C(N1CCOCC1)=NC(=O)C2=CC3C(F)=CC=CC=3
+BrC3=CC(NCC2=C1C(NC=C1)=CC=C2)=C(Cl)C=C3
+BrCCCCOC(C1=CC=CC=C1)=CC2=CC=CC=C2
+O3C(CNC2CN(C1CC1)CC2)=CC=C3C(O)=O
+OC(CNC1N=C(C=CC=1)C)C
+ClC2C=C(NC(=O)C1=CC(=CC(=C1)C)C)C=CC=2OC
+O(C(=O)C(CC)=C(N)C)CC
+O1OC(OOC(OOC1(CC)CC)(C)C)(C)C
+S=C(N)CCN(CC(C)C)C1=NC=C(C=C1)C(F)(F)F
+OC(=O)C(NC(=O)C1NC2C(C=1)=CC=CC=2)C(CC)C
+O1C3=C(N=C1C)C2N(OCC=C)C(=O)N(C2)C3
+BrC2=CC=C(OC1=CC=C(C(O)C)C=C1)C=C2
+S(OCC1(OCC(O)C(O)C1O)O)(=O)(=O)NC2CC2
+O2C1C=C(CNC(C)C(N)=NO)C=CC=1OC2
+ClC1=C(OC(Cl)(F)F)C=C(F)C=C1
+ClC(CNCC1CCC1)COC
+S2C1N=COC=1N=C2C
+BrC1=CC(C(=O)NCC(C)C)=C(Cl)C=C1
+BrC1C=C(SC=1)CN(C2N=CN=C(Cl)C=2CCC)C
+S(=O)(=O)(NCC(O)(CC)C)C1NC(=NC=1)CC
+O3N=CC(C(=O)NC2=CC1=C(NC=C1)C=C2)=C3C
+O1C2C(C=C(C(=O)NCC(N)C)C1=O)=CC=CC=2
+ClC2=CC=C(C1=NC(OC)=NC(Cl)=N1)C=C2
+BrC2SC(=S)N(C1=CC=C(OC)C=C1)C2=O
+BrC1=C(C(=O)NCCCC(C)C)C=C(OC)C=C1
+S(C1=CC=C(C=C1)C(=O)C)C2N=C(C=CN=2)C
+OC(=O)CC(N1N=C(C=C1C)C)C
+O=C1N(C(=O)N(C1C)C)CC(O)O
+O1NC(C(C1C)C(=O)N)C2=CCCC=C2
+O2CCC(NC(C1N(C=CN=1)C)C)CC2
+O2C(C1=CC=C(OC(=O)C=C)C=C1)=CC=C2
+O3C2C=C(CNCCCC1NN=CN=1)C=CC=2OC3
+O=C(NCCCC)C1NC=CN=1
+S2C(CC(=O)NCC1OC(=CN=1)C)=C(NC2=S)C
+OC(=O)C1C3CC(C1C(=O)NCC2=CC=NC=C2)C=C3
+O1C(=C(C(OC)C)C2=C1C=C(C(=C2)C#N)C#N)C
+FC(F)(F)CN(C(=O)C1NCC(NC1)C)CCC
+ClC1=C(C=C(C(=C1)C)C(=O)N=C(N)N)C(F)(F)F
+FC3=CC=C(C=C2C(N1CCC1)CCCC2)C=C3
+OC(C1C(C1)C2=C(OC)C=C(OC)C=C2)C
+O=C(NCC1=CN(N=C1)C)C2CC(N)CC2
+BrC1OC(C(=O)NCCC(C)C)=CC=1S(=O)(=O)N
+OC(=O)C(NC)CC1C=CC(C=CC=1)(C)C
+O=C1C(C(CCC1)C)(CC#C)C
+BrC2C=C(CSC1OC(=NN=1)CC)C=CC=2
+O(C2=CC=C(C(NCC(O)=O)C1CC1)C=C2)C
+PN1CC(C(C1=O)C2=CC=CC=C2)C3=CC=CC=C3
+ClC3C=C(C12C(C1)CC(N=O)C2)C=CC=3Cl
+O=C(N)C1(NC2=C(N1)C=CC(N)=C2)CCCCC
+O1C(NC(=O)C)(CC(C=C1C#N)C)C(OC)=O
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diff --git a/installation/MSC_1.0/TestSets/testSet2.txt b/installation/MSC_1.0/TestSets/testSet2.txt
new file mode 100644
index 0000000..76f70c6
--- /dev/null
+++ b/installation/MSC_1.0/TestSets/testSet2.txt
@@ -0,0 +1,50000 @@
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+O1CO(C1N2N=NC3=C2N=CC=C3)C(OC)=O
+ClCCOCCN(CC)C1=CC=C(C=C1)C
+ClC2C=C(NC1(CC)C=C(F)C(F)=CC=1F)C(=C2)C
+ClC=CC(F)=C(N)C(N)CC=C1CCC2C1=CC=CC=2
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+S14CCN(CC1)(CNC3C2NN=NC=2C=CC=3)CC4
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+O=C1N3CC(C1C2C(=C(C=CC=2)C)C)C4C3=CC=CC=4
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+FC(F)(F)CN(C1CC1)(C(=O)N(C2CC2)C3CC3)C(F)(F)F
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+BrC2C=CC(NCC1CCN(CC1)C)=NC=2
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+O=C(N)C(CCCCCCCC)C
+OCCC(C(C1NC2C(C=1)=CC=CC=2)C)CCC
+ClOC1CC(OS(=O)(=O)CCCOOOC)C=CC=1
+O=C1NC2C(C1)CC=CC=C2
+O=C(NC1C(C1)C)C(N(C(C)C)CC(O)=O)C
+OC(=O)C(NC(=O)C)(=CC1NC=NC=1)C
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diff --git a/installation/MSC_1.0/Tutorial/MSC_1.0_Tutorial.pdf b/installation/MSC_1.0/Tutorial/MSC_1.0_Tutorial.pdf
new file mode 100644
index 0000000..e1989fd
Binary files /dev/null and b/installation/MSC_1.0/Tutorial/MSC_1.0_Tutorial.pdf differ
diff --git a/installation/MSC_1.0/VersionHistory.txt b/installation/MSC_1.0/VersionHistory.txt
new file mode 100644
index 0000000..8167a40
--- /dev/null
+++ b/installation/MSC_1.0/VersionHistory.txt
@@ -0,0 +1,10 @@
+Molecule Set Comparator (MSC) Version 1.0
+
+Required Libraries:
+- cdk-2.3 for molecule encoding, molecule depiction and descriptor calculation
+- pdfbox-2.0.17 for image to pdf conversion
+- commons-logging-1.2 necessary for pdfbox-2.0.17
+- junit-4.12 for application testing
+- javaFX 14 for GUI and chart creation
+- batik-svggen-1.13 for image to svg conversion
+- batik-svg-dom-1.13 necessary for batik-svggen-1.13
diff --git a/installation/MSC_1.0/jdk-11.0.2/JDK download info.txt b/installation/MSC_1.0/jdk-11.0.2/JDK download info.txt
new file mode 100644
index 0000000..d533123
--- /dev/null
+++ b/installation/MSC_1.0/jdk-11.0.2/JDK download info.txt
@@ -0,0 +1,6 @@
+You need to download OpenJDK Version 11.0.2 from http://jdk.java.net/archive/ :
+- Go to the website and select download of version "11.0.2 (build 11.0.2+9)"
+ for your operating system (OS).
+- After download extract the zip or tar file (depending on your OS)
+ and copy the contents of extracted folder "jdk-11.0.2" (for Windows and Linux)
+ or "jdk-11.0.2.jdk" (for Mac) folder into this directory.
diff --git a/installation/MSC_1.0/lib/MoleculeSetComparator-fat-1.0.jar b/installation/MSC_1.0/lib/MoleculeSetComparator-fat-1.0.jar
new file mode 100644
index 0000000..ee6e0ff
Binary files /dev/null and b/installation/MSC_1.0/lib/MoleculeSetComparator-fat-1.0.jar differ
diff --git a/lib/batik-svg-dom-1.13.jar b/lib/batik-svg-dom-1.13.jar
new file mode 100644
index 0000000..e4972a8
Binary files /dev/null and b/lib/batik-svg-dom-1.13.jar differ
diff --git a/lib/batik-svggen-1.13.jar b/lib/batik-svggen-1.13.jar
new file mode 100644
index 0000000..24b3d69
Binary files /dev/null and b/lib/batik-svggen-1.13.jar differ
diff --git a/lib/cdk-2.3.jar b/lib/cdk-2.3.jar
new file mode 100644
index 0000000..20948b9
Binary files /dev/null and b/lib/cdk-2.3.jar differ
diff --git a/lib/commons-logging-1.2.jar b/lib/commons-logging-1.2.jar
new file mode 100644
index 0000000..93a3b9f
Binary files /dev/null and b/lib/commons-logging-1.2.jar differ
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.base/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Linux/legal/javafx.base/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.base/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
+package. Some of those programs are provided under licenses deemed
+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
+License, Version 2.0 and may include FreeType. Such programs are licensed
+to you under their original licenses.
+
+Oracle facilitates your further distribution of this package by adding the
+Classpath Exception to the necessary parts of its GPLv2 code, which permits
+you to use that code in combination with other independent modules not
+licensed under the GPLv2. However, note that this would not permit you to
+commingle code under an incompatible license with Oracle's GPLv2 licensed
+code by, for example, cutting and pasting such code into a file also
+containing Oracle's GPLv2 licensed code and then distributing the result.
+
+Additionally, if you were to remove the Classpath Exception from any of the
+files to which it applies and distribute the result, you would likely be
+required to license some or all of the other code in that distribution under
+the GPLv2 as well, and since the GPLv2 is incompatible with the license terms
+of some items included in the distribution by Oracle, removing the Classpath
+Exception could therefore effectively compromise your ability to further
+distribute the package.
+
+Failing to distribute notices associated with some files may also create
+unexpected legal consequences.
+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
+skilled in open source matters before removing the Classpath Exception or
+making modifications to this package which may subsequently be redistributed
+and/or involve the use of third party software.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.base/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Linux/legal/javafx.base/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.base/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
+ regardless of the license terms of the Designated Exception Modules,
+ and to copy and distribute the resulting executable under GPL2,
+ provided that the Designated Exception Modules continue to be
+ governed by the licenses under which they were offered by Oracle.
+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
+to build an executable that includes those portions of necessary code that
+Oracle could not provide under GPL2 (or that Oracle has provided under GPL2
+with the Classpath exception). If you modify or add to the OpenJDK code,
+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.base/LICENSE b/lib/javafx-sdk-14-Linux/legal/javafx.base/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.base/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
+by others will not reflect on the original authors' reputations.
+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
+everyone's free use or not licensed at all.
+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the source
+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.controls/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Linux/legal/javafx.controls/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.controls/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
+package. Some of those programs are provided under licenses deemed
+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
+License, Version 2.0 and may include FreeType. Such programs are licensed
+to you under their original licenses.
+
+Oracle facilitates your further distribution of this package by adding the
+Classpath Exception to the necessary parts of its GPLv2 code, which permits
+you to use that code in combination with other independent modules not
+licensed under the GPLv2. However, note that this would not permit you to
+commingle code under an incompatible license with Oracle's GPLv2 licensed
+code by, for example, cutting and pasting such code into a file also
+containing Oracle's GPLv2 licensed code and then distributing the result.
+
+Additionally, if you were to remove the Classpath Exception from any of the
+files to which it applies and distribute the result, you would likely be
+required to license some or all of the other code in that distribution under
+the GPLv2 as well, and since the GPLv2 is incompatible with the license terms
+of some items included in the distribution by Oracle, removing the Classpath
+Exception could therefore effectively compromise your ability to further
+distribute the package.
+
+Failing to distribute notices associated with some files may also create
+unexpected legal consequences.
+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
+skilled in open source matters before removing the Classpath Exception or
+making modifications to this package which may subsequently be redistributed
+and/or involve the use of third party software.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.controls/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Linux/legal/javafx.controls/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.controls/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
+ regardless of the license terms of the Designated Exception Modules,
+ and to copy and distribute the resulting executable under GPL2,
+ provided that the Designated Exception Modules continue to be
+ governed by the licenses under which they were offered by Oracle.
+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
+to build an executable that includes those portions of necessary code that
+Oracle could not provide under GPL2 (or that Oracle has provided under GPL2
+with the Classpath exception). If you modify or add to the OpenJDK code,
+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.controls/LICENSE b/lib/javafx-sdk-14-Linux/legal/javafx.controls/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.controls/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
+by others will not reflect on the original authors' reputations.
+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
+everyone's free use or not licensed at all.
+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the source
+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.fxml/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Linux/legal/javafx.fxml/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.fxml/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
+package. Some of those programs are provided under licenses deemed
+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
+License, Version 2.0 and may include FreeType. Such programs are licensed
+to you under their original licenses.
+
+Oracle facilitates your further distribution of this package by adding the
+Classpath Exception to the necessary parts of its GPLv2 code, which permits
+you to use that code in combination with other independent modules not
+licensed under the GPLv2. However, note that this would not permit you to
+commingle code under an incompatible license with Oracle's GPLv2 licensed
+code by, for example, cutting and pasting such code into a file also
+containing Oracle's GPLv2 licensed code and then distributing the result.
+
+Additionally, if you were to remove the Classpath Exception from any of the
+files to which it applies and distribute the result, you would likely be
+required to license some or all of the other code in that distribution under
+the GPLv2 as well, and since the GPLv2 is incompatible with the license terms
+of some items included in the distribution by Oracle, removing the Classpath
+Exception could therefore effectively compromise your ability to further
+distribute the package.
+
+Failing to distribute notices associated with some files may also create
+unexpected legal consequences.
+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
+skilled in open source matters before removing the Classpath Exception or
+making modifications to this package which may subsequently be redistributed
+and/or involve the use of third party software.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.fxml/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Linux/legal/javafx.fxml/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.fxml/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
+ regardless of the license terms of the Designated Exception Modules,
+ and to copy and distribute the resulting executable under GPL2,
+ provided that the Designated Exception Modules continue to be
+ governed by the licenses under which they were offered by Oracle.
+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
+to build an executable that includes those portions of necessary code that
+Oracle could not provide under GPL2 (or that Oracle has provided under GPL2
+with the Classpath exception). If you modify or add to the OpenJDK code,
+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.fxml/LICENSE b/lib/javafx-sdk-14-Linux/legal/javafx.fxml/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.fxml/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
+by others will not reflect on the original authors' reputations.
+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
+everyone's free use or not licensed at all.
+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the source
+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.graphics/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Linux/legal/javafx.graphics/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.graphics/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
+package. Some of those programs are provided under licenses deemed
+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
+License, Version 2.0 and may include FreeType. Such programs are licensed
+to you under their original licenses.
+
+Oracle facilitates your further distribution of this package by adding the
+Classpath Exception to the necessary parts of its GPLv2 code, which permits
+you to use that code in combination with other independent modules not
+licensed under the GPLv2. However, note that this would not permit you to
+commingle code under an incompatible license with Oracle's GPLv2 licensed
+code by, for example, cutting and pasting such code into a file also
+containing Oracle's GPLv2 licensed code and then distributing the result.
+
+Additionally, if you were to remove the Classpath Exception from any of the
+files to which it applies and distribute the result, you would likely be
+required to license some or all of the other code in that distribution under
+the GPLv2 as well, and since the GPLv2 is incompatible with the license terms
+of some items included in the distribution by Oracle, removing the Classpath
+Exception could therefore effectively compromise your ability to further
+distribute the package.
+
+Failing to distribute notices associated with some files may also create
+unexpected legal consequences.
+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
+skilled in open source matters before removing the Classpath Exception or
+making modifications to this package which may subsequently be redistributed
+and/or involve the use of third party software.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.graphics/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Linux/legal/javafx.graphics/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.graphics/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
+ regardless of the license terms of the Designated Exception Modules,
+ and to copy and distribute the resulting executable under GPL2,
+ provided that the Designated Exception Modules continue to be
+ governed by the licenses under which they were offered by Oracle.
+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
+to build an executable that includes those portions of necessary code that
+Oracle could not provide under GPL2 (or that Oracle has provided under GPL2
+with the Classpath exception). If you modify or add to the OpenJDK code,
+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.graphics/LICENSE b/lib/javafx-sdk-14-Linux/legal/javafx.graphics/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.graphics/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
+by others will not reflect on the original authors' reputations.
+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
+everyone's free use or not licensed at all.
+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the source
+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.graphics/jpeg_fx.md b/lib/javafx-sdk-14-Linux/legal/javafx.graphics/jpeg_fx.md
new file mode 100644
index 0000000..b98f177
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.graphics/jpeg_fx.md
@@ -0,0 +1,51 @@
+## Independent JPEG Group (IJG) JPEG v9c
+
+### IJG License
+```
+
+/*
+ * jcapimin.c
+ *
+ * Copyright (C) 1994-1998, Thomas G. Lane.
+ * Modified 2003-2010 by Guido Vollbeding.
+ * This file is part of the Independent JPEG Group's software.
+ * For conditions of distribution and use, see the accompanying README file.
+ */
+
+[From the README file]
+The authors make NO WARRANTY or representation, either express or implied,
+with respect to this software, its quality, accuracy, merchantability, or
+fitness for a particular purpose. This software is provided "AS IS", and you,
+its user, assume the entire risk as to its quality and accuracy.
+
+This software is copyright (C) 1991-2018, Thomas G. Lane, Guido Vollbeding.
+All Rights Reserved except as specified below.
+
+Permission is hereby granted to use, copy, modify, and distribute this
+software (or portions thereof) for any purpose, without fee, subject to these
+conditions:
+(1) If any part of the source code for this software is distributed, then this
+README file must be included, with this copyright and no-warranty notice
+unaltered; and any additions, deletions, or changes to the original files
+must be clearly indicated in accompanying documentation.
+(2) If only executable code is distributed, then the accompanying
+documentation must state that "this software is based in part on the work of
+the Independent JPEG Group".
+(3) Permission for use of this software is granted only if the user accepts
+full responsibility for any undesirable consequences; the authors accept
+NO LIABILITY for damages of any kind.
+
+These conditions apply to any software derived from or based on the IJG code,
+not just to the unmodified library. If you use our work, you ought to
+acknowledge us.
+
+Permission is NOT granted for the use of any IJG author's name or company name
+in advertising or publicity relating to this software or products derived from
+it. This software may be referred to only as "the Independent JPEG Group's
+software".
+
+We specifically permit and encourage the use of this software as the basis of
+commercial products, provided that all warranty or liability claims are
+assumed by the product vendor.
+
+```
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.graphics/mesa3d.md b/lib/javafx-sdk-14-Linux/legal/javafx.graphics/mesa3d.md
new file mode 100644
index 0000000..b3f32d8
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.graphics/mesa3d.md
@@ -0,0 +1,134 @@
+## Mesa 3-D Graphics Library v19.2.1
+
+### Mesa License
+
+```
+Copyright (C) 1999-2007 Brian Paul All Rights Reserved.
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the "Software"),
+to deal in the Software without restriction, including without limitation
+the rights to use, copy, modify, merge, publish, distribute, sublicense,
+and/or sell copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included
+in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+Attention, Contributors
+
+When contributing to the Mesa project you must agree to the licensing terms
+of the component to which you're contributing.
+The following section lists the primary components of the Mesa distribution
+and their respective licenses.
+Mesa Component Licenses
+
+
+
+Component Location License
+------------------------------------------------------------------
+Main Mesa code src/mesa/ MIT
+Device drivers src/mesa/drivers/* MIT, generally
+
+Gallium code src/gallium/ MIT
+
+Ext headers GL/glext.h Khronos
+ GL/glxext.h Khronos
+ GL/wglext.h Khronos
+ KHR/khrplatform.h Khronos
+
+*****************************************************************************
+
+----
+include/GL/gl.h :
+
+
+ Mesa 3-D graphics library
+
+ Copyright (C) 1999-2006 Brian Paul All Rights Reserved.
+ Copyright (C) 2009 VMware, Inc. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and associated documentation files (the "Software"),
+ to deal in the Software without restriction, including without limitation
+ the rights to use, copy, modify, merge, publish, distribute, sublicense,
+ and/or sell copies of the Software, and to permit persons to whom the
+ Software is furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+ THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
+ OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+ ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ OTHER DEALINGS IN THE SOFTWARE.
+
+ *****************************************************************************
+
+----
+include/GL/glext.h
+include/GL/glxext.h
+include/GL/wglxext.h :
+
+
+ Copyright (c) 2013 - 2018 The Khronos Group Inc.
+
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and/or associated documentation files (the
+ "Materials"), to deal in the Materials without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Materials, and to
+ permit persons to whom the Materials are furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Materials.
+
+ THE MATERIALS ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ MATERIALS OR THE USE OR OTHER DEALINGS IN THE MATERIALS.
+
+ *****************************************************************************
+
+----
+include/KHR/khrplatform.h :
+
+ Copyright (c) 2008 - 2018 The Khronos Group Inc.
+
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and/or associated documentation files (the
+ "Materials"), to deal in the Materials without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Materials, and to
+ permit persons to whom the Materials are furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Materials.
+
+ THE MATERIALS ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ MATERIALS OR THE USE OR OTHER DEALINGS IN THE MATERIALS.
+
+ *****************************************************************************
+
+```
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.media/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Linux/legal/javafx.media/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.media/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
+package. Some of those programs are provided under licenses deemed
+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
+License, Version 2.0 and may include FreeType. Such programs are licensed
+to you under their original licenses.
+
+Oracle facilitates your further distribution of this package by adding the
+Classpath Exception to the necessary parts of its GPLv2 code, which permits
+you to use that code in combination with other independent modules not
+licensed under the GPLv2. However, note that this would not permit you to
+commingle code under an incompatible license with Oracle's GPLv2 licensed
+code by, for example, cutting and pasting such code into a file also
+containing Oracle's GPLv2 licensed code and then distributing the result.
+
+Additionally, if you were to remove the Classpath Exception from any of the
+files to which it applies and distribute the result, you would likely be
+required to license some or all of the other code in that distribution under
+the GPLv2 as well, and since the GPLv2 is incompatible with the license terms
+of some items included in the distribution by Oracle, removing the Classpath
+Exception could therefore effectively compromise your ability to further
+distribute the package.
+
+Failing to distribute notices associated with some files may also create
+unexpected legal consequences.
+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
+skilled in open source matters before removing the Classpath Exception or
+making modifications to this package which may subsequently be redistributed
+and/or involve the use of third party software.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.media/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Linux/legal/javafx.media/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.media/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
+ regardless of the license terms of the Designated Exception Modules,
+ and to copy and distribute the resulting executable under GPL2,
+ provided that the Designated Exception Modules continue to be
+ governed by the licenses under which they were offered by Oracle.
+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
+to build an executable that includes those portions of necessary code that
+Oracle could not provide under GPL2 (or that Oracle has provided under GPL2
+with the Classpath exception). If you modify or add to the OpenJDK code,
+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.media/LICENSE b/lib/javafx-sdk-14-Linux/legal/javafx.media/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.media/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
+by others will not reflect on the original authors' reputations.
+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
+everyone's free use or not licensed at all.
+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
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+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.media/applecoreaudio.md b/lib/javafx-sdk-14-Linux/legal/javafx.media/applecoreaudio.md
new file mode 100644
index 0000000..5bf2a73
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.media/applecoreaudio.md
@@ -0,0 +1,53 @@
+## Apple Computer: CoreAudio Utility Classes v2.0
+
+### Apple Computer CoreAudio Notice
+This software is present only on Mac OS X systems.
+
+### Apple Computer CoreAudio License
+```
+
+File:
+Abstract: Part of CoreAudio Utility Classes
+Version: 1.1
+
+Disclaimer: IMPORTANT: This Apple software is supplied to you by Apple
+Inc. ("Apple") in consideration of your agreement to the following
+terms, and your use, installation, modification or redistribution of
+this Apple software constitutes acceptance of these terms. If you do
+not agree with these terms, please do not use, install, modify or
+redistribute this Apple software.
+
+In consideration of your agreement to abide by the following terms, and
+subject to these terms, Apple grants you a personal, non-exclusive
+license, under Apple's copyrights in this original Apple software (the
+"Apple Software"), to use, reproduce, modify and redistribute the Apple
+Software, with or without modifications, in source and/or binary forms;
+provided that if you redistribute the Apple Software in its entirety and
+without modifications, you must retain this notice and the following
+text and disclaimers in all such redistributions of the Apple Software.
+Neither the name, trademarks, service marks or logos of Apple Inc. may
+be used to endorse or promote products derived from the Apple Software
+without specific prior written permission from Apple. Except as
+expressly stated in this notice, no other rights or licenses, express or
+implied, are granted by Apple herein, including but not limited to any
+patent rights that may be infringed by your derivative works or by other
+works in which the Apple Software may be incorporated.
+
+The Apple Software is provided by Apple on an "AS IS" basis. APPLE
+MAKES NO WARRANTIES, EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION
+THE IMPLIED WARRANTIES OF NON-INFRINGEMENT, MERCHANTABILITY AND FITNESS
+FOR A PARTICULAR PURPOSE, REGARDING THE APPLE SOFTWARE OR ITS USE AND
+OPERATION ALONE OR IN COMBINATION WITH YOUR PRODUCTS.
+
+IN NO EVENT SHALL APPLE BE LIABLE FOR ANY SPECIAL, INDIRECT, INCIDENTAL
+OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) ARISING IN ANY WAY OUT OF THE USE, REPRODUCTION,
+MODIFICATION AND/OR DISTRIBUTION OF THE APPLE SOFTWARE, HOWEVER CAUSED
+AND WHETHER UNDER THEORY OF CONTRACT, TORT (INCLUDING NEGLIGENCE),
+STRICT LIABILITY OR OTHERWISE, EVEN IF APPLE HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.
+
+Copyright (C) 2014 Apple Inc. All Rights Reserved.
+
+```
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.media/glib.md b/lib/javafx-sdk-14-Linux/legal/javafx.media/glib.md
new file mode 100644
index 0000000..5858730
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.media/glib.md
@@ -0,0 +1,537 @@
+## GNU Glib v2.62.2
+
+### Glib Notice
+```
+
+You are receiving a copy of GNU Glib, Version: 2.62.2 in either source or
+object code in the JavaFX runtime or JavaFX SDK. The terms of the
+Oracle license do NOT apply to the GNU Glib, Version: 2.62.2; it is
+licensed under the following license, separately from the Oracle programs
+you receive. If you do not wish to install this library, you may delete
+this library:
+
+ - On Linux systems: N/A (library is not present)
+ - On Mac OS X systems: delete $(JAVA_HOME)/lib/libglib-lite.dylib
+ - On Windows systems: delete $(JAVA_HOME)\bin\glib-lite.dll
+
+A copy of the Oracle modified GNU Glib library source code is located
+in the following OpenJDK git repository:
+
+ https://github.com/openjdk/jfx
+
+You can use git to clone the repository or you can browse the
+source using a web browser. The root directory of the GNU Glib source
+code is here:
+
+ rt/modules/javafx.media/src/main/native/gstreamer/3rd_party/glib/
+
+
+```
+
+### LGPL 2.1
+```
+
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 2.1, February 1999
+
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+[This is the first released version of the Lesser GPL. It also counts
+ as the successor of the GNU Library Public License, version 2, hence
+ the version number 2.1.]
+
+ Preamble
+
+ The licenses for most software are designed to take away your
+freedom to share and change it. By contrast, the GNU General Public
+Licenses are intended to guarantee your freedom to share and change
+free software--to make sure the software is free for all its users.
+
+ This license, the Lesser General Public License, applies to some
+specially designated software packages--typically libraries--of the
+Free Software Foundation and other authors who decide to use it. You
+can use it too, but we suggest you first think carefully about whether
+this license or the ordinary General Public License is the better
+strategy to use in any particular case, based on the explanations below.
+
+ When we speak of free software, we are referring to freedom of use,
+not price. Our General Public Licenses are designed to make sure that
+you have the freedom to distribute copies of free software (and charge
+for this service if you wish); that you receive source code or can get
+it if you want it; that you can change the software and use pieces of
+it in new free programs; and that you are informed that you can do
+these things.
+
+ To protect your rights, we need to make restrictions that forbid
+distributors to deny you these rights or to ask you to surrender these
+rights. These restrictions translate to certain responsibilities for
+you if you distribute copies of the library or if you modify it.
+
+ For example, if you distribute copies of the library, whether gratis
+or for a fee, you must give the recipients all the rights that we gave
+you. You must make sure that they, too, receive or can get the source
+code. If you link other code with the library, you must provide
+complete object files to the recipients, so that they can relink them
+with the library after making changes to the library and recompiling
+it. And you must show them these terms so they know their rights.
+
+ We protect your rights with a two-step method: (1) we copyright the
+library, and (2) we offer you this license, which gives you legal
+permission to copy, distribute and/or modify the library.
+
+ To protect each distributor, we want to make it very clear that
+there is no warranty for the free library. Also, if the library is
+modified by someone else and passed on, the recipients should know
+that what they have is not the original version, so that the original
+author's reputation will not be affected by problems that might be
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+
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+
+
+ Copyright (C)
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Also add information on how to contact you by electronic and paper mail.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the library, if
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+That's all there is to it!
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+```
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.media/gstreamer.md b/lib/javafx-sdk-14-Linux/legal/javafx.media/gstreamer.md
new file mode 100644
index 0000000..8f77613
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.media/gstreamer.md
@@ -0,0 +1,535 @@
+## GStreamer v1.16.1
+
+### GStreamer Notice
+```
+
+You are receiving a copy of GStreamer, Version: 1.16.1 in either source or
+object code in the JavaFX runtime or JavaFX SDK. The terms of the
+Oracle license do NOT apply to the GStreamer, Version: 1.16.1; it is
+licensed under the following license, separately from the Oracle programs
+you receive. If you do not wish to install this library, you may delete
+this library:
+
+ - On Linux systems: delete $(JAVA_HOME)/lib/libgstreamer-lite.so
+ - On Mac OS X systems: delete $(JAVA_HOME)/lib/libgstreamer-lite.dylib
+ - On Windows systems: delete $(JAVA_HOME)\bin\gstreamer-lite.dll
+
+A copy of the Oracle modified GStreamer library source code is located
+in the following OpenJDK git repository:
+
+ https://github.com/openjdk/jfx
+
+You can use git to clone the repository or you can browse the
+source using a web browser. The root directory of the GStreamer source
+code is here:
+
+ rt/modules/javafx.media/src/main/native/gstreamer/gstreamer-lite/
+```
+
+### LGPL 2.1
+```
+
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 2.1, February 1999
+
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
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+
+ How to Apply These Terms to Your New Libraries
+
+ If you develop a new library, and you want it to be of the greatest
+possible use to the public, we recommend making it free software that
+everyone can redistribute and change. You can do so by permitting
+redistribution under these terms (or, alternatively, under the terms of the
+ordinary General Public License).
+
+ To apply these terms, attach the following notices to the library. It is
+safest to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least the
+"copyright" line and a pointer to where the full notice is found.
+
+
+ Copyright (C)
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Also add information on how to contact you by electronic and paper mail.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the library, if
+necessary. Here is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the
+ library `Frob' (a library for tweaking knobs) written by James Random Hacker.
+
+ , 1 April 1990
+ Ty Coon, President of Vice
+
+That's all there is to it!
+
+```
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.media/libffi.md b/lib/javafx-sdk-14-Linux/legal/javafx.media/libffi.md
new file mode 100644
index 0000000..6915bbc
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.media/libffi.md
@@ -0,0 +1,28 @@
+## LibFFI v3.2.1
+
+### LibFFI License
+```
+
+libffi - Copyright (c) 1996-2014 Anthony Green, Red Hat, Inc and others.
+See source files for details.
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+``Software''), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED ``AS IS'', WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+```
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.swing/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Linux/legal/javafx.swing/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.swing/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
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+based on the GNU Project exception for its Classpath libraries, known as the
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+
+Note that Oracle includes multiple, independent programs in this software
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+For example, the package includes programs licensed under the Apache
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+
+Failing to distribute notices associated with some files may also create
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+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
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diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.swing/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Linux/legal/javafx.swing/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.swing/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
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+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
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+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
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+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.swing/LICENSE b/lib/javafx-sdk-14-Linux/legal/javafx.swing/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.swing/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
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+
+Everyone is permitted to copy and distribute verbatim copies of this license
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+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the source
+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.web/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Linux/legal/javafx.web/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.web/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
+package. Some of those programs are provided under licenses deemed
+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
+License, Version 2.0 and may include FreeType. Such programs are licensed
+to you under their original licenses.
+
+Oracle facilitates your further distribution of this package by adding the
+Classpath Exception to the necessary parts of its GPLv2 code, which permits
+you to use that code in combination with other independent modules not
+licensed under the GPLv2. However, note that this would not permit you to
+commingle code under an incompatible license with Oracle's GPLv2 licensed
+code by, for example, cutting and pasting such code into a file also
+containing Oracle's GPLv2 licensed code and then distributing the result.
+
+Additionally, if you were to remove the Classpath Exception from any of the
+files to which it applies and distribute the result, you would likely be
+required to license some or all of the other code in that distribution under
+the GPLv2 as well, and since the GPLv2 is incompatible with the license terms
+of some items included in the distribution by Oracle, removing the Classpath
+Exception could therefore effectively compromise your ability to further
+distribute the package.
+
+Failing to distribute notices associated with some files may also create
+unexpected legal consequences.
+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
+skilled in open source matters before removing the Classpath Exception or
+making modifications to this package which may subsequently be redistributed
+and/or involve the use of third party software.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.web/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Linux/legal/javafx.web/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.web/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
+ regardless of the license terms of the Designated Exception Modules,
+ and to copy and distribute the resulting executable under GPL2,
+ provided that the Designated Exception Modules continue to be
+ governed by the licenses under which they were offered by Oracle.
+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
+to build an executable that includes those portions of necessary code that
+Oracle could not provide under GPL2 (or that Oracle has provided under GPL2
+with the Classpath exception). If you modify or add to the OpenJDK code,
+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.web/LICENSE b/lib/javafx-sdk-14-Linux/legal/javafx.web/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.web/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
+by others will not reflect on the original authors' reputations.
+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
+everyone's free use or not licensed at all.
+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the source
+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.web/icu_web.md b/lib/javafx-sdk-14-Linux/legal/javafx.web/icu_web.md
new file mode 100644
index 0000000..bbdc8d4
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.web/icu_web.md
@@ -0,0 +1,421 @@
+## IBM International Components for Unicode (ICU4C) v64.2
+
+### ICU License
+```
+
+COPYRIGHT AND PERMISSION NOTICE (ICU 58 and later)
+
+Copyright © 1991-2019 Unicode, Inc. All rights reserved.
+Distributed under the Terms of Use in https://www.unicode.org/copyright.html.
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of the Unicode data files and any associated documentation
+(the "Data Files") or Unicode software and any associated documentation
+(the "Software") to deal in the Data Files or Software
+without restriction, including without limitation the rights to use,
+copy, modify, merge, publish, distribute, and/or sell copies of
+the Data Files or Software, and to permit persons to whom the Data Files
+or Software are furnished to do so, provided that either
+(a) this copyright and permission notice appear with all copies
+of the Data Files or Software, or
+(b) this copyright and permission notice appear in associated
+Documentation.
+
+THE DATA FILES AND SOFTWARE ARE PROVIDED "AS IS", WITHOUT WARRANTY OF
+ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
+WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT OF THIRD PARTY RIGHTS.
+IN NO EVENT SHALL THE COPYRIGHT HOLDER OR HOLDERS INCLUDED IN THIS
+NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL INDIRECT OR CONSEQUENTIAL
+DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE,
+DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
+TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
+PERFORMANCE OF THE DATA FILES OR SOFTWARE.
+
+Except as contained in this notice, the name of a copyright holder
+shall not be used in advertising or otherwise to promote the sale,
+use or other dealings in these Data Files or Software without prior
+written authorization of the copyright holder.
+
+---------------------
+
+Third-Party Software Licenses
+
+This section contains third-party software notices and/or additional
+terms for licensed third-party software components included within ICU
+libraries.
+
+1. ICU License - ICU 1.8.1 to ICU 57.1
+
+COPYRIGHT AND PERMISSION NOTICE
+
+Copyright (c) 1995-2016 International Business Machines Corporation and others
+All rights reserved.
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, and/or sell copies of the Software, and to permit persons
+to whom the Software is furnished to do so, provided that the above
+copyright notice(s) and this permission notice appear in all copies of
+the Software and that both the above copyright notice(s) and this
+permission notice appear in supporting documentation.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
+OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY
+SPECIAL INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER
+RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF
+CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN
+CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+
+Except as contained in this notice, the name of a copyright holder
+shall not be used in advertising or otherwise to promote the sale, use
+or other dealings in this Software without prior written authorization
+of the copyright holder.
+
+All trademarks and registered trademarks mentioned herein are the
+property of their respective owners.
+
+2. Chinese/Japanese Word Break Dictionary Data (cjdict.txt)
+
+ # The Google Chrome software developed by Google is licensed under
+ # the BSD license. Other software included in this distribution is
+ # provided under other licenses, as set forth below.
+ #
+ # The BSD License
+ # http://opensource.org/licenses/bsd-license.php
+ # Copyright (C) 2006-2008, Google Inc.
+ #
+ # All rights reserved.
+ #
+ # Redistribution and use in source and binary forms, with or without
+ # modification, are permitted provided that the following conditions are met:
+ #
+ # Redistributions of source code must retain the above copyright notice,
+ # this list of conditions and the following disclaimer.
+ # Redistributions in binary form must reproduce the above
+ # copyright notice, this list of conditions and the following
+ # disclaimer in the documentation and/or other materials provided with
+ # the distribution.
+ # Neither the name of Google Inc. nor the names of its
+ # contributors may be used to endorse or promote products derived from
+ # this software without specific prior written permission.
+ #
+ #
+ # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ # CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ # INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+ # MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ # DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ # BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ # LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ # NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ #
+ #
+ # The word list in cjdict.txt are generated by combining three word lists
+ # listed below with further processing for compound word breaking. The
+ # frequency is generated with an iterative training against Google web
+ # corpora.
+ #
+ # * Libtabe (Chinese)
+ # - https://sourceforge.net/project/?group_id=1519
+ # - Its license terms and conditions are shown below.
+ #
+ # * IPADIC (Japanese)
+ # - http://chasen.aist-nara.ac.jp/chasen/distribution.html
+ # - Its license terms and conditions are shown below.
+ #
+ # ---------COPYING.libtabe ---- BEGIN--------------------
+ #
+ # /*
+ # * Copyright (c) 1999 TaBE Project.
+ # * Copyright (c) 1999 Pai-Hsiang Hsiao.
+ # * All rights reserved.
+ # *
+ # * Redistribution and use in source and binary forms, with or without
+ # * modification, are permitted provided that the following conditions
+ # * are met:
+ # *
+ # * . Redistributions of source code must retain the above copyright
+ # * notice, this list of conditions and the following disclaimer.
+ # * . Redistributions in binary form must reproduce the above copyright
+ # * notice, this list of conditions and the following disclaimer in
+ # * the documentation and/or other materials provided with the
+ # * distribution.
+ # * . Neither the name of the TaBE Project nor the names of its
+ # * contributors may be used to endorse or promote products derived
+ # * from this software without specific prior written permission.
+ # *
+ # * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ # * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ # * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+ # * FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+ # * REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ # * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ # * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ # * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ # * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ # * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ # * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+ # * OF THE POSSIBILITY OF SUCH DAMAGE.
+ # */
+ #
+ # /*
+ # * Copyright (c) 1999 Computer Systems and Communication Lab,
+ # * Institute of Information Science, Academia
+ # * Sinica. All rights reserved.
+ # *
+ # * Redistribution and use in source and binary forms, with or without
+ # * modification, are permitted provided that the following conditions
+ # * are met:
+ # *
+ # * . Redistributions of source code must retain the above copyright
+ # * notice, this list of conditions and the following disclaimer.
+ # * . Redistributions in binary form must reproduce the above copyright
+ # * notice, this list of conditions and the following disclaimer in
+ # * the documentation and/or other materials provided with the
+ # * distribution.
+ # * . Neither the name of the Computer Systems and Communication Lab
+ # * nor the names of its contributors may be used to endorse or
+ # * promote products derived from this software without specific
+ # * prior written permission.
+ # *
+ # * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ # * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ # * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+ # * FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+ # * REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ # * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ # * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ # * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ # * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ # * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ # * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+ # * OF THE POSSIBILITY OF SUCH DAMAGE.
+ # */
+ #
+ # Copyright 1996 Chih-Hao Tsai @ Beckman Institute,
+ # University of Illinois
+ # c-tsai4@uiuc.edu http://casper.beckman.uiuc.edu/~c-tsai4
+ #
+ # ---------------COPYING.libtabe-----END--------------------------------
+ #
+ #
+ # ---------------COPYING.ipadic-----BEGIN-------------------------------
+ #
+ # Copyright 2000, 2001, 2002, 2003 Nara Institute of Science
+ # and Technology. All Rights Reserved.
+ #
+ # Use, reproduction, and distribution of this software is permitted.
+ # Any copy of this software, whether in its original form or modified,
+ # must include both the above copyright notice and the following
+ # paragraphs.
+ #
+ # Nara Institute of Science and Technology (NAIST),
+ # the copyright holders, disclaims all warranties with regard to this
+ # software, including all implied warranties of merchantability and
+ # fitness, in no event shall NAIST be liable for
+ # any special, indirect or consequential damages or any damages
+ # whatsoever resulting from loss of use, data or profits, whether in an
+ # action of contract, negligence or other tortuous action, arising out
+ # of or in connection with the use or performance of this software.
+ #
+ # A large portion of the dictionary entries
+ # originate from ICOT Free Software. The following conditions for ICOT
+ # Free Software applies to the current dictionary as well.
+ #
+ # Each User may also freely distribute the Program, whether in its
+ # original form or modified, to any third party or parties, PROVIDED
+ # that the provisions of Section 3 ("NO WARRANTY") will ALWAYS appear
+ # on, or be attached to, the Program, which is distributed substantially
+ # in the same form as set out herein and that such intended
+ # distribution, if actually made, will neither violate or otherwise
+ # contravene any of the laws and regulations of the countries having
+ # jurisdiction over the User or the intended distribution itself.
+ #
+ # NO WARRANTY
+ #
+ # The program was produced on an experimental basis in the course of the
+ # research and development conducted during the project and is provided
+ # to users as so produced on an experimental basis. Accordingly, the
+ # program is provided without any warranty whatsoever, whether express,
+ # implied, statutory or otherwise. The term "warranty" used herein
+ # includes, but is not limited to, any warranty of the quality,
+ # performance, merchantability and fitness for a particular purpose of
+ # the program and the nonexistence of any infringement or violation of
+ # any right of any third party.
+ #
+ # Each user of the program will agree and understand, and be deemed to
+ # have agreed and understood, that there is no warranty whatsoever for
+ # the program and, accordingly, the entire risk arising from or
+ # otherwise connected with the program is assumed by the user.
+ #
+ # Therefore, neither ICOT, the copyright holder, or any other
+ # organization that participated in or was otherwise related to the
+ # development of the program and their respective officials, directors,
+ # officers and other employees shall be held liable for any and all
+ # damages, including, without limitation, general, special, incidental
+ # and consequential damages, arising out of or otherwise in connection
+ # with the use or inability to use the program or any product, material
+ # or result produced or otherwise obtained by using the program,
+ # regardless of whether they have been advised of, or otherwise had
+ # knowledge of, the possibility of such damages at any time during the
+ # project or thereafter. Each user will be deemed to have agreed to the
+ # foregoing by his or her commencement of use of the program. The term
+ # "use" as used herein includes, but is not limited to, the use,
+ # modification, copying and distribution of the program and the
+ # production of secondary products from the program.
+ #
+ # In the case where the program, whether in its original form or
+ # modified, was distributed or delivered to or received by a user from
+ # any person, organization or entity other than ICOT, unless it makes or
+ # grants independently of ICOT any specific warranty to the user in
+ # writing, such person, organization or entity, will also be exempted
+ # from and not be held liable to the user for any such damages as noted
+ # above as far as the program is concerned.
+ #
+ # ---------------COPYING.ipadic-----END----------------------------------
+
+3. Lao Word Break Dictionary Data (laodict.txt)
+
+ # Copyright (c) 2013 International Business Machines Corporation
+ # and others. All Rights Reserved.
+ #
+ # Project: http://code.google.com/p/lao-dictionary/
+ # Dictionary: http://lao-dictionary.googlecode.com/git/Lao-Dictionary.txt
+ # License: http://lao-dictionary.googlecode.com/git/Lao-Dictionary-LICENSE.txt
+ # (copied below)
+ #
+ # This file is derived from the above dictionary, with slight
+ # modifications.
+ # ----------------------------------------------------------------------
+ # Copyright (C) 2013 Brian Eugene Wilson, Robert Martin Campbell.
+ # All rights reserved.
+ #
+ # Redistribution and use in source and binary forms, with or without
+ # modification,
+ # are permitted provided that the following conditions are met:
+ #
+ #
+ # Redistributions of source code must retain the above copyright notice, this
+ # list of conditions and the following disclaimer. Redistributions in
+ # binary form must reproduce the above copyright notice, this list of
+ # conditions and the following disclaimer in the documentation and/or
+ # other materials provided with the distribution.
+ #
+ #
+ # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ # "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ # LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+ # FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+ # COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ # INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ # (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ # SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ # HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ # STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+ # OF THE POSSIBILITY OF SUCH DAMAGE.
+ # --------------------------------------------------------------------------
+
+4. Burmese Word Break Dictionary Data (burmesedict.txt)
+
+ # Copyright (c) 2014 International Business Machines Corporation
+ # and others. All Rights Reserved.
+ #
+ # This list is part of a project hosted at:
+ # github.com/kanyawtech/myanmar-karen-word-lists
+ #
+ # --------------------------------------------------------------------------
+ # Copyright (c) 2013, LeRoy Benjamin Sharon
+ # All rights reserved.
+ #
+ # Redistribution and use in source and binary forms, with or without
+ # modification, are permitted provided that the following conditions
+ # are met: Redistributions of source code must retain the above
+ # copyright notice, this list of conditions and the following
+ # disclaimer. Redistributions in binary form must reproduce the
+ # above copyright notice, this list of conditions and the following
+ # disclaimer in the documentation and/or other materials provided
+ # with the distribution.
+ #
+ # Neither the name Myanmar Karen Word Lists, nor the names of its
+ # contributors may be used to endorse or promote products derived
+ # from this software without specific prior written permission.
+ #
+ # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ # CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ # INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+ # MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ # DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS
+ # BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ # EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+ # TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ # DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ # ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
+ # TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF
+ # THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ # SUCH DAMAGE.
+ # --------------------------------------------------------------------------
+
+5. Time Zone Database
+
+ ICU uses the public domain data and code derived from Time Zone
+Database for its time zone support. The ownership of the TZ database
+is explained in BCP 175: Procedure for Maintaining the Time Zone
+Database section 7.
+
+ # 7. Database Ownership
+ #
+ # The TZ database itself is not an IETF Contribution or an IETF
+ # document. Rather it is a pre-existing and regularly updated work
+ # that is in the public domain, and is intended to remain in the
+ # public domain. Therefore, BCPs 78 [RFC5378] and 79 [RFC3979] do
+ # not apply to the TZ Database or contributions that individuals make
+ # to it. Should any claims be made and substantiated against the TZ
+ # Database, the organization that is providing the IANA
+ # Considerations defined in this RFC, under the memorandum of
+ # understanding with the IETF, currently ICANN, may act in accordance
+ # with all competent court orders. No ownership claims will be made
+ # by ICANN or the IETF Trust on the database or the code. Any person
+ # making a contribution to the database or code waives all rights to
+ # future claims in that contribution or in the TZ Database.
+
+6. Google double-conversion
+
+Copyright 2006-2011, the V8 project authors. All rights reserved.
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+ * Neither the name of Google Inc. nor the names of its
+ contributors may be used to endorse or promote products derived
+ from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+```
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.web/libxml2.md b/lib/javafx-sdk-14-Linux/legal/javafx.web/libxml2.md
new file mode 100644
index 0000000..2c21817
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.web/libxml2.md
@@ -0,0 +1,30 @@
+## xmlsoft.org: libxml2 v2.9.9
+
+### libxml2 License
+```
+
+Except where otherwise noted in the source code (e.g. the files hash.c,
+list.c and the trio files, which are covered by a similar licence but
+with different Copyright notices) all the files are:
+
+Copyright (C) 1998-2012 Daniel Veillard. All Rights Reserved.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+```
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.web/libxslt.md b/lib/javafx-sdk-14-Linux/legal/javafx.web/libxslt.md
new file mode 100644
index 0000000..c0e5bd6
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.web/libxslt.md
@@ -0,0 +1,60 @@
+## xmlsoft.org: libxslt v1.1.34
+
+### libxslt License
+```
+
+Licence for libxslt except libexslt
+----------------------------------------------------------------------
+ Copyright (C) 2001-2002 Daniel Veillard. All Rights Reserved.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is fur-
+nished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FIT-
+NESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+DANIEL VEILLARD BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CON-
+NECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+Except as contained in this notice, the name of Daniel Veillard shall not
+be used in advertising or otherwise to promote the sale, use or other deal-
+ings in this Software without prior written authorization from him.
+
+----------------------------------------------------------------------
+
+Licence for libexslt
+----------------------------------------------------------------------
+ Copyright (C) 2001-2002 Thomas Broyer, Charlie Bozeman and Daniel Veillard.
+ All Rights Reserved.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is fur-
+nished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FIT-
+NESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CON-
+NECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+Except as contained in this notice, the name of the authors shall not
+be used in advertising or otherwise to promote the sale, use or other deal-
+ings in this Software without prior written authorization from him.
+----------------------------------------------------------------------
+
+```
diff --git a/lib/javafx-sdk-14-Linux/legal/javafx.web/webkit.md b/lib/javafx-sdk-14-Linux/legal/javafx.web/webkit.md
new file mode 100644
index 0000000..e4cbc1e
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/legal/javafx.web/webkit.md
@@ -0,0 +1,535 @@
+## WebKit Open Source Project: WebKit v608.1
+
+### WebKit Notice
+```
+
+You are receiving a copy of WebKit in either source or
+object code in the JavaFX runtime or JavaFX SDK. The terms of the
+Oracle license do NOT apply to WebKit; it is
+licensed under the following license, separately from the Oracle programs
+you receive. If you do not wish to install this library, you may delete
+this library:
+
+ - On Linux systems: delete $(JAVA_HOME)/lib/libjfxwebkit.so
+ - On Mac OS X systems: delete $(JAVA_HOME)/lib/libjfxwebkit.dylib
+ - On Windows systems: delete $(JAVA_HOME)\bin\jfxwebkit.dll
+
+A copy of the Oracle modified WebKit library source code is located
+in the following OpenJDK git repository:
+
+ https://github.com/openjdk/jfx
+
+You can use git to clone the repository or you can browse the
+source using a web browser. The root directory of the WebKit source
+code is here:
+
+ rt/modules/javafx.web/src/main/native/
+```
+
+### LGPL 2.1
+```
+
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 2.1, February 1999
+
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+[This is the first released version of the Lesser GPL. It also counts
+ as the successor of the GNU Library Public License, version 2, hence
+ the version number 2.1.]
+
+ Preamble
+
+ The licenses for most software are designed to take away your
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+can use it too, but we suggest you first think carefully about whether
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+
+ When we speak of free software, we are referring to freedom of use,
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+ Copyright (C)
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+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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+
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+ library `Frob' (a library for tweaking knobs) written by James Random Hacker.
+
+ , 1 April 1990
+ Ty Coon, President of Vice
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+That's all there is to it!
+
+```
diff --git a/lib/javafx-sdk-14-Linux/lib/javafx-swt.jar b/lib/javafx-sdk-14-Linux/lib/javafx-swt.jar
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diff --git a/lib/javafx-sdk-14-Linux/lib/javafx.base.jar b/lib/javafx-sdk-14-Linux/lib/javafx.base.jar
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diff --git a/lib/javafx-sdk-14-Linux/lib/javafx.graphics.jar b/lib/javafx-sdk-14-Linux/lib/javafx.graphics.jar
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diff --git a/lib/javafx-sdk-14-Linux/lib/javafx.media.jar b/lib/javafx-sdk-14-Linux/lib/javafx.media.jar
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diff --git a/lib/javafx-sdk-14-Linux/lib/javafx.properties b/lib/javafx-sdk-14-Linux/lib/javafx.properties
new file mode 100644
index 0000000..942da72
--- /dev/null
+++ b/lib/javafx-sdk-14-Linux/lib/javafx.properties
@@ -0,0 +1,3 @@
+javafx.version=14
+javafx.runtime.version=14+9
+javafx.runtime.build=9
diff --git a/lib/javafx-sdk-14-Linux/lib/javafx.swing.jar b/lib/javafx-sdk-14-Linux/lib/javafx.swing.jar
new file mode 100644
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diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.base/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Mac/legal/javafx.base/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.base/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
+package. Some of those programs are provided under licenses deemed
+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
+License, Version 2.0 and may include FreeType. Such programs are licensed
+to you under their original licenses.
+
+Oracle facilitates your further distribution of this package by adding the
+Classpath Exception to the necessary parts of its GPLv2 code, which permits
+you to use that code in combination with other independent modules not
+licensed under the GPLv2. However, note that this would not permit you to
+commingle code under an incompatible license with Oracle's GPLv2 licensed
+code by, for example, cutting and pasting such code into a file also
+containing Oracle's GPLv2 licensed code and then distributing the result.
+
+Additionally, if you were to remove the Classpath Exception from any of the
+files to which it applies and distribute the result, you would likely be
+required to license some or all of the other code in that distribution under
+the GPLv2 as well, and since the GPLv2 is incompatible with the license terms
+of some items included in the distribution by Oracle, removing the Classpath
+Exception could therefore effectively compromise your ability to further
+distribute the package.
+
+Failing to distribute notices associated with some files may also create
+unexpected legal consequences.
+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
+skilled in open source matters before removing the Classpath Exception or
+making modifications to this package which may subsequently be redistributed
+and/or involve the use of third party software.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.base/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Mac/legal/javafx.base/ASSEMBLY_EXCEPTION
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index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.base/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
+ regardless of the license terms of the Designated Exception Modules,
+ and to copy and distribute the resulting executable under GPL2,
+ provided that the Designated Exception Modules continue to be
+ governed by the licenses under which they were offered by Oracle.
+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
+to build an executable that includes those portions of necessary code that
+Oracle could not provide under GPL2 (or that Oracle has provided under GPL2
+with the Classpath exception). If you modify or add to the OpenJDK code,
+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.base/LICENSE b/lib/javafx-sdk-14-Mac/legal/javafx.base/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.base/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
+by others will not reflect on the original authors' reputations.
+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
+everyone's free use or not licensed at all.
+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the source
+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.controls/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Mac/legal/javafx.controls/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.controls/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
+package. Some of those programs are provided under licenses deemed
+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
+License, Version 2.0 and may include FreeType. Such programs are licensed
+to you under their original licenses.
+
+Oracle facilitates your further distribution of this package by adding the
+Classpath Exception to the necessary parts of its GPLv2 code, which permits
+you to use that code in combination with other independent modules not
+licensed under the GPLv2. However, note that this would not permit you to
+commingle code under an incompatible license with Oracle's GPLv2 licensed
+code by, for example, cutting and pasting such code into a file also
+containing Oracle's GPLv2 licensed code and then distributing the result.
+
+Additionally, if you were to remove the Classpath Exception from any of the
+files to which it applies and distribute the result, you would likely be
+required to license some or all of the other code in that distribution under
+the GPLv2 as well, and since the GPLv2 is incompatible with the license terms
+of some items included in the distribution by Oracle, removing the Classpath
+Exception could therefore effectively compromise your ability to further
+distribute the package.
+
+Failing to distribute notices associated with some files may also create
+unexpected legal consequences.
+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
+skilled in open source matters before removing the Classpath Exception or
+making modifications to this package which may subsequently be redistributed
+and/or involve the use of third party software.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.controls/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Mac/legal/javafx.controls/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.controls/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
+ regardless of the license terms of the Designated Exception Modules,
+ and to copy and distribute the resulting executable under GPL2,
+ provided that the Designated Exception Modules continue to be
+ governed by the licenses under which they were offered by Oracle.
+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
+to build an executable that includes those portions of necessary code that
+Oracle could not provide under GPL2 (or that Oracle has provided under GPL2
+with the Classpath exception). If you modify or add to the OpenJDK code,
+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.controls/LICENSE b/lib/javafx-sdk-14-Mac/legal/javafx.controls/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.controls/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
+by others will not reflect on the original authors' reputations.
+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
+everyone's free use or not licensed at all.
+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the source
+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.fxml/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Mac/legal/javafx.fxml/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.fxml/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
+package. Some of those programs are provided under licenses deemed
+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
+License, Version 2.0 and may include FreeType. Such programs are licensed
+to you under their original licenses.
+
+Oracle facilitates your further distribution of this package by adding the
+Classpath Exception to the necessary parts of its GPLv2 code, which permits
+you to use that code in combination with other independent modules not
+licensed under the GPLv2. However, note that this would not permit you to
+commingle code under an incompatible license with Oracle's GPLv2 licensed
+code by, for example, cutting and pasting such code into a file also
+containing Oracle's GPLv2 licensed code and then distributing the result.
+
+Additionally, if you were to remove the Classpath Exception from any of the
+files to which it applies and distribute the result, you would likely be
+required to license some or all of the other code in that distribution under
+the GPLv2 as well, and since the GPLv2 is incompatible with the license terms
+of some items included in the distribution by Oracle, removing the Classpath
+Exception could therefore effectively compromise your ability to further
+distribute the package.
+
+Failing to distribute notices associated with some files may also create
+unexpected legal consequences.
+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
+skilled in open source matters before removing the Classpath Exception or
+making modifications to this package which may subsequently be redistributed
+and/or involve the use of third party software.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.fxml/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Mac/legal/javafx.fxml/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.fxml/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
+ regardless of the license terms of the Designated Exception Modules,
+ and to copy and distribute the resulting executable under GPL2,
+ provided that the Designated Exception Modules continue to be
+ governed by the licenses under which they were offered by Oracle.
+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
+to build an executable that includes those portions of necessary code that
+Oracle could not provide under GPL2 (or that Oracle has provided under GPL2
+with the Classpath exception). If you modify or add to the OpenJDK code,
+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.fxml/LICENSE b/lib/javafx-sdk-14-Mac/legal/javafx.fxml/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.fxml/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
+by others will not reflect on the original authors' reputations.
+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
+everyone's free use or not licensed at all.
+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the source
+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.graphics/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Mac/legal/javafx.graphics/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.graphics/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
+package. Some of those programs are provided under licenses deemed
+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
+License, Version 2.0 and may include FreeType. Such programs are licensed
+to you under their original licenses.
+
+Oracle facilitates your further distribution of this package by adding the
+Classpath Exception to the necessary parts of its GPLv2 code, which permits
+you to use that code in combination with other independent modules not
+licensed under the GPLv2. However, note that this would not permit you to
+commingle code under an incompatible license with Oracle's GPLv2 licensed
+code by, for example, cutting and pasting such code into a file also
+containing Oracle's GPLv2 licensed code and then distributing the result.
+
+Additionally, if you were to remove the Classpath Exception from any of the
+files to which it applies and distribute the result, you would likely be
+required to license some or all of the other code in that distribution under
+the GPLv2 as well, and since the GPLv2 is incompatible with the license terms
+of some items included in the distribution by Oracle, removing the Classpath
+Exception could therefore effectively compromise your ability to further
+distribute the package.
+
+Failing to distribute notices associated with some files may also create
+unexpected legal consequences.
+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
+skilled in open source matters before removing the Classpath Exception or
+making modifications to this package which may subsequently be redistributed
+and/or involve the use of third party software.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.graphics/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Mac/legal/javafx.graphics/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.graphics/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
+ regardless of the license terms of the Designated Exception Modules,
+ and to copy and distribute the resulting executable under GPL2,
+ provided that the Designated Exception Modules continue to be
+ governed by the licenses under which they were offered by Oracle.
+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
+to build an executable that includes those portions of necessary code that
+Oracle could not provide under GPL2 (or that Oracle has provided under GPL2
+with the Classpath exception). If you modify or add to the OpenJDK code,
+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.graphics/LICENSE b/lib/javafx-sdk-14-Mac/legal/javafx.graphics/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.graphics/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
+by others will not reflect on the original authors' reputations.
+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
+everyone's free use or not licensed at all.
+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the source
+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.graphics/jpeg_fx.md b/lib/javafx-sdk-14-Mac/legal/javafx.graphics/jpeg_fx.md
new file mode 100644
index 0000000..b98f177
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.graphics/jpeg_fx.md
@@ -0,0 +1,51 @@
+## Independent JPEG Group (IJG) JPEG v9c
+
+### IJG License
+```
+
+/*
+ * jcapimin.c
+ *
+ * Copyright (C) 1994-1998, Thomas G. Lane.
+ * Modified 2003-2010 by Guido Vollbeding.
+ * This file is part of the Independent JPEG Group's software.
+ * For conditions of distribution and use, see the accompanying README file.
+ */
+
+[From the README file]
+The authors make NO WARRANTY or representation, either express or implied,
+with respect to this software, its quality, accuracy, merchantability, or
+fitness for a particular purpose. This software is provided "AS IS", and you,
+its user, assume the entire risk as to its quality and accuracy.
+
+This software is copyright (C) 1991-2018, Thomas G. Lane, Guido Vollbeding.
+All Rights Reserved except as specified below.
+
+Permission is hereby granted to use, copy, modify, and distribute this
+software (or portions thereof) for any purpose, without fee, subject to these
+conditions:
+(1) If any part of the source code for this software is distributed, then this
+README file must be included, with this copyright and no-warranty notice
+unaltered; and any additions, deletions, or changes to the original files
+must be clearly indicated in accompanying documentation.
+(2) If only executable code is distributed, then the accompanying
+documentation must state that "this software is based in part on the work of
+the Independent JPEG Group".
+(3) Permission for use of this software is granted only if the user accepts
+full responsibility for any undesirable consequences; the authors accept
+NO LIABILITY for damages of any kind.
+
+These conditions apply to any software derived from or based on the IJG code,
+not just to the unmodified library. If you use our work, you ought to
+acknowledge us.
+
+Permission is NOT granted for the use of any IJG author's name or company name
+in advertising or publicity relating to this software or products derived from
+it. This software may be referred to only as "the Independent JPEG Group's
+software".
+
+We specifically permit and encourage the use of this software as the basis of
+commercial products, provided that all warranty or liability claims are
+assumed by the product vendor.
+
+```
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.graphics/mesa3d.md b/lib/javafx-sdk-14-Mac/legal/javafx.graphics/mesa3d.md
new file mode 100644
index 0000000..b3f32d8
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.graphics/mesa3d.md
@@ -0,0 +1,134 @@
+## Mesa 3-D Graphics Library v19.2.1
+
+### Mesa License
+
+```
+Copyright (C) 1999-2007 Brian Paul All Rights Reserved.
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the "Software"),
+to deal in the Software without restriction, including without limitation
+the rights to use, copy, modify, merge, publish, distribute, sublicense,
+and/or sell copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included
+in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+Attention, Contributors
+
+When contributing to the Mesa project you must agree to the licensing terms
+of the component to which you're contributing.
+The following section lists the primary components of the Mesa distribution
+and their respective licenses.
+Mesa Component Licenses
+
+
+
+Component Location License
+------------------------------------------------------------------
+Main Mesa code src/mesa/ MIT
+Device drivers src/mesa/drivers/* MIT, generally
+
+Gallium code src/gallium/ MIT
+
+Ext headers GL/glext.h Khronos
+ GL/glxext.h Khronos
+ GL/wglext.h Khronos
+ KHR/khrplatform.h Khronos
+
+*****************************************************************************
+
+----
+include/GL/gl.h :
+
+
+ Mesa 3-D graphics library
+
+ Copyright (C) 1999-2006 Brian Paul All Rights Reserved.
+ Copyright (C) 2009 VMware, Inc. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and associated documentation files (the "Software"),
+ to deal in the Software without restriction, including without limitation
+ the rights to use, copy, modify, merge, publish, distribute, sublicense,
+ and/or sell copies of the Software, and to permit persons to whom the
+ Software is furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+ THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
+ OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+ ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ OTHER DEALINGS IN THE SOFTWARE.
+
+ *****************************************************************************
+
+----
+include/GL/glext.h
+include/GL/glxext.h
+include/GL/wglxext.h :
+
+
+ Copyright (c) 2013 - 2018 The Khronos Group Inc.
+
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and/or associated documentation files (the
+ "Materials"), to deal in the Materials without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Materials, and to
+ permit persons to whom the Materials are furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Materials.
+
+ THE MATERIALS ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ MATERIALS OR THE USE OR OTHER DEALINGS IN THE MATERIALS.
+
+ *****************************************************************************
+
+----
+include/KHR/khrplatform.h :
+
+ Copyright (c) 2008 - 2018 The Khronos Group Inc.
+
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and/or associated documentation files (the
+ "Materials"), to deal in the Materials without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Materials, and to
+ permit persons to whom the Materials are furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Materials.
+
+ THE MATERIALS ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ MATERIALS OR THE USE OR OTHER DEALINGS IN THE MATERIALS.
+
+ *****************************************************************************
+
+```
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.media/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Mac/legal/javafx.media/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.media/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
+package. Some of those programs are provided under licenses deemed
+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
+License, Version 2.0 and may include FreeType. Such programs are licensed
+to you under their original licenses.
+
+Oracle facilitates your further distribution of this package by adding the
+Classpath Exception to the necessary parts of its GPLv2 code, which permits
+you to use that code in combination with other independent modules not
+licensed under the GPLv2. However, note that this would not permit you to
+commingle code under an incompatible license with Oracle's GPLv2 licensed
+code by, for example, cutting and pasting such code into a file also
+containing Oracle's GPLv2 licensed code and then distributing the result.
+
+Additionally, if you were to remove the Classpath Exception from any of the
+files to which it applies and distribute the result, you would likely be
+required to license some or all of the other code in that distribution under
+the GPLv2 as well, and since the GPLv2 is incompatible with the license terms
+of some items included in the distribution by Oracle, removing the Classpath
+Exception could therefore effectively compromise your ability to further
+distribute the package.
+
+Failing to distribute notices associated with some files may also create
+unexpected legal consequences.
+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
+skilled in open source matters before removing the Classpath Exception or
+making modifications to this package which may subsequently be redistributed
+and/or involve the use of third party software.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.media/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Mac/legal/javafx.media/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.media/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
+ regardless of the license terms of the Designated Exception Modules,
+ and to copy and distribute the resulting executable under GPL2,
+ provided that the Designated Exception Modules continue to be
+ governed by the licenses under which they were offered by Oracle.
+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
+to build an executable that includes those portions of necessary code that
+Oracle could not provide under GPL2 (or that Oracle has provided under GPL2
+with the Classpath exception). If you modify or add to the OpenJDK code,
+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.media/LICENSE b/lib/javafx-sdk-14-Mac/legal/javafx.media/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.media/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
+by others will not reflect on the original authors' reputations.
+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
+everyone's free use or not licensed at all.
+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
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diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.media/applecoreaudio.md b/lib/javafx-sdk-14-Mac/legal/javafx.media/applecoreaudio.md
new file mode 100644
index 0000000..5bf2a73
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.media/applecoreaudio.md
@@ -0,0 +1,53 @@
+## Apple Computer: CoreAudio Utility Classes v2.0
+
+### Apple Computer CoreAudio Notice
+This software is present only on Mac OS X systems.
+
+### Apple Computer CoreAudio License
+```
+
+File:
+Abstract: Part of CoreAudio Utility Classes
+Version: 1.1
+
+Disclaimer: IMPORTANT: This Apple software is supplied to you by Apple
+Inc. ("Apple") in consideration of your agreement to the following
+terms, and your use, installation, modification or redistribution of
+this Apple software constitutes acceptance of these terms. If you do
+not agree with these terms, please do not use, install, modify or
+redistribute this Apple software.
+
+In consideration of your agreement to abide by the following terms, and
+subject to these terms, Apple grants you a personal, non-exclusive
+license, under Apple's copyrights in this original Apple software (the
+"Apple Software"), to use, reproduce, modify and redistribute the Apple
+Software, with or without modifications, in source and/or binary forms;
+provided that if you redistribute the Apple Software in its entirety and
+without modifications, you must retain this notice and the following
+text and disclaimers in all such redistributions of the Apple Software.
+Neither the name, trademarks, service marks or logos of Apple Inc. may
+be used to endorse or promote products derived from the Apple Software
+without specific prior written permission from Apple. Except as
+expressly stated in this notice, no other rights or licenses, express or
+implied, are granted by Apple herein, including but not limited to any
+patent rights that may be infringed by your derivative works or by other
+works in which the Apple Software may be incorporated.
+
+The Apple Software is provided by Apple on an "AS IS" basis. APPLE
+MAKES NO WARRANTIES, EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION
+THE IMPLIED WARRANTIES OF NON-INFRINGEMENT, MERCHANTABILITY AND FITNESS
+FOR A PARTICULAR PURPOSE, REGARDING THE APPLE SOFTWARE OR ITS USE AND
+OPERATION ALONE OR IN COMBINATION WITH YOUR PRODUCTS.
+
+IN NO EVENT SHALL APPLE BE LIABLE FOR ANY SPECIAL, INDIRECT, INCIDENTAL
+OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) ARISING IN ANY WAY OUT OF THE USE, REPRODUCTION,
+MODIFICATION AND/OR DISTRIBUTION OF THE APPLE SOFTWARE, HOWEVER CAUSED
+AND WHETHER UNDER THEORY OF CONTRACT, TORT (INCLUDING NEGLIGENCE),
+STRICT LIABILITY OR OTHERWISE, EVEN IF APPLE HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.
+
+Copyright (C) 2014 Apple Inc. All Rights Reserved.
+
+```
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.media/glib.md b/lib/javafx-sdk-14-Mac/legal/javafx.media/glib.md
new file mode 100644
index 0000000..5858730
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.media/glib.md
@@ -0,0 +1,537 @@
+## GNU Glib v2.62.2
+
+### Glib Notice
+```
+
+You are receiving a copy of GNU Glib, Version: 2.62.2 in either source or
+object code in the JavaFX runtime or JavaFX SDK. The terms of the
+Oracle license do NOT apply to the GNU Glib, Version: 2.62.2; it is
+licensed under the following license, separately from the Oracle programs
+you receive. If you do not wish to install this library, you may delete
+this library:
+
+ - On Linux systems: N/A (library is not present)
+ - On Mac OS X systems: delete $(JAVA_HOME)/lib/libglib-lite.dylib
+ - On Windows systems: delete $(JAVA_HOME)\bin\glib-lite.dll
+
+A copy of the Oracle modified GNU Glib library source code is located
+in the following OpenJDK git repository:
+
+ https://github.com/openjdk/jfx
+
+You can use git to clone the repository or you can browse the
+source using a web browser. The root directory of the GNU Glib source
+code is here:
+
+ rt/modules/javafx.media/src/main/native/gstreamer/3rd_party/glib/
+
+
+```
+
+### LGPL 2.1
+```
+
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 2.1, February 1999
+
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+[This is the first released version of the Lesser GPL. It also counts
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+"copyright" line and a pointer to where the full notice is found.
+
+
+ Copyright (C)
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Also add information on how to contact you by electronic and paper mail.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the library, if
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+ , 1 April 1990
+ Ty Coon, President of Vice
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+That's all there is to it!
+
+```
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.media/gstreamer.md b/lib/javafx-sdk-14-Mac/legal/javafx.media/gstreamer.md
new file mode 100644
index 0000000..8f77613
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.media/gstreamer.md
@@ -0,0 +1,535 @@
+## GStreamer v1.16.1
+
+### GStreamer Notice
+```
+
+You are receiving a copy of GStreamer, Version: 1.16.1 in either source or
+object code in the JavaFX runtime or JavaFX SDK. The terms of the
+Oracle license do NOT apply to the GStreamer, Version: 1.16.1; it is
+licensed under the following license, separately from the Oracle programs
+you receive. If you do not wish to install this library, you may delete
+this library:
+
+ - On Linux systems: delete $(JAVA_HOME)/lib/libgstreamer-lite.so
+ - On Mac OS X systems: delete $(JAVA_HOME)/lib/libgstreamer-lite.dylib
+ - On Windows systems: delete $(JAVA_HOME)\bin\gstreamer-lite.dll
+
+A copy of the Oracle modified GStreamer library source code is located
+in the following OpenJDK git repository:
+
+ https://github.com/openjdk/jfx
+
+You can use git to clone the repository or you can browse the
+source using a web browser. The root directory of the GStreamer source
+code is here:
+
+ rt/modules/javafx.media/src/main/native/gstreamer/gstreamer-lite/
+```
+
+### LGPL 2.1
+```
+
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 2.1, February 1999
+
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+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply,
+and the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system which is
+implemented by public license practices. Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+ 12. If the distribution and/or use of the Library is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Library under this License may add
+an explicit geographical distribution limitation excluding those countries,
+so that distribution is permitted only in or among countries not thus
+excluded. In such case, this License incorporates the limitation as if
+written in the body of this License.
+
+ 13. The Free Software Foundation may publish revised and/or new
+versions of the Lesser General Public License from time to time.
+Such new versions will be similar in spirit to the present version,
+but may differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Library
+specifies a version number of this License which applies to it and
+"any later version", you have the option of following the terms and
+conditions either of that version or of any later version published by
+the Free Software Foundation. If the Library does not specify a
+license version number, you may choose any version ever published by
+the Free Software Foundation.
+
+ 14. If you wish to incorporate parts of the Library into other free
+programs whose distribution conditions are incompatible with these,
+write to the author to ask for permission. For software which is
+copyrighted by the Free Software Foundation, write to the Free
+Software Foundation; we sometimes make exceptions for this. Our
+decision will be guided by the two goals of preserving the free status
+of all derivatives of our free software and of promoting the sharing
+and reuse of software generally.
+
+ NO WARRANTY
+
+ 15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO
+WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
+EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR
+OTHER PARTIES PROVIDE THE LIBRARY "AS IS" WITHOUT WARRANTY OF ANY
+KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE
+LIBRARY IS WITH YOU. SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME
+THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN
+WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY
+AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU
+FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR
+CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
+LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING
+RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
+SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGES.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Libraries
+
+ If you develop a new library, and you want it to be of the greatest
+possible use to the public, we recommend making it free software that
+everyone can redistribute and change. You can do so by permitting
+redistribution under these terms (or, alternatively, under the terms of the
+ordinary General Public License).
+
+ To apply these terms, attach the following notices to the library. It is
+safest to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least the
+"copyright" line and a pointer to where the full notice is found.
+
+
+ Copyright (C)
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Also add information on how to contact you by electronic and paper mail.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the library, if
+necessary. Here is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the
+ library `Frob' (a library for tweaking knobs) written by James Random Hacker.
+
+ , 1 April 1990
+ Ty Coon, President of Vice
+
+That's all there is to it!
+
+```
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.media/libffi.md b/lib/javafx-sdk-14-Mac/legal/javafx.media/libffi.md
new file mode 100644
index 0000000..6915bbc
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.media/libffi.md
@@ -0,0 +1,28 @@
+## LibFFI v3.2.1
+
+### LibFFI License
+```
+
+libffi - Copyright (c) 1996-2014 Anthony Green, Red Hat, Inc and others.
+See source files for details.
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+``Software''), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED ``AS IS'', WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+```
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.swing/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Mac/legal/javafx.swing/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.swing/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
+package. Some of those programs are provided under licenses deemed
+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
+License, Version 2.0 and may include FreeType. Such programs are licensed
+to you under their original licenses.
+
+Oracle facilitates your further distribution of this package by adding the
+Classpath Exception to the necessary parts of its GPLv2 code, which permits
+you to use that code in combination with other independent modules not
+licensed under the GPLv2. However, note that this would not permit you to
+commingle code under an incompatible license with Oracle's GPLv2 licensed
+code by, for example, cutting and pasting such code into a file also
+containing Oracle's GPLv2 licensed code and then distributing the result.
+
+Additionally, if you were to remove the Classpath Exception from any of the
+files to which it applies and distribute the result, you would likely be
+required to license some or all of the other code in that distribution under
+the GPLv2 as well, and since the GPLv2 is incompatible with the license terms
+of some items included in the distribution by Oracle, removing the Classpath
+Exception could therefore effectively compromise your ability to further
+distribute the package.
+
+Failing to distribute notices associated with some files may also create
+unexpected legal consequences.
+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
+skilled in open source matters before removing the Classpath Exception or
+making modifications to this package which may subsequently be redistributed
+and/or involve the use of third party software.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.swing/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Mac/legal/javafx.swing/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.swing/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
+ regardless of the license terms of the Designated Exception Modules,
+ and to copy and distribute the resulting executable under GPL2,
+ provided that the Designated Exception Modules continue to be
+ governed by the licenses under which they were offered by Oracle.
+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
+to build an executable that includes those portions of necessary code that
+Oracle could not provide under GPL2 (or that Oracle has provided under GPL2
+with the Classpath exception). If you modify or add to the OpenJDK code,
+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.swing/LICENSE b/lib/javafx-sdk-14-Mac/legal/javafx.swing/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.swing/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
+by others will not reflect on the original authors' reputations.
+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
+everyone's free use or not licensed at all.
+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the source
+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.web/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Mac/legal/javafx.web/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.web/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
+package. Some of those programs are provided under licenses deemed
+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
+License, Version 2.0 and may include FreeType. Such programs are licensed
+to you under their original licenses.
+
+Oracle facilitates your further distribution of this package by adding the
+Classpath Exception to the necessary parts of its GPLv2 code, which permits
+you to use that code in combination with other independent modules not
+licensed under the GPLv2. However, note that this would not permit you to
+commingle code under an incompatible license with Oracle's GPLv2 licensed
+code by, for example, cutting and pasting such code into a file also
+containing Oracle's GPLv2 licensed code and then distributing the result.
+
+Additionally, if you were to remove the Classpath Exception from any of the
+files to which it applies and distribute the result, you would likely be
+required to license some or all of the other code in that distribution under
+the GPLv2 as well, and since the GPLv2 is incompatible with the license terms
+of some items included in the distribution by Oracle, removing the Classpath
+Exception could therefore effectively compromise your ability to further
+distribute the package.
+
+Failing to distribute notices associated with some files may also create
+unexpected legal consequences.
+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
+skilled in open source matters before removing the Classpath Exception or
+making modifications to this package which may subsequently be redistributed
+and/or involve the use of third party software.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.web/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Mac/legal/javafx.web/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.web/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
+ regardless of the license terms of the Designated Exception Modules,
+ and to copy and distribute the resulting executable under GPL2,
+ provided that the Designated Exception Modules continue to be
+ governed by the licenses under which they were offered by Oracle.
+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
+to build an executable that includes those portions of necessary code that
+Oracle could not provide under GPL2 (or that Oracle has provided under GPL2
+with the Classpath exception). If you modify or add to the OpenJDK code,
+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.web/LICENSE b/lib/javafx-sdk-14-Mac/legal/javafx.web/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.web/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
+by others will not reflect on the original authors' reputations.
+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
+everyone's free use or not licensed at all.
