diff --git a/LICENSE b/LICENSE
index 9cecc1d..7c057bf 100755
--- a/LICENSE
+++ b/LICENSE
@@ -659,7 +659,7 @@ notice like this when it starts in an interactive mode:
 
 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".
+might be different; for a org.damageprofiler.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.
diff --git a/README.md b/README.md
index f2a87e7..7e114c5 100755
--- a/README.md
+++ b/README.md
@@ -85,6 +85,6 @@ Maximal value on y axis (Default: flexible, adapts to the calculated damage).
 
 
 
-Running the jar file without any parameter starts a GUI to configure the run.
+Running the jar file without any parameter starts a org.damageprofiler.GUI to configure the run.
 
 Stay tuned, a more detailed description, manual and tutorial of DamageProfiler is coming soon.
\ No newline at end of file
diff --git a/build.gradle b/build.gradle
old mode 100644
new mode 100755
index 0386843..6af0c94
--- a/build.gradle
+++ b/build.gradle
@@ -1,105 +1,104 @@
-group 'com.uni-tuebingen.de.it.eager.damageprofiler'
-version '0.4.9'
+ plugins {
+    id 'application'
+    id 'org.openjfx.javafxplugin' version '0.0.8'
+    id 'org.beryx.jlink' version '2.12.0'
+ }
 
-buildscript {
-    repositories {
-        jcenter()
-    }
-    dependencies {
-        classpath 'com.jfrog.bintray.gradle:gradle-bintray-plugin:1.8+'
-    }
-}
+version '0.5.0-java11'
 
 
-allprojects {
-    repositories {
-        jcenter()
-    }
-    apply plugin: 'maven'
-    apply plugin: 'maven-publish'
-    apply plugin: 'java'
-    apply plugin: 'idea'
-    apply plugin: 'com.jfrog.bintray'
-    apply plugin: 'jacoco'
+repositories {
+    mavenCentral()
+    jcenter()
 }
 
 
-sourceCompatibility = 1.8
-
-
-sourceSets {
-    main {
-        java {
-            srcDir 'src'
-        }
-    }
-}
-
+ javafx {
+     version = "14"
+     modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.graphics', 'javafx.base', 'javafx.media', 'javafx.swing','javafx.web']
+ }
 
 dependencies {
+    compile group: 'log4j', name: 'log4j', version: '1.+'
     compile group: 'org.apache.commons', name: 'commons-lang3', version: '3.+'
     compile group: 'commons-cli', name: 'commons-cli', version: '1.3.+'
     compile group: 'com.itextpdf', name: 'itextpdf', version: '5.5.+'
-    compile group: 'org.jfree', name: 'jcommon', version: '1.0.+'
-    compile group: 'jfree', name: 'jfreechart', version: '1.0.13'
     compile group: 'com.github.samtools', name: 'htsjdk', version: '2.+'
-    compile group: 'com.intellij', name: 'forms_rt', version: '6.0.+'
-    compile group: 'log4j', name: 'log4j', version: '1.+'
+    compile group: 'com.intellij', name: 'forms_rt', version: '5.+'
     compile group: 'com.github.broadinstitute', name: 'picard', version: '2.+'
+    compile group: 'org.jfree', name: 'jfreesvg', version: '2.0'
+    compile group: 'org.apache.commons', name: 'commons-text', version: '1.+'
+    compile 'org.jfree:jfreechart-fx:1.+'
 }
 
-
-
 jar {
     manifest {
-        attributes("Implementation-Title": "DamageProfiler",
-                "Implementation-Version": version, "main-Class": "RunDamageProfiler")
+        attributes 'Main-Class': 'RunDamageProfiler'
     }
-    doFirst {
-        from { configurations.runtime.collect { it.isDirectory() ? it : zipTree(it) } }
+    from {
+        configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) }
     }
 }
 
 
-
-
-
-publishing {
-    publications {
-        MyPublication(MavenPublication) {
-            from components.java
-            groupId 'com.uni-tuebingen.de.it.eager'
-            artifactId 'DamageProfiler'
-        }
-    }
-}
-
-
-jacocoTestReport {
-    reports {
-        xml.enabled true
-    }
-}
-
-
-bintray {
-    user = System.getenv('BINTRAY_USER')
-	  key = System.getenv('BINTRAY_API_KEY')
-    publications = ['MyPublication']
-    publish = true
-    override = true
-    pkg {
-        repo = 'EAGER'
-        name = 'DamageProfiler'
-        licenses = ['GPL-3.0']
-        vcsUrl = "https://github.com/apeltzer/DamageProfiler"
-        version {
-            name = project.version
-            desc = 'Damage calculations for mapped reads.'
-            released  = new Date()
-            vcsTag = project.version
-            attributes = ['gradle-plugin': 'com.use.less:com.use.less.gradle:gradle-useless-plugin']
-        }
-
-    }
-}
+//// Uncomment when compiling with java8
+//version '0.5.0-java8'
+//buildscript {
+//    repositories {
+//        jcenter()
+//    }
+//    dependencies {
+//        classpath 'com.jfrog.bintray.gradle:gradle-bintray-plugin:1.8+'
+//    }
+//}
+//
+//allprojects {
+//    repositories {
+//        jcenter()
+//    }
+//    apply plugin: 'maven'
+//    apply plugin: 'maven-publish'
+//    apply plugin: 'java'
+//    apply plugin: 'idea'
+//    apply plugin: 'com.jfrog.bintray'
+//    apply plugin: 'jacoco'
+//}
+//
+//sourceCompatibility = 1.8
+//
+//sourceSets {
+//    main {
+//        java {
+//            srcDir 'src'
+//        }
+//
+//        resources {
+//            srcDirs "src/main/resources"
+//        }
+//    }
+//}
+//
+//
+//dependencies {
+//    compile group: 'org.apache.commons', name: 'commons-lang3', version: '3.+'
+//    compile group: 'commons-cli', name: 'commons-cli', version: '1.3.+'
+//    compile group: 'com.itextpdf', name: 'itextpdf', version: '5.5.+'
+//    compile group: 'com.github.samtools', name: 'htsjdk', version: '2.+'
+//    compile group: 'com.intellij', name: 'forms_rt', version: '6.0.+'
+//    compile group: 'log4j', name: 'log4j', version: '1.+'
+//    compile group: 'com.github.broadinstitute', name: 'picard', version: '2.+'
+//    compile group: 'org.jfree', name: 'jfreesvg', version: '2.0'
+//    compile group: 'org.apache.commons', name: 'commons-text', version: '1.+'
+//    compile 'org.jfree:jfreechart-fx:1.+'
+//}
+//
+//
+//jar {
+//    manifest {
+//        attributes("Implementation-Title": "DamageProfiler",
+//                "Implementation-Version": version, "main-Class": "RunDamageProfiler")
+//    }
+//    doFirst {
+//        from { configurations.runtime.collect { it.isDirectory() ? it : zipTree(it) } }
+//    }
+//}
\ No newline at end of file
diff --git a/docs/contents/generalUsage.rst b/docs/contents/generalUsage.rst
index 015c723..a65769d 100755
--- a/docs/contents/generalUsage.rst
+++ b/docs/contents/generalUsage.rst
@@ -40,7 +40,7 @@ Options:
 
 
 DamageProfiler can be used in offline mode.
-Running the jar file without any parameter starts a GUI to configure the run.
+Running the jar file without any parameter starts a org.damageprofiler.GUI to configure the run.
 
