Merge pull request #81 from mitobench/development

Development

build.gradle

@@ -1,22 +1,37 @@
 group 'com.uni-tuebingen.de.it.mitobench'
-version '1.6-beta'
+version '1.7-beta'
+
 
 apply plugin: 'java'
 apply plugin: 'idea'
-apply plugin: 'jacoco'
 apply plugin: 'maven'
 apply plugin: 'maven-publish'
 
 
 sourceCompatibility = 1.8
 
+
+
 repositories {
     jcenter()
     maven {
         url  "http://dl.bintray.com/apeltzer/Mitobench"
     }
 }
-
+//plugins {
+//    id 'application'
+//    id 'org.openjfx.javafxplugin' version '0.0.8'
+//    id 'org.beryx.jlink' version '2.12.0'
+//}
+//
+//
+//repositories {
+//    mavenCentral()
+//    jcenter()
+//    maven {url 'https://oss.sonatype.org/content/repositories/snapshots'}
+//}
+//
+//version '1.9-beta'
 
 sourceSets {
     main {
@@ -27,18 +42,13 @@ sourceSets {
             srcDirs "src/main/resources"
         }
     }
-    test {
-        java {
-            srcDir 'test'
-        }
-        resources {
-            srcDir 'resources'
-        }
-    }
 }
 
 
+
 dependencies {
+    //runtimeOnly "org.openjfx:javafx-graphics:$javafx.version:linux"
+    //implementation 'org.controlsfx:controlsfx:9.0.1-SNAPSHOT'
     compile 'org.slf4j:slf4j-simple:+'
     compile 'org.apache.poi:poi-ooxml:3.15'
     compile 'org.netbeans.html:net.java.html.boot.fx:1.4'
@@ -51,43 +61,27 @@ dependencies {
     compile group: 'org.javafxdata', name: 'datafx-flow', version: '8.0b5'
     compile group: 'guru.nidi', name: 'graphviz-java', version: '0.8.10'
     compile group: 'org.ojalgo', name: 'ojalgo', version: '47.2.0'
-    //compile files('src/main/resources/jars/FstCalculator-0.1.20.jar')
+    compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.10.1'
+    compile files('src/main/resources/jars/FstCalculator-0.1.21.jar')
     compile files('src/main/resources/jars/PhylotreeParser-0.4.4.jar')
     compile files('src/main/resources/jars/PGDSpider2.jar')
-    compile files('src/main/resources/jars/haplogrep-2.1.23.jar')
+    compile files('src/main/resources/jars/haplogrep-2.2.5.jar')
+    compile files('src/main/resources/jars/reverse-country-code.jar')
 
 }
 
+//javafx {
+//    version = "14"
+//    modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.graphics', 'javafx.base', 'javafx.media', 'javafx.swing','javafx.web']
+//}
 
-task copyTestResources(type: Copy) {
-    from "${projectDir}/src/test/resources"
-    into "${buildDir}/classes/test"
-}
-processTestResources.dependsOn copyTestResources
-
-//Required for headless testing here!!
-test {
-    if (!project.hasProperty("noHeadless")) {
-        jvmArgs = ["-Dheadless=true"]
-    } else {
-        jvmArgs = ["-Dheadless=false"]
-    }
-}
+//mainClassName = "Launcher"
 
 jar {
-
     manifest {
-        attributes("Implementation-Title": "MitoBench",
-                "Implementation-Version": version, "main-Class": "MitoBenchStarter")
+        attributes 'Main-Class': 'Launcher'
     }
-    doFirst {
-        from { configurations.runtime.collect { it.isDirectory() ? it : zipTree(it) } }
-    }
-}
-
-
-jacocoTestReport {
-    reports {
-        xml.enabled true
+    from {
+        configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) }
     }
 }

src/main/java/Launcher.java

@@ -0,0 +1,11 @@
+import javafx.application.Application;
+import view.MitoBenchWindow;
+
+
+public class Launcher {
+
+    public static void main(String[] args) {
+        new Thread(() -> Application.launch(MitoBenchWindow.class)).start();
+
+    }
+}

src/main/java/analysis/FstCalculationRunner.java

@@ -1,6 +1,6 @@
 package analysis;
 