+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the source
+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.web/icu_web.md b/lib/javafx-sdk-14-Mac/legal/javafx.web/icu_web.md
new file mode 100644
index 0000000..bbdc8d4
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.web/icu_web.md
@@ -0,0 +1,421 @@
+## IBM International Components for Unicode (ICU4C) v64.2
+
+### ICU License
+```
+
+COPYRIGHT AND PERMISSION NOTICE (ICU 58 and later)
+
+Copyright © 1991-2019 Unicode, Inc. All rights reserved.
+Distributed under the Terms of Use in https://www.unicode.org/copyright.html.
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of the Unicode data files and any associated documentation
+(the "Data Files") or Unicode software and any associated documentation
+(the "Software") to deal in the Data Files or Software
+without restriction, including without limitation the rights to use,
+copy, modify, merge, publish, distribute, and/or sell copies of
+the Data Files or Software, and to permit persons to whom the Data Files
+or Software are furnished to do so, provided that either
+(a) this copyright and permission notice appear with all copies
+of the Data Files or Software, or
+(b) this copyright and permission notice appear in associated
+Documentation.
+
+THE DATA FILES AND SOFTWARE ARE PROVIDED "AS IS", WITHOUT WARRANTY OF
+ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
+WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT OF THIRD PARTY RIGHTS.
+IN NO EVENT SHALL THE COPYRIGHT HOLDER OR HOLDERS INCLUDED IN THIS
+NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL INDIRECT OR CONSEQUENTIAL
+DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE,
+DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
+TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
+PERFORMANCE OF THE DATA FILES OR SOFTWARE.
+
+Except as contained in this notice, the name of a copyright holder
+shall not be used in advertising or otherwise to promote the sale,
+use or other dealings in these Data Files or Software without prior
+written authorization of the copyright holder.
+
+---------------------
+
+Third-Party Software Licenses
+
+This section contains third-party software notices and/or additional
+terms for licensed third-party software components included within ICU
+libraries.
+
+1. ICU License - ICU 1.8.1 to ICU 57.1
+
+COPYRIGHT AND PERMISSION NOTICE
+
+Copyright (c) 1995-2016 International Business Machines Corporation and others
+All rights reserved.
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, and/or sell copies of the Software, and to permit persons
+to whom the Software is furnished to do so, provided that the above
+copyright notice(s) and this permission notice appear in all copies of
+the Software and that both the above copyright notice(s) and this
+permission notice appear in supporting documentation.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
+OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY
+SPECIAL INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER
+RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF
+CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN
+CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+
+Except as contained in this notice, the name of a copyright holder
+shall not be used in advertising or otherwise to promote the sale, use
+or other dealings in this Software without prior written authorization
+of the copyright holder.
+
+All trademarks and registered trademarks mentioned herein are the
+property of their respective owners.
+
+2. Chinese/Japanese Word Break Dictionary Data (cjdict.txt)
+
+ # The Google Chrome software developed by Google is licensed under
+ # the BSD license. Other software included in this distribution is
+ # provided under other licenses, as set forth below.
+ #
+ # The BSD License
+ # http://opensource.org/licenses/bsd-license.php
+ # Copyright (C) 2006-2008, Google Inc.
+ #
+ # All rights reserved.
+ #
+ # Redistribution and use in source and binary forms, with or without
+ # modification, are permitted provided that the following conditions are met:
+ #
+ # Redistributions of source code must retain the above copyright notice,
+ # this list of conditions and the following disclaimer.
+ # Redistributions in binary form must reproduce the above
+ # copyright notice, this list of conditions and the following
+ # disclaimer in the documentation and/or other materials provided with
+ # the distribution.
+ # Neither the name of Google Inc. nor the names of its
+ # contributors may be used to endorse or promote products derived from
+ # this software without specific prior written permission.
+ #
+ #
+ # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ # CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ # INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+ # MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ # DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ # BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ # LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ # NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ #
+ #
+ # The word list in cjdict.txt are generated by combining three word lists
+ # listed below with further processing for compound word breaking. The
+ # frequency is generated with an iterative training against Google web
+ # corpora.
+ #
+ # * Libtabe (Chinese)
+ # - https://sourceforge.net/project/?group_id=1519
+ # - Its license terms and conditions are shown below.
+ #
+ # * IPADIC (Japanese)
+ # - http://chasen.aist-nara.ac.jp/chasen/distribution.html
+ # - Its license terms and conditions are shown below.
+ #
+ # ---------COPYING.libtabe ---- BEGIN--------------------
+ #
+ # /*
+ # * Copyright (c) 1999 TaBE Project.
+ # * Copyright (c) 1999 Pai-Hsiang Hsiao.
+ # * All rights reserved.
+ # *
+ # * Redistribution and use in source and binary forms, with or without
+ # * modification, are permitted provided that the following conditions
+ # * are met:
+ # *
+ # * . Redistributions of source code must retain the above copyright
+ # * notice, this list of conditions and the following disclaimer.
+ # * . Redistributions in binary form must reproduce the above copyright
+ # * notice, this list of conditions and the following disclaimer in
+ # * the documentation and/or other materials provided with the
+ # * distribution.
+ # * . Neither the name of the TaBE Project nor the names of its
+ # * contributors may be used to endorse or promote products derived
+ # * from this software without specific prior written permission.
+ # *
+ # * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ # * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ # * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+ # * FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+ # * REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ # * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ # * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ # * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ # * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ # * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ # * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+ # * OF THE POSSIBILITY OF SUCH DAMAGE.
+ # */
+ #
+ # /*
+ # * Copyright (c) 1999 Computer Systems and Communication Lab,
+ # * Institute of Information Science, Academia
+ # * Sinica. All rights reserved.
+ # *
+ # * Redistribution and use in source and binary forms, with or without
+ # * modification, are permitted provided that the following conditions
+ # * are met:
+ # *
+ # * . Redistributions of source code must retain the above copyright
+ # * notice, this list of conditions and the following disclaimer.
+ # * . Redistributions in binary form must reproduce the above copyright
+ # * notice, this list of conditions and the following disclaimer in
+ # * the documentation and/or other materials provided with the
+ # * distribution.
+ # * . Neither the name of the Computer Systems and Communication Lab
+ # * nor the names of its contributors may be used to endorse or
+ # * promote products derived from this software without specific
+ # * prior written permission.
+ # *
+ # * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ # * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ # * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+ # * FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+ # * REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ # * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ # * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ # * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ # * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ # * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ # * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+ # * OF THE POSSIBILITY OF SUCH DAMAGE.
+ # */
+ #
+ # Copyright 1996 Chih-Hao Tsai @ Beckman Institute,
+ # University of Illinois
+ # c-tsai4@uiuc.edu http://casper.beckman.uiuc.edu/~c-tsai4
+ #
+ # ---------------COPYING.libtabe-----END--------------------------------
+ #
+ #
+ # ---------------COPYING.ipadic-----BEGIN-------------------------------
+ #
+ # Copyright 2000, 2001, 2002, 2003 Nara Institute of Science
+ # and Technology. All Rights Reserved.
+ #
+ # Use, reproduction, and distribution of this software is permitted.
+ # Any copy of this software, whether in its original form or modified,
+ # must include both the above copyright notice and the following
+ # paragraphs.
+ #
+ # Nara Institute of Science and Technology (NAIST),
+ # the copyright holders, disclaims all warranties with regard to this
+ # software, including all implied warranties of merchantability and
+ # fitness, in no event shall NAIST be liable for
+ # any special, indirect or consequential damages or any damages
+ # whatsoever resulting from loss of use, data or profits, whether in an
+ # action of contract, negligence or other tortuous action, arising out
+ # of or in connection with the use or performance of this software.
+ #
+ # A large portion of the dictionary entries
+ # originate from ICOT Free Software. The following conditions for ICOT
+ # Free Software applies to the current dictionary as well.
+ #
+ # Each User may also freely distribute the Program, whether in its
+ # original form or modified, to any third party or parties, PROVIDED
+ # that the provisions of Section 3 ("NO WARRANTY") will ALWAYS appear
+ # on, or be attached to, the Program, which is distributed substantially
+ # in the same form as set out herein and that such intended
+ # distribution, if actually made, will neither violate or otherwise
+ # contravene any of the laws and regulations of the countries having
+ # jurisdiction over the User or the intended distribution itself.
+ #
+ # NO WARRANTY
+ #
+ # The program was produced on an experimental basis in the course of the
+ # research and development conducted during the project and is provided
+ # to users as so produced on an experimental basis. Accordingly, the
+ # program is provided without any warranty whatsoever, whether express,
+ # implied, statutory or otherwise. The term "warranty" used herein
+ # includes, but is not limited to, any warranty of the quality,
+ # performance, merchantability and fitness for a particular purpose of
+ # the program and the nonexistence of any infringement or violation of
+ # any right of any third party.
+ #
+ # Each user of the program will agree and understand, and be deemed to
+ # have agreed and understood, that there is no warranty whatsoever for
+ # the program and, accordingly, the entire risk arising from or
+ # otherwise connected with the program is assumed by the user.
+ #
+ # Therefore, neither ICOT, the copyright holder, or any other
+ # organization that participated in or was otherwise related to the
+ # development of the program and their respective officials, directors,
+ # officers and other employees shall be held liable for any and all
+ # damages, including, without limitation, general, special, incidental
+ # and consequential damages, arising out of or otherwise in connection
+ # with the use or inability to use the program or any product, material
+ # or result produced or otherwise obtained by using the program,
+ # regardless of whether they have been advised of, or otherwise had
+ # knowledge of, the possibility of such damages at any time during the
+ # project or thereafter. Each user will be deemed to have agreed to the
+ # foregoing by his or her commencement of use of the program. The term
+ # "use" as used herein includes, but is not limited to, the use,
+ # modification, copying and distribution of the program and the
+ # production of secondary products from the program.
+ #
+ # In the case where the program, whether in its original form or
+ # modified, was distributed or delivered to or received by a user from
+ # any person, organization or entity other than ICOT, unless it makes or
+ # grants independently of ICOT any specific warranty to the user in
+ # writing, such person, organization or entity, will also be exempted
+ # from and not be held liable to the user for any such damages as noted
+ # above as far as the program is concerned.
+ #
+ # ---------------COPYING.ipadic-----END----------------------------------
+
+3. Lao Word Break Dictionary Data (laodict.txt)
+
+ # Copyright (c) 2013 International Business Machines Corporation
+ # and others. All Rights Reserved.
+ #
+ # Project: http://code.google.com/p/lao-dictionary/
+ # Dictionary: http://lao-dictionary.googlecode.com/git/Lao-Dictionary.txt
+ # License: http://lao-dictionary.googlecode.com/git/Lao-Dictionary-LICENSE.txt
+ # (copied below)
+ #
+ # This file is derived from the above dictionary, with slight
+ # modifications.
+ # ----------------------------------------------------------------------
+ # Copyright (C) 2013 Brian Eugene Wilson, Robert Martin Campbell.
+ # All rights reserved.
+ #
+ # Redistribution and use in source and binary forms, with or without
+ # modification,
+ # are permitted provided that the following conditions are met:
+ #
+ #
+ # Redistributions of source code must retain the above copyright notice, this
+ # list of conditions and the following disclaimer. Redistributions in
+ # binary form must reproduce the above copyright notice, this list of
+ # conditions and the following disclaimer in the documentation and/or
+ # other materials provided with the distribution.
+ #
+ #
+ # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ # "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ # LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+ # FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+ # COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ # INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ # (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ # SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ # HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ # STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+ # OF THE POSSIBILITY OF SUCH DAMAGE.
+ # --------------------------------------------------------------------------
+
+4. Burmese Word Break Dictionary Data (burmesedict.txt)
+
+ # Copyright (c) 2014 International Business Machines Corporation
+ # and others. All Rights Reserved.
+ #
+ # This list is part of a project hosted at:
+ # github.com/kanyawtech/myanmar-karen-word-lists
+ #
+ # --------------------------------------------------------------------------
+ # Copyright (c) 2013, LeRoy Benjamin Sharon
+ # All rights reserved.
+ #
+ # Redistribution and use in source and binary forms, with or without
+ # modification, are permitted provided that the following conditions
+ # are met: Redistributions of source code must retain the above
+ # copyright notice, this list of conditions and the following
+ # disclaimer. Redistributions in binary form must reproduce the
+ # above copyright notice, this list of conditions and the following
+ # disclaimer in the documentation and/or other materials provided
+ # with the distribution.
+ #
+ # Neither the name Myanmar Karen Word Lists, nor the names of its
+ # contributors may be used to endorse or promote products derived
+ # from this software without specific prior written permission.
+ #
+ # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ # CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ # INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+ # MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ # DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS
+ # BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ # EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+ # TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ # DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ # ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
+ # TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF
+ # THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ # SUCH DAMAGE.
+ # --------------------------------------------------------------------------
+
+5. Time Zone Database
+
+ ICU uses the public domain data and code derived from Time Zone
+Database for its time zone support. The ownership of the TZ database
+is explained in BCP 175: Procedure for Maintaining the Time Zone
+Database section 7.
+
+ # 7. Database Ownership
+ #
+ # The TZ database itself is not an IETF Contribution or an IETF
+ # document. Rather it is a pre-existing and regularly updated work
+ # that is in the public domain, and is intended to remain in the
+ # public domain. Therefore, BCPs 78 [RFC5378] and 79 [RFC3979] do
+ # not apply to the TZ Database or contributions that individuals make
+ # to it. Should any claims be made and substantiated against the TZ
+ # Database, the organization that is providing the IANA
+ # Considerations defined in this RFC, under the memorandum of
+ # understanding with the IETF, currently ICANN, may act in accordance
+ # with all competent court orders. No ownership claims will be made
+ # by ICANN or the IETF Trust on the database or the code. Any person
+ # making a contribution to the database or code waives all rights to
+ # future claims in that contribution or in the TZ Database.
+
+6. Google double-conversion
+
+Copyright 2006-2011, the V8 project authors. All rights reserved.
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+ * Neither the name of Google Inc. nor the names of its
+ contributors may be used to endorse or promote products derived
+ from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+```
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.web/libxml2.md b/lib/javafx-sdk-14-Mac/legal/javafx.web/libxml2.md
new file mode 100644
index 0000000..2c21817
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.web/libxml2.md
@@ -0,0 +1,30 @@
+## xmlsoft.org: libxml2 v2.9.9
+
+### libxml2 License
+```
+
+Except where otherwise noted in the source code (e.g. the files hash.c,
+list.c and the trio files, which are covered by a similar licence but
+with different Copyright notices) all the files are:
+
+Copyright (C) 1998-2012 Daniel Veillard. All Rights Reserved.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+```
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.web/libxslt.md b/lib/javafx-sdk-14-Mac/legal/javafx.web/libxslt.md
new file mode 100644
index 0000000..c0e5bd6
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.web/libxslt.md
@@ -0,0 +1,60 @@
+## xmlsoft.org: libxslt v1.1.34
+
+### libxslt License
+```
+
+Licence for libxslt except libexslt
+----------------------------------------------------------------------
+ Copyright (C) 2001-2002 Daniel Veillard. All Rights Reserved.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is fur-
+nished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FIT-
+NESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+DANIEL VEILLARD BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CON-
+NECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+Except as contained in this notice, the name of Daniel Veillard shall not
+be used in advertising or otherwise to promote the sale, use or other deal-
+ings in this Software without prior written authorization from him.
+
+----------------------------------------------------------------------
+
+Licence for libexslt
+----------------------------------------------------------------------
+ Copyright (C) 2001-2002 Thomas Broyer, Charlie Bozeman and Daniel Veillard.
+ All Rights Reserved.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is fur-
+nished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FIT-
+NESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CON-
+NECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+Except as contained in this notice, the name of the authors shall not
+be used in advertising or otherwise to promote the sale, use or other deal-
+ings in this Software without prior written authorization from him.
+----------------------------------------------------------------------
+
+```
diff --git a/lib/javafx-sdk-14-Mac/legal/javafx.web/webkit.md b/lib/javafx-sdk-14-Mac/legal/javafx.web/webkit.md
new file mode 100644
index 0000000..e4cbc1e
--- /dev/null
+++ b/lib/javafx-sdk-14-Mac/legal/javafx.web/webkit.md
@@ -0,0 +1,535 @@
+## WebKit Open Source Project: WebKit v608.1
+
+### WebKit Notice
+```
+
+You are receiving a copy of WebKit in either source or
+object code in the JavaFX runtime or JavaFX SDK. The terms of the
+Oracle license do NOT apply to WebKit; it is
+licensed under the following license, separately from the Oracle programs
+you receive. If you do not wish to install this library, you may delete
+this library:
+
+ - On Linux systems: delete $(JAVA_HOME)/lib/libjfxwebkit.so
+ - On Mac OS X systems: delete $(JAVA_HOME)/lib/libjfxwebkit.dylib
+ - On Windows systems: delete $(JAVA_HOME)\bin\jfxwebkit.dll
+
+A copy of the Oracle modified WebKit library source code is located
+in the following OpenJDK git repository:
+
+ https://github.com/openjdk/jfx
+
+You can use git to clone the repository or you can browse the
+source using a web browser. The root directory of the WebKit source
+code is here:
+
+ rt/modules/javafx.web/src/main/native/
+```
+
+### LGPL 2.1
+```
+
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 2.1, February 1999
+
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+[This is the first released version of the Lesser GPL. It also counts
+ as the successor of the GNU Library Public License, version 2, hence
+ the version number 2.1.]
+
+ Preamble
+
+ The licenses for most software are designed to take away your
+freedom to share and change it. By contrast, the GNU General Public
+Licenses are intended to guarantee your freedom to share and change
+free software--to make sure the software is free for all its users.
+
+ This license, the Lesser General Public License, applies to some
+specially designated software packages--typically libraries--of the
+Free Software Foundation and other authors who decide to use it. You
+can use it too, but we suggest you first think carefully about whether
+this license or the ordinary General Public License is the better
+strategy to use in any particular case, based on the explanations below.
+
+ When we speak of free software, we are referring to freedom of use,
+not price. Our General Public Licenses are designed to make sure that
+you have the freedom to distribute copies of free software (and charge
+for this service if you wish); that you receive source code or can get
+it if you want it; that you can change the software and use pieces of
+it in new free programs; and that you are informed that you can do
+these things.
+
+ To protect your rights, we need to make restrictions that forbid
+distributors to deny you these rights or to ask you to surrender these
+rights. These restrictions translate to certain responsibilities for
+you if you distribute copies of the library or if you modify it.
+
+ For example, if you distribute copies of the library, whether gratis
+or for a fee, you must give the recipients all the rights that we gave
+you. You must make sure that they, too, receive or can get the source
+code. If you link other code with the library, you must provide
+complete object files to the recipients, so that they can relink them
+with the library after making changes to the library and recompiling
+it. And you must show them these terms so they know their rights.
+
+ We protect your rights with a two-step method: (1) we copyright the
+library, and (2) we offer you this license, which gives you legal
+permission to copy, distribute and/or modify the library.
+
+ To protect each distributor, we want to make it very clear that
+there is no warranty for the free library. Also, if the library is
+modified by someone else and passed on, the recipients should know
+that what they have is not the original version, so that the original
+author's reputation will not be affected by problems that might be
+introduced by others.
+
+ Finally, software patents pose a constant threat to the existence of
+any free program. We wish to make sure that a company cannot
+effectively restrict the users of a free program by obtaining a
+restrictive license from a patent holder. Therefore, we insist that
+any patent license obtained for a version of the library must be
+consistent with the full freedom of use specified in this license.
+
+ Most GNU software, including some libraries, is covered by the
+ordinary GNU General Public License. This license, the GNU Lesser
+General Public License, applies to certain designated libraries, and
+is quite different from the ordinary General Public License. We use
+this license for certain libraries in order to permit linking those
+libraries into non-free programs.
+
+ When a program is linked with a library, whether statically or using
+a shared library, the combination of the two is legally speaking a
+combined work, a derivative of the original library. The ordinary
+General Public License therefore permits such linking only if the
+entire combination fits its criteria of freedom. The Lesser General
+Public License permits more lax criteria for linking other code with
+the library.
+
+ We call this license the "Lesser" General Public License because it
+does Less to protect the user's freedom than the ordinary General
+Public License. It also provides other free software developers Less
+of an advantage over competing non-free programs. These disadvantages
+are the reason we use the ordinary General Public License for many
+libraries. However, the Lesser license provides advantages in certain
+special circumstances.
+
+ For example, on rare occasions, there may be a special need to
+encourage the widest possible use of a certain library, so that it becomes
+a de-facto standard. To achieve this, non-free programs must be
+allowed to use the library. A more frequent case is that a free
+library does the same job as widely used non-free libraries. In this
+case, there is little to gain by limiting the free library to free
+software only, so we use the Lesser General Public License.
+
+ In other cases, permission to use a particular library in non-free
+programs enables a greater number of people to use a large body of
+free software. For example, permission to use the GNU C Library in
+non-free programs enables many more people to use the whole GNU
+operating system, as well as its variant, the GNU/Linux operating
+system.
+
+ Although the Lesser General Public License is Less protective of the
+users' freedom, it does ensure that the user of a program that is
+linked with the Library has the freedom and the wherewithal to run
+that program using a modified version of the Library.
+
+ The precise terms and conditions for copying, distribution and
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+former contains code derived from the library, whereas the latter must
+be combined with the library in order to run.
+
+ GNU LESSER GENERAL PUBLIC LICENSE
+ TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+ 0. This License Agreement applies to any software library or other
+program which contains a notice placed by the copyright holder or
+other authorized party saying it may be distributed under the terms of
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+Each licensee is addressed as "you".
+
+ A "library" means a collection of software functions and/or data
+prepared so as to be conveniently linked with application programs
+(which use some of those functions and data) to form executables.
+
+ The "Library", below, refers to any such software library or work
+which has been distributed under these terms. A "work based on the
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+
+ "Source code" for a work means the preferred form of the work for
+making modifications to it. For a library, complete source code means
+all the source code for all modules it contains, plus any associated
+interface definition files, plus the scripts used to control compilation
+and installation of the library.
+
+ Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope. The act of
+running a program using the Library is not restricted, and output from
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+on the Library (independent of the use of the Library in a tool for
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+
+ 1. You may copy and distribute verbatim copies of the Library's
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+Library.
+
+ You may charge a fee for the physical act of transferring a copy,
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+above, provided that you also meet all of these conditions:
+
+ a) The modified work must itself be a software library.
+
+ b) You must cause the files modified to carry prominent notices
+ stating that you changed the files and the date of any change.
+
+ c) You must cause the whole of the work to be licensed at no
+ charge to all third parties under the terms of this License.
+
+ d) If a facility in the modified Library refers to a function or a
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+
+ (For example, a function in a library to compute square roots has
+ a purpose that is entirely well-defined independent of the
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+ be optional: if the application does not supply it, the square
+ root function must still compute square roots.)
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+on the Library, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote
+it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
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+
+In addition, mere aggregation of another work not based on the Library
+with the Library (or with a work based on the Library) on a volume of
+a storage or distribution medium does not bring the other work under
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+possible use to the public, we recommend making it free software that
+everyone can redistribute and change. You can do so by permitting
+redistribution under these terms (or, alternatively, under the terms of the
+ordinary General Public License).
+
+ To apply these terms, attach the following notices to the library. It is
+safest to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least the
+"copyright" line and a pointer to where the full notice is found.
+
+
+ Copyright (C)
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Also add information on how to contact you by electronic and paper mail.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the library, if
+necessary. Here is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the
+ library `Frob' (a library for tweaking knobs) written by James Random Hacker.
+
+ , 1 April 1990
+ Ty Coon, President of Vice
+
+That's all there is to it!
+
+```
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+javafx.runtime.build=9
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diff --git a/lib/javafx-sdk-14-Windows/bin/vcruntime140.dll b/lib/javafx-sdk-14-Windows/bin/vcruntime140.dll
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diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.base/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Windows/legal/javafx.base/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.base/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
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+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
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+Oracle facilitates your further distribution of this package by adding the
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+Failing to distribute notices associated with some files may also create
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+Proceed with caution and we recommend that you obtain the advice of a lawyer
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diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.base/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Windows/legal/javafx.base/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.base/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
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+
+ Linking this OpenJDK Code statically or dynamically with other code
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+
+ As a special exception, Oracle gives you permission to link this
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+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
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diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.base/LICENSE b/lib/javafx-sdk-14-Windows/legal/javafx.base/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.base/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
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+Preamble
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+The licenses for most software are designed to take away your freedom to share
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+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
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+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the source
+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.controls/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Windows/legal/javafx.controls/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.controls/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
+package. Some of those programs are provided under licenses deemed
+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
+License, Version 2.0 and may include FreeType. Such programs are licensed
+to you under their original licenses.
+
+Oracle facilitates your further distribution of this package by adding the
+Classpath Exception to the necessary parts of its GPLv2 code, which permits
+you to use that code in combination with other independent modules not
+licensed under the GPLv2. However, note that this would not permit you to
+commingle code under an incompatible license with Oracle's GPLv2 licensed
+code by, for example, cutting and pasting such code into a file also
+containing Oracle's GPLv2 licensed code and then distributing the result.
+
+Additionally, if you were to remove the Classpath Exception from any of the
+files to which it applies and distribute the result, you would likely be
+required to license some or all of the other code in that distribution under
+the GPLv2 as well, and since the GPLv2 is incompatible with the license terms
+of some items included in the distribution by Oracle, removing the Classpath
+Exception could therefore effectively compromise your ability to further
+distribute the package.
+
+Failing to distribute notices associated with some files may also create
+unexpected legal consequences.
+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
+skilled in open source matters before removing the Classpath Exception or
+making modifications to this package which may subsequently be redistributed
+and/or involve the use of third party software.
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.controls/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Windows/legal/javafx.controls/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.controls/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
+ regardless of the license terms of the Designated Exception Modules,
+ and to copy and distribute the resulting executable under GPL2,
+ provided that the Designated Exception Modules continue to be
+ governed by the licenses under which they were offered by Oracle.
+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
+to build an executable that includes those portions of necessary code that
+Oracle could not provide under GPL2 (or that Oracle has provided under GPL2
+with the Classpath exception). If you modify or add to the OpenJDK code,
+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.controls/LICENSE b/lib/javafx-sdk-14-Windows/legal/javafx.controls/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.controls/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
+by others will not reflect on the original authors' reputations.
+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
+everyone's free use or not licensed at all.
+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the source
+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.fxml/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Windows/legal/javafx.fxml/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.fxml/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
+package. Some of those programs are provided under licenses deemed
+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
+License, Version 2.0 and may include FreeType. Such programs are licensed
+to you under their original licenses.
+
+Oracle facilitates your further distribution of this package by adding the
+Classpath Exception to the necessary parts of its GPLv2 code, which permits
+you to use that code in combination with other independent modules not
+licensed under the GPLv2. However, note that this would not permit you to
+commingle code under an incompatible license with Oracle's GPLv2 licensed
+code by, for example, cutting and pasting such code into a file also
+containing Oracle's GPLv2 licensed code and then distributing the result.
+
+Additionally, if you were to remove the Classpath Exception from any of the
+files to which it applies and distribute the result, you would likely be
+required to license some or all of the other code in that distribution under
+the GPLv2 as well, and since the GPLv2 is incompatible with the license terms
+of some items included in the distribution by Oracle, removing the Classpath
+Exception could therefore effectively compromise your ability to further
+distribute the package.
+
+Failing to distribute notices associated with some files may also create
+unexpected legal consequences.
+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
+skilled in open source matters before removing the Classpath Exception or
+making modifications to this package which may subsequently be redistributed
+and/or involve the use of third party software.
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.fxml/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Windows/legal/javafx.fxml/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.fxml/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
+ regardless of the license terms of the Designated Exception Modules,
+ and to copy and distribute the resulting executable under GPL2,
+ provided that the Designated Exception Modules continue to be
+ governed by the licenses under which they were offered by Oracle.
+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
+to build an executable that includes those portions of necessary code that
+Oracle could not provide under GPL2 (or that Oracle has provided under GPL2
+with the Classpath exception). If you modify or add to the OpenJDK code,
+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.fxml/LICENSE b/lib/javafx-sdk-14-Windows/legal/javafx.fxml/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.fxml/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
+by others will not reflect on the original authors' reputations.
+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
+everyone's free use or not licensed at all.
+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the source
+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.graphics/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Windows/legal/javafx.graphics/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.graphics/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
+package. Some of those programs are provided under licenses deemed
+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
+License, Version 2.0 and may include FreeType. Such programs are licensed
+to you under their original licenses.
+
+Oracle facilitates your further distribution of this package by adding the
+Classpath Exception to the necessary parts of its GPLv2 code, which permits
+you to use that code in combination with other independent modules not
+licensed under the GPLv2. However, note that this would not permit you to
+commingle code under an incompatible license with Oracle's GPLv2 licensed
+code by, for example, cutting and pasting such code into a file also
+containing Oracle's GPLv2 licensed code and then distributing the result.
+
+Additionally, if you were to remove the Classpath Exception from any of the
+files to which it applies and distribute the result, you would likely be
+required to license some or all of the other code in that distribution under
+the GPLv2 as well, and since the GPLv2 is incompatible with the license terms
+of some items included in the distribution by Oracle, removing the Classpath
+Exception could therefore effectively compromise your ability to further
+distribute the package.
+
+Failing to distribute notices associated with some files may also create
+unexpected legal consequences.
+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
+skilled in open source matters before removing the Classpath Exception or
+making modifications to this package which may subsequently be redistributed
+and/or involve the use of third party software.
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.graphics/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Windows/legal/javafx.graphics/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.graphics/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
+ regardless of the license terms of the Designated Exception Modules,
+ and to copy and distribute the resulting executable under GPL2,
+ provided that the Designated Exception Modules continue to be
+ governed by the licenses under which they were offered by Oracle.
+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
+to build an executable that includes those portions of necessary code that
+Oracle could not provide under GPL2 (or that Oracle has provided under GPL2
+with the Classpath exception). If you modify or add to the OpenJDK code,
+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.graphics/LICENSE b/lib/javafx-sdk-14-Windows/legal/javafx.graphics/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.graphics/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
+by others will not reflect on the original authors' reputations.
+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
+everyone's free use or not licensed at all.
+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
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+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.graphics/jpeg_fx.md b/lib/javafx-sdk-14-Windows/legal/javafx.graphics/jpeg_fx.md
new file mode 100644
index 0000000..b98f177
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.graphics/jpeg_fx.md
@@ -0,0 +1,51 @@
+## Independent JPEG Group (IJG) JPEG v9c
+
+### IJG License
+```
+
+/*
+ * jcapimin.c
+ *
+ * Copyright (C) 1994-1998, Thomas G. Lane.
+ * Modified 2003-2010 by Guido Vollbeding.
+ * This file is part of the Independent JPEG Group's software.
+ * For conditions of distribution and use, see the accompanying README file.
+ */
+
+[From the README file]
+The authors make NO WARRANTY or representation, either express or implied,
+with respect to this software, its quality, accuracy, merchantability, or
+fitness for a particular purpose. This software is provided "AS IS", and you,
+its user, assume the entire risk as to its quality and accuracy.
+
+This software is copyright (C) 1991-2018, Thomas G. Lane, Guido Vollbeding.
+All Rights Reserved except as specified below.
+
+Permission is hereby granted to use, copy, modify, and distribute this
+software (or portions thereof) for any purpose, without fee, subject to these
+conditions:
+(1) If any part of the source code for this software is distributed, then this
+README file must be included, with this copyright and no-warranty notice
+unaltered; and any additions, deletions, or changes to the original files
+must be clearly indicated in accompanying documentation.
+(2) If only executable code is distributed, then the accompanying
+documentation must state that "this software is based in part on the work of
+the Independent JPEG Group".
+(3) Permission for use of this software is granted only if the user accepts
+full responsibility for any undesirable consequences; the authors accept
+NO LIABILITY for damages of any kind.
+
+These conditions apply to any software derived from or based on the IJG code,
+not just to the unmodified library. If you use our work, you ought to
+acknowledge us.
+
+Permission is NOT granted for the use of any IJG author's name or company name
+in advertising or publicity relating to this software or products derived from
+it. This software may be referred to only as "the Independent JPEG Group's
+software".
+
+We specifically permit and encourage the use of this software as the basis of
+commercial products, provided that all warranty or liability claims are
+assumed by the product vendor.
+
+```
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.graphics/mesa3d.md b/lib/javafx-sdk-14-Windows/legal/javafx.graphics/mesa3d.md
new file mode 100644
index 0000000..b3f32d8
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.graphics/mesa3d.md
@@ -0,0 +1,134 @@
+## Mesa 3-D Graphics Library v19.2.1
+
+### Mesa License
+
+```
+Copyright (C) 1999-2007 Brian Paul All Rights Reserved.
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the "Software"),
+to deal in the Software without restriction, including without limitation
+the rights to use, copy, modify, merge, publish, distribute, sublicense,
+and/or sell copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included
+in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+Attention, Contributors
+
+When contributing to the Mesa project you must agree to the licensing terms
+of the component to which you're contributing.
+The following section lists the primary components of the Mesa distribution
+and their respective licenses.
+Mesa Component Licenses
+
+
+
+Component Location License
+------------------------------------------------------------------
+Main Mesa code src/mesa/ MIT
+Device drivers src/mesa/drivers/* MIT, generally
+
+Gallium code src/gallium/ MIT
+
+Ext headers GL/glext.h Khronos
+ GL/glxext.h Khronos
+ GL/wglext.h Khronos
+ KHR/khrplatform.h Khronos
+
+*****************************************************************************
+
+----
+include/GL/gl.h :
+
+
+ Mesa 3-D graphics library
+
+ Copyright (C) 1999-2006 Brian Paul All Rights Reserved.
+ Copyright (C) 2009 VMware, Inc. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and associated documentation files (the "Software"),
+ to deal in the Software without restriction, including without limitation
+ the rights to use, copy, modify, merge, publish, distribute, sublicense,
+ and/or sell copies of the Software, and to permit persons to whom the
+ Software is furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+ THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
+ OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+ ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ OTHER DEALINGS IN THE SOFTWARE.
+
+ *****************************************************************************
+
+----
+include/GL/glext.h
+include/GL/glxext.h
+include/GL/wglxext.h :
+
+
+ Copyright (c) 2013 - 2018 The Khronos Group Inc.
+
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and/or associated documentation files (the
+ "Materials"), to deal in the Materials without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Materials, and to
+ permit persons to whom the Materials are furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Materials.
+
+ THE MATERIALS ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ MATERIALS OR THE USE OR OTHER DEALINGS IN THE MATERIALS.
+
+ *****************************************************************************
+
+----
+include/KHR/khrplatform.h :
+
+ Copyright (c) 2008 - 2018 The Khronos Group Inc.
+
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and/or associated documentation files (the
+ "Materials"), to deal in the Materials without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Materials, and to
+ permit persons to whom the Materials are furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Materials.
+
+ THE MATERIALS ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ MATERIALS OR THE USE OR OTHER DEALINGS IN THE MATERIALS.
+
+ *****************************************************************************
+
+```
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.media/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Windows/legal/javafx.media/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.media/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
+package. Some of those programs are provided under licenses deemed
+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
+License, Version 2.0 and may include FreeType. Such programs are licensed
+to you under their original licenses.
+
+Oracle facilitates your further distribution of this package by adding the
+Classpath Exception to the necessary parts of its GPLv2 code, which permits
+you to use that code in combination with other independent modules not
+licensed under the GPLv2. However, note that this would not permit you to
+commingle code under an incompatible license with Oracle's GPLv2 licensed
+code by, for example, cutting and pasting such code into a file also
+containing Oracle's GPLv2 licensed code and then distributing the result.
+
+Additionally, if you were to remove the Classpath Exception from any of the
+files to which it applies and distribute the result, you would likely be
+required to license some or all of the other code in that distribution under
+the GPLv2 as well, and since the GPLv2 is incompatible with the license terms
+of some items included in the distribution by Oracle, removing the Classpath
+Exception could therefore effectively compromise your ability to further
+distribute the package.
+
+Failing to distribute notices associated with some files may also create
+unexpected legal consequences.
+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
+skilled in open source matters before removing the Classpath Exception or
+making modifications to this package which may subsequently be redistributed
+and/or involve the use of third party software.
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.media/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Windows/legal/javafx.media/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.media/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
+ regardless of the license terms of the Designated Exception Modules,
+ and to copy and distribute the resulting executable under GPL2,
+ provided that the Designated Exception Modules continue to be
+ governed by the licenses under which they were offered by Oracle.
+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
+to build an executable that includes those portions of necessary code that
+Oracle could not provide under GPL2 (or that Oracle has provided under GPL2
+with the Classpath exception). If you modify or add to the OpenJDK code,
+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.media/LICENSE b/lib/javafx-sdk-14-Windows/legal/javafx.media/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.media/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
+by others will not reflect on the original authors' reputations.
+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
+everyone's free use or not licensed at all.
+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the source
+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.media/applecoreaudio.md b/lib/javafx-sdk-14-Windows/legal/javafx.media/applecoreaudio.md
new file mode 100644
index 0000000..5bf2a73
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.media/applecoreaudio.md
@@ -0,0 +1,53 @@
+## Apple Computer: CoreAudio Utility Classes v2.0
+
+### Apple Computer CoreAudio Notice
+This software is present only on Mac OS X systems.
+
+### Apple Computer CoreAudio License
+```
+
+File:
+Abstract: Part of CoreAudio Utility Classes
+Version: 1.1
+
+Disclaimer: IMPORTANT: This Apple software is supplied to you by Apple
+Inc. ("Apple") in consideration of your agreement to the following
+terms, and your use, installation, modification or redistribution of
+this Apple software constitutes acceptance of these terms. If you do
+not agree with these terms, please do not use, install, modify or
+redistribute this Apple software.
+
+In consideration of your agreement to abide by the following terms, and
+subject to these terms, Apple grants you a personal, non-exclusive
+license, under Apple's copyrights in this original Apple software (the
+"Apple Software"), to use, reproduce, modify and redistribute the Apple
+Software, with or without modifications, in source and/or binary forms;
+provided that if you redistribute the Apple Software in its entirety and
+without modifications, you must retain this notice and the following
+text and disclaimers in all such redistributions of the Apple Software.
+Neither the name, trademarks, service marks or logos of Apple Inc. may
+be used to endorse or promote products derived from the Apple Software
+without specific prior written permission from Apple. Except as
+expressly stated in this notice, no other rights or licenses, express or
+implied, are granted by Apple herein, including but not limited to any
+patent rights that may be infringed by your derivative works or by other
+works in which the Apple Software may be incorporated.
+
+The Apple Software is provided by Apple on an "AS IS" basis. APPLE
+MAKES NO WARRANTIES, EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION
+THE IMPLIED WARRANTIES OF NON-INFRINGEMENT, MERCHANTABILITY AND FITNESS
+FOR A PARTICULAR PURPOSE, REGARDING THE APPLE SOFTWARE OR ITS USE AND
+OPERATION ALONE OR IN COMBINATION WITH YOUR PRODUCTS.
+
+IN NO EVENT SHALL APPLE BE LIABLE FOR ANY SPECIAL, INDIRECT, INCIDENTAL
+OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) ARISING IN ANY WAY OUT OF THE USE, REPRODUCTION,
+MODIFICATION AND/OR DISTRIBUTION OF THE APPLE SOFTWARE, HOWEVER CAUSED
+AND WHETHER UNDER THEORY OF CONTRACT, TORT (INCLUDING NEGLIGENCE),
+STRICT LIABILITY OR OTHERWISE, EVEN IF APPLE HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.
+
+Copyright (C) 2014 Apple Inc. All Rights Reserved.
+
+```
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.media/glib.md b/lib/javafx-sdk-14-Windows/legal/javafx.media/glib.md
new file mode 100644
index 0000000..5858730
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.media/glib.md
@@ -0,0 +1,537 @@
+## GNU Glib v2.62.2
+
+### Glib Notice
+```
+
+You are receiving a copy of GNU Glib, Version: 2.62.2 in either source or
+object code in the JavaFX runtime or JavaFX SDK. The terms of the
+Oracle license do NOT apply to the GNU Glib, Version: 2.62.2; it is
+licensed under the following license, separately from the Oracle programs
+you receive. If you do not wish to install this library, you may delete
+this library:
+
+ - On Linux systems: N/A (library is not present)
+ - On Mac OS X systems: delete $(JAVA_HOME)/lib/libglib-lite.dylib
+ - On Windows systems: delete $(JAVA_HOME)\bin\glib-lite.dll
+
+A copy of the Oracle modified GNU Glib library source code is located
+in the following OpenJDK git repository:
+
+ https://github.com/openjdk/jfx
+
+You can use git to clone the repository or you can browse the
+source using a web browser. The root directory of the GNU Glib source
+code is here:
+
+ rt/modules/javafx.media/src/main/native/gstreamer/3rd_party/glib/
+
+
+```
+
+### LGPL 2.1
+```
+
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 2.1, February 1999
+
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+[This is the first released version of the Lesser GPL. It also counts
+ as the successor of the GNU Library Public License, version 2, hence
+ the version number 2.1.]
+
+ Preamble
+
+ The licenses for most software are designed to take away your
+freedom to share and change it. By contrast, the GNU General Public
+Licenses are intended to guarantee your freedom to share and change
+free software--to make sure the software is free for all its users.
+
+ This license, the Lesser General Public License, applies to some
+specially designated software packages--typically libraries--of the
+Free Software Foundation and other authors who decide to use it. You
+can use it too, but we suggest you first think carefully about whether
+this license or the ordinary General Public License is the better
+strategy to use in any particular case, based on the explanations below.
+
+ When we speak of free software, we are referring to freedom of use,
+not price. Our General Public Licenses are designed to make sure that
+you have the freedom to distribute copies of free software (and charge
+for this service if you wish); that you receive source code or can get
+it if you want it; that you can change the software and use pieces of
+it in new free programs; and that you are informed that you can do
+these things.
+
+ To protect your rights, we need to make restrictions that forbid
+distributors to deny you these rights or to ask you to surrender these
+rights. These restrictions translate to certain responsibilities for
+you if you distribute copies of the library or if you modify it.
+
+ For example, if you distribute copies of the library, whether gratis
+or for a fee, you must give the recipients all the rights that we gave
+you. You must make sure that they, too, receive or can get the source
+code. If you link other code with the library, you must provide
+complete object files to the recipients, so that they can relink them
+with the library after making changes to the library and recompiling
+it. And you must show them these terms so they know their rights.
+
+ We protect your rights with a two-step method: (1) we copyright the
+library, and (2) we offer you this license, which gives you legal
+permission to copy, distribute and/or modify the library.
+
+ To protect each distributor, we want to make it very clear that
+there is no warranty for the free library. Also, if the library is
+modified by someone else and passed on, the recipients should know
+that what they have is not the original version, so that the original
+author's reputation will not be affected by problems that might be
+introduced by others.
+
+ Finally, software patents pose a constant threat to the existence of
+any free program. We wish to make sure that a company cannot
+effectively restrict the users of a free program by obtaining a
+restrictive license from a patent holder. Therefore, we insist that
+any patent license obtained for a version of the library must be
+consistent with the full freedom of use specified in this license.
+
+ Most GNU software, including some libraries, is covered by the
+ordinary GNU General Public License. This license, the GNU Lesser
+General Public License, applies to certain designated libraries, and
+is quite different from the ordinary General Public License. We use
+this license for certain libraries in order to permit linking those
+libraries into non-free programs.
+
+ When a program is linked with a library, whether statically or using
+a shared library, the combination of the two is legally speaking a
+combined work, a derivative of the original library. The ordinary
+General Public License therefore permits such linking only if the
+entire combination fits its criteria of freedom. The Lesser General
+Public License permits more lax criteria for linking other code with
+the library.
+
+ We call this license the "Lesser" General Public License because it
+does Less to protect the user's freedom than the ordinary General
+Public License. It also provides other free software developers Less
+of an advantage over competing non-free programs. These disadvantages
+are the reason we use the ordinary General Public License for many
+libraries. However, the Lesser license provides advantages in certain
+special circumstances.
+
+ For example, on rare occasions, there may be a special need to
+encourage the widest possible use of a certain library, so that it becomes
+a de-facto standard. To achieve this, non-free programs must be
+allowed to use the library. A more frequent case is that a free
+library does the same job as widely used non-free libraries. In this
+case, there is little to gain by limiting the free library to free
+software only, so we use the Lesser General Public License.
+
+ In other cases, permission to use a particular library in non-free
+programs enables a greater number of people to use a large body of
+free software. For example, permission to use the GNU C Library in
+non-free programs enables many more people to use the whole GNU
+operating system, as well as its variant, the GNU/Linux operating
+system.
+
+ Although the Lesser General Public License is Less protective of the
+users' freedom, it does ensure that the user of a program that is
+linked with the Library has the freedom and the wherewithal to run
+that program using a modified version of the Library.
+
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+
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+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
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+Also add information on how to contact you by electronic and paper mail.
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+```
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.media/gstreamer.md b/lib/javafx-sdk-14-Windows/legal/javafx.media/gstreamer.md
new file mode 100644
index 0000000..8f77613
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.media/gstreamer.md
@@ -0,0 +1,535 @@
+## GStreamer v1.16.1
+
+### GStreamer Notice
+```
+
+You are receiving a copy of GStreamer, Version: 1.16.1 in either source or
+object code in the JavaFX runtime or JavaFX SDK. The terms of the
+Oracle license do NOT apply to the GStreamer, Version: 1.16.1; it is
+licensed under the following license, separately from the Oracle programs
+you receive. If you do not wish to install this library, you may delete
+this library:
+
+ - On Linux systems: delete $(JAVA_HOME)/lib/libgstreamer-lite.so
+ - On Mac OS X systems: delete $(JAVA_HOME)/lib/libgstreamer-lite.dylib
+ - On Windows systems: delete $(JAVA_HOME)\bin\gstreamer-lite.dll
+
+A copy of the Oracle modified GStreamer library source code is located
+in the following OpenJDK git repository:
+
+ https://github.com/openjdk/jfx
+
+You can use git to clone the repository or you can browse the
+source using a web browser. The root directory of the GStreamer source
+code is here:
+
+ rt/modules/javafx.media/src/main/native/gstreamer/gstreamer-lite/
+```
+
+### LGPL 2.1
+```
+
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 2.1, February 1999
+
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
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+
+ How to Apply These Terms to Your New Libraries
+
+ If you develop a new library, and you want it to be of the greatest
+possible use to the public, we recommend making it free software that
+everyone can redistribute and change. You can do so by permitting
+redistribution under these terms (or, alternatively, under the terms of the
+ordinary General Public License).
+
+ To apply these terms, attach the following notices to the library. It is
+safest to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least the
+"copyright" line and a pointer to where the full notice is found.
+
+
+ Copyright (C)
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Also add information on how to contact you by electronic and paper mail.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the library, if
+necessary. Here is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the
+ library `Frob' (a library for tweaking knobs) written by James Random Hacker.
+
+ , 1 April 1990
+ Ty Coon, President of Vice
+
+That's all there is to it!
+
+```
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.media/libffi.md b/lib/javafx-sdk-14-Windows/legal/javafx.media/libffi.md
new file mode 100644
index 0000000..6915bbc
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.media/libffi.md
@@ -0,0 +1,28 @@
+## LibFFI v3.2.1
+
+### LibFFI License
+```
+
+libffi - Copyright (c) 1996-2014 Anthony Green, Red Hat, Inc and others.
+See source files for details.
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+``Software''), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED ``AS IS'', WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+```
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.swing/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Windows/legal/javafx.swing/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.swing/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
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+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
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+
+Oracle facilitates your further distribution of this package by adding the
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+
+Failing to distribute notices associated with some files may also create
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+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
+skilled in open source matters before removing the Classpath Exception or
+making modifications to this package which may subsequently be redistributed
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diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.swing/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Windows/legal/javafx.swing/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.swing/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
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+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
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+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.swing/LICENSE b/lib/javafx-sdk-14-Windows/legal/javafx.swing/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.swing/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
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+Everyone is permitted to copy and distribute verbatim copies of this license
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+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the source
+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.web/ADDITIONAL_LICENSE_INFO b/lib/javafx-sdk-14-Windows/legal/javafx.web/ADDITIONAL_LICENSE_INFO
new file mode 100644
index 0000000..ff700cd
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.web/ADDITIONAL_LICENSE_INFO
@@ -0,0 +1,37 @@
+ ADDITIONAL INFORMATION ABOUT LICENSING
+
+Certain files distributed by Oracle America, Inc. and/or its affiliates are
+subject to the following clarification and special exception to the GPLv2,
+based on the GNU Project exception for its Classpath libraries, known as the
+GNU Classpath Exception.
+
+Note that Oracle includes multiple, independent programs in this software
+package. Some of those programs are provided under licenses deemed
+incompatible with the GPLv2 by the Free Software Foundation and others.
+For example, the package includes programs licensed under the Apache
+License, Version 2.0 and may include FreeType. Such programs are licensed
+to you under their original licenses.
+
+Oracle facilitates your further distribution of this package by adding the
+Classpath Exception to the necessary parts of its GPLv2 code, which permits
+you to use that code in combination with other independent modules not
+licensed under the GPLv2. However, note that this would not permit you to
+commingle code under an incompatible license with Oracle's GPLv2 licensed
+code by, for example, cutting and pasting such code into a file also
+containing Oracle's GPLv2 licensed code and then distributing the result.
+
+Additionally, if you were to remove the Classpath Exception from any of the
+files to which it applies and distribute the result, you would likely be
+required to license some or all of the other code in that distribution under
+the GPLv2 as well, and since the GPLv2 is incompatible with the license terms
+of some items included in the distribution by Oracle, removing the Classpath
+Exception could therefore effectively compromise your ability to further
+distribute the package.
+
+Failing to distribute notices associated with some files may also create
+unexpected legal consequences.
+
+Proceed with caution and we recommend that you obtain the advice of a lawyer
+skilled in open source matters before removing the Classpath Exception or
+making modifications to this package which may subsequently be redistributed
+and/or involve the use of third party software.
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.web/ASSEMBLY_EXCEPTION b/lib/javafx-sdk-14-Windows/legal/javafx.web/ASSEMBLY_EXCEPTION
new file mode 100644
index 0000000..065b8d9
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.web/ASSEMBLY_EXCEPTION
@@ -0,0 +1,27 @@
+
+OPENJDK ASSEMBLY EXCEPTION
+
+The OpenJDK source code made available by Oracle America, Inc. (Oracle) at
+openjdk.java.net ("OpenJDK Code") is distributed under the terms of the GNU
+General Public License version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
+ regardless of the license terms of the Designated Exception Modules,
+ and to copy and distribute the resulting executable under GPL2,
+ provided that the Designated Exception Modules continue to be
+ governed by the licenses under which they were offered by Oracle.
+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
+to build an executable that includes those portions of necessary code that
+Oracle could not provide under GPL2 (or that Oracle has provided under GPL2
+with the Classpath exception). If you modify or add to the OpenJDK code,
+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.web/LICENSE b/lib/javafx-sdk-14-Windows/legal/javafx.web/LICENSE
new file mode 100644
index 0000000..8b400c7
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.web/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
+by others will not reflect on the original authors' reputations.
+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
+everyone's free use or not licensed at all.
+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three years, to
+ give any third party, for a charge no more than your cost of physically
+ performing source distribution, a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of Sections 1
+ and 2 above on a medium customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer to
+ distribute corresponding source code. (This alternative is allowed only
+ for noncommercial distribution and only if you received the program in
+ object code or executable form with such an offer, in accord with
+ Subsection b above.)
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code
+distributed need not include anything that is normally distributed (in either
+source or binary form) with the major components (compiler, kernel, and so on)
+of the operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the source
+code from the same place counts as distribution of the source code, even though
+third parties are not compelled to copy the source along with the object code.
+
+4. You may not copy, modify, sublicense, or distribute the Program except as
+expressly provided under this License. Any attempt otherwise to copy, modify,
+sublicense or distribute the Program is void, and will automatically terminate
+your rights under this License. However, parties who have received copies, or
+rights, from you under this License will not have their licenses terminated so
+long as such parties remain in full compliance.
+
+5. You are not required to accept this License, since you have not signed it.
+However, nothing else grants you permission to modify or distribute the Program
+or its derivative works. These actions are prohibited by law if you do not
+accept this License. Therefore, by modifying or distributing the Program (or
+any work based on the Program), you indicate your acceptance of this License to
+do so, and all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+6. Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor to
+copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the
+rights granted herein. You are not responsible for enforcing compliance by
+third parties to this License.
+
+7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not distribute the Program at all.
+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
+distribution system, which is implemented by public license practices. Many
+people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing to
+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add an explicit
+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
+or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.web/icu_web.md b/lib/javafx-sdk-14-Windows/legal/javafx.web/icu_web.md
new file mode 100644
index 0000000..bbdc8d4
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.web/icu_web.md
@@ -0,0 +1,421 @@
+## IBM International Components for Unicode (ICU4C) v64.2
+
+### ICU License
+```
+
+COPYRIGHT AND PERMISSION NOTICE (ICU 58 and later)
+
+Copyright © 1991-2019 Unicode, Inc. All rights reserved.
+Distributed under the Terms of Use in https://www.unicode.org/copyright.html.
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of the Unicode data files and any associated documentation
+(the "Data Files") or Unicode software and any associated documentation
+(the "Software") to deal in the Data Files or Software
+without restriction, including without limitation the rights to use,
+copy, modify, merge, publish, distribute, and/or sell copies of
+the Data Files or Software, and to permit persons to whom the Data Files
+or Software are furnished to do so, provided that either
+(a) this copyright and permission notice appear with all copies
+of the Data Files or Software, or
+(b) this copyright and permission notice appear in associated
+Documentation.
+
+THE DATA FILES AND SOFTWARE ARE PROVIDED "AS IS", WITHOUT WARRANTY OF
+ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
+WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT OF THIRD PARTY RIGHTS.
+IN NO EVENT SHALL THE COPYRIGHT HOLDER OR HOLDERS INCLUDED IN THIS
+NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL INDIRECT OR CONSEQUENTIAL
+DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE,
+DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
+TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
+PERFORMANCE OF THE DATA FILES OR SOFTWARE.
+
+Except as contained in this notice, the name of a copyright holder
+shall not be used in advertising or otherwise to promote the sale,
+use or other dealings in these Data Files or Software without prior
+written authorization of the copyright holder.
+
+---------------------
+
+Third-Party Software Licenses
+
+This section contains third-party software notices and/or additional
+terms for licensed third-party software components included within ICU
+libraries.
+
+1. ICU License - ICU 1.8.1 to ICU 57.1
+
+COPYRIGHT AND PERMISSION NOTICE
+
+Copyright (c) 1995-2016 International Business Machines Corporation and others
+All rights reserved.
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, and/or sell copies of the Software, and to permit persons
+to whom the Software is furnished to do so, provided that the above
+copyright notice(s) and this permission notice appear in all copies of
+the Software and that both the above copyright notice(s) and this
+permission notice appear in supporting documentation.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
+OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY
+SPECIAL INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER
+RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF
+CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN
+CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+
+Except as contained in this notice, the name of a copyright holder
+shall not be used in advertising or otherwise to promote the sale, use
+or other dealings in this Software without prior written authorization
+of the copyright holder.
+
+All trademarks and registered trademarks mentioned herein are the
+property of their respective owners.
+
+2. Chinese/Japanese Word Break Dictionary Data (cjdict.txt)
+
+ # The Google Chrome software developed by Google is licensed under
+ # the BSD license. Other software included in this distribution is
+ # provided under other licenses, as set forth below.
+ #
+ # The BSD License
+ # http://opensource.org/licenses/bsd-license.php
+ # Copyright (C) 2006-2008, Google Inc.
+ #
+ # All rights reserved.
+ #
+ # Redistribution and use in source and binary forms, with or without
+ # modification, are permitted provided that the following conditions are met:
+ #
+ # Redistributions of source code must retain the above copyright notice,
+ # this list of conditions and the following disclaimer.
+ # Redistributions in binary form must reproduce the above
+ # copyright notice, this list of conditions and the following
+ # disclaimer in the documentation and/or other materials provided with
+ # the distribution.
+ # Neither the name of Google Inc. nor the names of its
+ # contributors may be used to endorse or promote products derived from
+ # this software without specific prior written permission.
+ #
+ #
+ # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ # CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ # INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+ # MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ # DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ # BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ # LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ # NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ #
+ #
+ # The word list in cjdict.txt are generated by combining three word lists
+ # listed below with further processing for compound word breaking. The
+ # frequency is generated with an iterative training against Google web
+ # corpora.
+ #
+ # * Libtabe (Chinese)
+ # - https://sourceforge.net/project/?group_id=1519
+ # - Its license terms and conditions are shown below.
+ #
+ # * IPADIC (Japanese)
+ # - http://chasen.aist-nara.ac.jp/chasen/distribution.html
+ # - Its license terms and conditions are shown below.
+ #
+ # ---------COPYING.libtabe ---- BEGIN--------------------
+ #
+ # /*
+ # * Copyright (c) 1999 TaBE Project.
+ # * Copyright (c) 1999 Pai-Hsiang Hsiao.
+ # * All rights reserved.
+ # *
+ # * Redistribution and use in source and binary forms, with or without
+ # * modification, are permitted provided that the following conditions
+ # * are met:
+ # *
+ # * . Redistributions of source code must retain the above copyright
+ # * notice, this list of conditions and the following disclaimer.
+ # * . Redistributions in binary form must reproduce the above copyright
+ # * notice, this list of conditions and the following disclaimer in
+ # * the documentation and/or other materials provided with the
+ # * distribution.
+ # * . Neither the name of the TaBE Project nor the names of its
+ # * contributors may be used to endorse or promote products derived
+ # * from this software without specific prior written permission.
+ # *
+ # * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ # * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ # * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+ # * FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+ # * REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ # * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ # * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ # * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ # * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ # * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ # * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+ # * OF THE POSSIBILITY OF SUCH DAMAGE.
+ # */
+ #
+ # /*
+ # * Copyright (c) 1999 Computer Systems and Communication Lab,
+ # * Institute of Information Science, Academia
+ # * Sinica. All rights reserved.
+ # *
+ # * Redistribution and use in source and binary forms, with or without
+ # * modification, are permitted provided that the following conditions
+ # * are met:
+ # *
+ # * . Redistributions of source code must retain the above copyright
+ # * notice, this list of conditions and the following disclaimer.
+ # * . Redistributions in binary form must reproduce the above copyright
+ # * notice, this list of conditions and the following disclaimer in
+ # * the documentation and/or other materials provided with the
+ # * distribution.
+ # * . Neither the name of the Computer Systems and Communication Lab
+ # * nor the names of its contributors may be used to endorse or
+ # * promote products derived from this software without specific
+ # * prior written permission.
+ # *
+ # * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ # * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ # * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+ # * FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+ # * REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ # * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ # * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ # * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ # * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ # * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ # * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+ # * OF THE POSSIBILITY OF SUCH DAMAGE.
+ # */
+ #
+ # Copyright 1996 Chih-Hao Tsai @ Beckman Institute,
+ # University of Illinois
+ # c-tsai4@uiuc.edu http://casper.beckman.uiuc.edu/~c-tsai4
+ #
+ # ---------------COPYING.libtabe-----END--------------------------------
+ #
+ #
+ # ---------------COPYING.ipadic-----BEGIN-------------------------------
+ #
+ # Copyright 2000, 2001, 2002, 2003 Nara Institute of Science
+ # and Technology. All Rights Reserved.
+ #
+ # Use, reproduction, and distribution of this software is permitted.
+ # Any copy of this software, whether in its original form or modified,
+ # must include both the above copyright notice and the following
+ # paragraphs.
+ #
+ # Nara Institute of Science and Technology (NAIST),
+ # the copyright holders, disclaims all warranties with regard to this
+ # software, including all implied warranties of merchantability and
+ # fitness, in no event shall NAIST be liable for
+ # any special, indirect or consequential damages or any damages
+ # whatsoever resulting from loss of use, data or profits, whether in an
+ # action of contract, negligence or other tortuous action, arising out
+ # of or in connection with the use or performance of this software.
+ #
+ # A large portion of the dictionary entries
+ # originate from ICOT Free Software. The following conditions for ICOT
+ # Free Software applies to the current dictionary as well.
+ #
+ # Each User may also freely distribute the Program, whether in its
+ # original form or modified, to any third party or parties, PROVIDED
+ # that the provisions of Section 3 ("NO WARRANTY") will ALWAYS appear
+ # on, or be attached to, the Program, which is distributed substantially
+ # in the same form as set out herein and that such intended
+ # distribution, if actually made, will neither violate or otherwise
+ # contravene any of the laws and regulations of the countries having
+ # jurisdiction over the User or the intended distribution itself.
+ #
+ # NO WARRANTY
+ #
+ # The program was produced on an experimental basis in the course of the
+ # research and development conducted during the project and is provided
+ # to users as so produced on an experimental basis. Accordingly, the
+ # program is provided without any warranty whatsoever, whether express,
+ # implied, statutory or otherwise. The term "warranty" used herein
+ # includes, but is not limited to, any warranty of the quality,
+ # performance, merchantability and fitness for a particular purpose of
+ # the program and the nonexistence of any infringement or violation of
+ # any right of any third party.
+ #
+ # Each user of the program will agree and understand, and be deemed to
+ # have agreed and understood, that there is no warranty whatsoever for
+ # the program and, accordingly, the entire risk arising from or
+ # otherwise connected with the program is assumed by the user.
+ #
+ # Therefore, neither ICOT, the copyright holder, or any other
+ # organization that participated in or was otherwise related to the
+ # development of the program and their respective officials, directors,
+ # officers and other employees shall be held liable for any and all
+ # damages, including, without limitation, general, special, incidental
+ # and consequential damages, arising out of or otherwise in connection
+ # with the use or inability to use the program or any product, material
+ # or result produced or otherwise obtained by using the program,
+ # regardless of whether they have been advised of, or otherwise had
+ # knowledge of, the possibility of such damages at any time during the
+ # project or thereafter. Each user will be deemed to have agreed to the
+ # foregoing by his or her commencement of use of the program. The term
+ # "use" as used herein includes, but is not limited to, the use,
+ # modification, copying and distribution of the program and the
+ # production of secondary products from the program.
+ #
+ # In the case where the program, whether in its original form or
+ # modified, was distributed or delivered to or received by a user from
+ # any person, organization or entity other than ICOT, unless it makes or
+ # grants independently of ICOT any specific warranty to the user in
+ # writing, such person, organization or entity, will also be exempted
+ # from and not be held liable to the user for any such damages as noted
+ # above as far as the program is concerned.
+ #
+ # ---------------COPYING.ipadic-----END----------------------------------
+
+3. Lao Word Break Dictionary Data (laodict.txt)
+
+ # Copyright (c) 2013 International Business Machines Corporation
+ # and others. All Rights Reserved.
+ #
+ # Project: http://code.google.com/p/lao-dictionary/
+ # Dictionary: http://lao-dictionary.googlecode.com/git/Lao-Dictionary.txt
+ # License: http://lao-dictionary.googlecode.com/git/Lao-Dictionary-LICENSE.txt
+ # (copied below)
+ #
+ # This file is derived from the above dictionary, with slight
+ # modifications.
+ # ----------------------------------------------------------------------
+ # Copyright (C) 2013 Brian Eugene Wilson, Robert Martin Campbell.
+ # All rights reserved.
+ #
+ # Redistribution and use in source and binary forms, with or without
+ # modification,
+ # are permitted provided that the following conditions are met:
+ #
+ #
+ # Redistributions of source code must retain the above copyright notice, this
+ # list of conditions and the following disclaimer. Redistributions in
+ # binary form must reproduce the above copyright notice, this list of
+ # conditions and the following disclaimer in the documentation and/or
+ # other materials provided with the distribution.
+ #
+ #
+ # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ # "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ # LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+ # FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+ # COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ # INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ # (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ # SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ # HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ # STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+ # OF THE POSSIBILITY OF SUCH DAMAGE.
+ # --------------------------------------------------------------------------
+
+4. Burmese Word Break Dictionary Data (burmesedict.txt)
+
+ # Copyright (c) 2014 International Business Machines Corporation
+ # and others. All Rights Reserved.
+ #
+ # This list is part of a project hosted at:
+ # github.com/kanyawtech/myanmar-karen-word-lists
+ #
+ # --------------------------------------------------------------------------
+ # Copyright (c) 2013, LeRoy Benjamin Sharon
+ # All rights reserved.
+ #
+ # Redistribution and use in source and binary forms, with or without
+ # modification, are permitted provided that the following conditions
+ # are met: Redistributions of source code must retain the above
+ # copyright notice, this list of conditions and the following
+ # disclaimer. Redistributions in binary form must reproduce the
+ # above copyright notice, this list of conditions and the following
+ # disclaimer in the documentation and/or other materials provided
+ # with the distribution.
+ #
+ # Neither the name Myanmar Karen Word Lists, nor the names of its
+ # contributors may be used to endorse or promote products derived
+ # from this software without specific prior written permission.
+ #
+ # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ # CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ # INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+ # MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ # DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS
+ # BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ # EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+ # TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ # DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ # ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
+ # TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF
+ # THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ # SUCH DAMAGE.
+ # --------------------------------------------------------------------------
+
+5. Time Zone Database
+
+ ICU uses the public domain data and code derived from Time Zone
+Database for its time zone support. The ownership of the TZ database
+is explained in BCP 175: Procedure for Maintaining the Time Zone
+Database section 7.
+
+ # 7. Database Ownership
+ #
+ # The TZ database itself is not an IETF Contribution or an IETF
+ # document. Rather it is a pre-existing and regularly updated work
+ # that is in the public domain, and is intended to remain in the
+ # public domain. Therefore, BCPs 78 [RFC5378] and 79 [RFC3979] do
+ # not apply to the TZ Database or contributions that individuals make
+ # to it. Should any claims be made and substantiated against the TZ
+ # Database, the organization that is providing the IANA
+ # Considerations defined in this RFC, under the memorandum of
+ # understanding with the IETF, currently ICANN, may act in accordance
+ # with all competent court orders. No ownership claims will be made
+ # by ICANN or the IETF Trust on the database or the code. Any person
+ # making a contribution to the database or code waives all rights to
+ # future claims in that contribution or in the TZ Database.
+
+6. Google double-conversion
+
+Copyright 2006-2011, the V8 project authors. All rights reserved.
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+ * Neither the name of Google Inc. nor the names of its
+ contributors may be used to endorse or promote products derived
+ from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+```
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.web/libxml2.md b/lib/javafx-sdk-14-Windows/legal/javafx.web/libxml2.md
new file mode 100644
index 0000000..2c21817
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.web/libxml2.md
@@ -0,0 +1,30 @@
+## xmlsoft.org: libxml2 v2.9.9
+
+### libxml2 License
+```
+
+Except where otherwise noted in the source code (e.g. the files hash.c,
+list.c and the trio files, which are covered by a similar licence but
+with different Copyright notices) all the files are:
+
+Copyright (C) 1998-2012 Daniel Veillard. All Rights Reserved.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+```
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.web/libxslt.md b/lib/javafx-sdk-14-Windows/legal/javafx.web/libxslt.md
new file mode 100644
index 0000000..c0e5bd6
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.web/libxslt.md
@@ -0,0 +1,60 @@
+## xmlsoft.org: libxslt v1.1.34
+
+### libxslt License
+```
+
+Licence for libxslt except libexslt
+----------------------------------------------------------------------
+ Copyright (C) 2001-2002 Daniel Veillard. All Rights Reserved.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is fur-
+nished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FIT-
+NESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+DANIEL VEILLARD BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CON-
+NECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+Except as contained in this notice, the name of Daniel Veillard shall not
+be used in advertising or otherwise to promote the sale, use or other deal-
+ings in this Software without prior written authorization from him.
+
+----------------------------------------------------------------------
+
+Licence for libexslt
+----------------------------------------------------------------------
+ Copyright (C) 2001-2002 Thomas Broyer, Charlie Bozeman and Daniel Veillard.
+ All Rights Reserved.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is fur-
+nished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FIT-
+NESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CON-
+NECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+Except as contained in this notice, the name of the authors shall not
+be used in advertising or otherwise to promote the sale, use or other deal-
+ings in this Software without prior written authorization from him.
+----------------------------------------------------------------------
+
+```
diff --git a/lib/javafx-sdk-14-Windows/legal/javafx.web/webkit.md b/lib/javafx-sdk-14-Windows/legal/javafx.web/webkit.md
new file mode 100644
index 0000000..e4cbc1e
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/legal/javafx.web/webkit.md
@@ -0,0 +1,535 @@
+## WebKit Open Source Project: WebKit v608.1
+
+### WebKit Notice
+```
+
+You are receiving a copy of WebKit in either source or
+object code in the JavaFX runtime or JavaFX SDK. The terms of the
+Oracle license do NOT apply to WebKit; it is
+licensed under the following license, separately from the Oracle programs
+you receive. If you do not wish to install this library, you may delete
+this library:
+
+ - On Linux systems: delete $(JAVA_HOME)/lib/libjfxwebkit.so
+ - On Mac OS X systems: delete $(JAVA_HOME)/lib/libjfxwebkit.dylib
+ - On Windows systems: delete $(JAVA_HOME)\bin\jfxwebkit.dll
+
+A copy of the Oracle modified WebKit library source code is located
+in the following OpenJDK git repository:
+
+ https://github.com/openjdk/jfx
+
+You can use git to clone the repository or you can browse the
+source using a web browser. The root directory of the WebKit source
+code is here:
+
+ rt/modules/javafx.web/src/main/native/
+```
+
+### LGPL 2.1
+```
+
+ GNU LESSER GENERAL PUBLIC LICENSE
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+ License as published by the Free Software Foundation; either
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+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
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+ Ty Coon, President of Vice
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+That's all there is to it!
+
+```
diff --git a/lib/javafx-sdk-14-Windows/lib/javafx-swt.jar b/lib/javafx-sdk-14-Windows/lib/javafx-swt.jar
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diff --git a/lib/javafx-sdk-14-Windows/lib/javafx.media.jar b/lib/javafx-sdk-14-Windows/lib/javafx.media.jar
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diff --git a/lib/javafx-sdk-14-Windows/lib/javafx.properties b/lib/javafx-sdk-14-Windows/lib/javafx.properties
new file mode 100644
index 0000000..942da72
--- /dev/null
+++ b/lib/javafx-sdk-14-Windows/lib/javafx.properties
@@ -0,0 +1,3 @@
+javafx.version=14
+javafx.runtime.version=14+9
+javafx.runtime.build=9
diff --git a/lib/javafx-sdk-14-Windows/lib/javafx.swing.jar b/lib/javafx-sdk-14-Windows/lib/javafx.swing.jar
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diff --git a/lib/javafx-sdk-14-Windows/lib/javafx.web.jar b/lib/javafx-sdk-14-Windows/lib/javafx.web.jar
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diff --git a/lib/javafx-sdk-14-Windows/lib/src.zip b/lib/javafx-sdk-14-Windows/lib/src.zip
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diff --git a/lib/junit-4.12.jar b/lib/junit-4.12.jar
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diff --git a/lib/pdfbox-2.0.17.jar b/lib/pdfbox-2.0.17.jar
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diff --git a/src/main/java/de/whs/ibci/msc/control/ApplicationController.java b/src/main/java/de/whs/ibci/msc/control/ApplicationController.java
new file mode 100644
index 0000000..b56775a
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/control/ApplicationController.java
@@ -0,0 +1,815 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.control;
+
+import de.whs.ibci.msc.model.JobTaskManager;
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.utility.MSCConstants;
+import de.whs.ibci.msc.model.HistogramDataManager;
+import de.whs.ibci.msc.model.ComparisonFeature;
+import de.whs.ibci.msc.model.ComparisonResult;
+import de.whs.ibci.msc.model.HistogramData;
+import de.whs.ibci.msc.utility.GuiUtilities;
+import de.whs.ibci.msc.view.MainView;
+import de.whs.ibci.msc.view.PreferencesConfigurationDialog;
+import java.awt.Desktop;
+import java.awt.Toolkit;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.util.Iterator;
+import java.util.Optional;
+import java.util.Queue;
+import java.util.Set;
+import java.util.concurrent.ConcurrentLinkedQueue;
+import java.util.logging.Level;
+import java.util.zip.GZIPInputStream;
+import java.util.zip.GZIPOutputStream;
+import javafx.application.Application;
+import javafx.application.Platform;
+import javafx.concurrent.Task;
+import javafx.event.ActionEvent;
+import javafx.event.Event;
+import javafx.scene.Cursor;
+import javafx.scene.control.Alert;
+import javafx.scene.control.Button;
+import javafx.scene.control.ButtonBar;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.TextFormatter;
+import javafx.scene.input.KeyCode;
+import javafx.scene.input.KeyCodeCombination;
+import javafx.scene.input.KeyCombination;
+import javafx.scene.input.KeyEvent;
+import javafx.stage.DirectoryChooser;
+import javafx.stage.Stage;
+import javafx.stage.WindowEvent;
+
+/**
+ * Entry point and main controller of this JavaFX application. Handles events
+ * for the menu-bar and general controls. Controls the creation and deletion of
+ * JobControllers
+ *
+ * @author Jan-Mathis Hein
+ */
+public class ApplicationController extends Application implements PropertyChangeListener {
+
+ //
+ /**
+ * True if the input for the number of parallel threads given by the user in
+ * the PreferencesConfigurationDialog is valid, false otherwise
+ */
+ private boolean isValidNumberOfParallelThreads;
+
+ /**
+ * True if the input for the default number of bins given by the user in
+ * the PreferencesConfigurationDialog is valid, false otherwise
+ */
+ private boolean isValidDefaultNumberOfBins;
+
+ /**
+ * True if the input for the maximal number of molecule pairs to save given
+ * by the user in the PreferencesConfigurationDialog is valid, false otherwise
+ */
+ private boolean isValidMaximalNumberOfMoleculePairsToSave;
+
+ /**
+ * DirectoryChooser that is used to choose the default directory for
+ * different file choosers
+ */
+ private final DirectoryChooser defaultDirectoryChooser = new DirectoryChooser();
+
+ /**
+ * Directory from where the last output file was loaded or directory where
+ * the last output file was saved
+ */
+ private File lastOutputDirectoryParent;
+
+ /**
+ * DirectoryChooser that is used to choose the directory for job saving and
+ * loading
+ */
+ private final DirectoryChooser outputDirectoryChooser = new DirectoryChooser();
+
+ /**
+ * Number of JobControllers created in this session of the application
+ */
+ private int numberOfCreatedJobControllers = 0;
+
+ /**
+ * The JobController which is currently active and shown
+ */
+ private JobController activeJobController;
+
+ /**
+ * Queue of currently opened JobControllers
+ */
+ private final Queue jobControllerList = new ConcurrentLinkedQueue<>();
+
+ /**
+ * Main window of this application. This variable must be effectively final
+ */
+ private MainView view;
+
+ /**
+ * Dialog in which some preferences can be configured by the user
+ */
+ private PreferencesConfigurationDialog preferencesConfigurationDialog;
+ //
+ //
+ //
+ /**
+ * The entry point for this JavaFX application. Starts and intializes the
+ * graphical user interface. Checks the screen size, the java version,
+ * whether this is the only currently running instance and whether the
+ * preferneces can be loaded. Sets up the file choosers and handles menu-bar
+ * and general controls events.
+ *
+ * NOTE: This method is called on the JavaFX Application Thread.