 
 Log file
diff --git a/src/main/java/GUI/CopyTask.java b/src/main/java/GUI/CopyTask.java
deleted file mode 100755
index b2e068a..0000000
--- a/src/main/java/GUI/CopyTask.java
+++ /dev/null
@@ -1,37 +0,0 @@
-package GUI;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-
-import javafx.concurrent.Task;
-
-// Copy all file in C:/Windows
-public class CopyTask extends Task<List<File>> {
-
-    @Override
-    protected List<File> call() throws Exception {
-
-        File dir = new File("C:/Windows");
-        File[] files = dir.listFiles();
-        int count = files.length;
-
-        List<File> copied = new ArrayList<File>();
-        int i = 0;
-        for (File file : files) {
-            if (file.isFile()) {
-                this.copy(file);
-                copied.add(file);
-            }
-            i++;
-            this.updateProgress(i, count);
-        }
-        return copied;
-    }
-
-    private void copy(File file) throws Exception {
-        this.updateMessage("Copying: " + file.getAbsolutePath());
-        Thread.sleep(500);
-    }
-
-}
\ No newline at end of file
diff --git a/src/main/java/GUI/MainGuiFX.java b/src/main/java/GUI/MainGuiFX.java
deleted file mode 100755
index 3aefba8..0000000
--- a/src/main/java/GUI/MainGuiFX.java
+++ /dev/null
@@ -1,273 +0,0 @@
-package GUI;
-
-import IO.Communicator;
-import calculations.StartCalculations;
-import javafx.application.Application;
-
-import javafx.concurrent.WorkerStateEvent;
-import javafx.event.EventHandler;
-import javafx.geometry.Pos;
-import javafx.scene.Scene;
-import javafx.scene.control.*;
-import javafx.scene.control.Button;
-import javafx.scene.control.Label;
-import javafx.scene.control.TextField;
-import javafx.scene.layout.GridPane;
-import javafx.scene.text.Font;
-import javafx.scene.text.FontWeight;
-import javafx.stage.Stage;
-import javafx.concurrent.Task;
-
-
-public class MainGuiFX extends Application {
-
-    private Button btn_inputfile;
-    private Button btn_reference;
-    private Button btn_output;
-    private Button btn_plotting_options;
-    private Button btn_run;
-    private Button btn_specieList;
-    private TextField textfield_threshold;
-    private TextField textfield_length;
-    private TextField textfield_specie;
-    private CheckBox checkbox_use_merged_reads;
-    private TextField textfield_title;
-    //private CheckBox checkbox_dynamic_y_axis_height;
-    private TextField textfield_y_axis_height;
-    private Communicator communicator = new Communicator();
-    private StartCalculations starter = new StartCalculations(null);
-    private Stage primaryStage;
-    private ProgressBar progressBar;
-    private Task startCalculuations;
-
-    @Override
-    public void start(Stage primaryStage) {
-        this.primaryStage = primaryStage;
-
-        this.primaryStage.setTitle("DamageProfiler configuration");
-
-        GridPane root = new GridPane();
-        root.setAlignment(Pos.CENTER);
-        root.setHgap(7);
-        root.setVgap(7);
-
-        addComponents(root);
-        addListener();
-
-        this.primaryStage.setScene(new Scene(root, 650, 400));
-        this.primaryStage.setResizable(true);
-        this.primaryStage.show();
-
-
-    }
-
-
-    public Task startCalculuations(Communicator communicator) {
-        return new Task() {
-            @Override
-            protected Object call() throws Exception {
-                starter.start(communicator);
-                return true;
-            }
-        };
-    }
-
-
-    private void addListener() {
-
-//        checkbox_dynamic_y_axis_height.selectedProperty().addListener((ov, old_val, new_val) -> {
-//            if(new_val){
-//                textfield_y_axis_height.setDisable(true);
-//            } else if(!new_val){
-//                textfield_y_axis_height.setDisable(false);
-//            }
-//        });
-
-
-
-        btn_inputfile.setOnAction(e -> {
-
-            BamFileChooserFX fqfc = new BamFileChooserFX(communicator);
-            //Check if some input was truly selected
-
-            if (checkIfInputWasSelected()) {
-                btn_run.setDisable(false);
-            } else {
-                btn_run.setDisable(true);
-            }
-
-        });
-
-        btn_reference.setOnAction(e -> {
-                ReferenceFileChooserFX rfc = new ReferenceFileChooserFX(communicator);
-                //Check if some input was truly selected
-
-            if (checkIfInputWasSelected()) {
-                btn_run.setDisable(false);
-            } else {
-                btn_run.setDisable(true);
-            }
-
-        });
-
-        btn_output.setOnAction(e -> {
-
-            OutputDirChooserFX rfc = new OutputDirChooserFX(communicator);
-
-            if (checkIfInputWasSelected()) {
-                btn_run.setDisable(false);
-            } else {
-                btn_run.setDisable(true);
-            }
-
-        });
-
-        btn_specieList.setOnAction(e -> {
-
-            SpeciesListFileChooser slfc = new SpeciesListFileChooser(communicator);
-            if (checkIfInputWasSelected()) {
-                btn_specieList.setDisable(false);
-            } else {
-                btn_specieList.setDisable(true);
-            }
-
-
-        });
-
-
-        btn_run.setOnAction(e -> {
-
-            // set all user options
-            communicator.setLength(Integer.parseInt(textfield_length.getText()));
-            communicator.setThreshold(Integer.parseInt(textfield_threshold.getText()));
-            communicator.setSpecies_ref_identifier(textfield_specie.getText());
-//            if(!checkbox_dynamic_y_axis_height.isSelected()){
-//                try {
-//                    communicator.setyAxis_damageplot(Double.parseDouble(textfield_y_axis_height.getText()));
-//                } catch (Exception ex){
-//                    System.out.println("Height value not valid.");
-//                }
-//            }
-
-
-            if(!textfield_title.getText().equals("")){
-                communicator.setTitle_plots(textfield_title.getText());
-            }
-
-
-            try {
-                // add progress indicator
-                progressBar.setProgress(0);
-                startCalculuations = startCalculuations(communicator);
-                progressBar.progressProperty().unbind();
-                progressBar.progressProperty().bind(startCalculuations.progressProperty());
-
-                startCalculuations.addEventHandler(WorkerStateEvent.WORKER_STATE_SUCCEEDED, //
-                        (EventHandler<WorkerStateEvent>) t -> {
-                            if(starter.isCalculationsDone()){
-                                primaryStage.close();
-                            }
-                        });
-                new Thread(startCalculuations).start();
-
-                //this.primaryStage.close();
-            } catch (Exception e1) {
-                e1.printStackTrace();
-            }
-
-        });
-
-
-    }
-
-
-
-    private void addComponents(GridPane root) {
-
-        btn_inputfile = new Button("Select input file");
-        btn_reference = new Button("Select reference");
-        btn_output = new Button("Select output");
-        btn_plotting_options = new Button("Plotting options");
-        btn_specieList = new Button("Set list");
-        btn_run = new Button("Run");
-
-        Label label_threshold = new Label("Number of bases (x-axis)");
-        Label label_yaxis = new Label("Height y-axis");
-        Label label_length = new Label("Set number of bases (calculations)");
-        Label label_specie = new Label("Filter for specie");
-        Label label_title = new Label("Set title");
-        Label label_plot = new Label("Plot");
-        label_plot.setFont(Font.font("Verdana", FontWeight.BOLD, 14));
-
-        Label label_calculations = new Label("Calculations");
-        label_calculations.setFont(Font.font("Verdana", FontWeight.BOLD, 14));
-
-        progressBar = new ProgressBar(0);
-
-        textfield_threshold = new TextField();
-        textfield_length = new TextField();
-        textfield_specie = new TextField();
-        textfield_title = new TextField();
-        textfield_y_axis_height = new TextField();
-
-        checkbox_use_merged_reads = new CheckBox("Use only merged reads");
-        //checkbox_dynamic_y_axis_height = new CheckBox("Dynamic");
-
-        btn_run.setDisable(true);
-        textfield_length.setText("100");
-        textfield_threshold.setText("25");
-        textfield_y_axis_height.setText("0.4");
-        //checkbox_dynamic_y_axis_height.setSelected(true);
-        //textfield_y_axis_height.setDisable(true);
-
-
-        // add components to grid
-
-        int row = 0;
-
-        root.add(btn_inputfile, 0, row,1,1);
-        root.add(btn_reference, 1, row,1,1);
-        root.add(btn_output, 2, row,1,1);
-        root.add(new Separator(), 0, ++row,3,1);
-
-        //          PLOT
-
-        root.add(label_plot, 0, ++row, 1,1);
-        root.add(label_title, 0, ++row, 1,1);
-        root.add(textfield_title, 1, row, 2,1);
-        root.add(label_yaxis, 0, ++row, 1,1);
-        //root.add(checkbox_dynamic_y_axis_height, 1, row, 1,1);
-        root.add(textfield_y_axis_height, 1, row, 2,1);
-        root.add(label_threshold, 0, ++row, 1,1);
-        root.add(textfield_threshold, 1, row, 2,1);
-        root.add(label_specie, 0, ++row, 1,1);
-        root.add(textfield_specie, 1, row, 2,1);
-        root.add(btn_specieList, 3, row, 1,1);
-        root.add(checkbox_use_merged_reads, 0, ++row,1,1);
-        root.add(new Separator(), 0, ++row,3,1);
-
-        //          CALCULATIONS
-
-        root.add(label_calculations, 0, ++row, 1,1);
-        root.add(label_length, 0, ++row, 1,1);
-        root.add(textfield_length, 1, row, 2,1);
-        root.add(new Separator(), 0, ++row,3,1);
-        root.add(btn_run, 0, ++row,1,1);
-        root.add(progressBar, 1, row,1,1);
-
-
-    }
-
-    private boolean checkIfInputWasSelected() {
-        boolean tmp = false;
-        if (communicator.getInput() != null && communicator.getReference() != null && communicator.getOutfolder() != null) {
-            if (communicator.getInput().length() != 0) {
-                tmp = true;
-            }
-        }
-        return tmp;
-    }
-
-
-
-}
diff --git a/src/main/java/GUI/Progress.java b/src/main/java/GUI/Progress.java
deleted file mode 100755
index cbc5a63..0000000
--- a/src/main/java/GUI/Progress.java
+++ /dev/null
@@ -1,128 +0,0 @@
-package GUI;
-
-import javafx.application.Application;
-import javafx.geometry.Insets;
-import javafx.scene.Scene;
-import javafx.scene.control.ProgressBar;
-import javafx.scene.control.ProgressIndicator;
-import javafx.scene.layout.FlowPane;
-import javafx.stage.Stage;
-
-import java.io.File;
-import java.util.List;
-
-import javafx.application.Application;
-import javafx.concurrent.WorkerStateEvent;
-import javafx.event.ActionEvent;
-import javafx.event.EventHandler;
-import javafx.geometry.Insets;
-import javafx.scene.Scene;
-import javafx.scene.control.Button;
-import javafx.scene.control.Label;
-import javafx.scene.control.ProgressBar;
-import javafx.scene.control.ProgressIndicator;
-import javafx.scene.layout.FlowPane;
-import javafx.scene.paint.Color;
-import javafx.stage.Stage;
-
-public class Progress extends Application {
-
-    private CopyTask copyTask;
-
-    @Override
-    public void start(Stage primaryStage) {
-
-        final Label label = new Label("Copy files:");
-        final ProgressBar progressBar = new ProgressBar(0);
-        final ProgressIndicator progressIndicator = new ProgressIndicator(0);
-
-        final Button startButton = new Button("Start");
-        final Button cancelButton = new Button("Cancel");
-
-        final Label statusLabel = new Label();
-        statusLabel.setMinWidth(250);
-        statusLabel.setTextFill(Color.BLUE);
-
-        // Start Button.
-        startButton.setOnAction(new EventHandler<ActionEvent>() {
-            @Override
-            public void handle(ActionEvent event) {
-                startButton.setDisable(true);
-                progressBar.setProgress(0);
-                progressIndicator.setProgress(0);
-                cancelButton.setDisable(false);
-
-                // Create a Task.
-                copyTask = new CopyTask();
-
-                // Unbind progress property
-                progressBar.progressProperty().unbind();
-
-                // Bind progress property
-                progressBar.progressProperty().bind(copyTask.progressProperty());
-
-                // Hủy bỏ kết nối thuộc tính progress
-                progressIndicator.progressProperty().unbind();
-
-                // Bind progress property.
-                progressIndicator.progressProperty().bind(copyTask.progressProperty());
-
-                // Unbind text property for Label.
-                statusLabel.textProperty().unbind();
-
-                // Bind the text property of Label
-                // with message property of Task
-                statusLabel.textProperty().bind(copyTask.messageProperty());
-
-                // When completed tasks
-                copyTask.addEventHandler(WorkerStateEvent.WORKER_STATE_SUCCEEDED, //
-                        new EventHandler<WorkerStateEvent>() {
-
-                            @Override
-                            public void handle(WorkerStateEvent t) {
-                                List<File> copied = copyTask.getValue();
-                                statusLabel.textProperty().unbind();
-                                statusLabel.setText("Copied: " + copied.size());
-                            }
-                        });
-
-                // Start the Task.
-                new Thread(copyTask).start();
-
-            }
-        });
-
-        // Cancel
-        cancelButton.setOnAction(new EventHandler<ActionEvent>() {
-            @Override
-            public void handle(ActionEvent event) {
-                startButton.setDisable(false);
-                cancelButton.setDisable(true);
-                copyTask.cancel(true);
-                progressBar.progressProperty().unbind();
-                progressIndicator.progressProperty().unbind();
-                statusLabel.textProperty().unbind();
-                //
-                progressBar.setProgress(0);
-                progressIndicator.setProgress(0);
-            }
-        });
-
-        FlowPane root = new FlowPane();
-        root.setPadding(new Insets(10));
-        root.setHgap(10);
-
-        root.getChildren().addAll(label, progressBar, progressIndicator, //
-                statusLabel, startButton, cancelButton);
-
-        Scene scene = new Scene(root, 500, 120, Color.WHITE);
-        primaryStage.setTitle("ProgressBar & ProgressIndicator");
-        primaryStage.setScene(scene);
-        primaryStage.show();
-    }
-
-    public static void main(String[] args) {
-        Application.launch(args);
-    }
-
-}
\ No newline at end of file
diff --git a/src/main/java/IO/Unzip.java b/src/main/java/IO/Unzip.java
deleted file mode 100755
index b8a0869..0000000
--- a/src/main/java/IO/Unzip.java
+++ /dev/null
@@ -1,45 +0,0 @@
-package IO;
-
-import org.apache.log4j.Logger;
-
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.OutputStream;
-import java.util.zip.GZIPInputStream;
-
-
-/**
- * Created by neukamm on 25.07.2016.
- */
-public class Unzip {
-
-    private final Logger LOG;
-
-    public Unzip(Logger LOG){
-        this.LOG = LOG;
-    }
-
-
-    /**
-     * decompress zipped/compressed file
-     *
-     * @param infile
-     * @return
-     * @throws Exception
-     */
-    public String decompress(String infile) throws Exception {
-
-        GZIPInputStream in = new GZIPInputStream(new FileInputStream(infile));
-        String outfile = infile.substring(0, infile.lastIndexOf('.'));
-        OutputStream out = new FileOutputStream(outfile);
-        byte[] buf = new byte[1024];
-        int len;
-        while ((len = in.read(buf)) > 0) {
-            out.write(buf, 0, len);
-        }
-        in.close();
-        out.close();
-
-        return outfile;
-    }
-}
diff --git a/src/main/java/IO/UserOptionsParser.java b/src/main/java/IO/UserOptionsParser.java
deleted file mode 100755
index ace9a28..0000000
--- a/src/main/java/IO/UserOptionsParser.java
+++ /dev/null
@@ -1,218 +0,0 @@
-package IO;
-
-import org.apache.commons.cli.*;
-
-
-/**
- * Created by neukamm on 01.08.16.
- */
-public class UserOptionsParser {
-
-    private static final String CLASS_NAME = "User option parser";
-    private final String version;
-    private String[] args;
-    private Communicator communicator;
-
-
-    public UserOptionsParser(String[] args, Communicator c, String version){
-        this.args = args;
-        this.communicator = c;
-        this.version = version;
-        parse();
-    }
-
-    private void parse() {
-
-        // create command line parameters
-        Options helpOptions = new Options();
-        helpOptions.addOption("h", "help", false, "show this help page");
-        Options options = new Options();
-        options.addOption("h", "help", false, "show this help page");
-
-        Option version = new Option("version", "version", false,
-                "Show version of DamageProfiler");
-        options.addOption(version);
-
-        options.addOption(OptionBuilder.withLongOpt("input")
-                .withArgName("INPUT")
-                .withDescription("The input sam/bam file")
-                .hasArg()
-                .create("i"));
-        options.addOption(OptionBuilder.withLongOpt("reference")
-                .withArgName("REFERENCE")
-                .withDescription("The reference file")
-                .hasArg()
-                .create("r"));
-        options.addOption(OptionBuilder.withLongOpt("output")
-                .withArgName("OUTPUT")
-                .withDescription("The output folder")
-                .hasArg()
-                .create("o"));
-        options.addOption(OptionBuilder.withLongOpt("threshold")
-                .withArgName("THRESHOLD")
-                .withDescription("Number of bases which are considered for plotting nucleotide misincorporations")
-                .hasArg()
-                .create("t"));
-        options.addOption(OptionBuilder.withLongOpt("specie")
-                .withArgName("SPECIE")
-                .withDescription("RNAME flag SAM record (Reference sequence name)")
-                .hasArg()
-                .create("s"));
-        options.addOption(OptionBuilder.withLongOpt("specieslist file")
-                .withArgName("SPECIES LIST")
-                .withDescription("List with species for which damage profile has to be calculated.")
-                .hasArg()
-                .create("sf"));
-        options.addOption(OptionBuilder.withLongOpt("length")
-                .withArgName("LENGTH")
-                .withDescription("Number of bases which are considered for frequency computations.")
-                .hasArg()
-                .create("l"));
-
-        options.addOption(OptionBuilder.withLongOpt("title")
-                .withArgName("TITLE")
-                .withDescription("Title used for all plots. Default: filepath of input SAM/BAM file.")
-                .hasArg()
-                .create("title"));
-
-        options.addOption(OptionBuilder.withLongOpt("yaxis_damageplot")
-                .withArgName("YAXIS_DAMAGEPLOT")
-                .withDescription("Maximal value on y axis of damage plot.")
-                .hasArg()
-                .create("yaxis_damageplot"));
-
-        options.addOption(OptionBuilder.withLongOpt("xaxis_histo_id_min")
-                .withArgName("XAXIS_HISTO_ID_MIN")
-                .withDescription("Minimal value x-axis of identity histogram.")
-                .hasArg()
-                .create("xaxis_histo_id_min"));
-
-        options.addOption(OptionBuilder.withLongOpt("xaxis_histo_id_max")
-                .withArgName("XAXIS_HISTO_ID_MAX")
-                .withDescription("Maximal value x-axis of identity histogram.")
-                .hasArg()
-                .create("xaxis_histo_id_max"));
-
-        options.addOption(OptionBuilder.withLongOpt("xaxis_histo_length_min")
-                .withArgName("XAXIS_HISTO_LENGTH_MIN")
-                .withDescription("Minimal value x-axis of length histogram.")
-                .hasArg()
-                .create("xaxis_histo_length_min"));
-
-        options.addOption(OptionBuilder.withLongOpt("xaxis_histo_length_max")
-                .withArgName("XAXIS_HISTO_LENGTH_MAX")
-                .withDescription("Maximal value x-axis of length histogram.")
-                .hasArg()
-                .create("xaxis_histo_length_max"));
-
-        Option mapped_and_merged = new Option("merged", "all_mapped_and_merged_reads", false,
-                "Use all mapped and merged reads to calculate damage plot instead of using all mapped reads. The SAM/BAM entry must start with 'M_', otherwise " +
-                        " it will be skipped. Default: false ");
-        options.addOption(mapped_and_merged);
-
-        Option use_all_reads = new Option("useall", "use_all_reads", false,
-                "Use all reads (mapped and unmapped) to calculate damage plot. Default: false ");
-        options.addOption(use_all_reads);
-
-
-        HelpFormatter helpformatter = new HelpFormatter();
-        CommandLineParser parser = new BasicParser();
-
-        if (args[0].equals("-version") || args[0].equals("--version")){
-            System.out.print("DamageProfiler v" + this.version);
-            System.exit(0);
-        } else if (args.length < 2) {
-            helpformatter.printHelp(CLASS_NAME, options);
-            System.exit(0);
-        }
-        try {
-            CommandLine cmd = parser.parse(helpOptions, args);
-            if (cmd.hasOption('h')) {
-                helpformatter.printHelp(CLASS_NAME, options);
-                System.exit(0);
-            }
-        } catch (ParseException e1) {
-        }
-
-
-        try {
-            CommandLine cmd = parser.parse(options, args);
-
-            if(cmd.hasOption("version")) {
-                System.out.print("DamageProfiler v" + this.version + "\n");
-                System.exit(0);
-            }
-
-            // input files
-
-            if (cmd.hasOption('i')) {
-                communicator.setInput(cmd.getOptionValue('i'));
-            }
-            if (cmd.hasOption('r')) {
-                communicator.setReference(cmd.getOptionValue('r'));
-            }
-            if (cmd.hasOption('o')) {
-                communicator.setOutfolder(cmd.getOptionValue('o'));
-            }
-
-            // damage calculation
-
-            if (cmd.hasOption('s')) {
-                communicator.setSpecies_ref_identifier(cmd.getOptionValue('s'));
-            }
-            if (cmd.hasOption("sf")) {
-                communicator.setSpecieslist_filepath(cmd.getOptionValue("sf"));
-            }
-            if (cmd.hasOption('l')) {
-                communicator.setLength(Integer.parseInt(cmd.getOptionValue('l')));
-            }
-            if(cmd.hasOption("all_mapped_and_merged_reads")) {
-                communicator.setUse_merged_and_mapped_reads(true);
-            }
-
-            if(cmd.hasOption("use_all_reads")) {
-                communicator.setUse_all_reads(false);
-            }
-
-            // Plotting
-
-            if(cmd.hasOption("title")) {
-                communicator.setTitle_plots(cmd.getOptionValue("title"));
-            }
-
-            if(cmd.hasOption("yaxis_damageplot")) {
-                communicator.setyAxis_damageplot(Double.parseDouble(cmd.getOptionValue("yaxis_damageplot")));
-            }
-
-            if(cmd.hasOption("xaxis_histo_id_min")) {
-                communicator.setXaxis_histo_id_min(Double.parseDouble(cmd.getOptionValue("xaxis_histo_id_min")));
-            }
-
-
-            if(cmd.hasOption("xaxis_histo_id_max")) {
-                communicator.setXaxis_histo_id_max(Double.parseDouble(cmd.getOptionValue("xaxis_histo_id_max")));
-            }
-
-            if(cmd.hasOption("xaxis_histo_length_min")) {
-                communicator.setXaxis_histo_length_min(Double.parseDouble(cmd.getOptionValue("xaxis_histo_length_min")));
-            }
-
-
-            if(cmd.hasOption("xaxis_histo_length_max")) {
-                communicator.setXaxis_histo_length_max(Double.parseDouble(cmd.getOptionValue("xaxis_histo_length_max")));
-            }
-
-
-            if (cmd.hasOption('t')) {
-                communicator.setThreshold(Integer.parseInt(cmd.getOptionValue('t')));
-            }
-
-
-        } catch (ParseException e) {
-            helpformatter.printHelp(CLASS_NAME, options);
-            System.err.println(e.getMessage());
-            System.exit(0);
-        }
-
-    }
-}
diff --git a/src/main/java/RunDamageProfiler.java b/src/main/java/RunDamageProfiler.java
old mode 100644
new mode 100755
index 446cef6..3315488
--- a/src/main/java/RunDamageProfiler.java
+++ b/src/main/java/RunDamageProfiler.java
@@ -1,6 +1,3 @@
-import GUI.MainGuiFX;
-import IO.*;
-import calculations.StartCalculations;
 import javafx.application.Application;
 