-import analysis.fstcalculation.FstCalculator;
+import Main.FstCalculator;
 import javafx.collections.ObservableList;
 import javafx.scene.control.ScrollPane;
 import javafx.scene.control.Tab;
@@ -114,8 +114,7 @@ public void run(boolean runSlatkin, boolean runReynolds, String field_level_miss
                 "Pairwise Difference",
                 numberOfPermutations,
                 gamma_a,
-                significance,
-                LOG
+                significance
                 );
 
         fsts = fstCalculator.runCaclulations();

src/main/java/analysis/HaplotypeCaller.java

@@ -4,16 +4,14 @@
 import Logging.LogClass;
 import genepi.haplogrep.main.Haplogrep;
 import htsjdk.samtools.SAMException;
-import io.Exceptions.HSDException;
-import io.reader.HSDInput;
+import io.reader.HSDParser;
 import io.writer.MultiFastaWriter;
 import org.apache.log4j.Logger;
 import model.MTStorage;
 import controller.TableControllerUserBench;
 
 import java.io.File;
 import java.io.IOException;
-import java.net.URL;
 import java.nio.file.Files;
 
 
@@ -25,16 +23,23 @@ public class HaplotypeCaller {
     private MTStorage mtStorage;
     private Logger LOG;
     private String phylotreeVersion = "17";
+    private String haplogrepversion = "2.2.5";
 
 
     public HaplotypeCaller(TableControllerUserBench tableControllerUserBench, LogClass logClass){
+
         this.mtStorage = tableControllerUserBench.getDataTable().getMtStorage();
         this.tableController = tableControllerUserBench;
         LOG = logClass.getLogger(this.getClass());
 
-
     }
 
+
+    /**
+     * Run HaploGrep2.
+     *
+     * @param lineage   Lineage parameter. Can be true or false (default = false). Creates dot file ('tree').
+     */
     public void call(String lineage) throws IOException {
         String file = "multifasta.fasta";
         //System.out.println("Writing fasta sequences to " + file);
@@ -44,30 +49,52 @@ public void call(String lineage) throws IOException {
         MultiFastaWriter multiFastaWriter = new MultiFastaWriter(this.mtStorage, tableController.getSelectedRows(), true);
         multiFastaWriter.writeData(file, tableController);
 
-        start(file, lineage);
+        // todo: error handling when task cancelled
+
+        String[] command = new String[] {
+                "classify",
+                "--format", "fasta",
+                "--in",file,
+                "--out", "haplogroups.hsd",
+                "--extend-report",
+                lineage};
+
+        try {
+            Haplogrep haplogrep = new Haplogrep(command);
+            haplogrep.start();
 
+            LOG.info("Calculate Haplogroups with Phylotree version " + phylotreeVersion + " and haplogrep-" + haplogrepversion);
+            System.out.println("Haplogrep finished");
+        } catch (SAMException e){
+            System.err.println("Task cancelled");
+        }
     }
 
 
+    /**
+     * Parse HaploGrep2 output file and update data.
+     */
     public void update() {
 
-        //HSDReaderIntern hsd_reader = new HSDReaderIntern("haplogroups.hsd", LOG, "Haplogroup Phylotree17", "Haplotype Phlyotree17");
-        HSDInput hsdInput = null;
+        HSDParser hsdInput;
+
         try {
             if(new File("haplogroups.hsd").exists()){
-                hsdInput = new HSDInput("haplogroups.hsd", LOG);
+                hsdInput = new HSDParser("haplogroups.hsd", LOG, null);
                 tableController.updateTable(hsdInput.getCorrespondingData());
             }    else {
-                LOG.info("Haplogrep did not run properly");
+                LOG.info("HaploGrep2 did not run properly, 'haplogroups.hsd' does not exists.");
             }
-        } catch (IOException e) {
-            e.printStackTrace();
-        } catch (HSDException e) {
+        } catch (Exception e) {
+            System.out.println("HaploGrep2 did not run properly, 'haplogroups.hsd' does not exists.");
             e.printStackTrace();
         }
 
     }
 
+    /**
+     * Delete all temporary files that were created while running HaploGrep2
+     */
     public void deleteTmpFiles() {
 
         try {
@@ -87,38 +114,4 @@ public void deleteTmpFiles() {
 
     }
 
-
-    private void start(String f, String lineage) {
-        // todo: error handling when task cancelled
-
-        String[] command = new String[] {
-                "--format", "fasta",
-                "--in",f,
-                "--out", "haplogroups.hsd",
-                "--extend-report",
-                lineage};
-
-
-            Haplogrep haplogrep = new Haplogrep(command);
-        try {
-            haplogrep.start();
-
-            LOG.info("Calculate Haplogroups with Phylotree version " + phylotreeVersion + " and haplogrep-2.1.18");
-        } catch (SAMException e){
-                System.err.println("Task cancelled");
-
-        }
-
-        // delete all temporary files
-
-        if(new File(f).exists()) {
-            try {
-                Files.delete(new File(f).toPath());
-            } catch (IOException e) {
-                e.printStackTrace();
-            }
-        }
-
-    }
-
 }