+ *
+ * @param primaryStage the primary stage for this application, onto which
+ * the application scene is set
+ */
+ @Override
+ public void start(Stage primaryStage) {
+ try {
+ //
+ String tmpJavaVersion = System.getProperty("java.version");
+ if (tmpJavaVersion.compareTo(MSCConstants.JAVA_VERSION) < 0) {
+ GeneralUtilities.showErrorDialog(null, String.format(
+ GeneralUtilities.getUIText("ErrorDescription.WrongVersion.text"),
+ tmpJavaVersion, MSCConstants.JAVA_VERSION),
+ "ApplicationController.start()"
+ );
+ System.exit(-1);
+ }
+ if (!MSCConstants.MSC_FILES_DIRECTORY.isDirectory()) {
+ MSCConstants.MSC_FILES_DIRECTORY.mkdirs();
+ }
+ if (!GeneralUtilities.isSingleInstance()) {
+ GeneralUtilities.showErrorDialog(
+ null,
+ GeneralUtilities.getUIText("ErrorDescription.NotSingleInstance.text") + " \n" + MSCConstants.MSC_FILES_DIRECTORY.getPath(),
+ "ApplicationController.start()"
+ );
+ System.exit(-1);
+ }
+ if (Toolkit.getDefaultToolkit().getScreenSize().height < MSCConstants.MINIMAL_MAIN_WINDOW_HEIGHT ||
+ Toolkit.getDefaultToolkit().getScreenSize().height < MSCConstants.MINIMAL_MOLECULE_DISPLAYER_HEIGHT ||
+ Toolkit.getDefaultToolkit().getScreenSize().width < MSCConstants.MINIMAL_MAIN_WINDOW_WIDTH ||
+ Toolkit.getDefaultToolkit().getScreenSize().width < MSCConstants.MINIMAL_MOLECULE_DISPLAYER_WIDTH) {
+ GeneralUtilities.showErrorDialog(null, GeneralUtilities.getUIText("ErrorDescription.ScreenTooSmall.text"), "ApplicationController.start()");
+ System.exit(-1);
+ }
+ // Do this after checking for single instance or
+ // otherwise an additional log-file will be created
+ GeneralUtilities.initializeLogger();
+ try {
+ // Check if the preferences are available
+ UserPreferences.getInstance();
+ } catch (SecurityException | IllegalStateException ex) {
+ GeneralUtilities.showErrorDialog(null, GeneralUtilities.getUIText("ErrorDescription.CanNotInstantiatePreferences.text"), "ApplicationController.start()");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ System.exit(-1);
+ }
+ //
+ //
+ GeneralUtilities.logMessage(Level.INFO, "", "", GeneralUtilities.getUIText("Logging.ApplicationStart.text"));
+ this.view = new MainView(primaryStage);
+ this.view.getPrimaryStage().setMinHeight(MSCConstants.MINIMAL_MAIN_WINDOW_HEIGHT);
+ this.view.getPrimaryStage().setMinWidth(MSCConstants.MINIMAL_MAIN_WINDOW_WIDTH);
+ this.view.getPrimaryStage().setHeight(MSCConstants.MINIMAL_MAIN_WINDOW_HEIGHT);
+ this.view.getPrimaryStage().setWidth(MSCConstants.MINIMAL_MAIN_WINDOW_WIDTH);
+ this.view.getPrimaryStage().show();
+ //
+ //
+ this.preferencesConfigurationDialog = new PreferencesConfigurationDialog(this.view.getPrimaryStage(), GeneralUtilities.getUIText("PreferencesConfigurationDialog.title.text"));
+ this.preferencesConfigurationDialog.getNumberOfParallelThreadsField().setTextFormatter(new TextFormatter<>((TextFormatter.Change tmpChange) -> {
+ if (!tmpChange.getControlNewText().matches("\\d*")) {
+ tmpChange.setText("");
+ }
+ try {
+ if (Integer.parseInt(tmpChange.getControlNewText()) == 0) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ this.isValidNumberOfParallelThreads = false;
+ }
+ tmpChange.getControl().setStyle("-fx-background-color: white;");
+ this.isValidNumberOfParallelThreads = true;
+ } catch (NumberFormatException ex) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ this.isValidNumberOfParallelThreads = false;
+ }
+ return tmpChange;
+ }));
+ this.preferencesConfigurationDialog.getDefaultNumberOfBinsField().setTextFormatter(new TextFormatter<>((TextFormatter.Change tmpChange) -> {
+ if (!tmpChange.getControlNewText().matches("\\d*")) {
+ tmpChange.setText("");
+ }
+ try {
+ if (Integer.parseInt(tmpChange.getControlNewText()) == 0) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ this.isValidDefaultNumberOfBins = false;
+ }
+ tmpChange.getControl().setStyle("-fx-background-color: white;");
+ this.isValidDefaultNumberOfBins = true;
+ } catch (NumberFormatException ex) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ this.isValidDefaultNumberOfBins = false;
+ }
+ return tmpChange;
+ }));
+ this.preferencesConfigurationDialog.getMaximalNumberOfMoleculePairsToSaveField().setTextFormatter(new TextFormatter<>((TextFormatter.Change tmpChange) -> {
+ if (!tmpChange.getControlNewText().matches("\\d*")) {
+ tmpChange.setText("");
+ }
+ try {
+ Integer.parseInt(tmpChange.getControlNewText());
+ tmpChange.getControl().setStyle("-fx-background-color: white;");
+ this.isValidMaximalNumberOfMoleculePairsToSave = true;
+ } catch (NumberFormatException ex) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ this.isValidMaximalNumberOfMoleculePairsToSave = false;
+ }
+ return tmpChange;
+ }));
+ //
+ //
+ //
+ this.view.getPrimaryStage().setOnCloseRequest((WindowEvent e) -> {
+ Optional tmpResult = GeneralUtilities.showConfirmationDialog(
+ this.view.getPrimaryStage(), GeneralUtilities.getUIText("ConfirmationDialog.ClosingApplicationContent.text"),
+ GeneralUtilities.getUIText("ConfirmationDialog.ClosingTitle.text"),
+ GeneralUtilities.getUIText("ConfirmationDialog.ClosingApplicationHeader.text")
+ );
+ if (tmpResult.isPresent() && tmpResult.get().getButtonData() == ButtonBar.ButtonData.APPLY) {
+ Platform.exit();
+ } else {
+ e.consume();
+ }
+ });
+ this.view.getCenterButton().setOnAction((ActionEvent e) -> {
+ this.view.getPrimaryStage().centerOnScreen();
+ });
+ this.view.getMinButton().setOnAction((ActionEvent e) -> {
+ this.view.getPrimaryStage().setMaximized(false);
+ this.view.getPrimaryStage().setHeight(MSCConstants.MINIMAL_MAIN_WINDOW_HEIGHT);
+ this.view.getPrimaryStage().setWidth(MSCConstants.MINIMAL_MAIN_WINDOW_WIDTH);
+ });
+ this.view.getMaxButton().setOnAction((ActionEvent e) -> {
+ this.view.getPrimaryStage().setMaximized(true);
+ });
+ //
+ //
+ this.view.getSaveJobMenuItem().setOnAction((ActionEvent e) -> {
+ if (this.activeJobController == null || this.activeJobController.getHistogramDataManager() == null) {
+ GeneralUtilities.showInfoDialog(this.view.getPrimaryStage(), GeneralUtilities.getUIText("InfoDescription.SavingNotPossible.text"));
+ return;
+ }
+ if (!UserPreferences.getInstance().getOutputDir().isEmpty() && new File(UserPreferences.getInstance().getOutputDir()).isDirectory()) {
+ this.outputDirectoryChooser.setInitialDirectory(new File(UserPreferences.getInstance().getOutputDir()));
+ } else {
+ this.outputDirectoryChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ if (this.lastOutputDirectoryParent != null && this.lastOutputDirectoryParent.isDirectory()) {
+ this.outputDirectoryChooser.setInitialDirectory(this.lastOutputDirectoryParent);
+ }
+ this.outputDirectoryChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.SaveOutput.text"));
+ final File tmpDirectory = this.outputDirectoryChooser.showDialog(this.view.getPrimaryStage());
+ if (tmpDirectory == null) {
+ return;
+ }
+ if (tmpDirectory.isDirectory()) {
+ if (tmpDirectory.list() != null && tmpDirectory.list().length != 0) {
+ Optional tmpResult = GeneralUtilities.showConfirmationDialog(
+ this.view.getPrimaryStage(), GeneralUtilities.getUIText("ConfirmationDialog.DirectoryAlreadyExistsContent.text"),
+ GeneralUtilities.getUIText("ConfirmationDialog.SelectionTitle.text"),
+ GeneralUtilities.getUIText("ConfirmationDialog.DirectoryAlreadyExistsHeader.text")
+ );
+ if (tmpResult.isPresent() && tmpResult.get().getButtonData() == ButtonBar.ButtonData.APPLY) {
+ new File(tmpDirectory.getAbsolutePath() + File.separator + "output.ser").delete();
+ new File(tmpDirectory.getAbsolutePath() + File.separator + "README.txt").delete();
+ new File(tmpDirectory.getAbsolutePath() + File.separator + "moleculeSet1.txt").delete();
+ new File(tmpDirectory.getAbsolutePath() + File.separator + "moleculeSet2.txt").delete();
+ } else {
+ return;
+ }
+ }
+ } else {
+ if (!tmpDirectory.mkdirs()) {
+ GeneralUtilities.showErrorDialog(this.view.getPrimaryStage(), GeneralUtilities.getUIText("ErrorDescription.CanNotCreateDirectory.text"), "ApplicationController.view.getSaveJobMenuItem().setOnAction()");
+ }
+ }
+ this.lastOutputDirectoryParent = tmpDirectory.getParentFile();
+ final JobController tmpJobController = this.activeJobController;
+ final HistogramDataManager tmpHistogramDataManager = tmpJobController.getHistogramDataManager();
+ Task tmpTask = new Task() {
+
+ @Override
+ protected Void call() throws Exception {
+ File tmpFirstMoleculeSetFile = new File(tmpDirectory.getAbsolutePath() + File.separator + MSCConstants.MOLECULE_SET_1_FILE);
+ File tmpSecondMoleculeSetFile = new File(tmpDirectory.getAbsolutePath() + File.separator + MSCConstants.MOLECULE_SET_2_FILE);
+ File tmpOutputFile = new File(tmpDirectory.getAbsolutePath() + File.separator + MSCConstants.OUTPUT_FILE_NAME);
+ File tmpInfoFile = new File(tmpDirectory.getAbsolutePath() + File.separator + MSCConstants.INFO_FILE_NAME);
+ try (
+ ObjectOutputStream tmpObjectOutputStream = new ObjectOutputStream(new GZIPOutputStream(new FileOutputStream(tmpOutputFile), 64 * 1024));
+ BufferedWriter tmpInfoFileWritter = new BufferedWriter(new FileWriter(tmpInfoFile));
+ BufferedWriter tmpFirstMoleculeSetFileWritter = new BufferedWriter(new FileWriter(tmpFirstMoleculeSetFile));
+ BufferedWriter tmpSecondMoleculeSetFileWritter = new BufferedWriter(new FileWriter(tmpSecondMoleculeSetFile));
+ ) {
+ //
+ synchronized (tmpHistogramDataManager) {
+ tmpObjectOutputStream.writeObject(tmpHistogramDataManager);
+ }
+ //
+ //
+ tmpInfoFileWritter.write(String.format(
+ GeneralUtilities.getUIText("SavingJob.InfoFile.text"),
+ tmpFirstMoleculeSetFile.getName(), tmpSecondMoleculeSetFile.getName(), tmpOutputFile.getName()
+ ));
+ //
+ //
+ Iterator tmpIterator = tmpHistogramDataManager.getNativeDataList().iterator();
+ ComparisonResult tmpComparisonResult;
+ int tmpCounter = 0;
+ while (tmpIterator.hasNext() && tmpCounter < UserPreferences.getInstance().getMaximalNumberOfMoleculePairsToSave()) {
+ tmpComparisonResult = tmpIterator.next();
+ tmpFirstMoleculeSetFileWritter.write(tmpComparisonResult.getMolecule1().trim());
+ tmpFirstMoleculeSetFileWritter.newLine();
+ tmpSecondMoleculeSetFileWritter.write(tmpComparisonResult.getMolecule2().trim());
+ tmpSecondMoleculeSetFileWritter.newLine();
+ tmpCounter++;
+ }
+ //
+ tmpJobController.setOutputIsSaved(true);
+ } catch (IOException ex) {
+ Platform.runLater(() -> {
+ ApplicationController.this.view.getScene().setCursor(Cursor.DEFAULT);
+ GeneralUtilities.showErrorDialog(ApplicationController.this.view.getPrimaryStage(), ex.toString(), "ApplicationController.view.getSaveJobMenuItem().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ });
+ } finally {
+ Platform.runLater(() -> {
+ ApplicationController.this.view.getScene().setCursor(Cursor.DEFAULT);
+ });
+ }
+ return null;
+ }
+
+ };
+ Thread tmpBackgroundThread = new Thread(tmpTask);
+ this.view.getScene().setCursor(Cursor.WAIT);
+ tmpBackgroundThread.start();
+ });
+ this.view.getLoadJobOutputMenuItem().setOnAction((ActionEvent e) -> {
+ if (!UserPreferences.getInstance().getOutputDir().isEmpty() && new File(UserPreferences.getInstance().getOutputDir()).isDirectory()) {
+ this.outputDirectoryChooser.setInitialDirectory(new File(UserPreferences.getInstance().getOutputDir()));
+ } else {
+ this.outputDirectoryChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ if (this.lastOutputDirectoryParent != null && this.lastOutputDirectoryParent.isDirectory()) {
+ this.outputDirectoryChooser.setInitialDirectory(this.lastOutputDirectoryParent);
+ }
+ this.outputDirectoryChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.LoadOutput.text"));
+ File tmpDirectory = this.outputDirectoryChooser.showDialog(this.view.getPrimaryStage());
+ if (tmpDirectory == null) {
+ return;
+ }
+ if (!tmpDirectory.isDirectory()) {
+ GeneralUtilities.showInfoDialog(this.view.getPrimaryStage(), GeneralUtilities.getUIText("InfoDescription.FileNotReadable.text"));
+ return;
+ }
+ this.lastOutputDirectoryParent = tmpDirectory.getParentFile();
+ Task tmpTask = new Task() {
+
+ @Override
+ protected Void call() throws Exception {
+ File tmpFirstMoleculeSetFile = new File(tmpDirectory.getAbsolutePath() + File.separator + MSCConstants.MOLECULE_SET_1_FILE);
+ File tmpSecondMoleculeSetFile = new File(tmpDirectory.getAbsolutePath() + File.separator + MSCConstants.MOLECULE_SET_2_FILE);
+ File tmpOutputFile = new File(tmpDirectory.getAbsolutePath() + File.separator + MSCConstants.OUTPUT_FILE_NAME);
+ try (
+ ObjectInputStream tmpObjectInputStream = new ObjectInputStream(new GZIPInputStream(new FileInputStream(tmpOutputFile), 64 * 1024));
+ BufferedReader tmpFirstMoleculeSetFileReader = new BufferedReader(new FileReader(tmpFirstMoleculeSetFile));
+ BufferedReader tmpSecondMoleculeSetFileReader = new BufferedReader(new FileReader(tmpSecondMoleculeSetFile));
+ ) {
+ //
+ HistogramDataManager tmpHistogramDataManager = (HistogramDataManager) tmpObjectInputStream.readObject();
+ //
+ //
+ Iterator tmpIterator = tmpHistogramDataManager.getNativeDataList().iterator();
+ ComparisonResult tmpComparisonResult;
+ String tmpLine1 = null;
+ String tmpLine2 = null;
+ while (
+ (tmpLine1 = tmpFirstMoleculeSetFileReader.readLine()) != null &&
+ (tmpLine2 = tmpSecondMoleculeSetFileReader.readLine()) != null &&
+ tmpIterator.hasNext()
+ ) {
+ tmpComparisonResult = tmpIterator.next();
+ tmpComparisonResult.setMolecule1(tmpLine1);
+ tmpComparisonResult.setMolecule2(tmpLine2);
+ }
+ //
+ //
+ tmpHistogramDataManager.getComparisonFeatureSet().forEach((ComparisonFeature tmpComparisonFeature) -> {
+ HistogramData tmpHistogramData = tmpHistogramDataManager.getHistogramData(tmpComparisonFeature);
+ double tmpLowerFrequencyBound = tmpHistogramData.getLowerFrequencyBound();
+ double tmpUpperFrequencyBound = tmpHistogramData.getUpperFrequencyBound();
+ // Resets the frequency bounds
+ tmpHistogramData.call();
+ // Set the pre-reset frequency bounds
+ tmpHistogramData.setLowerFrequencyBound(tmpLowerFrequencyBound);
+ tmpHistogramData.setUpperFrequencyBound(tmpUpperFrequencyBound);
+ });
+ //
+ Platform.runLater(() -> {
+ ApplicationController.this.createNewJobController(true, tmpHistogramDataManager);
+ ApplicationController.this.view.getScene().setCursor(Cursor.DEFAULT);
+ });
+ } catch (IOException | ClassNotFoundException | IllegalArgumentException ex) {
+ Platform.runLater(() -> {
+ ApplicationController.this.view.getScene().setCursor(Cursor.DEFAULT);
+ GeneralUtilities.showErrorDialog(ApplicationController.this.view.getPrimaryStage(), ex.toString(), "ApplicationController.view.getLoadJobOutputMenuItem().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ });
+ }
+ return null;
+ }
+
+ };
+ Thread tmpBackgroundThread = new Thread(tmpTask);
+ this.view.getScene().setCursor(Cursor.WAIT);
+ tmpBackgroundThread.start();
+ });
+ this.view.getNewJobMenuItem().setOnAction((ActionEvent e) -> {
+ this.createNewJobController(false, null);
+ });
+ this.view.getDefaultInputDirectoryMenuItem().setOnAction((ActionEvent e) -> {
+ try {
+ this.defaultDirectoryChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.DefaultInputDirectory.text"));
+ if (!UserPreferences.getInstance().getInputDir().isEmpty() && new File(UserPreferences.getInstance().getInputDir()).isDirectory()) {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(UserPreferences.getInstance().getInputDir()));
+ } else {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ File tmpFile = this.defaultDirectoryChooser.showDialog(this.view.getPrimaryStage());
+ if (tmpFile != null && tmpFile.isDirectory()) {
+ UserPreferences.getInstance().setInputDir(tmpFile.getAbsolutePath());
+ UserPreferences.savePreferences();
+ }
+ } catch (Exception ex) {
+ GeneralUtilities.showErrorDialog(this.view.getPrimaryStage(), ex.toString(), "ApplicationController.view.getInputDirectoryMenuItem().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ this.view.getDefaultOutputDirectoryMenuItem().setOnAction((ActionEvent e) -> {
+ try {
+ this.defaultDirectoryChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.DefaultOutputDirectory.text"));
+ if (!UserPreferences.getInstance().getOutputDir().isEmpty() && new File(UserPreferences.getInstance().getOutputDir()).isDirectory()) {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(UserPreferences.getInstance().getOutputDir()));
+ } else {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ File tmpFile = this.defaultDirectoryChooser.showDialog(this.view.getPrimaryStage());
+ if (tmpFile != null && tmpFile.isDirectory()) {
+ UserPreferences.getInstance().setOutputDir(tmpFile.getAbsolutePath());
+ UserPreferences.savePreferences();
+ }
+ } catch (Exception ex) {
+ GeneralUtilities.showErrorDialog(this.view.getPrimaryStage(), ex.toString(), "ApplicationController.view.getOutputDirectoryMenuItem().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ this.view.getDefaultImageDirectoryMenutItem().setOnAction((ActionEvent e) -> {
+ try {
+ this.defaultDirectoryChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.DefaultImageDirectory.text"));
+ if (!UserPreferences.getInstance().getImageDir().isEmpty() && new File(UserPreferences.getInstance().getImageDir()).isDirectory()) {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(UserPreferences.getInstance().getImageDir()));
+ } else {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ File tmpFile = this.defaultDirectoryChooser.showDialog(this.view.getPrimaryStage());
+ if (tmpFile != null && tmpFile.isDirectory()) {
+ UserPreferences.getInstance().setImageDir(tmpFile.getAbsolutePath());
+ UserPreferences.savePreferences();
+ }
+ } catch (Exception ex) {
+ GeneralUtilities.showErrorDialog(this.view.getPrimaryStage(), ex.toString(), "ApplicationController.view.getImageDirectoryMenuItem().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ this.view.getDefaultMoleculeListDirectoryMenuItem().setOnAction((ActionEvent e) -> {
+ try {
+ this.defaultDirectoryChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.DefaultMoleculeListDirectory.text"));
+ if (!UserPreferences.getInstance().getMoleculeListDir().isEmpty() && new File(UserPreferences.getInstance().getMoleculeListDir()).isDirectory()) {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(UserPreferences.getInstance().getMoleculeListDir()));
+ } else {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ File tmpFile = this.defaultDirectoryChooser.showDialog(this.view.getPrimaryStage());
+ if (tmpFile != null && tmpFile.isDirectory()) {
+ UserPreferences.getInstance().setMoleculeListDir(tmpFile.getAbsolutePath());
+ UserPreferences.savePreferences();
+ }
+ } catch (Exception ex) {
+ GeneralUtilities.showErrorDialog(this.view.getPrimaryStage(), ex.toString(), "ApplicationController.view.getMoleculeListDirectoryMenuItem().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ this.view.getDefaultSummaryReportDirectoryMenuItem().setOnAction((ActionEvent e) -> {
+ try {
+ this.defaultDirectoryChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.DefaultSummaryReportDirectory.text"));
+ if (!UserPreferences.getInstance().getSummaryReportDir().isEmpty() && new File(UserPreferences.getInstance().getSummaryReportDir()).isDirectory()) {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(UserPreferences.getInstance().getSummaryReportDir()));
+ } else {
+ this.defaultDirectoryChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ File tmpFile = this.defaultDirectoryChooser.showDialog(this.view.getPrimaryStage());
+ if (tmpFile != null && tmpFile.isDirectory()) {
+ UserPreferences.getInstance().setSummaryReportDir(tmpFile.getAbsolutePath());
+ UserPreferences.savePreferences();
+ }
+ } catch (Exception ex) {
+ GeneralUtilities.showErrorDialog(this.view.getPrimaryStage(), ex.toString(), "ApplicationController.view.getDefaultSummaryReportDirectoryMenuItem().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ this.view.getOtherPreferencesMenuItem().setOnAction((ActionEvent e) -> {
+ this.preferencesConfigurationDialog.getNumberOfParallelThreadsField().setText(Integer.toString(UserPreferences.getInstance().getNumberOfParallelThreads()));
+ this.preferencesConfigurationDialog.getDefaultNumberOfBinsField().setText(Integer.toString(UserPreferences.getInstance().getDefaultNumberOfBins()));
+ this.preferencesConfigurationDialog.getMaximalNumberOfMoleculePairsToSaveField().setText(Integer.toString(UserPreferences.getInstance().getMaximalNumberOfMoleculePairsToSave()));
+ this.preferencesConfigurationDialog.getImageQualitySlider().setValue(UserPreferences.getInstance().getImageQuality());
+ this.preferencesConfigurationDialog.showAndWait();
+ });
+ this.view.getBrowseLogMenuItem().setOnAction((ActionEvent e) -> {
+ File tmpLogFile = GeneralUtilities.getLogFile();
+ if (!Desktop.isDesktopSupported()) {
+ GeneralUtilities.showInfoDialog(this.view.getPrimaryStage(), GeneralUtilities.getUIText("InfoDescription.DesktopNotSupported.text"));
+ return;
+ }
+ if (!tmpLogFile.canRead()) {
+ GeneralUtilities.showInfoDialog(this.view.getPrimaryStage(), GeneralUtilities.getUIText("InfoDescription.LogFileNotReadable.text"));
+ return;
+ }
+ try {
+ Desktop.getDesktop().open(tmpLogFile);
+ } catch (IOException ex) {
+ GeneralUtilities.showErrorDialog(this.view.getPrimaryStage(), ex.toString(), "ApplicationController.view.getBrowseLogMenuItem().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ this.view.getResetLogMenuItem().setOnAction((ActionEvent e) -> {
+ // Also deletes the log file and then resets the handlers
+ GeneralUtilities.closeAndRemoveHandlersFromLogger(true);
+ GeneralUtilities.logMessage(Level.INFO, "", "", GeneralUtilities.getUIText("Logging.NewLoggingSession.text"));
+ });
+ this.view.getAboutMenuItem().setOnAction((ActionEvent e) -> {
+ Alert tmpAboutDialog = new Alert(Alert.AlertType.INFORMATION, "", ButtonType.OK);
+ tmpAboutDialog.initOwner(this.view.getPrimaryStage());
+ tmpAboutDialog.setTitle(GeneralUtilities.getUIText("InfoDialog.AboutTitle.text"));
+ tmpAboutDialog.setHeaderText(null);
+ tmpAboutDialog.getDialogPane().setContentText(String.format(GeneralUtilities.getUIText("InfoDescription.About.text"), MSCConstants.MSC_VERSION));
+ Button tmpButton = (Button) tmpAboutDialog.getDialogPane().lookupButton(ButtonType.OK);
+ GuiUtilities.setMinMaxPrefSize(tmpButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ tmpAboutDialog.showAndWait();
+ });
+ //
+ //
+ this.preferencesConfigurationDialog.getCancelButton().setOnAction((ActionEvent e) -> {
+ this.preferencesConfigurationDialog.hide();
+ });
+ this.preferencesConfigurationDialog.getApplyButton().setOnAction((ActionEvent e) -> {
+ if (this.isValidNumberOfParallelThreads) {
+ UserPreferences.getInstance().setNumberOfParallelThreads(Integer.parseInt(this.preferencesConfigurationDialog.getNumberOfParallelThreadsField().getText()));
+ UserPreferences.savePreferences();
+ this.jobControllerList.stream().filter((JobController tmpJobController) -> tmpJobController.getJobTaskManager() != null).forEach((JobController tmpJobController) -> {
+ tmpJobController.getJobTaskManager().setNumberOfParallelThreads(UserPreferences.getInstance().getNumberOfParallelThreads());
+ });
+ }
+ if (this.isValidDefaultNumberOfBins) {
+ UserPreferences.getInstance().setDefaultNumberOfBins(Integer.parseInt(this.preferencesConfigurationDialog.getDefaultNumberOfBinsField().getText()));
+ UserPreferences.savePreferences();
+ this.jobControllerList.stream().filter((JobController tmpJobController) -> tmpJobController.getJobTaskManager() != null).forEach((JobController tmpJobController) -> {
+ tmpJobController.getJobTaskManager().setDefaultNumberOfBins(UserPreferences.getInstance().getDefaultNumberOfBins());
+ });
+ }
+ if (this.isValidMaximalNumberOfMoleculePairsToSave) {
+ UserPreferences.getInstance().setMaximalNumberOfMoleculePairsToSave(Integer.parseInt(this.preferencesConfigurationDialog.getMaximalNumberOfMoleculePairsToSaveField().getText()));
+ UserPreferences.savePreferences();
+ }
+ UserPreferences.getInstance().setImageQuality(this.preferencesConfigurationDialog.getImageQualitySlider().getValue());
+ UserPreferences.savePreferences();
+ this.preferencesConfigurationDialog.hide();
+ });
+ this.preferencesConfigurationDialog.getDialogPane().addEventFilter(KeyEvent.KEY_PRESSED, (KeyEvent tmpEvent) -> {
+ KeyCombination tmpKeyCombination = new KeyCodeCombination(KeyCode.ENTER);
+ if (tmpKeyCombination.match(tmpEvent)) {
+ this.preferencesConfigurationDialog.getApplyButton().fire();
+ }
+ });
+ this.preferencesConfigurationDialog.getResetButton().setOnAction((ActionEvent e) -> {
+ this.preferencesConfigurationDialog.getNumberOfParallelThreadsField().setText(Integer.toString(UserPreferences.getInstance().getNumberOfParallelThreads()));
+ this.preferencesConfigurationDialog.getDefaultNumberOfBinsField().setText(Integer.toString(UserPreferences.getInstance().getDefaultNumberOfBins()));
+ this.preferencesConfigurationDialog.getMaximalNumberOfMoleculePairsToSaveField().setText(Integer.toString(UserPreferences.getInstance().getMaximalNumberOfMoleculePairsToSave()));
+ this.preferencesConfigurationDialog.getImageQualitySlider().setValue(UserPreferences.getInstance().getImageQuality());
+ });
+ //
+ //
+ } catch (Exception ex) {
+ GeneralUtilities.showErrorDialog(null, ex.toString(), "ApplicationController.start()");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ }
+
+ /**
+ * Handle PropertyChangeEvents that are coming from the JobControllers and
+ * update the GUI accordingly
+ *
+ * @param evt PropertyChangeEvent that was fired by one of the
+ * JobControllers
+ */
+ @Override
+ public void propertyChange(PropertyChangeEvent evt) {
+ try {
+ if (evt.getSource() instanceof JobController) {
+ JobController tmpJobController = (JobController) evt.getSource();
+ switch (evt.getPropertyName()) {
+ case "Created charts successfully":
+ this.view.getTabPane().getTabs().add(tmpJobController.getOutputTab());
+ this.view.getCenterPane().setStyle("-fx-background-color: rgb(200, 200, 200);");
+ this.view.getTabPane().getSelectionModel().select(tmpJobController.getOutputTab());
+ this.view.getTabPane().getTabs().remove(tmpJobController.getInputTab());
+ break;
+ case "Want to close InputTab":
+ if (tmpJobController.getJobTaskManager().isWorking()) {
+ Optional tmpResult = GeneralUtilities.showConfirmationDialog(
+ this.view.getPrimaryStage(), GeneralUtilities.getUIText("ConfirmationDialog.ClosingInputTabContent.text"),
+ GeneralUtilities.getUIText("ConfirmationDialog.ClosingTitle.text"),
+ GeneralUtilities.getUIText("ConfirmationDialog.ClosingInputTabHeader.text")
+ );
+ if (tmpResult.isPresent() && tmpResult.get().getButtonData() == ButtonBar.ButtonData.APPLY) {
+ this.closeJobController(tmpJobController);
+ // The Tab hasn't been closed yet
+ if (this.view.getTabPane().getTabs().size() <= 1) {
+ this.view.getCenterPane().setStyle("-fx-background-color: rgb(220, 220, 220);");
+ }
+ this.activeJobController = null;
+ } else {
+ // Destroy the closing event
+ if (evt.getNewValue() instanceof Event) {
+ Event tmpEvent = (Event) evt.getNewValue();
+ tmpEvent.consume();
+ }
+ }
+ } else {
+ this.closeJobController(tmpJobController);
+ // The Tab hasn't been closed yet
+ if (this.view.getTabPane().getTabs().size() <= 1) {
+ this.view.getCenterPane().setStyle("-fx-background-color: rgb(220, 220, 220);");
+ }
+ this.activeJobController = null;
+ }
+ break;
+ case "Want to close OutputTab":
+ if (!tmpJobController.outputIsSaved()) {
+ Optional tmpResult = GeneralUtilities.showConfirmationDialog(
+ this.view.getPrimaryStage(), GeneralUtilities.getUIText("ConfirmationDialog.ClosingOutputTabContent.text"),
+ GeneralUtilities.getUIText("ConfirmationDialog.ClosingTitle.text"),
+ GeneralUtilities.getUIText("ConfirmationDialog.ClosingOutputTabHeader.text")
+ );
+ if (tmpResult.isPresent() && tmpResult.get().getButtonData() == ButtonBar.ButtonData.APPLY) {
+ this.closeJobController(tmpJobController);
+ // The Tab hasn't been closed yet
+ if (this.view.getTabPane().getTabs().size() <= 1) {
+ this.view.getCenterPane().setStyle("-fx-background-color: rgb(220, 220, 220);");
+ }
+ this.activeJobController = null;
+ } else {
+ // Destroy the closing event
+ if (evt.getNewValue() instanceof Event) {
+ Event tmpEvent = (Event) evt.getNewValue();
+ tmpEvent.consume();
+ }
+ }
+ } else {
+ this.closeJobController(tmpJobController);
+ // The Tab hasn't been closed yet
+ if (this.view.getTabPane().getTabs().size() <= 1) {
+ this.view.getCenterPane().setStyle("-fx-background-color: rgb(220, 220, 220);");
+ }
+ this.activeJobController = null;
+ }
+ break;
+ case "JobController selected":
+ this.activeJobController = tmpJobController;
+ break;
+ default:
+ GeneralUtilities.logMessage(
+ Level.INFO, "ApplicationController", "propertyChange()",
+ String.format(GeneralUtilities.getUIText("Logging.UnexptectedPropertyChange.text"), evt.getPropertyName())
+ );
+ break;
+ }
+ }
+ } catch (Exception ex) {
+ GeneralUtilities.showErrorDialog(this.view.getPrimaryStage(), ex.toString(), "ApplicationController.propertyChange()");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ }
+
+ /**
+ * This is called whenever this JavaFX Application is closed and it closes
+ * all open JobControllers
+ */
+ @Override
+ public void stop() {
+ this.jobControllerList.forEach((tmpJobController) -> {
+ this.closeJobController(tmpJobController);
+ });
+ this.activeJobController = null;
+ GeneralUtilities.logMessage(Level.INFO, "", "", GeneralUtilities.getUIText("Logging.ApplicationClosed.text"));
+ // Closes the log file
+ GeneralUtilities.closeAndRemoveHandlersFromLogger(false);
+ }
+ //
+ //
+ //
+ /**
+ * Close the given JobController and its JobTaskManager
+ *
+ * @param tmpJobController the JobController that will be closed
+ */
+ private void closeJobController(JobController tmpJobController) {
+ tmpJobController.removePropertyChangeListener(this);
+ JobTaskManager tmpJobTaskManager = tmpJobController.getJobTaskManager();
+ if (tmpJobTaskManager != null) {
+ tmpJobTaskManager.cancelWorkingProcess();
+ }
+ this.jobControllerList.remove(tmpJobController);
+ }
+
+ /**
+ * Create a new JobController, add it to the JobController list and
+ * handle some related things
+ */
+ private synchronized void createNewJobController(boolean tmpIsLoaded, HistogramDataManager tmpHistogramDataManager) {
+ this.numberOfCreatedJobControllers++;
+ try {
+ JobController tmpController = new JobController(
+ this.view, tmpIsLoaded, Integer.toString(this.numberOfCreatedJobControllers)
+ );
+ tmpController.addPropertyChangeListener(this);
+ this.jobControllerList.add(tmpController);
+ if (tmpIsLoaded) {
+ tmpController.setHistogramDataManager(tmpHistogramDataManager);
+ // Set this first to avoid NullPointerExcpetions
+ tmpController.setCurrentlyChosenComparisonFeature(tmpHistogramDataManager.getComparisonFeatureSet().iterator().next());
+ tmpController.getOutputTab().setBinLabelChoiceBoxItems(Set.of(BinLabelType.values()));
+ tmpController.getOutputTab().setChartChoiceBoxItems(tmpController.getHistogramDataManager().getComparisonFeatureSet());
+ tmpController.getOutputTab().getBinLabelChoiceBox().setValue(BinLabelType.MAX);
+ tmpController.getOutputTab().getChartChoiceBox().setValue(tmpController.getHistogramDataManager().getComparisonFeatureSet().iterator().next());
+ tmpController.getOutputTab().getInfoLabel().setText(String.format(
+ GeneralUtilities.getUIText("OutputTab.infoLabel.text"),
+ tmpController.getJobNumber(),
+ tmpController.getHistogramDataManager().getNumberOfComparedPairs(),
+ tmpHistogramDataManager.getInputFile1(), tmpHistogramDataManager.getInputFile2()
+ ));
+ this.view.getTabPane().getTabs().add(tmpController.getOutputTab());
+ this.view.getCenterPane().setStyle("-fx-background-color: rgb(200, 200, 200);");
+ this.view.getTabPane().getSelectionModel().select(tmpController.getOutputTab());
+ } else {
+ this.view.getTabPane().getTabs().add(tmpController.getInputTab());
+ this.view.getCenterPane().setStyle("-fx-background-color: rgb(200, 200, 200);");
+ this.view.getTabPane().getSelectionModel().select(tmpController.getInputTab());
+ }
+ } catch (IllegalArgumentException ex) {
+ this.numberOfCreatedJobControllers--;
+ GeneralUtilities.showErrorDialog(this.view.getPrimaryStage(), ex.toString(), "ApplicationController.createNewJobController()");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/control/BinLabelType.java b/src/main/java/de/whs/ibci/msc/control/BinLabelType.java
new file mode 100644
index 0000000..42c9b1b
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/control/BinLabelType.java
@@ -0,0 +1,61 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.control;
+
+/**
+ * Defines different types of bin labels
+ *
+ * @author Jan-Mathis Hein
+ */
+public enum BinLabelType {
+
+ //
+ MIN ("Lower bin border"), MAX ("Upper bin border"), MEAN ("Mean of both borders"), INTERVAL ("Interval");
+ //
+ //
+ //
+ /**
+ * A more precise description for the BinLabelType
+ */
+ private final String description;
+ //
+ //
+ //
+ /**
+ * Initialize the instance variables
+ *
+ * @param tmpDescription a more precise description for the BinLabelType
+ */
+ private BinLabelType(String tmpDescription) {
+ this.description = tmpDescription;
+ }
+ //
+ //
+ //
+ /**
+ * Get a more precise description for the BinLabelType
+ *
+ * @return a more precise description for the BinLabelType
+ */
+ @Override
+ public String toString() {
+ return this.description;
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/control/JobController.java b/src/main/java/de/whs/ibci/msc/control/JobController.java
new file mode 100644
index 0000000..5c5f9e1
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/control/JobController.java
@@ -0,0 +1,1759 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.control;
+
+import de.whs.ibci.msc.model.ComparisonResult;
+import de.whs.ibci.msc.model.JobTaskManager;
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.model.MSCInputException;
+import de.whs.ibci.msc.view.ChartConfigurationDialog;
+import de.whs.ibci.msc.view.InputTab;
+import de.whs.ibci.msc.view.MainView;
+import de.whs.ibci.msc.view.OutputTab;
+import de.whs.ibci.msc.model.HistogramDataManager;
+import de.whs.ibci.msc.model.InputType;
+import de.whs.ibci.msc.model.ComparisonFeature;
+import de.whs.ibci.msc.model.HistogramData;
+import de.whs.ibci.msc.utility.ResultFormattingUtility;
+import de.whs.ibci.msc.view.BinBorderConfigurationBox;
+import de.whs.ibci.msc.view.BinBorderConfigurationDialog;
+import java.awt.Graphics2D;
+import java.awt.geom.AffineTransform;
+import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.nio.file.Files;
+import java.text.DecimalFormat;
+import java.util.Date;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.ListIterator;
+import java.util.Optional;
+import java.util.Set;
+import java.util.logging.Level;
+import javafx.application.Platform;
+import javafx.beans.value.ChangeListener;
+import javafx.beans.value.ObservableValue;
+import javafx.concurrent.Task;
+import javafx.embed.swing.SwingFXUtils;
+import javafx.event.ActionEvent;
+import javafx.event.Event;
+import javafx.event.EventHandler;
+import javafx.geometry.Insets;
+import javafx.geometry.Pos;
+import javafx.scene.Cursor;
+import javafx.scene.Scene;
+import javafx.scene.SnapshotParameters;
+import javafx.scene.chart.BarChart;
+import javafx.scene.chart.CategoryAxis;
+import javafx.scene.chart.NumberAxis;
+import javafx.scene.chart.XYChart;
+import javafx.scene.control.Button;
+import javafx.scene.control.ButtonBar;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.CheckBox;
+import javafx.scene.control.Label;
+import javafx.scene.control.TextFormatter;
+import javafx.scene.input.KeyCode;
+import javafx.scene.input.KeyCodeCombination;
+import javafx.scene.input.KeyCombination;
+import javafx.scene.input.KeyEvent;
+import javafx.scene.input.MouseEvent;
+import javafx.scene.layout.Region;
+import javafx.scene.layout.StackPane;
+import javafx.scene.layout.VBox;
+import javafx.scene.paint.Color;
+import javafx.scene.paint.Paint;
+import javafx.scene.transform.Transform;
+import javafx.stage.FileChooser;
+import javafx.stage.Stage;
+import javax.imageio.ImageIO;
+import org.apache.batik.dom.GenericDOMImplementation;
+import org.apache.batik.svggen.SVGGraphics2D;
+import org.apache.pdfbox.pdmodel.PDDocument;
+import org.apache.pdfbox.pdmodel.PDPage;
+import org.apache.pdfbox.pdmodel.PDPageContentStream;
+import org.apache.pdfbox.pdmodel.common.PDRectangle;
+import org.apache.pdfbox.pdmodel.graphics.image.LosslessFactory;
+import org.apache.pdfbox.pdmodel.graphics.image.PDImageXObject;
+import org.w3c.dom.DOMException;
+import org.w3c.dom.DOMImplementation;
+import org.w3c.dom.Document;
+
+/**
+ * Manages the ChartConfigurationDialog, the In and OutputTab as well as
+ * related events. Also directly communicates with the JobTaskManager and
+ * converts the resulting HistogramData objects in to charts.
+ *
+ * @author Jan-Mathis Hein
+ */
+public class JobController implements PropertyChangeListener{
+
+ //
+ /**
+ * Directory from where the last input file of any job was loaded
+ */
+ private static File lastInputFileDirectory;
+
+ /**
+ * Directory where the last chart file of any job was saved
+ */
+ private static File lastChartFileDirectory;
+
+ /**
+ * Directory where the last summary report of any job was saved
+ */
+ private static File lastSummaryReportDirectory;
+ //
+ //
+ //
+ /**
+ * A dialog that enables the user to specifically set the bin borders
+ */
+ private BinBorderConfigurationDialog binBorderConfigurationDialog;
+
+ /**
+ * False if there are changes that are not saved, true otherwise
+ */
+ private boolean outputIsSaved;
+
+ /**
+ * True if the input for the lower bin border given by the user in the
+ * ChartConfigurationDialog is valid, false: Otherwise
+ */
+ private boolean isValidLowerBinBorder;
+
+ /**
+ * True if the input for the upper bin border given by the user in the
+ * ChartConfigurationDialog is valid, false otherwise
+ */
+ private boolean isValidUpperBinBorder;
+
+ /**
+ * True if the input for the lower frequency bound given by the user in
+ * the ChartConfigurationDialog is valid, false: Otherwise
+ */
+ private boolean isValidLowerFrequencyBound;
+
+ /**
+ * True if the input for the upper frequency bound given by the user in
+ * the ChartConfigurationDialog is valid, false: Otherwise
+ */
+ private boolean isValidUpperFrequencyBound;
+
+ /**
+ * The BinLabelType that is currently chosen
+ */
+ private BinLabelType currentlyChosenBinLabelType = BinLabelType.MAX;
+
+ /**
+ * A dialog that enables the user to configure the chart
+ */
+ private ChartConfigurationDialog chartConfigurationDialog;
+
+ /**
+ * The ComparisonFeature that is currently chosen
+ */
+ private ComparisonFeature currentlyChosenComparisonFeature;
+
+ /**
+ * An EventHandler that handles the action of the user clicking any
+ * "Add"-button in the binBorderConfigurationDialog
+ */
+ private final EventHandler binBorderConfigurationDialogAddHandler;
+
+ /**
+ * An EventHandler that handles the action of the user clicking any
+ * "Remove"-button in the binBorderConfigurationDialog
+ */
+ private final EventHandler binBorderConfigurationDialogRemoveHandler;
+
+ /**
+ * A FileChooser that is used to choose files for loading and saving
+ */
+ private final FileChooser fileChooser = new FileChooser();
+
+ /**
+ * The InputTab that allows the user to enter his input
+ */
+ private InputTab inputTab;
+
+ /**
+ * The JobTaskManager that manages the task that is specified by the
+ * InputTab
+ */
+ private final JobTaskManager jobTaskManager;
+
+ /**
+ * Manages the data of the histograms for all ComparisonFeatures
+ */
+ private HistogramDataManager histogramDataManager;
+
+ /**
+ * List of BinBorderConfigurationBoxes for the BinBorderConfigurationDialog.
+ * Each box is for the configuration of one bin border
+ */
+ private final LinkedList binBorderConfigurationBoxList = new LinkedList<>();
+
+ /**
+ * The time difference, in milliseconds, between the time of the start of
+ * the job and midnight, January 1, 1970 UTC
+ */
+ private long calculationStartTime;
+
+ /**
+ * The OutputTab that displays the results of the task execution
+ */
+ private OutputTab outputTab;
+
+ /**
+ * PropertyChangeSupport that manages the firing of PropertyChangeEvents and
+ * the adding and removing of PropertyChangeListeners
+ */
+ private final PropertyChangeSupport propertyChangeSupport;
+
+ /**
+ * The chart that is currently shown. If the chart creation failed, this
+ * will be an error label
+ */
+ private Region currentlyShownChart;
+
+ /**
+ * The scene on which the In and OutputTab will be displayed
+ */
+ private final Scene scene;
+
+ /**
+ * A number that identifies this job in the current application session. It
+ * indicates the order in which different jobs have been opened or created
+ */
+ private String jobNumber;
+
+ /**
+ * The stage onto which the In and OutputTab will be projected
+ */
+ private final Stage applicationStage;
+ //
+ //
+ //
+ /**
+ * Initialize the instance variables, set TextFormatters for the
+ * ChartConfigurationDialog, add event handlers for the In and OutputTab and
+ * the ChartConfigurationDialog and set up the tab that will be shown
+ *
+ * @param tmpView main view of the application
+ * @param tmpIsLoaded true if the job is loaded, false otherwise
+ * @param tmpJobNumber identifies this job in this application session
+ */
+ public JobController (
+ MainView tmpView, boolean tmpIsLoaded, String tmpJobNumber
+ ) throws IllegalArgumentException {
+ //
+ if (tmpView == null) {
+ throw new IllegalArgumentException("tmpView is null");
+ }
+ if (tmpJobNumber == null || tmpJobNumber.matches("\\W*\\w*\\D+\\W*\\w*")) {
+ throw new IllegalArgumentException("tmpJobNumber is invalid");
+ }
+ //
+ //
+ this.applicationStage = tmpView.getPrimaryStage();
+ this.scene = tmpView.getScene();
+ this.jobNumber = tmpJobNumber;
+ if (!tmpIsLoaded) {
+ this.inputTab = new InputTab(this.jobNumber);
+ this.jobTaskManager = new JobTaskManager(
+ UserPreferences.getInstance().getNumberOfParallelThreads(),
+ UserPreferences.getInstance().getDefaultNumberOfBins()
+ );
+ this.jobTaskManager.addPropertyChangeListener(this);
+ } else {
+ this.jobTaskManager = null;
+ }
+ this.outputIsSaved = tmpIsLoaded;
+ this.outputTab = new OutputTab(this.jobNumber);
+ this.chartConfigurationDialog = new ChartConfigurationDialog(this.applicationStage, String.format(GeneralUtilities.getUIText("ChartConfigurationDialog.Title.text"), this.jobNumber));
+ this.propertyChangeSupport = new PropertyChangeSupport(this);
+ this.binBorderConfigurationDialog = new BinBorderConfigurationDialog(this.applicationStage, GeneralUtilities.getUIText("BinBorderConfigurationDialog.Title.text"));
+ this.binBorderConfigurationDialogRemoveHandler = (ActionEvent tmpEvent) -> {
+ Button tmpButton = (Button) tmpEvent.getSource();
+ int tmpIndex = JobController.this.binBorderConfigurationBoxList.indexOf(tmpButton.getParent());
+ JobController.this.binBorderConfigurationBoxList.remove(tmpIndex);
+ ListIterator tmpIterator = JobController.this.binBorderConfigurationBoxList.listIterator(tmpIndex);
+ while (tmpIterator.hasNext()) {
+ int tmpNextIndex = tmpIterator.nextIndex();
+ tmpIterator.next().getLabel().setText(Integer.toString(tmpNextIndex + 1));
+ }
+ if (JobController.this.binBorderConfigurationBoxList.size() <= 2) {
+ JobController.this.binBorderConfigurationBoxList.forEach((tmpBox1) -> {
+ // Removing is disabled if there are only two bin borders
+ tmpBox1.getRemoveButton().setDisable(true);
+ });
+ } else {
+ JobController.this.binBorderConfigurationBoxList.forEach((tmpBox1) -> {
+ // Removing is enabled if there are more than two bin borders
+ tmpBox1.getRemoveButton().setDisable(false);
+ });
+ }
+ JobController.this.binBorderConfigurationDialog.getBinBorderConfigurationBoxesBox().getChildren().setAll(JobController.this.binBorderConfigurationBoxList);
+ // Remove the insets because they were only a bug fix that is no longer necessary, because the ScrollPane has been resized
+ JobController.this.binBorderConfigurationDialog.getBinBorderConfigurationBoxesBox().setPadding(Insets.EMPTY);
+ };
+ this.binBorderConfigurationDialogAddHandler = new EventHandler() {
+
+ @Override
+ public void handle(ActionEvent tmpEvent) {
+ Button tmpButton = (Button) tmpEvent.getSource();
+ int tmpIndex = JobController.this.binBorderConfigurationBoxList.indexOf(tmpButton.getParent());
+ BinBorderConfigurationBox tmpBox = new BinBorderConfigurationBox("", Integer.toString(tmpIndex + 2));
+ tmpBox.getAddButton().setOnAction(this);
+ tmpBox.getRemoveButton().setOnAction(JobController.this.binBorderConfigurationDialogRemoveHandler);
+ tmpBox.getTextField().setTextFormatter(GeneralUtilities.getSignedDecimalNumberTextFormatter());
+ JobController.this.binBorderConfigurationBoxList.add(tmpIndex + 1, tmpBox);
+ ListIterator tmpIterator = JobController.this.binBorderConfigurationBoxList.listIterator(tmpIndex + 2);
+ while (tmpIterator.hasNext()) {
+ int tmpNextIndex = tmpIterator.nextIndex();
+ tmpIterator.next().getLabel().setText(Integer.toString(tmpNextIndex + 1));
+ }
+ if (JobController.this.binBorderConfigurationBoxList.size() <= 2) {
+ JobController.this.binBorderConfigurationBoxList.forEach((tmpBox1) -> {
+ // Removing is disabled if there are only two bin borders
+ tmpBox1.getRemoveButton().setDisable(true);
+ });
+ } else {
+ JobController.this.binBorderConfigurationBoxList.forEach((tmpBox1) -> {
+ // Removing is enabled if there are more than two bin borders
+ tmpBox1.getRemoveButton().setDisable(false);
+ });
+ }
+ JobController.this.binBorderConfigurationDialog.getBinBorderConfigurationBoxesBox().getChildren().setAll(JobController.this.binBorderConfigurationBoxList);
+ // Remove the insets because they were only a bug fix that is no longer necessary, because the ScrollPane has been resized
+ JobController.this.binBorderConfigurationDialog.getBinBorderConfigurationBoxesBox().setPadding(Insets.EMPTY);
+ }
+
+ };
+ //
+ //
+ this.outputTab.getNumberOfBinsTextField().setTextFormatter(GeneralUtilities.getUnsignedIntegerTextFormatter());
+ this.chartConfigurationDialog.getLowerBinBorderInputField().setTextFormatter(new TextFormatter<>((TextFormatter.Change tmpChange) -> {
+ if (!tmpChange.getControlNewText().matches("[-\\+]?\\d*\\.?\\d*E?\\d*")) {
+ tmpChange.setText("");
+ }
+ try {
+ Double.parseDouble(tmpChange.getControlNewText());
+ tmpChange.getControl().setStyle("-fx-background-color: white;");
+ this.isValidLowerBinBorder = true;
+ } catch (NumberFormatException ex) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ this.isValidLowerBinBorder = false;
+ }
+ return tmpChange;
+ }));
+ this.chartConfigurationDialog.getUpperBinBorderInputField().setTextFormatter(new TextFormatter<>((TextFormatter.Change tmpChange) -> {
+ if (!tmpChange.getControlNewText().matches("[-\\+]?\\d*\\.?\\d*E?\\d*")) {
+ tmpChange.setText("");
+ }
+ try {
+ Double.parseDouble(tmpChange.getControlNewText());
+ tmpChange.getControl().setStyle("-fx-background-color: white;");
+ this.isValidUpperBinBorder = true;
+ } catch (NumberFormatException ex) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ this.isValidUpperBinBorder = false;
+ }
+ return tmpChange;
+ }));
+ this.chartConfigurationDialog.getLowerFrequencyBoundInputField().setTextFormatter(new TextFormatter<>((TextFormatter.Change tmpChange) -> {
+ if (!tmpChange.getControlNewText().matches("\\d*\\.?\\d*E?\\d*")) {
+ tmpChange.setText("");
+ }
+ try {
+ Double.parseDouble(tmpChange.getControlNewText());
+ tmpChange.getControl().setStyle("-fx-background-color: white;");
+ this.isValidLowerFrequencyBound = true;
+ } catch (NumberFormatException ex) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ this.isValidLowerFrequencyBound = false;
+ }
+ return tmpChange;
+ }));
+ this.chartConfigurationDialog.getUpperFrequencyBoundInputField().setTextFormatter(new TextFormatter<>((TextFormatter.Change tmpChange) -> {
+ if (!tmpChange.getControlNewText().matches("\\d*\\.?\\d*E?\\d*")) {
+ tmpChange.setText("");
+ }
+ try {
+ Double.parseDouble(tmpChange.getControlNewText());
+ tmpChange.getControl().setStyle("-fx-background-color: white;");
+ this.isValidUpperFrequencyBound = true;
+ } catch (NumberFormatException ex) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ this.isValidUpperFrequencyBound = false;
+ }
+ return tmpChange;
+ }));
+ //
+ //
+ //
+ if (!tmpIsLoaded) {
+ //
+ this.inputTab.setOnCloseRequest((Event e) -> {
+ this.propertyChangeSupport.firePropertyChange("Want to close InputTab", null, e);
+ });
+ this.inputTab.setOnSelectionChanged((Event e) -> {
+ this.propertyChangeSupport.firePropertyChange("JobController selected", false, this.inputTab.isSelected());
+ });
+ //
+ //
+ this.inputTab.getChooseFile1Button().setOnAction((ActionEvent e) -> {
+ try {
+ this.fileChooser.getExtensionFilters().clear();
+ this.fileChooser.getExtensionFilters().addAll(
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.All.text"), "*.*"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.Text.text"), "*.txt")
+ );
+ if (!UserPreferences.getInstance().getInputDir().isEmpty() && new File(UserPreferences.getInstance().getInputDir()).isDirectory()) {
+ this.fileChooser.setInitialDirectory(new File(UserPreferences.getInstance().getInputDir()));
+ } else {
+ this.fileChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ synchronized (JobController.class) {
+ if (JobController.lastInputFileDirectory != null && JobController.lastInputFileDirectory.isDirectory()) {
+ this.fileChooser.setInitialDirectory(JobController.lastInputFileDirectory);
+ }
+ }
+ this.fileChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.MoleculeFile.text"));
+ File tmpFile = this.fileChooser.showOpenDialog(this.applicationStage);
+ if (tmpFile != null && tmpFile.canRead()) {
+ this.inputTab.getInputFile1Label().setText(GeneralUtilities.getUIText("InputTab.inputFile1Label.text") + " " + tmpFile.getName());
+ this.jobTaskManager.setInputFile1(tmpFile);
+ this.inputTab.getJobInfoLabel().setText(GeneralUtilities.getUIText("InfoDescription.InputFile1.text"));
+ synchronized (JobController.class) {
+ JobController.lastInputFileDirectory = tmpFile.getParentFile();
+ }
+ }
+ for (CheckBox tmpCheckBox : this.inputTab.getComparisonFeatureCheckBoxes()) {
+ if (tmpCheckBox.isSelected() && this.jobTaskManager.canReadInput()) {
+ this.inputTab.getJobStartButton().setDisable(false);
+ return;
+ }
+ }
+ this.inputTab.getJobStartButton().setDisable(true);
+ } catch (IllegalArgumentException ex) {
+ GeneralUtilities.showErrorDialog(this.applicationStage, ex.toString(), "JobController.inputTab.getChooseFile1Button().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ this.inputTab.getChooseFile2Button().setOnAction((ActionEvent e) -> {
+ try {
+ this.fileChooser.getExtensionFilters().clear();
+ this.fileChooser.getExtensionFilters().addAll(
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.All.text"), "*.*"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.Text.text"), "*.txt")
+ );
+ if (!UserPreferences.getInstance().getInputDir().isEmpty() && new File(UserPreferences.getInstance().getInputDir()).isDirectory()) {
+ this.fileChooser.setInitialDirectory(new File(UserPreferences.getInstance().getInputDir()));
+ } else {
+ this.fileChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ synchronized (JobController.class) {
+ if (JobController.lastInputFileDirectory != null && JobController.lastInputFileDirectory.isDirectory()) {
+ this.fileChooser.setInitialDirectory(JobController.lastInputFileDirectory);
+ }
+ }
+ this.fileChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.MoleculeFile.text"));
+ File tmpFile = this.fileChooser.showOpenDialog(this.applicationStage);
+ if (tmpFile != null && tmpFile.canRead()) {
+ this.inputTab.getInputFile2Label().setText(GeneralUtilities.getUIText("InputTab.inputFile2Label.text") + " " + tmpFile.getName());
+ this.jobTaskManager.setInputFile2(tmpFile);
+ this.inputTab.getJobInfoLabel().setText(GeneralUtilities.getUIText("InfoDescription.InputFile2.text"));
+ synchronized (JobController.class) {
+ JobController.lastInputFileDirectory = tmpFile.getParentFile();
+ }
+ }
+ for (CheckBox tmpCheckBox : this.inputTab.getComparisonFeatureCheckBoxes()) {
+ if (tmpCheckBox.isSelected() && this.jobTaskManager.canReadInput()) {
+ this.inputTab.getJobStartButton().setDisable(false);
+ return;
+ }
+ }
+ this.inputTab.getJobStartButton().setDisable(true);
+ } catch (IllegalArgumentException ex) {
+ GeneralUtilities.showErrorDialog(this.applicationStage, ex.toString(), "JobController.inputTab.getChooseFile2Button().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ this.inputTab.getInputType1ChoiceBox().setOnAction((ActionEvent e) -> {
+ InputType tmpType = this.inputTab.getInputType1ChoiceBox().getValue();
+ if (tmpType != null) {
+ this.jobTaskManager.setInputType1(tmpType);
+ }
+ this.inputTab.getJobStartButton().setDisable(!this.jobTaskManager.canReadInput());
+ });
+ this.inputTab.getInputType2ChoiceBox().setOnAction((ActionEvent e) -> {
+ InputType tmpType = this.inputTab.getInputType2ChoiceBox().getValue();
+ if (tmpType != null) {
+ this.jobTaskManager.setInputType2(tmpType);
+ }
+ this.inputTab.getJobStartButton().setDisable(!this.jobTaskManager.canReadInput());
+ });
+ //
+ //
+ this.inputTab.getSelectAllComparisonFeaturesButton().setOnAction((ActionEvent e) -> {
+ for (CheckBox tmpCheckBox : this.inputTab.getComparisonFeatureCheckBoxes()) {
+ tmpCheckBox.setSelected(true);
+ }
+ for (CheckBox tmpCheckBox : this.inputTab.getSelectAllCheckBoxes()) {
+ tmpCheckBox.setSelected(true);
+ }
+ });
+ this.inputTab.getReverseComparisonFeatureSelectionButton().setOnAction((ActionEvent e) -> {
+ for (CheckBox tmpCheckBox : this.inputTab.getComparisonFeatureCheckBoxes()) {
+ tmpCheckBox.setSelected(!tmpCheckBox.isSelected());
+ }
+ });
+ for (CheckBox tmpCheckBox1 : this.inputTab.getComparisonFeatureCheckBoxes()) {
+ tmpCheckBox1.selectedProperty().addListener((ObservableValue tmpObservableValue, Boolean tmpOldValue, Boolean tmpNewValue) -> {
+ int tmpInt = 0;
+ for (CheckBox tmpCheckBox2 : this.inputTab.getComparisonFeatureCheckBoxes()) {
+ if (tmpCheckBox2.isSelected()) {
+ tmpInt++;
+ }
+ }
+ if (tmpInt == 0) {
+ this.inputTab.getJobInfoLabel().setText(GeneralUtilities.getUIText("InfoDescription.noFeaturesSelected.text"));
+ this.inputTab.getJobStartButton().setDisable(true);
+ } else {
+ this.inputTab.getJobInfoLabel().setText(String.format(GeneralUtilities.getUIText("InfoDescription.xFeaturesSelected.text"), tmpInt));
+ if (this.jobTaskManager.canReadInput()) {
+ this.inputTab.getJobStartButton().setDisable(false);
+ } else {
+ this.inputTab.getJobStartButton().setDisable(true);
+ }
+ }
+
+ });
+ }
+ ListIterator tmpCheckBoxIterator = this.inputTab.getSelectAllCheckBoxes().listIterator();
+ Iterator tmpVBoxIterator = this.inputTab.getCheckBoxesBoxes().iterator();
+ while (tmpCheckBoxIterator.hasNext() && tmpVBoxIterator.hasNext()) {
+ tmpCheckBoxIterator.next().setOnAction(new EventHandler() {
+
+ private final VBox box = tmpVBoxIterator.next();
+
+ private final CheckBox checkBox = tmpCheckBoxIterator.previous();
+
+ {
+ tmpCheckBoxIterator.next();
+ }
+
+ @Override
+ public void handle(ActionEvent e) {
+ boolean tmpIsChecked = this.checkBox.isSelected();
+ this.box.getChildren().stream().map((tmpNode) -> (CheckBox) tmpNode).forEach((tmpCheckBox) -> {
+ tmpCheckBox.setSelected(tmpIsChecked);
+ });
+ }
+ });
+ }
+ //
+ //
+ this.inputTab.getJobStartButton().setOnAction((ActionEvent e) -> {
+ //
+ if (this.jobTaskManager.isWorking()) {
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.JobStillWorking.text"));
+ this.inputTab.getJobStartButton().setDisable(true);
+ return;
+ }
+ if (!this.jobTaskManager.canReadInput()) {
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.InputConfigurationNotReadable.text"));
+ this.inputTab.getJobStartButton().setDisable(true);
+ return;
+ }
+ //
+ boolean[] tmpChoosenComparisonFeatures = new boolean[this.inputTab.getComparisonFeatureCheckBoxes().length];
+ for (int i = 0; i < tmpChoosenComparisonFeatures.length; i++) {
+ tmpChoosenComparisonFeatures[i] = this.inputTab.getComparisonFeatureCheckBoxes()[i].isSelected();
+ }
+ try {
+ // Checks if at least one ComparisonFeature is chosen
+ this.jobTaskManager.setComparisonFeatures(tmpChoosenComparisonFeatures);
+ } catch (MSCInputException | IllegalArgumentException ex) {
+ GeneralUtilities.showInfoDialog(this.applicationStage, ex.toString());
+ return;
+ }
+ this.inputTab.getJobStartButton().setVisible(false);
+ this.inputTab.getJobCancelButton().setVisible(true);
+ this.inputTab.getChooseFile1Button().setDisable(true);
+ this.inputTab.getChooseFile2Button().setDisable(true);
+ this.inputTab.getInputType1ChoiceBox().setDisable(true);
+ this.inputTab.getInputType2ChoiceBox().setDisable(true);
+ this.inputTab.getInputFile1Label().setDisable(true);
+ this.inputTab.getInputFile2Label().setDisable(true);
+ this.inputTab.getJobCancelButton().setDisable(false);
+ this.inputTab.getReverseComparisonFeatureSelectionButton().setDisable(true);
+ for (CheckBox tmpCheckBox : this.inputTab.getSelectAllCheckBoxes()) {
+ tmpCheckBox.setDisable(true);
+ }
+ this.inputTab.getSelectAllComparisonFeaturesButton().setDisable(true);
+ for (CheckBox tmpCheckBox : this.inputTab.getComparisonFeatureCheckBoxes()) {
+ tmpCheckBox.setDisable(true);
+ }
+ this.inputTab.getJobProgressBar().setVisible(true);
+ this.inputTab.getJobProgressBar().setProgress(0);
+ this.inputTab.getJobInfoLabel().setText(GeneralUtilities.getUIText("InfoDescription.JobStarted.text"));
+ try {
+ Task tmpTask = new Task() {
+ @Override
+ protected Void call() throws Exception {
+ JobController.this.jobTaskManager.startTasks();
+ return null;
+ }
+ };
+ Thread tmpBackgroundThread = new Thread(tmpTask);
+ this.calculationStartTime = System.currentTimeMillis();
+ tmpBackgroundThread.start();
+ } catch (Exception ex) {
+ GeneralUtilities.logException(Level.SEVERE, ex);
+ GeneralUtilities.showErrorDialog(this.applicationStage, ex.toString(), "JobController.inputTab.getJobStartButton().setOnAction($lambda)");
+ this.jobTaskManager.cancelWorkingProcess();
+ this.inputTab.getJobStartButton().setVisible(true);
+ this.inputTab.getJobCancelButton().setVisible(false);
+ this.inputTab.getChooseFile1Button().setDisable(false);
+ this.inputTab.getChooseFile2Button().setDisable(false);
+ this.inputTab.getInputType1ChoiceBox().setDisable(false);
+ this.inputTab.getInputType2ChoiceBox().setDisable(false);
+ this.inputTab.getInputFile1Label().setDisable(false);
+ this.inputTab.getInputFile2Label().setDisable(false);
+ this.inputTab.getReverseComparisonFeatureSelectionButton().setDisable(false);
+ for (CheckBox tmpCheckBox : this.inputTab.getSelectAllCheckBoxes()) {
+ tmpCheckBox.setDisable(false);
+ }
+ this.inputTab.getSelectAllComparisonFeaturesButton().setDisable(false);
+ for (CheckBox tmpCheckBox : this.inputTab.getComparisonFeatureCheckBoxes()) {
+ tmpCheckBox.setDisable(false);
+ }
+ this.inputTab.getJobProgressBar().setVisible(false);
+ this.inputTab.getJobProgressBar().setProgress(0);
+ this.inputTab.getJobInfoLabel().setText(GeneralUtilities.getUIText("InfoDescription.StartingJobFailed.text"));
+ }
+ });
+ this.inputTab.getJobCancelButton().setOnAction((ActionEvent e) -> {
+ this.jobTaskManager.cancelWorkingProcess();
+ this.inputTab.getJobStartButton().setVisible(true);
+ this.inputTab.getJobCancelButton().setVisible(false);
+ this.inputTab.getChooseFile1Button().setDisable(false);
+ this.inputTab.getChooseFile2Button().setDisable(false);
+ this.inputTab.getInputType1ChoiceBox().setDisable(false);
+ this.inputTab.getInputType2ChoiceBox().setDisable(false);
+ this.inputTab.getInputFile1Label().setDisable(false);
+ this.inputTab.getInputFile2Label().setDisable(false);
+ this.inputTab.getReverseComparisonFeatureSelectionButton().setDisable(false);
+ for (CheckBox tmpCheckBox : this.inputTab.getSelectAllCheckBoxes()) {
+ tmpCheckBox.setDisable(false);
+ }
+ this.inputTab.getSelectAllComparisonFeaturesButton().setDisable(false);
+ for (CheckBox tmpCheckBox : this.inputTab.getComparisonFeatureCheckBoxes()) {
+ tmpCheckBox.setDisable(false);
+ }
+ this.inputTab.getJobProgressBar().setVisible(false);
+ this.inputTab.getJobProgressBar().setProgress(0);
+ synchronized (this) {
+ // Guarantees that the label is set correctly
+ Platform.runLater(() -> {
+ this.inputTab.getJobInfoLabel().setText(GeneralUtilities.getUIText("InfoDescription.JobCanceled.text"));
+ });
+ }
+ });
+ //
+ }
+ //
+ //
+ //
+ this.outputTab.setOnCloseRequest((Event e) -> {
+ this.propertyChangeSupport.firePropertyChange("Want to close OutputTab", null, e);
+ });
+ this.outputTab.setOnSelectionChanged((Event e) -> {
+ this.propertyChangeSupport.firePropertyChange("JobController selected", false, this.outputTab.isSelected());
+ });
+ //
+ //
+ this.outputTab.getSummaryReportButton().setOnAction((ActionEvent e) -> {
+ try {
+ this.fileChooser.getExtensionFilters().clear();
+ this.fileChooser.getExtensionFilters().addAll(
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.All.text"), "*.*"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.Text.text"), "*.txt")
+ );
+ if (!UserPreferences.getInstance().getSummaryReportDir().isEmpty() && new File(UserPreferences.getInstance().getSummaryReportDir()).isDirectory()) {
+ this.fileChooser.setInitialDirectory(new File(UserPreferences.getInstance().getSummaryReportDir()));
+ } else {
+ this.fileChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ synchronized (JobController.class) {
+ if (JobController.lastSummaryReportDirectory != null && JobController.lastSummaryReportDirectory.isDirectory()) {
+ this.fileChooser.setInitialDirectory(JobController.lastSummaryReportDirectory);
+ }
+ }
+ this.fileChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.SaveSummaryReport.text"));
+ final File tmpFile = this.fileChooser.showSaveDialog(this.applicationStage);
+ if (tmpFile == null) {
+ return;
+ }
+ boolean tmpIsNewFile = tmpFile.createNewFile();
+ if (!tmpFile.canWrite()) {
+ if (tmpIsNewFile) {
+ Files.delete(tmpFile.toPath());
+ }
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.FileNotWritable.text"));
+ return;
+ }
+ synchronized (JobController.class) {
+ JobController.lastSummaryReportDirectory = tmpFile.getParentFile();
+ }
+ String tmpFormat = tmpFile.getAbsolutePath().substring(tmpFile.getAbsolutePath().lastIndexOf(".")).toLowerCase();
+ switch (tmpFormat) {
+ case ".txt":
+ try (BufferedWriter tmpBufferedWriter = new BufferedWriter(new FileWriter(tmpFile))) {
+ for (String tmpString : ResultFormattingUtility.getResultSummaryReportHeader()) {
+ tmpBufferedWriter.write(tmpString);
+ tmpBufferedWriter.newLine();
+ }
+ for (String tmpString : ResultFormattingUtility.getGeneralInfoBlock(
+ new Date(this.histogramDataManager.getCalculationFinishTime()),
+ (this.histogramDataManager.getCalculationFinishTime() - this.histogramDataManager.getCalculationStartTime()) / 1000,
+ this.histogramDataManager.getNumberOfComparedPairs(), this.histogramDataManager.getInputFile1(), this.histogramDataManager.getInputFile2()
+ )) {
+ tmpBufferedWriter.write(tmpString);
+ tmpBufferedWriter.newLine();
+ }
+ for (ComparisonFeature tmpComparisonFeature : this.histogramDataManager.getComparisonFeatureSet()) {
+ for (String tmpString : ResultFormattingUtility.getVerticalHistogramBlock(this.histogramDataManager.getHistogramData(tmpComparisonFeature))) {
+ tmpBufferedWriter.write(tmpString);
+ tmpBufferedWriter.newLine();
+ }
+ }
+ }
+ break;
+ default:
+ GeneralUtilities.showInfoDialog(JobController.this.applicationStage, GeneralUtilities.getUIText("InfoDescription.FileFormatNotSupported.text"));
+ break;
+ }
+ } catch (IOException ex) {
+ GeneralUtilities.showErrorDialog(this.applicationStage, ex.toString(), "JobController.outputTab.getSummaryReportButton().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ //
+ //
+ this.outputTab.getImageButton().setOnAction((ActionEvent e) -> {
+ try {
+ this.fileChooser.getExtensionFilters().clear();
+ this.fileChooser.getExtensionFilters().addAll(
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.All.text"), "*.*"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.pdf.text"), "*.pdf"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.png.text"), "*.png"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.jpeg.text"), "*.jpeg"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.svg.text"), "*.svg")
+ );
+ if (!UserPreferences.getInstance().getImageDir().isEmpty() && new File(UserPreferences.getInstance().getImageDir()).isDirectory()) {
+ this.fileChooser.setInitialDirectory(new File(UserPreferences.getInstance().getImageDir()));
+ } else {
+ this.fileChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ synchronized (JobController.class) {
+ if (JobController.lastChartFileDirectory != null && JobController.lastChartFileDirectory.isDirectory()) {
+ this.fileChooser.setInitialDirectory(JobController.lastChartFileDirectory);
+ }
+ }
+ this.fileChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.SaveChart.text"));
+ final File tmpFile = this.fileChooser.showSaveDialog(this.applicationStage);
+ if (tmpFile == null) {
+ return;
+ }
+ boolean tmpIsNewFile = tmpFile.createNewFile();
+ if (!tmpFile.canWrite()) {
+ if (tmpIsNewFile) {
+ Files.delete(tmpFile.toPath());
+ }
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.FileNotWritable.text"));
+ return;
+ }
+ synchronized (JobController.class) {
+ JobController.lastChartFileDirectory = tmpFile.getParentFile();
+ }
+ SnapshotParameters tmpSnapshotParameters = new SnapshotParameters();
+ // IMPORTANT: Setting tmpScalingFactor too low will cause the program to throw an exception
+ final float tmpScalingFactor = (float) ((-0.91) * UserPreferences.getInstance().getImageQuality() + 1);
+ tmpSnapshotParameters.setTransform(Transform.scale(1 / tmpScalingFactor, 1 / tmpScalingFactor));
+ final BufferedImage tmpBufferedImage = SwingFXUtils.fromFXImage(this.currentlyShownChart.snapshot(tmpSnapshotParameters, null), null);
+ final String tmpFormat = tmpFile.getAbsolutePath().substring(tmpFile.getAbsolutePath().lastIndexOf(".")).toLowerCase();
+ Task tmpTask = new Task() {
+ @Override
+ protected Void call() throws Exception {
+ try {
+ switch (tmpFormat) {
+ case ".png":
+ ImageIO.write(tmpBufferedImage, "PNG", tmpFile);
+ break;
+ case ".jpg":
+ case ".jpeg":
+ BufferedImage tmpImage = new BufferedImage(tmpBufferedImage.getWidth(), tmpBufferedImage.getHeight(), BufferedImage.TYPE_INT_RGB);
+ // Change the color model of the BufferedImage for the jpeg format
+ Graphics2D tmpGraphics2D = tmpImage.createGraphics();
+ tmpGraphics2D.drawImage(tmpBufferedImage, 0, 0, null);
+ tmpGraphics2D.dispose();
+ ImageIO.write(tmpImage, "JPG", tmpFile);
+ break;
+ case ".svg":
+ DOMImplementation domImpl = GenericDOMImplementation.getDOMImplementation();
+ Document document = domImpl.createDocument("http://www.w3.org/2000/svg", "svg", null);
+ SVGGraphics2D tmpSvgGenerator = new SVGGraphics2D(document);
+ tmpSvgGenerator.drawImage(tmpBufferedImage, AffineTransform.getScaleInstance(tmpScalingFactor, tmpScalingFactor), null);
+ try (BufferedWriter tmpWriter = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(tmpFile)))) {
+ tmpSvgGenerator.stream(tmpWriter);
+ }
+ break;
+ case ".pdf":
+ try (PDDocument tmpDocument = new PDDocument()) {
+ PDPage tmpPage = new PDPage();
+ tmpDocument.addPage(tmpPage);
+ PDImageXObject tmpPDImage = LosslessFactory.createFromImage(tmpDocument, tmpBufferedImage);
+ try (PDPageContentStream tmpStream = new PDPageContentStream(tmpDocument, tmpPage)) {
+ float tmpWidth = tmpBufferedImage.getWidth() * tmpScalingFactor;
+ float tmpHeight = tmpBufferedImage.getHeight() * tmpScalingFactor;
+ tmpPage.setMediaBox(new PDRectangle(tmpWidth, tmpHeight));
+ tmpStream.drawImage(tmpPDImage, 0, 0, tmpWidth, tmpHeight);
+ }
+ tmpDocument.save(tmpFile);
+ }
+ break;
+ default:
+ Platform.runLater(() -> {
+ GeneralUtilities.showInfoDialog(JobController.this.applicationStage, GeneralUtilities.getUIText("InfoDescription.FileFormatNotSupported.text"));
+ });
+ }
+ } catch (IOException | DOMException ex) {
+ Platform.runLater(() -> {
+ JobController.this.scene.setCursor(Cursor.DEFAULT);
+ GeneralUtilities.showErrorDialog(JobController.this.applicationStage, ex.toString(), "JobController.outputTab.getSaveButton().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ });
+ } finally {
+ Platform.runLater(() -> {
+ JobController.this.scene.setCursor(Cursor.DEFAULT);
+ });
+ }
+ return null;
+ }
+ };
+ Thread tmpBackgroundThread = new Thread(tmpTask);
+ this.scene.setCursor(Cursor.WAIT);
+ tmpBackgroundThread.start();
+ } catch (StringIndexOutOfBoundsException ex) {
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.FileFormatNotSupported.text"));
+ } catch (Exception ex) {
+ GeneralUtilities.showErrorDialog(this.applicationStage, ex.toString(), "JobController.outputTab.getSaveButton().setOnAction($lambda)");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ });
+ //
+ //
+ this.outputTab.getRelativeFrequenciesCheckBox().setOnAction((ActionEvent e) -> {
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ tmpHistogramData.setUseRelativeFrequencies(this.outputTab.getRelativeFrequenciesCheckBox().isSelected());
+ this.outputTab.getFrequency1Slider().setMin(0.0);
+ this.outputTab.getFrequency1Slider().setMax(tmpHistogramData.getMaxFrequency());
+ this.outputTab.getFrequency2Slider().setMin(0.0);
+ this.outputTab.getFrequency2Slider().setMax(tmpHistogramData.getMaxFrequency());
+ double tmpTickUnit;
+ tmpTickUnit = (tmpHistogramData.getMaxFrequency() - 0.0) / 10;
+ if (tmpTickUnit > 0) {
+ this.outputTab.getFrequency1Slider().setMajorTickUnit(tmpTickUnit);
+ this.outputTab.getFrequency2Slider().setMajorTickUnit(tmpTickUnit);
+ }
+ this.updateOutputTab();
+ });
+ //
+ //
+ this.outputTab.getChartChoiceBox().setOnAction((ActionEvent e) -> {
+ ComparisonFeature tmpComparisonFeature = this.outputTab.getChartChoiceBox().getValue();
+ //
+ if (!this.histogramDataManager.getComparisonFeatureSet().contains(tmpComparisonFeature)) {
+ GeneralUtilities.showErrorDialog(this.applicationStage, GeneralUtilities.getUIText("ErrorDescription.InvalidComparisonFeatureSelection.text"), "JobController.outputTab.getChartChoiceBox().setOnAction($lambda)");
+ GeneralUtilities.logMessage(Level.WARNING, "JobController", "Constructor()", GeneralUtilities.getUIText("Logging.InvalidComparisonFeatureSelection.text"));
+ return;
+ }
+ //
+ this.currentlyChosenComparisonFeature = tmpComparisonFeature;
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ //
+ double tmpMin = Double.isNaN(this.currentlyChosenComparisonFeature.getMinimalValue()) ? tmpHistogramData.getMinComparisonFeatureValue() : this.currentlyChosenComparisonFeature.getMinimalValue();
+ double tmpMax = Double.isNaN(this.currentlyChosenComparisonFeature.getMaximalValue()) ? tmpHistogramData.getMaxComparisonFeatureValue() : this.currentlyChosenComparisonFeature.getMaximalValue();
+ this.outputTab.getBinBorder1Slider().setMin(tmpMin);
+ this.outputTab.getBinBorder1Slider().setMax(tmpMax);
+ this.outputTab.getBinBorder2Slider().setMin(tmpMin);
+ this.outputTab.getBinBorder2Slider().setMax(tmpMax);
+ double tmpTickUnit1;
+ tmpTickUnit1 = (tmpMax - tmpMin) / 10;
+ if (tmpTickUnit1 > 0) {
+ this.outputTab.getBinBorder1Slider().setMajorTickUnit(tmpTickUnit1);
+ this.outputTab.getBinBorder2Slider().setMajorTickUnit(tmpTickUnit1);
+ }
+ this.outputTab.getFrequency1Slider().setMin(0.0);
+ this.outputTab.getFrequency1Slider().setMax(tmpHistogramData.getMaxFrequency());
+ this.outputTab.getFrequency2Slider().setMin(0.0);
+ this.outputTab.getFrequency2Slider().setMax(tmpHistogramData.getMaxFrequency());
+ double tmpTickUnit2;
+ tmpTickUnit2 = (tmpHistogramData.getMaxFrequency() - 0.0) / 10;
+ if (tmpTickUnit2 > 0) {
+ this.outputTab.getFrequency1Slider().setMajorTickUnit(tmpTickUnit2);
+ this.outputTab.getFrequency2Slider().setMajorTickUnit(tmpTickUnit2);
+ }
+ //
+ this.updateOutputTab();
+ if (this.currentlyShownChart instanceof BarChart) {
+ this.outputTab.getBinBorder1Slider().setDisable(!(tmpTickUnit1 > 0));
+ this.outputTab.getBinBorder2Slider().setDisable(!(tmpTickUnit1 > 0));
+ this.outputTab.getFrequency1Slider().setDisable(!(tmpTickUnit2 > 0));
+ this.outputTab.getFrequency2Slider().setDisable(!(tmpTickUnit2 > 0));
+ }
+ });
+ //
+ //
+ this.outputTab.getNumberOfBinsTextField().addEventFilter(KeyEvent.KEY_PRESSED, (KeyEvent tmpEvent) -> {
+ KeyCombination tmpKeyCombination = new KeyCodeCombination(KeyCode.ENTER);
+ if (tmpKeyCombination.match(tmpEvent)) {
+ int tmpNumberOfBins;
+ try {
+ tmpNumberOfBins = Integer.parseInt(this.outputTab.getNumberOfBinsTextField().getText());
+ } catch (NumberFormatException ex) {
+ // This happens if the text field is empty or the input is too large
+ if (!this.outputTab.getNumberOfBinsTextField().getText().isEmpty()) {
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.NumberInputTooHigh.text"));
+ }
+ return;
+ }
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ if (tmpNumberOfBins >= 500) {
+ // Confirm, because binning could take a while
+ Optional tmpResult = GeneralUtilities.showConfirmationDialog(
+ this.applicationStage, GeneralUtilities.getUIText("ConfirmationDialog.ManyBinsContent.text"),
+ GeneralUtilities.getUIText("ConfirmationDialog.SelectionTitle.text"),
+ String.format(GeneralUtilities.getUIText("ConfirmationDialog.ManyBinsHeader.text"), tmpNumberOfBins)
+ );
+ if (tmpResult.isPresent() && tmpResult.get().getButtonData() == ButtonBar.ButtonData.APPLY) {
+ tmpHistogramData.setNumberOfBins(tmpNumberOfBins);
+ this.outputIsSaved = false;
+ } else {
+ return;
+ }
+ } else {
+ tmpHistogramData.setNumberOfBins(tmpNumberOfBins);
+ this.outputIsSaved = false;
+ }
+ // Resets the frequency bounds
+ tmpHistogramData.call();
+ // Update the reseted frequency bounds
+ this.updateOutputTab();
+ }
+ });
+ //
+ //
+ this.outputTab.getBinBorder1Slider().setOnMouseReleased((MouseEvent e) -> {
+ double tmpBinBorder1 = this.outputTab.getBinBorder1Slider().getValue();
+ double tmpBinBorder2 = this.outputTab.getBinBorder2Slider().getValue();
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ tmpHistogramData.setUpperBinBorder(tmpBinBorder1 > tmpBinBorder2 ? tmpBinBorder1 : tmpBinBorder2);
+ tmpHistogramData.setLowerBinBorder(tmpBinBorder1 < tmpBinBorder2 ? tmpBinBorder1 : tmpBinBorder2);
+ double tmpFrequency1SliderValue = this.outputTab.getFrequency1Slider().getValue();
+ double tmpFrequency2SliderValue = this.outputTab.getFrequency2Slider().getValue();
+ // Resets the frequency bounds
+ tmpHistogramData.call();
+ // Set the pre-reset frequency bounds
+ tmpHistogramData.setUpperFrequencyBound(tmpFrequency1SliderValue);
+ tmpHistogramData.setLowerFrequencyBound(tmpFrequency2SliderValue);
+ this.updateOutputTab();
+ this.outputIsSaved = false;
+ });
+ this.outputTab.getBinBorder2Slider().setOnMouseReleased((MouseEvent e) -> {
+ double tmpBinBorder1 = this.outputTab.getBinBorder1Slider().getValue();
+ double tmpBinBorder2 = this.outputTab.getBinBorder2Slider().getValue();
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ tmpHistogramData.setUpperBinBorder(tmpBinBorder1 > tmpBinBorder2 ? tmpBinBorder1 : tmpBinBorder2);
+ tmpHistogramData.setLowerBinBorder(tmpBinBorder1 < tmpBinBorder2 ? tmpBinBorder1 : tmpBinBorder2);
+ double tmpFrequency1SliderValue = this.outputTab.getFrequency1Slider().getValue();
+ double tmpFrequency2SliderValue = this.outputTab.getFrequency2Slider().getValue();
+ // Resets the frequency bounds
+ tmpHistogramData.call();
+ // Set the pre-reset frequency bounds
+ tmpHistogramData.setUpperFrequencyBound(tmpFrequency1SliderValue);
+ tmpHistogramData.setLowerFrequencyBound(tmpFrequency2SliderValue);
+ this.updateOutputTab();
+ this.outputIsSaved = false;
+ });
+ //
+ //
+ this.outputTab.getFrequency1Slider().setOnMouseReleased((MouseEvent e) -> {
+ double tmpFrequencyBound1 = this.outputTab.getFrequency1Slider().getValue();
+ double tmpFrequencyBound2 = this.outputTab.getFrequency2Slider().getValue();
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ tmpHistogramData.setUpperFrequencyBound(
+ tmpFrequencyBound1 > tmpFrequencyBound2 ? tmpFrequencyBound1 : tmpFrequencyBound2
+ );
+ tmpHistogramData.setLowerFrequencyBound(
+ tmpFrequencyBound1 < tmpFrequencyBound2 ? tmpFrequencyBound1 : tmpFrequencyBound2
+ );
+ this.updateOutputTab();
+ this.outputIsSaved = false;
+ });
+ this.outputTab.getFrequency2Slider().setOnMouseReleased((MouseEvent e) -> {
+ double tmpFrequencyBound1 = this.outputTab.getFrequency1Slider().getValue();
+ double tmpFrequencyBound2 = this.outputTab.getFrequency2Slider().getValue();
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ tmpHistogramData.setUpperFrequencyBound(
+ tmpFrequencyBound1 > tmpFrequencyBound2 ? tmpFrequencyBound1 : tmpFrequencyBound2
+ );
+ tmpHistogramData.setLowerFrequencyBound(
+ tmpFrequencyBound1 < tmpFrequencyBound2 ? tmpFrequencyBound1 : tmpFrequencyBound2
+ );
+ this.updateOutputTab();
+ this.outputIsSaved = false;
+ });
+ //
+ //
+ this.outputTab.getBarLabelCheckBox().setOnAction((ActionEvent e) -> {
+ this.updateOutputTab();
+ });
+ //
+ //
+ this.outputTab.getBinLabelChoiceBox().setOnAction((ActionEvent e) -> {
+ this.currentlyChosenBinLabelType = this.outputTab.getBinLabelChoiceBox().getValue();
+ this.updateOutputTab();
+ });
+ //
+ //
+ this.outputTab.getDefaultButton().setOnAction((ActionEvent e) -> {
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ tmpHistogramData.setNumberOfBins(UserPreferences.getInstance().getDefaultNumberOfBins());
+ tmpHistogramData.setUseRelativeFrequencies(false);
+ tmpHistogramData.setLowerBinBorder(tmpHistogramData.getMinComparisonFeatureValue());
+ tmpHistogramData.setUpperBinBorder(tmpHistogramData.getMaxComparisonFeatureValue());
+ // Resets the frequency bounds
+ tmpHistogramData.call();
+ this.updateOutputTab();
+ });
+ //
+ //
+ this.outputTab.getChartConfigurationButton().setOnAction((ActionEvent e) -> {
+ //
+ if (this.currentlyChosenComparisonFeature == null) {
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.NoComparisonFeatureChosen.text"));
+ return;
+ }
+ //
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ this.chartConfigurationDialog.getLowerBinBorderInputField().setText(Double.toString(tmpHistogramData.getLowerBinBorder()));
+ this.chartConfigurationDialog.getUpperBinBorderInputField().setText(Double.toString(tmpHistogramData.getUpperBinBorder()));
+ this.chartConfigurationDialog.getLowerFrequencyBoundInputField().setText(Double.toString(tmpHistogramData.getLowerFrequencyBound()));
+ this.chartConfigurationDialog.getUpperFrequencyBoundInputField().setText(Double.toString(tmpHistogramData.getUpperFrequencyBound()));
+ this.chartConfigurationDialog.setHeaderText(String.format(GeneralUtilities.getUIText("ChartConfigurationDialog.Header.text"), this.currentlyChosenComparisonFeature.toString()));
+ this.chartConfigurationDialog.showAndWait();
+ });
+ //
+ //
+ this.outputTab.getBinBorderConfigurationButton().setOnAction((ActionEvent e) -> {
+ BinBorderConfigurationBox tmpBox;
+ this.binBorderConfigurationBoxList.clear();
+ int tmpIndex = 0;
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ for (double tmpDouble : tmpHistogramData.getBinBorders()) {
+ tmpBox = new BinBorderConfigurationBox(Double.toString(tmpDouble), Integer.toString(++tmpIndex));
+ tmpBox.getAddButton().setOnAction(this.binBorderConfigurationDialogAddHandler);
+ tmpBox.getRemoveButton().setOnAction(this.binBorderConfigurationDialogRemoveHandler);
+ tmpBox.getTextField().setTextFormatter(GeneralUtilities.getSignedDecimalNumberTextFormatter());
+ this.binBorderConfigurationBoxList.add(tmpBox);
+ // Removing is disabled if there are only two bin borders
+ tmpBox.getRemoveButton().setDisable(tmpHistogramData.getBinBorders().length <= 2);
+ }
+ this.binBorderConfigurationDialog.getBinBorderConfigurationBoxesBox().getChildren().setAll(this.binBorderConfigurationBoxList);
+ this.binBorderConfigurationDialog.showAndWait();
+ });
+ //
+ //
+ //
+ this.binBorderConfigurationDialog.getCancelButton().setOnAction((ActionEvent e) -> {
+ this.binBorderConfigurationDialog.hide();
+ });
+ this.binBorderConfigurationDialog.getApplyButton().setOnAction((ActionEvent e) -> {
+ ListIterator tmpIterator = this.binBorderConfigurationBoxList.listIterator();
+ while (tmpIterator.hasNext()) {
+ BinBorderConfigurationBox tmpBox = tmpIterator.next();
+ // Remove all BinConfigurationBoxs with invalid textfields
+ if (tmpBox.getTextField().getText() != null) {
+ try {
+ Double.parseDouble(tmpBox.getTextField().getText());
+ } catch (NumberFormatException ex) {
+ tmpIterator.remove();
+ }
+ } else {
+ tmpIterator.remove();
+ }
+ }
+ if (this.binBorderConfigurationBoxList.size() <= 1) {
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.InvalidBinBorders.text"));
+ return;
+ }
+ double[] tmpBinBorders = new double[this.binBorderConfigurationBoxList.size()];
+ int tmpIndex = 0;
+ for (BinBorderConfigurationBox tmpBox : this.binBorderConfigurationBoxList) {
+ tmpBinBorders[tmpIndex] = Double.parseDouble(tmpBox.getTextField().getText());
+ if (tmpIndex != 0 && tmpBinBorders[tmpIndex] <= tmpBinBorders[tmpIndex - 1]) {
+ // Every bin border has to be greater than the previous bin border
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.InvalidBinBorders.text"));
+ return;
+ }
+ tmpIndex++;
+ }
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ // Important: Do this first or else the new borders will not be used
+ tmpHistogramData.setNumberOfBins(tmpBinBorders.length - 1);
+ tmpHistogramData.setSpecificBinBorders(tmpBinBorders);
+ this.outputIsSaved = false;
+ // Resets the frequency bounds
+ tmpHistogramData.call();
+ // Update the reseted frequency bounds
+ this.updateOutputTab();
+ this.binBorderConfigurationDialog.hide();
+ });
+ this.binBorderConfigurationDialog.getDialogPane().addEventFilter(KeyEvent.KEY_PRESSED, (KeyEvent tmpEvent) -> {
+ KeyCombination tmpKeyCombination = new KeyCodeCombination(KeyCode.ENTER);
+ if (tmpKeyCombination.match(tmpEvent)) {
+ this.binBorderConfigurationDialog.getApplyButton().fire();
+ }
+ });
+ this.binBorderConfigurationDialog.getResetButton().setOnAction((ActionEvent e) -> {
+ BinBorderConfigurationBox tmpBox;
+ this.binBorderConfigurationBoxList.clear();
+ int tmpIndex = 0;
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ for (double tmpDouble : tmpHistogramData.getBinBorders()) {
+ tmpBox = new BinBorderConfigurationBox(Double.toString(tmpDouble), Integer.toString(++tmpIndex));
+ tmpBox.getAddButton().setOnAction(this.binBorderConfigurationDialogAddHandler);
+ tmpBox.getRemoveButton().setOnAction(this.binBorderConfigurationDialogRemoveHandler);
+ tmpBox.getTextField().setTextFormatter(GeneralUtilities.getSignedDecimalNumberTextFormatter());
+ this.binBorderConfigurationBoxList.add(tmpBox);
+ // Removing is disabled if there are only two bin borders
+ tmpBox.getRemoveButton().setDisable(tmpHistogramData.getBinBorders().length <= 2);
+ }
+ this.binBorderConfigurationDialog.getBinBorderConfigurationBoxesBox().getChildren().setAll(this.binBorderConfigurationBoxList);
+ });
+ this.chartConfigurationDialog.getCancelButton().setOnAction((ActionEvent e) -> {
+ this.chartConfigurationDialog.hide();
+ });
+ this.chartConfigurationDialog.getApplyButton().setOnAction((ActionEvent e) -> {
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ if (this.isValidLowerBinBorder) {
+ tmpHistogramData.setLowerBinBorder(Double.parseDouble(this.chartConfigurationDialog.getLowerBinBorderInputField().getText()));
+ this.outputIsSaved = false;
+ }
+ if (this.isValidUpperBinBorder) {
+ tmpHistogramData.setUpperBinBorder(Double.parseDouble(this.chartConfigurationDialog.getUpperBinBorderInputField().getText()));
+ this.outputIsSaved = false;
+ }
+ // Resets the frequency bounds
+ tmpHistogramData.call();
+ // Set the new frequency bounds AFTER the binning
+ if (this.isValidLowerFrequencyBound) {
+ double tmpDouble = Double.parseDouble(this.chartConfigurationDialog.getLowerFrequencyBoundInputField().getText());
+ if (tmpHistogramData.isUseRelativeFrequencies() && tmpDouble > 1.5) {
+ GeneralUtilities.showInfoDialog(
+ this.applicationStage, String.format(GeneralUtilities.getUIText("InfoDescription.RelativeFrequencyTooHigh.text"), tmpDouble)
+ );
+ } else {
+ tmpHistogramData.setLowerFrequencyBound(tmpDouble);
+ this.outputIsSaved = false;
+ }
+ }
+ if (this.isValidUpperFrequencyBound) {
+ double tmpDouble = Double.parseDouble(this.chartConfigurationDialog.getUpperFrequencyBoundInputField().getText());
+ if (tmpHistogramData.isUseRelativeFrequencies() && tmpDouble > 1.5) {
+ GeneralUtilities.showInfoDialog(
+ this.applicationStage, String.format(GeneralUtilities.getUIText("InfoDescription.RelativeFrequencyTooHigh.text"), tmpDouble)
+ );
+ } else {
+ tmpHistogramData.setUpperFrequencyBound(tmpDouble);
+ this.outputIsSaved = false;
+ }
+ }
+ this.updateOutputTab();
+ this.chartConfigurationDialog.hide();
+ });
+ this.chartConfigurationDialog.getDialogPane().addEventFilter(KeyEvent.KEY_PRESSED, (KeyEvent tmpEvent) -> {
+ KeyCombination tmpKeyCombination = new KeyCodeCombination(KeyCode.ENTER);
+ if (tmpKeyCombination.match(tmpEvent)) {
+ this.chartConfigurationDialog.getApplyButton().fire();
+ }
+ });
+ this.chartConfigurationDialog.getResetButton().setOnAction((ActionEvent e) -> {
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ this.chartConfigurationDialog.getLowerBinBorderInputField().setText(Double.toString(this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature).getLowerBinBorder()));
+ this.chartConfigurationDialog.getUpperBinBorderInputField().setText(Double.toString(tmpHistogramData.getUpperBinBorder()));
+ this.chartConfigurationDialog.getLowerFrequencyBoundInputField().setText(Double.toString(tmpHistogramData.getLowerFrequencyBound()));
+ this.chartConfigurationDialog.getUpperFrequencyBoundInputField().setText(Double.toString(tmpHistogramData.getUpperFrequencyBound()));
+ });
+ this.chartConfigurationDialog.getDefaultButton().setOnAction((ActionEvent e) -> {
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ this.chartConfigurationDialog.getLowerBinBorderInputField().setText(Double.toString(tmpHistogramData.getMinComparisonFeatureValue()));
+ this.chartConfigurationDialog.getUpperBinBorderInputField().setText(Double.toString(tmpHistogramData.getMaxComparisonFeatureValue()));
+ this.chartConfigurationDialog.getLowerFrequencyBoundInputField().setText(Double.toString(0.0));
+ this.chartConfigurationDialog.getUpperFrequencyBoundInputField().setText(Double.toString(tmpHistogramData.getMaxFrequency()));
+ });
+ //
+ //
+ //
+ if (!tmpIsLoaded) {
+ this.inputTab.getButtonsTitledPane().setExpanded(true);
+ this.inputTab.getInputType1ChoiceBox().setValue(InputType.SMILES);
+ this.inputTab.getInputType2ChoiceBox().setValue(InputType.SMILES);
+ this.inputTab.getJobStartButton().setDisable(true);
+ this.inputTab.getJobCancelButton().setDisable(true);
+ this.inputTab.getJobProgressBar().setVisible(false);
+ this.inputTab.getJobInfoLabel().setText(GeneralUtilities.getUIText("InfoDescription.NewJob.text"));
+ }
+ //
+ }
+ //
+ //
+ //
+ //
+ //
+ /**
+ * True if the output of this JobController is saved, false otherwise
+ *
+ * @return true if the output of this JobController is saved,
+ * false otherwise
+ */
+ public boolean outputIsSaved() {
+ return this.outputIsSaved;
+ }
+
+ /**
+ * Get the InputTab of this JobController
+ *
+ * @return the InputTab
+ */
+ public InputTab getInputTab() {
+ return this.inputTab;
+ }
+
+ /**
+ * Get the JobTaskManager of this JobController or null if this
+ * JobController was loaded
+ *
+ * @return the JobTaskManager
+ */
+ public JobTaskManager getJobTaskManager() {
+ return this.jobTaskManager;
+ }
+
+ /**
+ * Get the HistogramDataManager
+ *
+ * @return the HistogramDataManager
+ */
+ public HistogramDataManager getHistogramDataManager() {
+ return this.histogramDataManager;
+ }
+
+ /**
+ * Get the ComparisonFeature that is currently selected in the OutputTab
+ *
+ * @return the currently selected ComparisonFeature
+ */
+ public ComparisonFeature getCurrentlyChosenComparisonFeature() {
+ return this.currentlyChosenComparisonFeature;
+ }
+
+ /**
+ * Get the OutputTab of this JobController
+ *
+ * @return the OutputTab
+ */
+ public OutputTab getOutputTab() {
+ return this.outputTab;
+ }
+
+ /**
+ * Get the number that identifies this JobController in the current
+ * application session
+ *
+ * @return the number of this JobController
+ */
+ public String getJobNumber() {
+ return this.jobNumber;
+ }
+ //
+ //
+ /**
+ * Set the HistogramDataManager
+ *
+ * @param tmpHistogramDataManager a HistogramDataManager
+ */
+ public void setHistogramDataManager(HistogramDataManager tmpHistogramDataManager) {
+ this.histogramDataManager = tmpHistogramDataManager;
+ }
+
+ /**
+ * Set whether the result of this JobController is saved or not
+ *
+ * @param tmpOutputIsSaved true if the output is saved, false otherwise
+ */
+ public void setOutputIsSaved(boolean tmpOutputIsSaved) {
+ this.outputIsSaved = tmpOutputIsSaved;
+ }
+
+ /**
+ * Set a value for the currentlyChosenComparisonFeature
+ *
+ * @param tmpCurrentlyChosenComparisonFeature the value to be set
+ */
+ public void setCurrentlyChosenComparisonFeature(ComparisonFeature tmpCurrentlyChosenComparisonFeature) {
+ this.currentlyChosenComparisonFeature = tmpCurrentlyChosenComparisonFeature;
+ }
+ //
+ //
+ //
+ /**
+ * Adds a PropertyChangeListener that listens for changes fired from this
+ * JobController
+ *
+ * @param tmpListener a listener to be added
+ */
+ public void addPropertyChangeListener(PropertyChangeListener tmpListener) {
+ this.propertyChangeSupport.addPropertyChangeListener(tmpListener);
+ }
+
+ /**
+ * Removes a PropertyChangeListener
+ *
+ * @param tmpListener a listener to be removed
+ */
+ public void removePropertyChangeListener(PropertyChangeListener tmpListener) {
+ this.propertyChangeSupport.removePropertyChangeListener(tmpListener);
+ }
+
+ /**
+ * Handle all PropertyChangeEvents that reach this JobController.