 /**
@@ -8,37 +5,24 @@
  */
 public class RunDamageProfiler {
 
-    private static final String VERSION = "0.4.9";
+    private static final String VERSION = "0.5.0";
 
-
-    @SuppressWarnings("static-access")
     public static void main(String[] args) throws Exception {
 
          /*
-
                   get input parameters
 
-                    $ damageprofiler                    :   starts GUI
+                    $ damageprofiler                    :   starts org.damageprofiler.GUI
 
                     $ damageprofiler -i <> -o <> ....   :   parse command line arguments
-
           */
 
-
         if(args.length==0){
-            //MainDP damageProfilerGUI = new MainDP(c, starter, VERSION);
-            System.out.println(VERSION);
-            new Thread(() -> Application.launch(MainGuiFX.class)).start();
+            new Thread(() -> Application.launch(StarterGUI.class)).start();
 
         } else {
-            Communicator c = new Communicator();
-            StartCalculations starter = new StartCalculations(VERSION);
-            UserOptionsParser userOptions = new UserOptionsParser(args, c, VERSION);
-            starter.start(c);
-
+            System.setProperty("java.awt.headless", "true");
+            StarterCLI starterCLI = new StarterCLI(VERSION, args);
         }
-
-
     }
-
 }
diff --git a/src/main/java/StarterCLI.java b/src/main/java/StarterCLI.java
new file mode 100755
index 0000000..46caa76
--- /dev/null
+++ b/src/main/java/StarterCLI.java
@@ -0,0 +1,15 @@
+import org.damageprofiler.calculations.StartCalculations;
+import org.damageprofiler.IO.Communicator;
+import org.damageprofiler.IO.UserOptionsParser;
+
+public class StarterCLI {
+
+    public StarterCLI(String version, String[] args) throws Exception {
+        Communicator c = new Communicator();
+        StartCalculations starter = new StartCalculations();
+        starter.setVERSION(version);
+        UserOptionsParser userOptions = new UserOptionsParser(args, c, version);
+        starter.start(c);
+        System.exit(0);
+    }
+}
diff --git a/src/main/java/StarterGUI.java b/src/main/java/StarterGUI.java
new file mode 100755
index 0000000..e37b4e0
--- /dev/null
+++ b/src/main/java/StarterGUI.java
@@ -0,0 +1,28 @@
+import org.damageprofiler.controller.DamageProfilerMainController;
+import org.damageprofiler.GUI.DamageProfilerMainGUI;
+import org.damageprofiler.controller.PlottingSettingController;
+import org.damageprofiler.controller.ProgressBarController;
+import javafx.application.Application;
+import javafx.stage.Stage;
+
+
+public class StarterGUI extends Application {
+
+    private static final String VERSION = "0.5.0";
+
+    @Override
+    public void start(Stage primaryStage) {
+
+        ProgressBarController progressBarController = new ProgressBarController();
+        progressBarController.create();
+
+        DamageProfilerMainGUI damageProfilerMainGUI = new DamageProfilerMainGUI(VERSION, progressBarController);
+        damageProfilerMainGUI.init(primaryStage);
+
+        PlottingSettingController plottingSettingController = new PlottingSettingController();
+        new DamageProfilerMainController(damageProfilerMainGUI, progressBarController, plottingSettingController);
+
+    }
+
+
+}
diff --git a/src/main/java/calculations/Aligner.java b/src/main/java/calculations/Aligner.java
deleted file mode 100755
index 38b0f5f..0000000
--- a/src/main/java/calculations/Aligner.java
+++ /dev/null
@@ -1,97 +0,0 @@
-package calculations;
-
-import htsjdk.samtools.CigarElement;
-import htsjdk.samtools.SAMRecord;
-import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-/**
- * Created by neukamm on 06.10.2016.
- */
-public class Aligner {
-
-    private final Logger LOG;
-
-    public Aligner(Logger LOG){
-        this.LOG = LOG;
-
-    }
-
-    /*
-    # from Martin Kircher, description of CIGAR operations
-    # BAM Description
-    #M 0 alignment match (can be a sequence match or mismatch)
-    #I 1 insertion to the reference
-    #D 2 deletion from the reference
-    #N 3 skipped region from the reference
-    #S 4 soft clipping (clipped sequences present in SEQ)
-    #H 5 hard clipping (clipped sequences NOT present in SEQ)
-    #P 6 padding (silent deletion from padded reference)
-    #= 7 sequence match
-    #X 8 sequence mismatch
-     */
-
-    /**
-     * align reference and read according cigar string
-     *
-     * @param seq
-     * @param ref
-     * @param record
-     * @return
-     */
-    public String[] align(String seq, String ref, SAMRecord record){
-
-        List<CigarElement> cigar_elements = record.getCigar().getCigarElements();
-
-        String ref_aligned = ref;
-        List<double[]> coord = parseCigar(cigar_elements,1);
-        for(int i = 0; i < coord.size(); i++){
-            double[] entry = coord.get(i);
-            ref_aligned = new StringBuilder(ref_aligned).insert((int)entry[1], StringUtils.repeat("-", (int)entry[0])).toString();
-        }
-        String read_aligned = seq;
-        coord.clear();
-        coord = parseCigar(cigar_elements,2);
-        for(int i = 0; i < coord.size(); i++){
-            double[] entry = coord.get(i);
-            read_aligned = new StringBuilder(read_aligned).insert((int)entry[1]-1, StringUtils.repeat("-", (int)entry[0])).toString();
-        }
-
-        return new String[]{read_aligned, ref_aligned};
-
-    }
-
-
-    /**
-     * parse CIGAR string, get length of each operation and position of operation in read
-     *
-     * @param cigar
-     * @param ope
-     * @return double[] coordinates = position in record sequence and number of occurrences
-     */
-    private List<double[]> parseCigar(List<CigarElement> cigar, int ope){
-        List<double[]> coordinates = new ArrayList<>();
-        int tlength = 0;
-
-        //count matches, indels and mismatches
-        List<Integer> oplist = Arrays.asList(0, 1, 2, 7, 8);
-
-        for(int i = 0; i < cigar.size(); i++){
-            int length = cigar.get(i).getLength();
-            int op = cigar.get(i).getOperator().ordinal();
-            if(op == ope){
-                coordinates.add(new double[]{length, tlength});
-
-            }
-            if(oplist.contains(op)){
-                tlength+= length;
-            }
-        }
-
-        return coordinates;
-    }
-}
diff --git a/src/main/java/calculations/Functions.java b/src/main/java/calculations/Functions.java
deleted file mode 100755
index 2a62748..0000000
--- a/src/main/java/calculations/Functions.java
+++ /dev/null
@@ -1,46 +0,0 @@
-package calculations;
-
-import org.apache.log4j.Logger;
-
-/**
- * Created by neukamm on 13.03.17.
- */
-public class Functions {
-
-    private final Logger LOG;
-
-    public Functions(Logger LOG){
-        this.LOG = LOG;
-    }
-
-
-    /**
-     * Get the hamming distance between two string sequences
-     *
-     * @param sequence1 - the first sequence
-     * @param sequence2 - the second sequence
-     * @return the hamming distance
-     */
-    public static int getHammingDistance(String sequence1, String sequence2){
-        int distance =0;
-        if(sequence1 == null || sequence2==null)
-            System.exit(0);
-
-        sequence1 = sequence1.toUpperCase();
-        sequence2 = sequence2.toUpperCase();
-
-        if(sequence1.length() != sequence2.length())
-        {
-            System.out.println("The string are not equal in length ,Please enter the strings wit equal lengths ");
-        }
-
-        for(int i=0;i < sequence1.length();i++)
-        {
-            if(sequence1.charAt(i)!=sequence2.charAt(i))
-                distance++;
-        }
-
-        return distance;
-
-    }
-}
diff --git a/src/main/java/GUI/BamFileChooserFX.java b/src/main/java/org/damageprofiler/GUI/BamFileChooser.java
similarity index 75%
rename from src/main/java/GUI/BamFileChooserFX.java
rename to src/main/java/org/damageprofiler/GUI/BamFileChooser.java
index c91b333..81fbd0c 100755
--- a/src/main/java/GUI/BamFileChooserFX.java
+++ b/src/main/java/org/damageprofiler/GUI/BamFileChooser.java
@@ -1,6 +1,6 @@
-package GUI;
+package org.damageprofiler.GUI;
 
-import IO.Communicator;
+import org.damageprofiler.IO.Communicator;
 import javafx.stage.FileChooser;
 import javafx.stage.Stage;
 
@@ -8,11 +8,11 @@
 import java.util.ArrayList;
 import java.util.List;
 
-public class BamFileChooserFX {
+public class BamFileChooser {
 
     private FileChooser fileChooser = new FileChooser();
 
-    public BamFileChooserFX(Communicator c){
+    public BamFileChooser(Communicator c){
 
         fileChooser.getExtensionFilters().addAll(
                 new FileChooser.ExtensionFilter("BAM", "*.bam"),
@@ -31,9 +31,10 @@ public BamFileChooserFX(Communicator c){
             }
 
             c.setInput(files.get(0));
-            System.out.println(files.get(0));
+            System.out.println("Input file: " + files.get(0));
 
         } catch (Exception e){
+            System.err.println(e);
 
         }
 
diff --git a/src/main/java/org/damageprofiler/GUI/DamageProfilerMainGUI.java b/src/main/java/org/damageprofiler/GUI/DamageProfilerMainGUI.java
new file mode 100755
index 0000000..f1f096e
--- /dev/null
+++ b/src/main/java/org/damageprofiler/GUI/DamageProfilerMainGUI.java
@@ -0,0 +1,132 @@
+package org.damageprofiler.GUI;
+
+import org.damageprofiler.GUI.Dialogues.ConfigurationDialogue;
+import org.damageprofiler.IO.Communicator;
+import org.damageprofiler.controller.ProgressBarController;
+import javafx.geometry.Insets;
+import javafx.scene.Scene;
+import javafx.scene.control.*;
+import javafx.scene.image.Image;
+import javafx.scene.image.ImageView;
+import javafx.scene.layout.BorderPane;
+import javafx.scene.layout.VBox;
+import javafx.stage.Stage;
+
+import java.io.InputStream;
+
+public class DamageProfilerMainGUI {
+
+
+    private final String version;
+    private final ProgressBarController progressBarController;
+    private Stage primaryStage;
+    private Communicator communicator = new Communicator();
+    private BorderPane root;
+    private ConfigurationDialogue config_dialogue;
+    private Button btn_leftpane_identityDist;
+    private Button btn_leftpane_info;
+    private Button btn_leftpane_damageProfile;
+    private Button btn_leftpane_lengthDist;
+    private Button btn_help;
+
+
+    public DamageProfilerMainGUI(String version, ProgressBarController progressBarController) {
+        this.version = version;
+        this.progressBarController = progressBarController;
+    }
+
+    public void init(Stage primaryStage) {
+
+        this.primaryStage = primaryStage;
+        this.primaryStage.setTitle("DamageProfiler v" + version);
+
+        root = new BorderPane();
+
+        config_dialogue = new ConfigurationDialogue(progressBarController.getProgressBar());
+
+        ScrollPane scrollPane_adv_config = new ScrollPane();
+        scrollPane_adv_config.setPadding(new Insets(10,10,10,10));
+        scrollPane_adv_config.setContent(config_dialogue.getConfig_gridpane());
+        root.setCenter(scrollPane_adv_config);
+        root.setLeft(generateLeftPane());
+
+        this.primaryStage.setScene(new Scene(root, 950, 700));
+        this.primaryStage.setResizable(true);
+        this.primaryStage.show();
+
+    }
+
+    private VBox generateLeftPane() {
+
+        // Image Source
+        InputStream input= getClass().getClassLoader().getResourceAsStream("logo.png");
+        Image image = new Image(input);
+        ImageView imageView = new ImageView(image);
+
+        // Create a Label with label and Icon
+        Label label = new Label("", imageView);
+
+
+
+        VBox leftPanel = new VBox();
+        btn_leftpane_damageProfile = new Button("Damage Plot");
+        btn_leftpane_info = new Button("Run Configuration");
+        btn_help = new Button("Show help");
+        btn_leftpane_lengthDist = new Button("Length Distribution");
+        btn_leftpane_identityDist = new Button("Edit distance");
+
+        // style buttons
+        btn_leftpane_info.setPrefHeight(30);
+        btn_leftpane_info.setPrefWidth(200);
+
+        btn_help.setPrefHeight(30);
+        btn_help.setPrefWidth(200);
+
+        btn_leftpane_damageProfile.setPrefHeight(30);
+        btn_leftpane_damageProfile.setPrefWidth(200);
+        btn_leftpane_damageProfile.setDisable(true);
+
+        btn_leftpane_lengthDist.setPrefHeight(30);
+        btn_leftpane_lengthDist.setPrefWidth(200);
+        btn_leftpane_lengthDist.setDisable(true);
+
+        btn_leftpane_identityDist.setPrefHeight(30);
+        btn_leftpane_identityDist.setPrefWidth(200);
+        btn_leftpane_identityDist.setDisable(true);
+
+        leftPanel.getChildren().addAll(label, btn_leftpane_info, btn_leftpane_damageProfile, btn_leftpane_lengthDist, btn_leftpane_identityDist, btn_help);
+        leftPanel.setPadding(new Insets(10,10,10,10));
+
+        return leftPanel;
+    }
+
+
+
+    public Communicator getCommunicator() {
+        return communicator;
+    }
+
+    public BorderPane getRoot() {
+        return root;
+    }
+
+    public Button getBtn_leftpane_identityDist() {
+        return btn_leftpane_identityDist;
+    }
+
+    public Button getBtn_leftpane_info() { return btn_leftpane_info; }
+
+    public Button getBtn_leftpane_damageProfile() {
+        return btn_leftpane_damageProfile;
+    }
+
+    public Button getBtn_leftpane_lengthDist() {
+        return btn_leftpane_lengthDist;
+    }
+
+    public Button getBtn_help() { return btn_help; }
+
+    public ConfigurationDialogue getConfig_dialogue() { return config_dialogue; }
+
+    public String getVersion() { return version; }
+}
diff --git a/src/main/java/org/damageprofiler/GUI/Dialogues/AbstractApplication.java b/src/main/java/org/damageprofiler/GUI/Dialogues/AbstractApplication.java
new file mode 100755
index 0000000..117d430
--- /dev/null
+++ b/src/main/java/org/damageprofiler/GUI/Dialogues/AbstractApplication.java
@@ -0,0 +1,48 @@
+package org.damageprofiler.GUI.Dialogues;
+
+import javafx.geometry.Pos;
+import javafx.scene.Scene;
+import javafx.scene.control.Label;
+import javafx.scene.control.Separator;
+import javafx.scene.layout.GridPane;
+import javafx.stage.Modality;
+import javafx.stage.Stage;
+
+public class AbstractApplication {
+
+    private final Stage stage;
+    protected GridPane gridPane;
+    protected int row;
+
+    public AbstractApplication(String header, String message){
+
+        stage = new Stage();
+        stage.setTitle(header);
+        stage.initModality(Modality.APPLICATION_MODAL);
+        stage.initOwner(new Stage());
+
+        gridPane = new GridPane();
+        gridPane.setAlignment(Pos.CENTER);
+        gridPane.setHgap(10);
+        gridPane.setVgap(10);
+
+        fillGrid(message);
+
+    }
+
+    private void fillGrid(String message) {
+        row = 0;
+        gridPane.add(new Label(message), 0,row,2,1);
+        gridPane.add(new Separator(), 0,++row,2,1);
+    }
+
+    public void show(){
+        Scene dialogScene = new Scene(gridPane, 600, 200);
+        stage.setScene(dialogScene);
+        stage.show();
+    }
+
+    public void close() {
+        stage.close();
+    }
+}
diff --git a/src/main/java/org/damageprofiler/GUI/Dialogues/AbstractDialogue.java b/src/main/java/org/damageprofiler/GUI/Dialogues/AbstractDialogue.java
new file mode 100755
index 0000000..535f52b
--- /dev/null
+++ b/src/main/java/org/damageprofiler/GUI/Dialogues/AbstractDialogue.java
@@ -0,0 +1,39 @@
+package org.damageprofiler.GUI.Dialogues;
+
+import javafx.geometry.Insets;
+import javafx.geometry.Pos;
+import javafx.scene.control.Label;
+import javafx.scene.control.Separator;
+import javafx.scene.layout.GridPane;
+import javafx.scene.text.Font;
+import javafx.scene.text.FontWeight;
+
+public class AbstractDialogue {
+
+    protected GridPane gridPane;
+    protected int row;
+
+    public AbstractDialogue(String message){
+        gridPane = new GridPane();
+        gridPane.setAlignment(Pos.CENTER);
+        gridPane.setHgap(10);
+        gridPane.setVgap(10);
+        gridPane.setPadding(new Insets(15,15,15,15));
+
+        fillGrid(message);
+    }
+
+    private void fillGrid(String message) {
+
+        Label label_message = new Label(message);
+        label_message.setFont(Font.font("Verdana", FontWeight.BOLD, 14));
+
+        row = 0;
+        gridPane.add(label_message, 0,row,2,1);
+        gridPane.add(new Separator(), 0,++row,2,1);
+    }
+
+    public GridPane getGridPane() {
+        return gridPane;
+    }
+}
diff --git a/src/main/java/org/damageprofiler/GUI/Dialogues/AdvancedPlottingOptionsDialogue.java b/src/main/java/org/damageprofiler/GUI/Dialogues/AdvancedPlottingOptionsDialogue.java
new file mode 100755
index 0000000..8f52061
--- /dev/null
+++ b/src/main/java/org/damageprofiler/GUI/Dialogues/AdvancedPlottingOptionsDialogue.java
@@ -0,0 +1,45 @@
+package org.damageprofiler.GUI.Dialogues;
+
+import javafx.scene.control.Tab;
+import javafx.scene.control.TabPane;
+
+
+public class AdvancedPlottingOptionsDialogue {
+
+    private TabPane tabPane;
+    private Tab tab_DP;
+    private TabAdvancedSettingsDamagePlot tabAdvancedSettingsDamagePlot;
+
+    /**
+     * Tab for the configuration of all colours of the damage patterns
+     */
+    public AdvancedPlottingOptionsDialogue(){
+
+        fill();
+    }
+
+    /**
+     * Fill the empty tab pane with all components
+     */
+    private void fill() {
+
+        tabAdvancedSettingsDamagePlot = new TabAdvancedSettingsDamagePlot("Damage Profile");
+        tab_DP = tabAdvancedSettingsDamagePlot.getTab();
+
+        tabPane = new TabPane();
+        tabPane.getTabs().addAll(tab_DP);
+
+    }
+
+
+    /*
+            Getter
+     */
+    public TabPane getGridPane() {
+        return tabPane;
+    }
+    public TabAdvancedSettingsDamagePlot getTabAdvancedSettingsDamagePlot() {
+        return tabAdvancedSettingsDamagePlot;
+    }
+
+}
diff --git a/src/main/java/org/damageprofiler/GUI/Dialogues/ColorPickerPane.java b/src/main/java/org/damageprofiler/GUI/Dialogues/ColorPickerPane.java
new file mode 100755
index 0000000..c71d232
--- /dev/null
+++ b/src/main/java/org/damageprofiler/GUI/Dialogues/ColorPickerPane.java
@@ -0,0 +1,17 @@
+package org.damageprofiler.GUI.Dialogues;
+
+import javafx.scene.control.ColorPicker;
+import javafx.scene.paint.Color;
+
+public class ColorPickerPane {
+    private ColorPicker colorPicker;
+
+    public ColorPickerPane(Color color){
+        colorPicker = new ColorPicker();
+        colorPicker.setValue(color);
+    }
+
+    public ColorPicker getPicker() {
+       return colorPicker;
+    }
+}
diff --git a/src/main/java/org/damageprofiler/GUI/Dialogues/ConfigurationDialogue.java b/src/main/java/org/damageprofiler/GUI/Dialogues/ConfigurationDialogue.java
new file mode 100755
index 0000000..ddcc4fe
--- /dev/null
+++ b/src/main/java/org/damageprofiler/GUI/Dialogues/ConfigurationDialogue.java
@@ -0,0 +1,220 @@
+package org.damageprofiler.GUI.Dialogues;
+
+import javafx.geometry.Insets;
+import javafx.geometry.Pos;
+import javafx.scene.control.*;
+import javafx.scene.layout.GridPane;
+import javafx.scene.layout.HBox;
+import javafx.scene.text.Font;
+import javafx.scene.text.FontWeight;
+
+public class ConfigurationDialogue {
+
+
+    private GridPane config_gridpane;
+
+    private Button btn_inputfile;
+    private Button btn_reference;
+    private Button btn_output;
+    private Button btn_run;
+    private Button btn_estimate_runtime;
+    private Button btn_speciesList;
+
+    private TextField textfield_threshold;
+    private TextField textfield_length;
+    private TextField textfield_species;
+    private CheckBox checkbox_use_merged_reads;
+    private CheckBox checkbox_ssLibs_protocol;
+    private TextField textfield_title;
+    private TextField textfield_y_axis_height;
+
+    private ProgressBar progressBar;
+    private AdvancedPlottingOptionsDialogue advancedPlottingOptionsDialogue;
+    private Button btn_loadSpecies;
+
+
+    public ConfigurationDialogue(ProgressBar progressBar){
+
+        config_gridpane = new GridPane();
+        config_gridpane.setAlignment(Pos.CENTER);
+        config_gridpane.setHgap(7);
+        config_gridpane.setVgap(7);
+        config_gridpane.setPadding(new Insets(10,10,10,10));
+
+        this.progressBar = progressBar;
+        addComponents();
+
+    }
+
+    private void addComponents() {
+
+        btn_inputfile = new Button("Select input file");
+        btn_reference = new Button("Select reference");
+        btn_output = new Button("Select output");
+        btn_speciesList = new Button("Set species file");
+        btn_loadSpecies = new Button("Load Species");
+        btn_run = new Button("Run");
+        btn_estimate_runtime = new Button("Estimate Runtime");
+
+        Label label_threshold = new Label("Number of bases (x-axis)");
+        Label label_yaxis = new Label("Height y-axis");
+        Label label_length = new Label("Set number of bases");
+        Label label_specie = new Label("Enter RefSeq ID ");
+        Label label_title = new Label("Set title");
+
+        Label label_plot = new Label("Plot");
+        label_plot.setFont(Font.font("Verdana", FontWeight.BOLD, 14));
+
+        Label label_files = new Label("Files");
+        label_files.setFont(Font.font("Verdana", FontWeight.BOLD, 14));
+
+        Label label_calculations = new Label("Calculations");
+        label_calculations.setFont(Font.font("Verdana", FontWeight.BOLD, 14));
+
+        Label label_title_config = new Label("Configuration");
+        label_title_config.setFont(Font.font("Verdana", FontWeight.BOLD, 14));
+
+        textfield_threshold = new TextField();
+        textfield_length = new TextField();
+        textfield_species = new TextField();
+        textfield_title = new TextField();
+        textfield_y_axis_height = new TextField();
+
+        checkbox_use_merged_reads = new CheckBox("Only merged reads");
+        checkbox_ssLibs_protocol = new CheckBox("Single-stranded library protocol");
+
+        btn_run.setDisable(true);
+        btn_estimate_runtime.setDisable(true);
+        textfield_length.setText("100");
+        textfield_threshold.setText("25");
+        textfield_y_axis_height.setText("0.4");
+
+        TitledPane pane_advanced_plotting_options = new TitledPane();
+        pane_advanced_plotting_options.setText("Advanced options (Plotting)");
+
+
+        advancedPlottingOptionsDialogue = new AdvancedPlottingOptionsDialogue();
+        pane_advanced_plotting_options.setContent(advancedPlottingOptionsDialogue.getGridPane());
+        pane_advanced_plotting_options.setExpanded(false);
+
+        TitledPane pane_advanced_calculation_options = new TitledPane();
+        pane_advanced_calculation_options.setText("Advanced options (Calculation)");
+        HBox hbox_length_calc = new HBox();
+        hbox_length_calc.setPadding(new Insets(10,10,10,10));
+        hbox_length_calc.getChildren().addAll(label_length, textfield_length);
+        pane_advanced_calculation_options.setContent(hbox_length_calc);
+        pane_advanced_calculation_options.setExpanded(false);
+
+
+        // add components to grid
+
+        int row = 0;
+
+        config_gridpane.add(label_title_config, 0, row, 1,1);
+        config_gridpane.add(new Separator(), 0, ++row,3,1);
+
+
+        config_gridpane.add(label_files, 0, ++row, 1,1);
+        config_gridpane.add(btn_inputfile, 0, ++row,1,1);
+        config_gridpane.add(btn_reference, 1, row,1,1);
+        config_gridpane.add(btn_output, 2, row,1,1);
+        config_gridpane.add(new Separator(), 0, ++row,3,1);
+
+        //          PLOT
+
+        config_gridpane.add(label_plot, 0, ++row, 1,1);
+        config_gridpane.add(label_title, 0, ++row, 1,1);
+        config_gridpane.add(textfield_title, 1, row, 2,1);
+        config_gridpane.add(label_yaxis, 0, ++row, 1,1);
+        //config_gridpane.add(checkbox_dynamic_y_axis_height, 1, row, 1,1);
+        config_gridpane.add(textfield_y_axis_height, 1, row, 2,1);
+        config_gridpane.add(label_threshold, 0, ++row, 1,1);
+        config_gridpane.add(textfield_threshold, 1, row, 2,1);
+        config_gridpane.add(pane_advanced_plotting_options, 0,++row, 3,1);
+        config_gridpane.add(new Separator(), 0, ++row,3,1);
+
+        //          CALCULATIONS
+        config_gridpane.add(label_calculations, 0, ++row, 1,1);
+        config_gridpane.add(checkbox_use_merged_reads, 0, ++row,1,1);
+        config_gridpane.add(checkbox_ssLibs_protocol, 0, ++row, 1,1);
+        config_gridpane.add(label_specie, 0, ++row, 1,1);
+        config_gridpane.add(textfield_species, 1, row, 2,1);
+        config_gridpane.add(btn_speciesList, 1, ++row, 1,1);