+ *
+ * @param evt a PropertyChangeEvent that reached this JobController
+ */
+ @Override
+ public void propertyChange(PropertyChangeEvent evt) {
+ try {
+ if (evt.getSource() instanceof JobTaskManager) {
+ switch (evt.getPropertyName()) {
+ case "Exception":
+ this.jobTaskManager.cancelWorkingProcess();
+ Exception tmpException = (Exception) evt.getNewValue();
+ String tmpOrigin = (String) evt.getOldValue();
+ Platform.runLater(() -> {
+ GeneralUtilities.showErrorDialog(this.applicationStage, tmpException.toString(), tmpOrigin);
+ GeneralUtilities.logException(Level.WARNING, tmpException);
+ });
+ break;
+ case "ParseAndCompareTasks progress":
+ synchronized (this) {
+ if (this.jobTaskManager.isWorking()) {
+ double tmpProgressValue = (double) evt.getNewValue();
+ Platform.runLater(() -> {
+ // The JavaFX Application can be only updated from the JavaFX Application Thread.
+ // NOTE: Applications should avoid flooding JavaFX with too many pending Runnables. Otherwise, the application may become unresponsive.
+ this.inputTab.getJobProgressBar().setProgress(tmpProgressValue);
+ this.inputTab.getJobInfoLabel().setText(
+ String.format(GeneralUtilities.getUIText("InfoDescription.ReadingInputProgress.text"), (int) (tmpProgressValue * 100))
+ );
+ });
+ }
+ }
+ break;
+ case "ParseAndCompareTasks finished":
+ synchronized (this) {
+ if (this.jobTaskManager.isWorking()) {
+ this.jobTaskManager.cancelWorkingProcess();
+ this.histogramDataManager = this.jobTaskManager.getHistogramDataManager();
+ this.histogramDataManager.setCalculationStartTime(this.calculationStartTime);
+ this.histogramDataManager.setCalculationFinishTime(System.currentTimeMillis());
+ Platform.runLater(() -> {
+ this.inputTab.getJobStartButton().setVisible(true);
+ this.inputTab.getJobCancelButton().setVisible(false);
+ this.inputTab.getJobProgressBar().setVisible(false);
+ this.inputTab.getJobInfoLabel().setText(GeneralUtilities.getUIText("InfoDescription.FinishedJob.text"));
+ // Set this first to avoid NullPointerExcpetions
+ this.currentlyChosenComparisonFeature = this.histogramDataManager.getComparisonFeatureSet().iterator().next();
+ this.outputTab.setBinLabelChoiceBoxItems(Set.of(BinLabelType.values()));
+ this.outputTab.setChartChoiceBoxItems(this.histogramDataManager.getComparisonFeatureSet());
+ this.outputTab.getBinLabelChoiceBox().setValue(this.currentlyChosenBinLabelType);
+ this.outputTab.getChartChoiceBox().setValue(this.currentlyChosenComparisonFeature);
+ this.outputTab.getInfoLabel().setText(String.format(
+ GeneralUtilities.getUIText("OutputTab.infoLabel.text"), this.jobNumber,
+ this.histogramDataManager.getNumberOfComparedPairs(), this.histogramDataManager.getInputFile1(),
+ this.histogramDataManager.getInputFile2()
+ ));
+ // Displays OutputTab and closes InputTab
+ this.propertyChangeSupport.firePropertyChange("Created charts successfully", false, true);
+ });
+ }
+ }
+ break;
+ case "Unpaired inputs":
+ Platform.runLater(() -> {
+ GeneralUtilities.showInfoDialog(this.applicationStage, String.format(
+ GeneralUtilities.getUIText("InfoDescription.UnpairedStrings.text"),
+ evt.getNewValue()
+ ));
+ });
+ break;
+ default:
+ GeneralUtilities.logMessage(
+ Level.INFO, "JobController", "propertyChange()",
+ String.format(GeneralUtilities.getUIText("Logging.UnexptectedPropertyChange.text"), evt.getPropertyName())
+ );
+ break;
+ }
+ }
+ } catch (Exception ex) {
+ Platform.runLater(() -> {
+ GeneralUtilities.showErrorDialog(this.applicationStage, ex.toString(), "JobController.propertyChange()");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ });
+ }
+ }
+ //
+ //
+ /**
+ * Create a BarChart from the given HistogramData. Also add a mouse click
+ * listener to every bar.
+ *
+ * @param tmpHistogramData the HistogramData from which the chart will be
+ * created
+ * @param tmpBinLabelType specifies the type of labeling used for the bins
+ * @return the created BarChart or an error label if something went wrong
+ */
+ public Region createChart(HistogramData tmpHistogramData, BinLabelType tmpBinLabelType) {
+ try {
+ //
+ CategoryAxis tmpXAxis = new CategoryAxis();
+ tmpXAxis.setLabel(GeneralUtilities.getUIText("OutputTab.xAxisLabel.text"));
+ tmpXAxis.setTickLabelFill(Color.color(0.2, 0.2, 0.2));
+ final NumberAxis tmpYAxis = new NumberAxis();
+ tmpYAxis.setLabel(GeneralUtilities.getUIText("OutputTab.yAxisLabel.text"));
+ tmpYAxis.setTickLabelFill(Color.color(0.2, 0.2, 0.2));
+ tmpYAxis.setAutoRanging(false);
+ BarChart tmpChart = new BarChart<>(tmpXAxis, tmpYAxis);
+ tmpChart.setBarGap(0.0);
+ tmpChart.setLegendVisible(false);
+ //
+ //
+ tmpYAxis.heightProperty().addListener(new ChangeListener() {
+
+ /**
+ * True if the last resize of the chart pane was done
+ * automatically, false otherwise
+ */
+ private boolean lastResizeWasAutomatic1 = false;
+
+ /**
+ * True if the last resize of the application stage was done
+ * automatically, false otherwise
+ */
+ private boolean lastResizeWasAutomatic2 = false;
+
+ @Override
+ public void changed(ObservableValue tmpObservableValue, Number tmpOldAxisHeight, Number tmpNewAxisHeight) {
+ double tmpUpperBound = tmpHistogramData.getUpperFrequencyBound();
+ double tmpLowerBound = tmpHistogramData.getLowerFrequencyBound();
+ double tmpBoundDifference = tmpUpperBound - tmpLowerBound;
+ double tmpTickSpacing = 25.0;
+ int tmpMaxTickNumber = (int) ((double) tmpNewAxisHeight / tmpTickSpacing);
+ double[] tmpTickUnits = {1, 2.5, 5};
+ double tmpResultTickUnit = -1;
+ if (JobController.this.outputTab.getRelativeFrequenciesCheckBox().isSelected()) {
+ double[] tmpFactors = {0.0000001, 0.000001, 0.00001, 0.0001, 0.001, 0.01, 0.1};
+ outerLoop:
+ for (double tmpFactor : tmpFactors) {
+ for (double tmpTickUnit : tmpTickUnits) {
+ if (tmpMaxTickNumber * tmpFactor * tmpTickUnit >= tmpBoundDifference) {
+ tmpResultTickUnit = tmpFactor * tmpTickUnit;
+ break outerLoop;
+ }
+ }
+ }
+ tmpResultTickUnit = tmpResultTickUnit == -1 ? 0.0000001 : tmpResultTickUnit;
+ tmpYAxis.setMinorTickVisible(true);
+ } else {
+ long[] tmpFactors = {1L, 10L, 100L, 1000L, 10000L, 100000L, 1000000L, 10000000L, 100000000L, 1000000000L, 10000000000L, 100000000000L, 1000000000000L, 10000000000000L, 100000000000000L};
+ outerLoop:
+ for (long tmpFactor : tmpFactors) {
+ for (double tmpTickUnit : tmpTickUnits) {
+ if (tmpMaxTickNumber * tmpFactor * tmpTickUnit >= tmpBoundDifference) {
+ tmpResultTickUnit = tmpFactor * tmpTickUnit;
+ break outerLoop;
+ }
+ }
+ }
+ tmpResultTickUnit = tmpResultTickUnit == -1 ? 1000000000000000L : tmpResultTickUnit;
+ tmpYAxis.setMinorTickVisible(tmpResultTickUnit >= 5);
+ }
+ tmpYAxis.setTickUnit(tmpResultTickUnit);
+ tmpYAxis.setLowerBound(tmpLowerBound);
+ tmpYAxis.setUpperBound((((int) (tmpUpperBound * 1.02 / tmpResultTickUnit)) + 1) * tmpResultTickUnit);
+ //
+ // If a chart has just been created the layout of the y-axis may be incorrect.
+ // This section tries to resize the y-axis and later undo the resize in an attempt to thus correct the layout of the y-axis
+ if ((double) tmpOldAxisHeight == 0.0 && JobController.this.applicationStage.isMaximized() && !JobController.this.histogramDataManager.getHistogramData(currentlyChosenComparisonFeature).isUseRelativeFrequencies()) {
+ JobController.this.outputTab.getChartPane().setMaxHeight(JobController.this.outputTab.getChartPane().getHeight() - 10);
+ this.lastResizeWasAutomatic1 = true;
+ } else if (this.lastResizeWasAutomatic1) {
+ JobController.this.outputTab.getChartPane().setMaxHeight(Double.MAX_VALUE);
+ JobController.this.outputTab.getChartPane().autosize();
+ this.lastResizeWasAutomatic1 = false;
+ } else if ((double) tmpOldAxisHeight == 0.0 || this.lastResizeWasAutomatic2) {
+ JobController.this.applicationStage.setHeight(JobController.this.applicationStage.getHeight() + (this.lastResizeWasAutomatic2 ? -5.8 : 5));
+ this.lastResizeWasAutomatic2 = !this.lastResizeWasAutomatic2;
+ }
+ //
+ }
+ });
+ //
+ double[] tmpFrequencyData = tmpHistogramData.getFrequencies();
+ List> tmpDataList = new LinkedList<>();
+ for (int i = tmpFrequencyData.length - 1; i >= 0; i--) {
+ //
+ double tmpFrequency = tmpFrequencyData[i];
+ String tmpCategory;
+ int tmpPrecision = tmpHistogramData.getComparisonFeauture().isContinuous() ? 3 : 2;
+ switch (tmpBinLabelType) {
+ case MIN:
+ tmpCategory = tmpHistogramData.getComparisonFeauture().isContinuous() ?
+ String.format("%." + tmpPrecision + "f", tmpHistogramData.getBinBorders()[i]) :
+ String.format("%d", (int) Math.ceil(tmpHistogramData.getBinBorders()[i]));
+ // Check for and eliminate duplicate categories
+ outerLoop:
+ while (true) {
+ for (XYChart.Data tmpData : tmpDataList) {
+ if (Double.parseDouble(tmpData.getXValue()) == Double.parseDouble((tmpCategory))) {
+ tmpCategory = String.format("%." + (++tmpPrecision) + "f", tmpHistogramData.getBinBorders()[i]);
+ continue outerLoop;
+ }
+ }
+ break;
+ }
+ break;
+ case MAX:
+ tmpCategory = tmpHistogramData.getComparisonFeauture().isContinuous() ?
+ String.format("%." + tmpPrecision + "f", tmpHistogramData.getBinBorders()[i + 1]) :
+ String.format("%d", (int) Math.ceil(tmpHistogramData.getBinBorders()[i + 1]));
+ // Check for and eliminate duplicate categories
+ outerLoop:
+ while (true) {
+ for (XYChart.Data tmpData : tmpDataList) {
+ if (Double.parseDouble(tmpData.getXValue()) == Double.parseDouble((tmpCategory))) {
+ tmpCategory = String.format("%." + (++tmpPrecision) + "f", tmpHistogramData.getBinBorders()[i + 1]);
+ continue outerLoop;
+ }
+ }
+ break;
+ }
+ break;
+ case MEAN:
+ tmpPrecision = tmpHistogramData.getComparisonFeauture().isContinuous() ? 3 : 1;
+ tmpCategory = String.format("%." + tmpPrecision + "f", (tmpHistogramData.getBinBorders()[i] + tmpHistogramData.getBinBorders()[i + 1]) / 2.0);
+ // Check for and eliminate duplicate categories
+ outerLoop:
+ while (true) {
+ for (XYChart.Data tmpData : tmpDataList) {
+ if (Double.parseDouble(tmpData.getXValue()) == Double.parseDouble((tmpCategory))) {
+ tmpCategory = String.format("%." + (++tmpPrecision) + "f", (tmpHistogramData.getBinBorders()[i] + tmpHistogramData.getBinBorders()[i + 1]) / 2.0);
+ continue outerLoop;
+ }
+ }
+ break;
+ }
+ break;
+ case INTERVAL:
+ if (i == tmpFrequencyData.length - 1 && tmpHistogramData.getComparisonFeauture().isContinuous()) {
+ tmpCategory = String.format(
+ "[%." + tmpPrecision + "f - %." + tmpPrecision + "f]",
+ tmpHistogramData.getBinBorders()[i], tmpHistogramData.getBinBorders()[i + 1]
+ );
+ } else if (i == tmpFrequencyData.length - 1) {
+ tmpCategory = String.format(
+ "[%d - %d]",
+ (int) Math.ceil(tmpHistogramData.getBinBorders()[i]), (int) Math.ceil(tmpHistogramData.getBinBorders()[i + 1])
+ );
+ } else if (tmpHistogramData.getComparisonFeauture().isContinuous()) {
+ tmpCategory = String.format(
+ "[%." + tmpPrecision + "f - %." + tmpPrecision + "f)",
+ tmpHistogramData.getBinBorders()[i], tmpHistogramData.getBinBorders()[i + 1]
+ );
+ } else {
+ tmpCategory = String.format(
+ "[%d - %d)",
+ (int) Math.ceil(tmpHistogramData.getBinBorders()[i]), (int) Math.ceil(tmpHistogramData.getBinBorders()[i + 1])
+ );
+ }
+ // Check for and eliminate duplicate categories
+ outerLoop:
+ while (true) {
+ for (XYChart.Data tmpData : tmpDataList) {
+ if (tmpData.getXValue().equals(tmpCategory)) {
+ tmpCategory = String.format(
+ "[%." + (++tmpPrecision) + "f - %." + (++tmpPrecision) + "f)",
+ tmpHistogramData.getBinBorders()[i], tmpHistogramData.getBinBorders()[i + 1]
+ );
+ continue outerLoop;
+ }
+ }
+ break;
+ }
+ break;
+ default:
+ tmpCategory = "";
+ }
+ XYChart.Data tmpData = new XYChart.Data<>(tmpCategory, tmpFrequency);
+ tmpDataList.add(tmpData);
+ //
+ //
+ StackPane tmpMouseClickListener = new StackPane();
+ tmpMouseClickListener.setAlignment(Pos.TOP_CENTER);
+ //
+ if (this.outputTab.getBarLabelCheckBox().isSelected()) {
+ Label tmpBarLabel = tmpHistogramData.isUseRelativeFrequencies() ? new Label(new DecimalFormat("0.000").format(tmpFrequency)) : new Label(new DecimalFormat("###").format(tmpFrequency));
+ tmpMouseClickListener.getChildren().add(tmpBarLabel);
+ tmpYAxis.heightProperty().addListener((ObservableValue tmpObservableValue, Number tmpOldAxisHeight, Number tmpNewAxisHeight) -> {
+ double tmpMouseClickListenerHeight = tmpMouseClickListener.boundsInParentProperty().getValue().getHeight();
+ if (tmpMouseClickListenerHeight >= (double) tmpNewAxisHeight) {
+ tmpBarLabel.setTranslateY((tmpMouseClickListenerHeight + 5) - (double) tmpNewAxisHeight);
+ tmpBarLabel.setTextFill(Paint.valueOf("White"));
+ } else {
+ tmpBarLabel.setTranslateY(-20);
+ tmpBarLabel.setTextFill(Paint.valueOf("Black"));
+ }
+ });
+ }
+ //
+ List tmpComparisonResultList = tmpHistogramData.getBin(i);
+ int tmpBinNumber = i + 1;
+ // The list may be empty even though the bin is not
+ if (!tmpComparisonResultList.isEmpty()) {
+ tmpMouseClickListener.setOnMouseClicked((MouseEvent e) -> {
+ MoleculePairDisplayerController tmpController = new MoleculePairDisplayerController(
+ tmpComparisonResultList, this.applicationStage, this.fileChooser,
+ tmpBinNumber, tmpHistogramData.getComparisonFeauture(), tmpFrequency,
+ tmpHistogramData.getBinBorders()[tmpBinNumber - 1], tmpHistogramData.getBinBorders()[tmpBinNumber]
+ );
+ });
+ tmpMouseClickListener.setOnMouseEntered((MouseEvent e) -> {
+ this.scene.setCursor(Cursor.HAND);
+ });
+ tmpMouseClickListener.setOnMouseExited((MouseEvent e) -> {
+ this.scene.setCursor(Cursor.DEFAULT);
+ });
+ } else {
+ tmpMouseClickListener.setOnMouseClicked((MouseEvent e) -> {
+ GeneralUtilities.showInfoDialog(this.applicationStage, GeneralUtilities.getUIText("InfoDescription.NoMoleculesPairs.text"));
+ });
+ }
+ tmpData.setNode(tmpMouseClickListener);
+ //
+ }
+ //
+ XYChart.Series tmpSeries = new XYChart.Series<>();
+ ListIterator> tmpIterator = tmpDataList.listIterator(tmpDataList.size());
+ while (tmpIterator.hasPrevious()) {
+ tmpSeries.getData().add(tmpIterator.previous());
+ }
+ tmpChart.getData().add(tmpSeries);
+ //
+ return tmpChart;
+ } catch (Exception ex) {
+ GeneralUtilities.showErrorDialog(
+ this.applicationStage,
+ String.format(GeneralUtilities.getUIText("ErrorDescription.ChartCreationFailed.text"), tmpHistogramData.getComparisonFeauture().toString()),
+ "JobController.createChart()"
+ );
+ GeneralUtilities.logException(Level.WARNING, ex);
+ return new Label(String.format(GeneralUtilities.getUIText("InfoDescription.ChartPlaceHolder.text"), tmpHistogramData.getComparisonFeauture().toString()));
+ }
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Update the outputTab. Set the new chart and the states of some controls
+ */
+ private void updateOutputTab() {
+ HistogramData tmpHistogramData = this.histogramDataManager.getHistogramData(this.currentlyChosenComparisonFeature);
+ this.outputTab.getFrequency1Slider().setValue(tmpHistogramData.getUpperFrequencyBound());
+ this.outputTab.getFrequency2Slider().setValue(tmpHistogramData.getLowerFrequencyBound());
+ this.outputTab.getBinBorder1Slider().setValue(tmpHistogramData.getUpperBinBorder());
+ this.outputTab.getBinBorder2Slider().setValue(tmpHistogramData.getLowerBinBorder());
+ this.outputTab.getNumberOfBinsTextField().setText(Integer.toString(tmpHistogramData.getNumberOfBins()));
+ this.outputTab.getRelativeFrequenciesCheckBox().setSelected(tmpHistogramData.isUseRelativeFrequencies());
+ this.currentlyShownChart = this.createChart(tmpHistogramData, this.currentlyChosenBinLabelType);
+ this.outputTab.setComparisonFeatureChart(this.currentlyShownChart);
+ if (this.currentlyShownChart instanceof Label) {
+ this.outputTab.getImageButton().setDisable(true);
+ this.outputTab.getSummaryReportButton().setDisable(true);
+ this.outputTab.getBinLabelChoiceBox().setDisable(true);
+ this.outputTab.getChartConfigurationButton().setDisable(true);
+ this.outputTab.getDefaultButton().setDisable(true);
+ this.outputTab.getBinBorderConfigurationButton().setDisable(true);
+ this.outputTab.getRelativeFrequenciesCheckBox().setDisable(true);
+ this.outputTab.getNumberOfBinsTextField().setDisable(true);
+ this.outputTab.getBinBorder1Slider().setDisable(true);
+ this.outputTab.getBinBorder2Slider().setDisable(true);
+ this.outputTab.getFrequency1Slider().setDisable(true);
+ this.outputTab.getFrequency2Slider().setDisable(true);
+ } else if (this.currentlyShownChart instanceof BarChart) {
+ this.outputTab.getImageButton().setDisable(false);
+ this.outputTab.getSummaryReportButton().setDisable(false);
+ this.outputTab.getBinLabelChoiceBox().setDisable(false);
+ this.outputTab.getChartConfigurationButton().setDisable(false);
+ this.outputTab.getDefaultButton().setDisable(false);
+ this.outputTab.getBinBorderConfigurationButton().setDisable(false);
+ this.outputTab.getRelativeFrequenciesCheckBox().setDisable(false);
+ this.outputTab.getNumberOfBinsTextField().setDisable(false);
+ this.outputTab.getBinBorder1Slider().setDisable(false);
+ this.outputTab.getBinBorder2Slider().setDisable(false);
+ this.outputTab.getFrequency1Slider().setDisable(false);
+ this.outputTab.getFrequency2Slider().setDisable(false);
+ }
+ }
+ //
+
+}
\ No newline at end of file
diff --git a/src/main/java/de/whs/ibci/msc/control/MoleculePairDisplayerController.java b/src/main/java/de/whs/ibci/msc/control/MoleculePairDisplayerController.java
new file mode 100644
index 0000000..377863a
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/control/MoleculePairDisplayerController.java
@@ -0,0 +1,723 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.control;
+
+import de.whs.ibci.msc.model.ComparisonUtility;
+import de.whs.ibci.msc.model.ComparisonFeature;
+import de.whs.ibci.msc.model.ComparisonResult;
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.utility.GuiUtilities;
+import de.whs.ibci.msc.utility.MSCConstants;
+import de.whs.ibci.msc.view.MoleculePairDisplayerStage;
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.geom.AffineTransform;
+import java.awt.image.BufferedImage;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.nio.file.Files;
+import java.text.DecimalFormat;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
+import java.util.ListIterator;
+import java.util.logging.Level;
+import javafx.application.Platform;
+import javafx.beans.value.ObservableValue;
+import javafx.concurrent.Task;
+import javafx.embed.swing.SwingFXUtils;
+import javafx.scene.Cursor;
+import javafx.scene.control.CheckBox;
+import javafx.scene.control.Control;
+import javafx.scene.control.Labeled;
+import javafx.scene.input.KeyCode;
+import javafx.scene.input.KeyCodeCombination;
+import javafx.scene.input.KeyCombination;
+import javafx.scene.input.KeyEvent;
+import javafx.stage.FileChooser;
+import javafx.stage.Modality;
+import javafx.stage.Window;
+import javax.imageio.ImageIO;
+import org.apache.batik.dom.GenericDOMImplementation;
+import org.apache.batik.svggen.SVGGraphics2D;
+import org.apache.pdfbox.pdmodel.PDDocument;
+import org.apache.pdfbox.pdmodel.PDPage;
+import org.apache.pdfbox.pdmodel.PDPageContentStream;
+import org.apache.pdfbox.pdmodel.common.PDRectangle;
+import org.apache.pdfbox.pdmodel.graphics.image.LosslessFactory;
+import org.apache.pdfbox.pdmodel.graphics.image.PDImageXObject;
+import org.openscience.cdk.depict.DepictionGenerator;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
+import org.openscience.cdk.smiles.SmilesParser;
+import org.w3c.dom.DOMException;
+import org.w3c.dom.DOMImplementation;
+import org.w3c.dom.Document;
+
+/**
+ * Controller for a MoleculePairDisplayerStage that handles related events. This
+ * is used to display a list of molecule pairs
+ *
+ * @author Jan-Mathis Hein
+ */
+public class MoleculePairDisplayerController {
+
+ //
+ /**
+ * If true the MoleculePairDisplayerStage will be maximized,
+ * if false it will not
+ */
+ private static boolean isMaximized = false;
+
+ /**
+ * The MoleculePairDisplayerStage's initial width
+ */
+ private static double stageWidth = Double.NaN;
+
+ /**
+ * The MoleculePairDisplayerStage's initial height
+ */
+ private static double stageHeight = Double.NaN;
+
+ /**
+ * The MoleculePairDisplayerStage's initial X position
+ */
+ private static double stageXPosition = Double.NaN;
+
+ /**
+ * The MoleculePairDisplayerStage's initial Y position
+ */
+ private static double stageYPosition = Double.NaN;
+
+ /**
+ * Directory where the last molecule list file of any
+ * MoleculePairDisplayerController was saved
+ */
+ private static File lastMoleculeListFileDirectory;
+
+ /**
+ * Directory where the last molecule image file of any
+ * MoleculePairDisplayerController was saved
+ */
+ private static File lastMoleculeImageFileDirectory;
+ //
+ //
+ //
+ /**
+ * True if the last move of the comparisonResultListIterator was forward,
+ * false otherwise
+ */
+ private boolean wasLastIteratorStepForward;
+
+ /**
+ * The ComparisonFeature which was used for the comparison of the molecule
+ * pairs
+ */
+ private ComparisonFeature comparisonFeature;
+
+ /**
+ * The ComparisonResult that is currently displayed
+ */
+ private ComparisonResult currentComparisonResult;
+
+ /**
+ * Formats numerical input to fit the given pattern
+ */
+ private final DecimalFormat formatter = new DecimalFormat("###.##");
+
+ /**
+ * The lower border of the bin from which the molecule pairs will be
+ * displayed
+ */
+ private final double lowerBorder;
+
+ /**
+ * The upper border of the bin from which the molecule pairs will be
+ * displayed
+ */
+ private final double upperBorder;
+
+ /**
+ * The frequency-value of the bin from which the molecule pairs will be
+ * displayed
+ */
+ private final double frequencyValue;
+
+ /**
+ * Depicts molecules contained in IAtomContainers as BufferedImages
+ */
+ private DepictionGenerator depictionGenerator;
+
+ /**
+ * FileChooser to choose a location where images and lists of molecules will
+ * be saved
+ */
+ private FileChooser fileChooser;
+
+ /**
+ * List of ComparisonResults which contain the molecule pairs
+ * that will be displayed
+ */
+ private final List comparisonResultList;
+
+ /**
+ * Iterator for iterating through the comparisonResultList
+ */
+ private ListIterator comparisonResultListIterator;
+
+ /**
+ * MoleculePairDisplayerStage that is being controlled
+ */
+ private MoleculePairDisplayerStage moleculePairDisplayerStage;
+
+ /**
+ * Object that takes a SMILES string as input and parses it to the
+ * corresponding IAtomContainer
+ */
+ private final SmilesParser smilesParser = new SmilesParser(SilentChemObjectBuilder.getInstance());
+ //
+ //
+ //
+ /**
+ * Initialize instance variables, add event handlers, set up and show the
+ * MoleculePairDisplayerStage
+ *
+ * @param tmpMoleculePairList list of ComparisonResults which contain
+ * molecule pairs
+ * @param tmpOwner specifies the owner window of the
+ * MoleculePairDisplayerStage
+ * @param tmpFileChooser a FileChooser to choose a file where the molecule
+ * pair list will be saved
+ * @param tmpBinNumber specifies the number of the bin from which the
+ * molecule pairs will be displayed
+ * @param tmpComparisonFeature the ComparisonFeature which was used for the
+ * comparison of the molecule pairs
+ * @param tmpFrequencyValue the frequency-value of the bin from which the
+ * molecule pairs will be displayed
+ * @param tmpLowerBorder the lower border of the bin from which the
+ * molecule pairs will be displayed
+ * @param tmpUpperBorder the upper border of the bin from which the
+ * molecule pairs will be displayed
+ * @throws IllegalArgumentException if the tmpMoleculePairList is empty or
+ * null
+ */
+ public MoleculePairDisplayerController(
+ List tmpMoleculePairList, Window tmpOwner,
+ FileChooser tmpFileChooser, int tmpBinNumber, ComparisonFeature tmpComparisonFeature, double tmpFrequencyValue,
+ double tmpLowerBorder, double tmpUpperBorder
+ ) throws IllegalArgumentException {
+ //
+ if (tmpMoleculePairList == null || tmpMoleculePairList.isEmpty()) {
+ throw new IllegalArgumentException("Invalid moleculePairList");
+ }
+ //
+ //
+ this.comparisonResultList = tmpMoleculePairList;
+ this.comparisonResultListIterator = this.comparisonResultList.listIterator();
+ this.currentComparisonResult = this.comparisonResultListIterator.next();
+ this.wasLastIteratorStepForward = true;
+ this.moleculePairDisplayerStage = new MoleculePairDisplayerStage();
+ this.moleculePairDisplayerStage.setTitle(String.format(GeneralUtilities.getUIText("MoleculePairDisplayerStage.title.text"), tmpBinNumber));
+ this.moleculePairDisplayerStage.initOwner(tmpOwner);
+ this.moleculePairDisplayerStage.initModality(Modality.APPLICATION_MODAL);
+ this.fileChooser = tmpFileChooser;
+ this.comparisonFeature = tmpComparisonFeature;
+ this.frequencyValue = tmpFrequencyValue;
+ this.lowerBorder = tmpLowerBorder;
+ this.upperBorder = tmpUpperBorder;
+ this.depictionGenerator = new DepictionGenerator().withAtomColors().withSize(200, 200).withFillToFit().withBackgroundColor(Color.WHITE).withMargin(10);
+ //
+ //
+ this.updateDisplay();
+ //
+ //
+ this.moleculePairDisplayerStage.getNextButton().setOnAction((ActionEvent) -> {
+ if (!this.wasLastIteratorStepForward) {
+ // Iterator has to move one step further because of change of direction
+ this.comparisonResultListIterator.next();
+ }
+ this.currentComparisonResult = this.comparisonResultListIterator.next();
+ this.wasLastIteratorStepForward = true;
+ this.updateDisplay();
+ });
+ this.moleculePairDisplayerStage.getLastButton().setOnAction((ActionEvent) -> {
+ boolean tmpHadNext = this.comparisonResultListIterator.hasNext();
+ while (this.comparisonResultListIterator.hasNext()) {
+ this.currentComparisonResult = this.comparisonResultListIterator.next();
+ }
+ if (tmpHadNext) {
+ this.wasLastIteratorStepForward = true;
+ } else {
+ return;
+ }
+ this.updateDisplay();
+ });
+ this.moleculePairDisplayerStage.getPreviousButton().setOnAction((ActionEvent) -> {
+ if (this.wasLastIteratorStepForward) {
+ // Iterator has to move one step further because of change of direction
+ this.comparisonResultListIterator.previous();
+ }
+ this.currentComparisonResult = this.comparisonResultListIterator.previous();
+ this.wasLastIteratorStepForward = false;
+ this.updateDisplay();
+ });
+ this.moleculePairDisplayerStage.getFirstButton().setOnAction((ActionEvent) -> {
+ boolean tmpHadPrevious = this.comparisonResultListIterator.hasPrevious();
+ while (this.comparisonResultListIterator.hasPrevious()) {
+ this.currentComparisonResult = this.comparisonResultListIterator.previous();
+ }
+ if (tmpHadPrevious) {
+ this.wasLastIteratorStepForward = false;
+ } else {
+ return;
+ }
+ this.updateDisplay();
+ });
+ this.moleculePairDisplayerStage.getPositionTextField().addEventFilter(KeyEvent.KEY_PRESSED, (KeyEvent tmpEvent) -> {
+ KeyCombination tmpKeyCombination = new KeyCodeCombination(KeyCode.ENTER);
+ if (tmpKeyCombination.match(tmpEvent)) {
+ int tmpDesiredIndex;
+ try {
+ tmpDesiredIndex = Integer.parseInt(this.moleculePairDisplayerStage.getPositionTextField().getText());
+ } catch (NumberFormatException ex) {
+ // This happens if the text field is empty or the input is too large
+ if (!this.moleculePairDisplayerStage.getPositionTextField().getText().isEmpty()) {
+ GeneralUtilities.showInfoDialog(this.moleculePairDisplayerStage, GeneralUtilities.getUIText("InfoDescription.NumberInputTooHigh.text"));
+ }
+ return;
+ }
+ int tmpCurrentIndex = this.wasLastIteratorStepForward ? this.comparisonResultListIterator.nextIndex() : this.comparisonResultListIterator.nextIndex() + 1;
+ if (tmpDesiredIndex < tmpCurrentIndex && this.comparisonResultListIterator.hasPrevious()) {
+ if (this.wasLastIteratorStepForward) {
+ // Iterator has to move one step further because of change of direction
+ this.comparisonResultListIterator.previous();
+ }
+ do {
+ this.currentComparisonResult = this.comparisonResultListIterator.previous();
+ tmpCurrentIndex--;
+ } while (tmpDesiredIndex != tmpCurrentIndex && this.comparisonResultListIterator.hasPrevious());
+ this.wasLastIteratorStepForward = false;
+ } else if (tmpDesiredIndex > tmpCurrentIndex && this.comparisonResultListIterator.hasNext()) {
+ if (!this.wasLastIteratorStepForward) {
+ // Iterator has to move one step further because of change of direction
+ this.comparisonResultListIterator.next();
+ }
+ do {
+ this.currentComparisonResult = this.comparisonResultListIterator.next();
+ tmpCurrentIndex++;
+ } while (tmpDesiredIndex != tmpCurrentIndex && this.comparisonResultListIterator.hasNext());
+ this.wasLastIteratorStepForward = true;
+ } else {
+ return;
+ }
+ this.updateDisplay();
+ }
+ });
+ this.moleculePairDisplayerStage.getSaveLeftListButton().setOnAction((ActionEvent) -> {
+ this.saveMoleculeList(true);
+ });
+ this.moleculePairDisplayerStage.getSaveRightListButton().setOnAction((ActionEvent) -> {
+ this.saveMoleculeList(false);
+ });
+ this.moleculePairDisplayerStage.getSaveLeftImageButton().setOnAction((ActionEvent) -> {
+ this.saveMoleculeImage(true);
+ });
+ this.moleculePairDisplayerStage.getSaveRightImageButton().setOnAction((ActionEvent) -> {
+ this.saveMoleculeImage(false);
+ });
+ for (int i = 0; i < this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls().length; i++) {
+ Control[] tmpControlArray = this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls()[i];
+ int tmpIndex = i;
+ ((CheckBox) tmpControlArray[0]).selectedProperty().addListener((ObservableValue tmpObservableValue, Boolean tmpOldValue, Boolean tmpNewValue) -> {
+ try {
+ if (tmpNewValue) {
+ boolean[] tmpCalculateFeature = new boolean[this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls().length];
+ Arrays.fill(tmpCalculateFeature, false);
+ tmpCalculateFeature[tmpIndex] = true;
+ double[][] tmpCalculations = ComparisonUtility.compareMoleculePair(
+ tmpCalculateFeature, this.currentComparisonResult.getMolecule1(), this.currentComparisonResult.getMolecule2()
+ );
+ // This can be NaN if there aren't two seperate values for each molecule
+ if (!Double.isNaN(tmpCalculations[tmpIndex][0])) {
+ if (tmpCalculations[tmpIndex][1] < 0) {
+ ((Labeled) tmpControlArray[1]).setText(
+ "| " + this.formatter.format(tmpCalculations[tmpIndex][0])
+ + " - (" + this.formatter.format(tmpCalculations[tmpIndex][1])
+ + ") | = " + this.formatter.format(tmpCalculations[tmpIndex][2])
+ );
+ } else {
+ ((Labeled) tmpControlArray[1]).setText(
+ "| " + this.formatter.format(tmpCalculations[tmpIndex][0])
+ + " - " + this.formatter.format(tmpCalculations[tmpIndex][1])
+ + " | = " + this.formatter.format(tmpCalculations[tmpIndex][2])
+ );
+ }
+ } else {
+ ((Labeled) tmpControlArray[1]).setText(this.formatter.format(tmpCalculations[tmpIndex][2]));
+ }
+ } else {
+ ((Labeled) tmpControlArray[1]).setText("");
+ }
+ } catch (CDKException CDKException) {
+ ((Labeled) tmpControlArray[1]).setText("");
+ }
+ });
+ }
+ //
+ //
+ this.moleculePairDisplayerStage.getScene().addEventFilter(KeyEvent.KEY_PRESSED, (KeyEvent tmpEvent) -> {
+ KeyCombination tmpKeyCombination = new KeyCodeCombination(KeyCode.LEFT);
+ if (!this.moleculePairDisplayerStage.getPreviousButton().isDisabled() && tmpKeyCombination.match(tmpEvent)) {
+ this.moleculePairDisplayerStage.getPreviousButton().fire();
+ tmpEvent.consume();
+ }
+ tmpKeyCombination = new KeyCodeCombination(KeyCode.RIGHT);
+ if (!this.moleculePairDisplayerStage.getNextButton().isDisabled() && tmpKeyCombination.match(tmpEvent)) {
+ this.moleculePairDisplayerStage.getNextButton().fire();
+ tmpEvent.consume();
+ }
+ });
+ //
+ //
+ this.moleculePairDisplayerStage.getPositionTextField().setTextFormatter(GeneralUtilities.getUnsignedIntegerTextFormatter());
+ //
+ //
+ this.moleculePairDisplayerStage.setMinWidth(MSCConstants.MINIMAL_MOLECULE_DISPLAYER_WIDTH);
+ this.moleculePairDisplayerStage.setWidth(
+ Double.isNaN(MoleculePairDisplayerController.stageWidth) ?
+ MSCConstants.MINIMAL_MOLECULE_DISPLAYER_WIDTH :
+ MoleculePairDisplayerController.stageWidth
+ );
+ this.moleculePairDisplayerStage.setMinHeight(MSCConstants.MINIMAL_MOLECULE_DISPLAYER_HEIGHT);
+ this.moleculePairDisplayerStage.setHeight(
+ Double.isNaN(MoleculePairDisplayerController.stageHeight) ?
+ MSCConstants.MINIMAL_MOLECULE_DISPLAYER_HEIGHT :
+ MoleculePairDisplayerController.stageHeight
+ );
+ if (!Double.isNaN(MoleculePairDisplayerController.stageXPosition)) {
+ this.moleculePairDisplayerStage.setX(MoleculePairDisplayerController.stageXPosition);
+ }
+ if (!Double.isNaN(MoleculePairDisplayerController.stageXPosition)) {
+ this.moleculePairDisplayerStage.setY(MoleculePairDisplayerController.stageYPosition);
+ }
+ this.moleculePairDisplayerStage.setMaximized(MoleculePairDisplayerController.isMaximized);
+ this.moleculePairDisplayerStage.showAndWait();
+ MoleculePairDisplayerController.stageWidth = this.moleculePairDisplayerStage.getWidth();
+ MoleculePairDisplayerController.stageHeight = this.moleculePairDisplayerStage.getHeight();
+ MoleculePairDisplayerController.stageXPosition = this.moleculePairDisplayerStage.getX();
+ MoleculePairDisplayerController.stageYPosition = this.moleculePairDisplayerStage.getY();
+ MoleculePairDisplayerController.isMaximized = this.moleculePairDisplayerStage.isMaximized();
+ //
+ }
+ //
+ //
+ //
+ /**
+ * Save one of the molecule images in a file that the user chooses.
+ *
+ * @param tmpSaveLeft if true the image of the left molecule will be saved,
+ * if false the image of the right molecule will be saved
+ */
+ private void saveMoleculeImage(boolean tmpSaveLeft) {
+ try {
+ this.fileChooser.getExtensionFilters().clear();
+ this.fileChooser.getExtensionFilters().addAll(
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.All.text"), "*.*"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.pdf.text"), "*.pdf"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.png.text"), "*.png"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.jpeg.text"), "*.jpeg"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.svg.text"), "*.svg")
+ );
+ if (!UserPreferences.getInstance().getImageDir().isEmpty() && new File(UserPreferences.getInstance().getImageDir()).isDirectory()) {
+ this.fileChooser.setInitialDirectory(new File(UserPreferences.getInstance().getImageDir()));
+ } else {
+ this.fileChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ synchronized (MoleculePairDisplayerController.class) {
+ if (MoleculePairDisplayerController.lastMoleculeImageFileDirectory != null && MoleculePairDisplayerController.lastMoleculeImageFileDirectory.isDirectory()) {
+ this.fileChooser.setInitialDirectory(MoleculePairDisplayerController.lastMoleculeImageFileDirectory);
+ }
+ }
+ this.fileChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.MoleculeList.text"));
+ final File tmpFile = this.fileChooser.showSaveDialog(this.moleculePairDisplayerStage);
+ if (tmpFile == null) {
+ return;
+ }
+ boolean tmpIsNewFile = tmpFile.createNewFile();
+ if (!tmpFile.canWrite()) {
+ if (tmpIsNewFile) {
+ Files.delete(tmpFile.toPath());
+ }
+ return;
+ }
+ synchronized (MoleculePairDisplayerController.class) {
+ MoleculePairDisplayerController.lastMoleculeImageFileDirectory = tmpFile.getParentFile();
+ }
+ BufferedImage tmpBufferedImage;
+ // IMPORTANT: Setting tmpSideLength too high will cause the program to throw an exception
+ double tmpSideLength = 9800 * UserPreferences.getInstance().getImageQuality() + 200;
+ DepictionGenerator tmpDepictionGenerator = new DepictionGenerator().withAtomColors().withSize(tmpSideLength, tmpSideLength).withFillToFit().withBackgroundColor(Color.WHITE).withMargin(tmpSideLength / 20);
+ if (tmpSaveLeft) {
+ tmpBufferedImage = tmpDepictionGenerator.depict(this.smilesParser.parseSmiles(this.currentComparisonResult.getMolecule1())).toImg();
+ } else {
+ tmpBufferedImage = tmpDepictionGenerator.depict(this.smilesParser.parseSmiles(this.currentComparisonResult.getMolecule2())).toImg();
+ }
+ final String tmpFormat = tmpFile.getAbsolutePath().substring(tmpFile.getAbsolutePath().lastIndexOf(".")).toLowerCase();
+ Task tmpTask = new Task() {
+ @Override
+ protected Void call() throws Exception {
+ try {
+ switch (tmpFormat) {
+ case ".png":
+ ImageIO.write(tmpBufferedImage, "PNG", tmpFile);
+ break;
+ case ".jpg":
+ case ".jpeg":
+ BufferedImage tmpImage = new BufferedImage(tmpBufferedImage.getWidth(), tmpBufferedImage.getHeight(), BufferedImage.TYPE_INT_RGB);
+ // Change the color model of the BufferedImage for the jpeg format
+ Graphics2D tmpGraphics2D = tmpImage.createGraphics();
+ tmpGraphics2D.drawImage(tmpBufferedImage, 0, 0, null);
+ tmpGraphics2D.dispose();
+ ImageIO.write(tmpImage, "JPG", tmpFile);
+ break;
+ case ".svg":
+ DOMImplementation domImpl = GenericDOMImplementation.getDOMImplementation();
+ Document document = domImpl.createDocument("http://www.w3.org/2000/svg", "svg", null);
+ SVGGraphics2D tmpSvgGenerator = new SVGGraphics2D(document);
+ tmpSvgGenerator.drawImage(tmpBufferedImage, AffineTransform.getScaleInstance(100 / tmpSideLength, 100 / tmpSideLength), null);
+ try (BufferedWriter tmpWriter = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(tmpFile)))) {
+ tmpSvgGenerator.stream(tmpWriter);
+ }
+ break;
+ case ".pdf":
+ try (PDDocument tmpDocument = new PDDocument()) {
+ PDPage tmpPage = new PDPage();
+ tmpDocument.addPage(tmpPage);
+ PDImageXObject tmpPDImage = LosslessFactory.createFromImage(tmpDocument, tmpBufferedImage);
+ try (PDPageContentStream tmpStream = new PDPageContentStream(tmpDocument, tmpPage)) {
+ float tmpWidth = tmpBufferedImage.getWidth();
+ float tmpHeight = tmpBufferedImage.getHeight();
+ tmpPage.setMediaBox(new PDRectangle(tmpWidth, tmpHeight));
+ tmpStream.drawImage(tmpPDImage, 0, 0, tmpWidth, tmpHeight);
+ }
+ tmpDocument.save(tmpFile);
+ }
+ break;
+ default:
+ Platform.runLater(() -> {
+ GeneralUtilities.showInfoDialog(MoleculePairDisplayerController.this.moleculePairDisplayerStage, GeneralUtilities.getUIText("InfoDescription.FileFormatNotSupported.text"));
+ });
+ }
+ } catch (IOException | DOMException ex) {
+ Platform.runLater(() -> {
+ MoleculePairDisplayerController.this.moleculePairDisplayerStage.getScene().setCursor(Cursor.DEFAULT);
+ GeneralUtilities.showErrorDialog(MoleculePairDisplayerController.this.moleculePairDisplayerStage, ex.toString(), "MoleculePairDisplayerController.saveMoleculeImage()");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ });
+ } finally {
+ Platform.runLater(() -> {
+ MoleculePairDisplayerController.this.moleculePairDisplayerStage.getScene().setCursor(Cursor.DEFAULT);
+ });
+ }
+ return null;
+ }
+ };
+ Thread tmpBackgroundThread = new Thread(tmpTask);
+ this.moleculePairDisplayerStage.getScene().setCursor(Cursor.WAIT);
+ tmpBackgroundThread.start();
+ } catch (StringIndexOutOfBoundsException ex) {
+ GeneralUtilities.showInfoDialog(this.moleculePairDisplayerStage, GeneralUtilities.getUIText("InfoDescription.FileFormatNotSupported.text"));
+ } catch (IOException | CDKException ex) {
+ GeneralUtilities.showErrorDialog(
+ this.moleculePairDisplayerStage, ex.toString(),
+ "MoleculePairDisplayerController.saveMoleculeImage()"
+ );
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ }
+
+ /**
+ * Save either the left or the right list of molecules in a file that the
+ * user chooses.
+ *
+ * @param tmpSaveLeft if true the left list of molecules will be saved,
+ * if false the right list of molecules will be saved
+ */
+ private void saveMoleculeList(boolean tmpSaveLeft) {
+ try {
+ this.fileChooser.getExtensionFilters().clear();
+ this.fileChooser.getExtensionFilters().addAll(
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.All.text"), "*.*"),
+ new FileChooser.ExtensionFilter(GeneralUtilities.getUIText("FileExtensionFilter.Text.text"), "*.txt")
+ );
+ if (!UserPreferences.getInstance().getMoleculeListDir().isEmpty() && new File(UserPreferences.getInstance().getMoleculeListDir()).isDirectory()) {
+ this.fileChooser.setInitialDirectory(new File(UserPreferences.getInstance().getMoleculeListDir()));
+ } else {
+ this.fileChooser.setInitialDirectory(new File(System.getProperty("user.dir")));
+ }
+ synchronized (MoleculePairDisplayerController.class) {
+ if (MoleculePairDisplayerController.lastMoleculeListFileDirectory != null && MoleculePairDisplayerController.lastMoleculeListFileDirectory.isDirectory()) {
+ this.fileChooser.setInitialDirectory(MoleculePairDisplayerController.lastMoleculeListFileDirectory);
+ }
+ }
+ this.fileChooser.setTitle(GeneralUtilities.getUIText("FileChooserTitle.MoleculeList.text"));
+ final File tmpFile = this.fileChooser.showSaveDialog(this.moleculePairDisplayerStage);
+ if (tmpFile == null) {
+ return;
+ }
+ boolean tmpIsNewFile = tmpFile.createNewFile();
+ if (!tmpFile.canWrite()) {
+ if (tmpIsNewFile) {
+ Files.delete(tmpFile.toPath());
+ }
+ return;
+ }
+ synchronized (MoleculePairDisplayerController.class) {
+ MoleculePairDisplayerController.lastMoleculeListFileDirectory = tmpFile.getParentFile();
+ }
+ Task tmpTask = new Task() {
+ @Override
+ protected Void call() throws Exception {
+ try (BufferedWriter tmpMoleculeWriter = new BufferedWriter(new FileWriter(tmpFile))) {
+ Iterator tmpIterator = MoleculePairDisplayerController.this.comparisonResultList.iterator();
+ while (tmpIterator.hasNext()) {
+ ComparisonResult tmpResult = tmpIterator.next();
+ tmpMoleculeWriter.write(tmpSaveLeft ? tmpResult.getMolecule1().strip() : tmpResult.getMolecule2().strip());
+ tmpMoleculeWriter.newLine();
+ }
+ } catch (IOException ex) {
+ Platform.runLater(() -> {
+ MoleculePairDisplayerController.this.moleculePairDisplayerStage.getScene().setCursor(Cursor.DEFAULT);
+ });
+ try {
+ Files.delete(tmpFile.toPath());
+ } catch (IOException tmpEx) {
+ }
+ Platform.runLater(() -> {
+ GeneralUtilities.showErrorDialog(
+ MoleculePairDisplayerController.this.moleculePairDisplayerStage, ex.toString(),
+ "MoleculePairDisplayerController.saveMoleculeList()"
+ );
+ GeneralUtilities.logException(Level.WARNING, ex);
+ });
+ } finally {
+ Platform.runLater(() -> {
+ MoleculePairDisplayerController.this.moleculePairDisplayerStage.getScene().setCursor(Cursor.DEFAULT);
+ });
+ }
+ return null;
+ }
+ };
+ Thread tmpBackgroundThread = new Thread(tmpTask);
+ this.moleculePairDisplayerStage.getScene().setCursor(Cursor.WAIT);
+ tmpBackgroundThread.start();
+ } catch (IOException ex) {
+ GeneralUtilities.showErrorDialog(
+ this.moleculePairDisplayerStage, ex.toString(),
+ "MoleculePairDisplayerController.saveMoleculeList()"
+ );
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ }
+
+ /**
+ * Update the MoleculePairDisplayerStage
+ */
+ private void updateDisplay() {
+ DecimalFormat tmpFormat = new DecimalFormat("#.####");
+ try {
+ BufferedImage tmpBufferedImage;
+ tmpBufferedImage = this.depictionGenerator.depict(this.smilesParser.parseSmiles(this.currentComparisonResult.getMolecule1())).toImg();
+ this.moleculePairDisplayerStage.getLeftMoleculeImageView().setImage(SwingFXUtils.toFXImage(tmpBufferedImage, null));
+ tmpBufferedImage = this.depictionGenerator.depict(this.smilesParser.parseSmiles(this.currentComparisonResult.getMolecule2())).toImg();
+ this.moleculePairDisplayerStage.getRightMoleculeImageView().setImage(SwingFXUtils.toFXImage(tmpBufferedImage, null));
+ this.moleculePairDisplayerStage.getInfoLabel().setText(String.format(
+ GeneralUtilities.getUIText("MoleculePairDisplayerStage.infoLabel.text"),
+ this.comparisonFeature, this.comparisonResultList.size(),
+ tmpFormat.format(this.frequencyValue),
+ tmpFormat.format(this.lowerBorder), tmpFormat.format(this.upperBorder),
+ this.currentComparisonResult.getMolecule1().strip(), this.currentComparisonResult.getMolecule2().strip(),
+ this.currentComparisonResult.getSimilarities()[this.comparisonFeature.getFeatureNumber()]
+ ));
+ this.moleculePairDisplayerStage.getPositionTextField().setText(Integer.toString(
+ this.wasLastIteratorStepForward ?
+ this.comparisonResultListIterator.nextIndex() :
+ this.comparisonResultListIterator.nextIndex() + 1)
+ );
+ } catch (CDKException ex) {
+ this.moleculePairDisplayerStage.getRightMoleculeImageView().setImage(GuiUtilities.WHITE_SQUARE);
+ this.moleculePairDisplayerStage.getLeftMoleculeImageView().setImage(GuiUtilities.WHITE_SQUARE);
+ this.moleculePairDisplayerStage.getInfoLabel().setText(String.format(
+ GeneralUtilities.getUIText("MoleculePairDisplayerStage.infoLabel.text"),
+ this.comparisonFeature, this.comparisonResultList.size(),
+ tmpFormat.format(this.frequencyValue),
+ tmpFormat.format(this.lowerBorder), tmpFormat.format(this.upperBorder),
+ "", "", ""
+ ));
+ this.moleculePairDisplayerStage.getPositionTextField().setText("");
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ try {
+ boolean[] tmpCalculateFeature = new boolean[this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls().length];
+ for (int i = 0; i < this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls().length; i++) {
+ tmpCalculateFeature[i] = ((CheckBox) this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls()[i][0]).isSelected();
+ }
+ double[][] tmpCalculations = ComparisonUtility.compareMoleculePair(
+ tmpCalculateFeature, this.currentComparisonResult.getMolecule1(), this.currentComparisonResult.getMolecule2()
+ );
+ for (int i = 0; i < this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls().length; i++) {
+ if (tmpCalculateFeature[i]) {
+ // This can be NaN if there aren't two seperate values for each molecule
+ if (!Double.isNaN(tmpCalculations[i][0])) {
+ if (tmpCalculations[i][1] < 0) {
+ ((Labeled) this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls()[i][1]).setText(
+ "| " + this.formatter.format(tmpCalculations[i][0]) +
+ " - (" + this.formatter.format(tmpCalculations[i][1]) +
+ ") | = " + this.formatter.format(tmpCalculations[i][2])
+ );
+ } else {
+ ((Labeled) this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls()[i][1]).setText(
+ "| " + this.formatter.format(tmpCalculations[i][0]) +
+ " - " + this.formatter.format(tmpCalculations[i][1]) +
+ " | = " + this.formatter.format(tmpCalculations[i][2])
+ );
+ }
+ } else {
+ ((Labeled) this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls()[i][1]).setText(this.formatter.format(tmpCalculations[i][2]));
+ }
+ } else {
+ ((Labeled) this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls()[i][1]).setText("");
+ }
+ }
+ } catch (CDKException ex) {
+ for (Control[] additionalComparisonFeatureControl : this.moleculePairDisplayerStage.getAdditionalComparisonFeatureControls()) {
+ ((Labeled) additionalComparisonFeatureControl[1]).setText("");
+ }
+ }
+ this.moleculePairDisplayerStage.getNextButton().setDisable(!this.comparisonResultListIterator.hasNext());
+ this.moleculePairDisplayerStage.getLastButton().setDisable(!this.comparisonResultListIterator.hasNext());
+ this.moleculePairDisplayerStage.getPreviousButton().setDisable(!this.comparisonResultListIterator.hasPrevious());
+ this.moleculePairDisplayerStage.getFirstButton().setDisable(!this.comparisonResultListIterator.hasPrevious());
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/control/UserPreferences.java b/src/main/java/de/whs/ibci/msc/control/UserPreferences.java
new file mode 100644
index 0000000..df80605
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/control/UserPreferences.java
@@ -0,0 +1,334 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.control;
+
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.utility.MSCConstants;
+import java.beans.XMLDecoder;
+import java.beans.XMLEncoder;
+import java.io.BufferedInputStream;
+import java.io.BufferedOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.logging.Level;
+
+/**
+ * Handles, loads and permanently saves preferences of the user.
+ *
+ * @author Jan-Mathis Hein
+ */
+public class UserPreferences {
+
+ //
+ /**
+ * Instance of this class. Other instances should not exist
+ */
+ private static UserPreferences instance;
+
+ /**
+ * File where the user preferences will be saved
+ */
+ private static final File USER_PREFERENCE_FILE = new File(MSCConstants.MSC_FILES_DIRECTORY.getAbsolutePath() + File.separator + "UserPreferences.xml");
+ //
+ //
+ //
+ static {
+ if (UserPreferences.USER_PREFERENCE_FILE.canRead()) {
+ try {
+ try (XMLDecoder tmpDecoder = new XMLDecoder(new BufferedInputStream(new FileInputStream(UserPreferences.USER_PREFERENCE_FILE)))) {
+ UserPreferences.instance = (UserPreferences) tmpDecoder.readObject();
+ }
+ } catch (Exception ex) {
+ GeneralUtilities.logMessage(Level.INFO, "", "", GeneralUtilities.getUIText("Logging.PreferencesLoadingNotPossible.text"));
+ GeneralUtilities.logException(Level.WARNING, ex);
+ // Sets default values
+ UserPreferences.instance = new UserPreferences();
+ }
+ } else {
+ // Sets default values
+ UserPreferences.instance = new UserPreferences();
+ }
+ }
+ //
+ //
+ //
+ /**
+ * The preference for the input directory
+ */
+ private String inputDir = "";
+
+ /**
+ * The preference for the output directory
+ */
+ private String outputDir = "";
+
+ /**
+ * The preference for the image directory
+ */
+ private String imageDir = "";
+
+ /**
+ * The preference for the molecule list directory
+ */
+ private String moleculeListDir = "";
+
+ /**
+ * The preference for the summary report directory
+ */
+ private String summaryReportDir = "";
+
+ /**
+ * The preference for the number of parallel threads
+ */
+ private int numberOfParallelThreads = 1;
+
+ /**
+ * The preference for the default number of bins
+ */
+ private int defaultNumberOfBins = 10;
+
+ /**
+ * The preference for the maximal number of molecule pairs to be saved when
+ * saving a job
+ */
+ private int maximalNumberOfMoleculePairsToSave = 1000;
+
+ /**
+ * The preference for the quality of images. 0.0 corresponds to a low
+ * quality and 1.0 to a high quality.