+        //config_gridpane.add(btn_loadSpecies, 3, row, 1,1);
+        config_gridpane.add(pane_advanced_calculation_options, 0,++row, 3,1);
+
+        config_gridpane.add(new Separator(), 0, ++row,3,1);
+        config_gridpane.add(btn_estimate_runtime, 0, ++row,1,1);
+        config_gridpane.add(btn_run, 1, row,1,1);
+        config_gridpane.add(progressBar, 2, row,1,1);
+
+    }
+
+    public GridPane getConfig_gridpane() {
+        return config_gridpane;
+    }
+
+    public Button getBtn_inputfile() {
+        return btn_inputfile;
+    }
+
+    public Button getBtn_reference() {
+        return btn_reference;
+    }
+
+    public Button getBtn_output() {
+        return btn_output;
+    }
+
+    public Button getBtn_run() {
+        return btn_run;
+    }
+
+    public Button getBtn_speciesList() {
+        return btn_speciesList;
+    }
+
+    public TextField getTextfield_threshold() {
+        return textfield_threshold;
+    }
+
+    public TextField getTextfield_length() {
+        return textfield_length;
+    }
+
+    public TextField getTextfield_species() {
+        return textfield_species;
+    }
+
+    public CheckBox getCheckbox_use_merged_reads() {
+        return checkbox_use_merged_reads;
+    }
+
+    public CheckBox getCheckbox_ssLibs_protocol() {
+        return checkbox_ssLibs_protocol;
+    }
+
+    public TextField getTextfield_title() {
+        return textfield_title;
+    }
+
+    public void setTextfield_title(String textfield_title) {
+        this.textfield_title.setText(textfield_title);
+    }
+
+    public TextField getTextfield_y_axis_height() {
+        return textfield_y_axis_height;
+    }
+
+    public Button getBtn_estimate_runtime() {
+        return btn_estimate_runtime;
+    }
+
+    public AdvancedPlottingOptionsDialogue getAdvancedPlottingOptionsDialogue() {
+        return advancedPlottingOptionsDialogue;
+    }
+
+    public Button getBtn_loadSpecies() {
+        return btn_loadSpecies;
+    }
+}
diff --git a/src/main/java/org/damageprofiler/GUI/Dialogues/HelpDialogue.java b/src/main/java/org/damageprofiler/GUI/Dialogues/HelpDialogue.java
new file mode 100755
index 0000000..4862a61
--- /dev/null
+++ b/src/main/java/org/damageprofiler/GUI/Dialogues/HelpDialogue.java
@@ -0,0 +1,101 @@
+package org.damageprofiler.GUI.Dialogues;
+
+
+import javafx.geometry.Insets;
+import javafx.geometry.Pos;
+import javafx.scene.control.Hyperlink;
+import javafx.scene.control.Label;
+import javafx.scene.control.Separator;
+import javafx.scene.layout.GridPane;
+import javafx.scene.text.Font;
+import javafx.scene.text.FontWeight;
+
+import java.awt.*;
+import java.io.IOException;
+import java.net.URI;
+import java.net.URISyntaxException;
+
+public class HelpDialogue {
+
+    private final GridPane gridPane;
+    private Hyperlink link;
+
+    public HelpDialogue(){
+
+        gridPane = new GridPane();
+        gridPane.setAlignment(Pos.CENTER);
+        gridPane.setHgap(10);
+        gridPane.setVgap(10);
+        gridPane.setPadding(new Insets(15,15,15,15));
+
+        fill();
+    }
+
+    /**
+     * Fill dialogue with help content
+     */
+    private void fill() {
+        Label label_title = new Label("Welcome to DamageProfiler help page");
+        label_title.setFont(Font.font("Verdana", FontWeight.BOLD, 14));
+
+        Label label_usage = new Label("Usage:\n");
+        label_usage.setFont(Font.font("Verdana", FontWeight.BOLD, 12));
+
+        Label label_help = new Label();
+        label_help.setText("DamageProfiler [-h] [-version] [-i <INPUT>] [-r <REFERENCE>] [-o <OUTPUT>] [-t <THRESHOLD>]\n[-s <SPECIES>] [-sf <SPECIESLIST>] " +
+        "[-l <LENGTH>] [-title <TITLE>] [-yaxis_dp_max <MAX_VALUE>]\n[-xaxis_id_min <MIN_VALUE>] [-xaxis_id_max <MAX_VALUE>] [-xaxis_length_min <MIN_VALUE>]\n" +
+                "[-xaxis_length_max <MAX_VALUE>] [-only_merged] [-ssLib]" +
+                "\n\n" );
+
+        Label label_details = new Label("Detailed description:\n");
+        label_details.setFont(Font.font("Verdana", FontWeight.BOLD, 12));
+
+        link = new Hyperlink();
+        link.setText("Documentation");
+        link.setOnAction(event -> new Thread(() -> {
+            try {
+                Desktop.getDesktop().browse(new URI("http://damageprofiler.readthedocs.io/en/latest/"));
+            } catch (IOException | URISyntaxException e1) {
+                e1.printStackTrace();
+            }
+        }).start());
+
+        Label label_helppage = new Label(" -h\t\t\t\t\t\t\tShows this help page.\n" +
+                " -version\t\t\t\t\t\tShows the version of DamageProfiler.\n" +
+                " -i <INPUT>\t\t\t\t\tREQUIRED: The input sam/bam/cram file.\n" +
+                " -r <REFERENCE>\t\t\t\tThe reference file (fasta format).\n" +
+                " -o <OUTPUT>\t\t\t\t\tREQUIRED: The output folder.\n" +
+                " -t <THRESHOLD>\t\t\t\tDamagePlot: Number of bases which are considered for plotting\n\t\t\t\t\t\t\tnucleotide misincorporations. Default: 25\n" +
+                " -s <SPECIES>\t\t\t\t\tReference sequence name (RNAME flag of SAM record).\n\t\t\t\t\t\t\tFor more details see Documentation.\n" +
+                " -sf <SPECIES LIST>\t\t\t\tList with species for which damage profile has to be calculated.\n\t\t\t\t\t\t\tFor more details see Documentation.\n" +
+                " -l <LENGTH>\t\t\t\t\tNumber of bases which are considered for frequency\n\t\t\t\t\t\t\tcomputations. Default: 100.\n" +
+                " -title <TITLE>\t\t\t\t\tTitle used for all plots. Default: input filename.\n" +
+                " -yaxis_dp_max <MAX_VALUE>\tDamagePlot: Maximal y-axis value.\n" +
+                " -xaxis_id_min <MIN_VALUE>\t\tIdentity Distribution: Minimal value x-axis.\n" +
+                " -xaxis_id_max <MAX_VALUE>\tIdentity Distribution: Maximal value x-axis.\n" +
+                " -xaxis_length_min <MIN_VALUE>\tLength Distribution: Minimal value x-axis.\n" +
+                " -xaxis_length_max <MAX_VALUE>\tLength Distribution: Maximal value x-axis.\n" +
+                " -only_merged\t\t\t\t\tUse only mapped and merged reads to calculate damage plot\n\t\t\t\t\t\t\tinstead of using all mapped reads.\n\t\t\t\t\t\t\tThe SAM/BAM entry must start with 'M_', otherwise  it will\n\t\t\t\t\t\t\tbe skipped. Default: false\n" +
+                " -ssLib\t\t\t\t\t\tSingle-stranded library protocol was used. Default: false");
+
+        int row=0;
+
+        gridPane.add(label_title,0,row,2,1);
+        gridPane.add(new Label("If you need more information, please check the documentation or contact the developers."),0, ++row,2,1);
+        gridPane.add(link,0, ++row,2,1);
+        gridPane.add(new Separator(),0, ++row,2,1);
+
+        gridPane.add(label_usage,0, ++row,2,1);
+        gridPane.add(label_help,0, ++row,2,1);
+        gridPane.add(label_details,0, ++row,2,1);
+        gridPane.add(label_helppage, 0,++row, 2,1);
+
+    }
+
+
+    // Getter
+
+    public GridPane getGridPane() {
+        return this.gridPane;
+    }
+}
diff --git a/src/main/java/org/damageprofiler/GUI/Dialogues/RunInfoDialogue.java b/src/main/java/org/damageprofiler/GUI/Dialogues/RunInfoDialogue.java
new file mode 100755
index 0000000..9821f0f
--- /dev/null
+++ b/src/main/java/org/damageprofiler/GUI/Dialogues/RunInfoDialogue.java
@@ -0,0 +1,65 @@
+package org.damageprofiler.GUI.Dialogues;
+
+import org.damageprofiler.IO.Communicator;
+import javafx.scene.control.Button;
+import javafx.scene.control.Label;
+import javafx.scene.control.ScrollPane;
+import javafx.scene.control.Separator;
+
+public class RunInfoDialogue extends AbstractDialogue {
+
+    private final Communicator communicator;
+    private Button btn_new_config;
+    private ScrollPane scrollPaneRef;
+    private ScrollPane scrollPaneInput;
+    private ScrollPane scrollPaneOutput;
+
+    public RunInfoDialogue(String message, Communicator communicator){
+        super(message);
+        this.communicator = communicator;
+        btn_new_config = new Button("New configuration");
+        init();
+    }
+
+
+    public void init() {
+
+        scrollPaneInput = new ScrollPane( new Label(communicator.getInput()));
+        scrollPaneOutput = new ScrollPane( new Label(communicator.getOutfolder()));
+        scrollPaneRef = new ScrollPane( new Label(communicator.getReference()));
+
+
+        Label label_input = new Label("Input file: ");
+        Label label_output = new Label("Output folder: ");
+        Label label_ref = new Label("Reference file: ");
+
+
+        gridPane.add(label_input, 0,++row, 1,1);
+        gridPane.add(scrollPaneInput, 1,row, 2,1);
+
+        gridPane.add(label_output, 0,++row, 1,1);
+        gridPane.add(scrollPaneOutput, 1,row, 2,1);
+
+        gridPane.add(label_ref, 0,++row, 1,1);
+        gridPane.add(scrollPaneRef, 1,row, 2,1);
+
+        gridPane.add(new Separator(), 0,++row, 1,2);
+
+
+
+        gridPane.add(btn_new_config, 0, ++row, 1,1);
+
+    }
+
+    public void updateParameters(){
+        scrollPaneInput.setContent(new Label(communicator.getInput()));
+        scrollPaneOutput.setContent( new Label(communicator.getOutfolder()));
+        scrollPaneRef.setContent(new Label(communicator.getReference()));
+
+    }
+
+
+    public Button getBtn_new_config() {
+        return btn_new_config;
+    }
+}
diff --git a/src/main/java/org/damageprofiler/GUI/Dialogues/RuntimeEstimatorDialogue.java b/src/main/java/org/damageprofiler/GUI/Dialogues/RuntimeEstimatorDialogue.java
new file mode 100755
index 0000000..10b9e0e
--- /dev/null
+++ b/src/main/java/org/damageprofiler/GUI/Dialogues/RuntimeEstimatorDialogue.java
@@ -0,0 +1,49 @@
+package org.damageprofiler.GUI.Dialogues;
+
+import javafx.scene.control.Button;
+import javafx.scene.control.Label;
+
+public class RuntimeEstimatorDialogue extends AbstractApplication {
+
+    private final Button btn_proceed;
+    private final Button btn_cancel;
+    private int numberOfRecords;
+    private String text_estimatedRuntime;
+
+    public RuntimeEstimatorDialogue(String header, String message) {
+        super(header, message);
+
+
+        btn_proceed = new Button("Proceed");
+        btn_cancel = new Button("Cancel");
+
+
+    }
+
+    public void setNumberOfRecords(int numberOfRecords) {
+        this.numberOfRecords = numberOfRecords;
+    }
+
+    public void setResultText(String text_estimatedRuntime) {
+        this.text_estimatedRuntime = text_estimatedRuntime;
+    }
+
+    public void addComponents(){
+        this.gridPane.add(new Label("Number of reads: " + numberOfRecords), 0, ++row, 2,1);
+        this.gridPane.add(new Label(text_estimatedRuntime), 0, ++row, 2,1);
+        this.gridPane.add(btn_cancel, 0, ++row, 1,1);
+        this.gridPane.add(btn_proceed, 1, row, 1,1);
+
+
+    }
+
+
+    public Button getBtn_proceed() {
+        return btn_proceed;
+    }
+
+    public Button getBtn_cancel() {
+        return btn_cancel;
+    }
+
+}
diff --git a/src/main/java/org/damageprofiler/GUI/Dialogues/TabAdvancedSettingsDamagePlot.java b/src/main/java/org/damageprofiler/GUI/Dialogues/TabAdvancedSettingsDamagePlot.java
new file mode 100755
index 0000000..dd67833
--- /dev/null
+++ b/src/main/java/org/damageprofiler/GUI/Dialogues/TabAdvancedSettingsDamagePlot.java
@@ -0,0 +1,143 @@
+package org.damageprofiler.GUI.Dialogues;
+
+import javafx.geometry.Insets;
+import javafx.geometry.Pos;
+import javafx.scene.control.Button;
+import javafx.scene.control.ColorPicker;
+import javafx.scene.control.Label;
+import javafx.scene.control.Tab;
+import javafx.scene.layout.GridPane;
+import javafx.scene.paint.Color;
+
+public class TabAdvancedSettingsDamagePlot {
+
+    private final Tab tab;
+    private ColorPicker colorPicker_C_to_T;
+    private ColorPicker colorPicker_G_to_A;
+    private ColorPicker colorPicker_insertions;
+    private ColorPicker colorPicker_deletions;
+    private ColorPicker colorPicker_others;
+    private Button btn_reset;
+    private GridPane gridpane;
+
+    /**
+     * Tab pane to configure the visualization of the damage profile
+     *  (misincorporation frequencies)
+     * @param title
+     */
+    public TabAdvancedSettingsDamagePlot(String title){
+
+        this.tab = new Tab(title);
+        btn_reset = new Button("Reset");
+
+        fill(   generateColorPicker(Color.RED),
+                generateColorPicker(Color.BLUE),
+                generateColorPicker(Color.valueOf("FF00FF")),
+                generateColorPicker(Color.GREEN),
+                generateColorPicker(Color.GREY));
+
+    }
+
+
+
+    /**
+     * Fill grid pane with all components
+     *
+     * @param c_t
+     * @param g_a
+     * @param insertions
+     * @param deletions
+     * @param others
+     */
+    public void fill(ColorPicker c_t, ColorPicker g_a, ColorPicker insertions, ColorPicker deletions, ColorPicker others) {
+        gridpane = new GridPane();
+        gridpane.setAlignment(Pos.BOTTOM_LEFT);
+        gridpane.setHgap(7);
+        gridpane.setVgap(7);
+        gridpane.setPadding(new Insets(10,10,10,10));
+
+
+        colorPicker_C_to_T = c_t;
+        colorPicker_G_to_A = g_a;
+        colorPicker_insertions = insertions;
+        colorPicker_deletions = deletions;
+        colorPicker_others = others;
+
+        gridpane.add(new Label("C->T"), 0,0,1,1);
+        gridpane.add(colorPicker_C_to_T, 0,1,1,1);
+
+        gridpane.add(new Label("G->A"), 1,0,1,1);
+        gridpane.add(colorPicker_G_to_A, 1,1,1,1);
+
+        gridpane.add(new Label("Insertions"), 0,2,1,1);
+        gridpane.add(colorPicker_insertions, 0,3,1,1);
+
+        gridpane.add(new Label("Deletions"), 1,2,1,1);
+        gridpane.add(colorPicker_deletions, 1,3,1,1);
+
+        gridpane.add(new Label("Others"), 0,4,1,1);
+        gridpane.add(colorPicker_others, 0,5,1,1);
+
+        gridpane.add(btn_reset, 2,5,1,1);
+
+        tab.setContent(gridpane);
+    }
+
+
+    /**
+     * Generate and return color picker
+     *
+     * @param color
+     * @return
+     */
+    public ColorPicker generateColorPicker(Color color) {
+        ColorPickerPane colorPickerPane = new ColorPickerPane(color);
+        return colorPickerPane.getPicker();
+    }
+
+    /*
+            Getter
+     */
+    public Tab getTab() {
+        return tab;
+    }
+
+    public ColorPicker getColorPicker_C_to_T() {
+        return colorPicker_C_to_T;
+    }
+
+    public ColorPicker getColorPicker_G_to_A() {
+        return colorPicker_G_to_A;
+    }
+
+    public ColorPicker getColorPicker_insertions() {
+        return colorPicker_insertions;
+    }
+
+    public ColorPicker getColorPicker_deletions() {
+        return colorPicker_deletions;
+    }
+
+    public ColorPicker getColorPicker_others() {
+        return colorPicker_others;
+    }
+
+    public Button getBtn_reset() {
+        return btn_reset;
+    }
+
+    public GridPane getGridpane() {
+        return gridpane;
+    }
+
+    public void reset() {
+
+        this.gridpane.getChildren().clear();
+        fill(   generateColorPicker(Color.RED),
+                generateColorPicker(Color.BLUE),
+                generateColorPicker(Color.valueOf("FF00FF")),
+                generateColorPicker(Color.GREEN),
+                generateColorPicker(Color.GREY));
+
+    }
+}
diff --git a/src/main/java/GUI/OutputDirChooserFX.java b/src/main/java/org/damageprofiler/GUI/OutputDirChooser.java
similarity index 57%
rename from src/main/java/GUI/OutputDirChooserFX.java
rename to src/main/java/org/damageprofiler/GUI/OutputDirChooser.java
index 9141f5f..b9ab610 100755
--- a/src/main/java/GUI/OutputDirChooserFX.java
+++ b/src/main/java/org/damageprofiler/GUI/OutputDirChooser.java
@@ -1,20 +1,20 @@
-package GUI;
+package org.damageprofiler.GUI;
 