+ * NOTE: The value can't be higher than 1 or lower than 0
+ */
+ private double imageQuality = 0.5;
+ //
+ //
+ //
+ /**
+ * Public empty constructor that does nothing. Should only be invoked in
+ * this class and by the XMLDecoder
+ */
+ public UserPreferences() {
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Get an instance. Other instances should not exist
+ *
+ * @return an instance
+ */
+ public static UserPreferences getInstance() {
+ return UserPreferences.instance;
+ }
+
+ /**
+ * Get the preference for the input directory
+ *
+ * @return the preference for the input directory
+ */
+ public String getInputDir() {
+ return this.inputDir;
+ }
+
+ /**
+ * Get the preference for the output directory
+ *
+ * @return the preference for the output directory
+ */
+ public String getOutputDir() {
+ return this.outputDir;
+ }
+
+ /**
+ * Get the preference for the image directory
+ *
+ * @return the preference for the image directory
+ */
+ public String getImageDir() {
+ return this.imageDir;
+ }
+
+ /**
+ * Get the preference for the molecule list directory
+ *
+ * @return the preference for the molecule list directory
+ */
+ public String getMoleculeListDir() {
+ return this.moleculeListDir;
+ }
+
+ /**
+ * Get the preference for the summary report directory
+ *
+ * @return the preference for the summary report directory
+ */
+ public String getSummaryReportDir() {
+ return this.summaryReportDir;
+ }
+
+ /**
+ * Get the preference for the number of parallel threads
+ *
+ * @return the preference for the number of parallel threads
+ */
+ public int getNumberOfParallelThreads() {
+ return this.numberOfParallelThreads;
+ }
+
+ /**
+ * Get the preference for the default number of bins
+ *
+ * @return the preference for the default number of bins
+ */
+ public int getDefaultNumberOfBins() {
+ return this.defaultNumberOfBins;
+ }
+
+ /**
+ * Get the preference for the maximal number of molecule pairs to be saved
+ *
+ * @return the preference for the maximal number of molecule pairs to be
+ * saved
+ */
+ public int getMaximalNumberOfMoleculePairsToSave() {
+ return this.maximalNumberOfMoleculePairsToSave;
+ }
+
+ /**
+ * Get the preference for the quality of images. 0.0 corresponds to a low
+ * quality and 1.0 to a high quality
+ *
+ * @return a value between 0.0 and 1.0 that represents the
+ * imageQuality preference
+ */
+ public double getImageQuality() {
+ return this.imageQuality;
+ }
+ //
+ //
+ /**
+ * Set the preference for the input directory
+ *
+ * @param tmpInputDir the input directory
+ */
+ public void setInputDir(String tmpInputDir) {
+ this.inputDir = tmpInputDir;
+ }
+
+ /**
+ * Set the preference for the output directory
+ *
+ * @param tmpOutputDir the output directory
+ */
+ public void setOutputDir(String tmpOutputDir) {
+ this.outputDir = tmpOutputDir;
+ }
+
+ /**
+ * Set the preference for the image directory
+ *
+ * @param tmpImageDir the image directory
+ */
+ public void setImageDir(String tmpImageDir) {
+ this.imageDir = tmpImageDir;
+ }
+
+ /**
+ * Set the preference for the molecule list directory
+ *
+ * @param tmpMoleculeListDir the molecule list directory
+ */
+ public void setMoleculeListDir(String tmpMoleculeListDir) {
+ this.moleculeListDir = tmpMoleculeListDir;
+ }
+
+ /**
+ * Set the preference for the summary report directory
+ *
+ * @param tmpSummaryReportDir the summary report directory
+ */
+ public void setSummaryReportDir(String tmpSummaryReportDir) {
+ this.summaryReportDir = tmpSummaryReportDir;
+ }
+
+ /**
+ * Set the preference for the number of parallel threads
+ *
+ * @param tmpNumberOfParallelThreads the number of parallel threads
+ */
+ public void setNumberOfParallelThreads(int tmpNumberOfParallelThreads) {
+ this.numberOfParallelThreads = tmpNumberOfParallelThreads;
+ }
+
+ /**
+ * Set the preference for the dafault number of bins
+ *
+ * @param tmpDefaultNumberOfBins the deafult number of bins
+ */
+ public void setDefaultNumberOfBins(int tmpDefaultNumberOfBins) {
+ this.defaultNumberOfBins = tmpDefaultNumberOfBins;
+ }
+
+ /**
+ * Set the preference for the maximal number of molecule pairs to be saved
+ *
+ * @param tmpMaximalNumberOfMoleculePairsToSave the maximal number of
+ * molecule pairs to be saved
+ */
+ public void setMaximalNumberOfMoleculePairsToSave(int tmpMaximalNumberOfMoleculePairsToSave) {
+ this.maximalNumberOfMoleculePairsToSave = tmpMaximalNumberOfMoleculePairsToSave;
+ }
+
+ /**
+ * Set the preference for the quality of images. 0.0 corresponds to a low
+ * quality and 1.0 to a high quality. If the value is higher than 1.0 or
+ * lower than 0.0, 1.0 or 0.0 is used instead
+ *
+ * @param tmpImageQuality the new value for the imageQuality preference
+ */
+ public void setImageQuality(double tmpImageQuality) {
+ if (tmpImageQuality < 0.0) {
+ tmpImageQuality = 0.0;
+ } else if (tmpImageQuality > 1.0) {
+ tmpImageQuality = 1.0;
+ }
+ this.imageQuality = tmpImageQuality;
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Permanently save the preferences as an XML file
+ */
+ public static synchronized void savePreferences() {
+ try {
+ UserPreferences.USER_PREFERENCE_FILE.createNewFile();
+ try (XMLEncoder tmpEncoder = new XMLEncoder(new BufferedOutputStream(new FileOutputStream(UserPreferences.USER_PREFERENCE_FILE)))) {
+ tmpEncoder.writeObject(UserPreferences.getInstance());
+ }
+ } catch (IOException ex) {
+ GeneralUtilities.logMessage(Level.INFO, "", "", GeneralUtilities.getUIText("Logging.PreferencesSavingNotPossible.text"));
+ GeneralUtilities.logException(Level.WARNING, ex);
+ }
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/main/Main.java b/src/main/java/de/whs/ibci/msc/main/Main.java
new file mode 100644
index 0000000..a9d4dec
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/main/Main.java
@@ -0,0 +1,47 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.main;
+
+import de.whs.ibci.msc.control.ApplicationController;
+import java.util.Locale;
+import java.util.Properties;
+import javafx.application.Application;
+
+/**
+ * Main class of the application
+ *
+ * @author Jan-Mathis Hein
+ */
+public class Main {
+
+ //
+ /**
+ * Set the default locale and some properties and start the application
+ *
+ * @param args the command line arguments
+ */
+ public static void main(String[] args) {
+ Properties tmpProperties = new Properties(System.getProperties());
+ tmpProperties.setProperty("CdkUseLegacyAtomContainer", "f");
+ System.setProperties(tmpProperties);
+ Locale.setDefault(Locale.US);
+ Application.launch(ApplicationController.class, args);
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/model/ComparisonFeature.java b/src/main/java/de/whs/ibci/msc/model/ComparisonFeature.java
new file mode 100644
index 0000000..98e7b5d
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/model/ComparisonFeature.java
@@ -0,0 +1,244 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+/**
+ * Defines different features that can be used to compare molecules
+ *
+ * @author Jan-Mathis Hein
+ */
+public enum ComparisonFeature {
+
+ //
+ TANIMOTO_BASIC_FINGERPRINTER ("Basic fingerprint", true, 0.0, 1.0, "The Tanimoto coefficient with the basic CDK fingerprint"),
+ TANIMOTO_LINGO_FINGERPRINTER ("LINGO fingerprint", true, 0.0, 1.0, "The Tanimoto coefficient with the LINGO fingerprint"),
+ TANIMOTO_EXTENDED_FINGERPRINTER ("Extended fingerprint", true, 0.0, 1.0, "The Tanimoto coefficient with the extended CDK fingerprint"),
+ TANIMOTO_ESTATE_FINGERPRINTER ("E-State fingerprint", true, 0.0, 1.0, "The Tanimoto coefficient with the E-State fingerprint"),
+ TANIMOTO_PUBCHEM_FINGERPRINTER ("PubChem fingerprint", true, 0.0, 1.0, "The Tanimoto coefficient with the pubchem fingerprint"),
+ TANIMOTO_SHORTEST_PATH_FINGERPRINTER ("Shortest path fingerprint", true, 0.0, 1.0, "The Tanimoto coefficient with the shortest path fingerprint"),
+ TANIMOTO_SUBSTRUCTURE_FINGERPRINTER ("Substructure fingerprint", true, 0.0, 1.0, "The Tanimoto coefficient with default substructure fingerprint"),
+ ATOM_COUNT ("Atom count", false, 0.0, Double.NaN, "The difference of the counts of all atoms"),
+ CARBON_COUNT ("C count", false, 0.0, Double.NaN, "The difference of the counts of all carbon atoms"),
+ OXYGEN_COUNT ("O count", false, 0.0, Double.NaN, "The difference of the counts of all oyxgen atoms"),
+ SULFUR_COUNT ("S count", false, 0.0, Double.NaN, "The difference of the counts of all sulfur atoms"),
+ NITROGEN_COUNT ("N count", false, 0.0, Double.NaN, "The difference of the counts of all nitrogen atoms"),
+ PHOSPHOR_COUNT ("P count", false, 0.0, Double.NaN, "The difference of the counts of all phosphor atoms"),
+ MOLECULAR_WEIGHT ("Molecular weight", true, 0.0, Double.NaN, "The difference of molecular weights"),
+ MANNHOLD_LOGP ("Mannhold LogP", true, Double.NaN, Double.NaN, "The difference of Mannhold LogP values"),
+ APOL ("Atomic polarizability", true, Double.NaN, Double.NaN, "The difference of atomic polarizabilites"),
+ ACIDIC_GROUP_COUNT ("Acidic group count", false, 0.0, Double.NaN, "The difference of the acidic group counts"),
+ AROMATIC_ATOM_COUNT ("Aromatic atom count", false, 0.0, Double.NaN, "The difference of the counts of all aromatic atoms"),
+ BASIC_GROUP_COUNT ("Basic group count", false, 0.0, Double.NaN, "The difference of basic group counts"),
+ BOND_COUNT ("Bond count", false, 0.0, Double.NaN, "The difference of counts of all bonds"),
+ AROMATIC_BOND_COUNT ("Aromatic bond count", false, 0.0, Double.NaN, "The difference of counts of all aromatic bonds"),
+ SINGLE_BOND_COUNT ("Single bond count", false, 0.0, Double.NaN, "The difference of counts of all single bonds"),
+ DOUBLE_BOND_COUNT ("Double bond count", false, 0.0, Double.NaN, "The difference of counts of all double bonds"),
+ TRIPLE_BOND_COUNT ("Triple bond count", false, 0.0, Double.NaN, "The difference of counts of all triple bonds"),
+ QUADRUPLE_BOND_COUNT ("Quadruple bond count", false, 0.0, Double.NaN, "The difference of counts of all quadruple bonds"),
+ ALL_SMALL_RINGS_COUNT ("Small rings count", false, 0.0, Double.NaN, "The difference of the counts of all rings with a size of 9 or smaller"),
+ AROMATIC_RINGS_COUNT ("Aromatic rings count", false, 0.0, Double.NaN, "The difference of the counts of all aromatic rings with a size of 9 or smaller"),
+ SIZE_3_RINGS_COUNT ("Size 3 rings count", false, 0.0, Double.NaN, "The difference of the counts of all rings with size 3"),
+ SIZE_4_RINGS_COUNT ("Size 4 rings count", false, 0.0, Double.NaN, "The difference of the counts of all rings with size 4"),
+ SIZE_5_RINGS_COUNT ("Size 5 rings count", false, 0.0, Double.NaN, "The difference of the counts of all rings with size 5"),
+ SIZE_6_RINGS_COUNT ("Size 6 rings count", false, 0.0, Double.NaN, "The difference of the counts of all rings with size 6"),
+ SIZE_7_RINGS_COUNT ("Size 7 rings count", false, 0.0, Double.NaN, "The difference of the counts of all rings with size 7"),
+ SIZE_8_RINGS_COUNT ("Size 8 rings count", false, 0.0, Double.NaN, "The difference of the counts of all rings with size 8"),
+ SIZE_9_RINGS_COUNT ("Size 9 rings count", false, 0.0, Double.NaN, "The difference of the counts of all rings with size 9"),
+ ALL_RINGS_COUNT ("All rings count", false, 0.0, Double.NaN, "The difference of the counts of all rings (no size limitation"),
+ ATS_CHARGE1 ("ATS charge", true, Double.NaN, Double.NaN, "The difference of the autocorrelations of a topological structure, where the weights are equal to the charges"),
+ ATS_MASS1 ("ATS mass", true, Double.NaN, Double.NaN, "The difference of the autocorrelations of a topological structure, where the weights are equal to the masses"),
+ ATS_POLARIZABILITY1 ("ATS polarizability", true, Double.NaN, Double.NaN, "The difference of the autocorrelations of a topological structure, where the weights are equal to the polarizabilities"),
+ BPOL ("Bond polarizabilities", true, Double.NaN, Double.NaN, "The difference of the bond polarizabilites"),
+ C1SP1_COUNT ("C1SP1 count", false, 0.0, Double.NaN, "The difference of the counts of sp1 hybridized carbons bound to 1 other carbon"),
+ C2SP1_COUNT ("C2SP1 count", false, 0.0, Double.NaN, "The difference of the counts of sp1 hybridized carbons bound to 2 other carbons"),
+ C1SP2_COUNT ("C1SP2 count", false, 0.0, Double.NaN, "The difference of the counts of sp2 hybridized carbons bound to 1 other carbon"),
+ C2SP2_COUNT ("C2SP2 count", false, 0.0, Double.NaN, "The difference of the counts of sp2 hybridized carbons bound to 2 other carbons"),
+ C3SP2_COUNT ("C3SP2 count", false, 0.0, Double.NaN, "The difference of the counts of sp2 hybridized carbons bound to 3 other carbons"),
+ C1SP3_COUNT ("C1SP3 count", false, 0.0, Double.NaN, "The difference of the counts of sp3 hybridized carbons bound to 1 other carbon"),
+ C2SP3_COUNT ("C2SP3 count", false, 0.0, Double.NaN, "The difference of the counts of sp3 hybridized carbons bound to 2 other carbons"),
+ C3SP3_COUNT ("C3SP3 count", false, 0.0, Double.NaN, "The difference of the counts of sp3 hybridized carbons bound to 3 other carbons"),
+ C4SP3_COUNT ("C4SP3 count", false, 0.0, Double.NaN, "The difference of the counts of sp3 hybridized carbons bound to 4 other carbons"),
+ ECCENTRIC_CONNECTIVITY_INDEX ("Eccentric connectivity", false, Double.NaN, Double.NaN, "The difference of the eccentric conectivity indices"),
+ FMF ("Fraction of MF", true, 0.0, 1.0, "The difference of the fractions of the number of heavy atoms in the molecular framework to the total number of heavy atoms"),
+ FCSP3 ("Fraction of SP3 carbons", true, 0.0, 1.0, "The difference of the fractions of the number of sp3 hybridized carbons to the total number of carbons"),
+ FPSA ("Fractional PSA", true, 0.0, 1.0, "The difference of the polar surface areas expressed as a ratio to the molecular size"),
+ FRAGMENT_COMPLEXITY ("Fragment complexity", true, Double.NaN, Double.NaN, "The difference of the values of the FragmentComplexityDescriptor of the CDK"),
+ H_BOND_ACCEPTOR_COUNT ("H-bond acceptor count", false, 0.0, Double.NaN, "The difference of the counts of H-bond acceptors"),
+ H_BOND_DONOR_COUNT ("H-bond donor count", false, 0.0, Double.NaN, "The difference of the counts of H-bond donors"),
+ JP_LOGP ("JPLogP", true, Double.NaN, Double.NaN, "The difference of the JPLogP values"),
+ KAPPA_SHAPE_INDEX_1 ("1. kappa shape index", true, Double.NaN, Double.NaN, "The difference of the first kappa shape indices"),
+ KAPPA_SHAPE_INDEX_2 ("2. kappa shape index", true, Double.NaN, Double.NaN, "The difference of the second kappa shape indices"),
+ KAPPA_SHAPE_INDEX_3 ("3. kappa shape index", true, Double.NaN, Double.NaN, "The difference of the third kappa shape indices"),
+ LARGEST_CHAIN ("Largest chain", false, 0.0, Double.NaN, "The difference of the lengths of the longest chains"),
+ LARGEST_PI_SYSTEM ("Largest pi system", false, 0.0, Double.NaN, "The difference of the sizes of the largest pi-systems"),
+ LONGEST_ALIPHATIC_CHAIN ("Longest aliphatic chain", false, 0.0, Double.NaN, "The difference of the lengths of the longest aliphatic chains"),
+ PETITJEAN_NUMBER ("Petitjean number", true, Double.NaN, Double.NaN, "The difference of the Petitjean numbers"),
+ PETITJEAN_SHAPE_INDEX ("Petitjean shape index", true, Double.NaN, Double.NaN, "The difference of the topological Petitjean shape indices"),
+ ROTATABLE_BOND_COUNT ("Rotatable bond count", false, 0.0, Double.NaN, "The difference of the counts of rotatable bonds"),
+ SPIRO_ATOM_COUNT ("Spiro atom count", false, 0.0, Double.NaN, "The difference of the coutns of spiro-atoms"),
+ TPSA ("Topolgical PSA", true, 0.0, Double.NaN, "The difference of the topological polar surface areas"),
+ VABC ("VdW volume (using VABC)", true, 0.0, Double.NaN, "The difference of the Van der Waals volumes calculated using VABC method"),
+ V_ADJ_MA ("Vertex adjacency", true, Double.NaN, Double.NaN, "The difference of the vertex adjacency numbers"),
+ WEIGHTED_PATH_1 ("Weighted path descriptor", true, Double.NaN, Double.NaN, "The difference of the values of the weighted path descriptor which characterizes molecular branching"),
+ WIENER_PATH ("Wiener path number", true, Double.NaN, Double.NaN, "The difference of the Wiener path numbers"),
+ WIENER_POLARITY ("Wiener polarity number", true, Double.NaN, Double.NaN, "The difference of the Wiener polarity numbers"),
+ X_LOGP ("XLogP", true, Double.NaN, Double.NaN, "The difference of the XLogP values"),
+ ZAGREB_INDEX ("Zagreb index", false, Double.NaN, Double.NaN, "The difference of the Zagreb indices"),
+ A_LOGP ("Ghose-Crippen LogP", true, Double.NaN, Double.NaN, "The difference of the ALogP values (Ghose-Crippen LogKow)"),
+ A_LOGP_2 ("Ghose-Crippen LogP 2", true, Double.NaN, Double.NaN, "The difference of the ALogP2 values (Ghose-Crippen LogKow)"),
+ MOLAR_REFRACTIVITY ("Molar refractivity", true, Double.NaN, Double.NaN, "The difference of the molar refractivities"),
+ EQUALITY ("Equality", false, 0.0, 1.0, "Returns 1 if the unique SMILES are the same, else returns 0");
+ //
+ //
+ //
+ /**
+ * If true this ComparisonFeature has continuous values, if false it has
+ * discrete values
+ */
+ private final boolean isContinuous;
+
+ /**
+ * The minimal value this ComparisonFeature can take on or NaN if no such
+ * value is defined
+ */
+ private final double minimalValue;
+
+ /**
+ * The maximal value this ComparisonFeature can take on or NaN if no such
+ * value is defined
+ */
+ private final double maximalValue;
+
+ /**
+ * A number that uniquely corresponds to a ComparisonFeature
+ */
+ private final int featureNumber;
+
+ /**
+ * The value for the featureNumber of the next ComparisonFeature
+ */
+ private static int nextFeatureNumber = 0;
+
+ /**
+ * A more userfriendly name for the ComparisonFeature
+ */
+ private final String name;
+
+ /**
+ * A detailed description for the ComparisonFeature
+ */
+ private final String detailedDescription;
+ //
+ //
+ //
+ /**
+ * Initialize the instance variables
+ *
+ * @param tmpName specifies a more userfriendly name for the
+ * ComparisonFeature
+ * @param tmpIsContinuous if true this ComparisonFeature has continuous
+ * values, if false it has discrete values
+ * @param tmpMinValue the minimal value this ComparisonFeature can take on
+ * or NaN if no such value is defined
+ * @param tmpMaxValue the minimal value this ComparisonFeature can take on
+ * or NaN if no such value is defined
+ * @param tmpDescription a detailed description for the ComparisonFeature
+ */
+ private ComparisonFeature(String tmpName, boolean tmpIsContinuous, double tmpMinValue, double tmpMaxValue, String tmpDescription) {
+ this.featureNumber = ComparisonFeature.getNextFeatureNumber();
+ this.isContinuous = tmpIsContinuous;
+ this.name = tmpName;
+ this.minimalValue = tmpMinValue;
+ this.maximalValue = tmpMaxValue;
+ this.detailedDescription = tmpDescription;
+ }
+ //
+ //
+ //
+ /**
+ * If true this ComparisonFeature has continuous values, if false it has
+ * discrete values
+ *
+ * @return true if this ComparisonFeature has continuous values,
+ * false if it has discrete values
+ */
+ public boolean isContinuous() {
+ return this.isContinuous;
+ }
+
+ /**
+ * Get the minimal value this ComparisonFeature can take on or NaN if no
+ * such value is defined
+ *
+ * @return the minimal value this ComparisonFeature can take on or NaN if no
+ * such value is defined
+ */
+ public double getMinimalValue() {
+ return this.minimalValue;
+ }
+
+ /**
+ * Get the maximal value this ComparisonFeature can take on or NaN if no
+ * such value is defined
+ *
+ * @return the maximal value this ComparisonFeature can take on or NaN if no
+ * such value is defined
+ */
+ public double getMaximalValue() {
+ return this.maximalValue;
+ }
+
+ /**
+ * Get the feature number corresponding to the ComparisonFeature
+ *
+ * @return the feature number
+ */
+ public int getFeatureNumber() {
+ return this.featureNumber;
+ }
+
+ /**
+ * Get the value for the next featureNumber an increment nextFeatureNumber
+ * by one
+ *
+ * @return the value for the next featureNumber
+ */
+ private static int getNextFeatureNumber() {
+ return ComparisonFeature.nextFeatureNumber++;
+ }
+
+ /**
+ * Get a detailed description for the ComparisonFeature
+ *
+ * @return a detailed description for the ComparisonFeature
+ */
+ public String getDetailedDescription() {
+ return this.detailedDescription;
+ }
+
+ /**
+ * Return a string representation of the ComparisonFeature
+ *
+ * @return a string representation of the ComparisonFeature
+ */
+ @Override
+ public String toString() {
+ return this.name;
+ }
+ //
+}
diff --git a/src/main/java/de/whs/ibci/msc/model/ComparisonResult.java b/src/main/java/de/whs/ibci/msc/model/ComparisonResult.java
new file mode 100644
index 0000000..4560144
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/model/ComparisonResult.java
@@ -0,0 +1,169 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+/**
+ * Represents the result of a molecule pair comparison. Also stores the two
+ * compared molecules as SMILES.
+ *
+ * @author Jan-Mathis Hein
+ */
+public class ComparisonResult {
+
+ //
+ /**
+ * Array with the different comparison results. The index corresponds to the
+ * number of the ComparisonFeature. If the computation of a comparison
+ * failed, Double.NaN is put instead
+ */
+ private final double[] similarities;
+
+ /**
+ * SMILES encoding of the first compared molecule
+ */
+ private String molecule1;
+
+ /**
+ * SMILES encoding of the second compared molecule
+ */
+ private String molecule2;
+
+ /**
+ * Unique identifier for this object
+ */
+ private final int identifier;
+
+ /**
+ * Reason why the comparison may have failed
+ */
+ private final String reasonOfFailure;
+ //
+ //
+ //
+ /**
+ * Initialize the instance variables
+ *
+ * @param tmpSimilarities the comparsion results in array form
+ * @param tmpMolecule1 SMILES encoding of the first compared molecule,
+ * should never be null
+ * @param tmpMolecule2 SMILES encoding of the second compared molecule,
+ * should never be null
+ * @param tmpIdentifier specifies an unique identifier for this object
+ */
+ public ComparisonResult(double[] tmpSimilarities, String tmpMolecule1, String tmpMolecule2, int tmpIdentifier) {
+ this.similarities = tmpSimilarities;
+ this.molecule1 = tmpMolecule1;
+ this.molecule2 = tmpMolecule2;
+ this.identifier = tmpIdentifier;
+ this.reasonOfFailure = "";
+ }
+
+ /**
+ * Initialize the instance variables
+ *
+ * @param tmpString reason why the comparison failed
+ * @param tmpIdentifier specifies an unique identifier for this object
+ */
+ public ComparisonResult(String tmpString, int tmpIdentifier) {
+ this.similarities = null;
+ this.molecule1 = "";
+ this.molecule2 = "";
+ this.reasonOfFailure = tmpString;
+ this.identifier = tmpIdentifier;
+ }
+ //
+ //
+ //
+ /**
+ * Get the comparison results. The index corresponds to the number of the
+ * ComparisonFeature. If the computation of a comparison failed, Double.NaN
+ * is put instead
+ *
+ * @return the comparison results
+ */
+ public double[] getSimilarities() {
+ return this.similarities;
+ }
+
+ /**
+ * Get the SMILES encoding of the first compared molecule
+ *
+ * @return the first molecule
+ */
+ public String getMolecule1() {
+ return this.molecule1;
+ }
+
+ /**
+ * Get the SMILES encoding of the second compared molecule
+ *
+ * @return the second molecule
+ */
+ public String getMolecule2() {
+ return this.molecule2;
+ }
+
+ /**
+ * Get the unique identifier of this object
+ *
+ * @return the unique identifier of this object
+ */
+ public int getIdentifier() {
+ return this.identifier;
+ }
+
+ /**
+ * Get the reason why the comparison failed
+ *
+ * @return the reason why the comparison failed
+ */
+ public String getReasonOfFailure() {
+ return this.reasonOfFailure;
+ }
+
+ /**
+ * True if for both molecules a SMILES encoding is available,
+ * false otherwise
+ *
+ * @return true if for both molecules a SMILES encoding is available,
+ * false otherwise
+ */
+ public boolean hasMoleculePair() {
+ return !this.molecule1.isBlank()&& !this.molecule2.isBlank();
+ }
+
+ /**
+ * Set the first molecule
+ *
+ * @param tmpMolecule specifies the molecule to set
+ */
+ public void setMolecule1(String tmpMolecule) {
+ this.molecule1 = tmpMolecule;
+ }
+
+ /**
+ * Set the second molecule
+ *
+ * @param tmpMolecule specifies the molecule to set
+ */
+ public void setMolecule2(String tmpMolecule) {
+ this.molecule2 = tmpMolecule;
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/model/ComparisonUtility.java b/src/main/java/de/whs/ibci/msc/model/ComparisonUtility.java
new file mode 100644
index 0000000..7a7f72c
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/model/ComparisonUtility.java
@@ -0,0 +1,938 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.aromaticity.Aromaticity;
+import org.openscience.cdk.aromaticity.ElectronDonation;
+import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.fingerprint.*;
+import org.openscience.cdk.graph.Cycles;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IAtomType;
+import org.openscience.cdk.qsar.IMolecularDescriptor;
+import org.openscience.cdk.qsar.descriptors.molecular.*;
+import org.openscience.cdk.ringsearch.AllRingsFinder;
+import org.openscience.cdk.ringsearch.RingSearch;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
+import org.openscience.cdk.similarity.Tanimoto;
+import org.openscience.cdk.smiles.SmiFlavor;
+import org.openscience.cdk.smiles.SmilesGenerator;
+import org.openscience.cdk.smiles.SmilesParser;
+import org.openscience.cdk.tools.CDKHydrogenAdder;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
+import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
+
+/**
+ * This abstract class provides utility methods for the comparison of
+ * molecule pairs
+ *
+ * @author Jan-Mathis Hein
+ */
+public abstract class ComparisonUtility {
+
+ //
+ /**
+ * A molecular descriptor that calculates the number of acidic groups
+ */
+ private static final AcidicGroupCountDescriptor ACIDIC_GROUP_COUNT_DESCRIPTOR = new AcidicGroupCountDescriptor();
+
+ /**
+ * Calculates the total number of rings in a molecule
+ */
+ private static final AllRingsFinder ALL_RINGS_FINDER = new AllRingsFinder();
+
+ /**
+ * A molecular descriptor that calculates the number of aromatic atoms
+ */
+ private static final AromaticAtomsCountDescriptor AROMATIC_ATOMS_COUNTS_DESCRIPTOR = new AromaticAtomsCountDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the number of aromatic bonds
+ */
+ private static final AromaticBondsCountDescriptor AROMATIC_BONDS_COUNT_DESCRIPTOR = new AromaticBondsCountDescriptor();
+
+ /**
+ * Used to set the aromaticity flags of atoms in molecules
+ */
+ private static final Aromaticity AROMATICITY = new Aromaticity(ElectronDonation.cdk(), Cycles.or(Cycles.all(), Cycles.cdkAromaticSet()));
+
+ /**
+ * A molecular descriptor that calculates the number of atoms
+ */
+ private static final AtomCountDescriptor ATOM_COUNT_DESCRIPTOR = new AtomCountDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the atomic polarizability
+ */
+ private static final APolDescriptor A_POL_DESCRIPTOR = new APolDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the autocorrelation of a
+ * topological structure, where the weight is equal to the charges.
+ */
+ private static final AutocorrelationDescriptorCharge AUTOCORRELATION_DESCRIPTOR_CHARGE = new AutocorrelationDescriptorCharge();
+
+ /**
+ * A molecular descriptor that calculates the autocorrelation of a
+ * topological structure, where the weight is equal to the mass.
+ */
+ private static final AutocorrelationDescriptorMass AUTOCORRELATION_DESCRIPTOR_MASS = new AutocorrelationDescriptorMass();
+
+ /**
+ * A molecular descriptor that calculates the autocorrelation of a
+ * topological structure, where the weight is equal to the polarizability.
+ */
+ private static final AutocorrelationDescriptorPolarizability AUTOCORRELATION_DESCRIPTOR_POLARIZABILITY = new AutocorrelationDescriptorPolarizability();
+
+ /**
+ * A molecular descriptor that calculates the number of basic groups
+ */
+ private static final BasicGroupCountDescriptor BASCIS_GROUP_COUNT_DESCRIPTOR = new BasicGroupCountDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the number of bonds
+ */
+ private static final BondCountDescriptor BOND_COUNT_DESCRIPTOR = new BondCountDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the bond polarizability
+ */
+ private static final BPolDescriptor B_POL_DESCRIPTOR = new BPolDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the number of different carbon
+ * types
+ */
+ private static final CarbonTypesDescriptor CARBON_TYPES_DESCRIPTOR = new CarbonTypesDescriptor();
+
+ /**
+ * Matches atom types to atoms
+ */
+ private static final CDKAtomTypeMatcher CDK_ATOM_TYPE_MATCHER = CDKAtomTypeMatcher.getInstance(DefaultChemObjectBuilder.getInstance());
+
+ /**
+ * Adds implicit hydrogens to a molecule
+ */
+ private static final CDKHydrogenAdder CDK_HYDROGEN_ADDER = CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance());
+
+ /**
+ * A molecular descriptor that calculates the eccentric connectivity
+ */
+ private static final EccentricConnectivityIndexDescriptor ECCENTRIC_CONNECTIVITY_DESCRIPTOR = new EccentricConnectivityIndexDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the fraction of the molecular
+ * framework
+ */
+ private static final FMFDescriptor FMF_DESCRIPTOR = new FMFDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the fraction of CSP3 atoms
+ */
+ private static final FractionalCSP3Descriptor FRACTIONAL_CSP3_DESCRIPTOR = new FractionalCSP3Descriptor();
+
+ /**
+ * A molecular descriptor that calculates the fraction of the PSA
+ */
+ private static final FractionalPSADescriptor FRACTIONAL_PSA_DESCRIPTOR = new FractionalPSADescriptor();
+
+ /**
+ * A molecular descriptor that calculates the fragment complexity
+ */
+ private static final FragmentComplexityDescriptor FRAGMENT_COMPLEXITY_DESCRIPTOR = new FragmentComplexityDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the number of H-bond acceptors
+ */
+ private static final HBondAcceptorCountDescriptor HBOND_ACCEPTOR_COUNT_DESCRIPTOR = new HBondAcceptorCountDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the number of H-bond donors
+ */
+ private static final HBondDonorCountDescriptor HBOND_DONOR_COUNT_DESCRIPTOR = new HBondDonorCountDescriptor();
+
+ /**
+ * Generates a basic fingerprint for a molecule
+ */
+ private static final IFingerprinter BASIC_FINGERPRINTER = new Fingerprinter();
+
+ /**
+ * Generates a LINGO fingerprint for a molecule
+ */
+ private static final IFingerprinter LINGO_FINGERPRINTER = new LingoFingerprinter();
+
+ /**
+ * Generates an extended fingerprint for a molecule
+ */
+ private static final IFingerprinter EXTENDED_FINGERPRINTER = new ExtendedFingerprinter();
+
+ /**
+ * Generates a E-State fingerprint for a molecule
+ */
+ private static final IFingerprinter ESTATE_FINGERPRINTER = new EStateFingerprinter();
+
+ /**
+ * Generates a PubChem fingerprint for a molecule
+ */
+ private static final IFingerprinter PUBCHEM_FINGERPRINTER = new PubchemFingerprinter(DefaultChemObjectBuilder.getInstance());
+
+ /**
+ * Generates a shortest path fingerprint for a molecule
+ */
+ private static final IFingerprinter SHORTEST_PATH_FINGERPRINTER = new ShortestPathFingerprinter();
+
+ /**
+ * Generates a fingerprint for a molecule based on a given substructure set
+ */
+ private static final IFingerprinter SUBSTRUCTURE_FINGERPRINTER = new SubstructureFingerprinter();
+
+ /**
+ * A molecular descriptor that calculates the JP-logP value
+ */
+ private static final JPlogPDescriptor JP_LOGP_DESCRIPTOR = new JPlogPDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the kappa shape indices
+ */
+ private static final KappaShapeIndicesDescriptor KAPPA_SHAPE_INDICES_DESCRIPTOR = new KappaShapeIndicesDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the length of the largest chain
+ */
+ private static final LargestChainDescriptor LARGEST_CHAIN_DESCRIPTOR = new LargestChainDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the size of the largest pi system
+ */
+ private static final LargestPiSystemDescriptor LARGEST_PI_SYSTEM_DESCRIPTOR = new LargestPiSystemDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the lenght of the longest
+ * aliphatic chain
+ */
+ private static final LongestAliphaticChainDescriptor LONGEST_ALIPHATIC_CHAIN_DESCRIPTOR = new LongestAliphaticChainDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the Mannhold-logP value
+ */
+ private static final MannholdLogPDescriptor MANNHOLD_LOG_P_DESCRIPTOR = new MannholdLogPDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the Petitjean number
+ */
+ private static final PetitjeanNumberDescriptor PETITJEAN_NUMBER_DESCRIPTOR = new PetitjeanNumberDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the Petitjean shape index
+ */
+ private static final PetitjeanShapeIndexDescriptor PETITJEAN_SHAPE_INDEX_DESCRIPTOR = new PetitjeanShapeIndexDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the number of rotatable bonds
+ */
+ private static final RotatableBondsCountDescriptor ROTATABLE_BOND_COUNT = new RotatableBondsCountDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the number of small rings
+ */
+ private static final SmallRingDescriptor SMALL_RING_DESCRIPTOR = new SmallRingDescriptor();
+
+ /**
+ * Generates unique and canoncical SMILES
+ */
+ private static final SmilesGenerator SMILES_GENERATOR = new SmilesGenerator(SmiFlavor.Unique);
+
+ /**
+ * Parses SMILES to IAtomContainers
+ */
+ private static final SmilesParser SMILES_PARSER = new SmilesParser(SilentChemObjectBuilder.getInstance());
+
+ /**
+ * A molecular descriptor that calculates the number of spiro atoms
+ */
+ private static final SpiroAtomCountDescriptor SPIRO_ATOM_COUNT_DESCRIPTOR = new SpiroAtomCountDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the TPSA
+ */
+ private static final TPSADescriptor TPSA_DESCRIPTOR = new TPSADescriptor();
+
+ /**
+ * A molecular descriptor that calculates the VdW volume
+ */
+ private static final VABCDescriptor VABC_DESCRIPTOR = new VABCDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the vertex adjacency
+ */
+ private static final VAdjMaDescriptor V_ADJ_MA_DESCRIPTOR = new VAdjMaDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the molecular weight
+ */
+ private static final WeightDescriptor WEIGHT_DESCRIPTOR = new WeightDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the weighted path
+ */
+ private static final WeightedPathDescriptor WEIGHTER_PATH_DESCRIPTOR = new WeightedPathDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the Wiener numbers
+ */
+ private static final WienerNumbersDescriptor WIENER_NUMBERS_DESCRIPTOR = new WienerNumbersDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the X-logP value
+ */
+ private static final XLogPDescriptor X_LOGP_DESCRIPTOR = new XLogPDescriptor();
+
+ /**
+ * A molecular descriptor that calculates the Zagreb index
+ */
+ private static final ZagrebIndexDescriptor ZAGREB_INDEY_DESCRIPTOR = new ZagrebIndexDescriptor();
+ //
+ //
+ //
+ static {
+ ComparisonUtility.ACIDIC_GROUP_COUNT_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ AllRingsFinder.usingThreshold(AllRingsFinder.Threshold.PubChem_99);
+ ComparisonUtility.A_POL_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.AROMATIC_ATOMS_COUNTS_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.AROMATIC_BONDS_COUNT_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.AUTOCORRELATION_DESCRIPTOR_CHARGE.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.AUTOCORRELATION_DESCRIPTOR_MASS.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.AUTOCORRELATION_DESCRIPTOR_POLARIZABILITY.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.BASCIS_GROUP_COUNT_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.B_POL_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.CARBON_TYPES_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.ECCENTRIC_CONNECTIVITY_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.FMF_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.FRACTIONAL_CSP3_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.FRAGMENT_COMPLEXITY_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.HBOND_ACCEPTOR_COUNT_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.HBOND_DONOR_COUNT_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.JP_LOGP_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.KAPPA_SHAPE_INDICES_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.LARGEST_CHAIN_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.LARGEST_PI_SYSTEM_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.LONGEST_ALIPHATIC_CHAIN_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.MANNHOLD_LOG_P_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.PETITJEAN_NUMBER_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.PETITJEAN_SHAPE_INDEX_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.ROTATABLE_BOND_COUNT.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.SMALL_RING_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.SPIRO_ATOM_COUNT_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.TPSA_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.VABC_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.V_ADJ_MA_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.WEIGHT_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.WEIGHTER_PATH_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.WIENER_NUMBERS_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.X_LOGP_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ ComparisonUtility.ZAGREB_INDEY_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ }
+ //
+ //
+ //
+ /**
+ * Compare the given molecule based on the specified ComparisonFeatures and
+ * return an array containing the individual values
+ * (if available, else return NaN) and the resulting similarity for every
+ * ComparisonFeature
+ *
+ * @param tmpCalculateFeature specifies the ComparisonFeatures which will be
+ * calculated
+ * @param tmpSmiles1 the first molecule in SMILES form
+ * @param tmpSmiles2 the second molecule in SMILES form
+ * @return an array where each element is an array of the form
+ * {firstComparisonFeatureValue, secondComparisonFeatureValue,
+ * resultingSimilarity}. The index of the element corresponds to the
+ * featureNumber of the corresponding ComparisonFeature. If there are no
+ * individual values available for the molecules, NaN is returned instead.
+ * @throws org.openscience.cdk.exception.CDKException if there is something
+ * wrong with the molecules
+ */
+ public static synchronized double[][] compareMoleculePair(boolean[] tmpCalculateFeature, String tmpSmiles1, String tmpSmiles2) throws CDKException {
+ double[][] tmpResult = new double[tmpCalculateFeature.length][3];
+ //
+ IAtomContainer tmpMolecule1 = ComparisonUtility.SMILES_PARSER.parseSmiles(tmpSmiles1);
+ IAtomContainer tmpMolecule2 = ComparisonUtility.SMILES_PARSER.parseSmiles(tmpSmiles2);
+ RingSearch tmpRingSearch = new RingSearch(tmpMolecule1);
+ for (IAtom tmpAtom : tmpMolecule1.atoms()) {
+ tmpAtom.setIsInRing(tmpRingSearch.cyclic(tmpAtom));
+ IAtomType tmpType = ComparisonUtility.CDK_ATOM_TYPE_MATCHER.findMatchingAtomType(tmpMolecule1, tmpAtom);
+ AtomTypeManipulator.configure(tmpAtom, tmpType);
+ }
+ ComparisonUtility.CDK_HYDROGEN_ADDER.addImplicitHydrogens(tmpMolecule1);
+ AtomContainerManipulator.convertImplicitToExplicitHydrogens(tmpMolecule1);
+ // Set aromaticity flags
+ ComparisonUtility.AROMATICITY.apply(tmpMolecule1);
+ tmpRingSearch = new RingSearch(tmpMolecule2);
+ for (IAtom tmpAtom : tmpMolecule2.atoms()) {
+ tmpAtom.setIsInRing(tmpRingSearch.cyclic(tmpAtom));
+ IAtomType tmpType = ComparisonUtility.CDK_ATOM_TYPE_MATCHER.findMatchingAtomType(tmpMolecule2, tmpAtom);
+ AtomTypeManipulator.configure(tmpAtom, tmpType);
+ }
+ ComparisonUtility.CDK_HYDROGEN_ADDER.addImplicitHydrogens(tmpMolecule2);
+ AtomContainerManipulator.convertImplicitToExplicitHydrogens(tmpMolecule2);
+ // Set aromaticity flags
+ ComparisonUtility.AROMATICITY.apply(tmpMolecule2);
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.ACIDIC_GROUP_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.ACIDIC_GROUP_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ACIDIC_GROUP_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.ALL_RINGS_COUNT.getFeatureNumber()]) {
+ try {
+ int tmpRingCount1 = ComparisonUtility.ALL_RINGS_FINDER.findAllRings(tmpMolecule1).getAtomContainerCount();
+ int tmpRingCount2 = ComparisonUtility.ALL_RINGS_FINDER.findAllRings(tmpMolecule2).getAtomContainerCount();
+ tmpResult[ComparisonFeature.ALL_RINGS_COUNT.getFeatureNumber()] = new double[] {tmpRingCount1, tmpRingCount2, Math.abs(tmpRingCount1 - tmpRingCount2)};
+ } catch (CDKException CDKException) {
+ tmpResult[ComparisonFeature.ALL_RINGS_COUNT.getFeatureNumber()] = new double[] {Double.NaN, Double.NaN, Double.NaN};
+ }
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.A_LOGP.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.A_LOGP_2.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.MOLAR_REFRACTIVITY.getFeatureNumber()]) {
+ ALOGPDescriptor tmpALOGPDescriptor = new ALOGPDescriptor();
+ tmpALOGPDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpALOGPDescriptor.calculate(tmpMolecule1).getValue().toString().split(",");
+ String[] tmpArray2 = tmpALOGPDescriptor.calculate(tmpMolecule2).getValue().toString().split(",");
+ // Ghose-Grippen logP
+ if (tmpCalculateFeature[ComparisonFeature.A_LOGP.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.A_LOGP.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[0]), Double.parseDouble(tmpArray2[0]), Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]))};
+ }
+ // Ghose-Grippen logP 2
+ if (tmpCalculateFeature[ComparisonFeature.A_LOGP_2.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.A_LOGP_2.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[1]), Double.parseDouble(tmpArray2[1]), Math.abs(Double.parseDouble(tmpArray1[1]) - Double.parseDouble(tmpArray2[1]))};
+ }
+ // Molar refractivity
+ if (tmpCalculateFeature[ComparisonFeature.MOLAR_REFRACTIVITY.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.MOLAR_REFRACTIVITY.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[2]), Double.parseDouble(tmpArray2[2]), Math.abs(Double.parseDouble(tmpArray1[2]) - Double.parseDouble(tmpArray2[2]))};
+ }
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.APOL.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.APOL.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.A_POL_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.AROMATIC_ATOM_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.AROMATIC_ATOMS_COUNTS_DESCRIPTOR.setParameters(new Object[] {true});
+ tmpResult[ComparisonFeature.AROMATIC_ATOM_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.AROMATIC_ATOMS_COUNTS_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.AROMATIC_BOND_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.AROMATIC_BONDS_COUNT_DESCRIPTOR.setParameters(new Object[] {true});
+ tmpResult[ComparisonFeature.AROMATIC_BOND_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.AROMATIC_BONDS_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ // Atom count
+ if (tmpCalculateFeature[ComparisonFeature.ATOM_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR.setParameters(new Object[] {"*"});
+ tmpResult[ComparisonFeature.ATOM_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Carbon count
+ if (tmpCalculateFeature[ComparisonFeature.CARBON_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR.setParameters(new Object[] {"C"});
+ tmpResult[ComparisonFeature.CARBON_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Oxygen count
+ if (tmpCalculateFeature[ComparisonFeature.OXYGEN_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR.setParameters(new Object[] {"O"});
+ tmpResult[ComparisonFeature.OXYGEN_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Sulfur count
+ if (tmpCalculateFeature[ComparisonFeature.SULFUR_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR.setParameters(new Object[] {"S"});
+ tmpResult[ComparisonFeature.SULFUR_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Nitrogen count
+ if (tmpCalculateFeature[ComparisonFeature.NITROGEN_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR.setParameters(new Object[] {"N"});
+ tmpResult[ComparisonFeature.NITROGEN_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Phosphor count
+ if (tmpCalculateFeature[ComparisonFeature.PHOSPHOR_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR.setParameters(new Object[] {"P"});
+ tmpResult[ComparisonFeature.PHOSPHOR_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ATOM_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.ATS_CHARGE1.getFeatureNumber()]) {
+ String[] tmpArray1 = ComparisonUtility.AUTOCORRELATION_DESCRIPTOR_CHARGE.calculate(tmpMolecule1).getValue().toString().split(",");
+ String[] tmpArray2 = ComparisonUtility.AUTOCORRELATION_DESCRIPTOR_CHARGE.calculate(tmpMolecule2).getValue().toString().split(",");
+ tmpResult[ComparisonFeature.ATS_CHARGE1.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[0]), Double.parseDouble(tmpArray2[0]), Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]))};
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.ATS_MASS1.getFeatureNumber()]) {
+ String[] tmpArray1 = ComparisonUtility.AUTOCORRELATION_DESCRIPTOR_MASS.calculate(tmpMolecule1).getValue().toString().split(",");
+ String[] tmpArray2 = ComparisonUtility.AUTOCORRELATION_DESCRIPTOR_MASS.calculate(tmpMolecule2).getValue().toString().split(",");
+ tmpResult[ComparisonFeature.ATS_MASS1.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[0]), Double.parseDouble(tmpArray2[0]), Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]))};
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.ATS_POLARIZABILITY1.getFeatureNumber()]) {
+ String[] tmpArray1 = ComparisonUtility.AUTOCORRELATION_DESCRIPTOR_POLARIZABILITY.calculate(tmpMolecule1).getValue().toString().split(",");
+ String[] tmpArray2 = ComparisonUtility.AUTOCORRELATION_DESCRIPTOR_POLARIZABILITY.calculate(tmpMolecule2).getValue().toString().split(",");
+ tmpResult[ComparisonFeature.ATS_POLARIZABILITY1.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[0]), Double.parseDouble(tmpArray2[0]), Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]))};
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.BASIC_GROUP_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.BASIC_GROUP_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.BASCIS_GROUP_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ // Bond count
+ if (tmpCalculateFeature[ComparisonFeature.BOND_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR.setParameters(new Object[] {""});
+ tmpResult[ComparisonFeature.BOND_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Single bond count
+ if (tmpCalculateFeature[ComparisonFeature.SINGLE_BOND_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR.setParameters(new Object[] {"s"});
+ tmpResult[ComparisonFeature.SINGLE_BOND_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Double bond count
+ if (tmpCalculateFeature[ComparisonFeature.DOUBLE_BOND_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR.setParameters(new Object[] {"d"});
+ tmpResult[ComparisonFeature.DOUBLE_BOND_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Triple bond count
+ if (tmpCalculateFeature[ComparisonFeature.TRIPLE_BOND_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR.setParameters(new Object[] {"t"});
+ tmpResult[ComparisonFeature.TRIPLE_BOND_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Quadruple bond count
+ if (tmpCalculateFeature[ComparisonFeature.QUADRUPLE_BOND_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR.setParameters(new Object[] {"q"});
+ tmpResult[ComparisonFeature.QUADRUPLE_BOND_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.BOND_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.BPOL.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.BPOL.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.B_POL_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.C1SP1_COUNT.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.C2SP1_COUNT.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.C1SP2_COUNT.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.C2SP2_COUNT.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.C3SP2_COUNT.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.C1SP3_COUNT.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.C2SP3_COUNT.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.C3SP3_COUNT.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.C4SP3_COUNT.getFeatureNumber()]) {
+ String[] tmpArray1 = ComparisonUtility.CARBON_TYPES_DESCRIPTOR.calculate(tmpMolecule1).getValue().toString().split(",");
+ String[] tmpArray2 = ComparisonUtility.CARBON_TYPES_DESCRIPTOR.calculate(tmpMolecule2).getValue().toString().split(",");
+ // C1SP1 count
+ if (tmpCalculateFeature[ComparisonFeature.C1SP1_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.C1SP1_COUNT.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[0]), Double.parseDouble(tmpArray2[0]), Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]))};
+ }
+ // C2SP1 count
+ if (tmpCalculateFeature[ComparisonFeature.C2SP1_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.C2SP1_COUNT.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[1]), Double.parseDouble(tmpArray2[1]), Math.abs(Double.parseDouble(tmpArray1[1]) - Double.parseDouble(tmpArray2[1]))};
+ }
+ // C1SP2 count
+ if (tmpCalculateFeature[ComparisonFeature.C1SP2_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.C1SP2_COUNT.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[2]), Double.parseDouble(tmpArray2[2]), Math.abs(Double.parseDouble(tmpArray1[2]) - Double.parseDouble(tmpArray2[2]))};
+ }
+ // C2SP2 count
+ if (tmpCalculateFeature[ComparisonFeature.C2SP2_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.C2SP2_COUNT.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[3]), Double.parseDouble(tmpArray2[3]), Math.abs(Double.parseDouble(tmpArray1[3]) - Double.parseDouble(tmpArray2[3]))};
+ }
+ // C3SP2 count
+ if (tmpCalculateFeature[ComparisonFeature.C3SP2_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.C3SP2_COUNT.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[4]), Double.parseDouble(tmpArray2[4]), Math.abs(Double.parseDouble(tmpArray1[4]) - Double.parseDouble(tmpArray2[4]))};
+ }
+ // C1SP3 count
+ if (tmpCalculateFeature[ComparisonFeature.C1SP3_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.C1SP3_COUNT.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[5]), Double.parseDouble(tmpArray2[5]), Math.abs(Double.parseDouble(tmpArray1[5]) - Double.parseDouble(tmpArray2[5]))};
+ }
+ // C2SP3 count
+ if (tmpCalculateFeature[ComparisonFeature.C2SP3_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.C2SP3_COUNT.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[6]), Double.parseDouble(tmpArray2[6]), Math.abs(Double.parseDouble(tmpArray1[6]) - Double.parseDouble(tmpArray2[6]))};
+ }
+ // C3SP3 count
+ if (tmpCalculateFeature[ComparisonFeature.C3SP3_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.C3SP3_COUNT.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[7]), Double.parseDouble(tmpArray2[7]), Math.abs(Double.parseDouble(tmpArray1[7]) - Double.parseDouble(tmpArray2[7]))};
+ }
+ // C4SP3 count
+ if (tmpCalculateFeature[ComparisonFeature.C4SP3_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.C4SP3_COUNT.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[8]), Double.parseDouble(tmpArray2[8]), Math.abs(Double.parseDouble(tmpArray1[8]) - Double.parseDouble(tmpArray2[8]))};
+ }
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.EQUALITY.getFeatureNumber()]) {
+ String tmpUniqueSmiles1 = ComparisonUtility.SMILES_GENERATOR.create(tmpMolecule1);
+ String tmpUniqueSmiles2 = ComparisonUtility.SMILES_GENERATOR.create(tmpMolecule2);
+ tmpResult[ComparisonFeature.EQUALITY.getFeatureNumber()] = new double[] {Double.NaN, Double.NaN, tmpUniqueSmiles1.equals(tmpUniqueSmiles2) ? 1 : 0};
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.ECCENTRIC_CONNECTIVITY_INDEX.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.ECCENTRIC_CONNECTIVITY_INDEX.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ECCENTRIC_CONNECTIVITY_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.FMF.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.FMF.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.FMF_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.FCSP3.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.FCSP3.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.FRACTIONAL_CSP3_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.FPSA.getFeatureNumber()]) {
+ ComparisonUtility.FRACTIONAL_PSA_DESCRIPTOR.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpResult[ComparisonFeature.FPSA.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.FRACTIONAL_PSA_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.FRAGMENT_COMPLEXITY.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.FRAGMENT_COMPLEXITY.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.FRAGMENT_COMPLEXITY_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.H_BOND_ACCEPTOR_COUNT.getFeatureNumber()]) {
+ ComparisonUtility.HBOND_ACCEPTOR_COUNT_DESCRIPTOR.setParameters(new Object[] {true});
+ tmpResult[ComparisonFeature.H_BOND_ACCEPTOR_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.HBOND_ACCEPTOR_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.H_BOND_DONOR_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.H_BOND_DONOR_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.HBOND_DONOR_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.JP_LOGP.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.JP_LOGP.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.JP_LOGP_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_1.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_2.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_3.getFeatureNumber()]) {
+ String[] tmpArray1 = ComparisonUtility.KAPPA_SHAPE_INDICES_DESCRIPTOR.calculate(tmpMolecule1).getValue().toString().split(",");
+ String[] tmpArray2 = ComparisonUtility.KAPPA_SHAPE_INDICES_DESCRIPTOR.calculate(tmpMolecule2).getValue().toString().split(",");
+ // First kappa shape index
+ if (tmpCalculateFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_1.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.KAPPA_SHAPE_INDEX_1.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[0]), Double.parseDouble(tmpArray2[0]), Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]))};
+ }
+ // Second kappa shape index
+ if (tmpCalculateFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_2.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.KAPPA_SHAPE_INDEX_2.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[1]), Double.parseDouble(tmpArray2[1]), Math.abs(Double.parseDouble(tmpArray1[1]) - Double.parseDouble(tmpArray2[1]))};
+ }
+ // Third kappa shape index
+ if (tmpCalculateFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_3.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.KAPPA_SHAPE_INDEX_3.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[2]), Double.parseDouble(tmpArray2[2]), Math.abs(Double.parseDouble(tmpArray1[2]) - Double.parseDouble(tmpArray2[2]))};
+ }
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.LARGEST_CHAIN.getFeatureNumber()]) {
+ // Doesn't need to check for rings because that is done in the preproccesing
+ ComparisonUtility.LARGEST_CHAIN_DESCRIPTOR.setParameters(new Object[] {false, false});
+ tmpResult[ComparisonFeature.LARGEST_CHAIN.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.LARGEST_CHAIN_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.LARGEST_PI_SYSTEM.getFeatureNumber()]) {
+ // Doesn't need to check for aromaticity because that is done in the preproccesing
+ ComparisonUtility.LARGEST_PI_SYSTEM_DESCRIPTOR.setParameters(new Object[] {false});
+ tmpResult[ComparisonFeature.LARGEST_PI_SYSTEM.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.LARGEST_PI_SYSTEM_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.LONGEST_ALIPHATIC_CHAIN.getFeatureNumber()]) {
+ // Doesn't need to check for rings because that is done in the preproccesing
+ ComparisonUtility.LONGEST_ALIPHATIC_CHAIN_DESCRIPTOR.setParameters(new Object[] {false});
+ tmpResult[ComparisonFeature.LONGEST_ALIPHATIC_CHAIN.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.LONGEST_ALIPHATIC_CHAIN_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.MANNHOLD_LOGP.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.MANNHOLD_LOGP.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.MANNHOLD_LOG_P_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.PETITJEAN_NUMBER.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.PETITJEAN_NUMBER.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.PETITJEAN_NUMBER_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.PETITJEAN_SHAPE_INDEX.getFeatureNumber()]) {
+ String[] tmpArray1 = ComparisonUtility.PETITJEAN_SHAPE_INDEX_DESCRIPTOR.calculate(tmpMolecule1).getValue().toString().split(",");
+ String[] tmpArray2 = ComparisonUtility.PETITJEAN_SHAPE_INDEX_DESCRIPTOR.calculate(tmpMolecule2).getValue().toString().split(",");
+ tmpResult[ComparisonFeature.PETITJEAN_SHAPE_INDEX.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[0]), Double.parseDouble(tmpArray2[0]), Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]))};
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.ROTATABLE_BOND_COUNT.getFeatureNumber()]) {
+ // Don't include terminal bonds and don't exclude amide bonds
+ ComparisonUtility.ROTATABLE_BOND_COUNT.setParameters(new Object[] {false, false});
+ tmpResult[ComparisonFeature.ROTATABLE_BOND_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ROTATABLE_BOND_COUNT, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.ALL_SMALL_RINGS_COUNT.getFeatureNumber()]) {
+ int tmpRingCount1 = Integer.parseInt(ComparisonUtility.SMALL_RING_DESCRIPTOR.calculate(tmpMolecule1).getValue().toString().split(",")[0]);
+ int tmpRingCount2 = Integer.parseInt(ComparisonUtility.SMALL_RING_DESCRIPTOR.calculate(tmpMolecule2).getValue().toString().split(",")[0]);
+ tmpResult[ComparisonFeature.ALL_SMALL_RINGS_COUNT.getFeatureNumber()] = new double[] {tmpRingCount1, tmpRingCount2, Math.abs(tmpRingCount1 - tmpRingCount2)};
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.SPIRO_ATOM_COUNT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.SPIRO_ATOM_COUNT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.SPIRO_ATOM_COUNT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ // Basic fingerprint
+ if (tmpCalculateFeature[ComparisonFeature.TANIMOTO_BASIC_FINGERPRINTER.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.TANIMOTO_BASIC_FINGERPRINTER.getFeatureNumber()] = calculateTanimotoCoefficient(
+ ComparisonUtility.BASIC_FINGERPRINTER, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // LINGO fingerprint
+ if (tmpCalculateFeature[ComparisonFeature.TANIMOTO_LINGO_FINGERPRINTER.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.TANIMOTO_LINGO_FINGERPRINTER.getFeatureNumber()] = calculateTanimotoCoefficient(
+ ComparisonUtility.LINGO_FINGERPRINTER, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Extended fingerprint
+ if (tmpCalculateFeature[ComparisonFeature.TANIMOTO_EXTENDED_FINGERPRINTER.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.TANIMOTO_EXTENDED_FINGERPRINTER.getFeatureNumber()] = calculateTanimotoCoefficient(
+ ComparisonUtility.EXTENDED_FINGERPRINTER, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // E-State fingerprint
+ if (tmpCalculateFeature[ComparisonFeature.TANIMOTO_ESTATE_FINGERPRINTER.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.TANIMOTO_ESTATE_FINGERPRINTER.getFeatureNumber()] = calculateTanimotoCoefficient(
+ ComparisonUtility.ESTATE_FINGERPRINTER, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // PubChem fingerprint
+ if (tmpCalculateFeature[ComparisonFeature.TANIMOTO_PUBCHEM_FINGERPRINTER.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.TANIMOTO_PUBCHEM_FINGERPRINTER.getFeatureNumber()] = calculateTanimotoCoefficient(
+ ComparisonUtility.PUBCHEM_FINGERPRINTER, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Shortest path fingerprint
+ if (tmpCalculateFeature[ComparisonFeature.TANIMOTO_SHORTEST_PATH_FINGERPRINTER.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.TANIMOTO_SHORTEST_PATH_FINGERPRINTER.getFeatureNumber()] = calculateTanimotoCoefficient(
+ ComparisonUtility.SHORTEST_PATH_FINGERPRINTER, tmpMolecule1, tmpMolecule2
+ );
+ }
+ // Substructure fingerprint
+ if (tmpCalculateFeature[ComparisonFeature.TANIMOTO_SUBSTRUCTURE_FINGERPRINTER.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.TANIMOTO_SUBSTRUCTURE_FINGERPRINTER.getFeatureNumber()] = calculateTanimotoCoefficient(
+ ComparisonUtility.SUBSTRUCTURE_FINGERPRINTER, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.TPSA.getFeatureNumber()]) {
+ // Doesn't need to check for aromaticity because that is done in the preproccesing
+ ComparisonUtility.TPSA_DESCRIPTOR.setParameters(new Object[] {false});
+ tmpResult[ComparisonFeature.TPSA.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.TPSA_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.VABC.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.VABC.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.VABC_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.V_ADJ_MA.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.V_ADJ_MA.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.V_ADJ_MA_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.MOLECULAR_WEIGHT.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.MOLECULAR_WEIGHT.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.WEIGHT_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.WEIGHTED_PATH_1.getFeatureNumber()]) {
+ String[] tmpArray1 = ComparisonUtility.WEIGHTER_PATH_DESCRIPTOR.calculate(tmpMolecule1).getValue().toString().split(",");
+ String[] tmpArray2 = ComparisonUtility.WEIGHTER_PATH_DESCRIPTOR.calculate(tmpMolecule2).getValue().toString().split(",");
+ tmpResult[ComparisonFeature.WEIGHTED_PATH_1.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[0]), Double.parseDouble(tmpArray2[0]), Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]))};
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.WIENER_PATH.getFeatureNumber()] ||
+ tmpCalculateFeature[ComparisonFeature.WIENER_POLARITY.getFeatureNumber()]) {
+ String[] tmpArray1 = ComparisonUtility.WIENER_NUMBERS_DESCRIPTOR.calculate(tmpMolecule1).getValue().toString().split(",");
+ String[] tmpArray2 = ComparisonUtility.WIENER_NUMBERS_DESCRIPTOR.calculate(tmpMolecule2).getValue().toString().split(",");
+ // Wiener path number
+ if (tmpCalculateFeature[ComparisonFeature.WIENER_PATH.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.WIENER_PATH.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[0]), Double.parseDouble(tmpArray2[0]), Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]))};
+ }
+ // Wiener polarity number
+ if (tmpCalculateFeature[ComparisonFeature.WIENER_POLARITY.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.WIENER_POLARITY.getFeatureNumber()] = new double[] {Double.parseDouble(tmpArray1[1]), Double.parseDouble(tmpArray2[1]), Math.abs(Double.parseDouble(tmpArray1[1]) - Double.parseDouble(tmpArray2[1]))};
+ }
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.X_LOGP.getFeatureNumber()]) {
+ // Aromaticity is already checked in preprocessing; use the salicyl acid correction factor
+ ComparisonUtility.X_LOGP_DESCRIPTOR.setParameters(new Object[] {false, true});
+ tmpResult[ComparisonFeature.X_LOGP.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.X_LOGP_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ //
+ if (tmpCalculateFeature[ComparisonFeature.ZAGREB_INDEX.getFeatureNumber()]) {
+ tmpResult[ComparisonFeature.ZAGREB_INDEX.getFeatureNumber()] = calculateDescriptorDifference(
+ ComparisonUtility.ZAGREB_INDEY_DESCRIPTOR, tmpMolecule1, tmpMolecule2
+ );
+ }
+ //
+ return tmpResult;
+ }
+ //
+ //
+ //
+ /**
+ * Calculate the individual descriptor values and their difference of the
+ * two given molecules and the given descriptor
+ *
+ * @param tmpDescriptor specifies the descriptor
+ * @param tmpMolecule1 the first molecule
+ * @param tmpMolecule2 the second molecule
+ * @return an array of the form
+ * {firstDescriptorValue, secondDescriptorValue, difference}
+ */
+ private static double[] calculateDescriptorDifference(IMolecularDescriptor tmpDescriptor, IAtomContainer tmpMolecule1, IAtomContainer tmpMolecule2) {
+ double tmpResult1 = Double.parseDouble(tmpDescriptor.calculate(tmpMolecule1).getValue().toString());
+ double tmpResult2 = Double.parseDouble(tmpDescriptor.calculate(tmpMolecule2).getValue().toString());
+ return new double[] {tmpResult1, tmpResult2, Math.abs(tmpResult1 - tmpResult2)};
+ };
+
+ /**
+ * Calculate the Tanimoto coefficient for the two given molecules with
+ * the given fingerprint
+ *
+ * @param tmpFingerprinter specifies the fingerprint
+ * @param tmpMolecule1 the first molecule
+ * @param tmpMolecule2 the second molecule
+ * @return an array of the form {NaN, NaN, Tanimoto coefficient}
+ */
+ private static double[] calculateTanimotoCoefficient(IFingerprinter tmpFingerprinter, IAtomContainer tmpMolecule1, IAtomContainer tmpMolecule2) {
+ try {
+ return new double[] {Double.NaN, Double.NaN, Tanimoto.calculate(tmpFingerprinter.getBitFingerprint(tmpMolecule1), tmpFingerprinter.getBitFingerprint(tmpMolecule2))};
+ } catch (CDKException ex) {
+ return new double[] {Double.NaN, Double.NaN, Double.NaN};
+ }
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/model/HistogramData.java b/src/main/java/de/whs/ibci/msc/model/HistogramData.java
new file mode 100644
index 0000000..7bfb872
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/model/HistogramData.java
@@ -0,0 +1,603 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+import java.io.IOException;
+import java.io.ObjectStreamException;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.concurrent.Callable;
+
+/**
+ * Handles the frequency data, the bin borders and the bins list for one
+ * particular ComparisonFeature which is represented by its corresponding number
+ *
+ * @author Jan-Mathis Hein
+ */
+public class HistogramData implements Callable, Serializable {
+
+ //
+ /**
+ * A serial version UID to check whether loaded data is compatible
+ */
+ private static final long serialVersionUID = 5L;
+ //
+ //
+ //
+ /**
+ * If true the specifically set bin borders will be used, if false the bin
+ * borders are calculated automatically
+ */
+ private boolean useSpecificBinBorders;
+
+ /**
+ * If true all returning frequencies will be relative ones and all
+ * inputted frequencies will be regarded as relative ones;
+ * if false all returning frequencies will be absolute ones and all
+ * inputted frequencies will be regarded as absolute ones
+ */
+ private boolean useRelativeFrequencies;
+
+ /**
+ * Maximal value of all comparison results
+ */
+ private double maxComparisonFeatureValue;
+
+ /**
+ * Minimal value of all comparison results
+ */
+ private double minComparisonFeatureValue;
+
+ /**
+ * The average value off all comparison results
+ */
+ private transient double averageComparisonFeatureValue;
+
+ /**
+ * The lower border of the first bin
+ */
+ private double lowerBinBorder;
+
+ /**
+ * The upper border of the last bin
+ */
+ private double upperBinBorder;
+
+ /**
+ * The lower boundary for frequency values. Is set to NaN if the data is
+ * binned
+ */
+ private double lowerFrequencyBound;
+
+ /**
+ * The upper boundary for frequency values. Is set to NaN if the data is
+ * binned
+ */
+ private double upperFrequencyBound;
+
+ /**
+ * The current maximal frequency value of any bin
+ */
+ private double currentMaxFrequencyValue;
+
+ /**
+ * Borders of the bins
+ */
+ private double[] binBorders;
+
+ /**
+ * Number which represents a ComparisonFeature
+ */
+ private int comparisonFeatureNumber;
+
+ /**
+ * Number of bins into which the comparison results will be devided.
+ * This will always be positive
+ */
+ private int numberOfBins;
+
+ /**
+ * The number of invalid similarity values
+ */
+ private int numberOfInvalidComparisonFeatureValues;
+
+ /**
+ * This frequency data. The value at each index represents the frequency of
+ * ComparisonResults in the corresponding bin.
+ */
+ private transient int[] frequencies;
+
+ /**
+ * List of all the ComparisonResults (the native data) that belong to the
+ * data set
+ */
+ private transient List nativeDataList;
+
+ /**
+ * List of lists where each list corresponds to a bin and contains
+ * a sample of molecule pairs whos comparison result belongs to this bin
+ */
+ private transient List> binsList;
+ //
+ //
+ //
+ /**
+ * Initialize some instance variables
+ *
+ * @param tmpComparisonFeatureNumber specifies the ComparisonFeature to which
+ * this HistogramData belongs
+ * @param tmpList reference to the native data
+ */
+ public HistogramData(int tmpComparisonFeatureNumber, List tmpList) {
+ this.comparisonFeatureNumber = tmpComparisonFeatureNumber;
+ this.nativeDataList = tmpList;
+ this.lowerBinBorder = Double.NaN;
+ this.upperBinBorder = Double.NaN;
+ this.lowerFrequencyBound = Double.NaN;
+ this.upperFrequencyBound = Double.NaN;
+ this.currentMaxFrequencyValue = 0.0;
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Calculate the bin borders and the corresponding frequency data. Also
+ * reset upperFrequencyBound and lowerFrequencyBound to NaN
+ */
+ @Override
+ public Void call() {
+ this.lowerFrequencyBound = Double.NaN;
+ this.upperFrequencyBound = Double.NaN;
+ int tmpNumberOfBins;
+ //
+ if (!this.useSpecificBinBorders) {
+ double tmpLowestBinBorder = Double.isNaN(this.lowerBinBorder) ? this.minComparisonFeatureValue : this.lowerBinBorder;
+ double tmpHighestBinBorder = Double.isNaN(this.upperBinBorder) ? this.maxComparisonFeatureValue : this.upperBinBorder;
+ double tmpBinSize = (tmpHighestBinBorder - tmpLowestBinBorder) / this.numberOfBins;
+ if (tmpBinSize < 0) {
+ // If binSize is negative, reasonable values are inferred
+ tmpBinSize = Math.abs(tmpBinSize);
+ this.lowerBinBorder = tmpHighestBinBorder;
+ this.upperBinBorder = tmpLowestBinBorder;
+ tmpLowestBinBorder = this.lowerBinBorder;
+ tmpHighestBinBorder = this.upperBinBorder;
+ }
+ if (tmpBinSize == 0) {
+ tmpNumberOfBins = 1;
+ } else {
+ tmpNumberOfBins= this.numberOfBins;
+ }
+ this.binBorders = new double[tmpNumberOfBins + 1];
+ for (int i = 0; i < tmpNumberOfBins; i++) {
+ this.binBorders[i] = tmpLowestBinBorder + (tmpBinSize * i);
+ }
+ this.binBorders[tmpNumberOfBins] = tmpHighestBinBorder;
+ } else {
+ tmpNumberOfBins = this.numberOfBins;
+ }
+ //
+ this.binsList = new ArrayList<>(tmpNumberOfBins);
+ for (int i = 0; i < tmpNumberOfBins; i++) {
+ this.binsList.add(i, new LinkedList<>());
+ }
+ this.frequencies = new int[tmpNumberOfBins];
+ Arrays.fill(this.frequencies, 0);
+ Iterator tmpIterator = this.nativeDataList.iterator();
+ ComparisonResult tmpResult;
+ double tmpValue;
+ this.averageComparisonFeatureValue = 0.0;
+ this.numberOfInvalidComparisonFeatureValues = 0;
+ iteratorLoop:
+ while (tmpIterator.hasNext()) {
+ tmpResult = tmpIterator.next();
+ tmpValue = tmpResult.getSimilarities()[this.comparisonFeatureNumber];
+ if (Double.isNaN(tmpValue)) {
+ this.numberOfInvalidComparisonFeatureValues++;
+ continue;
+ }
+ this.averageComparisonFeatureValue += tmpValue;
+ for (int i = 1; i < this.binBorders.length; i++) {
+ // Lower bound included, upper bound excluded
+ if (tmpValue < this.binBorders[i] && tmpValue >= this.binBorders[i - 1]) {
+ this.frequencies[i - 1]++;
+ if (tmpResult.hasMoleculePair()) {
+ List tmpBin = this.binsList.get(i - 1);
+ tmpBin.add(tmpResult);
+ }
+ continue iteratorLoop;
+ }
+ }
+ // If tmpValue exactly matches the highest bin border it contributes to the last bin
+ if (tmpValue == this.binBorders[tmpNumberOfBins]) {
+ this.frequencies[tmpNumberOfBins - 1]++;
+ if (tmpResult.hasMoleculePair()) {
+ List tmpBin = this.binsList.get(tmpNumberOfBins - 1);
+ tmpBin.add(tmpResult);
+ }
+ }
+ }
+ this.averageComparisonFeatureValue /= (this.nativeDataList.size() - this.numberOfInvalidComparisonFeatureValues);
+ this.currentMaxFrequencyValue = this.frequencies[0];
+ for (int tmpInt : this.frequencies) {
+ this.currentMaxFrequencyValue = this.currentMaxFrequencyValue >= tmpInt ? this.currentMaxFrequencyValue : tmpInt;
+ }
+ return null;
+ }
+ //
+ //
+ /**
+ * If true all returning frequencies will be relative ones and all
+ * inputted frequencies will be regarded as relative ones;
+ * if false all returning frequencies will be absolute ones and all
+ * inputted frequencies will be regarded as absolute ones
+ *
+ * @return true if all returning frequencies will be relative ones and all
+ * inputted frequencies will be regarded as relative ones;
+ * return false if all returning frequencies will be absolute ones and all
+ * inputted frequencies will be regarded as absolute ones
+ */
+ public boolean isUseRelativeFrequencies() {
+ return this.useRelativeFrequencies;
+ }
+
+ /**
+ * Get a copy of the bin borders.
+ *
+ * @return a copy of the bin borders
+ */
+ public double[] getBinBorders() {
+ return Arrays.copyOf(this.binBorders, this.binBorders.length);
+ }
+
+ /**
+ * Get the maximal ComparisonFeature value
+ *
+ * @return the maximal ComparisonFeature value
+ */
+ public double getMaxComparisonFeatureValue() {
+ return this.maxComparisonFeatureValue;
+ }
+
+ /**
+ * Get the minimal ComparisonFeature value
+ *
+ * @return the minmal ComparisonFeature value
+ */
+ public double getMinComparisonFeatureValue() {
+ return this.minComparisonFeatureValue;
+ }
+
+ /**
+ * Get the average ComparisonFeature value
+ *
+ * @return the average ComparisonFeature value
+ */
+ public double getAverageComparisonFeatureValue() {
+ return this.averageComparisonFeatureValue;
+ }
+
+ /**
+ * Get the value that will be or is the lowest bin border
+ *
+ * @return the lowest bin border
+ */
+ public double getLowerBinBorder() {
+ return Double.isNaN(this.lowerBinBorder) ? this.minComparisonFeatureValue : this.lowerBinBorder;
+ }
+
+ /**
+ * Get the value that will be or is the highest bin border
+ *
+ * @return the highest bin border
+ */
+ public double getUpperBinBorder() {
+ return Double.isNaN(this.upperBinBorder) ? this.maxComparisonFeatureValue : this.upperBinBorder;
+ }
+
+ /**
+ * Get the lower bound for the frequency values
+ *
+ * @return the lower bound for the frequency values
+ */
+ public double getLowerFrequencyBound() {
+ if (this.useRelativeFrequencies) {
+ return Double.isNaN(this.lowerFrequencyBound) ?
+ (0.0 / (this.nativeDataList.size() - this.numberOfInvalidComparisonFeatureValues)) :
+ (this.lowerFrequencyBound / (this.nativeDataList.size() - this.numberOfInvalidComparisonFeatureValues));
+ } else {
+ return Double.isNaN(this.lowerFrequencyBound) ? 0.0 : this.lowerFrequencyBound;
+ }
+ }
+
+ /**
+ * Get the upper bound for the frequency values
+ *
+ * @return the upper bound for the frequency values
+ */
+ public double getUpperFrequencyBound() {
+ if (this.useRelativeFrequencies) {
+ return Double.isNaN(this.upperFrequencyBound) ?
+ (this.currentMaxFrequencyValue / (this.nativeDataList.size() - this.numberOfInvalidComparisonFeatureValues)) :
+ (this.upperFrequencyBound / (this.nativeDataList.size() - this.numberOfInvalidComparisonFeatureValues));
+ } else {
+ return Double.isNaN(this.upperFrequencyBound) ? this.currentMaxFrequencyValue : this.upperFrequencyBound;
+ }
+ }
+
+ /**
+ * Get the maximal possible frequency value
+ *
+ * @return the maximal possible frequency value
+ */
+ public double getMaxFrequency() {
+ if (this.useRelativeFrequencies) {
+ return 1;
+ } else {
+ return (this.nativeDataList.size() - this.numberOfInvalidComparisonFeatureValues);
+ }
+ }
+
+ /**
+ * Get the number of bins
+ *
+ * @return the number of bins
+ */
+ public int getNumberOfBins() {
+ return this.numberOfBins;
+ }
+
+ /**
+ * Get the frequencies as an array where each index corresponds to a bin
+ *
+ * @return the frequencies
+ */
+ public double[] getFrequencies() {
+ double tmpScaling = 1.0;
+ if (this.useRelativeFrequencies) {
+ tmpScaling = (this.nativeDataList.size() - this.numberOfInvalidComparisonFeatureValues);
+ }
+ double[] tmpResult = new double[this.frequencies.length];
+ for (int i = 0; i < tmpResult.length; i++) {
+ tmpResult[i] = (this.frequencies[i] / tmpScaling);
+ }
+ return tmpResult;
+ }
+
+ /**
+ * Get the bin specified by the index as a list that contains
+ * associated ComparisonResults.
+ * NOTE: If this HistogramData is loaded, this list can be empty even
+ * though the frequency of the bin is not zero
+ *
+ * @param tmpBinIndex specifies the bin
+ * @return the specified bin as a list of IAtomContainer arrays
+ */
+ public List getBin(int tmpBinIndex) {
+ return this.binsList.get(tmpBinIndex);
+ }
+
+ /**
+ * Get the number corresponding to the ComparisonFeature of this
+ * HistogramData
+ *
+ * @return the number corresponding to the ComparisonFeature
+ */
+ public int getComparisonFeautureNumber() {
+ return this.comparisonFeatureNumber;
+ }
+
+ /**
+ * Get the ComparisonFeature of this HistogramData
+ *
+ * @return the ComparisonFeature of this HistogramData
+ */
+ public ComparisonFeature getComparisonFeauture() {
+ return ComparisonFeature.values()[this.comparisonFeatureNumber];
+ }
+ //
+ //
+ /**
+ * Set the useRelativeFrequencies flag. If this flag is true all
+ * returning and inputted frequencies will be realtive ones, if false all
+ * returning and inputted frequencies will be absolute ones
+ *
+ * @param tmpUseRelativeFrequencies the value to which the flag will
+ * be set
+ */
+ public synchronized void setUseRelativeFrequencies(boolean tmpUseRelativeFrequencies) {
+ this.useRelativeFrequencies = tmpUseRelativeFrequencies;
+ }
+
+ /**
+ * Set the lower bin border
+ *
+ * @param tmpBorder specifies the new value of the lower bin border
+ */
+ public synchronized void setLowerBinBorder(double tmpBorder) {
+ this.lowerBinBorder = tmpBorder;
+ this.useSpecificBinBorders = false;
+ }
+
+ /**
+ * Set the upper bin border
+ *
+ * @param tmpBorder specifies the new value of the upper bin border
+ */
+ public synchronized void setUpperBinBorder(double tmpBorder) {
+ this.upperBinBorder = tmpBorder;
+ this.useSpecificBinBorders = false;
+ }
+
+ /**
+ * Set the number of bins. If the given value is smaller than one,
+ * one is used instead.
+ *
+ * @param tmpNumberOfBins specifies the new number of bins
+ */
+ public synchronized void setNumberOfBins(int tmpNumberOfBins) {
+ this.numberOfBins = tmpNumberOfBins > 1 ? tmpNumberOfBins : 1;
+ this.useSpecificBinBorders = false;
+ }
+
+ /**
+ * Set the lower frequency bound. If the resulting frequency bounds
+ * would be irrational, reasonable values are inferred. If the given
+ * bound is not a number the method returns without doing anything
+ *
+ * @param tmpLowerBound specifies the new value of the lower frequency bound
+ */
+ public synchronized void setLowerFrequencyBound(double tmpLowerBound) {
+ if (Double.isNaN(tmpLowerBound)) {
+ return;
+ }
+ if (this.useRelativeFrequencies) {
+ tmpLowerBound *= (this.nativeDataList.size() - this.numberOfInvalidComparisonFeatureValues);
+ }
+ double tmpUpperBound = this.upperFrequencyBound;
+ if (tmpLowerBound > tmpUpperBound) {
+ this.lowerFrequencyBound = tmpUpperBound;
+ this.upperFrequencyBound = tmpLowerBound;
+ } else {
+ this.lowerFrequencyBound = tmpLowerBound;
+ this.upperFrequencyBound = tmpUpperBound;
+ }
+ }
+
+ /**
+ * Set the upper frequency bound. If the resulting frequency bounds
+ * would be irrational, reasonable values are inferred. If the given
+ * bound is not a number the method returns without doing anything
+ *
+ * @param tmpUpperBound specifies the new value of the upper frequency bound
+ */
+ public synchronized void setUpperFrequencyBound(double tmpUpperBound) {
+ if (Double.isNaN(tmpUpperBound)) {
+ return;
+ }
+ if (this.useRelativeFrequencies) {
+ tmpUpperBound *= (this.nativeDataList.size() - this.numberOfInvalidComparisonFeatureValues);
+ }
+ double tmpLowerBound = this.lowerFrequencyBound;
+ if (tmpLowerBound > tmpUpperBound) {
+ this.lowerFrequencyBound = tmpUpperBound;
+ this.upperFrequencyBound = tmpLowerBound;
+ } else {
+ this.lowerFrequencyBound = tmpLowerBound;
+ this.upperFrequencyBound = tmpUpperBound;
+ }
+ }
+
+ /**
+ * Set the maximal ComparisonFeature value
+ *
+ * @param tmpValue specifies the value to set
+ */
+ public void setMaxComparisonFeatureValue(double tmpValue) {
+ this.maxComparisonFeatureValue = tmpValue;
+ }
+
+ /**
+ * Set the minimal ComparisonFeature value
+ *
+ * @param tmpValue specifies the value to set
+ */
+ public void setMinComparisonFeatureValue(double tmpValue) {
+ this.minComparisonFeatureValue = tmpValue;
+ }
+
+ /**
+ * Set the native data list
+ *
+ * @param tmpList the native data list to be set
+ */
+ public void setNativeDataList(List tmpList) {
+ this.nativeDataList = tmpList;
+ }
+
+ /**
+ * Set the bin borders
+ *
+ * @param tmpBinBorders the bin borders to be set
+ */
+ public void setSpecificBinBorders(double[] tmpBinBorders) {
+ this.binBorders = Arrays.copyOf(tmpBinBorders, tmpBinBorders.length);
+ this.useSpecificBinBorders = true;
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Write the state of this object to the given ObjectOutputStream
+ *
+ * @param tmpObjectOutputStream the ObjectOutputStream to which information
+ * will be written
+ * @throws IOException if an I/O error occurs
+ */
+ private synchronized void writeObject(java.io.ObjectOutputStream tmpObjectOutputStream) throws IOException {
+ tmpObjectOutputStream.writeBoolean(this.useRelativeFrequencies);
+ tmpObjectOutputStream.writeBoolean(this.useSpecificBinBorders);
+ tmpObjectOutputStream.writeDouble(this.lowerBinBorder);
+ tmpObjectOutputStream.writeDouble(this.lowerFrequencyBound);
+ tmpObjectOutputStream.writeDouble(this.maxComparisonFeatureValue);
+ tmpObjectOutputStream.writeDouble(this.minComparisonFeatureValue);
+ tmpObjectOutputStream.writeDouble(this.upperBinBorder);
+ tmpObjectOutputStream.writeDouble(this.upperFrequencyBound);
+ tmpObjectOutputStream.writeDouble(this.currentMaxFrequencyValue);
+ tmpObjectOutputStream.writeInt(this.comparisonFeatureNumber);
+ tmpObjectOutputStream.writeInt(this.numberOfBins);
+ tmpObjectOutputStream.writeObject(this.binBorders);
+ }
+
+ /**
+ * Read the state of an object from the given ObjectInputStream
+ *
+ * @param tmpObjectInputStream ObjectInputStream from which to read
+ * @throws IOException if an I/O error occurs
+ * @throws ClassNotFoundException Class of a serialized object cannot be
+ * found
+ */
+ private void readObject(java.io.ObjectInputStream tmpObjectInputStream) throws IOException, ClassNotFoundException {
+ this.useRelativeFrequencies = tmpObjectInputStream.readBoolean();
+ this.useSpecificBinBorders = tmpObjectInputStream.readBoolean();
+ this.lowerBinBorder = tmpObjectInputStream.readDouble();
+ this.lowerFrequencyBound = tmpObjectInputStream.readDouble();
+ this.maxComparisonFeatureValue = tmpObjectInputStream.readDouble();
+ this.minComparisonFeatureValue = tmpObjectInputStream.readDouble();
+ this.upperBinBorder = tmpObjectInputStream.readDouble();
+ this.upperFrequencyBound = tmpObjectInputStream.readDouble();
+ this.currentMaxFrequencyValue = tmpObjectInputStream.readDouble();
+ this.comparisonFeatureNumber = tmpObjectInputStream.readInt();
+ this.numberOfBins = tmpObjectInputStream.readInt();
+ this.binBorders = (double[]) tmpObjectInputStream.readObject();
+ }
+
+ /**
+ * This method is not implemented
+ */
+ private void readObjectNoData() {
+ throw new RuntimeException("Method \"readObjectNoData\" is not implemented");
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/model/HistogramDataManager.java b/src/main/java/de/whs/ibci/msc/model/HistogramDataManager.java
new file mode 100644
index 0000000..978d378
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/model/HistogramDataManager.java
@@ -0,0 +1,335 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.ObjectStreamException;
+import java.io.Serializable;
+import java.util.EnumMap;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+/**
+ * Stores and manages the histogram data for multiple ComparisonFeatures.
+ * Also handles the saving and loading of the histogram data
+ *
+ * @author Jan-Mathis Hein
+ */
+public class HistogramDataManager implements Serializable {
+
+ //
+ /**
+ * A serial version UID to check whether loaded data is compatible
+ */
+ private static final long serialVersionUID = 5L;
+ //
+ //
+ //
+ /**
+ * List of all the ComparisonResults (the native data) that belong to the
+ * data set
+ */
+ private transient List nativeDataList;
+
+ /**
+ * Maps all the HistogramData objects to their corresponding
+ * ComparisonFeature
+ */
+ private transient Map comparisonFeatureToDataMap;
+
+ /**
+ * The time difference, in milliseconds, between the data's calculation
+ * start time and midnight, January 1, 1970 UTC
+ */
+ private long calculationStartTime;
+
+ /**
+ * The time difference, in milliseconds, between the data's calculation
+ * finish time and midnight, January 1, 1970 UTC
+ */
+ private long calculationFinishTime;
+
+ /**
+ * Name of the first input file which was used for the comparison
+ */
+ private String inputFile1;
+
+ /**
+ * Name of the second input file which was used for the comparison
+ */
+ private String inputFile2;
+ //
+ //
+ //
+ /**
+ * Initialize the instance variables and add the first ComparisonResult to
+ * the data set
+ *
+ * @param tmpConsideredComparisonFeaturesList list of ComparisonFeatures for
+ * which histogram data will be stored
+ * @param tmpNumberOfInitialBins initial number of bins
+ * @param tmpFirstResult first ComparisonResult for the data set
+ * @param tmpInputFile1 the name of the first input file
+ * @param tmpInputFile2 the name of the second input file
+ */
+ public HistogramDataManager(
+ List tmpConsideredComparisonFeaturesList, int tmpNumberOfInitialBins,
+ ComparisonResult tmpFirstResult, String tmpInputFile1, String tmpInputFile2
+ ) throws IllegalArgumentException {
+ //
+ if (tmpConsideredComparisonFeaturesList == null || tmpFirstResult == null) {
+ throw new IllegalArgumentException("An argument is null");
+ }
+ //
+ this.comparisonFeatureToDataMap = new EnumMap<>(ComparisonFeature.class);
+ this.nativeDataList = new LinkedList<>();
+ this.nativeDataList.add(tmpFirstResult);
+ tmpConsideredComparisonFeaturesList.forEach((ComparisonFeature tmpComparisonFeature) -> {
+ this.comparisonFeatureToDataMap.putIfAbsent(tmpComparisonFeature, new HistogramData(tmpComparisonFeature.getFeatureNumber(), this.nativeDataList));
+ });
+ this.comparisonFeatureToDataMap.values().forEach((HistogramData tmpHistogramData) -> {
+ tmpHistogramData.setMinComparisonFeatureValue(tmpFirstResult.getSimilarities()[tmpHistogramData.getComparisonFeautureNumber()]);
+ tmpHistogramData.setMaxComparisonFeatureValue(tmpFirstResult.getSimilarities()[tmpHistogramData.getComparisonFeautureNumber()]);
+ tmpHistogramData.setNumberOfBins(tmpNumberOfInitialBins < 1 ? 1 : tmpNumberOfInitialBins);
+ });
+ this.inputFile1 = tmpInputFile1;
+ this.inputFile2 = tmpInputFile2;
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Add a new ComparisonResult to the data set
+ *
+ * @param tmpResult ComparisonResult to be added
+ */
+ public synchronized void addDatum(ComparisonResult tmpResult) {
+ //
+ if (tmpResult == null) {
+ return;
+ }
+ //
+ this.comparisonFeatureToDataMap.values().forEach((HistogramData tmpData) -> {
+ if (Double.isNaN(tmpResult.getSimilarities()[tmpData.getComparisonFeautureNumber()])) {
+ return;
+ }
+ tmpData.setMinComparisonFeatureValue(
+ tmpData.getMinComparisonFeatureValue() < tmpResult.getSimilarities()[tmpData.getComparisonFeautureNumber()] ?
+ tmpData.getMinComparisonFeatureValue() : tmpResult.getSimilarities()[tmpData.getComparisonFeautureNumber()]
+ );
+ tmpData.setMaxComparisonFeatureValue(
+ tmpData.getMaxComparisonFeatureValue() > tmpResult.getSimilarities()[tmpData.getComparisonFeautureNumber()] ?
+ tmpData.getMaxComparisonFeatureValue() : tmpResult.getSimilarities()[tmpData.getComparisonFeautureNumber()]
+ );
+ });
+ this.nativeDataList.add(tmpResult);
+ }
+ //
+ public synchronized ByteArrayOutputStream getObjectAsByteStream() throws IOException {
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+
+ baos.write(toBytes(this.inputFile1.length()));
+ baos.write(this.inputFile1.getBytes());
+ baos.write(toBytes(this.inputFile2.length()));
+ baos.write(this.inputFile2.getBytes());
+
+ return baos;
+ }
+ private byte[] toBytes(int i) {
+ byte[] result = new byte[4];
+
+ result[0] = (byte) (i >> 24);
+ result[1] = (byte) (i >> 16);
+ result[2] = (byte) (i >> 8);
+ result[3] = (byte) (i /*>> 0*/);
+
+ return result;
+ }
+ //
+ /**
+ * Get the number of data that were added to the data set
+ *
+ * @return number of added data
+ */
+ public int getNumberOfComparedPairs() {
+ return this.nativeDataList.size();
+ }
+
+ /**
+ * Get the set of ComparisonFeatures for which histogram data is available
+ *
+ * @return the set of ComparisonFeatures for which histogram data is
+ * available
+ */
+ public Set getComparisonFeatureSet() {
+ return this.comparisonFeatureToDataMap.keySet();
+ }
+
+ /**
+ * Get the HistogramData object corresponding to the given ComparisonFeature
+ *
+ * @param tmpComparisonFeature specifies which HistogramData object
+ * to return
+ * @return the HistogramData object corresponding to the given
+ * ComparisonFeature
+ */
+ public HistogramData getHistogramData(ComparisonFeature tmpComparisonFeature) {
+ return this.comparisonFeatureToDataMap.get(tmpComparisonFeature);
+ }
+
+ /**
+ * Get the list of all the ComparisonResults (the native data) that belong
+ * to the data set
+ *
+ * @return a list of ComparisonResults
+ */
+ public List getNativeDataList() {
+ return this.nativeDataList;
+ }
+
+ /**
+ * Get the name of the first input file
+ *
+ * @return the name of the first input file
+ */
+ public String getInputFile1() {
+ return this.inputFile1;
+ }
+
+ /**
+ * Get the name of the second input file
+ *
+ * @return the name of the second input file
+ */
+ public String getInputFile2() {
+ return this.inputFile2;
+ }
+
+ /**
+ * Get the time difference, in milliseconds, between the data's calculation
+ * start time and midnight, January 1, 1970 UTC
+ *
+ * @return the calculationStartTime in milliseconds
+ */
+ public long getCalculationStartTime() {
+ return this.calculationStartTime;
+ }
+
+ /**
+ * Get the time difference, in milliseconds, between the data's calculation
+ * finish time and midnight, January 1, 1970 UTC
+ *
+ * @return the calculationFinishTime in milliseconds
+ */
+ public long getCalculationFinishTime() {
+ return this.calculationFinishTime;
+ }
+
+ /**
+ * Set the time difference, in milliseconds, between the data's calculation
+ * start time and midnight, January 1, 1970 UTC
+ *
+ * @param tmpStartTime the difference to be set in milliseconds
+ */
+ public void setCalculationStartTime(long tmpStartTime) {
+ this.calculationStartTime = tmpStartTime;
+ }
+
+ /**
+ * Set the time difference, in milliseconds, between the data's calculation
+ * finish time and midnight, January 1, 1970 UTC
+ *
+ * @param tmpFinishTime the difference to be set in milliseconds
+ */
+ public void setCalculationFinishTime(long tmpFinishTime) {
+ this.calculationFinishTime = tmpFinishTime;
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Write the important contents of this HistogramDataManager to an
+ * ObjectOutputStream so this HistogramDataManager can be loaded at
+ * a later point in time. Important contents are the HistogramData
+ * objects, the previously calculated similarities and the origirnal input
+ * files
+ *
+ * @param tmpObjectOutputStream ObjectOutputStream to which the contents
+ * will be written
+ * @throws IOException any exception thrown by the underlying OutputStream
+ */
+ private synchronized void writeObject(java.io.ObjectOutputStream tmpObjectOutputStream) throws IOException {
+ tmpObjectOutputStream.writeObject(this.comparisonFeatureToDataMap.values().toArray(new HistogramData[this.comparisonFeatureToDataMap.values().size()]));
+ Iterator tmpIterator = this.nativeDataList.iterator();
+ double[][] tmpSimilaritiesArray = new double[this.nativeDataList.size()][this.nativeDataList.get(0).getSimilarities().length];
+ int tmpCounter = 0;
+ while (tmpIterator.hasNext()) {
+ tmpSimilaritiesArray[tmpCounter] = tmpIterator.next().getSimilarities();
+ tmpCounter++;
+ }
+ tmpObjectOutputStream.writeObject(tmpSimilaritiesArray);
+ tmpObjectOutputStream.writeUTF(this.inputFile1);
+ tmpObjectOutputStream.writeUTF(this.inputFile2);
+ tmpObjectOutputStream.writeLong(this.calculationStartTime);
+ tmpObjectOutputStream.writeLong(this.calculationFinishTime);
+ }
+
+ /**
+ * Read the contents of the given ObjectInputStream and use them to recreate
+ * the corresponding HistogramDataManager.
+ *
+ * @param tmpObjectInputStream ObjectInputStream from which the contents
+ * will be read
+ * @throws IOException any of the usual Input/Output related exceptions
+ * @throws ClassNotFoundException Class of a serialized object cannot be
+ * found
+ */
+ private void readObject(java.io.ObjectInputStream tmpObjectInputStream) throws IOException, ClassNotFoundException {
+ HistogramData[] tmpDataAray = (HistogramData[]) tmpObjectInputStream.readObject();
+ this.nativeDataList = new LinkedList<>();
+ this.comparisonFeatureToDataMap = new EnumMap<>(ComparisonFeature.class);
+ for (HistogramData tmpData : tmpDataAray) {
+ // Set nativeDataList because it transient in HistogramData
+ tmpData.setNativeDataList(this.nativeDataList);
+ this.comparisonFeatureToDataMap.putIfAbsent(ComparisonFeature.values()[tmpData.getComparisonFeautureNumber()], tmpData);
+ }
+ double[][] tmpSimilaritiesArray = (double[][]) tmpObjectInputStream.readObject();
+ for (int i = 0; i < tmpSimilaritiesArray.length; i++) {
+ this.nativeDataList.add(new ComparisonResult(tmpSimilaritiesArray[i], "", "", i));
+ }
+ this.inputFile1 = tmpObjectInputStream.readUTF();
+ this.inputFile2 = tmpObjectInputStream.readUTF();
+ this.calculationStartTime = tmpObjectInputStream.readLong();
+ this.calculationFinishTime = tmpObjectInputStream.readLong();
+ }
+
+ /**
+ * This method is not implemented
+ */
+ private void readObjectNoData() {
+ throw new RuntimeException("Method \"readObjectNoData\" is not implemented");
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/model/InputType.java b/src/main/java/de/whs/ibci/msc/model/InputType.java
new file mode 100644
index 0000000..8987a06
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/model/InputType.java
@@ -0,0 +1,32 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+/**
+ * Defines different supported data types for the molecule set input
+ *
+ * @author Jan-Mathis Hein
+ */
+public enum InputType {
+
+ //
+ SMILES,
+ SDF;
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/model/JobTaskManager.java b/src/main/java/de/whs/ibci/msc/model/JobTaskManager.java
new file mode 100644
index 0000000..86706b6
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/model/JobTaskManager.java
@@ -0,0 +1,680 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.Reader;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.concurrent.ConcurrentLinkedQueue;
+import java.util.Queue;
+import java.util.concurrent.Executors;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.ThreadLocalRandom;
+
+/**
+ * Manages the cancelation and execution of the ParseAndCompareTasks. This class
+ * also communicates its progress and handles the task's inputs.
+ *
+ * @author Jan-Mathis Hein
+ */
+public class JobTaskManager implements PropertyChangeListener{
+
+ //
+ /**
+ * True if this TaskManager is initializing task, executing tasks or
+ * processing the results of tasks, false otherwise. Is also used for
+ * cancelation
+ */
+ private boolean isStillWorking;
+
+ /**
+ * True if a valid first input type has been set, false otherwise
+ */
+ private boolean hasValidInputType1;
+
+ /**
+ * True if a valid second input type has been set, false otherwise
+ */
+ private boolean hasValidInputType2;
+
+ /**
+ * True if a valid first input file has been chosen, false otherwise
+ */
+ private boolean hasValidInputFile1;
+
+ /**
+ * True if a valid second input file has been chosen, false otherwise
+ */
+ private boolean hasValidInputFile2;
+
+ /**
+ * True if the HistogramDataManager has been created, false otherwise
+ */
+ private boolean hasCreatedHistogramDataManager;
+
+ /**
+ * An array that defines which features will be considered for
+ * the comparison. The index corresponds to the number of the feature
+ */
+ private boolean[] considerFeature;
+
+ /**
+ * Highest task progress value reached so far
+ */
+ private double highestProgressValue;
+
+ /**
+ * Number of created ParseAndCompareTasks
+ */
+ private double numberOfParseAndCompareTasks;
+
+ /**
+ * ExecutorService that handles threads and the execution of the tasks
+ */
+ private ExecutorService executorService;
+
+ /**
+ * First input file which contains a string encoding of the molecule set
+ */
+ private File inputFile1;
+
+ /**
+ * Second input file which contains a string encoding of the molecule set
+ */
+ private File inputFile2;
+
+ /**
+ * Manages the histogram data for each ComparisonFeature
+ */
+ private HistogramDataManager histogramDataManager;
+
+ /**
+ * Type of input of the first input file
+ */
+ private InputType inputType1;
+
+ /**
+ * Type of input of the second input file
+ */
+ private InputType inputType2;
+
+ /**
+ * Number of threads that can be used concurrently by the ExecutorService
+ */
+ private int numberOfParallelThreads;
+
+ /**
+ * Default number of bins in a histogram
+ */
+ private int defaultNumberOfBins;
+
+ /**
+ * Number of inputs that one set has as a surplus
+ */
+ private int numberOfUnpairedInputs;
+
+ /**
+ * List of features that are considered for the comparison. Is never null
+ */
+ private final List consideredFeaturesList = new LinkedList<>();
+
+ /**
+ * PropertyChangeSupport that manages the firing of PropertyChangeEvents and
+ * the adding and removing of PropertyChangeListeners
+ */
+ private final PropertyChangeSupport propertyChangeSupport;
+
+ /**
+ * Queue of ComparisonResults of ParseAndCompareTasks that finished
+ * successfully. Is never null
+ */
+ private final Queue comparisonResultsQueue = new ConcurrentLinkedQueue<>();
+
+ /**
+ * Queue of ComparisonResults of ParseAndCompareTask that did not finish
+ * successfully. Is never null
+ */
+ private final Queue failedComparisonsQueue = new ConcurrentLinkedQueue<>();
+
+ /**
+ * Queue of ParseAndCompareTasks that were initialized but not
+ * submitted for execution yet. Is never null
+ */
+ private final Queue remainingParseAndCompareTasksQueue = new ConcurrentLinkedQueue<>();
+
+ /**
+ * Queue of ParseAndCompareTasks that have been submitted for
+ * execution. Is never null
+ */
+ private final Queue submittedParseAndCompareTasksQueue = new ConcurrentLinkedQueue<>();
+ //
+ //
+ //
+ /**
+ * Initialize the instance variables
+ *
+ * @param tmpNumberOfParallelThreads number of threads that will be used in
+ * parallel
+ * @param tmpDefaultNumberOfBins default number of bins used for histograms
+ */
+ public JobTaskManager(int tmpNumberOfParallelThreads, int tmpDefaultNumberOfBins) {
+ this.hasCreatedHistogramDataManager = false;
+ this.isStillWorking = false;
+ this.hasValidInputType1 = false;
+ this.hasValidInputType2 = false;
+ this.hasValidInputFile1 = false;
+ this.hasValidInputFile2 = false;
+ this.propertyChangeSupport = new PropertyChangeSupport(this);
+ this.numberOfParallelThreads = tmpNumberOfParallelThreads;
+ this.defaultNumberOfBins = tmpDefaultNumberOfBins;
+ }
+ //
+ //
+ //
+ //
+ /**
+ * True if this JobTaskManager is initializing tasks, executing tasks or
+ * processing the results of tasks AND was not canceled, false otherwise
+ *
+ * @return true if this JobTaskManager is initializing tasks, executing
+ * tasks or processing the results of tasks AND was not canceled,
+ * false otherwise
+ */
+ public boolean isWorking() {
+ return this.isStillWorking;
+ }
+
+ /**
+ * Cancel the working process of this JobTaskManager i.e. the
+ * initialization, execution or result processing of tasks. The
+ * ExecutorService will be shutdown and disposed of. After cancelation the
+ * JobTaskManager can be reused.
+ */
+ public void cancelWorkingProcess() {
+ this.isStillWorking = false;
+ synchronized (this) {
+ int tmpNumberOfSubmittedTasks = this.submittedParseAndCompareTasksQueue.size();
+ for (int i = 0; i < tmpNumberOfSubmittedTasks; i++) {
+ try {
+ ParseAndCompareTask tmpTask = this.submittedParseAndCompareTasksQueue.poll();
+ tmpTask.cancel();
+ tmpTask.removePropertyChangeListener(this);
+ } catch (NullPointerException ex) {
+ // This can happen if the task finishes and in the process removes itself from the queue
+ }
+ }
+ this.remainingParseAndCompareTasksQueue.clear();
+ this.comparisonResultsQueue.clear();
+ this.failedComparisonsQueue.clear();
+ if (this.executorService != null) {
+ this.executorService.shutdown();
+ this.executorService = null;
+ }
+ }
+ }
+
+ /**
+ * Initialize the tasks and start their execution
+ *
+ * @throws IOException if there is something wrong with the input files
+ * @throws MSCInputException if the input is not sufficient
+ */
+ public synchronized void startTasks() throws IOException, MSCInputException {
+ //
+ if (!(this.hasValidInputFile1 && this.hasValidInputFile2)) {
+ throw new MSCInputException("Can't read these files");
+ }
+ if (this.consideredFeaturesList.isEmpty()) {
+ throw new MSCInputException("There are no features to compare");
+ }
+ if (!(this.hasValidInputType1 && this.hasValidInputType2)) {
+ throw new MSCInputException("The input types are invalid");
+ }
+ //
+ try (Reader tmpReader1 = new BufferedReader(new FileReader(this.inputFile1));
+ Reader tmpReader2 = new BufferedReader(new FileReader(this.inputFile2));) {
+ // Clears all queues
+ this.cancelWorkingProcess();
+ this.executorService = Executors.newFixedThreadPool(this.numberOfParallelThreads);
+ this.isStillWorking = true;
+ this.hasCreatedHistogramDataManager = false;
+ this.highestProgressValue = 0;
+ this.numberOfParseAndCompareTasks = 0;
+ this.numberOfUnpairedInputs = 0;
+ int tmpIdentifier = 0;
+ // Byte value of the new line character
+ int tmpSeperator = 10;
+ boolean tmpReachedEOF1, tmpReachedEOF2;
+ String tmpMolecule1, tmpMolecule2;
+ Object[] tmpArray1, tmpArray2;
+ outerLoop:
+ while (true) {
+ //
+ switch (this.inputType1) {
+ case SMILES:
+ tmpArray1 = this.readCharactersUntilSeperator(tmpReader1, tmpSeperator);
+ tmpMolecule1 = (String) tmpArray1[0];
+ tmpReachedEOF1 = (boolean) tmpArray1[1];
+ break;
+ case SDF:
+ tmpArray1 = this.readCharactersUntil$$$$(tmpReader1);
+ tmpMolecule1 = (String) tmpArray1[0];
+ tmpReachedEOF1 = (boolean) tmpArray1[1];
+ break;
+ default:
+ throw new MSCInputException("The first input type is invalid");
+ }
+ switch (this.inputType2) {
+ case SMILES:
+ tmpArray2 = this.readCharactersUntilSeperator(tmpReader2, tmpSeperator);
+ tmpMolecule2 = (String) tmpArray2[0];
+ tmpReachedEOF2 = (boolean) tmpArray2[1];
+ break;
+ case SDF:
+ tmpArray2 = this.readCharactersUntil$$$$(tmpReader2);
+ tmpMolecule2 = (String) tmpArray2[0];
+ tmpReachedEOF2 = (boolean) tmpArray2[1];
+ break;
+ default:
+ throw new MSCInputException("The second input type is invalid");
+ }
+ //
+ if (!tmpMolecule1.isEmpty() && !tmpMolecule2.isEmpty()) {
+ ParseAndCompareTask tmpTask = new ParseAndCompareTask(tmpMolecule1, tmpMolecule2, this.inputType1, this.inputType2, this.considerFeature, tmpIdentifier++);
+ tmpTask.addPropertyChangeListener(this);
+ this.remainingParseAndCompareTasksQueue.add(tmpTask);
+ this.numberOfParseAndCompareTasks++;
+ } else if (tmpMolecule1.isEmpty() ^ tmpMolecule2.isEmpty()) {
+ this.numberOfUnpairedInputs++;
+ }
+ if (!this.isStillWorking) {
+ return;
+ }
+ if (tmpReachedEOF1 && tmpReachedEOF2) {
+ break;
+ }
+ }
+ this.propertyChangeSupport.firePropertyChange("Unpaired inputs", 0, this.numberOfUnpairedInputs);
+ if (this.isStillWorking) {
+ for (int i = 0; i < this.numberOfParallelThreads; i++) {
+ ParseAndCompareTask tmpNextTask;
+ if ((tmpNextTask = this.remainingParseAndCompareTasksQueue.poll()) != null) {
+ this.submittedParseAndCompareTasksQueue.add(tmpNextTask);
+ this.executorService.submit(tmpNextTask);
+ }
+ }
+ }
+ } catch (Exception ex) {
+ throw ex;
+ }
+ }
+ //
+ //
+ /**
+ * Add a PropertyChangeListener that listens for changes fired from this
+ * JobTaskManager
+ *
+ * @param tmpListener a listener to be added
+ */
+ public void addPropertyChangeListener(PropertyChangeListener tmpListener) {
+ this.propertyChangeSupport.addPropertyChangeListener(tmpListener);
+ }
+
+ /**
+ * Remove a PropertyChangeListener
+ *
+ * @param tmpListener a listener to be removed
+ */
+ public void removePropertyChangeListener(PropertyChangeListener tmpListener) {
+ this.propertyChangeSupport.removePropertyChangeListener(tmpListener);
+ }
+
+ /**
+ * Handle all PropertyChangeEvents that reach this JobTaskManager.
+ *
+ * @param evt PropertyChangeEvent that reached this JobTaskManager
+ */
+ @Override
+ public void propertyChange(PropertyChangeEvent evt) {
+ try {
+ if (evt.getSource() instanceof ParseAndCompareTask) {
+ ParseAndCompareTask tmpTask = (ParseAndCompareTask) evt.getSource();
+ if (!tmpTask.isFinished()) {
+ return;
+ }
+ switch1:
+ switch (evt.getPropertyName()) {
+ case "Task completed":
+ if ((boolean) evt.getNewValue()) {
+ this.comparisonResultsQueue.add(tmpTask.getResult());
+ } else {
+ this.failedComparisonsQueue.add(tmpTask.getResult());
+ }
+ tmpTask.removePropertyChangeListener(this);
+ this.submittedParseAndCompareTasksQueue.remove(tmpTask);
+ double tmpProgress = tmpTask.getIdentifier() / this.numberOfParseAndCompareTasks;
+ if (tmpProgress > this.highestProgressValue && ThreadLocalRandom.current().nextInt(0, 100) < 5) {
+ this.highestProgressValue = tmpProgress;
+ this.propertyChangeSupport.firePropertyChange("ParseAndCompareTasks progress", 0.0, tmpProgress);
+ }
+ synchronized (this) {
+ if (this.isStillWorking && !this.remainingParseAndCompareTasksQueue.isEmpty()) {
+ ParseAndCompareTask tmpNextTask;
+ if ((tmpNextTask = this.remainingParseAndCompareTasksQueue.poll()) != null) {
+ this.submittedParseAndCompareTasksQueue.add(tmpNextTask);
+ this.executorService.submit(tmpNextTask);
+ }
+ } else if (this.remainingParseAndCompareTasksQueue.isEmpty() && this.submittedParseAndCompareTasksQueue.isEmpty() &&
+ this.isStillWorking && !this.hasCreatedHistogramDataManager) {
+ Iterator tmpIterator = this.comparisonResultsQueue.iterator();
+ if (!tmpIterator.hasNext()) {
+ throw new MSCInputException("At least one result is required");
+ }
+ ComparisonResult tmpResult = tmpIterator.next();
+ this.histogramDataManager = new HistogramDataManager(
+ this.consideredFeaturesList, this.defaultNumberOfBins, tmpResult,
+ this.inputFile1.getName(), this.inputFile2.getName()
+ );
+ while(tmpIterator.hasNext()) {
+ if (!this.isStillWorking) {
+ this.comparisonResultsQueue.clear();
+ this.failedComparisonsQueue.clear();
+ this.histogramDataManager = null;
+ break switch1;
+ }
+ tmpResult = tmpIterator.next();
+ this.histogramDataManager.addDatum(tmpResult);
+ }
+ for (ComparisonFeature tmpComparisonFeature : this.consideredFeaturesList) {
+ if (!this.isStillWorking) {
+ this.comparisonResultsQueue.clear();
+ this.failedComparisonsQueue.clear();
+ this.histogramDataManager = null;
+ break switch1;
+ }
+ this.histogramDataManager.getHistogramData(tmpComparisonFeature).call();
+ }
+ this.comparisonResultsQueue.clear();
+ this.hasCreatedHistogramDataManager = true;
+ this.propertyChangeSupport.firePropertyChange("ParseAndCompareTasks finished", false, true);
+ this.isStillWorking = false;
+ }
+ }
+ break;
+ default:
+ this.propertyChangeSupport.firePropertyChange("Exception", "JobTaskManager.propertyChange()", new RuntimeException("Unexpected PropertyChange:" + evt.getPropertyName()));
+ break;
+ }
+ }
+ } catch (Exception ex) {
+ this.propertyChangeSupport.firePropertyChange("Exception", "JobTaskManager.propertyChange(): " + evt.getPropertyName(), ex);
+ }
+ }
+ //
+ //
+ //
+ /**
+ * Get the HistogramDataManager that manages the histogram data for each
+ * ComparisonFeature
+ *
+ * @return the HistogramDataManager that manages the histogram data for each
+ * ComparisonFeature or null if the task execution has not been
+ * finished successfully
+ */
+ public synchronized HistogramDataManager getHistogramDataManager() {
+ return this.hasCreatedHistogramDataManager ? this.histogramDataManager : null;
+ }
+ //
+ //
+ /**
+ * Set the ComparisonFeatures which will be considered during the
+ * comparison.
+ *
+ * @param tmpConsideredFeatures specifies which ComparisonFeatures
+ * will be considered
+ * @throws MSCInputException if no ComparisonFeatures are being considered
+ */
+ public synchronized void setComparisonFeatures(boolean[] tmpConsideredFeatures) throws MSCInputException, IllegalArgumentException {
+ //
+ if (tmpConsideredFeatures == null || tmpConsideredFeatures.length < 1) {
+ throw new IllegalArgumentException("tmpConsideredFeatures is invalid");
+ }
+ //
+ this.considerFeature = tmpConsideredFeatures;
+ this.consideredFeaturesList.clear();
+ for (int i = 0; i < this.considerFeature.length; i++) {
+ if (this.considerFeature[i]) {
+ this.consideredFeaturesList.add(ComparisonFeature.values()[i]);
+ }
+ }
+ if (this.consideredFeaturesList.size() < 1 || this.consideredFeaturesList.isEmpty()) {
+ throw new MSCInputException("There are no features for the comparison");
+ }
+ }
+
+ /**
+ * Set the first input file
+ *
+ * @param tmpFile the input file
+ */
+ public synchronized void setInputFile1(File tmpFile) throws IllegalArgumentException {
+ //
+ if (tmpFile == null) {
+ throw new IllegalArgumentException("tmpFile is null");
+ }
+ //
+ this.inputFile1 = tmpFile;
+ this.hasValidInputFile1 = this.inputFile1.canRead();
+ }
+
+ /**
+ * Set the second input file
+ *
+ * @param tmpFile the input file
+ */
+ public synchronized void setInputFile2(File tmpFile) throws IllegalArgumentException {
+ //
+ if (tmpFile == null) {
+ throw new IllegalArgumentException("tmpFile is null");
+ }
+ //
+ this.inputFile2 = tmpFile;
+ this.hasValidInputFile2 = this.inputFile2.canRead();
+ }
+
+ /**
+ * Set the first input type
+ *
+ * @param tmpInputType the input type
+ */
+ public synchronized void setInputType1(InputType tmpInputType) {
+ this.inputType1 = tmpInputType;
+ this.hasValidInputType1 = this.inputType1 == InputType.SMILES || this.inputType1 == InputType.SDF;
+ }
+
+ /**
+ * Set the second input type
+ *
+ * @param tmpInputType the input type
+ */
+ public synchronized void setInputType2(InputType tmpInputType) {
+ this.inputType2 = tmpInputType;
+ this.hasValidInputType2 = this.inputType2 == InputType.SMILES || this.inputType2 == InputType.SDF;
+ }
+
+ /**
+ * Set the number of parallel threads to be used by the executor service and
+ * initialize a new executor service
+ *
+ * @param tmpNumberOfParallelThreads specifies the number of parallel
+ * threads
+ */
+ public synchronized void setNumberOfParallelThreads(int tmpNumberOfParallelThreads) {
+ this.numberOfParallelThreads = tmpNumberOfParallelThreads;
+ if (this.executorService != null) {
+ this.executorService.shutdown();
+ this.executorService = Executors.newFixedThreadPool(this.numberOfParallelThreads);
+ }
+ }
+
+ /**
+ * Set the default number of bins used for histograms
+ *
+ * @param tmpDefaultNumberOfBins specifies the default number of bins used
+ * for histograms
+ */
+ public void setDefaultNumberOfBins(int tmpDefaultNumberOfBins) {
+ this.defaultNumberOfBins = tmpDefaultNumberOfBins;
+ }
+ //
+ //
+ //
+ /**
+ * True if input file configuration can be read, false otherwise
+ *
+ * @return true if input file configuration can be read, false otherwise
+ */
+ public boolean canReadInput() {
+ return this.hasValidInputType1 && this.hasValidInputType2 && this.hasValidInputFile1 && this.hasValidInputFile2;
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Finalize this object by stopping the working process, shuting down the
+ * ExecutorService and calling Object.finalize()
+ */
+ @Override
+ @SuppressWarnings("deprecation")
+ protected void finalize() throws Throwable {
+ this.cancelWorkingProcess();
+ super.finalize();
+ }
+ //
+ //
+ //
+ /**
+ * Read characters from the stream of the given reader until the given
+ * seperator is read. Concatenate all read characters to a String. Return
+ * the String and true if the end of the stream has been reached and false
+ * otherwise
+ *
+ * @param tmpReader the reader from whos stream the characters will be read
+ * @param tmpSeperator specifies the seperator as its byte value
+ * @return an Object array where the first element is the concatenated
+ * String and the second element is a Boolean that is true if the end of
+ * the stream has been reached and false otherwise
+ * @throws IOException
+ */
+ private Object[] readCharactersUntilSeperator(Reader tmpReader, int tmpSeperator) throws IOException {
+ String tmpMolecule = "";
+ Boolean tmpReachedEndOfStream = false;
+ int tmpByte;
+ while (true) {
+ tmpByte = tmpReader.read();
+ if (tmpByte == tmpSeperator) {
+ break;
+ } else if (tmpByte == -1) {
+ tmpReachedEndOfStream = true;
+ break;
+ } else {
+ tmpMolecule += (char) tmpByte;
+ }
+ }
+ return new Object[]{tmpMolecule, tmpReachedEndOfStream};
+ }
+
+ /**
+ * Read characters from the stream of the given reader until '$$$$' is read.
+ * Concatenate all read characters to a String. Return the String and true
+ * if the end of the stream has been reached and false otherwise
+ *
+ * @param tmpReader the reader from whos stream the characters will be read
+ * @return an Object array where the first element is the concatenated
+ * String and the second element is a Boolean that is true if the end of
+ * the stream has been reached and false otherwise
+ * @throws IOException
+ */
+ private Object[] readCharactersUntil$$$$(Reader tmpReader) throws IOException {
+ String tmpMolecule = "";
+ Boolean tmpReachedEndOfStream = false;
+ int tmpByte;
+ int tmp$Counter = 0;
+ loop:
+ while (true) {
+ tmpByte = tmpReader.read();
+ outerSwitch:
+ switch (tmpByte) {
+ case -1:
+ tmpReachedEndOfStream = true;
+ break loop;
+ case 36:
+ tmpMolecule += (char) tmpByte;
+ tmp$Counter++;
+ while (true) {
+ tmpByte = tmpReader.read();
+ switch (tmpByte) {
+ case -1:
+ tmpReachedEndOfStream = true;
+ break loop;
+ case 36:
+ tmpMolecule += (char) tmpByte;
+ tmp$Counter++;
+ break;
+ case 10:
+ tmpMolecule += (char) tmpByte;
+ if (tmp$Counter == 4) {
+ tmp$Counter = 0;
+ break loop;
+ }
+ tmp$Counter = 0;
+ break outerSwitch;
+ // Characters that are allowed to follow '$$$$' like \r
+ case 13:
+ tmpMolecule += (char) tmpByte;
+ if (tmp$Counter != 4) {
+ tmp$Counter = 0;
+ break outerSwitch;
+ }
+ break;
+ default:
+ tmpMolecule += (char) tmpByte;
+ tmp$Counter = 0;
+ break outerSwitch;
+ }
+ }
+ default:
+ tmpMolecule += (char) tmpByte;
+ tmp$Counter = 0;
+ break;
+ }
+ }
+ return new Object[]{tmpMolecule, tmpReachedEndOfStream};
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/model/MSCInputException.java b/src/main/java/de/whs/ibci/msc/model/MSCInputException.java
new file mode 100644
index 0000000..9c41e57
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/model/MSCInputException.java
@@ -0,0 +1,73 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+/**
+ * An Exception that is thrown whenever the Molecule Set Comparator application
+ * received unexpected input with which it can't continue operating
+ *
+ * @author Jan-Mathis Hein
+ */
+public class MSCInputException extends Exception {
+
+ //
+ /**
+ * A serial version UID to check whether the loaded data is compatible
+ */
+ private static final long serialVersionUID = 1L;
+ //
+ //
+ //
+ /**
+ * A message that furhter describes the exception
+ */
+ private String message;
+ //
+ //
+ //
+ /**
+ * Create an Exception without a message
+ */
+ public MSCInputException() {
+ super();
+ }
+
+ /**
+ * Create an Exception with the specified message
+ *
+ * @param tmpMessage specifies the message
+ */
+ public MSCInputException(String tmpMessage) {
+ super(tmpMessage);
+ this.message = tmpMessage;
+ }
+ //
+ //
+ //
+ /**
+ * Return a string representation of the MSCInputException
+ *
+ * @return a string representation of the MSCInputException
+ */
+ @Override
+ public String toString() {
+ return "InsufficientDataException: " + this.message;
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/model/ParseAndCompareTask.java b/src/main/java/de/whs/ibci/msc/model/ParseAndCompareTask.java
new file mode 100644
index 0000000..3d47182
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/model/ParseAndCompareTask.java
@@ -0,0 +1,1390 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.util.concurrent.Callable;
+import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.aromaticity.Aromaticity;
+import org.openscience.cdk.aromaticity.ElectronDonation;
+import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.fingerprint.*;
+import org.openscience.cdk.graph.Cycles;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IAtomType;
+import org.openscience.cdk.io.SMILESWriter;
+import org.openscience.cdk.io.iterator.IIteratingChemObjectReader;
+import org.openscience.cdk.io.iterator.IteratingSDFReader;
+import org.openscience.cdk.qsar.descriptors.molecular.*;
+import org.openscience.cdk.ringsearch.AllRingsFinder;
+import org.openscience.cdk.ringsearch.RingSearch;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
+import org.openscience.cdk.similarity.Tanimoto;
+import org.openscience.cdk.smiles.SmiFlavor;
+import org.openscience.cdk.smiles.SmilesGenerator;
+import org.openscience.cdk.smiles.SmilesParser;
+import org.openscience.cdk.tools.CDKHydrogenAdder;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
+import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
+
+/**
+ * A task that parses a pair of string encodings to a molecule pair and compares
+ * the pair on the basis of specified ComparisonFeatures.
+ *
+ * @author Jan-Mathis Hein
+ */
+public class ParseAndCompareTask implements Callable {
+
+ //
+ /**
+ * True if this task has finished in any way, false otherwise
+ */
+ private boolean isFinished;
+
+ /**
+ * True if this task has been started, false otherwise
+ */
+ private boolean isStarted;
+
+ /**
+ * True if this task has been cancelled, false otherwise
+ */
+ private boolean isCancelled;
+
+ /**
+ * An array that defines on the basis of which ComparisonFeatures the
+ * comparison will be made. The index corresponds to the number of the
+ * ComparisonFeature
+ */
+ private final boolean[] consideredComparisonFeature;
+
+ /**
+ * The result of the comparison
+ */
+ private ComparisonResult result;
+
+ /**
+ * InputType of the first molecule
+ */
+ private final InputType type1;
+
+ /**
+ * InputType of the second molecule
+ */
+ private final InputType type2;
+
+ /**
+ * Number that identifies this task
+ */
+ private final int identifier;
+
+ /**
+ * PropertyChangeSupport that manages the firing of PropertyChangeEvents and
+ * the adding and removing of PropertyChangeListeners
+ */
+ private final PropertyChangeSupport propertyChangeSupport;
+
+ /**
+ * String encoding of the first molecule
+ */
+ private String molecule1;
+
+ /**
+ * String encoding of the second molecule
+ */
+ private String molecule2;
+ //
+ //
+ //
+ /**
+ * Initialize the instance variables
+ *
+ * @param tmpInput1 specifies the first input string
+ * @param tmpInput2 specifies the second input string
+ * @param tmpType1 specifies the first input type
+ * @param tmpType2 specifies the first input type
+ * @param tmpConsiderFeature specifies on the basis of which
+ * ComparisonFeatures the comparison will be made
+ * @param tmpIdentifier unique identifier for this task
+ */
+ public ParseAndCompareTask(String tmpInput1, String tmpInput2, InputType tmpType1, InputType tmpType2, boolean[] tmpConsiderFeature, int tmpIdentifier) {
+ this.isStarted = false;
+ this.isFinished = false;
+ this.isCancelled = false;
+ this.molecule1 = tmpInput1;
+ this.molecule2 = tmpInput2;
+ this.type1 = tmpType1;
+ this.type2 = tmpType2;
+ this.consideredComparisonFeature = tmpConsiderFeature;
+ this.identifier = tmpIdentifier;
+ this.propertyChangeSupport = new PropertyChangeSupport(this);
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Parse the input strings to molecules and compare them on the basis of the
+ * specified ComparisonFeatures
+ *
+ * @return null
+ */
+ @Override
+ public Void call() {
+ try {
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ this.isStarted = true;
+ double[] tmpSimilarities = new double[this.consideredComparisonFeature.length];
+ IAtomContainer[] tmpMoleculePair = new IAtomContainer[2];
+ SmilesParser tmpSmilesParser = new SmilesParser(SilentChemObjectBuilder.getInstance());
+ IIteratingChemObjectReader tmpSdfParser = new IteratingSDFReader(new StringReader(""), DefaultChemObjectBuilder.getInstance());
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ switch (this.type1) {
+ case SMILES:
+ tmpMoleculePair[0] = tmpSmilesParser.parseSmiles(this.molecule1);
+ break;
+ case SDF:
+ tmpSdfParser.setReader(new StringReader(this.molecule1));
+ tmpMoleculePair[0] = tmpSdfParser.next();
+ break;
+ default:
+ break;
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ switch (this.type2) {
+ case SMILES:
+ tmpMoleculePair[1] = tmpSmilesParser.parseSmiles(this.molecule2);
+ break;
+ case SDF:
+ tmpSdfParser.setReader(new StringReader(this.molecule2));
+ tmpMoleculePair[1] = tmpSdfParser.next();
+ break;
+ default:
+ break;
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ CDKAtomTypeMatcher tmpCDKAtomTypeMatcher = CDKAtomTypeMatcher.getInstance(DefaultChemObjectBuilder.getInstance());
+ CDKHydrogenAdder tmpCDKHydrogenAdder = CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance());
+ Aromaticity tmpAromaticity = new Aromaticity(ElectronDonation.cdk(), Cycles.or(Cycles.all(), Cycles.cdkAromaticSet()));
+ RingSearch tmpRingSearch;
+ for (IAtomContainer tmpMolecule : tmpMoleculePair) {
+ tmpRingSearch = new RingSearch(tmpMolecule);
+ for (IAtom tmpAtom : tmpMolecule.atoms()) {
+ tmpAtom.setIsInRing(tmpRingSearch.cyclic(tmpAtom));
+ IAtomType tmpType = tmpCDKAtomTypeMatcher.findMatchingAtomType(tmpMolecule, tmpAtom);
+ AtomTypeManipulator.configure(tmpAtom, tmpType);
+ }
+ tmpCDKHydrogenAdder.addImplicitHydrogens(tmpMolecule);
+ AtomContainerManipulator.convertImplicitToExplicitHydrogens(tmpMolecule);
+ // Sets aromaticity flags
+ tmpAromaticity.apply(tmpMolecule);
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.ACIDIC_GROUP_COUNT.getFeatureNumber()]) {
+ AcidicGroupCountDescriptor tmpAcidicGroupCountDescriptor = new AcidicGroupCountDescriptor();
+ tmpAcidicGroupCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.ACIDIC_GROUP_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAcidicGroupCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAcidicGroupCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.ALL_RINGS_COUNT.getFeatureNumber()]) {
+ try {
+ AllRingsFinder.usingThreshold(AllRingsFinder.Threshold.PubChem_99);
+ AllRingsFinder tmpAllRingsFinder = new AllRingsFinder();
+ int tmpAllRingsCount1 = tmpAllRingsFinder.findAllRings(tmpMoleculePair[0]).getAtomContainerCount();
+ int tmpAllRingsCount2 = tmpAllRingsFinder.findAllRings(tmpMoleculePair[1]).getAtomContainerCount();
+ tmpSimilarities[ComparisonFeature.ALL_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpAllRingsCount1 - tmpAllRingsCount2);
+ } catch (CDKException CDKException) {
+ tmpSimilarities[ComparisonFeature.ALL_RINGS_COUNT.getFeatureNumber()] = Double.NaN;
+ }
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.A_LOGP.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.A_LOGP_2.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.MOLAR_REFRACTIVITY.getFeatureNumber()]) {
+ ALOGPDescriptor tmpALOGPDescriptor = new ALOGPDescriptor();
+ tmpALOGPDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpALOGPDescriptor.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpALOGPDescriptor.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ // Ghose-Grippen logP
+ if (this.consideredComparisonFeature[ComparisonFeature.A_LOGP.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.A_LOGP.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]));
+ }
+ // Ghose-Grippen logP 2
+ if (this.consideredComparisonFeature[ComparisonFeature.A_LOGP_2.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.A_LOGP_2.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[1]) - Double.parseDouble(tmpArray2[1]));
+ }
+ // Molar refractivity
+ if (this.consideredComparisonFeature[ComparisonFeature.MOLAR_REFRACTIVITY.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.MOLAR_REFRACTIVITY.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[2]) - Double.parseDouble(tmpArray2[2]));
+ }
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.APOL.getFeatureNumber()]) {
+ APolDescriptor tmpAPolDescriptor = new APolDescriptor();
+ tmpAPolDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.APOL.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAPolDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAPolDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.AROMATIC_ATOM_COUNT.getFeatureNumber()]) {
+ AromaticAtomsCountDescriptor tmpAromaticAtomsCountDescriptor = new AromaticAtomsCountDescriptor();
+ tmpAromaticAtomsCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpAromaticAtomsCountDescriptor.setParameters(new Object[] {true});
+ tmpSimilarities[ComparisonFeature.AROMATIC_ATOM_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAromaticAtomsCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAromaticAtomsCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.AROMATIC_BOND_COUNT.getFeatureNumber()]) {
+ AromaticBondsCountDescriptor tmpAromaticBondsCountDescriptor = new AromaticBondsCountDescriptor();
+ tmpAromaticBondsCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpAromaticBondsCountDescriptor.setParameters(new Object[] {true});
+ tmpSimilarities[ComparisonFeature.AROMATIC_BOND_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAromaticBondsCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAromaticBondsCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ AtomCountDescriptor tmpAtomCountDescriptor = new AtomCountDescriptor();
+ tmpAtomCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ // Atom count
+ if (this.consideredComparisonFeature[ComparisonFeature.ATOM_COUNT.getFeatureNumber()]) {
+ tmpAtomCountDescriptor.setParameters(new Object[] {"*"});
+ tmpSimilarities[ComparisonFeature.ATOM_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ // Carbon count
+ if (this.consideredComparisonFeature[ComparisonFeature.CARBON_COUNT.getFeatureNumber()]) {
+ tmpAtomCountDescriptor.setParameters(new Object[] {"C"});
+ tmpSimilarities[ComparisonFeature.CARBON_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ // Oxygen count
+ if (this.consideredComparisonFeature[ComparisonFeature.OXYGEN_COUNT.getFeatureNumber()]) {
+ tmpAtomCountDescriptor.setParameters(new Object[] {"O"});
+ tmpSimilarities[ComparisonFeature.OXYGEN_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ // Sulfur count
+ if (this.consideredComparisonFeature[ComparisonFeature.SULFUR_COUNT.getFeatureNumber()]) {
+ tmpAtomCountDescriptor.setParameters(new Object[] {"S"});
+ tmpSimilarities[ComparisonFeature.SULFUR_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ // Nitrogen count
+ if (this.consideredComparisonFeature[ComparisonFeature.NITROGEN_COUNT.getFeatureNumber()]) {
+ tmpAtomCountDescriptor.setParameters(new Object[] {"N"});
+ tmpSimilarities[ComparisonFeature.NITROGEN_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ // Phosphor count
+ if (this.consideredComparisonFeature[ComparisonFeature.PHOSPHOR_COUNT.getFeatureNumber()]) {
+ tmpAtomCountDescriptor.setParameters(new Object[] {"P"});
+ tmpSimilarities[ComparisonFeature.PHOSPHOR_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpAtomCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.ATS_CHARGE1.getFeatureNumber()]) {
+ AutocorrelationDescriptorCharge tmpAutocorrelationDescriptorCharge = new AutocorrelationDescriptorCharge();
+ tmpAutocorrelationDescriptorCharge.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpAutocorrelationDescriptorCharge.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpAutocorrelationDescriptorCharge.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ tmpSimilarities[ComparisonFeature.ATS_CHARGE1.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]));
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.ATS_MASS1.getFeatureNumber()]) {
+ AutocorrelationDescriptorMass tmpAutocorrelationDescriptorMass = new AutocorrelationDescriptorMass();
+ tmpAutocorrelationDescriptorMass.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpAutocorrelationDescriptorMass.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpAutocorrelationDescriptorMass.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ tmpSimilarities[ComparisonFeature.ATS_MASS1.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]));
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.ATS_POLARIZABILITY1.getFeatureNumber()]) {
+ AutocorrelationDescriptorPolarizability tmpAutocorrelationDescriptorPolarizability = new AutocorrelationDescriptorPolarizability();
+ tmpAutocorrelationDescriptorPolarizability.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpAutocorrelationDescriptorPolarizability.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpAutocorrelationDescriptorPolarizability.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ tmpSimilarities[ComparisonFeature.ATS_POLARIZABILITY1.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]));
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.BASIC_GROUP_COUNT.getFeatureNumber()]) {
+ BasicGroupCountDescriptor tmpBasicGroupCountDescriptor = new BasicGroupCountDescriptor();
+ tmpBasicGroupCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.BASIC_GROUP_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpBasicGroupCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpBasicGroupCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ BondCountDescriptor tmpBondCountDescriptor = new BondCountDescriptor();
+ tmpBondCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ // Bond count
+ if (this.consideredComparisonFeature[ComparisonFeature.BOND_COUNT.getFeatureNumber()]) {
+ tmpBondCountDescriptor.setParameters(new Object[] {""});
+ tmpSimilarities[ComparisonFeature.BOND_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ // Single bond count
+ if (this.consideredComparisonFeature[ComparisonFeature.SINGLE_BOND_COUNT.getFeatureNumber()]) {
+ tmpBondCountDescriptor.setParameters(new Object[] {"s"});
+ tmpSimilarities[ComparisonFeature.SINGLE_BOND_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ // Double bond count
+ if (this.consideredComparisonFeature[ComparisonFeature.DOUBLE_BOND_COUNT.getFeatureNumber()]) {
+ tmpBondCountDescriptor.setParameters(new Object[] {"d"});
+ tmpSimilarities[ComparisonFeature.DOUBLE_BOND_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ // Triple bond count
+ if (this.consideredComparisonFeature[ComparisonFeature.TRIPLE_BOND_COUNT.getFeatureNumber()]) {
+ tmpBondCountDescriptor.setParameters(new Object[] {"t"});
+ tmpSimilarities[ComparisonFeature.TRIPLE_BOND_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ // Quadruple bond count
+ if (this.consideredComparisonFeature[ComparisonFeature.QUADRUPLE_BOND_COUNT.getFeatureNumber()]) {
+ tmpBondCountDescriptor.setParameters(new Object[] {"q"});
+ tmpSimilarities[ComparisonFeature.QUADRUPLE_BOND_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpBondCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.BPOL.getFeatureNumber()]) {
+ BPolDescriptor tmpBPolDescriptor = new BPolDescriptor();
+ tmpBPolDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.BPOL.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpBPolDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpBPolDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.C1SP1_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.C2SP1_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.C1SP2_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.C2SP2_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.C3SP2_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.C1SP3_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.C2SP3_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.C3SP3_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.C4SP3_COUNT.getFeatureNumber()]) {
+ CarbonTypesDescriptor tmpCarbonTypesDescriptor = new CarbonTypesDescriptor();
+ tmpCarbonTypesDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpCarbonTypesDescriptor.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpCarbonTypesDescriptor.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ // C1SP1 count
+ if (this.consideredComparisonFeature[ComparisonFeature.C1SP1_COUNT.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.C1SP1_COUNT.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]));
+ }
+ // C2SP1 count
+ if (this.consideredComparisonFeature[ComparisonFeature.C2SP1_COUNT.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.C2SP1_COUNT.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[1]) - Double.parseDouble(tmpArray2[1]));
+ }
+ // C1SP2 count
+ if (this.consideredComparisonFeature[ComparisonFeature.C1SP2_COUNT.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.C1SP2_COUNT.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[2]) - Double.parseDouble(tmpArray2[2]));
+ }
+ // C2SP2 count
+ if (this.consideredComparisonFeature[ComparisonFeature.C2SP2_COUNT.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.C2SP2_COUNT.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[3]) - Double.parseDouble(tmpArray2[3]));
+ }
+ // C3SP2 count
+ if (this.consideredComparisonFeature[ComparisonFeature.C3SP2_COUNT.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.C3SP2_COUNT.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[4]) - Double.parseDouble(tmpArray2[4]));
+ }
+ // C1SP3 count
+ if (this.consideredComparisonFeature[ComparisonFeature.C1SP3_COUNT.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.C1SP3_COUNT.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[5]) - Double.parseDouble(tmpArray2[5]));
+ }
+ // C2SP3 count
+ if (this.consideredComparisonFeature[ComparisonFeature.C2SP3_COUNT.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.C2SP3_COUNT.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[6]) - Double.parseDouble(tmpArray2[6]));
+ }
+ // C3SP3 count
+ if (this.consideredComparisonFeature[ComparisonFeature.C3SP3_COUNT.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.C3SP3_COUNT.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[7]) - Double.parseDouble(tmpArray2[7]));
+ }
+ // C4SP3 count
+ if (this.consideredComparisonFeature[ComparisonFeature.C4SP3_COUNT.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.C4SP3_COUNT.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[8]) - Double.parseDouble(tmpArray2[8]));
+ }
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.EQUALITY.getFeatureNumber()]) {
+ SmilesGenerator tmpSmilesGenerator = new SmilesGenerator(SmiFlavor.Unique);
+ String tmpUniqueSmiles1 = tmpSmilesGenerator.create(tmpMoleculePair[0]);
+ String tmpUniqueSmiles2 = tmpSmilesGenerator.create(tmpMoleculePair[1]);
+ tmpSimilarities[ComparisonFeature.EQUALITY.getFeatureNumber()] = tmpUniqueSmiles1.equals(tmpUniqueSmiles2) ? 1 : 0;
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.ECCENTRIC_CONNECTIVITY_INDEX.getFeatureNumber()]) {
+ EccentricConnectivityIndexDescriptor tmpEccentricConnectivityIndexDescriptor = new EccentricConnectivityIndexDescriptor();
+ tmpEccentricConnectivityIndexDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.ECCENTRIC_CONNECTIVITY_INDEX.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpEccentricConnectivityIndexDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpEccentricConnectivityIndexDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.FMF.getFeatureNumber()]) {
+ FMFDescriptor tmpFMFDescriptor = new FMFDescriptor();
+ tmpFMFDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.FMF.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpFMFDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpFMFDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.FCSP3.getFeatureNumber()]) {
+ FractionalCSP3Descriptor tmpFractionalCSP3Descriptor = new FractionalCSP3Descriptor();
+ tmpFractionalCSP3Descriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.FCSP3.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpFractionalCSP3Descriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpFractionalCSP3Descriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.FPSA.getFeatureNumber()]) {
+ FractionalPSADescriptor tmpFractionalPSADescriptor = new FractionalPSADescriptor();
+ tmpFractionalPSADescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.FPSA.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpFractionalPSADescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpFractionalPSADescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.FRAGMENT_COMPLEXITY.getFeatureNumber()]) {
+ FragmentComplexityDescriptor tmpFragmentComplexityDescriptor = new FragmentComplexityDescriptor();
+ tmpFragmentComplexityDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.FRAGMENT_COMPLEXITY.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpFragmentComplexityDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpFragmentComplexityDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.H_BOND_ACCEPTOR_COUNT.getFeatureNumber()]) {
+ HBondAcceptorCountDescriptor tmpHBondAcceptorCountDescriptor = new HBondAcceptorCountDescriptor();
+ tmpHBondAcceptorCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpHBondAcceptorCountDescriptor.setParameters(new Object[] {true});
+ tmpSimilarities[ComparisonFeature.H_BOND_ACCEPTOR_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpHBondAcceptorCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpHBondAcceptorCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.H_BOND_DONOR_COUNT.getFeatureNumber()]) {
+ HBondDonorCountDescriptor tmpHBondDonorCountDescriptor = new HBondDonorCountDescriptor();
+ tmpHBondDonorCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.H_BOND_DONOR_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpHBondDonorCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpHBondDonorCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.JP_LOGP.getFeatureNumber()]) {
+ JPlogPDescriptor tmpJPlogPDescriptor = new JPlogPDescriptor();
+ tmpJPlogPDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.JP_LOGP.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpJPlogPDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpJPlogPDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_1.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_2.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_3.getFeatureNumber()]) {
+ KappaShapeIndicesDescriptor tmpKappaShapeIndicesDescriptor = new KappaShapeIndicesDescriptor();
+ tmpKappaShapeIndicesDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpKappaShapeIndicesDescriptor.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpKappaShapeIndicesDescriptor.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ // First kappa shape index
+ if (this.consideredComparisonFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_1.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.KAPPA_SHAPE_INDEX_1.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]));
+ }
+ // Second kappa shape index
+ if (this.consideredComparisonFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_2.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.KAPPA_SHAPE_INDEX_2.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[1]) - Double.parseDouble(tmpArray2[1]));
+ }
+ // Third kappa shape index
+ if (this.consideredComparisonFeature[ComparisonFeature.KAPPA_SHAPE_INDEX_3.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.KAPPA_SHAPE_INDEX_3.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[2]) - Double.parseDouble(tmpArray2[2]));
+ }
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.LARGEST_CHAIN.getFeatureNumber()]) {
+ LargestChainDescriptor tmpLargestChainDescriptor = new LargestChainDescriptor();
+ tmpLargestChainDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ // Doesn't need to check for rings because that is done in the preproccesing
+ tmpLargestChainDescriptor.setParameters(new Object[] {false, false});
+ tmpSimilarities[ComparisonFeature.LARGEST_CHAIN.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpLargestChainDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpLargestChainDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.LARGEST_PI_SYSTEM.getFeatureNumber()]) {
+ LargestPiSystemDescriptor tmpLargestPiSystemDescriptor = new LargestPiSystemDescriptor();
+ tmpLargestPiSystemDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ // Doesn't need to check for aromaticity because that is done in the preproccesing
+ tmpLargestPiSystemDescriptor.setParameters(new Object[] {false});
+ tmpSimilarities[ComparisonFeature.LARGEST_PI_SYSTEM.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpLargestPiSystemDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpLargestPiSystemDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.LONGEST_ALIPHATIC_CHAIN.getFeatureNumber()]) {
+ LongestAliphaticChainDescriptor tmpLongestAliphaticChainDescriptor = new LongestAliphaticChainDescriptor();
+ tmpLongestAliphaticChainDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ // Doesn't need to check for rings because that is done in the preproccesing
+ tmpLongestAliphaticChainDescriptor.setParameters(new Object[] {false});
+ tmpSimilarities[ComparisonFeature.LONGEST_ALIPHATIC_CHAIN.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpLongestAliphaticChainDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpLongestAliphaticChainDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.MANNHOLD_LOGP.getFeatureNumber()]) {
+ MannholdLogPDescriptor tmpMannholdLogPDescriptor = new MannholdLogPDescriptor();
+ tmpMannholdLogPDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.MANNHOLD_LOGP.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpMannholdLogPDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpMannholdLogPDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.PETITJEAN_NUMBER.getFeatureNumber()]) {
+ PetitjeanNumberDescriptor tmpPetitjeanNumberDescriptor = new PetitjeanNumberDescriptor();
+ tmpPetitjeanNumberDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.PETITJEAN_NUMBER.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpPetitjeanNumberDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpPetitjeanNumberDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.PETITJEAN_SHAPE_INDEX.getFeatureNumber()]) {
+ PetitjeanShapeIndexDescriptor tmpPetitjeanShapeIndexDescriptor = new PetitjeanShapeIndexDescriptor();
+ tmpPetitjeanShapeIndexDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpPetitjeanShapeIndexDescriptor.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpPetitjeanShapeIndexDescriptor.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ tmpSimilarities[ComparisonFeature.PETITJEAN_SHAPE_INDEX.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]));
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.ROTATABLE_BOND_COUNT.getFeatureNumber()]) {
+ RotatableBondsCountDescriptor tmpRotatableBondsCountDescriptor = new RotatableBondsCountDescriptor();
+ tmpRotatableBondsCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ // Don't include terminal bonds and don't exclude amide bonds
+ tmpRotatableBondsCountDescriptor.setParameters(new Object[] {false, false});
+ tmpSimilarities[ComparisonFeature.ROTATABLE_BOND_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpRotatableBondsCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpRotatableBondsCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.ALL_SMALL_RINGS_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.AROMATIC_RINGS_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.SIZE_3_RINGS_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.SIZE_4_RINGS_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.SIZE_5_RINGS_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.SIZE_6_RINGS_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.SIZE_7_RINGS_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.SIZE_8_RINGS_COUNT.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.SIZE_9_RINGS_COUNT.getFeatureNumber()]) {
+ SmallRingDescriptor tmpSmallRingDescriptor = new SmallRingDescriptor();
+ tmpSmallRingDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ double tmpRingCount1, tmpRingCount2;
+ String[] tmpArray1 = tmpSmallRingDescriptor.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpSmallRingDescriptor.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ //All small rings count
+ if (this.consideredComparisonFeature[ComparisonFeature.ALL_SMALL_RINGS_COUNT.getFeatureNumber()]) {
+ tmpRingCount1 = Double.parseDouble(tmpArray1[0]);
+ tmpRingCount2 = Double.parseDouble(tmpArray2[0]);
+ tmpSimilarities[ComparisonFeature.ALL_SMALL_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpRingCount1 - tmpRingCount2);
+ }
+ //Aromatic rings count
+ if (this.consideredComparisonFeature[ComparisonFeature.AROMATIC_RINGS_COUNT.getFeatureNumber()]) {
+ tmpRingCount1 = Double.parseDouble(tmpArray1[1]);
+ tmpRingCount2 = Double.parseDouble(tmpArray2[1]);
+ tmpSimilarities[ComparisonFeature.AROMATIC_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpRingCount1 - tmpRingCount2);
+ }
+ //Size 3 rings count
+ if (this.consideredComparisonFeature[ComparisonFeature.SIZE_3_RINGS_COUNT.getFeatureNumber()]) {
+ tmpRingCount1 = Double.parseDouble(tmpArray1[4]);
+ tmpRingCount2 = Double.parseDouble(tmpArray2[4]);
+ tmpSimilarities[ComparisonFeature.SIZE_3_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpRingCount1 - tmpRingCount2);
+ }
+ //Size 4 rings count
+ if (this.consideredComparisonFeature[ComparisonFeature.SIZE_4_RINGS_COUNT.getFeatureNumber()]) {
+ tmpRingCount1 = Double.parseDouble(tmpArray1[5]);
+ tmpRingCount2 = Double.parseDouble(tmpArray2[5]);
+ tmpSimilarities[ComparisonFeature.SIZE_4_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpRingCount1 - tmpRingCount2);
+ }
+ //Size 5 rings count
+ if (this.consideredComparisonFeature[ComparisonFeature.SIZE_5_RINGS_COUNT.getFeatureNumber()]) {
+ tmpRingCount1 = Double.parseDouble(tmpArray1[6]);
+ tmpRingCount2 = Double.parseDouble(tmpArray2[6]);
+ tmpSimilarities[ComparisonFeature.SIZE_5_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpRingCount1 - tmpRingCount2);
+ }
+ //Size 6 rings count
+ if (this.consideredComparisonFeature[ComparisonFeature.SIZE_6_RINGS_COUNT.getFeatureNumber()]) {
+ tmpRingCount1 = Double.parseDouble(tmpArray1[7]);
+ tmpRingCount2 = Double.parseDouble(tmpArray2[7]);
+ tmpSimilarities[ComparisonFeature.SIZE_6_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpRingCount1 - tmpRingCount2);
+ }
+ //Size 7 rings count
+ if (this.consideredComparisonFeature[ComparisonFeature.SIZE_7_RINGS_COUNT.getFeatureNumber()]) {
+ tmpRingCount1 = Double.parseDouble(tmpArray1[8]);
+ tmpRingCount2 = Double.parseDouble(tmpArray2[8]);
+ tmpSimilarities[ComparisonFeature.SIZE_7_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpRingCount1 - tmpRingCount2);
+ }
+ //Size 8 rings count
+ if (this.consideredComparisonFeature[ComparisonFeature.SIZE_8_RINGS_COUNT.getFeatureNumber()]) {
+ tmpRingCount1 = Double.parseDouble(tmpArray1[9]);
+ tmpRingCount2 = Double.parseDouble(tmpArray2[9]);
+ tmpSimilarities[ComparisonFeature.SIZE_8_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpRingCount1 - tmpRingCount2);
+ }
+ //Size 9 rings count
+ if (this.consideredComparisonFeature[ComparisonFeature.SIZE_9_RINGS_COUNT.getFeatureNumber()]) {
+ tmpRingCount1 = Double.parseDouble(tmpArray1[10]);
+ tmpRingCount2 = Double.parseDouble(tmpArray2[10]);
+ tmpSimilarities[ComparisonFeature.SIZE_9_RINGS_COUNT.getFeatureNumber()] = Math.abs(tmpRingCount1 - tmpRingCount2);
+ }
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.SPIRO_ATOM_COUNT.getFeatureNumber()]) {
+ SpiroAtomCountDescriptor tmpSpiroAtomCountDescriptor = new SpiroAtomCountDescriptor();
+ tmpSpiroAtomCountDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.SPIRO_ATOM_COUNT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpSpiroAtomCountDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpSpiroAtomCountDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ // Basic
+ IFingerprinter tmpFingerprinter;
+ if (this.consideredComparisonFeature[ComparisonFeature.TANIMOTO_BASIC_FINGERPRINTER.getFeatureNumber()]) {
+ tmpFingerprinter = new Fingerprinter();
+ tmpSimilarities[ComparisonFeature.TANIMOTO_BASIC_FINGERPRINTER.getFeatureNumber()] = Tanimoto.calculate(
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[0]),
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[1])
+ );
+ }
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ // LINGO
+ if (this.consideredComparisonFeature[ComparisonFeature.TANIMOTO_LINGO_FINGERPRINTER.getFeatureNumber()]) {
+ tmpFingerprinter = new LingoFingerprinter();
+ tmpSimilarities[ComparisonFeature.TANIMOTO_LINGO_FINGERPRINTER.getFeatureNumber()] = Tanimoto.calculate(
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[0]),
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[1])
+ );
+ }
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ // Extended
+ if (this.consideredComparisonFeature[ComparisonFeature.TANIMOTO_EXTENDED_FINGERPRINTER.getFeatureNumber()]) {
+ tmpFingerprinter = new ExtendedFingerprinter();
+ tmpSimilarities[ComparisonFeature.TANIMOTO_EXTENDED_FINGERPRINTER.getFeatureNumber()] = Tanimoto.calculate(
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[0]),
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[1])
+ );
+ }
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ // E-State
+ if (this.consideredComparisonFeature[ComparisonFeature.TANIMOTO_ESTATE_FINGERPRINTER.getFeatureNumber()]) {
+ tmpFingerprinter = new EStateFingerprinter();
+ tmpSimilarities[ComparisonFeature.TANIMOTO_ESTATE_FINGERPRINTER.getFeatureNumber()] = Tanimoto.calculate(
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[0]),
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[1])
+ );
+ }
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ // PubChem
+ if (this.consideredComparisonFeature[ComparisonFeature.TANIMOTO_PUBCHEM_FINGERPRINTER.getFeatureNumber()]) {
+ tmpFingerprinter = new PubchemFingerprinter(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.TANIMOTO_PUBCHEM_FINGERPRINTER.getFeatureNumber()] = Tanimoto.calculate(
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[0]),
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[1])
+ );
+ }
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ // Shortest path
+ if (this.consideredComparisonFeature[ComparisonFeature.TANIMOTO_SHORTEST_PATH_FINGERPRINTER.getFeatureNumber()]) {
+ tmpFingerprinter = new ShortestPathFingerprinter();
+ tmpSimilarities[ComparisonFeature.TANIMOTO_SHORTEST_PATH_FINGERPRINTER.getFeatureNumber()] = Tanimoto.calculate(
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[0]),
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[1])
+ );
+ }
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ // Substructure
+ if (this.consideredComparisonFeature[ComparisonFeature.TANIMOTO_SUBSTRUCTURE_FINGERPRINTER.getFeatureNumber()]) {
+ tmpFingerprinter = new SubstructureFingerprinter();
+ tmpSimilarities[ComparisonFeature.TANIMOTO_SUBSTRUCTURE_FINGERPRINTER.getFeatureNumber()] = Tanimoto.calculate(
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[0]),
+ tmpFingerprinter.getBitFingerprint(tmpMoleculePair[1])
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.TPSA.getFeatureNumber()]) {
+ TPSADescriptor tmpTPSADescriptor = new TPSADescriptor();
+ tmpTPSADescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ // Doesn't need to check for aromaticity because that is done in the preproccesing
+ tmpTPSADescriptor.setParameters(new Object[] {false});
+ tmpSimilarities[ComparisonFeature.TPSA.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpTPSADescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpTPSADescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.VABC.getFeatureNumber()]) {
+ VABCDescriptor tmpVABCDescriptor = new VABCDescriptor();
+ tmpVABCDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.VABC.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpVABCDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpVABCDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.V_ADJ_MA.getFeatureNumber()]) {
+ VAdjMaDescriptor tmpVAdjMaDescriptor = new VAdjMaDescriptor();
+ tmpVAdjMaDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.V_ADJ_MA.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpVAdjMaDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpVAdjMaDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.MOLECULAR_WEIGHT.getFeatureNumber()]) {
+ WeightDescriptor tmpWeightDescriptor = new WeightDescriptor();
+ tmpWeightDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ // Calculate the weight of all atoms
+ tmpWeightDescriptor.setParameters(new Object[] {"*"});
+ tmpSimilarities[ComparisonFeature.MOLECULAR_WEIGHT.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpWeightDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpWeightDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.WEIGHTED_PATH_1.getFeatureNumber()]) {
+ WeightedPathDescriptor tmpWeightedPathDescriptor = new WeightedPathDescriptor();
+ tmpWeightedPathDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpWeightedPathDescriptor.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpWeightedPathDescriptor.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ tmpSimilarities[ComparisonFeature.WEIGHTED_PATH_1.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]));
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.WIENER_PATH.getFeatureNumber()] ||
+ this.consideredComparisonFeature[ComparisonFeature.WIENER_POLARITY.getFeatureNumber()]) {
+ WienerNumbersDescriptor tmpWienerNumbersDescriptor = new WienerNumbersDescriptor();
+ tmpWienerNumbersDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ String[] tmpArray1 = tmpWienerNumbersDescriptor.calculate(tmpMoleculePair[0]).getValue().toString().split(",");
+ String[] tmpArray2 = tmpWienerNumbersDescriptor.calculate(tmpMoleculePair[1]).getValue().toString().split(",");
+ // Wiener path number
+ if (this.consideredComparisonFeature[ComparisonFeature.WIENER_PATH.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.WIENER_PATH.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[0]) - Double.parseDouble(tmpArray2[0]));
+ }
+ // Wiener polarity number
+ if (this.consideredComparisonFeature[ComparisonFeature.WIENER_POLARITY.getFeatureNumber()]) {
+ tmpSimilarities[ComparisonFeature.WIENER_POLARITY.getFeatureNumber()] = Math.abs(Double.parseDouble(tmpArray1[1]) - Double.parseDouble(tmpArray2[1]));
+ }
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.X_LOGP.getFeatureNumber()]) {
+ XLogPDescriptor tmpXLogPDescriptor = new XLogPDescriptor();
+ tmpXLogPDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ // Aromaticity is already checked in preprocessing; use the salicyl acid correction factor
+ tmpXLogPDescriptor.setParameters(new Object[] {false, true});
+ tmpSimilarities[ComparisonFeature.X_LOGP.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpXLogPDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpXLogPDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.consideredComparisonFeature[ComparisonFeature.ZAGREB_INDEX.getFeatureNumber()]) {
+ ZagrebIndexDescriptor tmpZagrebIndexDescriptor = new ZagrebIndexDescriptor();
+ tmpZagrebIndexDescriptor.initialise(DefaultChemObjectBuilder.getInstance());
+ tmpSimilarities[ComparisonFeature.ZAGREB_INDEX.getFeatureNumber()] = Math.abs(
+ Double.parseDouble(tmpZagrebIndexDescriptor.calculate(tmpMoleculePair[0]).getValue().toString()) -
+ Double.parseDouble(tmpZagrebIndexDescriptor.calculate(tmpMoleculePair[1]).getValue().toString())
+ );
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ //
+ if (this.type1 != InputType.SMILES) {
+ StringWriter tmpWriter = new StringWriter();
+ SMILESWriter tmpSmilesWriter = new SMILESWriter(tmpWriter);
+ tmpSmilesWriter.writeAtomContainer(tmpMoleculePair[0]);
+ this.molecule1 = tmpWriter.toString();
+ }
+ if (this.type2 != InputType.SMILES) {
+ StringWriter tmpWriter = new StringWriter();
+ SMILESWriter tmpSmilesWriter = new SMILESWriter(tmpWriter);
+ tmpSmilesWriter.writeAtomContainer(tmpMoleculePair[1]);
+ this.molecule2 = tmpWriter.toString();
+ }
+ //
+ //
+ if (this.isCancelled) {
+ this.result = new ComparisonResult("The comparison was cancelled", this.identifier);
+ this.isFinished = true;
+ return null;
+ }
+ //
+ this.result = new ComparisonResult(tmpSimilarities, this.molecule1, this.molecule2, this.identifier);
+ this.isFinished = true;
+ this.propertyChangeSupport.firePropertyChange("Task completed", false, true);
+ return null;
+ } catch (Exception ex) {
+ this.result = new ComparisonResult(ex.toString(), this.identifier);
+ this.isFinished = true;
+ this.propertyChangeSupport.firePropertyChange("Task completed", true, false);
+ return null;
+ }
+ }
+
+ /**
+ * Cancel the execution of this task
+ */
+ public void cancel(){
+ this.isCancelled = true;
+ }
+
+ /**
+ * True if this task finished its execution in any way, false otherwise
+ *
+ * @return true if this task finished its execution in any way,
+ * false otherwise
+ */
+ public boolean isFinished() {
+ return this.isFinished;
+ }
+
+ /**
+ * True if this task is still working, false otherwise
+ *
+ * @return true if this task is still working, false otherwise
+ */
+ public boolean isWorking() {
+ return this.isStarted && !this.isFinished;
+ }
+
+ /**
+ * True is this task has been started, false otherwise
+ *
+ * @return true is this task has been started, false otherwise
+ */
+ public boolean isStarted() {
+ return this.isStarted;
+ }
+ //
+ //
+ /**
+ * Get the result of the execution of this task
+ *
+ * @return the result of the execution of this task
+ */
+ public ComparisonResult getResult() {
+ return this.result;
+ }
+
+ /**
+ * Get the identifier of this task
+ *
+ * @return the identifier of this task
+ */
+ public int getIdentifier() {
+ return this.identifier;
+ }
+ //
+ //
+ /**
+ * Add a PropertyChangeListener that listens for changes from this
+ * CompareAtomContainerPairTask
+ *
+ * @param tmpListener a listener to be added
+ */
+ public void addPropertyChangeListener(PropertyChangeListener tmpListener) {
+ this.propertyChangeSupport.addPropertyChangeListener(tmpListener);
+ }
+
+ /**
+ * Remove a PropertyChangeListener
+ *
+ * @param tmpListener a listener to be removed
+ */
+ public void removePropertyChangeListener(PropertyChangeListener tmpListener) {
+ this.propertyChangeSupport.removePropertyChangeListener(tmpListener);
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Cancel the execution of this task and call Object.finialize()
+ */
+ @Override
+ @SuppressWarnings("deprecation")
+ protected void finalize() throws Throwable {
+ this.cancel();
+ super.finalize();
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/utility/GeneralUtilities.java b/src/main/java/de/whs/ibci/msc/utility/GeneralUtilities.java
new file mode 100644
index 0000000..e550d96
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/utility/GeneralUtilities.java
@@ -0,0 +1,375 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.utility;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.RandomAccessFile;
+import java.io.StringWriter;
+import java.nio.channels.FileChannel;
+import java.nio.channels.FileLock;
+import java.util.Date;
+import java.util.MissingResourceException;
+import java.util.Optional;
+import java.util.ResourceBundle;
+import java.util.logging.FileHandler;
+import java.util.logging.Formatter;
+import java.util.logging.Handler;
+import java.util.logging.Level;
+import java.util.logging.LogRecord;
+import java.util.logging.Logger;
+import javafx.scene.control.Alert;
+import javafx.scene.control.Button;
+import javafx.scene.control.ButtonBar;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.TextFormatter;
+import javafx.stage.Window;
+
+/**
+ * This class provides utility methods for the MSC application. The methods in
+ * this class are used for logging, to show various dialogs, to get Strings from
+ * property files and for checking whether only a single instance of the
+ * application is running
+ *
+ * @author Jan-Mathis Hein
+ */
+public final class GeneralUtilities {
+
+ //
+ /**
+ * Resource bundle for the user interface texts
+ */
+ private static final ResourceBundle RESOURCE_BUNDLE = ResourceBundle.getBundle("resources/UIText");
+
+ /**
+ * A logger that documents exceptions and information about the execution of
+ * the application
+ */
+ private static final Logger LOGGER = Logger.getLogger(GeneralUtilities.class.getName());
+
+ /**
+ * File used to check whether only a single instance of the application is
+ * running
+ */
+ private static File singleInstanceFile;
+
+ /**
+ * FileChannel used to attempt to acquire an exclusive lock on the
+ * singleInstanceFile
+ */
+ private static FileChannel fileChannel;
+
+ /**
+ * A token representing a lock on the singleInstanceFile
+ */
+ private static FileLock fileLock;
+ //
+ //
+ //
+ //
+ /**
+ * Return false if the calling application is not the only currently running
+ * instance or if an error occurs, true otherwise
+ *
+ * @return false if the calling application is not the only currently
+ * running instance or if an error occurs, true otherwise
+ */
+ public static boolean isSingleInstance() {
+ try {
+ GeneralUtilities.singleInstanceFile = new File(MSCConstants.MSC_FILES_DIRECTORY.getAbsolutePath() + File.separator + "MSC_SingleInstance.lck");
+ if (GeneralUtilities.singleInstanceFile.exists()) {
+ GeneralUtilities.singleInstanceFile.delete();
+ }
+ GeneralUtilities.fileChannel = new RandomAccessFile(GeneralUtilities.singleInstanceFile, "rw").getChannel();
+ GeneralUtilities.fileLock = GeneralUtilities.fileChannel.tryLock();
+ if (GeneralUtilities.fileLock == null) {
+ GeneralUtilities.fileChannel.close();
+ return false;
+ }
+ Thread tmpThread = new Thread(() -> {
+ try {
+ if (GeneralUtilities.fileLock != null) {
+ GeneralUtilities.fileLock.release();
+ GeneralUtilities.fileChannel.close();
+ GeneralUtilities.singleInstanceFile.delete();
+ }
+ } catch (IOException ex) {
+ // Can't log this because the log-handlers were already removed
+ ex.printStackTrace();
+ }
+ });
+ Runtime.getRuntime().addShutdownHook(tmpThread);
+ return true;
+ } catch (IOException ex) {
+ return false;
+ }
+ }
+ //
+ //
+ /**
+ * Initialize the logger by setting the level, adding the handlers and
+ * creating the log-file.