-import IO.Communicator;
+import org.damageprofiler.IO.Communicator;
 import javafx.stage.DirectoryChooser;
 import javafx.stage.Stage;
 
 import java.io.File;
 
-public class OutputDirChooserFX {
+public class OutputDirChooser {
 
     private DirectoryChooser dirChooser = new DirectoryChooser();
 
-    public OutputDirChooserFX(Communicator c) {
+    public OutputDirChooser(Communicator c) {
         File f = dirChooser.showDialog(new Stage());
         if (f != null){
             c.setOutfolder(f.getAbsolutePath());
-            System.out.println(f.getAbsolutePath());
+            System.out.println("Output folder: " + f.getAbsolutePath());
         }
 
     }
diff --git a/src/main/java/GUI/ReferenceFileChooserFX.java b/src/main/java/org/damageprofiler/GUI/ReferenceFileChooser.java
similarity index 73%
rename from src/main/java/GUI/ReferenceFileChooserFX.java
rename to src/main/java/org/damageprofiler/GUI/ReferenceFileChooser.java
index 632458b..384df7b 100755
--- a/src/main/java/GUI/ReferenceFileChooserFX.java
+++ b/src/main/java/org/damageprofiler/GUI/ReferenceFileChooser.java
@@ -1,16 +1,16 @@
-package GUI;
+package org.damageprofiler.GUI;
 
-import IO.Communicator;
+import org.damageprofiler.IO.Communicator;
 import javafx.stage.FileChooser;
 import javafx.stage.Stage;
 
 import java.io.File;
 
-public class ReferenceFileChooserFX {
+public class ReferenceFileChooser {
 
     private FileChooser fileChooser = new FileChooser();
 
-    public ReferenceFileChooserFX(Communicator c){
+    public ReferenceFileChooser(Communicator c){
 
         fileChooser.getExtensionFilters().addAll(
                 new FileChooser.ExtensionFilter("Fasta", "*.fa","*.fasta", ".fas")
diff --git a/src/main/java/GUI/SpeciesListFileChooser.java b/src/main/java/org/damageprofiler/GUI/SpeciesListFileChooser.java
similarity index 83%
rename from src/main/java/GUI/SpeciesListFileChooser.java
rename to src/main/java/org/damageprofiler/GUI/SpeciesListFileChooser.java
index a9e894a..c33feb9 100755
--- a/src/main/java/GUI/SpeciesListFileChooser.java
+++ b/src/main/java/org/damageprofiler/GUI/SpeciesListFileChooser.java
@@ -1,6 +1,6 @@
-package GUI;
+package org.damageprofiler.GUI;
 
-import IO.Communicator;
+import org.damageprofiler.IO.Communicator;
 import javafx.stage.FileChooser;
 import javafx.stage.Stage;
 
@@ -16,6 +16,5 @@ public SpeciesListFileChooser(Communicator c){
         if(f != null){
             c.setSpecieslist_filepath(f.getAbsolutePath());
         }
-
     }
 }
diff --git a/src/main/java/IO/Communicator.java b/src/main/java/org/damageprofiler/IO/Communicator.java
similarity index 66%
rename from src/main/java/IO/Communicator.java
rename to src/main/java/org/damageprofiler/IO/Communicator.java
index 88226d1..faf04db 100755
--- a/src/main/java/IO/Communicator.java
+++ b/src/main/java/org/damageprofiler/IO/Communicator.java
@@ -1,4 +1,6 @@
-package IO;
+package org.damageprofiler.IO;
+
+import javafx.scene.paint.Color;
 
 /**
  * Created by neukamm on 11.11.2016.
@@ -14,27 +16,28 @@ public class Communicator {
     // damage calculation
     private int threshold = 25;
 
-    private double yAxis_damageplot=0.4;
-    private double xaxis_histo_id_min =-1;
-    private double xaxis_histo_id_max =-1;
-    private double xaxis_histo_length_min=-1;
-    private double xaxis_histo_length_max=-1;
+    private double yAxis_damageplot = 0.4;
+    private double xaxis_histo_id_min = -1;
+    private double xaxis_histo_id_max = -1;
+    private double xaxis_histo_length_min = -1;
+    private double xaxis_histo_length_max = -1;
     private int length = 100;
     private boolean use_merged_and_mapped_reads = false;
     private boolean use_all_reads = false;
+    private boolean ssLibsProtocolUsed = false;
 
     // specie filtering
     private String species_ref_identifier = null;
 
     // plot settings
     private String title_plots;
+    private Color color_DP_C_to_T = Color.RED;
+    private Color color_DP_G_to_A = Color.BLUE;
+    private Color color_DP_insertions = Color.valueOf("FF00FF");
+    private Color color_DP_deletions = Color.GREEN;
+    private Color color_DP_other = Color.GREY;
 
 
-
-    public Communicator(){
-
-    }
-
     public String getInput() {
         return input;
     }
@@ -99,6 +102,14 @@ public void setUse_all_reads(boolean use_all_reads) {
         this.use_all_reads = use_all_reads;
     }
 
+    public boolean isSsLibsProtocolUsed() {
+        return ssLibsProtocolUsed;
+    }
+
+    public void setSsLibsProtocolUsed(boolean ssLibsProtocolUsed) {
+        this.ssLibsProtocolUsed = ssLibsProtocolUsed;
+    }
+
     public void setyAxis_damageplot(double yAxis_damageplot) {
         this.yAxis_damageplot = yAxis_damageplot;
     }
@@ -123,7 +134,6 @@ public void setSpecieslist_filepath(String specieslist_filepath) {
         this.specieslist_filepath = specieslist_filepath;
     }
 
-
     public double getXaxis_histo_id_min() {
         return xaxis_histo_id_min;
     }
@@ -155,4 +165,45 @@ public double getXaxis_histo_length_max() {
     public void setXaxis_histo_length_max(double xaxis_histo_length_max) {
         this.xaxis_histo_length_max = xaxis_histo_length_max;
     }
+
+    public void setColor_DP_C_to_T(Color color_c_to_t) {
+        this.color_DP_C_to_T = color_c_to_t;
+    }
+
+    public void setColor_DP_G_to_A(Color color_g_to_a) {
+        this.color_DP_G_to_A = color_g_to_a;
+    }
+
+    public void setColor_DP_insertions(Color color_insertions) {
+        this.color_DP_insertions = color_insertions;
+    }
+
+    public void setColor_DP_deletions(Color color_deletions) {
+        this.color_DP_deletions = color_deletions;
+    }
+
+    public void setColor_DP_other(Color color_other) {
+        this.color_DP_other = color_other;
+    }
+
+    public Color getColor_DP_C_to_T() {
+        return color_DP_C_to_T;
+    }
+
+    public Color getColor_DP_G_to_A() {
+        return color_DP_G_to_A;
+    }
+
+    public Color getColor_DP_insertions() {
+        return color_DP_insertions;
+    }
+
+    public Color getColor_DP_deletions() {
+        return color_DP_deletions;
+    }
+
+    public Color getColor_DP_other() {
+        return color_DP_other;
+    }
+
 }
diff --git a/src/main/java/IO/DOMParser.java b/src/main/java/org/damageprofiler/IO/DOMParser.java
similarity index 89%
rename from src/main/java/IO/DOMParser.java
rename to src/main/java/org/damageprofiler/IO/DOMParser.java
index 71dd54b..fc30ae0 100755
--- a/src/main/java/IO/DOMParser.java
+++ b/src/main/java/org/damageprofiler/IO/DOMParser.java
@@ -1,4 +1,4 @@
-package IO;
+package org.damageprofiler.IO;
 
 import org.apache.log4j.Logger;
 import org.w3c.dom.Document;
@@ -25,6 +25,13 @@ public DOMParser(Logger LOG){
         this.LOG = LOG;
 
     }
+
+    /**
+     * Parse file from NCBI with species information to filter species name information.
+     *
+     * @param filepathXML
+     * @return
+     */
     public String parse(String filepathXML) {
 
         String species = null;
diff --git a/src/main/java/IO/FastACacher.java b/src/main/java/org/damageprofiler/IO/FastACacher.java
similarity index 71%
rename from src/main/java/IO/FastACacher.java
rename to src/main/java/org/damageprofiler/IO/FastACacher.java
index 99c8929..31dfffe 100755
--- a/src/main/java/IO/FastACacher.java
+++ b/src/main/java/org/damageprofiler/IO/FastACacher.java
@@ -1,10 +1,9 @@
-package IO;
+package org.damageprofiler.IO;
 
 import htsjdk.samtools.reference.*;
 import org.apache.log4j.Logger;
 
 import java.io.File;
-import java.io.FileNotFoundException;
 import java.util.HashMap;
 
 /**
@@ -12,10 +11,11 @@
  */
 public class FastACacher {
     private final Logger LOG;
+    private final ReferenceSequenceFile refSeq;
     private HashMap<String,byte[]> data = new HashMap<>();
 
-    public FastACacher(File f, Logger LOG) throws FileNotFoundException {
-        ReferenceSequenceFile refSeq = ReferenceSequenceFileFactory.getReferenceSequenceFile(f);
+    public FastACacher(File f, Logger LOG) {
+        refSeq = ReferenceSequenceFileFactory.getReferenceSequenceFile(f);
         this.LOG = LOG;
 
 
@@ -24,7 +24,6 @@ public FastACacher(File f, Logger LOG) throws FileNotFoundException {
             if(rs == null){
                 break;
             } else {
-
                 data.put(getKeyName(rs.getName()), rs.getBases());
             }
         }
@@ -34,6 +33,11 @@ public HashMap<String, byte[]> getData() {
         return data;
     }
 