+ */
+ public static synchronized void initializeLogger() {
+ GeneralUtilities.LOGGER.setLevel(Level.INFO);
+ GeneralUtilities.addNewHandlersToLogger();
+ }
+
+ /**
+ * Write information about the excpetion to the log-file
+ *
+ * @param tmpLevel the severity of the exception
+ * @param tmpException the exception that has been thrown and that will be
+ * logged
+ * @return false if the logging failed and true otherwise
+ */
+ public static synchronized boolean logException(Level tmpLevel, Exception tmpException) {
+ //
+ if (tmpException == null || tmpLevel == null) {
+ return false;
+ }
+ if (GeneralUtilities.LOGGER.getHandlers().length == 0 || GeneralUtilities.LOGGER.getHandlers()[0] == null) {
+ if(!GeneralUtilities.addNewHandlersToLogger()) {
+ return false;
+ }
+ }
+ //
+ StringWriter tmpStringWriter = new StringWriter();
+ tmpException.printStackTrace(new PrintWriter(tmpStringWriter));
+ LogRecord tmpLogRecord = new LogRecord(tmpLevel, tmpStringWriter.toString());
+ Handler tmpFileHandler = GeneralUtilities.LOGGER.getHandlers()[0];
+ tmpFileHandler.setFormatter(new Formatter() {
+ @Override
+ public String format(LogRecord tmpLogRecord) {
+ return tmpLogRecord.getThreadID() + ": " + new Date(tmpLogRecord.getMillis()) + ": " + tmpLogRecord.getMessage() + "\n";
+ }
+ });
+ tmpFileHandler.publish(tmpLogRecord);
+ return true;
+ }
+
+ /**
+ * Write a given message to the log-file
+ *
+ * @param tmpLevel the importance of the message
+ * @param tmpSourceClass the class from where the message originated
+ * @param tmpSourceMethod the method from where the message originated
+ * @param tmpMessage the message that will be logged
+ * @return false if the logging failed and true otherwise
+ */
+ public static synchronized boolean logMessage(Level tmpLevel, String tmpSourceClass, String tmpSourceMethod, String tmpMessage) {
+ //
+ if (tmpLevel == null || tmpSourceClass == null || tmpSourceMethod == null || tmpMessage == null) {
+ return false;
+ }
+ if (GeneralUtilities.LOGGER.getHandlers().length == 0 || GeneralUtilities.LOGGER.getHandlers()[0] == null) {
+ if(!GeneralUtilities.addNewHandlersToLogger()) {
+ return false;
+ }
+ }
+ //
+ LogRecord tmpLogRecord = new LogRecord(tmpLevel, tmpMessage);
+ tmpLogRecord.setSourceClassName(tmpSourceClass);
+ tmpLogRecord.setSourceMethodName(tmpSourceMethod);
+ Handler tmpFileHandler = GeneralUtilities.LOGGER.getHandlers()[0];
+ tmpFileHandler.setFormatter(new Formatter() {
+ @Override
+ public String format(LogRecord tmpLogRecord) {
+ return tmpLogRecord.getThreadID() + ": " + tmpLogRecord.getSourceClassName() +
+ ": " + tmpLogRecord.getSourceMethodName() + ": " + new Date(tmpLogRecord.getMillis()) +
+ ": " + tmpLogRecord.getLevel().toString() + ": " + tmpLogRecord.getMessage() + "\n";
+ }
+ });
+ tmpFileHandler.publish(tmpLogRecord);
+ return true;
+ }
+
+ /**
+ * Get an abstract representation of the log-file
+ *
+ * @return an abstract representation of the log-file
+ */
+ public static synchronized File getLogFile() {
+ return new File(MSCConstants.MSC_FILES_DIRECTORY.getAbsolutePath() + File.separator + "MSC_LOG.log");
+ }
+
+ /**
+ * Close and remove all the handlers from the logger. Optionaly you
+ * can reset the log-file and logger by deleting and reconstructing the
+ * log-file and adding new handlers to the logger.
+ *
+ * @param tmpResetLogFile if true, the log-file and logger will be reset
+ * otherwise not
+ * @return true if everything went as intended
+ */
+ public static synchronized boolean closeAndRemoveHandlersFromLogger(boolean tmpResetLogFile) {
+ for (Handler tmpFileHandler : GeneralUtilities.LOGGER.getHandlers()) {
+ tmpFileHandler.flush();
+ tmpFileHandler.close();
+ GeneralUtilities.LOGGER.removeHandler(tmpFileHandler);
+ }
+ if (tmpResetLogFile) {
+ GeneralUtilities.getLogFile().delete();
+ // Creates a new file
+ return(GeneralUtilities.addNewHandlersToLogger());
+ }
+ return true;
+ }
+ //
+ //
+ /**
+ * Show an error dialog with the specified information.
+ *
+ * @param tmpOwner specifies the owner window of this dialog
+ * @param tmpContentText a text that describes the error
+ * @param tmpOrigin origin of the error
+ */
+ public static void showErrorDialog(Window tmpOwner, String tmpContentText , String tmpOrigin) {
+ Alert tmpErrorDialog = new Alert(Alert.AlertType.ERROR, tmpContentText, ButtonType.OK);
+ tmpErrorDialog.initOwner(tmpOwner);
+ tmpErrorDialog.setTitle(GeneralUtilities.getUIText("ErrorAlertDialog.Title.text"));
+ tmpErrorDialog.getDialogPane().setHeaderText(String.format(GeneralUtilities.getUIText("ErrorAlertDialog.Header.text"), tmpOrigin));
+ Button tmpButton = (Button) tmpErrorDialog.getDialogPane().lookupButton(ButtonType.OK);
+ GuiUtilities.setMinMaxPrefSize(tmpButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ tmpErrorDialog.showAndWait();
+ }
+
+ /**
+ * Show an info dialog with the specified information
+ *
+ * @param tmpOwner specifies the owner window of this dialog
+ * @param tmpInfoText the information that will be displayes
+ */
+ public static void showInfoDialog(Window tmpOwner, String tmpInfoText) {
+ Alert tmpInfoDialog = new Alert(Alert.AlertType.INFORMATION, "", ButtonType.OK);
+ tmpInfoDialog.initOwner(tmpOwner);
+ tmpInfoDialog.setTitle(GeneralUtilities.getUIText("InfoDialog.Title.text"));
+ tmpInfoDialog.getDialogPane().setHeaderText(tmpInfoText);
+ Button tmpButton = (Button) tmpInfoDialog.getDialogPane().lookupButton(ButtonType.OK);
+ GuiUtilities.setMinMaxPrefSize(tmpButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ tmpInfoDialog.showAndWait();
+ }
+
+ /**
+ * Show a confirmation dialog with the specified information
+ *
+ * @param tmpOwner specifies the owner window of this dialog
+ * @param tmpContentText specifies the content area's text
+ * @param tmpTitle the title of the dialog
+ * @param tmpHeaderText specifies the header's text
+ * @return the ButtonType the user chose (APPLY or CANCEL)
+ */
+ public static Optional showConfirmationDialog(Window tmpOwner, String tmpContentText, String tmpTitle, String tmpHeaderText) {
+ ButtonType tmpYesButtonType = new ButtonType(GeneralUtilities.getUIText("ConfirmationDialog.Yes.text"), ButtonBar.ButtonData.APPLY);
+ ButtonType tmpNoButtonType = new ButtonType(GeneralUtilities.getUIText("ConfirmationDialog.No.text"), ButtonBar.ButtonData.CANCEL_CLOSE);
+ Alert tmpConfirmationDialog = new Alert(Alert.AlertType.CONFIRMATION, tmpContentText, tmpYesButtonType, tmpNoButtonType);
+ tmpConfirmationDialog.initOwner(tmpOwner);
+ tmpConfirmationDialog.setTitle(tmpTitle);
+ tmpConfirmationDialog.getDialogPane().setHeaderText(tmpHeaderText);
+ Button tmpButton = (Button) tmpConfirmationDialog.getDialogPane().lookupButton(tmpYesButtonType);
+ GuiUtilities.setMinMaxPrefSize(tmpButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ tmpButton = (Button) tmpConfirmationDialog.getDialogPane().lookupButton(tmpNoButtonType);
+ GuiUtilities.setMinMaxPrefSize(tmpButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ return tmpConfirmationDialog.showAndWait();
+ }
+ //
+ //
+ /**
+ * Get the text specified by the key from the resource bundle
+ *
+ * @param tmpKey specifies the text which to get
+ * @return the retrieved text or an exception message if the retrieval was
+ * not possible
+ */
+ public static String getUIText(String tmpKey) {
+ try {
+ return RESOURCE_BUNDLE.getString(tmpKey).trim();
+ } catch (MissingResourceException ex) {
+ return "Key '" + tmpKey + "' not found.";
+ }
+ }
+ //
+ //
+ /**
+ * Get a TextFormatter that formats all input so that the resulting
+ * text will always represent an unsigned whole number
+ *
+ * @return a TextFormatter that formats all input so that the resulting
+ * text will always represent an unsigned whole number
+ */
+ public static TextFormatter getUnsignedIntegerTextFormatter() {
+ return new TextFormatter<>((TextFormatter.Change tmpChange) -> {
+ if (!tmpChange.getControlNewText().matches("\\d*")) {
+ tmpChange.setText("");
+ }
+ try {
+ Integer.parseInt(tmpChange.getControlNewText());
+ tmpChange.getControl().setStyle("-fx-background-color: white;");
+ } catch (NumberFormatException ex) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ }
+ return tmpChange;
+ });
+ }
+
+ /**
+ * Get a TextFormatter that formats all input so that the resulting
+ * text will always represent a signed decimal number.
+ *
+ * @return a TextFormatter that formats all input so that the resulting
+ * text will always represent a signed decimal number
+ */
+ public static TextFormatter getSignedDecimalNumberTextFormatter() {
+ return new TextFormatter<>((TextFormatter.Change tmpChange) -> {
+ if (!tmpChange.getControlNewText().matches("[-\\+]?\\d*\\.?\\d*E?\\d*")) {
+ tmpChange.setText("");
+ }
+ try {
+ Double.parseDouble(tmpChange.getControlNewText());
+ tmpChange.getControl().setStyle("-fx-background-color: white;");
+ } catch (NumberFormatException ex) {
+ tmpChange.getControl().setStyle("-fx-background-color: red;");
+ }
+ return tmpChange;
+ });
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Add new handlers to the logger and create a new log-file
+ *
+ * @return true if all new handlers have been added
+ */
+ private static synchronized boolean addNewHandlersToLogger() {
+ try {
+ GeneralUtilities.getLogFile().createNewFile();
+ // Appends to already exisiting file
+ FileHandler tmpFileHandler = new FileHandler(GeneralUtilities.getLogFile().getAbsolutePath(), true);
+ GeneralUtilities.LOGGER.addHandler(tmpFileHandler);
+ return true;
+ } catch (IOException | SecurityException ex) {
+ ex.printStackTrace();
+ return false;
+ }
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/utility/GuiUtilities.java b/src/main/java/de/whs/ibci/msc/utility/GuiUtilities.java
new file mode 100644
index 0000000..9e64579
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/utility/GuiUtilities.java
@@ -0,0 +1,185 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.utility;
+
+import java.awt.Graphics2D;
+import java.awt.image.BufferedImage;
+import javafx.embed.swing.SwingFXUtils;
+import javafx.geometry.Insets;
+import javafx.scene.image.Image;
+import javafx.scene.layout.Border;
+import javafx.scene.layout.BorderStroke;
+import javafx.scene.layout.BorderStrokeStyle;
+import javafx.scene.layout.BorderWidths;
+import javafx.scene.layout.CornerRadii;
+import javafx.scene.layout.Region;
+import javafx.scene.paint.Color;
+import javafx.scene.paint.Paint;
+
+/**
+ * Defines some constants and utility methods for a graphical user interface.
+ * This class can't be instantiated
+ *
+ * @author Jan-Mathis Hein
+ */
+public final class GuiUtilities {
+
+ //
+ /**
+ * Standard horizontal gap between controls that are located in the same
+ * region
+ */
+ public static final double HORIZONTAL_GAP_BETWEEN_CONTROLS = 10;
+
+ /**
+ * Standard vertical gap between controls that are located in the same
+ * region
+ */
+ public static final double VERTICAL_GAP_BETWEEN_CONTROLS = 10;
+
+ /**
+ * Standard insets that are used to isolate different regions from
+ * each other
+ */
+ public static final Insets STANDARD_INSETS = new Insets(10);
+
+ /**
+ * An image of a white square with a dimension of 200 x 200
+ */
+ public static final Image WHITE_SQUARE;
+
+ /**
+ * A border that lets a region appear as if it is lowered
+ */
+ public static final Border LOWERED_BORDER = new Border(new BorderStroke(
+ Color.color(0.4, 0.4, 0.4), Color.color(0.99, 0.99, 0.99),
+ Color.color(0.99, 0.99, 0.99), Color.color(0.4, 0.4, 0.4),
+ BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ BorderStrokeStyle.SOLID, new CornerRadii(0), new BorderWidths(2), new Insets(0)
+ ));
+
+ /**
+ * A border that lets a region appear as if it is raised
+ */
+ public static final Border RAISED_BORDER = new Border(new BorderStroke(
+ Color.color(0.99, 0.99, 0.99), Color.color(0.4, 0.4, 0.4),
+ Color.color(0.4, 0.4, 0.4), Color.color(0.99, 0.99, 0.99),
+ BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ BorderStrokeStyle.SOLID, new CornerRadii(0), new BorderWidths(2), new Insets(0)
+ ));
+
+ /**
+ * A thin red border
+ */
+ public static final Border RED_BORDER = new Border(new BorderStroke(
+ Paint.valueOf("Red"), Paint.valueOf("Red"), Paint.valueOf("Red"),
+ Paint.valueOf("Red"), BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ new CornerRadii(0), new BorderWidths(2), new Insets(0)
+ ));
+
+ /**
+ * A thin green border
+ */
+ public static final Border GREEN_BORDER = new Border(new BorderStroke(
+ Paint.valueOf("Green"), Paint.valueOf("Green"), Paint.valueOf("Green"),
+ Paint.valueOf("Green"), BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ new CornerRadii(0), new BorderWidths(2), new Insets(0)
+ ));
+
+ /**
+ * A thin black border
+ */
+ public static final Border BLACK_BORDER = new Border(new BorderStroke(
+ Paint.valueOf("Black"), Paint.valueOf("Black"), Paint.valueOf("Black"),
+ Paint.valueOf("Black"), BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ new CornerRadii(0), new BorderWidths(2), new Insets(0)
+ ));
+
+ /**
+ * The standard width of a button
+ */
+ public static final double BUTTON_WIDTH = 100;
+
+ /**
+ * The standard width of a textfield
+ */
+ public static final double TEXT_FIELD_WIDTH = 160;
+
+ /**
+ * The standard width of a small button
+ */
+ public static final double SMALL_BUTTON_WIDTH = 75.2;
+
+ /**
+ * The standard height of a button
+ */
+ public static final double BUTTON_HEIGHT = 25;
+ //
+ //
+ //
+ static {
+ BufferedImage tmpImage = new BufferedImage(200, 200, BufferedImage.TYPE_INT_RGB);
+ Graphics2D tmpGraphics2D = tmpImage.createGraphics();
+ tmpGraphics2D.setColor(java.awt.Color.WHITE);
+ tmpGraphics2D.fillRect(0, 0, tmpImage.getWidth(), tmpImage.getHeight());
+ WHITE_SQUARE = SwingFXUtils.toFXImage(tmpImage, null);
+ }
+ //
+ //
+ //
+ /**
+ * Set the maximal, minimal and prefered size of a specified region
+ *
+ * @param tmpRegion specifies the region
+ * @param tmpWidth specifies the height
+ * @param tmpHeight specifies the width
+ */
+ public static void setMinMaxPrefSize(Region tmpRegion, double tmpWidth, double tmpHeight) {
+ GuiUtilities.setMinMaxPrefWidth(tmpRegion, tmpWidth);
+ GuiUtilities.setMinMaxPrefHeight(tmpRegion, tmpHeight);
+ }
+
+ /**
+ * Set the maximal, minimal and prefered width of a specified region
+ *
+ * @param tmpRegion specifies the region
+ * @param tmpWidth specifies the width
+ */
+ public static void setMinMaxPrefWidth(Region tmpRegion, double tmpWidth) {
+ tmpRegion.setMinWidth(tmpWidth);
+ tmpRegion.setMaxWidth(tmpWidth);
+ tmpRegion.setPrefWidth(tmpWidth);
+ }
+
+ /**
+ * Set the maximal, minimal and prefered height of a specified region
+ *
+ * @param tmpRegion specifies the region
+ * @param tmpHeight specifies the height
+ */
+ public static void setMinMaxPrefHeight(Region tmpRegion, double tmpHeight) {
+ tmpRegion.setMinHeight(tmpHeight);
+ tmpRegion.setMaxHeight(tmpHeight);
+ tmpRegion.setPrefHeight(tmpHeight);
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/utility/MSCConstants.java b/src/main/java/de/whs/ibci/msc/utility/MSCConstants.java
new file mode 100644
index 0000000..863834f
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/utility/MSCConstants.java
@@ -0,0 +1,87 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.utility;
+
+import java.io.File;
+
+/**
+ * Defines some constants for the MSC application.
+ * This class can't be instantiated
+ *
+ * @author Jan-Mathis Hein
+ */
+public final class MSCConstants {
+
+ //
+ /**
+ * The main window's minimal width
+ */
+ public final static double MINIMAL_MAIN_WINDOW_WIDTH = 514.0;
+
+ /**
+ * The main window's minimal height
+ */
+ public final static double MINIMAL_MAIN_WINDOW_HEIGHT = 686.0;
+
+ /**
+ * The MoleculePairDisplayerStage's minimal width
+ */
+ public final static double MINIMAL_MOLECULE_DISPLAYER_WIDTH = 859.0;
+
+ /**
+ * The MoleculePairDisplayerStage's minimal height
+ */
+ public final static double MINIMAL_MOLECULE_DISPLAYER_HEIGHT = 444.0;
+
+ /**
+ * Directory where important MSC files will be saved
+ */
+ public static final File MSC_FILES_DIRECTORY = new File(System.getProperty("user.dir") + File.separator + "MSC_Files");
+
+ /**
+ * A String representing the current version of the MSC
+ */
+ public final static String MSC_VERSION = "1.0";
+
+ /**
+ * Minimal java version needed to run the application.
+ */
+ public final static String JAVA_VERSION = "11";
+
+ /**
+ * String representing the name of an info file
+ */
+ public final static String INFO_FILE_NAME = "README.txt";
+
+ /**
+ * String representing the name of an output file
+ */
+ public final static String OUTPUT_FILE_NAME = "jobOutput.mosc";
+
+ /**
+ * String representing the name of an molecule set 1 file
+ */
+ public final static String MOLECULE_SET_1_FILE = "moleculeSet1.txt";
+
+ /**
+ * String representing the name of an molecule set 2 file
+ */
+ public final static String MOLECULE_SET_2_FILE = "moleculeSet2.txt";
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/utility/ResultFormattingUtility.java b/src/main/java/de/whs/ibci/msc/utility/ResultFormattingUtility.java
new file mode 100644
index 0000000..24e11c1
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/utility/ResultFormattingUtility.java
@@ -0,0 +1,259 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.utility;
+
+import de.whs.ibci.msc.model.HistogramData;
+import java.text.DecimalFormat;
+import java.util.Date;
+
+/**
+ * Utility class that provides methods to convert job results into formatted
+ * texts
+ *
+ * @author Jan-Mathis Hein
+ */
+public abstract class ResultFormattingUtility {
+
+ //
+ /**
+ * Get the header for a result summary report
+ *
+ * @return an array that contains the individual lines of text
+ */
+ public static String[] getResultSummaryReportHeader() {
+ String[] tmpLines = new String[6];
+ tmpLines[0] = "Molecule Set Comparator";
+ tmpLines[1] = "Version: " + MSCConstants.MSC_VERSION;
+ tmpLines[2] = "Covered under the GNU GPLv3, copyright Jan-Mahis Hein";
+ tmpLines[3] = "";
+ tmpLines[4] = "Result summary report";
+ tmpLines[5] = "";
+ //tmpLines[5] = "Job ID:";
+ return tmpLines;
+ }
+
+ /**
+ * Get the general information block for a job
+ *
+ * @param tmpDateOfCompletion specifies the date of completion of the job
+ * @param tmpComputingTime specifies the computing time of the job
+ * @param tmpNumberOfPairs specifies the number of pairs of the job
+ * @param tmpInputFile1 specifies the job's first input file
+ * @param tmpInputFile2 specifies the job's second input file
+ * @return an array that contains the individual lines of text
+ */
+ public static String[] getGeneralInfoBlock(Date tmpDateOfCompletion, double tmpComputingTime, int tmpNumberOfPairs, String tmpInputFile1, String tmpInputFile2) {
+ String[] tmpLines = new String[9];
+ tmpLines[0] = "Date of completion: " + tmpDateOfCompletion.toString();
+ tmpLines[1] = "Computing time: " + Double.toString(tmpComputingTime) + " (Seconds)";
+ tmpLines[2] = "";
+ tmpLines[3] = "Number of pairs: " + Integer.toString(tmpNumberOfPairs);
+ tmpLines[4] = "";
+ tmpLines[5] = "Input set files:";
+ tmpLines[6] = tmpInputFile1;
+ tmpLines[7] = tmpInputFile2;
+ tmpLines[8] = "";
+ return tmpLines;
+ }
+
+ /**
+ * Get a text representation of an HistogramData object in vertical form.
+ * This representation contains a table with the frequencies and the min,
+ * max and average ComparisonFeature values
+ *
+ * @param tmpHistogramData contains the histogram data
+ * @return an array that contains the individual lines of text
+ */
+ public static String[] getVerticalHistogramBlock(HistogramData tmpHistogramData) {
+ //
+ String[] tmpLines = new String[(tmpHistogramData.getBinBorders().length * 2) + 8];
+ String tmpSpace;
+ //
+ //
+ String[] tmpBinBorders = new String[tmpHistogramData.getBinBorders().length];
+ DecimalFormat tmpBinBorderFormatter = new DecimalFormat("##0.00000");
+ int tmpMaxLength = 0;
+ if (tmpHistogramData.getComparisonFeauture().isContinuous()) {
+ for (int i = 0; i < tmpBinBorders.length; i++) {
+ tmpBinBorders[i] = tmpBinBorderFormatter.format(tmpHistogramData.getBinBorders()[i]);
+ tmpMaxLength = tmpBinBorders[i].length() > tmpMaxLength ? tmpBinBorders[i].length() : tmpMaxLength;
+ }
+ } else {
+ for (int i = 0; i < tmpBinBorders.length; i++) {
+ if (i < (tmpBinBorders.length - 1)) {
+ tmpBinBorders[i] = Integer.toString((int) Math.ceil(tmpHistogramData.getBinBorders()[i]));
+ } else {
+ tmpBinBorders[i] = Integer.toString((int) Math.ceil(tmpHistogramData.getBinBorders()[i] + 1));
+ }
+ tmpMaxLength = tmpBinBorders[i].length() > tmpMaxLength ? tmpBinBorders[i].length() : tmpMaxLength;
+ }
+ }
+ //
+ tmpLines[0] = tmpHistogramData.getComparisonFeauture().toString() + ":";
+ tmpLines[1] = "";
+ //
+ tmpLines[2] = "bin borders | frequency of pairs";
+ int tmpLinePosition = tmpLines[2].indexOf("|");
+ if ((tmpLinePosition - 2) < tmpMaxLength) {
+ tmpLinePosition = tmpMaxLength + 2;
+ }
+ tmpSpace = "";
+ while (tmpLines[2].indexOf("|") < tmpLinePosition) {
+ tmpSpace += " ";
+ tmpLines[2] = "bin borders " + tmpSpace + "| frequency of pairs";
+ }
+ //
+ //
+ tmpLines[3] = "";
+ while (tmpLines[3].length() < tmpLines[2].length()) {
+ tmpLines[3] += "-";
+ }
+ //
+ //
+ for (int i = 0; i < tmpBinBorders.length; i++) {
+ tmpSpace = "";
+ while ((tmpSpace.length() + tmpBinBorders[i].length() + 2) < tmpLinePosition) {
+ tmpSpace += " ";
+ }
+ tmpLines[4 + (i * 2)] = tmpSpace + tmpBinBorders[i] + " |";
+ }
+ //
+ //
+ int tmpInt;
+ DecimalFormat tmpFrequencyFormatter = tmpHistogramData.isUseRelativeFrequencies() ? new DecimalFormat("##0.00000") : new DecimalFormat("###");
+ int tmpMaxPrePointLength = 0;
+ String[] tmpFrequencies = new String[tmpHistogramData.getFrequencies().length];
+ for (int i = 0; i < tmpFrequencies.length; i++) {
+ tmpFrequencies[i] = tmpFrequencyFormatter.format(tmpHistogramData.getFrequencies()[i]);
+ tmpInt = tmpFrequencies[i].indexOf('.') == -1 ? tmpFrequencies[i].length() : tmpFrequencies[i].indexOf('.');
+ tmpMaxPrePointLength = tmpInt > tmpMaxPrePointLength ? tmpInt : tmpMaxPrePointLength;
+ }
+ //
+ //
+ String[] tmpArray;
+ for (int i = 0; i < tmpHistogramData.getFrequencies().length; i++) {
+ tmpArray = tmpFrequencies[i].split("\\.");
+ tmpSpace = "";
+ while (tmpSpace.length() < tmpLinePosition) {
+ tmpSpace += " ";
+ }
+ tmpLines[5 + (i * 2)] = tmpSpace + "| ";
+ tmpSpace = "";
+ while (tmpSpace.length() < (tmpMaxPrePointLength - tmpArray[0].length())) {
+ tmpSpace += " ";
+ }
+ tmpLines[5 + (i * 2)] += tmpSpace + tmpFrequencies[i] + (tmpHistogramData.isUseRelativeFrequencies() ? "%" : "");
+ }
+ //
+ tmpLines[3 + (tmpHistogramData.getBinBorders().length * 2)] = "";
+ tmpLines[4 + (tmpHistogramData.getBinBorders().length * 2)] = "min: " + Double.toString(tmpHistogramData.getMinComparisonFeatureValue());
+ tmpLines[5 + (tmpHistogramData.getBinBorders().length * 2)] = "max: " + Double.toString(tmpHistogramData.getMaxComparisonFeatureValue());
+ tmpLines[6 + (tmpHistogramData.getBinBorders().length * 2)] = "average: " + Double.toString(tmpHistogramData.getAverageComparisonFeatureValue());
+ tmpLines[7 + (tmpHistogramData.getBinBorders().length * 2)] = "";
+ return tmpLines;
+ }
+
+ /**
+ * Get a text representation of an HistogramData object in horizontal form.
+ * This representation contains a table with the frequencies and the min,
+ * max and average ComparisonFeature values
+ *
+ * @param tmpHistogramData contains the histogram data
+ * @return an array that contains the individual lines of text
+ */
+ public static String[] getHorizontalHistogramBlock(HistogramData tmpHistogramData) {
+ //
+ String[] tmpStringArray;
+ String[] tmpLines = new String[5];
+ String tmpSpaceBetweenNumbers = " ";
+ String tmpString;
+ String tmpSpace;
+ String tmpPattern = "####0.0####";
+ DecimalFormat tmpFormatter = new DecimalFormat(tmpPattern);
+ int tmpMaxPrePointLength = 0;
+ int tmpMaxPostPointLength = 0;
+ int tmpMaxFrequencyLength = 0;
+ int tmpNumberOfLeadingSpaces;
+ //
+ //
+ for (double tmpBinBorder : tmpHistogramData.getBinBorders()) {
+ tmpStringArray = tmpFormatter.format(tmpBinBorder).split("\\.");
+ tmpMaxPrePointLength = tmpStringArray[0].length() > tmpMaxPrePointLength ? tmpStringArray[0].length() : tmpMaxPrePointLength;
+ tmpMaxPostPointLength = tmpStringArray[1].length() > tmpMaxPostPointLength ? tmpStringArray[1].length() : tmpMaxPostPointLength;
+ }
+ for (double tmpFrequency : tmpHistogramData.getFrequencies()) {
+ tmpString = Double.toString(tmpFrequency);
+ tmpMaxFrequencyLength = tmpString.length() > tmpMaxFrequencyLength ? tmpString.length() : tmpMaxFrequencyLength;
+ }
+ while ((tmpMaxPostPointLength + tmpSpaceBetweenNumbers.length() + tmpMaxPrePointLength) < tmpMaxFrequencyLength + 2) {
+ tmpSpaceBetweenNumbers += " ";
+ }
+ while ((tmpMaxPostPointLength + tmpSpaceBetweenNumbers.length() + tmpMaxPrePointLength) > tmpMaxFrequencyLength + 2) {
+ tmpMaxFrequencyLength++;
+ }
+ //
+ //
+ tmpLines[0] = tmpHistogramData.getComparisonFeauture().toString() + ":";
+ tmpLines[1] = "";
+ //
+ //
+ for (double tmpBorder : tmpHistogramData.getBinBorders()) {
+ tmpString = tmpFormatter.format(tmpBorder);
+ while (tmpString.split("\\.")[0].length() < tmpMaxPrePointLength) {
+ tmpString = " " + tmpString;
+ }
+ while (tmpString.split("\\.")[1].length() < tmpMaxPostPointLength) {
+ tmpString += " ";
+ }
+ tmpLines[2] += tmpString + tmpSpaceBetweenNumbers;
+ }
+ tmpLines[2] = tmpLines[2].trim();
+ //
+ //
+ char[] tmpArray = new char[tmpLines[2].split("\\.")[0].length()];
+ for (int i = 0; i < tmpArray.length; i++) {
+ tmpArray[i] = ' ';
+ }
+ tmpLines[3] += new String(tmpArray);
+ for (double tmpFrequencyValue : tmpHistogramData.getFrequencies()) {
+ tmpString = Double.toString(tmpFrequencyValue);
+ tmpLines[3] += "| ";
+ if (tmpString.length() < tmpMaxFrequencyLength) {
+ tmpNumberOfLeadingSpaces = (tmpMaxFrequencyLength - tmpString.length()) / 2;
+ tmpNumberOfLeadingSpaces += (tmpMaxFrequencyLength - tmpString.length()) % 2;
+ tmpSpace = "";
+ while (tmpSpace.length() != tmpNumberOfLeadingSpaces) {
+ tmpSpace += " ";
+ }
+ tmpString = tmpSpace + tmpString;
+ tmpSpace = "";
+ while (tmpSpace.length() != (tmpMaxFrequencyLength - tmpString.length())) {
+ tmpSpace += " ";
+ }
+ tmpString += tmpSpace;
+ }
+ tmpLines[3] += tmpString + " ";
+ }
+ tmpLines[3] += "|";
+ tmpLines[4] = "";
+ //
+ return tmpLines;
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/view/BinBorderConfigurationBox.java b/src/main/java/de/whs/ibci/msc/view/BinBorderConfigurationBox.java
new file mode 100644
index 0000000..fa92c42
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/view/BinBorderConfigurationBox.java
@@ -0,0 +1,104 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.view;
+
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.utility.GuiUtilities;
+import javafx.scene.control.Button;
+import javafx.scene.control.Label;
+import javafx.scene.control.TextField;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.HBox;
+
+/**
+ * Box for the configuration of a single bin border
+ *
+ * @author Jan-Mathis Hein
+ */
+public class BinBorderConfigurationBox extends HBox {
+
+ //
+ private final Label label;
+
+ private final TextField textField;
+
+ private final Button removeButton, addButton;
+ //
+ //
+ //
+ /**
+ * Initializes the instance variables
+ *
+ * @param tmpTextFieldValue initial value for the textField
+ * @param tmpLabelText specifies the text for the label
+ */
+ public BinBorderConfigurationBox(String tmpTextFieldValue, String tmpLabelText) {
+ super(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.label = new Label(tmpLabelText);
+ GuiUtilities.setMinMaxPrefSize(this.label, 20, GuiUtilities.BUTTON_HEIGHT);
+ this.textField = new TextField(tmpTextFieldValue);
+ GuiUtilities.setMinMaxPrefSize(this.textField, 150, GuiUtilities.BUTTON_HEIGHT);
+ this.removeButton = new Button(GeneralUtilities.getUIText("BinBorderConfigurationBox.removeButton.text"));
+ this.removeButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("BinBorderConfigurationBox.removeButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.removeButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.addButton = new Button(GeneralUtilities.getUIText("BinBorderConfigurationBox.addButton.text"));
+ this.addButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("BinBorderConfigurationBox.addButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.addButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.getChildren().addAll(this.label, this.textField, this.removeButton, this.addButton);
+ }
+ //
+ //
+ //
+ /**
+ * Get the textField
+ *
+ * @return the textField
+ */
+ public TextField getTextField() {
+ return this.textField;
+ }
+
+ /**
+ * Get the label
+ *
+ * @return the label
+ */
+ public Label getLabel() {
+ return this.label;
+ }
+
+ /**
+ * Get the removeButton
+ *
+ * @return the removeButton
+ */
+ public Button getRemoveButton() {
+ return this.removeButton;
+ }
+
+ /**
+ * Get the addButton
+ *
+ * @return the addButton
+ */
+ public Button getAddButton() {
+ return this.addButton;
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/view/BinBorderConfigurationDialog.java b/src/main/java/de/whs/ibci/msc/view/BinBorderConfigurationDialog.java
new file mode 100644
index 0000000..a1ff84d
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/view/BinBorderConfigurationDialog.java
@@ -0,0 +1,108 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.view;
+
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.utility.GuiUtilities;
+import javafx.geometry.Insets;
+import javafx.geometry.Pos;
+import javafx.scene.control.Button;
+import javafx.scene.control.ScrollPane;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.GridPane;
+import javafx.scene.layout.HBox;
+import javafx.scene.layout.VBox;
+import javafx.stage.Window;
+
+/**
+ * A configuration-dialog in which the user can specify any number of bin
+ * borders with specifically set values.
+ *
+ * @author Jan-Mathis Hein
+ */
+public class BinBorderConfigurationDialog extends ConfigurationDialog {
+
+ //
+ private final Button resetButton;
+
+ private final ScrollPane scrollPane;
+
+ private final VBox binBorderConfigurationBoxesBox;
+
+ private final HBox controlsBox;
+
+ private final GridPane inputPane;
+ //
+ //
+ //
+ /**
+ * Create the Dialog with all its controls and handle their layout and size
+ *
+ * @param tmpOwner specifies the window that owns the ConfigurationDialog
+ * @param tmpTitle specifies the title of the ConfigurationDialog
+ */
+ public BinBorderConfigurationDialog(Window tmpOwner, String tmpTitle) {
+ super(tmpOwner, tmpTitle);
+ this.inputPane = new GridPane();
+ this.inputPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.inputPane.setBorder(GuiUtilities.RAISED_BORDER);
+ this.inputPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.scrollPane = new ScrollPane();
+ this.scrollPane.setVbarPolicy(ScrollPane.ScrollBarPolicy.ALWAYS);
+ this.scrollPane.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER);
+ this.scrollPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.binBorderConfigurationBoxesBox = new VBox(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ // This fixes a bug where the ScrollPane cuts off its content at the bottom
+ this.binBorderConfigurationBoxesBox.setPadding(new Insets(0, 0, 10, 0));
+ this.scrollPane.setContent(this.binBorderConfigurationBoxesBox);
+ this.inputPane.add(this.scrollPane, 0, 0);
+ this.controlsBox = new HBox(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.controlsBox.setAlignment(Pos.CENTER_RIGHT);
+ this.resetButton = new Button(GeneralUtilities.getUIText("BinBorderConfigurationDialog.resetButton.text"));
+ this.resetButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("BinBorderConfigurationDialog.resetButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.resetButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.controlsBox.getChildren().add(this.resetButton);
+ this.inputPane.add(this.controlsBox, 0, 1);
+ this.getContentPane().getChildren().add(this.inputPane);
+ this.setHeaderText(GeneralUtilities.getUIText("BinBorderConfigurationDialog.Header.text"));
+ GuiUtilities.setMinMaxPrefHeight(this.getDialogPane(), 500);
+ }
+ //
+ //
+ //
+ /**
+ * Get the resetButton
+ *
+ * @return the resetButton
+ */
+ public Button getResetButton() {
+ return this.resetButton;
+ }
+
+
+ /**
+ * Get the binBorderConfigurationBoxesBox
+ *
+ * @return the binBorderConfigurationBoxesBox
+ */
+ public VBox getBinBorderConfigurationBoxesBox() {
+ return this.binBorderConfigurationBoxesBox;
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/view/ChartConfigurationDialog.java b/src/main/java/de/whs/ibci/msc/view/ChartConfigurationDialog.java
new file mode 100644
index 0000000..3b31f00
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/view/ChartConfigurationDialog.java
@@ -0,0 +1,166 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.view;
+
+import de.whs.ibci.msc.utility.GuiUtilities;
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import javafx.geometry.Insets;
+import javafx.geometry.Pos;
+import javafx.scene.control.Button;
+import javafx.scene.control.Label;
+import javafx.scene.control.TextField;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.GridPane;
+import javafx.scene.layout.HBox;
+import javafx.stage.Window;
+
+/**
+ * A configuration-dialog in which the user can specify the upper and lower bin
+ * borders as well as the upper and lower frequency bounds of a chart.
+ *
+ * @author Jan-Mathis Hein
+ */
+public class ChartConfigurationDialog extends ConfigurationDialog {
+
+ //
+ private final GridPane inputPane;
+
+ private final Label lowerBinBorderLabel, upperBinBorderLabel, lowerFrequencyBoundLabel, upperFrequencyBoundLabel;
+
+ private final TextField lowerBinBorderInputField, upperBinBorderInputField, lowerFrequencyBoundInputField, upperFrequencyBoundInputField;
+
+ private final Button resetButton, defaultButton;
+
+ private final HBox buttonBox;
+ //
+ //
+ //
+ /**
+ * Create the Dialog with all its controls and handle their layout and size
+ *
+ * @param tmpOwner specifies the window that owns the ConfigurationDialog
+ * @param tmpTitle specifies the title of the ConfigurationDialog
+ */
+ public ChartConfigurationDialog(Window tmpOwner, String tmpTitle) {
+ super(tmpOwner, tmpTitle);
+ this.inputPane = new GridPane();
+ this.inputPane.setBorder(GuiUtilities.RAISED_BORDER);
+ this.inputPane.setPadding(new Insets(10, 10, 10, 10));
+ this.inputPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.inputPane.setHgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.lowerBinBorderInputField = new TextField();
+ this.lowerBinBorderInputField.setTooltip(new Tooltip(GeneralUtilities.getUIText("ChartConfigurationDialog.lowerBinBorderInputField.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.lowerBinBorderInputField, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.lowerBinBorderLabel = new Label(GeneralUtilities.getUIText("ChartConfigurationDialog.lowerBinBorderLabel.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.lowerBinBorderLabel, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.lowerBinBorderInputField, 1, 0);
+ this.inputPane.add(this.lowerBinBorderLabel, 0, 0);
+ this.upperBinBorderInputField = new TextField();
+ this.upperBinBorderInputField.setTooltip(new Tooltip(GeneralUtilities.getUIText("ChartConfigurationDialog.upperBinBorderInputField.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.upperBinBorderInputField, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.upperBinBorderLabel = new Label(GeneralUtilities.getUIText("ChartConfigurationDialog.upperBinBorderLabel.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.upperBinBorderLabel, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.upperBinBorderInputField, 1, 1);
+ this.inputPane.add(this.upperBinBorderLabel, 0, 1);
+ this.lowerFrequencyBoundInputField = new TextField();
+ this.lowerFrequencyBoundInputField.setTooltip(new Tooltip(GeneralUtilities.getUIText("ChartConfigurationDialog.lowerFrequencyBoundInputField.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.lowerFrequencyBoundInputField, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.lowerFrequencyBoundLabel = new Label(GeneralUtilities.getUIText("ChartConfigurationDialog.lowerFrequencyBoundLabel.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.lowerFrequencyBoundLabel, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(lowerFrequencyBoundInputField, 1, 2);
+ this.inputPane.add(lowerFrequencyBoundLabel, 0, 2);
+ this.upperFrequencyBoundInputField = new TextField();
+ this.upperFrequencyBoundInputField.setTooltip(new Tooltip(GeneralUtilities.getUIText("ChartConfigurationDialog.upperFrequencyBoundInputField.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.upperFrequencyBoundInputField, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.upperFrequencyBoundLabel = new Label(GeneralUtilities.getUIText("ChartConfigurationDialog.upperFrequencyBoundLabel.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.upperFrequencyBoundLabel, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(upperFrequencyBoundInputField, 1, 3);
+ this.inputPane.add(upperFrequencyBoundLabel, 0, 3);
+ this.buttonBox = new HBox(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.buttonBox.setAlignment(Pos.CENTER_RIGHT);
+ this.defaultButton = new Button(GeneralUtilities.getUIText("ChartConfigurationDialog.defaultButton.text"));
+ this.defaultButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("ChartConfigurationDialog.defaultButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.defaultButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.buttonBox.getChildren().add(this.defaultButton);
+ this.resetButton = new Button(GeneralUtilities.getUIText("ChartConfigurationDialog.resetButton.text"));
+ this.resetButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("ChartConfigurationDialog.resetButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.resetButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.buttonBox.getChildren().add(this.resetButton);
+ this.inputPane.add(this.buttonBox, 1, 4);
+ this.getContentPane().getChildren().add(this.inputPane);
+ GuiUtilities.setMinMaxPrefHeight(this.getDialogPane(), 304);
+ }
+ //
+ //
+ //
+ /**
+ * Get the lowerBinBorderInputField
+ *
+ * @return the lowerBinBorderInputField
+ */
+ public TextField getLowerBinBorderInputField() {
+ return this.lowerBinBorderInputField;
+ }
+
+ /**
+ * Get the upperBinBorderInputField
+ *
+ * @return the upperBinBorderInputField
+ */
+ public TextField getUpperBinBorderInputField() {
+ return this.upperBinBorderInputField;
+ }
+
+ /**
+ * Get the lowerFrequencyBoundInputField
+ *
+ * @return the lowerFrequencyBoundInputField
+ */
+ public TextField getLowerFrequencyBoundInputField() {
+ return this.lowerFrequencyBoundInputField;
+ }
+
+ /**
+ * Get the upperFrequencyBoundInputField
+ *
+ * @return the upperFrequencyBoundInputField
+ */
+ public TextField getUpperFrequencyBoundInputField() {
+ return this.upperFrequencyBoundInputField;
+ }
+
+ /**
+ * Get the resetButton
+ *
+ * @return the resetButton
+ */
+ public Button getResetButton() {
+ return this.resetButton;
+ }
+
+ /**
+ * Get the defaultButton
+ *
+ * @return the defaultButton
+ */
+ public Button getDefaultButton() {
+ return this.defaultButton;
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/view/ConfigurationDialog.java b/src/main/java/de/whs/ibci/msc/view/ConfigurationDialog.java
new file mode 100644
index 0000000..7efd1de
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/view/ConfigurationDialog.java
@@ -0,0 +1,113 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.view;
+
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.utility.GuiUtilities;
+import javafx.geometry.Insets;
+import javafx.scene.control.Button;
+import javafx.scene.control.ButtonBar;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.Dialog;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.Border;
+import javafx.scene.layout.BorderStroke;
+import javafx.scene.layout.BorderStrokeStyle;
+import javafx.scene.layout.BorderWidths;
+import javafx.scene.layout.CornerRadii;
+import javafx.scene.layout.StackPane;
+import javafx.scene.paint.Color;
+import javafx.stage.Window;
+
+/**
+ * A base framework for a Dialog for configuration purposes
+ *
+ * @author Jan-Mathis Hein
+ */
+public abstract class ConfigurationDialog extends Dialog {
+
+ //
+ private final Button applyButton, cancelButton;
+
+ private final StackPane contentPane;
+ //
+ //
+ //
+ /**
+ * Create the Dialog with all its controls and handle their layout and size
+ *
+ * @param tmpOwner specifies the window that owns the Dialog
+ * @param tmpTitle specifies the title of the Dialog
+ */
+ public ConfigurationDialog(Window tmpOwner, String tmpTitle) {
+ super();
+ this.initOwner(tmpOwner);
+ this.setTitle(tmpTitle);
+ this.setHeaderText(GeneralUtilities.getUIText("ConfigurationDialog.Header.text"));
+ ButtonType tmpApplyButtonType = new ButtonType(GeneralUtilities.getUIText("ConfigurationDialog.applyButtonType.text"), ButtonBar.ButtonData.APPLY);
+ ButtonType tmpCancelButtonType = new ButtonType(GeneralUtilities.getUIText("ConfigurationDialog.cancelButtonType.text"), ButtonBar.ButtonData.CANCEL_CLOSE);
+ this.getDialogPane().getButtonTypes().addAll(tmpApplyButtonType, tmpCancelButtonType);
+ this.applyButton = (Button) this.getDialogPane().lookupButton(tmpApplyButtonType);
+ GuiUtilities.setMinMaxPrefSize(this.applyButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.applyButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("ConfigurationDialog.applyButton.tooltipText")));
+ this.cancelButton = (Button) this.getDialogPane().lookupButton(tmpCancelButtonType);
+ GuiUtilities.setMinMaxPrefSize(this.cancelButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.cancelButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("ConfigurationDialog.cancelButton.tooltipText")));
+ this.contentPane = new StackPane();
+ this.contentPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.contentPane.setBorder(new Border(new BorderStroke(
+ Color.WHITE, Color.WHITE, Color.color(0.1, 0.1, 0.1),
+ Color.WHITE, BorderStrokeStyle.NONE, BorderStrokeStyle.NONE,
+ BorderStrokeStyle.SOLID, BorderStrokeStyle.NONE,
+ new CornerRadii(0), new BorderWidths(0, 0, 2, 0), new Insets(0)
+ )));
+ this.getDialogPane().setContent(this.contentPane);
+
+ }
+ //
+ //
+ //
+ /**
+ * Get the cancelButton
+ *
+ * @return the cancelButton
+ */
+ public final Button getCancelButton() {
+ return this.cancelButton;
+ }
+
+ /**
+ * Get the applyButton
+ *
+ * @return the applyButton
+ */
+ public final Button getApplyButton() {
+ return this.applyButton;
+ }
+
+ /**
+ * Get the contentPane
+ *
+ * @return the contentPane
+ */
+ public final StackPane getContentPane() {
+ return this.contentPane;
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/view/InputTab.java b/src/main/java/de/whs/ibci/msc/view/InputTab.java
new file mode 100644
index 0000000..af0e79d
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/view/InputTab.java
@@ -0,0 +1,561 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.view;
+
+import de.whs.ibci.msc.utility.GuiUtilities;
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.model.InputType;
+import de.whs.ibci.msc.model.ComparisonFeature;
+import java.util.Arrays;
+import java.util.LinkedList;
+import java.util.List;
+import javafx.collections.FXCollections;
+import javafx.collections.ObservableList;
+import javafx.geometry.HPos;
+import javafx.geometry.Insets;
+import javafx.geometry.Pos;
+import javafx.geometry.VPos;
+import javafx.scene.control.Button;
+import javafx.scene.control.CheckBox;
+import javafx.scene.control.ChoiceBox;
+import javafx.scene.control.Label;
+import javafx.scene.control.ProgressBar;
+import javafx.scene.control.ScrollPane;
+import javafx.scene.control.Tab;
+import javafx.scene.control.TitledPane;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.AnchorPane;
+import javafx.scene.layout.ColumnConstraints;
+import javafx.scene.layout.GridPane;
+import javafx.scene.layout.HBox;
+import javafx.scene.layout.Priority;
+import javafx.scene.layout.RowConstraints;
+import javafx.scene.layout.StackPane;
+import javafx.scene.layout.VBox;
+
+/**
+ * A Tab in which the user can specify his input for a job
+ *
+ * @author Jan-Mathis Hein
+ */
+public class InputTab extends Tab {
+
+ //
+ private final ChoiceBox inputType1ChoiceBox, inputType2ChoiceBox;
+
+ private final Button chooseFile1Button, chooseFile2Button, jobStartButton,
+ reverseComparisonFeatureSelectionButton, jobCancelButton, selectAllComparisonFeaturesButton;
+
+ private final StackPane startCancelPane;
+
+ private final ProgressBar jobProgressBar;
+
+ private final Label inputFile1Label, inputFile2Label, jobInfoLabel;
+
+ private final ScrollPane scrollPane;
+
+ private final GridPane mainPane, inputFilesPane;
+
+ private final HBox startProgressCancelBox;
+
+ private final VBox tanimotoCheckBoxesBox, atomCountsCheckBoxesBox, bondCountsCheckBoxesBox, functionalGroupCountsCheckBoxesBox,
+ logPValuesCheckBoxesBox, autocorrelationCheckBoxesBox, electronicDescriptorsCheckBoxesBox, miscellaneousCheckBoxesBox,
+ comparisonFeatureSelectionBox;
+
+ private final AnchorPane comparisonFeaturePane, comparisonFeatureButtonsPane, infoStartProgressCancelPane;
+
+ private final CheckBox[] comparisonFeatureCheckBoxes;
+
+ private final CheckBox selectAllTanimotoCheckBox, selectAllAtomCountsCheckBox, selectAllMiscellaneousCheckBox,
+ selectAllBondCountsCheckBox, selectAllFunctionalGroupCountsCheckBox, selectAllLogPValuesCheckBox,
+ selectAllAutocorrelationCheckBox, selectAllElectronicDescriptorsCheckBox;
+
+ private final TitledPane buttonsTitledPane, tanimotoTitledPane, atomCountsTitledPane,
+ miscellaneousTitledPane, bondCountsTitledPane, functionalGroupCountsTitledPane, logPValuesTitledPane,
+ autocorrelationTitledPane, electronicDescriptorsTitledPane;
+ //
+ //
+ //
+ /**
+ * Create the Tab with all its controls and handle their layout and size
+ *
+ * @param tmpJobNumber specifies the title of the Tab
+ */
+ public InputTab(String tmpJobNumber) {
+ super(GeneralUtilities.getUIText("InputTab.title.text") + tmpJobNumber);
+ this.setClosable(true);
+ this.mainPane = new GridPane();
+ this.mainPane.setHgap(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.mainPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.mainPane.getColumnConstraints().addAll(
+ new ColumnConstraints(),
+ new ColumnConstraints(234.0, 234.0, Double.MAX_VALUE, Priority.ALWAYS, HPos.LEFT, true)
+ );
+ this.mainPane.getRowConstraints().addAll(
+ new RowConstraints(142.4, 142.4, Double.MAX_VALUE, Priority.ALWAYS, VPos.CENTER, true),
+ new RowConstraints()
+ );
+ // The 12 is intentional
+ this.mainPane.setPadding(new Insets(10, 10, 12, 10));
+ //
+ this.inputFilesPane = new GridPane();
+ this.inputFilesPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.inputFilesPane.setHgap(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.inputFilesPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.inputFilesPane.setBorder(GuiUtilities.RAISED_BORDER);
+ ObservableList inputTypeCollection = FXCollections.observableArrayList(new LinkedList<>(Arrays.asList(InputType.values())));
+ this.inputType1ChoiceBox = new ChoiceBox<>(inputTypeCollection);
+ this.inputType1ChoiceBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.inputType1ChoiceBox.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.inputType1ChoiceBox, GuiUtilities.BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.inputType2ChoiceBox = new ChoiceBox<>(inputTypeCollection);
+ this.inputType2ChoiceBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.inputType2ChoiceBox.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.inputType2ChoiceBox, GuiUtilities.BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.chooseFile1Button = new Button(GeneralUtilities.getUIText("InputTab.chooseFile1Button.text"));
+ this.chooseFile1Button.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.chooseFile1Button.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.chooseFile1Button, GuiUtilities.BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.chooseFile2Button = new Button(GeneralUtilities.getUIText("InputTab.chooseFile2Button.text"));
+ this.chooseFile2Button.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.chooseFile2Button.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.chooseFile2Button, GuiUtilities.BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.inputFile1Label = new Label(GeneralUtilities.getUIText("InputTab.inputFile1Label.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.inputFile1Label, GuiUtilities.BUTTON_WIDTH * 2 + GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.inputFile2Label = new Label(GeneralUtilities.getUIText("InputTab.inputFile2Label.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.inputFile2Label, GuiUtilities.BUTTON_WIDTH * 2 + GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.inputFilesPane.add(this.inputType1ChoiceBox, 0, 0);
+ this.inputFilesPane.add(this.chooseFile1Button, 1, 0);
+ this.inputFilesPane.add(this.inputFile1Label, 0, 1, 2, 1);
+ this.inputFilesPane.add(this.inputType2ChoiceBox, 0, 2);
+ this.inputFilesPane.add(this.chooseFile2Button, 1, 2);
+ this.inputFilesPane.add(this.inputFile2Label, 0, 3, 2, 1);
+ this.mainPane.add(this.inputFilesPane, 0, 0);
+ //
+ //
+ this.comparisonFeaturePane = new AnchorPane();
+ this.comparisonFeaturePane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.comparisonFeaturePane.setBorder(GuiUtilities.RAISED_BORDER);
+ this.scrollPane = new ScrollPane();
+ this.scrollPane.setVbarPolicy(ScrollPane.ScrollBarPolicy.ALWAYS);
+ // The content node is resized to fit the width of the scrollpane
+ this.scrollPane.setFitToWidth(true);
+ this.comparisonFeatureSelectionBox = new VBox();
+ this.comparisonFeatureSelectionBox.setStyle("-fx-background-color: rgb(200, 200, 200);");
+ this.buttonsTitledPane = new TitledPane();
+ this.buttonsTitledPane.setText(GeneralUtilities.getUIText("InputTab.comparisonFeatureButtonsTitlePane.text"));
+ this.buttonsTitledPane.setAnimated(false);
+ this.buttonsTitledPane.setExpanded(false);
+ this.comparisonFeatureButtonsPane = new AnchorPane();
+ this.comparisonFeatureButtonsPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.selectAllComparisonFeaturesButton = new Button(GeneralUtilities.getUIText("InputTab.selectAllComparisonFeaturesButton.text"));
+ this.selectAllComparisonFeaturesButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.selectAllComparisonFeaturesButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.selectAllComparisonFeaturesButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ AnchorPane.setLeftAnchor(this.selectAllComparisonFeaturesButton, 0.0);
+ AnchorPane.setTopAnchor(this.selectAllComparisonFeaturesButton, 0.0);
+ this.reverseComparisonFeatureSelectionButton = new Button(GeneralUtilities.getUIText("InputTab.reverseComparisonFeatureSelectionButton.text"));
+ this.reverseComparisonFeatureSelectionButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.reverseComparisonFeatureSelectionButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.reverseComparisonFeatureSelectionButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ AnchorPane.setRightAnchor(this.reverseComparisonFeatureSelectionButton, 0.0);
+ AnchorPane.setTopAnchor(this.reverseComparisonFeatureSelectionButton, 0.0);
+ this.comparisonFeatureButtonsPane.getChildren().setAll(this.selectAllComparisonFeaturesButton, this.reverseComparisonFeatureSelectionButton);
+ this.buttonsTitledPane.setContent(this.comparisonFeatureButtonsPane);
+ this.comparisonFeatureSelectionBox.getChildren().add(this.buttonsTitledPane);
+ //
+ this.tanimotoTitledPane = new TitledPane();
+ this.tanimotoTitledPane.setText(GeneralUtilities.getUIText("InputTab.tanimotoTitledPane.text"));
+ this.tanimotoTitledPane.setAnimated(false);
+ this.tanimotoTitledPane.setExpanded(false);
+ this.atomCountsTitledPane = new TitledPane();
+ this.atomCountsTitledPane.setText(GeneralUtilities.getUIText("InputTab.atomCountsTitledPane.text"));
+ this.atomCountsTitledPane.setAnimated(false);
+ this.atomCountsTitledPane.setExpanded(false);
+ this.bondCountsTitledPane = new TitledPane();
+ this.bondCountsTitledPane.setText(GeneralUtilities.getUIText("InputTab.bondCountsTitledPane.text"));
+ this.bondCountsTitledPane.setAnimated(false);
+ this.bondCountsTitledPane.setExpanded(false);
+ this.functionalGroupCountsTitledPane = new TitledPane();
+ this.functionalGroupCountsTitledPane.setText(GeneralUtilities.getUIText("InputTab.functionalGroupCountsTitledPane.text"));
+ this.functionalGroupCountsTitledPane.setAnimated(false);
+ this.functionalGroupCountsTitledPane.setExpanded(false);
+ this.logPValuesTitledPane = new TitledPane();
+ this.logPValuesTitledPane.setText(GeneralUtilities.getUIText("InputTab.logPValuesTitledPane.text"));
+ this.logPValuesTitledPane.setAnimated(false);
+ this.logPValuesTitledPane.setExpanded(false);
+ this.autocorrelationTitledPane = new TitledPane();
+ this.autocorrelationTitledPane.setText(GeneralUtilities.getUIText("InputTab.autocorrelationTitledPane.text"));
+ this.autocorrelationTitledPane.setAnimated(false);
+ this.autocorrelationTitledPane.setExpanded(false);
+ this.electronicDescriptorsTitledPane = new TitledPane();
+ this.electronicDescriptorsTitledPane.setText(GeneralUtilities.getUIText("InputTab.electricsDescriptorsTitledPane.text"));
+ this.electronicDescriptorsTitledPane.setAnimated(false);
+ this.electronicDescriptorsTitledPane.setExpanded(false);
+ this.miscellaneousTitledPane = new TitledPane();
+ this.miscellaneousTitledPane.setText(GeneralUtilities.getUIText("InputTab.miscellaneousTitledPane.text"));
+ this.miscellaneousTitledPane.setAnimated(false);
+ this.miscellaneousTitledPane.setExpanded(false);
+ //
+ //
+ this.tanimotoCheckBoxesBox = new VBox();
+ this.tanimotoCheckBoxesBox.setSpacing(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.tanimotoCheckBoxesBox.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.selectAllTanimotoCheckBox = new CheckBox(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.text"));
+ this.selectAllTanimotoCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.tooltipText")));
+ this.tanimotoCheckBoxesBox.getChildren().add(this.selectAllTanimotoCheckBox);
+ this.atomCountsCheckBoxesBox = new VBox();
+ this.atomCountsCheckBoxesBox.setSpacing(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.atomCountsCheckBoxesBox.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.selectAllAtomCountsCheckBox = new CheckBox(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.text"));
+ this.selectAllAtomCountsCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.tooltipText")));
+ this.atomCountsCheckBoxesBox.getChildren().add(this.selectAllAtomCountsCheckBox);
+ this.bondCountsCheckBoxesBox = new VBox();
+ this.bondCountsCheckBoxesBox.setSpacing(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.bondCountsCheckBoxesBox.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.selectAllBondCountsCheckBox = new CheckBox(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.text"));
+ this.selectAllBondCountsCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.tooltipText")));
+ this.bondCountsCheckBoxesBox.getChildren().add(this.selectAllBondCountsCheckBox);
+ this.functionalGroupCountsCheckBoxesBox = new VBox();
+ this.functionalGroupCountsCheckBoxesBox.setSpacing(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.functionalGroupCountsCheckBoxesBox.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.selectAllFunctionalGroupCountsCheckBox = new CheckBox(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.text"));
+ this.selectAllFunctionalGroupCountsCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.tooltipText")));
+ this.functionalGroupCountsCheckBoxesBox.getChildren().add(this.selectAllFunctionalGroupCountsCheckBox);
+ this.logPValuesCheckBoxesBox = new VBox();
+ this.logPValuesCheckBoxesBox .setSpacing(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.logPValuesCheckBoxesBox .setPadding(GuiUtilities.STANDARD_INSETS);
+ this.selectAllLogPValuesCheckBox = new CheckBox(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.text"));
+ this.selectAllLogPValuesCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.tooltipText")));
+ this.logPValuesCheckBoxesBox.getChildren().add(this.selectAllLogPValuesCheckBox);
+ this.autocorrelationCheckBoxesBox = new VBox();
+ this.autocorrelationCheckBoxesBox .setSpacing(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.autocorrelationCheckBoxesBox .setPadding(GuiUtilities.STANDARD_INSETS);
+ this.selectAllAutocorrelationCheckBox = new CheckBox(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.text"));
+ this.selectAllAutocorrelationCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.tooltipText")));
+ this.autocorrelationCheckBoxesBox.getChildren().add(this.selectAllAutocorrelationCheckBox);
+ this.electronicDescriptorsCheckBoxesBox = new VBox();
+ this.electronicDescriptorsCheckBoxesBox .setSpacing(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.electronicDescriptorsCheckBoxesBox .setPadding(GuiUtilities.STANDARD_INSETS);
+ this.selectAllElectronicDescriptorsCheckBox = new CheckBox(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.text"));
+ this.selectAllElectronicDescriptorsCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.tooltipText")));
+ this.electronicDescriptorsCheckBoxesBox.getChildren().add(this.selectAllElectronicDescriptorsCheckBox);
+ this.miscellaneousCheckBoxesBox = new VBox();
+ this.miscellaneousCheckBoxesBox.setSpacing(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.miscellaneousCheckBoxesBox.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.selectAllMiscellaneousCheckBox = new CheckBox(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.text"));
+ this.selectAllMiscellaneousCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.selectAllCheckBox.tooltipText")));
+ this.miscellaneousCheckBoxesBox.getChildren().add(this.selectAllMiscellaneousCheckBox);
+ //
+ //
+ this.comparisonFeatureCheckBoxes = new CheckBox[ComparisonFeature.values().length];
+ CheckBox tmpCheckBox;
+ for (int i = 0; i < this.comparisonFeatureCheckBoxes.length; i++) {
+ tmpCheckBox = new CheckBox(ComparisonFeature.values()[i].toString());
+ tmpCheckBox.setTooltip(new Tooltip(ComparisonFeature.values()[i].getDetailedDescription()));
+ if (i == ComparisonFeature.TANIMOTO_BASIC_FINGERPRINTER.getFeatureNumber() ||
+ i == ComparisonFeature.TANIMOTO_LINGO_FINGERPRINTER.getFeatureNumber() ||
+ i == ComparisonFeature.TANIMOTO_EXTENDED_FINGERPRINTER.getFeatureNumber() ||
+ i == ComparisonFeature.TANIMOTO_ESTATE_FINGERPRINTER.getFeatureNumber() ||
+ i == ComparisonFeature.TANIMOTO_PUBCHEM_FINGERPRINTER.getFeatureNumber() ||
+ i == ComparisonFeature.TANIMOTO_SHORTEST_PATH_FINGERPRINTER.getFeatureNumber() ||
+ i == ComparisonFeature.TANIMOTO_SUBSTRUCTURE_FINGERPRINTER.getFeatureNumber()) {
+ this.tanimotoCheckBoxesBox.getChildren().add(tmpCheckBox);
+ } else if (i == ComparisonFeature.ATOM_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.CARBON_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.NITROGEN_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.OXYGEN_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.PHOSPHOR_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SULFUR_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.AROMATIC_ATOM_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.C1SP1_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.C1SP2_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.C1SP3_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.C2SP1_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.C2SP2_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.C2SP3_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.C3SP2_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.C3SP3_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.C4SP3_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SPIRO_ATOM_COUNT.getFeatureNumber()) {
+ this.atomCountsCheckBoxesBox.getChildren().add(tmpCheckBox);
+ } else if (i == ComparisonFeature.BOND_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SINGLE_BOND_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.DOUBLE_BOND_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.TRIPLE_BOND_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.QUADRUPLE_BOND_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.AROMATIC_BOND_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.ROTATABLE_BOND_COUNT.getFeatureNumber()) {
+ this.bondCountsCheckBoxesBox.getChildren().add(tmpCheckBox);
+ } else if (i == ComparisonFeature.ACIDIC_GROUP_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.BASIC_GROUP_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.H_BOND_ACCEPTOR_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.H_BOND_DONOR_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SIZE_3_RINGS_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SIZE_4_RINGS_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SIZE_5_RINGS_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SIZE_6_RINGS_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SIZE_7_RINGS_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SIZE_8_RINGS_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.SIZE_9_RINGS_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.AROMATIC_RINGS_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.ALL_RINGS_COUNT.getFeatureNumber() ||
+ i == ComparisonFeature.ALL_SMALL_RINGS_COUNT.getFeatureNumber()) {
+ this.functionalGroupCountsCheckBoxesBox.getChildren().add(tmpCheckBox);
+ } else if (i == ComparisonFeature.A_LOGP.getFeatureNumber() ||
+ i == ComparisonFeature.A_LOGP_2.getFeatureNumber() ||
+ i == ComparisonFeature.X_LOGP.getFeatureNumber() ||
+ i == ComparisonFeature.MANNHOLD_LOGP.getFeatureNumber() ||
+ i == ComparisonFeature.JP_LOGP.getFeatureNumber()) {
+ this.logPValuesCheckBoxesBox.getChildren().add(tmpCheckBox);
+ } else if (i == ComparisonFeature.ATS_CHARGE1.getFeatureNumber() ||
+ i == ComparisonFeature.ATS_MASS1.getFeatureNumber() ||
+ i == ComparisonFeature.ATS_POLARIZABILITY1.getFeatureNumber()) {
+ this.autocorrelationCheckBoxesBox.getChildren().add(tmpCheckBox);
+ } else if (i == ComparisonFeature.APOL.getFeatureNumber() ||
+ i == ComparisonFeature.BPOL.getFeatureNumber() ||
+ i == ComparisonFeature.FPSA.getFeatureNumber() ||
+ i == ComparisonFeature.TPSA.getFeatureNumber() ||
+ i == ComparisonFeature.MOLAR_REFRACTIVITY.getFeatureNumber()) {
+ this.electronicDescriptorsCheckBoxesBox.getChildren().add(tmpCheckBox);
+ } else {
+ this.miscellaneousCheckBoxesBox.getChildren().add(tmpCheckBox);
+ }
+ this.comparisonFeatureCheckBoxes[i] = tmpCheckBox;
+ }
+ //
+ this.tanimotoTitledPane.setContent(this.tanimotoCheckBoxesBox);
+ this.atomCountsTitledPane.setContent(this.atomCountsCheckBoxesBox);
+ this.bondCountsTitledPane.setContent(this.bondCountsCheckBoxesBox);
+ this.functionalGroupCountsTitledPane.setContent(this.functionalGroupCountsCheckBoxesBox);
+ this.logPValuesTitledPane.setContent(this.logPValuesCheckBoxesBox);
+ this.autocorrelationTitledPane.setContent(this.autocorrelationCheckBoxesBox);
+ this.electronicDescriptorsTitledPane.setContent(this.electronicDescriptorsCheckBoxesBox);
+ this.miscellaneousTitledPane.setContent(this.miscellaneousCheckBoxesBox);
+ this.comparisonFeatureSelectionBox.getChildren().add(this.tanimotoTitledPane);
+ this.comparisonFeatureSelectionBox.getChildren().add(this.atomCountsTitledPane);
+ this.comparisonFeatureSelectionBox.getChildren().add(this.bondCountsTitledPane);
+ this.comparisonFeatureSelectionBox.getChildren().add(this.functionalGroupCountsTitledPane);
+ this.comparisonFeatureSelectionBox.getChildren().add(this.logPValuesTitledPane);
+ this.comparisonFeatureSelectionBox.getChildren().add(this.autocorrelationTitledPane);
+ this.comparisonFeatureSelectionBox.getChildren().add(this.electronicDescriptorsTitledPane);
+ this.comparisonFeatureSelectionBox.getChildren().add(this.miscellaneousTitledPane);
+ this.scrollPane.setContent(this.comparisonFeatureSelectionBox);
+ AnchorPane.setLeftAnchor(this.scrollPane, 0.0);
+ AnchorPane.setTopAnchor(this.scrollPane, 0.0);
+ AnchorPane.setRightAnchor(this.scrollPane, 0.0);
+ AnchorPane.setBottomAnchor(this.scrollPane, 0.0);
+ this.comparisonFeaturePane.getChildren().add(this.scrollPane);
+ this.mainPane.add(this.comparisonFeaturePane, 1, 0);
+ //
+ //
+ this.infoStartProgressCancelPane = new AnchorPane();
+ this.infoStartProgressCancelPane.setBorder(GuiUtilities.RAISED_BORDER);
+ this.infoStartProgressCancelPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.jobInfoLabel = new Label("");
+ AnchorPane.setLeftAnchor(this.jobInfoLabel, 0.0);
+ AnchorPane.setTopAnchor(this.jobInfoLabel, 0.0);
+ AnchorPane.setBottomAnchor(this.jobInfoLabel, 0.0);
+ this.infoStartProgressCancelPane.getChildren().add(this.jobInfoLabel);
+ this.startProgressCancelBox = new HBox(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.startProgressCancelBox.setAlignment(Pos.CENTER);
+ AnchorPane.setRightAnchor(this.startProgressCancelBox, 0.0);
+ AnchorPane.setBottomAnchor(this.startProgressCancelBox, 0.0);
+ AnchorPane.setTopAnchor(this.startProgressCancelBox, 0.0);
+ this.jobProgressBar = new ProgressBar(0);
+ GuiUtilities.setMinMaxPrefWidth(this.jobProgressBar, GuiUtilities.BUTTON_WIDTH);
+ this.startProgressCancelBox.getChildren().add(this.jobProgressBar);
+ this.startCancelPane = new StackPane();
+ this.jobCancelButton = new Button(GeneralUtilities.getUIText("InputTab.jobCancelButton.text"));
+ this.jobCancelButton.setVisible(false);
+ this.jobCancelButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.jobCancelButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.jobCancelButton, GuiUtilities.BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.startCancelPane.getChildren().add(this.jobCancelButton);
+ this.jobStartButton = new Button(GeneralUtilities.getUIText("InputTab.jobStartButton.text"));
+ this.jobStartButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("InputTab.jobStartButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.jobStartButton, GuiUtilities.BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.startCancelPane.getChildren().add(this.jobStartButton);
+ this.startProgressCancelBox.getChildren().add(this.startCancelPane);
+ this.infoStartProgressCancelPane.getChildren().add(this.startProgressCancelBox);
+ this.mainPane.add(this.infoStartProgressCancelPane, 0, 1, 2, 1);
+ //
+ this.setContent(this.mainPane);
+ }
+ //
+ //
+ //
+ /**
+ * Get the reverseComparisonFeatureSelectionButton
+ *
+ * @return the reverseComparisonFeatureSelectionButton
+ */
+ public Button getReverseComparisonFeatureSelectionButton() {
+ return this.reverseComparisonFeatureSelectionButton;
+ }
+
+ /**
+ * Get the selectAllComparisonFeaturesButton
+ *
+ * @return the selectAllComparisonFeaturesButton
+ */
+ public Button getSelectAllComparisonFeaturesButton() {
+ return this.selectAllComparisonFeaturesButton;
+ }
+
+ /**
+ * Get the buttonsTitledPane
+ *
+ * @return the buttonsTitledPane
+ */
+ public TitledPane getButtonsTitledPane() {
+ return this.buttonsTitledPane;
+ }
+
+ /**
+ * Get a list containing all xxxCheckBoxesBox boxes. Order corresponds
+ * to the one of getSelectAllCheckBoxes()
+ *
+ * @return a list containing all xxxCheckBoxesBox boxes
+ */
+ public List getCheckBoxesBoxes() {
+ LinkedList tmpList = new LinkedList<>();
+ tmpList.add(this.atomCountsCheckBoxesBox);
+ tmpList.add(this.autocorrelationCheckBoxesBox);
+ tmpList.add(this.bondCountsCheckBoxesBox);
+ tmpList.add(this.electronicDescriptorsCheckBoxesBox);
+ tmpList.add(this.functionalGroupCountsCheckBoxesBox);
+ tmpList.add(this.logPValuesCheckBoxesBox);
+ tmpList.add(this.miscellaneousCheckBoxesBox);
+ tmpList.add(this.tanimotoCheckBoxesBox);
+ return tmpList;
+ }
+
+ /**
+ * Get a list containing all selectAllXxxCheckBox check boxes. Order
+ * corresponds to the one of getCheckBoxesBoxes()
+ *
+ * @return a list containing all selectAllXxxCheckBox check boxes
+ */
+ public List getSelectAllCheckBoxes() {
+ LinkedList tmpList = new LinkedList<>();
+ tmpList.add(this.selectAllAtomCountsCheckBox);
+ tmpList.add(this.selectAllAutocorrelationCheckBox);
+ tmpList.add(this.selectAllBondCountsCheckBox);
+ tmpList.add(this.selectAllElectronicDescriptorsCheckBox);
+ tmpList.add(this.selectAllFunctionalGroupCountsCheckBox);
+ tmpList.add(this.selectAllLogPValuesCheckBox);
+ tmpList.add(this.selectAllMiscellaneousCheckBox);
+ tmpList.add(this.selectAllTanimotoCheckBox);
+ return tmpList;
+ }
+
+ /**
+ * Get the comparisonFeatureCheckBoxes
+ *
+ * @return the comparisonFeatureCheckBoxes
+ */
+ public CheckBox[] getComparisonFeatureCheckBoxes() {
+ return this.comparisonFeatureCheckBoxes;
+ }
+
+ /**
+ * Get the chooseFile1Button
+ *
+ * @return the chooseFile1Button
+ */
+ public Button getChooseFile1Button() {
+ return this.chooseFile1Button;
+ }
+
+ /**
+ * Get the compareSetsButton
+ *
+ * @return the compareSetsButton
+ */
+ public Button getJobStartButton() {
+ return this.jobStartButton;
+ }
+
+ /**
+ * Get the inputFile1Label
+ *
+ * @return the inputFile1Label
+ */
+ public Label getInputFile1Label() {
+ return this.inputFile1Label;
+ }
+
+ /**
+ * Get the inputFile2Label
+ *
+ * @return the inputFile2Label
+ */
+ public Label getInputFile2Label() {
+ return this.inputFile2Label;
+ }
+
+ /**
+ * Get the chooseFile2Button
+ *
+ * @return the chooseFile2Button
+ */
+ public Button getChooseFile2Button() {
+ return chooseFile2Button;
+ }
+
+ /**
+ * Get the inputType1ChoiceBox
+ *
+ * @return the inputType1ChoiceBox
+ */
+ public ChoiceBox getInputType1ChoiceBox() {
+ return this.inputType1ChoiceBox;
+ }
+
+ /**
+ * Get the inputType2ChoiceBox
+ *
+ * @return the inputType2ChoiceBox
+ */
+ public ChoiceBox getInputType2ChoiceBox() {
+ return this.inputType2ChoiceBox;
+ }
+
+ /**
+ * Get the jobCancelButton
+ *
+ * @return the jobCancelButton
+ */
+ public Button getJobCancelButton() {
+ return this.jobCancelButton;
+ }
+
+ /**
+ * Get the jobProgressBar
+ *
+ * @return the jobProgressBar
+ */
+ public ProgressBar getJobProgressBar() {
+ return this.jobProgressBar;
+ }
+
+ /**
+ * Get the jobInfoLabel
+ *
+ * @return the jobInfoLabel
+ */
+ public Label getJobInfoLabel() {
+ return this.jobInfoLabel;
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/view/MainView.java b/src/main/java/de/whs/ibci/msc/view/MainView.java
new file mode 100644
index 0000000..24e2bf6
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/view/MainView.java
@@ -0,0 +1,335 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.view;
+
+import de.whs.ibci.msc.utility.GuiUtilities;
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.utility.MSCConstants;
+import javafx.geometry.Insets;
+import javafx.scene.control.Button;
+import javafx.scene.control.Menu;
+import javafx.scene.control.MenuBar;
+import javafx.scene.control.MenuItem;
+import javafx.scene.control.TabPane;
+import javafx.scene.layout.BorderPane;
+import javafx.scene.layout.HBox;
+import javafx.scene.Scene;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.Border;
+import javafx.scene.layout.BorderStroke;
+import javafx.scene.layout.BorderStrokeStyle;
+import javafx.scene.layout.BorderWidths;
+import javafx.scene.layout.CornerRadii;
+import javafx.scene.layout.StackPane;
+import javafx.scene.paint.Color;
+import javafx.stage.Stage;
+
+/**
+ * The MainView holds the main application window which contains a MenuBar,
+ * the TabPane in which the In and OutputTabs will be displayed and
+ * some Controls
+ *
+ * @author Jan-Mathis Hein
+ */
+public class MainView {
+
+ //
+ private final Button centerButton, minButton, maxButton;
+
+ private final MenuBar menuBar;
+
+ private final Menu preferencesMenu, logMenu, helpMenu, jobMenu, directoryMenu;
+
+ private final MenuItem saveJobMenuItem, otherPreferencesMenuItem, newJobMenuItem,
+ loadJobOutputMenuItem, defaultInputDirectoryMenuItem, defaultOutputDirectoryMenuItem,
+ defaultImageDirectoryMenutItem, defaultMoleculeListDirectoryMenuItem, browseLogMenuItem,
+ resetLogMenuItem, aboutMenuItem, defaultSummaryReportDirectoryMenuItem;
+
+ private final Stage primaryStage;
+
+ private final Scene scene;
+
+ private final BorderPane mainPane;
+
+ private final TabPane tabPane;
+
+ private final HBox windowControlsBox;
+
+ private final StackPane centerPane;
+ //
+ //
+ //
+ /**
+ * Set up the main window with all its controls and
+ * handle their layout and size
+ *
+ * @param tmpPrimaryStage the main application window or more specifically
+ * the primary stage of the application
+ */
+ public MainView(Stage tmpPrimaryStage) {
+ this.primaryStage = tmpPrimaryStage;
+ this.primaryStage.setTitle(GeneralUtilities.getUIText("MainView.title.text") + " " + MSCConstants.MSC_VERSION);
+ this.mainPane = new BorderPane();
+ //
+ this.menuBar = new MenuBar();
+ this.jobMenu = new Menu(GeneralUtilities.getUIText("MainView.jobMenu.text"));
+ this.jobMenu.setStyle("-fx-background-color: rgb(180, 180, 180);-fx-border-color: rgb(150, 150, 150);");
+ this.newJobMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.newJobMenuItem.text"));
+ this.jobMenu.getItems().add(this.newJobMenuItem);
+ this.saveJobMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.saveJobMenuItem.text"));
+ this.jobMenu.getItems().add(this.saveJobMenuItem);
+ this.loadJobOutputMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.loadJobOutputMenuItem.text"));
+ this.jobMenu.getItems().add(this.loadJobOutputMenuItem);
+ this.menuBar.getMenus().add(this.jobMenu);
+ this.preferencesMenu = new Menu(GeneralUtilities.getUIText("MainView.preferencesMenu.text"));
+ this.preferencesMenu.setStyle("-fx-background-color: rgb(180, 180, 180);-fx-border-color: rgb(150, 150, 150);");
+ this.directoryMenu = new Menu(GeneralUtilities.getUIText("MainView.directoryMenu.text"));
+ this.defaultInputDirectoryMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.inputDirectoryMenuItem.text"));
+ this.defaultOutputDirectoryMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.outputDirectoryMenuItem.text"));
+ this.defaultImageDirectoryMenutItem = new MenuItem(GeneralUtilities.getUIText("MainView.imageDirectoryMenuItem.text"));
+ this.defaultMoleculeListDirectoryMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.moleculeListDirectoryMenuItem.text"));
+ this.defaultSummaryReportDirectoryMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.summaryReportDirectoryMenuItem.text"));
+ this.directoryMenu.getItems().addAll(
+ this.defaultInputDirectoryMenuItem, this.defaultOutputDirectoryMenuItem,
+ this.defaultImageDirectoryMenutItem, this.defaultMoleculeListDirectoryMenuItem,
+ this.defaultSummaryReportDirectoryMenuItem
+ );
+ this.preferencesMenu.getItems().add(this.directoryMenu);
+ this.otherPreferencesMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.otherPreferencesMenuItem.text"));
+ this.preferencesMenu.getItems().add(this.otherPreferencesMenuItem);
+ this.menuBar.getMenus().add(this.preferencesMenu);
+ this.helpMenu = new Menu(GeneralUtilities.getUIText("MainView.helpMenu.text"));
+ this.helpMenu.setStyle("-fx-background-color: rgb(180, 180, 180);-fx-border-color: rgb(150, 150, 150);");
+ this.logMenu = new Menu(GeneralUtilities.getUIText("MainView.logMenu.text"));
+ this.browseLogMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.browseLogMenuItem.text"));
+ this.resetLogMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.resetLogMenuItem.text"));
+ this.logMenu.getItems().addAll(this.browseLogMenuItem, this.resetLogMenuItem);
+ this.helpMenu.getItems().add(this.logMenu);
+ this.aboutMenuItem = new MenuItem(GeneralUtilities.getUIText("MainView.aboutMenuItem.text"));
+ this.helpMenu.getItems().add(this.aboutMenuItem);
+ this.menuBar.getMenus().add(this.helpMenu);
+ this.mainPane.setTop(this.menuBar);
+ //
+ //
+ this.centerPane = new StackPane();
+ this.centerPane.setStyle("-fx-background-color: rgb(220, 220, 220);");
+ this.tabPane = new TabPane();
+ this.centerPane.getChildren().add(this.tabPane);
+ this.mainPane.setCenter(this.centerPane);
+ //
+ //
+ this.windowControlsBox = new HBox(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.windowControlsBox.setBorder(new Border(new BorderStroke(
+ Color.color(0.1, 0.1, 0.1), Color.WHITE, Color.WHITE,
+ Color.WHITE, BorderStrokeStyle.SOLID, BorderStrokeStyle.NONE,
+ BorderStrokeStyle.NONE, BorderStrokeStyle.NONE,
+ new CornerRadii(0), new BorderWidths(2, 0, 0, 0), new Insets(0)
+ )));
+ this.windowControlsBox.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.maxButton = new Button(GeneralUtilities.getUIText("MainView.maxButton.text"));
+ GuiUtilities.setMinMaxPrefSize(this.maxButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.maxButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MainView.maxButton.tooltipText")));
+ this.minButton = new Button(GeneralUtilities.getUIText("MainView.minButton.text"));
+ GuiUtilities.setMinMaxPrefSize(this.minButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.minButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MainView.minButton.tooltipText")));
+ this.centerButton = new Button(GeneralUtilities.getUIText("MainView.centerButton.text"));
+ GuiUtilities.setMinMaxPrefSize(this.centerButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.centerButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MainView.centerButton.tooltipText")));
+ this.windowControlsBox.getChildren().addAll(this.maxButton, this.minButton, this.centerButton);
+ this.mainPane.setBottom(this.windowControlsBox);
+ //
+ this.scene = new Scene(this.mainPane);
+ this.scene.getStylesheets().add("resources/MainStyle.css");
+ this.primaryStage.setScene(this.scene);
+ }
+ //
+ //
+ //
+ /**
+ * Get the browseLogMenuItem
+ *
+ * @return the browseLogMenuItem
+ */
+ public MenuItem getBrowseLogMenuItem() {
+ return this.browseLogMenuItem;
+ }
+
+ /**
+ * Get the resetLogMenuItem
+ *
+ * @return the resetLogMenuItem
+ */
+ public MenuItem getResetLogMenuItem() {
+ return this.resetLogMenuItem;
+ }
+
+ /**
+ * Get the otherPreferencesMenuItem
+ *
+ * @return the otherPreferencesMenuItem
+ */
+ public MenuItem getOtherPreferencesMenuItem() {
+ return this.otherPreferencesMenuItem;
+ }
+
+ /**
+ * Get the defaultOutputDirectoryMenuItem
+ *
+ * @return the defaultOutputDirectoryMenuItem
+ */
+ public MenuItem getDefaultOutputDirectoryMenuItem() {
+ return this.defaultOutputDirectoryMenuItem;
+ }
+
+ /**
+ * Get the defaultImageDirectoryMenutItem
+ *
+ * @return the defaultImageDirectoryMenutItem
+ */
+ public MenuItem getDefaultImageDirectoryMenutItem() {
+ return this.defaultImageDirectoryMenutItem;
+ }
+
+ /**
+ * Get the defaultMoleculeListDirectoryMenuItem
+ *
+ * @return the defaultMoleculeListDirectoryMenuItem
+ */
+ public MenuItem getDefaultMoleculeListDirectoryMenuItem() {
+ return this.defaultMoleculeListDirectoryMenuItem;
+ }
+
+ /**
+ * Get the defaultSummaryReportDirectoryMenuItem
+ *
+ * @return the defaultSummaryReportDirectoryMenuItem
+ */
+ public MenuItem getDefaultSummaryReportDirectoryMenuItem() {
+ return this.defaultSummaryReportDirectoryMenuItem;
+ }
+
+ /**
+ * Get the newJobMenuItem
+ *
+ * @return the newJobMenuItem
+ */
+ public MenuItem getNewJobMenuItem() {
+ return this.newJobMenuItem;
+ }
+
+ /**
+ * Get the loadJobOutputMenuItem
+ *
+ * @return the loadJobOutputMenuItem
+ */
+ public MenuItem getLoadJobOutputMenuItem() {
+ return this.loadJobOutputMenuItem;
+ }
+
+ /**
+ * Get the defaultInputDirectoryMenuItem
+ *
+ * @return the defaultInputDirectoryMenuItem
+ */
+ public MenuItem getDefaultInputDirectoryMenuItem() {
+ return this.defaultInputDirectoryMenuItem;
+ }
+
+ /**
+ * Get the saveJobMenuItem
+ *
+ * @return the saveJobMenuItem
+ */
+ public MenuItem getSaveJobMenuItem() {
+ return this.saveJobMenuItem;
+ }
+
+ /**
+ * Get the aboutMenuItem
+ *
+ * @return the aboutMenuItem
+ */
+ public MenuItem getAboutMenuItem() {
+ return this.aboutMenuItem;
+ }
+
+ /**
+ * Get the centerButton
+ *
+ * @return the centerButton
+ */
+ public Button getCenterButton() {
+ return this.centerButton;
+ }
+
+ /**
+ * Get the minButton
+ *
+ * @return the minButton
+ */
+ public Button getMinButton() {
+ return this.minButton;
+ }
+
+ /**
+ * Get the maxButton
+ *
+ * @return the maxButton
+ */
+ public Button getMaxButton() {
+ return this.maxButton;
+ }
+
+ /**
+ * Get the primaryStage
+ *
+ * @return the primaryStage
+ */
+ public Stage getPrimaryStage() {
+ return this.primaryStage;
+ }
+
+ /**
+ * Get the scene
+ *
+ * @return the scene
+ */
+ public Scene getScene() {
+ return this.scene;
+ }
+
+ /**
+ * Get the centerPane
+ *
+ * @return the centerPane
+ */
+ public StackPane getCenterPane() {
+ return this.centerPane;
+ }
+
+ /**
+ * Get the tabPane
+ *
+ * @return the tabPane
+ */
+ public TabPane getTabPane() {
+ return this.tabPane;
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/view/MoleculePairDisplayerStage.java b/src/main/java/de/whs/ibci/msc/view/MoleculePairDisplayerStage.java
new file mode 100644
index 0000000..174f082
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/view/MoleculePairDisplayerStage.java
@@ -0,0 +1,355 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.view;
+
+import de.whs.ibci.msc.model.ComparisonFeature;
+import de.whs.ibci.msc.utility.GuiUtilities;
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import javafx.geometry.HPos;
+import javafx.geometry.Insets;
+import javafx.geometry.Pos;
+import javafx.geometry.VPos;
+import javafx.scene.Scene;
+import javafx.scene.control.Button;
+import javafx.scene.control.CheckBox;
+import javafx.scene.control.Control;
+import javafx.scene.control.Label;
+import javafx.scene.control.ScrollPane;
+import javafx.scene.control.TextField;
+import javafx.scene.control.Tooltip;
+import javafx.scene.image.ImageView;
+import javafx.scene.layout.Border;
+import javafx.scene.layout.BorderStroke;
+import javafx.scene.layout.BorderStrokeStyle;
+import javafx.scene.layout.BorderWidths;
+import javafx.scene.layout.ColumnConstraints;
+import javafx.scene.layout.CornerRadii;
+import javafx.scene.layout.FlowPane;
+import javafx.scene.layout.GridPane;
+import javafx.scene.layout.HBox;
+import javafx.scene.layout.Priority;
+import javafx.scene.layout.RowConstraints;
+import javafx.scene.layout.StackPane;
+import javafx.scene.layout.VBox;
+import javafx.scene.paint.Paint;
+import javafx.stage.Stage;
+
+/**
+ * A window or more specifically a Stage on which a collection of molecule pairs
+ * can be displayed.