+    public ReferenceSequence getSubSequence(String chr, int start, int end){
+        ReferenceSequence subsequenceAt = refSeq.getSubsequenceAt(chr, start, end);
+        return subsequenceAt;
+    }
+
     public String getKeyName(String reference_name){
         String name=reference_name;
         String[] reference_name_splitted = reference_name.split("ref");
@@ -42,10 +46,7 @@ public String getKeyName(String reference_name){
             name = reference_name_splitted[1].substring(1, reference_name_splitted[1].length()-1);
 
         }
-
         return name;
-
-
     }
 }
 
diff --git a/src/main/java/IO/LogClass.java b/src/main/java/org/damageprofiler/IO/LogClass.java
similarity index 96%
rename from src/main/java/IO/LogClass.java
rename to src/main/java/org/damageprofiler/IO/LogClass.java
index b657234..458dc74 100755
--- a/src/main/java/IO/LogClass.java
+++ b/src/main/java/org/damageprofiler/IO/LogClass.java
@@ -1,4 +1,4 @@
-package IO;
+package org.damageprofiler.IO;
 
 import org.apache.log4j.Logger;
 import org.apache.log4j.PropertyConfigurator;
diff --git a/src/main/java/org/damageprofiler/IO/MetagenomicOutput.java b/src/main/java/org/damageprofiler/IO/MetagenomicOutput.java
new file mode 100644
index 0000000..5043674
--- /dev/null
+++ b/src/main/java/org/damageprofiler/IO/MetagenomicOutput.java
@@ -0,0 +1,98 @@
+package org.damageprofiler.IO;
+
+import com.itextpdf.awt.PdfGraphics2D;
+import com.itextpdf.text.*;
+import com.itextpdf.text.Font;
+import com.itextpdf.text.pdf.PdfContentByte;
+import com.itextpdf.text.pdf.PdfTemplate;
+import com.itextpdf.text.pdf.PdfWriter;
+import org.jfree.chart.JFreeChart;
+
+import java.awt.*;
+import java.awt.geom.Rectangle2D;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.util.HashMap;
+import java.util.List;
+
+public class MetagenomicOutput {
+
+    /**
+     * Writes summary of the metagenomic results. Only a overview of the results is presented for
+     * each species.
+     *
+     * @param output_folder
+     * @param species_output_summary
+     * @param sample_name
+     * @param mapped_reads
+     * @throws FileNotFoundException
+     * @throws DocumentException
+     */
+    public void generate(String output_folder, HashMap<String, List<JFreeChart>> species_output_summary, String sample_name,
+                         HashMap<String, Integer> mapped_reads)
+            throws FileNotFoundException, DocumentException {
+
+        // step 1
+        Document document = new Document(PageSize.A4);
+
+        // step 2
+        PdfWriter writer = PdfWriter.getInstance(document, new FileOutputStream(output_folder + File.separator + sample_name +"_summary.pdf"));
+        // step 3
+        document.open();
+
+        Font fontbold = FontFactory.getFont("Times-Roman", 24, Font.BOLD);
+
+        Paragraph para = new Paragraph();
+        Chunk c_title = new Chunk("\n\n\n\nSummary of damage patterns\n\n" + sample_name, fontbold);
+
+        Phrase p1 = new Phrase(c_title);
+        para.add(p1);
+        para.setAlignment(1);
+
+        document.add(para);
+        document.addTitle("Summary_damage_patterns");
+
+
+
+        document.newPage();
+
+        PdfContentByte cb = writer.getDirectContent();
+        float height = PageSize.A4.getHeight() * (float)0.25;
+        float width = PageSize.A4.getWidth() / 2;
+
+        for(String species : species_output_summary.keySet()){
+            Paragraph para2 = new Paragraph();
+            Phrase p2 = new Phrase("Results for species:\n\n" + species, FontFactory.getFont("Times-Roman", 22));
+            Phrase p3 = new Phrase("\n\nNumber of mapped reads:" + mapped_reads.get(species), FontFactory.getFont("Times-Roman", 18));
+            para2.add(p2);
+            para2.add(p3);
+            document.add(para2);
+
+            double xpos = 0;
+            for(int i = 0; i < species_output_summary.get(species).size(); i++){
+                JFreeChart chart = species_output_summary.get(species).get(i);
+                PdfTemplate plot = cb.createTemplate(width, height);
+                Graphics2D g2d = new PdfGraphics2D(plot, width, height);
+                Rectangle2D r2d = new Rectangle2D.Double(0, 0, width, height);
+                chart.draw(g2d, r2d);
+                g2d.dispose();
+
+
+                if(i==0){
+                    cb.addTemplate(plot, xpos, 500);
+                } else if(i==1){
+                    cb.addTemplate(plot, width, 500);
+                } else if(i==2){
+                    cb.addTemplate(plot, xpos, 500-height);
+                } else if(i==3){
+                    cb.addTemplate(plot, width, 500-height);
+                }
+
+            }
+            document.newPage();
+        }
+        // step 5
+        document.close();
+    }
+}
diff --git a/src/main/java/IO/OutputGenerator.java b/src/main/java/org/damageprofiler/IO/OutputGenerator.java
similarity index 81%
rename from src/main/java/IO/OutputGenerator.java
rename to src/main/java/org/damageprofiler/IO/OutputGenerator.java
index 32e15eb..3a9ae86 100755
--- a/src/main/java/IO/OutputGenerator.java
+++ b/src/main/java/org/damageprofiler/IO/OutputGenerator.java
@@ -1,7 +1,9 @@
-package IO;
+package org.damageprofiler.IO;
 
-import calculations.DamageProfiler;
-import calculations.Frequencies;
+import org.damageprofiler.IO.PDFoutput.Histogram;
+import org.damageprofiler.IO.PDFoutput.LinePlot;
+import org.damageprofiler.calculations.DamageProfiler;
+import org.damageprofiler.calculations.Frequencies;
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
 import com.itextpdf.awt.PdfGraphics2D;
@@ -10,14 +12,19 @@
 import com.itextpdf.text.pdf.PdfContentByte;
 import com.itextpdf.text.pdf.PdfTemplate;
 import com.itextpdf.text.pdf.PdfWriter;
+import javafx.scene.paint.Color;
 import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
 import org.apache.log4j.Logger;
 import org.jfree.chart.JFreeChart;
+import org.jfree.chart.title.LegendTitle;
+import org.jfree.chart.ui.RectangleEdge;
 import org.jfree.data.statistics.HistogramDataset;
 import org.jfree.data.xy.XYDataset;
-
+import org.jfree.graphics2d.svg.SVGGraphics2D;
+import org.jfree.graphics2d.svg.SVGUtils;
 
 import java.awt.*;
+import java.awt.Rectangle;
 import java.io.*;
 import java.math.BigDecimal;
 import java.text.DecimalFormat;
@@ -37,25 +44,44 @@ public class OutputGenerator {
     private final double x_axis_max_id_histo;
     private final double x_axis_min_length_histo;
     private final double x_axis_max_length_histo;
+    private final boolean ssLibProtocolUsed;
     private int numberOfUsedReads;
     private final double height;
     private final Logger LOG;
     private String outpath;
     private Frequencies frequencies;
     private DamageProfiler damageProfiler;
-    private int max_length;
-    private int min_length;
-    private String specie;
+    private int numberOfRecords;
+    private double max_length;
+    private double min_length;
+    private String species;
     private int threshold;
     private int length;
     private String input;
     private HashMap<String,Object> json_map = new HashMap<>();
+    private double[] three_C_to_T_reverse;
+    private double[] three_G_to_A_reverse;
+    private JFreeChart chart_DP_5prime;
+    private JFreeChart chart_DP_3prime;
+    private JFreeChart length_chart_all;
+    private JFreeChart length_chart_separated;
+    private JFreeChart editDist_chart;
+
+    private Color color_DP_C_to_T;
+    private Color color_DP_G_to_A;
+    private Color color_DP_insertions;
+    private Color color_DP_deletions;
+    private Color color_DP_other;
+
 
 
 
-    public OutputGenerator(String outputFolder, DamageProfiler damageProfiler, String specie, int threshold,
+    public OutputGenerator(String outputFolder, DamageProfiler damageProfiler, String species, int threshold,
                            int length, double height, double x_axis_min_id_histo, double x_axis_max_id_histo,
-                           double x_axis_min_length_histo, double x_axis_max_length_histo, String input, Logger LOG) {
+                           double x_axis_min_length_histo, double x_axis_max_length_histo, String input, Logger LOG,
+                           int numberOfRecords, boolean ssLibProtocolUsed, Color color_DP_C_to_T,
+                           Color color_DP_deletions, Color color_DP_G_to_A, Color color_DP_insertions,
+                           Color color_DP_other) {
 
         this.outpath = outputFolder;
         this.frequencies = damageProfiler.getFrequencies();
@@ -70,10 +96,18 @@ public OutputGenerator(String outputFolder, DamageProfiler damageProfiler, Strin
         this.x_axis_max_length_histo = x_axis_max_length_histo;
         this.input = input;
         this.LOG = LOG;
+        this.numberOfRecords = numberOfRecords;
+        this.ssLibProtocolUsed = ssLibProtocolUsed;
+
+        this.color_DP_C_to_T = color_DP_C_to_T;
+        this.color_DP_deletions = color_DP_deletions;
+        this.color_DP_G_to_A = color_DP_G_to_A;
+        this.color_DP_other = color_DP_other;
+        this.color_DP_insertions = color_DP_insertions;
 
         // set tax id if specified by user
-        if(specie != null && !specie.equals("")){
-            this.specie = specie;
+        if(species != null && !species.equals("")){
+            this.species = species;
         }
     }
 
@@ -117,10 +151,10 @@ public void writeJSON(String version) throws IOException {
     public void writeLengthDistribution() throws IOException{
 
         BufferedWriter lgdist = new BufferedWriter(new FileWriter(this.outpath + "/lgdistribution.txt"));
-        HashMap<Integer, Integer> map_forward = damageProfiler.getLength_distribution_map_forward();
-        HashMap<Integer, Integer> map_reverse = damageProfiler.getLength_distribution_map_reverse();
+        HashMap<Double, Integer> map_forward = damageProfiler.getLength_distribution_map_forward();
+        HashMap<Double, Integer> map_reverse = damageProfiler.getLength_distribution_map_reverse();
 
-        lgdist.write("# table produced by calculations.DamageProfiler\n");
+        lgdist.write("# table produced by org.damageprofiler.calculations.DamageProfiler\n");
         lgdist.write("# using mapped file " + input + "\n");
         lgdist.write("# Sample ID: " + input.split("/")[input.split("/").length-1] + "\n");
         lgdist.write("# Std: strand of reads\n");
@@ -128,17 +162,17 @@ public void writeLengthDistribution() throws IOException{
 
         // fill file
 
-        List<Integer> key_list = new ArrayList<>();
+        List<Double> key_list = new ArrayList<>();
         key_list.addAll(map_forward.keySet());
         Collections.sort(key_list);
 
-        HashMap<Integer,Integer> yaml_dump_fw = new HashMap<>();
+        HashMap<Double,Integer> yaml_dump_fw = new HashMap<>();
 
         if(key_list.size()>0){
             min_length = key_list.get(0);
             max_length = key_list.get(key_list.size()-1);
 
-            for(int key : key_list){
+            for(double key : key_list){
                 lgdist.write("+\t" + key + "\t" + map_forward.get(key) + "\n");
                 yaml_dump_fw.put(key, map_forward.get(key));
             }
@@ -149,7 +183,7 @@ public void writeLengthDistribution() throws IOException{
         key_list.addAll(map_reverse.keySet());
         Collections.sort(key_list);
 
-        HashMap<Integer,Integer> yaml_dump_rv = new HashMap<>();
+        HashMap<Double,Integer> yaml_dump_rv = new HashMap<>();
 
 
         if(key_list.size()>0){
@@ -160,7 +194,7 @@ public void writeLengthDistribution() throws IOException{
                 max_length = key_list.get(key_list.size()-1);
 
             }
-            for(int key : key_list){
+            for(double key : key_list){
                 lgdist.write("-\t" + key + "\t" + map_reverse.get(key) + "\n");
                 yaml_dump_rv.put(key, map_reverse.get(key));
             }
@@ -176,7 +210,7 @@ public void writeDNAcomp_genome(Frequencies frequencies) throws IOException{
 
         BufferedWriter file_dna_comp = new BufferedWriter(new FileWriter(outpath + File.separator + "DNA_comp_genome.txt"));
 
-        file_dna_comp.write("# table produced by calculations.DamageProfiler\n");
+        file_dna_comp.write("# table produced by org.damageprofiler.calculations.DamageProfiler\n");
         file_dna_comp.write("# using mapped file " + input + "\n");
         file_dna_comp.write("# Sample ID: " + input.split("/")[input.split("/").length-1] + "\n");
         file_dna_comp.write("DNA base frequencies Sample\n");
@@ -224,7 +258,7 @@ public void writeDNAComp(Frequencies frequencies) throws IOException{
 
           */
 
-        freq_file_sample.write("# table produced by calculations.DamageProfiler\n");
+        freq_file_sample.write("# table produced by org.damageprofiler.calculations.DamageProfiler\n");
         freq_file_sample.write("# using mapped file " + input + "\n");
         freq_file_sample.write("# Sample ID: " + input.split("/")[input.split("/").length-1] + "\n");
 
@@ -252,7 +286,6 @@ public void writeDNAComp(Frequencies frequencies) throws IOException{
                     +(int)frequencies.getCountG_reverse_3()[i]+"\t"+(int)frequencies.getCountT_reverse_3()[i]+"\t"
                     +(int)sum+"\n"
             );
-
         }
 
 
@@ -286,7 +319,7 @@ public void writeFrequenciesReference(Frequencies frequencies) throws IOExceptio
         BufferedWriter freq_file_ref = new BufferedWriter(new FileWriter(outpath + File.separator + "misincorporation.txt"));
 
 
-        freq_file_ref.write("# table produced by calculations.DamageProfiler\n");
+        freq_file_ref.write("# table produced by org.damageprofiler.calculations.DamageProfiler\n");
         freq_file_ref.write("# using mapped file " + input + "\n");
         freq_file_ref.write("# Sample ID: " + input.split("/")[input.split("/").length-1] + "\n");
 