+ *
+ * @author Jan-Mathis Hein
+ */
+public class MoleculePairDisplayerStage extends Stage {
+
+ //
+ private final Button saveLeftListButton, saveRightListButton, saveLeftImageButton, saveRightImageButton, nextButton, previousButton, lastButton, firstButton;
+
+ private final Scene scene;
+
+ private final TextField positionTextField;
+
+ private final ImageView leftMoleculeImageView, rightMoleculeImageView;
+
+ private final Label infoLabel;
+
+ private final HBox moleculePairBox, positionControlsBox, otherControlsBox;
+
+ private final VBox controlsBox;
+
+ private final GridPane mainPane, infoPane, savingControlsPane;
+
+ private final FlowPane additionalComparisonFeatureControlsPane;
+
+ private final ScrollPane additionalComparisonFeaturesScrollPane;
+
+ private final StackPane leftMoleculePane, rightMoleculePane;
+
+ private final Control[][] additionalComparisonFeatureControls;
+ //
+ //
+ //
+ /**
+ * Creates the stage with all its controls and handle their layout and size
+ */
+ public MoleculePairDisplayerStage() {
+ super();
+ this.mainPane = new GridPane();
+ this.mainPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.mainPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.mainPane.setHgap(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.mainPane.getColumnConstraints().addAll(
+ new ColumnConstraints(60, 100, Double.MAX_VALUE, Priority.ALWAYS, HPos.LEFT, true),
+ new ColumnConstraints()
+ );
+ this.mainPane.getRowConstraints().addAll(
+ new RowConstraints(),
+ new RowConstraints(49.6, 49.6, Double.MAX_VALUE, Priority.ALWAYS, VPos.TOP, true)
+ );
+ this.moleculePairBox = new HBox();
+ this.moleculePairBox.setBorder(GuiUtilities.RAISED_BORDER);
+ this.leftMoleculePane = new StackPane();
+ this.leftMoleculePane.setBorder(new Border(new BorderStroke(
+ Paint.valueOf("Black"), Paint.valueOf("Black"), Paint.valueOf("Black"),
+ Paint.valueOf("Black"), BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ new CornerRadii(0), new BorderWidths(2, 1, 2, 2), new Insets(10, 0, 10, 10)
+ )));
+ this.leftMoleculeImageView = new ImageView();
+ this.leftMoleculeImageView.setPreserveRatio(true);
+ this.leftMoleculePane.getChildren().add(this.leftMoleculeImageView);
+ this.rightMoleculePane = new StackPane();
+ this.rightMoleculePane.setBorder(new Border(new BorderStroke(
+ Paint.valueOf("Black"), Paint.valueOf("Black"), Paint.valueOf("Black"),
+ Paint.valueOf("Black"), BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ BorderStrokeStyle.SOLID, BorderStrokeStyle.SOLID,
+ new CornerRadii(0), new BorderWidths(2, 2, 2, 1), new Insets(10, 10, 10, 0)
+ )));
+ this.rightMoleculeImageView = new ImageView();
+ this.rightMoleculeImageView.setPreserveRatio(true);
+ this.rightMoleculePane.getChildren().add(this.rightMoleculeImageView);
+ this.moleculePairBox.getChildren().addAll(this.leftMoleculePane, this.rightMoleculePane);
+ this.mainPane.add(this.moleculePairBox, 1, 0, 1, 1);
+ this.infoPane = new GridPane();
+ this.infoPane.setBorder(GuiUtilities.RAISED_BORDER);
+ this.infoPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.infoPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.infoPane.setMaxWidth(Double.MAX_VALUE);
+ this.infoPane.getRowConstraints().addAll(
+ new RowConstraints(),
+ new RowConstraints(20, 20, Double.MAX_VALUE, Priority.ALWAYS, VPos.TOP, true)
+ );
+ this.infoPane.getColumnConstraints().addAll(
+ new ColumnConstraints(40, 80, Double.MAX_VALUE, Priority.ALWAYS, HPos.LEFT, true)
+ );
+ this.infoLabel = new Label();
+ this.infoLabel.setWrapText(true);
+ this.infoLabel.setAlignment(Pos.TOP_LEFT);
+ this.infoLabel.setMaxSize(Double.MAX_VALUE, Double.MAX_VALUE);
+ this.infoPane.add(this.infoLabel, 0, 0);
+ this.additionalComparisonFeaturesScrollPane = new ScrollPane();
+ this.additionalComparisonFeaturesScrollPane.setFitToWidth(true);
+ this.additionalComparisonFeaturesScrollPane.setVbarPolicy(ScrollPane.ScrollBarPolicy.ALWAYS);
+ this.additionalComparisonFeaturesScrollPane.setHbarPolicy(ScrollPane.ScrollBarPolicy.AS_NEEDED);
+ this.additionalComparisonFeaturesScrollPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.additionalComparisonFeatureControlsPane = new FlowPane();
+ this.additionalComparisonFeatureControlsPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.additionalComparisonFeatureControlsPane.setHgap(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.additionalComparisonFeatureControls = new Control[ComparisonFeature.values().length][2];
+ CheckBox tmpCheckBox;
+ Label tmpLabel;
+ HBox tmpBox;
+ for (int i = 0; i < this.additionalComparisonFeatureControls.length; i++) {
+ tmpBox = new HBox(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ GuiUtilities.setMinMaxPrefWidth(tmpBox, 320);
+ tmpCheckBox = new CheckBox(ComparisonFeature.values()[i].toString());
+ tmpCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.additionalComparisonFeatureCheckBox.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(tmpCheckBox, 160);
+ this.additionalComparisonFeatureControls[i][0] = tmpCheckBox;
+ tmpBox.getChildren().add(tmpCheckBox);
+ tmpLabel = new Label("");
+ this.additionalComparisonFeatureControls[i][1] = tmpLabel;
+ tmpBox.getChildren().add(tmpLabel);
+ this.additionalComparisonFeatureControlsPane.getChildren().add(tmpBox);
+ }
+ this.additionalComparisonFeaturesScrollPane.setContent(this.additionalComparisonFeatureControlsPane);
+ this.infoPane.add(this.additionalComparisonFeaturesScrollPane, 0, 1);
+ this.mainPane.add(this.infoPane, 0, 0, 1, 2);
+ this.controlsBox = new VBox(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.controlsBox.setBorder(GuiUtilities.RAISED_BORDER);
+ this.controlsBox.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.positionControlsBox = new HBox(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.positionControlsBox.setAlignment(Pos.TOP_CENTER);
+ this.firstButton = new Button(GeneralUtilities.getUIText("MoleculePairDisplayerStage.firstButton.text"));
+ this.firstButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.firstButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.firstButton, 30, GuiUtilities.BUTTON_HEIGHT);
+ this.previousButton = new Button(GeneralUtilities.getUIText("MoleculePairDisplayerStage.previousButton.text"));
+ this.previousButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.previousButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.previousButton, 30, GuiUtilities.BUTTON_HEIGHT);
+ this.positionTextField = new TextField();
+ this.positionTextField.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.positionTextField.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.positionTextField, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.nextButton = new Button(GeneralUtilities.getUIText("MoleculePairDisplayerStage.nextButton.text"));
+ this.nextButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.nextButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.nextButton, 30, GuiUtilities.BUTTON_HEIGHT);
+ this.lastButton = new Button(GeneralUtilities.getUIText("MoleculePairDisplayerStage.lastButton.text"));
+ this.lastButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.lastButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.lastButton, 30, GuiUtilities.BUTTON_HEIGHT);
+ this.positionControlsBox.getChildren().addAll(this.firstButton, this.previousButton, this.positionTextField, this.nextButton, this.lastButton);
+ this.controlsBox.getChildren().addAll(this.positionControlsBox);
+ this.otherControlsBox = new HBox(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.savingControlsPane = new GridPane();
+ this.savingControlsPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.savingControlsPane.setHgap(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.savingControlsPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.savingControlsPane.setBorder(GuiUtilities.LOWERED_BORDER);
+ this.saveLeftListButton = new Button(GeneralUtilities.getUIText("MoleculePairDisplayerStage.saveLeftListButton.text"));
+ this.saveLeftListButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.saveLeftListButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.saveLeftListButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.savingControlsPane.add(this.saveLeftListButton, 0, 0);
+ this.saveRightListButton = new Button(GeneralUtilities.getUIText("MoleculePairDisplayerStage.saveRightListButton.text"));
+ this.saveRightListButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.saveRightListButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.saveRightListButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.savingControlsPane.add(this.saveRightListButton, 0, 1);
+ this.saveLeftImageButton = new Button(GeneralUtilities.getUIText("MoleculePairDisplayerStage.saveLeftImageButton.text"));
+ this.saveLeftImageButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.saveLeftImageButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.saveLeftImageButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.savingControlsPane.add(this.saveLeftImageButton, 1, 0);
+ this.saveRightImageButton = new Button(GeneralUtilities.getUIText("MoleculePairDisplayerStage.saveRightImageButton.text"));
+ this.saveRightImageButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("MoleculePairDisplayerStage.saveRightImageButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.saveRightImageButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.savingControlsPane.add(this.saveRightImageButton, 1, 1);
+ this.otherControlsBox.getChildren().add(this.savingControlsPane);
+ this.controlsBox.getChildren().add(this.otherControlsBox);
+ this.mainPane.add(this.controlsBox, 1, 1, 1, 1);
+ this.scene = new Scene(this.mainPane);
+ this.scene.getStylesheets().add("resources/MainStyle.css");
+ this.setScene(this.scene);
+ }
+ //
+ //
+ //
+ /**
+ * Get the nextButton
+ *
+ * @return the nextButton
+ */
+ public Button getNextButton() {
+ return this.nextButton;
+ }
+
+ /**
+ * Get the previousButton
+ *
+ * @return the previousButton
+ */
+ public Button getPreviousButton() {
+ return this.previousButton;
+ }
+
+ /**
+ * Get the saveLeftListButton
+ *
+ * @return the saveLeftListButton
+ */
+ public Button getSaveLeftListButton() {
+ return this.saveLeftListButton;
+ }
+
+ /**
+ * Get the saveRightListButton
+ *
+ * @return the saveRightListButton
+ */
+ public Button getSaveRightListButton() {
+ return this.saveRightListButton;
+ }
+
+ /**
+ * Get the saveLeftImageButton
+ *
+ * @return the saveLeftImageButton
+ */
+ public Button getSaveLeftImageButton() {
+ return this.saveLeftImageButton;
+ }
+
+ /**
+ * Get the saveRightImageButton
+ *
+ * @return the saveRightImageButton
+ */
+ public Button getSaveRightImageButton() {
+ return this.saveRightImageButton;
+ }
+
+ /**
+ * Get the lastButton
+ *
+ * @return the lastButton
+ */
+ public Button getLastButton() {
+ return this.lastButton;
+ }
+
+ /**
+ * Get the firstButton
+ *
+ * @return the firstButton
+ */
+ public Button getFirstButton() {
+ return this.firstButton;
+ }
+
+ /**
+ * Get the infoPane
+ *
+ * @return the infoPane
+ */
+ public GridPane getInfoPane() {
+ return this.infoPane;
+ }
+
+ /**
+ * Get the leftMoleculeImageView
+ *
+ * @return the leftMoleculeImageView
+ */
+ public ImageView getLeftMoleculeImageView() {
+ return this.leftMoleculeImageView;
+ }
+
+ /**
+ * Get the rightMoleculeImageView
+ *
+ * @return the rightMoleculeImageView
+ */
+ public ImageView getRightMoleculeImageView() {
+ return this.rightMoleculeImageView;
+ }
+
+ /**
+ * Get the infoLabel
+ *
+ * @return the infoLabel
+ */
+ public Label getInfoLabel() {
+ return infoLabel;
+ }
+
+ /**
+ * Get the positionTextField
+ *
+ * @return the positionTextField
+ */
+ public TextField getPositionTextField() {
+ return this.positionTextField;
+ }
+
+ /**
+ * Get the additionalComparisonFeatureControls array where each element is
+ * an array of the form {checkbox, label}
+ *
+ * @return the additionalComparisonFeatureControls array
+ */
+ public Control[][] getAdditionalComparisonFeatureControls() {
+ return this.additionalComparisonFeatureControls;
+ }
+ //
+
+}
diff --git a/src/main/java/de/whs/ibci/msc/view/OutputTab.java b/src/main/java/de/whs/ibci/msc/view/OutputTab.java
new file mode 100644
index 0000000..536708e
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/view/OutputTab.java
@@ -0,0 +1,383 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.view;
+
+import de.whs.ibci.msc.control.BinLabelType;
+import de.whs.ibci.msc.control.JobController;
+import de.whs.ibci.msc.utility.GuiUtilities;
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import de.whs.ibci.msc.model.ComparisonFeature;
+import java.util.Set;
+import javafx.collections.FXCollections;
+import javafx.geometry.Insets;
+import javafx.geometry.Orientation;
+import javafx.geometry.Pos;
+import javafx.scene.control.Button;
+import javafx.scene.control.CheckBox;
+import javafx.scene.control.ChoiceBox;
+import javafx.scene.control.Label;
+import javafx.scene.control.Slider;
+import javafx.scene.control.Tab;
+import javafx.scene.control.TextField;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.AnchorPane;
+import javafx.scene.layout.GridPane;
+import javafx.scene.layout.HBox;
+import javafx.scene.layout.Region;
+import javafx.scene.layout.VBox;
+
+/**
+ * A Tab in which a job's output is displayed and that contains some controls
+ * with which the user can interact with the output
+ *
+ * @author Jan-Mathis Hein
+ */
+public class OutputTab extends Tab {
+
+ //
+ private final HBox contentPane;
+
+ private final VBox binBorderSlidersBox, frequencySlidersBox, binBorderBox, frequencyBox;
+
+ private final AnchorPane chartPane;
+
+ private final Label infoLabel, binBorderSlidersLabel, frequencySlidersLabel, numberOfBinsLabel;
+
+ private final GridPane controlsPane, chartConfigurationPane;
+
+ private final ChoiceBox chartChoiceBox;
+
+ private final TextField numberOfBinsTextField;
+
+ private final ChoiceBox binLabelChoiceBox;
+
+ private final Button imageButton, chartConfigurationButton, defaultButton, binBorderConfigurationButton, summaryReportButton;
+
+ private final Slider binBorder1Slider, binBorder2Slider, frequency1Slider, frequency2Slider;
+
+ private final CheckBox relativeFrequenciesCheckBox, barLabelCheckBox;
+ //
+ //
+ //
+ /**
+ * Create the Tab with all its controls and handle their layout and size
+ *
+ * @param tmpJobNumber the job's identifier number
+ */
+ public OutputTab(String tmpJobNumber) {
+ super(GeneralUtilities.getUIText("OutputTab.title.text") + tmpJobNumber);
+ this.setClosable(true);
+ this.contentPane = new HBox(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ // The 11 is intentional
+ this.contentPane.setPadding(new Insets(10, 10, 11, 10));
+ this.controlsPane = new GridPane();
+ this.controlsPane.setHgap(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.controlsPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.controlsPane.setBorder(GuiUtilities.RAISED_BORDER);
+ this.controlsPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.infoLabel = new Label("");
+ this.infoLabel.setWrapText(true);
+ this.infoLabel.setAlignment(Pos.TOP_LEFT);
+ this.controlsPane.add(this.infoLabel, 0, 0, 2, 1);
+ this.summaryReportButton = new Button(GeneralUtilities.getUIText("OutputTab.summaryReportButton.text"));
+ this.summaryReportButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.summaryReportButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.summaryReportButton, GuiUtilities.BUTTON_WIDTH);
+ this.controlsPane.add(this.summaryReportButton, 0, 1, 1, 1);
+ this.barLabelCheckBox = new CheckBox(GeneralUtilities.getUIText("OutputTab.barLabelCheckBox.text"));
+ this.barLabelCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.barLabelCheckBox.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.barLabelCheckBox, GuiUtilities.BUTTON_WIDTH);
+ this.controlsPane.add(this.barLabelCheckBox, 1, 1, 1, 1);
+ this.chartChoiceBox = new ChoiceBox<>();
+ this.chartChoiceBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.chartChoiceBox.tooltipText")));
+ this.chartChoiceBox.setMaxWidth(Double.MAX_VALUE);
+ this.controlsPane.add(this.chartChoiceBox, 0, 2, 2, 1);
+ this.binLabelChoiceBox = new ChoiceBox<>();
+ this.binLabelChoiceBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.binLabelChoiceBox.tooltipText")));
+ this.binLabelChoiceBox.setMaxWidth(Double.MAX_VALUE);
+ this.controlsPane.add(this.binLabelChoiceBox, 0, 3, 2, 1);
+ this.chartConfigurationPane = new GridPane();
+ this.chartConfigurationPane.setHgap(GuiUtilities.HORIZONTAL_GAP_BETWEEN_CONTROLS);
+ this.chartConfigurationPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.chartConfigurationPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.chartConfigurationPane.setBorder(GuiUtilities.LOWERED_BORDER);
+ this.chartConfigurationButton = new Button(GeneralUtilities.getUIText("OutputTab.configureButton.text"));
+ this.chartConfigurationButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.configureButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.chartConfigurationButton, GuiUtilities.BUTTON_WIDTH);
+ this.chartConfigurationPane.add(this.chartConfigurationButton, 0, 0, 1, 1);
+ this.defaultButton = new Button(GeneralUtilities.getUIText("ChartConfigurationDialog.defaultButton.text"));
+ this.defaultButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("ChartConfigurationDialog.defaultButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.defaultButton, GuiUtilities.BUTTON_WIDTH);
+ this.chartConfigurationPane.add(this.defaultButton, 1, 0, 1, 1);
+ this.binBorderConfigurationButton = new Button(GeneralUtilities.getUIText("OutputTab.binBorderConfigurationButton.text"));
+ this.binBorderConfigurationButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.binBorderConfigurationButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.binBorderConfigurationButton, GuiUtilities.BUTTON_WIDTH);
+ this.chartConfigurationPane.add(this.binBorderConfigurationButton, 0, 1, 1, 1);
+ this.relativeFrequenciesCheckBox = new CheckBox(GeneralUtilities.getUIText("OutputTab.relativeFrequenciesCheckBox.text"));
+ this.relativeFrequenciesCheckBox.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.relativeFrequenciesCheckBox.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.relativeFrequenciesCheckBox, GuiUtilities.BUTTON_WIDTH);
+ this.chartConfigurationPane.add(this.relativeFrequenciesCheckBox, 1, 1, 1, 1);
+ this.numberOfBinsLabel = new Label(GeneralUtilities.getUIText("OutputTab.numberOfBinsLabel.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.numberOfBinsLabel, GuiUtilities.BUTTON_WIDTH);
+ this.chartConfigurationPane.add(this.numberOfBinsLabel, 0, 2, 1, 1);
+ this.numberOfBinsTextField = new TextField();
+ this.numberOfBinsTextField.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.numberOfBinsTextField.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.numberOfBinsTextField, GuiUtilities.BUTTON_WIDTH);
+ this.chartConfigurationPane.add(this.numberOfBinsTextField, 1, 2, 1, 1);
+ this.binBorderBox = new VBox(-5);
+ this.binBorderSlidersLabel = new Label(GeneralUtilities.getUIText("OutputTab.binBorderSlidersLabel.text"));
+ this.binBorderBox.getChildren().add(this.binBorderSlidersLabel);
+ this.binBorderSlidersBox = new VBox(-10);
+ this.binBorder1Slider = new Slider();
+ this.binBorder1Slider.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.binBorderSlider.tooltipText")));
+ this.binBorder1Slider.setOrientation(Orientation.HORIZONTAL);
+ GuiUtilities.setMinMaxPrefHeight(this.binBorder1Slider, 50);
+ this.binBorder1Slider.setShowTickMarks(true);
+ this.binBorder1Slider.setShowTickLabels(true);
+ this.binBorderSlidersBox.getChildren().add(this.binBorder1Slider);
+ this.binBorder2Slider = new Slider();
+ this.binBorder2Slider.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.binBorderSlider.tooltipText")));
+ this.binBorder2Slider.setOrientation(Orientation.HORIZONTAL);
+ GuiUtilities.setMinMaxPrefHeight(this.binBorder2Slider, 20);
+ this.binBorder2Slider.setShowTickMarks(false);
+ this.binBorder2Slider.setShowTickLabels(false);
+ this.binBorderSlidersBox.getChildren().add(this.binBorder2Slider);
+ this.binBorderBox.getChildren().add(this.binBorderSlidersBox);
+ this.chartConfigurationPane.add(this.binBorderBox, 0, 3, 2, 1);
+ this.frequencyBox = new VBox(-5);
+ this.frequencySlidersLabel = new Label(GeneralUtilities.getUIText("OutputTab.frequencySlidersLabel.text"));
+ this.frequencyBox.getChildren().add(this.frequencySlidersLabel);
+ this.frequencySlidersBox = new VBox(-10);
+ this.frequency1Slider = new Slider();
+ this.frequency1Slider.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.frequencySlider.tooltipText")));
+ this.frequency1Slider.setOrientation(Orientation.HORIZONTAL);
+ GuiUtilities.setMinMaxPrefHeight(this.frequency1Slider, 50);
+ this.frequency1Slider.setShowTickMarks(true);
+ this.frequency1Slider.setShowTickLabels(true);
+ this.frequencySlidersBox.getChildren().add(this.frequency1Slider);
+ this.frequency2Slider = new Slider();
+ this.frequency2Slider.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.frequencySlider.tooltipText")));
+ this.frequency2Slider.setOrientation(Orientation.HORIZONTAL);
+ GuiUtilities.setMinMaxPrefHeight(this.frequency2Slider, 20);
+ this.frequency2Slider.setShowTickMarks(false);
+ this.frequency2Slider.setShowTickLabels(false);
+ this.frequencySlidersBox.getChildren().add(this.frequency2Slider);
+ this.frequencyBox.getChildren().add(this.frequencySlidersBox);
+ this.chartConfigurationPane.add(this.frequencyBox, 0, 4, 2, 1);
+ this.controlsPane.add(this.chartConfigurationPane, 0, 4, 2, 1);
+ this.contentPane.getChildren().add(this.controlsPane);
+ this.chartPane = new AnchorPane();
+ this.chartPane.setBorder(GuiUtilities.RAISED_BORDER);
+ this.chartPane.setPrefWidth(999999);
+ this.imageButton = new Button(GeneralUtilities.getUIText("OutputTab.saveButton.text"));
+ this.imageButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("OutputTab.saveButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.imageButton, GuiUtilities.BUTTON_WIDTH);
+ AnchorPane.setRightAnchor(this.imageButton, 10.0);
+ AnchorPane.setTopAnchor(this.imageButton, 10.0);
+ this.chartPane.getChildren().add(this.imageButton);
+ this.contentPane.getChildren().add(this.chartPane);
+ this.setContent(this.contentPane);
+ }
+ //
+ //
+ //
+ //
+ /**
+ * Get the chartChoiceBox
+ *
+ * @return the chartChoiceBox
+ */
+ public ChoiceBox getChartChoiceBox() {
+ return this.chartChoiceBox;
+ }
+
+ /**
+ * Get the binLabelChoiceBox
+ *
+ * @return the binLabelChoiceBox
+ */
+ public ChoiceBox getBinLabelChoiceBox() {
+ return this.binLabelChoiceBox;
+ }
+
+ /**
+ * Get the numberOfBinsTextField
+ *
+ * @return the numberOfBinsTextField
+ */
+ public TextField getNumberOfBinsTextField() {
+ return this.numberOfBinsTextField;
+ }
+
+ /**
+ * Get the chartConfigurationButton
+ *
+ * @return the chartConfigurationButton
+ */
+ public Button getChartConfigurationButton() {
+ return this.chartConfigurationButton;
+ }
+
+ /**
+ * Get the imageButton
+ *
+ * @return the imageButton
+ */
+ public Button getImageButton() {
+ return this.imageButton;
+ }
+
+ /**
+ * Get the summaryReportButton
+ *
+ * @return the summaryReportButton
+ */
+ public Button getSummaryReportButton() {
+ return this.summaryReportButton;
+ }
+
+ /**
+ * Get the defaultButton
+ *
+ * @return the defaultButton
+ */
+ public Button getDefaultButton() {
+ return this.defaultButton;
+ }
+
+ /**
+ * Get the binBorderConfigurationButton
+ *
+ * @return the binBorderConfigurationButton
+ */
+ public Button getBinBorderConfigurationButton() {
+ return this.binBorderConfigurationButton;
+ }
+
+ /**
+ * Get the relativeFrequenciesCheckBox
+ *
+ * @return the relativeFrequenciesCheckBox
+ */
+ public CheckBox getRelativeFrequenciesCheckBox() {
+ return this.relativeFrequenciesCheckBox;
+ }
+
+ /**
+ * Get the barLabelCheckBox
+ *
+ * @return the barLabelCheckBox
+ */
+ public CheckBox getBarLabelCheckBox() {
+ return this.barLabelCheckBox;
+ }
+
+ /**
+ * Get the infoLabel
+ *
+ * @return the infoLabel
+ */
+ public Label getInfoLabel() {
+ return this.infoLabel;
+ }
+
+ /**
+ * Get the frequency1Slider
+ *
+ * @return the frequency1Slider
+ */
+ public Slider getFrequency1Slider() {
+ return this.frequency1Slider;
+ }
+
+ /**
+ * Get the frequency2Slider
+ *
+ * @return the frequency2Slider
+ */
+ public Slider getFrequency2Slider() {
+ return this.frequency2Slider;
+ }
+
+ /**
+ * Get the binBorder1Slider
+ *
+ * @return the binBorder1Slider
+ */
+ public Slider getBinBorder1Slider() {
+ return this.binBorder1Slider;
+ }
+
+ /**
+ * Get the binBorder2Slider
+ *
+ * @return the binBorder2Slider
+ */
+ public Slider getBinBorder2Slider() {
+ return this.binBorder2Slider;
+ }
+
+ /**
+ * Get the chartPane
+ *
+ * @return the chartPane
+ */
+ public AnchorPane getChartPane() {
+ return this.chartPane;
+ }
+ //
+ //
+ /**
+ * Set the set of ComparisonFeatures that will be the items of the
+ * chartChoiceBox
+ *
+ * @param tmpComparisonFeatureSet specifies the set of ComparisonFeatures
+ */
+ public void setChartChoiceBoxItems(Set tmpComparisonFeatureSet) {
+ this.chartChoiceBox.setItems(FXCollections.observableArrayList(tmpComparisonFeatureSet));
+ }
+
+ /**
+ * Set the set of BinLabelTypes that will be the items of the
+ * binLabelChoiceBox
+ *
+ * @param tmpBinLabelTypeSet specifies the set of BinLabelTypes
+ */
+ public void setBinLabelChoiceBoxItems(Set tmpBinLabelTypeSet) {
+ this.binLabelChoiceBox.setItems(FXCollections.observableArrayList(tmpBinLabelTypeSet));
+ }
+
+ /**
+ * Set a region that will be displayed in the chartPane
+ *
+ * @param tmpRegion specifies the region
+ */
+ public void setComparisonFeatureChart(Region tmpRegion){
+ this.chartPane.getChildren().clear();
+ AnchorPane.setRightAnchor(this.imageButton, 10.0);
+ AnchorPane.setTopAnchor(this.imageButton, 10.0);
+ this.chartPane.getChildren().add(this.imageButton);
+ AnchorPane.setLeftAnchor(tmpRegion, 0.0);
+ AnchorPane.setTopAnchor(tmpRegion, 38.0);
+ // Alignes the chart with the button
+ AnchorPane.setRightAnchor(tmpRegion, 3.0);
+ AnchorPane.setBottomAnchor(tmpRegion, 0.0);
+ this.chartPane.getChildren().add(tmpRegion);
+ }
+ //
+ //
+}
diff --git a/src/main/java/de/whs/ibci/msc/view/PreferencesConfigurationDialog.java b/src/main/java/de/whs/ibci/msc/view/PreferencesConfigurationDialog.java
new file mode 100644
index 0000000..981ddcc
--- /dev/null
+++ b/src/main/java/de/whs/ibci/msc/view/PreferencesConfigurationDialog.java
@@ -0,0 +1,161 @@
+/*
+ * MSC - Molecule Set Comparator
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.view;
+
+import de.whs.ibci.msc.utility.GuiUtilities;
+import de.whs.ibci.msc.utility.GeneralUtilities;
+import javafx.geometry.Orientation;
+import javafx.geometry.Pos;
+import javafx.scene.control.Button;
+import javafx.scene.control.Label;
+import javafx.scene.control.Slider;
+import javafx.scene.control.TextField;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.GridPane;
+import javafx.scene.layout.HBox;
+import javafx.stage.Window;
+
+/**
+ * A Dialog in which the user can configure some of the application's
+ * preferences
+ *
+ * @author Jan-Mathis Hein
+ */
+public class PreferencesConfigurationDialog extends ConfigurationDialog {
+
+ //
+ private final GridPane inputPane;
+
+ private final Label numberOfParallelThreadsLabel, defaultNumberOfBinsLabel, maximalNumberOfMoleculePairsToSaveLabel, imageQualityLabel;
+
+ private final TextField numberOfParallelThreadsField, defaultNumberOfBinsField, maximalNumberOfMoleculePairsToSaveField;
+
+ private final Button resetButton;
+
+ private final Slider imageQualitySlider;
+
+ private final HBox resetButtonBox;
+ //
+ //
+ //
+ /**
+ * Create the Dialog with all its controls and handle their layout and size
+ *
+ * @param tmpOwner specifies the window that owns the Dialog
+ * @param tmpTitle specifies the title of the Dialog
+ */
+ public PreferencesConfigurationDialog(Window tmpOwner, String tmpTitle) {
+ super(tmpOwner, tmpTitle);
+ this.inputPane = new GridPane();
+ this.inputPane.setBorder(GuiUtilities.RAISED_BORDER);
+ this.inputPane.setPadding(GuiUtilities.STANDARD_INSETS);
+ this.inputPane.setVgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.inputPane.setHgap(GuiUtilities.VERTICAL_GAP_BETWEEN_CONTROLS);
+ this.numberOfParallelThreadsLabel = new Label(GeneralUtilities.getUIText("PreferencesConfigurationDialog.numberOfParallelThreadsLabel.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.numberOfParallelThreadsLabel, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.numberOfParallelThreadsLabel, 0, 0);
+ this.numberOfParallelThreadsField = new TextField();
+ this.numberOfParallelThreadsField.setTooltip(new Tooltip(GeneralUtilities.getUIText("PreferencesConfigurationDialog.numberOfParallelThreadsField.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.numberOfParallelThreadsField, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.numberOfParallelThreadsField, 1, 0);
+ this.defaultNumberOfBinsLabel = new Label(GeneralUtilities.getUIText("PreferencesConfigurationDialog.defaultNumberOfBinsLabel.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.defaultNumberOfBinsLabel, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.defaultNumberOfBinsLabel, 0, 1);
+ this.defaultNumberOfBinsField = new TextField();
+ this.defaultNumberOfBinsField.setTooltip(new Tooltip(GeneralUtilities.getUIText("PreferencesConfigurationDialog.defaultNumberOfBinsField.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.defaultNumberOfBinsField, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.defaultNumberOfBinsField, 1, 1);
+ this.maximalNumberOfMoleculePairsToSaveLabel = new Label(GeneralUtilities.getUIText("PreferencesConfigurationDialog.maximalNumberOfMoleculePairsToSaveLabel.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.maximalNumberOfMoleculePairsToSaveLabel, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.maximalNumberOfMoleculePairsToSaveLabel, 0, 2);
+ this.maximalNumberOfMoleculePairsToSaveField = new TextField();
+ this.maximalNumberOfMoleculePairsToSaveField.setTooltip(new Tooltip(GeneralUtilities.getUIText("PreferencesConfigurationDialog.maximalNumberOfMoleculePairsToSaveField.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.maximalNumberOfMoleculePairsToSaveField, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.maximalNumberOfMoleculePairsToSaveField, 1, 2);
+ this.imageQualityLabel = new Label(GeneralUtilities.getUIText("PreferencesConfigurationDialog.imageQualityLabel.text"));
+ GuiUtilities.setMinMaxPrefWidth(this.imageQualityLabel, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.imageQualityLabel, 0, 3);
+ this.imageQualitySlider = new Slider(0.0, 1.0, 0.5);
+ this.imageQualitySlider.setMajorTickUnit(0.25);
+ this.imageQualitySlider.setOrientation(Orientation.HORIZONTAL);
+ this.imageQualitySlider.setShowTickLabels(true);
+ this.imageQualitySlider.setShowTickMarks(true);
+ this.imageQualitySlider.setTooltip(new Tooltip(GeneralUtilities.getUIText("PreferencesConfigurationDialog.imageQualitySlider.tooltipText")));
+ GuiUtilities.setMinMaxPrefWidth(this.imageQualitySlider, GuiUtilities.TEXT_FIELD_WIDTH);
+ this.inputPane.add(this.imageQualitySlider, 1, 3);
+ this.resetButtonBox = new HBox();
+ this.resetButtonBox.setAlignment(Pos.CENTER_RIGHT);
+ this.resetButton = new Button(GeneralUtilities.getUIText("PreferencesConfigurationDialog.resetButton.text"));
+ this.resetButton.setTooltip(new Tooltip(GeneralUtilities.getUIText("PreferencesConfigurationDialog.resetButton.tooltipText")));
+ GuiUtilities.setMinMaxPrefSize(this.resetButton, GuiUtilities.SMALL_BUTTON_WIDTH, GuiUtilities.BUTTON_HEIGHT);
+ this.resetButtonBox.getChildren().add(this.resetButton);
+ this.inputPane.add(this.resetButtonBox, 1, 4);
+ this.getContentPane().getChildren().add(this.inputPane);
+ this.setHeaderText(GeneralUtilities.getUIText("PreferencesConfigurationDialog.Header.text"));
+ GuiUtilities.setMinMaxPrefHeight(this.getDialogPane(), 317.0);
+ }
+ //
+ //
+ //
+ /**
+ * Get the numberOfParallelThreadsField
+ *
+ * @return the numberOfParallelThreadsField
+ */
+ public TextField getNumberOfParallelThreadsField() {
+ return this.numberOfParallelThreadsField;
+ }
+
+ /**
+ * Get the defaultNumberOfBinsField
+ *
+ * @return the defaultNumberOfBinsField
+ */
+ public TextField getDefaultNumberOfBinsField() {
+ return this.defaultNumberOfBinsField;
+ }
+
+ /**
+ * Get the maximalNumberOfMoleculePairsToSaveField
+ *
+ * @return the maximalNumberOfMoleculePairsToSaveField
+ */
+ public TextField getMaximalNumberOfMoleculePairsToSaveField() {
+ return this.maximalNumberOfMoleculePairsToSaveField;
+ }
+
+ /**
+ * Get the resetButton
+ *
+ * @return the resetButton
+ */
+ public Button getResetButton() {
+ return this.resetButton;
+ }
+
+ /**
+ * Get the imageQualitySlider
+ *
+ * @return the imageQualitySlider
+ */
+ public Slider getImageQualitySlider() {
+ return this.imageQualitySlider;
+ }
+ //
+
+}
diff --git a/src/main/java/resources/MainStyle.css b/src/main/java/resources/MainStyle.css
new file mode 100644
index 0000000..3ef12ad
--- /dev/null
+++ b/src/main/java/resources/MainStyle.css
@@ -0,0 +1,70 @@
+/*
+ Created on : 09.11.2019, 12:42:54
+ Author : Jan-Mathis Hein
+*/
+
+.axis {
+ -fx-tick-label-fill: rgb(50, 50, 50);
+ -fx-start-margin: 4;
+ -fx-end-margin: 4;
+ -fx-tick-label-gap: 5;
+ -fx-tick-length: 6;
+ -fx-minor-tick-length: 3;
+ -fx-tick-mark-visible: true;
+}
+
+.axis-minor-tick-mark {
+ -fx-stroke: rgb(50, 50, 50);
+ -fx-stroke-width: 1;
+ -fx-opacity: 0.5;
+}
+
+.axis-tick-mark {
+ -fx-stroke: rgb(50, 50, 50);
+ -fx-stroke-width: 1;
+ -fx-opacity: 0.5;
+}
+
+.chart {
+ -fx-padding: 0px;
+ -fx-vertical-grid-lines-visible: false;
+ -fx-category-gap: 8;
+}
+
+.chart-bar {
+ -fx-background-color: rgb(50, 50, 170);
+}
+
+.chart-content {
+ -fx-padding: 10px;
+}
+
+.dialog-pane:header .header-panel {
+ -fx-background-color: rgb(220, 220, 220);
+}
+
+.menu-bar {
+ -fx-background-color: rgb(160, 160, 160);
+}
+
+.root {
+ default-color: rgb(200, 200, 200);
+ -fx-background-color: default-color;
+ -fx-base-color: default-color;
+}
+
+.tab {
+ -fx-background-color: rgb(160, 160, 160);
+}
+
+.tab:selected {
+ -fx-background-color: rgb(140, 140, 140);
+}
+
+.tab-header-background {
+ -fx-background-color: rgb(220, 220, 220);
+}
+
+.tab-label {
+ -fx-text-fill: rgb(250, 250, 250);
+}
\ No newline at end of file
diff --git a/src/main/java/resources/UIText.properties b/src/main/java/resources/UIText.properties
new file mode 100644
index 0000000..6145291
--- /dev/null
+++ b/src/main/java/resources/UIText.properties
@@ -0,0 +1,239 @@
+BinBorderConfigurationBox.addButton.text=Add
+BinBorderConfigurationBox.addButton.tooltipText=Add a new BinBorderConfigurationBox under this one
+BinBorderConfigurationBox.removeButton.text=Remove
+BinBorderConfigurationBox.removeButton.tooltipText=Remove this BinBorderConfigurationBox
+
+BinBorderConfigurationDialog.Title.text=Bin border configuration
+BinBorderConfigurationDialog.Header.text=Specify the bin borders
+BinBorderConfigurationDialog.resetButton.text=Reset
+BinBorderConfigurationDialog.resetButton.tooltipText=Reset the bin borders to their original number and to their original values (state at the time of the opening of this dialog)
+
+ChartConfigurationDialog.lowerBinBorderLabel.text=Lower binning border
+ChartConfigurationDialog.upperBinBorderLabel.text=Upper binning border
+ChartConfigurationDialog.lowerFrequencyBoundLabel.text=Lower frequency bound
+ChartConfigurationDialog.upperFrequencyBoundLabel.text=Upper frequency bound
+ChartConfigurationDialog.resetButton.text=Reset
+ChartConfigurationDialog.resetButton.tooltipText=Reset all configurations to their initial state (state at the time of the opening of this dialog)
+ChartConfigurationDialog.defaultButton.text=Default
+ChartConfigurationDialog.defaultButton.tooltipText=Reset all configurations to their default state (state at the time of the creation of the chart)
+ChartConfigurationDialog.Title.text=Output%s: Chart configuration
+ChartConfigurationDialog.Header.text=Configure the %s-chart
+ChartConfigurationDialog.lowerBinBorderInputField.tooltipText=Set the lower border of the first bin
+ChartConfigurationDialog.upperBinBorderInputField.tooltipText=Set the upper border of the last bin
+ChartConfigurationDialog.lowerFrequencyBoundInputField.tooltipText=Set the lower bound for the frequency range that will be displayed
+ChartConfigurationDialog.upperFrequencyBoundInputField.tooltipText=Set the upper bound for the frequency range that will be displayed
+
+ConfigurationDialog.Header.text=Configure
+ConfigurationDialog.applyButtonType.text=Apply
+ConfigurationDialog.applyButton.tooltipText=Apply all valid configurations
+ConfigurationDialog.cancelButtonType.text=Cancel
+ConfigurationDialog.cancelButton.tooltipText=Close this dialog and apply no configurations
+
+ConfirmationDialog.ClosingTitle.text=Confirm closing
+ConfirmationDialog.SelectionTitle.text=Confirm selection
+ConfirmationDialog.ClosingApplicationHeader.text=You are about to close the application
+ConfirmationDialog.ClosingApplicationContent.text=Do you really want to close the application?
+ConfirmationDialog.ClosingInputTabHeader.text=This job is still working
+ConfirmationDialog.ClosingInputTabContent.text=Do you still want to close this input tab?
+ConfirmationDialog.ClosingOutputTabHeader.text=This job is not saved
+ConfirmationDialog.ClosingOutputTabContent.text=Do you still want to close this output tab?
+ConfirmationDialog.ManyBinsHeader.text=The given number of bins is %s. Therefore the binning could take a while
+ConfirmationDialog.ManyBinsContent.text=Do you still want to use this amount of bins?
+ConfirmationDialog.DirectoryAlreadyExistsHeader.text=The selected directory already contains some files. These may be overwritten
+ConfirmationDialog.DirectoryAlreadyExistsContent.text=Do you still want to use this directory?
+ConfirmationDialog.Yes.text=Yes
+ConfirmationDialog.No.text=No
+
+ErrorAlertDialog.Header.text=An error has occured while calling: %s
+ErrorAlertDialog.Title.text=Warning: Exception
+
+ErrorDescription.WrongVersion.text=Found version: %s%nNecessary version: %s
+ErrorDescription.ScreenTooSmall.text=The screen size is too small for this application
+ErrorDescription.CanNotInstantiatePreferences.text=Preferences could not be instantiated
+ErrorDescription.InvalidComparisonFeatureSelection.text=Invalid ComparisonFeature selection. Please select something else
+ErrorDescription.InvalidBinLabelTypeSelection.text=Invalid bin label type selection. Please select something else
+ErrorDescription.NoDataForComparisonFeature.text=No data for the given ComparisonFeature is accessible
+ErrorDescription.ChartCreationFailed.text=Could not create the %s chart
+ErrorDescription.NotSingleInstance.text=Another MSC application seems to be already running.\nIf this not the case try to delete the MSC_SingleInstance.lck\nfile in the directory:
+ErrorDescription.CanNotCreateDirectory.text=The given directory does not exist and can't be created
+
+FileChooserTitle.SaveChart.text=Select a file where to save the chart as an image
+FileChooserTitle.SaveOutput.text=Select a folder where the output files will be saved
+FileChooserTitle.LoadOutput.text=Select a folder from where the output files will be loaded
+FileChooserTitle.DefaultInputDirectory.text=Select a default input directory
+FileChooserTitle.DefaultOutputDirectory.text=Select a default output directory
+FileChooserTitle.DefaultImageDirectory.text=Select a default image directory
+FileChooserTitle.DefaultMoleculeListDirectory.text=Select a default molecule list directory
+FileChooserTitle.DefaultSummaryReportDirectory.text=Select a default summary report directory
+FileChooserTitle.MoleculeFile.text=Select a file that contains a molecule set
+FileChooserTitle.MoleculeList.text=Select a file where to save the molecule list
+FileChooserTitle.SaveSummaryReport.text=Select a file where to save the summary report
+
+FileExtensionFilter.All.text=All
+FileExtensionFilter.Text.text=Text
+FileExtensionFilter.pdf.text=PDF
+FileExtensionFilter.png.text=PNG
+FileExtensionFilter.jpeg.text=JPEG
+FileExtensionFilter.svg.text=SVG
+FileExtensionFilter.xml.text=XML
+
+InfoDescription.SavingNotPossible.text=Saving the input is not possible
+InfoDescription.FileNotWritable.text=Writing to this file is not possible
+InfoDescription.FileNotReadable.text=Reading from this file is not possible
+InfoDescription.DesktopNotSupported.text=Desktop is not supported, log file can't be shown
+InfoDescription.LogFileNotReadable.text=Log file can't be read
+InfoDescription.ReadingInputCanceled.text=Reading input was canceled
+InfoDescription.ReadingInputFailed.text=Reading the input failed
+InfoDescription.NoComparisonFeatureChosen.text=Please choose a ComparisonFeature first
+InfoDescription.ChartPlaceHolder.text=Could not create the chart for%n the ComparisonFeature %s.%nThis is just a placeholder
+InfoDescription.UnpairedStrings.text=One input file contains %s more input string(s) than the other
+InfoDescription.NoMoleculesPairs.text=There were no molecule pairs loaded for this bin
+InfoDescription.FileFormatNotSupported.text=The chosen file format is not supported
+InfoDescription.InputConfigurationNotReadable.text=Can't read this input configuration. Please try again
+InfoDescription.JobStillWorking.text=This job is still working
+InfoDescription.About.text=MSC Version %s%n%nDeveloped and managed by Jan-Mathis Hein%n%nMany thanks to Kohulan Rajan, Christoph%nSteinbeck, Achim Zielesny and the communities%nthat created the open libraries%n%nThe MSC is published under the GNU GPL V3%n%nThe source code is available at GitHub%n(https://github.com/zielesny/MSC)
+InfoDescription.JobStarted.text=The job has been started
+InfoDescription.StartingJobFailed.text=Starting the job failed
+InfoDescription.JobFinished.text=The job has been finished
+InfoDescription.NewJob.text=A new job has been created
+InfoDescription.JobCanceled.text=The job has been canceled
+InfoDescription.ReadingInputProgress.text=Comparing molecules: %d%%
+InfoDescription.InputFile1.text=The first input file has been chosen
+InfoDescription.InputFile2.text=The second input file has been chosen
+InfoDescription.xFeaturesSelected.text=%d comparison features are selected
+InfoDescription.noFeaturesSelected.text=No comparison features are selected
+InfoDescription.InvalidBinBorders.text=The given bin borders are invalid and can't be applied
+InfoDescription.RelativeFrequencyTooHigh.text=The given relative frequency of %f is too high and will not be used
+InfoDescription.NumberInputTooHigh.text=The given numeric input is too high and can't be parsed and will thus not be used
+
+InfoDialog.Title.text=Information
+InfoDialog.AboutTitle.text=Application information
+
+InputTab.title.text=Input
+InputTab.selectAllComparisonFeaturesButton.text=All
+InputTab.selectAllComparisonFeaturesButton.tooltipText=Select all ComparisonFeatures
+InputTab.reverseComparisonFeatureSelectionButton.text=Reverse
+InputTab.reverseComparisonFeatureSelectionButton.tooltipText=Reverse all selections
+InputTab.selectAllCheckBox.text=Select all
+InputTab.selectAllCheckBox.tooltipText=Select/Deselect all check boxes of this section
+InputTab.jobStartButton.text=Start
+InputTab.jobStartButton.tooltipText=Start the reading and comparing of the two molecule sets
+InputTab.chooseFile1Button.text=Choose File
+InputTab.chooseFile1Button.tooltipText=Choose the file that contains the first molecule set
+InputTab.inputType1ChoiceBox.tooltipText=Select the encoding used for the first molecule set
+InputTab.inputType2ChoiceBox.tooltipText=Select the encoding used for the second molecule set
+InputTab.chooseFile2Button.text=Choose File
+InputTab.chooseFile2Button.tooltipText=Choose the file that contains the second molecule set
+InputTab.inputFile1Label.text=Filename:
+InputTab.inputFile2Label.text=Filename:
+InputTab.jobCancelButton.text=Cancel
+InputTab.jobCancelButton.tooltipText=Cancel the currently ongoing process
+InputTab.comparisonFeatureButtonsTitlePane.text=General
+InputTab.tanimotoTitledPane.text=Tanimoto
+InputTab.atomCountsTitledPane.text=Atom counts
+InputTab.bondCountsTitledPane.text=Bond counts
+InputTab.functionalGroupCountsTitledPane.text=Group counts
+InputTab.logPValuesTitledPane.text=LogP values
+InputTab.autocorrelationTitledPane.text=Autocorrelation
+InputTab.electricsDescriptorsTitledPane.text=Electronic descriptors
+InputTab.chiIndicesTitledPane.text=Chi indices
+InputTab.miscellaneousTitledPane.text=Miscellaneous
+
+Logging.ApplicationStart.text=The application has been started
+Logging.NewLoggingSession.text=A new logging session has been started
+Logging.UnexptectedPropertyChange.text=Unexpected PropertyChange: %s
+Logging.CompareBeforeReadingInput.text=Tried to compare sets before reading them
+Logging.InvalidComparisonFeatureSelection.text=An invalid ComparisonFeature has been chosen
+Logging.InvalidBinLabelTypeSelection.text=An invalid bin label type has been chosen
+Logging.PreferencesSavingNotPossible.text=The user preferences could not be saved
+Logging.PreferencesLoadingNotPossible.text=The user preferences could not be loaded
+Logging.ApplicationClosed.text=The application has been closed
+
+MainView.title.text=Molecule Set Comparator
+MainView.fileMenu.text=File
+MainView.saveJobMenuItem.text=Save
+MainView.loadJobOutputMenuItem.text=Load
+MainView.newJobMenuItem.text=New
+MainView.preferencesMenu.text=Preferences
+MainView.inputDirectoryMenuItem.text=Input directory
+MainView.outputDirectoryMenuItem.text=Output directory
+MainView.imageDirectoryMenuItem.text=Image directory
+MainView.moleculeListDirectoryMenuItem.text=Molecule list directory
+MainView.summaryReportDirectoryMenuItem.text=Summary report directory
+MainView.otherPreferencesMenuItem.text=Others
+MainView.logMenu.text=Logging
+MainView.browseLogMenuItem.text=Browse
+MainView.resetLogMenuItem.text=Reset
+MainView.maxButton.text=Large
+MainView.maxButton.tooltipText=Maximize the application window
+MainView.minButton.text=Small
+MainView.minButton.tooltipText=Minimize the application window
+MainView.centerButton.text=Center
+MainView.centerButton.tooltipText=Put the application window in the center of the screen
+MainView.jobMenu.text=Job
+MainView.directoryMenu.text=Directories
+MainView.helpMenu.text=Help
+MainView.aboutMenuItem.text=About
+
+MoleculePairDisplayerStage.title.text=Molecule pairs of bin %s
+MoleculePairDisplayerStage.saveLeftListButton.text=L list
+MoleculePairDisplayerStage.saveLeftListButton.tooltipText=Save the left list of molecules
+MoleculePairDisplayerStage.saveRightListButton.text=R list
+MoleculePairDisplayerStage.saveRightListButton.tooltipText=Save the right list of molecules
+MoleculePairDisplayerStage.saveLeftImageButton.text=L image
+MoleculePairDisplayerStage.saveLeftImageButton.tooltipText=Save the molecule image on the left
+MoleculePairDisplayerStage.saveRightImageButton.text=R image
+MoleculePairDisplayerStage.saveRightImageButton.tooltipText=Save the molecule image on the right
+MoleculePairDisplayerStage.highlightDifferencesCheckBox.text=Highlight
+MoleculePairDisplayerStage.highlightDifferencesCheckBox.tooltipText=Graphically highlight the molecule pair's differences
+MoleculePairDisplayerStage.firstButton.text=|<
+MoleculePairDisplayerStage.firstButton.tooltipText=Go to the first molecule pair
+MoleculePairDisplayerStage.previousButton.text=<
+MoleculePairDisplayerStage.previousButton.tooltipText=Go to the previous molecule pair
+MoleculePairDisplayerStage.nextButton.text=>
+MoleculePairDisplayerStage.nextButton.tooltipText=Go to the next molecule pair
+MoleculePairDisplayerStage.lastButton.text=>|
+MoleculePairDisplayerStage.lastButton.tooltipText=Go to the last molecule pair
+MoleculePairDisplayerStage.positionTextField.tooltipText=Press enter to go the specified molecule pair
+MoleculePairDisplayerStage.additionalComparisonFeatureCheckBox.tooltipText=Calculate and display the similarity of the currently shown molecule pair based on this ComparisonFeature
+MoleculePairDisplayerStage.infoLabel.text=Used ComparisonFeature: %s%nNumber of displayed pairs: %d%nFrequency value of this bin: %s%nLower bin border: %s%nUpper bin border: %s%nSMILES of the first molecule: %s%nSMILES of the second molecule: %s%nComparison result: %f
+
+OutputTab.title.text=Output
+OutputTab.summaryReportButton.text=Summarize
+OutputTab.summaryReportButton.tooltipText=Create and save a short summary report for this job result
+OutputTab.saveButton.text=Image
+OutputTab.saveButton.tooltipText=Save this chart as an image
+OutputTab.configureButton.text=Configure
+OutputTab.configureButton.tooltipText=Open the configuration dialog for charts
+OutputTab.binBorderConfigurationButton.text=Bin borders
+OutputTab.binBorderConfigurationButton.tooltipText=Open a dialog with which all bin borders can explicity be specified
+OutputTab.infoLabel.text=Chart: %s%nNumber of pairs: %d%nInput files: %n%s, %n%s
+OutputTab.xAxisLabel.text=Bins
+OutputTab.yAxisLabel.text=Frequency
+OutputTab.numberOfBinsLabel.text=Number of bins:
+OutputTab.binBorderSlidersLabel.text=Upper and lower bin border:
+OutputTab.frequencySlidersLabel.text=Frequency range:
+OutputTab.chartChoiceBox.tooltipText=Select a ComparisonFeature whose chart will be displayed
+OutputTab.binLabelChoiceBox.tooltipText=Select a bin label type which will be used to label the bins in the chart
+OutputTab.binBorderSlider.tooltipText=Move the slider to change the lower and upper bin border of the first and last bin respectively
+OutputTab.frequencySlider.tooltipText=Move the slider to change the displayed range of the y axis
+OutputTab.numberOfBinsTextField.tooltipText=Set the number of bins for this histogram
+OutputTab.relativeFrequenciesCheckBox.text=Rel. Freq.
+OutputTab.relativeFrequenciesCheckBox.tooltipText=If this is selected all returned and inputted frequencies will be given in relative terms, otherwise in absolute terms
+OutputTab.barLabelCheckBox.text=Bar labels
+OutputTab.barLabelCheckBox.tooltipText=If this is selected all bars will be labeled with their respective y-value
+
+PreferencesConfigurationDialog.title.text=Other preferences
+PreferencesConfigurationDialog.Header.text=Configure the preferences
+PreferencesConfigurationDialog.numberOfParallelThreadsLabel.text=Parallel threads
+PreferencesConfigurationDialog.defaultNumberOfBinsLabel.text=Number of bins
+PreferencesConfigurationDialog.maximalNumberOfMoleculePairsToSaveLabel.text=Pairs to save
+PreferencesConfigurationDialog.imageQualityLabel.text=Image quality
+PreferencesConfigurationDialog.resetButton.text=Reset
+PreferencesConfigurationDialog.resetButton.tooltipText=Reset all preferences to their initial state (state at the time of the opening of this dialog)
+PreferencesConfigurationDialog.numberOfParallelThreadsField.tooltipText=Set the number of threads that will be used concurrently for calculations
+PreferencesConfigurationDialog.defaultNumberOfBinsField.tooltipText=Set the default number of bins a histogram will have
+PreferencesConfigurationDialog.maximalNumberOfMoleculePairsToSaveField.tooltipText=Set the number of molecule pairs that will be saved when a job is being saved
+PreferencesConfigurationDialog.imageQualitySlider.tooltipText=Set the image quality preference where 0 and 1 represent low and high quality respectively
+
+SavingJob.InfoFile.text=The files \"%s\", \"%s\" and \"%s\" should not be %nrenamed or removed. This whole folder can be %nmoved anywhere and can also be renamed. %nEvery saved job has to have its own folder
\ No newline at end of file
diff --git a/src/test/java/de/whs/ibci/msc/model/GeneralTestSuite.java b/src/test/java/de/whs/ibci/msc/model/GeneralTestSuite.java
new file mode 100644
index 0000000..73ea621
--- /dev/null
+++ b/src/test/java/de/whs/ibci/msc/model/GeneralTestSuite.java
@@ -0,0 +1,34 @@
+/*
+ * Copyright (C) 2019 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+
+/**
+ * Test suite that combines all test classes
+ *
+ * @author Jan-Mathis Hein
+ */
+@RunWith(Suite.class)
+@Suite.SuiteClasses({
+ de.whs.ibci.msc.model.ParseAndCompareTaskTest.class,
+ de.whs.ibci.msc.model.HistogramDataManagerTest.class
+})
+public class GeneralTestSuite {
+
+}
diff --git a/src/test/java/de/whs/ibci/msc/model/HistogramDataManagerTest.java b/src/test/java/de/whs/ibci/msc/model/HistogramDataManagerTest.java
new file mode 100644
index 0000000..965a057
--- /dev/null
+++ b/src/test/java/de/whs/ibci/msc/model/HistogramDataManagerTest.java
@@ -0,0 +1,179 @@
+/*
+ * Copyright (C) 2019 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+import de.whs.ibci.msc.utility.MSCConstants;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.util.Collections;
+import org.junit.Test;
+import static org.junit.Assert.*;
+
+/**
+ * Test class of the HistogramDataManager class
+ *
+ * @author Jan-Mathis Hein
+ */
+public class HistogramDataManagerTest {
+
+ //
+ /**
+ * The tolerance used when two double values are compared. Every deviation
+ * that is smaller than this is still accepted as equal
+ */
+ private static final double TOLERANCE = 0.00001;
+
+ /**
+ * The histogram's expected bin borders
+ */
+ private static final double[] EXPECTED_BIN_BORDERS = {0, 0.8, 1.6, 2.4, 3.2, 4};
+
+ /**
+ * A HistogramDataManager instance on which the tests are done
+ */
+ private HistogramDataManager histogramDataManager;
+
+ /**
+ * The number of pairs that were added to the HistogramDataManager
+ */
+ private final int numberOfPairs;
+
+ /**
+ * The histogram's expected frequency data
+ */
+ private static final int[] EXPECTED_FREQUENCY_DATA = {1, 0, 0, 6, 1};
+
+ /**
+ * The ComparisonFeature that is used in this test
+ */
+ private static final ComparisonFeature MOLECULAR_DESCRIPTOR = ComparisonFeature.ATOM_COUNT;
+ //
+ //
+ //
+ /**
+ * Initialize a HistogramDataManager and add some comparison results to it
+ *
+ * @throws java.lang.Exception
+ */
+ public HistogramDataManagerTest() throws Exception {
+ String[][] tmpInputPairs = {
+ {"CC\n", "CC\n"}, {"C\n", "CC\n"}, {"C\n", "CC\n"}, {"C\n", "CC\n"},
+ {"C\n", "CC\n"}, {"C\n", "CC\n"}, {"C\n", "CC\n"}
+ };
+ int tmpIdentifier = 0;
+ final boolean[] tmpCompareAspects = new boolean[ComparisonFeature.values().length];
+ tmpCompareAspects[HistogramDataManagerTest.MOLECULAR_DESCRIPTOR.getFeatureNumber()] = true;
+ ParseAndCompareTask tmpTask = new ParseAndCompareTask("CC\n", "OO\n", InputType.SMILES, InputType.SMILES, tmpCompareAspects, tmpIdentifier++);
+ tmpTask.call();
+ this.histogramDataManager = new HistogramDataManager(
+ Collections.singletonList(HistogramDataManagerTest.MOLECULAR_DESCRIPTOR),
+ HistogramDataManagerTest.EXPECTED_BIN_BORDERS.length - 1, tmpTask.getResult(),
+ "", ""
+ );
+ for (String[] tmpPair : tmpInputPairs) {
+ tmpTask = new ParseAndCompareTask(tmpPair[0], tmpPair[1], InputType.SMILES, InputType.SMILES, tmpCompareAspects, tmpIdentifier++);
+ tmpTask.call();
+ this.histogramDataManager.addDatum(tmpTask.getResult());
+ }
+ this.numberOfPairs = tmpIdentifier;
+ }
+ //
+ //
+ //
+ /**
+ * Test of binData method, of class HistogramDataManager. Also assert that
+ * the borders, the number of added data and the histogram data are as
+ * expected
+ */
+ @Test
+ public void testBinDataAndCheckResults() {
+ this.histogramDataManager.getHistogramData(HistogramDataManagerTest.MOLECULAR_DESCRIPTOR).call();
+ assertEquals("Test number of added data", this.numberOfPairs, this.histogramDataManager.getNumberOfComparedPairs());
+ for (int i = 0; i < HistogramDataManagerTest.EXPECTED_BIN_BORDERS.length; i++) {
+ assertEquals(
+ "Test bin border " + Integer.toString(i),
+ HistogramDataManagerTest.EXPECTED_BIN_BORDERS[i],
+ this.histogramDataManager.getHistogramData(HistogramDataManagerTest.MOLECULAR_DESCRIPTOR).getBinBorders()[i], TOLERANCE
+ );
+ }
+ for (int i = 0; i < HistogramDataManagerTest.EXPECTED_FREQUENCY_DATA.length; i++) {
+ assertEquals(
+ HistogramDataManagerTest.EXPECTED_FREQUENCY_DATA[i],
+ this.histogramDataManager.getHistogramData(HistogramDataManagerTest.MOLECULAR_DESCRIPTOR).getFrequencies()[i],
+ HistogramDataManagerTest.TOLERANCE
+ );
+ }
+ }
+
+ /**
+ * Test of the writeObject and readObject methods or rather the
+ * serialization and deserialization, of class HistogramDataManager. Also
+ * assert that the borders and the histogram data are as expected.
+ * NOTE: Created files and directories will normaly be deleted upon
+ * completion
+ *
+ * @throws IOException
+ * @throws ClassNotFoundException
+ */
+ @Test
+ public void testSerializationAndDeserialization() throws IOException, ClassNotFoundException {
+ File tmpTemporaryFile = new File(System.getProperty("user.dir") + File.separator + MSCConstants.OUTPUT_FILE_NAME);
+ try {
+ tmpTemporaryFile.createNewFile();
+ assertTrue("Test if file is readable", tmpTemporaryFile.canRead());
+ assertTrue("Test if file is writable", tmpTemporaryFile.canWrite());
+ try (
+ FileOutputStream tmpFileOutputStream = new FileOutputStream(tmpTemporaryFile);
+ ObjectOutputStream tmpObjectOutputStream = new ObjectOutputStream(tmpFileOutputStream)
+ ) {
+ tmpObjectOutputStream.writeObject(this.histogramDataManager);
+ }
+ this.histogramDataManager = null;
+ try (
+ FileInputStream tmpFileInputStream = new FileInputStream(tmpTemporaryFile);
+ ObjectInputStream tmpOutputStream = new ObjectInputStream(tmpFileInputStream)
+ ) {
+ this.histogramDataManager = (HistogramDataManager) tmpOutputStream.readObject();
+ }
+ this.histogramDataManager.getComparisonFeatureSet().forEach((ComparisonFeature tmpComparisonFeature) -> {
+ this.histogramDataManager.getHistogramData(tmpComparisonFeature).call();
+ });
+ for (int i = 0; i < HistogramDataManagerTest.EXPECTED_BIN_BORDERS.length; i++) {
+ assertEquals(
+ "Test bin border " + Integer.toString(i),
+ HistogramDataManagerTest.EXPECTED_BIN_BORDERS[i],
+ this.histogramDataManager.getHistogramData(HistogramDataManagerTest.MOLECULAR_DESCRIPTOR).getBinBorders()[i], TOLERANCE
+ );
+ }
+ for (int i = 0; i < HistogramDataManagerTest.EXPECTED_FREQUENCY_DATA.length; i++) {
+ assertEquals(
+ HistogramDataManagerTest.EXPECTED_FREQUENCY_DATA[i],
+ this.histogramDataManager.getHistogramData(HistogramDataManagerTest.MOLECULAR_DESCRIPTOR).getFrequencies()[i],
+ HistogramDataManagerTest.TOLERANCE
+ );
+ }
+ } finally {
+ tmpTemporaryFile.delete();
+ }
+ }
+ //
+
+}
diff --git a/src/test/java/de/whs/ibci/msc/model/ParseAndCompareTaskTest.java b/src/test/java/de/whs/ibci/msc/model/ParseAndCompareTaskTest.java
new file mode 100644
index 0000000..90589e9
--- /dev/null
+++ b/src/test/java/de/whs/ibci/msc/model/ParseAndCompareTaskTest.java
@@ -0,0 +1,145 @@
+/*
+ * Copyright (C) 2020 Jan-Mathis Hein
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see .
+ */
+package de.whs.ibci.msc.model;
+
+import java.util.Arrays;
+import java.util.Collection;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameter;
+import org.junit.runners.Parameterized.Parameters;
+
+/**
+ * Test class of the ParseAndCompareTask class
+ *
+ * @author Jan-Mathis Hein
+ */
+@RunWith(Parameterized.class)
+public class ParseAndCompareTaskTest {
+
+ //
+ /**
+ * The tolerance used when two double values are compared. Every deviation
+ * that is smaller than this is still accepted as equal
+ */
+ private static final double TOLERANCE = 0.00001;
+ //
+ //
+ //
+ /**
+ * The first input molecule
+ */
+ @Parameter(0)
+ public String molecule1;
+
+ /**
+ * The second input molecule
+ */
+ @Parameter(1)
+ public String molecule2;
+
+ /**
+ * The first input type
+ */
+ @Parameter(2)
+ public InputType inputType1;
+
+ /**
+ * The second input type
+ */
+ @Parameter(3)
+ public InputType inputType2;
+
+ /**
+ * Defines which descriptors will be used for the molecule comparison
+ */
+ @Parameter(4)
+ public boolean[] useDescriptors;
+
+ /**
+ * The the expected results of the comparison
+ */
+ @Parameter(5)
+ public Double[] expectedResults;
+ //
+ //
+ //
+ /**
+ * Create the parameter sets that contain the inputs and the expected
+ * outputs that will be used for testing
+ *
+ * @return a collection where each item is an array that contains a
+ * parameter set
+ * @throws java.lang.Exception
+ */
+ @Parameters
+ public static Collection createParameterSets() throws Exception {
+ //
+ String tmpMolecule1 = "COC(N)CP\n";
+ String tmpMolecule2 = "COC(O)CS\n";
+ InputType tmpInputType1 = InputType.SMILES;
+ InputType tmpInputType2 = InputType.SMILES;
+ boolean[] tmpCompareAspects = new boolean[ComparisonFeature.values().length];
+ Double[] tmpExpectedResults = new Double[ComparisonFeature.values().length];
+ // If a result is not set, that descriptor will not be used
+ tmpExpectedResults[ComparisonFeature.TANIMOTO_BASIC_FINGERPRINTER.getFeatureNumber()] = 0.277777;
+ tmpExpectedResults[ComparisonFeature.ATOM_COUNT.getFeatureNumber()] = 2.0;
+ tmpExpectedResults[ComparisonFeature.CARBON_COUNT.getFeatureNumber()] = 0.0;
+ tmpExpectedResults[ComparisonFeature.OXYGEN_COUNT.getFeatureNumber()] = 1.0;
+ tmpExpectedResults[ComparisonFeature.SULFUR_COUNT.getFeatureNumber()] = 1.0;
+ tmpExpectedResults[ComparisonFeature.NITROGEN_COUNT.getFeatureNumber()] = 1.0;
+ tmpExpectedResults[ComparisonFeature.PHOSPHOR_COUNT.getFeatureNumber()] = 1.0;
+ tmpExpectedResults[ComparisonFeature.MOLECULAR_WEIGHT.getFeatureNumber()] = 1.069143575;
+ for (int i = 0; i < tmpExpectedResults.length; i++) {
+ tmpCompareAspects[i] = tmpExpectedResults[i] != null;
+ }
+ //
+ Object[][] tmpData = {
+ {tmpMolecule1, tmpMolecule2, tmpInputType1, tmpInputType2, tmpCompareAspects, tmpExpectedResults}
+ };
+ return Arrays.asList(tmpData);
+ }
+
+ /**
+ * Test of call method, of class ParseAndCompareTask. Also assert that the
+ * results and state of the task are as expected
+ */
+ @Test
+ public void testCall() throws Exception {
+ ParseAndCompareTask tmpTask = new ParseAndCompareTask(this.molecule1, this.molecule2, this.inputType1, this.inputType2, this.useDescriptors, 0);
+ tmpTask.call();
+ assertFalse("Test if this is working", tmpTask.isWorking());
+ assertTrue("Test if this is finished", tmpTask.isFinished());
+ assertTrue("Test if this was started", tmpTask.isStarted());
+ ComparisonResult tmpResult = tmpTask.getResult();
+ assertEquals("Test for exceptions that occured during comparing", tmpResult.getReasonOfFailure(), "");
+ Arrays.stream(ComparisonFeature.values()).filter((ComparisonFeature descriptor) -> this.useDescriptors[descriptor.getFeatureNumber()]).forEach((ComparisonFeature descriptor) -> {
+ assertEquals(
+ "Test " + descriptor.toString(),
+ tmpTask.getResult().getSimilarities()[descriptor.getFeatureNumber()],
+ this.expectedResults[descriptor.getFeatureNumber()],
+ ParseAndCompareTaskTest.TOLERANCE
+ );
+ });
+ }
+ //
+
+}