@@ -360,6 +393,7 @@ public void writeFrequenciesReference(Frequencies frequencies) throws IOExceptio
         }
 
 
+
         // fill '5p +'
         for(int i = 0; i < this.length; i++){
             double sum = frequencies.getCountA_ref_forward_5()[i]+frequencies.getCountC_ref_forward_5()[i]+
@@ -434,8 +468,8 @@ public void plotLengthHistogram(List<Double> length_all, List<Double> length_for
         Histogram hist_all = new Histogram(LOG);
         hist_all.addData(length_all);
         HistogramDataset dataset_all = hist_all.createDataset(new String[]{"all reads"}, max_length);
-        JFreeChart chart_all = hist_all.createChart(dataset_all, "Read length distribution", "Read length",
-                "Occurrences",  x_axis_min_length_histo, x_axis_max_length_histo);
+        length_chart_all = hist_all.createChart(dataset_all, "", "Read length",
+                "Occurrences",  x_axis_min_length_histo, x_axis_max_length_histo, false);
 
         Histogram hist_separated = new Histogram(LOG);
         if(length_forward.size()>0){
@@ -445,10 +479,15 @@ public void plotLengthHistogram(List<Double> length_all, List<Double> length_for
             hist_separated.addData(length_reverse);
         }
         HistogramDataset dataset_separated = hist_separated.createDataset(new String[]{"+ strand", "- strand"}, max_length);
-        JFreeChart chart_separated = hist_separated.createChart(dataset_separated, "Read length distribution",
-                "Read length", "Occurrences",  x_axis_min_length_histo, x_axis_max_length_histo);
+        length_chart_separated = hist_separated.createChart(dataset_separated, "",
+                "Read length", "Occurrences",  x_axis_min_length_histo, x_axis_max_length_histo, true);
+
+        LegendTitle lt = length_chart_separated.getLegend();
+        lt.setPosition(RectangleEdge.RIGHT);
 
-        createPdf("/Length_plot.pdf", new JFreeChart[]{chart_all, chart_separated}, file);
+        createPdf("/Length_plot.pdf", new JFreeChart[]{length_chart_all, length_chart_separated}, file);
+        createSVG("/Length_plot_combined_data.svg", length_chart_all);
+        createSVG("/Length_plot_forward_reverse_separated.svg", length_chart_separated);
 
 
     }
@@ -462,16 +501,20 @@ public void plotLengthHistogram(List<Double> length_all, List<Double> length_for
      * @throws DocumentException
      * @throws IOException
      */
-    public void plotIdentitiyHistogram(ArrayList distances, String title, String file) throws DocumentException, IOException{
+    public void plotEditDistanceHistogram(List<Double> distances, String title, String file) throws DocumentException, IOException{
         Histogram hist_all = new Histogram(LOG);
         hist_all.addData(distances);
+
         HistogramDataset dataset = hist_all.createDataset(new String[]{title}, 100);
-        JFreeChart chart_all = hist_all.createChart(dataset,  "Read identity distribution", "Identity", "Occurrences",
-                x_axis_min_id_histo, x_axis_max_id_histo);
-        createPdf("/identity_histogram.pdf", new JFreeChart[]{chart_all}, file);
+        editDist_chart = hist_all.createChart(dataset,  "", "Edit distance", "Occurrences",
+                x_axis_min_id_histo, x_axis_max_id_histo, false);
+
+        createPdf("/edit_distance.pdf", new JFreeChart[]{editDist_chart}, file);
+        createSVG("/edit_distance.svg", editDist_chart);
 
     }
 
+
     /**
      * write percentage of misincorporations per read position
      *
@@ -481,28 +524,30 @@ public void plotIdentitiyHistogram(ArrayList distances, String title, String fil
      */
     public void writeDamageFiles(double[] gToA_reverse, double[] cToT) throws IOException{
 
+        BufferedWriter writer3Prime;
+
 
-        BufferedWriter writer3Prime = new BufferedWriter(new FileWriter(this.outpath + "/3pGtoA_freq.txt"));
         BufferedWriter writer5Prime = new BufferedWriter(new FileWriter(this.outpath + "/5pCtoT_freq.txt"));
 
         //Add stuff to json output file
         json_map.put("dmg_5p",getSubArray(cToT, this.threshold));
+
+        // 3p end always included in json file, as it's needed for EAGER2.0 report
         json_map.put("dmg_3p",getSubArray(gToA_reverse,this.threshold));
 
 
-        writer3Prime.write("# table produced by calculations.DamageProfiler\n");
+        writer3Prime = new BufferedWriter(new FileWriter(this.outpath + "/3pGtoA_freq.txt"));
+        writer3Prime.write("# table produced by DamageProfiler\n");
         writer3Prime.write("# using mapped file " + input + "\n");
         writer3Prime.write("# Sample ID: " + input.split("/")[input.split("/").length-1] + "\n");
+        writeDamagePattern("pos\t3pG>A\n", getSubArray(gToA_reverse, this.threshold), writer3Prime);
+        writer3Prime.close();
 
 
-        writer5Prime.write("# table produced by calculations.DamageProfiler\n");
+        writer5Prime.write("# table produced by DamageProfiler\n");
         writer5Prime.write("# using mapped file " + input + "\n");
         writer5Prime.write("# Sample ID: " + input.split("/")[input.split("/").length-1] + "\n");
-
         writeDamagePattern("pos\t5pC>T\n", getSubArray(cToT, this.threshold), writer5Prime);
-        writeDamagePattern("pos\t3pG>A\n", getSubArray(gToA_reverse, this.threshold), writer3Prime);
-
-        writer3Prime.close();
         writer5Prime.close();
 
     }
@@ -523,20 +568,20 @@ private void writeDamagePattern(String title, double[] values, BufferedWriter wr
     }
 
     public void computeSummaryMetrics(){
-        HashMap<Integer,Integer> forwardMap = damageProfiler.getLength_distribution_map_forward(); // key = length, value = occurences
-        HashMap<Integer, Integer>reverseMap = damageProfiler.getLength_distribution_map_reverse();
+        HashMap<Double,Integer> forwardMap = damageProfiler.getLength_distribution_map_forward(); // key = length, value = occurrences
+        HashMap<Double, Integer>reverseMap = damageProfiler.getLength_distribution_map_reverse();
 
         //Create ArrayList<Integer> of read lengths
         DescriptiveStatistics descriptiveStatistics = new DescriptiveStatistics();
 
-        for (int key : forwardMap.keySet()){
+        for (double key : forwardMap.keySet()){
             int occurences = forwardMap.get(key);
             for (int i = 0; i <= occurences; i++) {
                 descriptiveStatistics.addValue(key);
             }
         }
 
-        for (int key : reverseMap.keySet()){
+        for (double key : reverseMap.keySet()){
             int occurences = reverseMap.get(key);
             for (int i = 0; i <= occurences; i++) {
                 descriptiveStatistics.addValue(key);
@@ -564,17 +609,11 @@ public void writeMisincorporations(Frequencies frequencies, int threshold) throw
         Locale.setDefault(Locale.US);
 
         BufferedWriter writer5PrimeAll = new BufferedWriter(new FileWriter(this.outpath + "/5p_freq_misincorporations.txt"));
-        BufferedWriter writer3PrimeAll = new BufferedWriter(new FileWriter(this.outpath + "/3p_freq_misincorporations.txt"));
 
-        writer5PrimeAll.write("# table produced by calculations.DamageProfiler\n");
+        writer5PrimeAll.write("# table produced by org.damageprofiler.calculations.DamageProfiler\n");
         writer5PrimeAll.write("# using mapped file " + input + "\n");
         writer5PrimeAll.write("# Sample ID: " + input.split("/")[input.split("/").length-1] + "\n");
 
-        writer3PrimeAll.write("# table produced by calculations.DamageProfiler\n");
-        writer3PrimeAll.write("# using mapped file " + input + "\n");
-        writer3PrimeAll.write("# Sample ID: " + input.split("/")[input.split("/").length-1] + "\n");
-
-
            /*
 
                         5 prime end
@@ -629,13 +668,18 @@ public void writeMisincorporations(Frequencies frequencies, int threshold) throw
                     String.format("%.6f",deletions_mean5[pos])+ "\n");
 
         }
-
+        writer5PrimeAll.close();
 
         /*
 
                         3 prime end
          */
 
+        BufferedWriter writer3PrimeAll = new BufferedWriter(new FileWriter(this.outpath + "/3p_freq_misincorporations.txt"));
+        writer3PrimeAll.write("# table produced by DamageProfiler\n");
+        writer3PrimeAll.write("# using mapped file " + input + "\n");
+        writer3PrimeAll.write("# Sample ID: " + input.split("/")[input.split("/").length-1] + "\n");
+
 
         double[] three_A_to_C_reverse = getSubArray(frequencies.getCount_A_C_3_norm(),threshold);
         double[] three_A_to_G_reverse = getSubArray(frequencies.getCount_A_G_3_norm(),threshold);
@@ -653,21 +697,6 @@ public void writeMisincorporations(Frequencies frequencies, int threshold) throw
         double[] three_T_to_C_reverse = getSubArray(frequencies.getCount_T_C_3_norm(),threshold);
         double[] three_T_to_G_reverse = getSubArray(frequencies.getCount_T_G_3_norm(),threshold);
 
-//        three_A_to_C_reverse = reverseArray(three_A_to_C_reverse);
-//        three_A_to_G_reverse = reverseArray(three_A_to_G_reverse);
-//        three_A_to_T_reverse = reverseArray(three_A_to_T_reverse);
-//
-//        three_C_to_A_reverse = reverseArray(three_C_to_A_reverse);
-//        three_C_to_G_reverse = reverseArray(three_C_to_G_reverse);
-//        three_C_to_T_reverse = reverseArray(three_C_to_T_reverse);
-//
-//        three_G_to_A_reverse = reverseArray(three_G_to_A_reverse);
-//        three_G_to_C_reverse = reverseArray(three_G_to_C_reverse);
-//        three_G_to_T_reverse = reverseArray(three_G_to_T_reverse);
-//
-//        three_T_to_A_reverse = reverseArray(three_T_to_A_reverse);
-//        three_T_to_C_reverse = reverseArray(three_T_to_C_reverse);
-//        three_T_to_G_reverse = reverseArray(three_T_to_G_reverse);
 
 
         double[] insertions_mean_3 = getMean(frequencies.getCount_0_A_3_norm(),frequencies.getCount_0_C_3_norm(),
@@ -701,12 +730,32 @@ public void writeMisincorporations(Frequencies frequencies, int threshold) throw
         }
 
         writer3PrimeAll.close();
-        writer5PrimeAll.close();
+
+
 
     }
 
 
 
+    public void writeEditDistance(List<Double> editDistances) throws IOException {
+        Collections.sort(editDistances);
+        Set<Double> distances_sorted = new HashSet<Double>(editDistances);
+        HashMap<Double, Integer> edit_occurrences_map = new HashMap<>();
+        for(double dist : distances_sorted){
+            int occurrences = Collections.frequency(editDistances, dist);
+            edit_occurrences_map.put(dist, occurrences);
+
+        }
+
+        BufferedWriter writerEditDistance = new BufferedWriter(new FileWriter(this.outpath + "/editDistance.txt"));
+        writerEditDistance.write("#Edit distances for file:" + input + "\n");
+        writerEditDistance.write("Edit distance\tOccurrences\n");
+
+        for(double dist : edit_occurrences_map.keySet())
+            writerEditDistance.write(dist + "\t" + edit_occurrences_map.get(dist) + "\n");
+
+        writerEditDistance.close();
+    }
 
     /**
      * create damage plot
@@ -724,9 +773,9 @@ public void plotMisincorporations(String file) throws IOException, DocumentExcep
 
         double[] three_C_to_A_reverse = getSubArray(frequencies.getCount_C_A_3_norm(), threshold);
         double[] three_C_to_G_reverse = getSubArray(frequencies.getCount_C_G_3_norm(), threshold);
-        double[] three_C_to_T_reverse = getSubArray(frequencies.getCount_C_T_3_norm(), threshold);
+        three_C_to_T_reverse = getSubArray(frequencies.getCount_C_T_3_norm(), threshold);
 
-        double[] three_G_to_A_reverse = getSubArray(frequencies.getCount_G_A_3_norm(),threshold);
+        three_G_to_A_reverse = getSubArray(frequencies.getCount_G_A_3_norm(),threshold);
         double[] three_G_to_C_reverse = getSubArray(frequencies.getCount_G_C_3_norm(),threshold);
         double[] three_G_to_T_reverse = getSubArray(frequencies.getCount_G_T_3_norm(),threshold);
 
@@ -750,11 +799,45 @@ public void plotMisincorporations(String file) throws IOException, DocumentExcep
         three_T_to_C_reverse = reverseArray(three_T_to_C_reverse);
         three_T_to_G_reverse = reverseArray(three_T_to_G_reverse);
 
-
+        LinePlot damagePlot_three=null;
 
         // create plots
-        LinePlot damagePlot_three = new LinePlot("3' end", threshold, height, LOG);
-        LinePlot damagePlot_five  = new LinePlot("5' end", threshold, height, LOG);
+        damagePlot_three = new LinePlot(threshold, height, LOG, color_DP_C_to_T, color_DP_G_to_A,
+                color_DP_insertions, color_DP_deletions, color_DP_other);
+
+        // three prime end
+        // red
+        damagePlot_three.addData(three_C_to_T_reverse, "3'C>T");
+        // blue
+        damagePlot_three.addData(three_G_to_A_reverse, "3'G>A");
+
+        // purple (insertions)
+        double[] insertions_mean_3 = getMean(frequencies.getCount_0_A_3_norm(),frequencies.getCount_0_C_3_norm(),
+                frequencies.getCount_0_G_3_norm(),frequencies.getCount_0_T_3_norm());
+        damagePlot_three.addData(insertions_mean_3, "insertions");
+
+        // green (deletions)
+        double[] deletions_mean_3 = getMean(frequencies.getCount_A_0_3_norm(), frequencies.getCount_C_0_3_norm() ,
+                frequencies.getCount_G_0_3_norm(), frequencies.getCount_T_0_3_norm());
+        damagePlot_three.addData(deletions_mean_3, "deletions");
+
+
+        // gray
+        damagePlot_three.addData(three_A_to_C_reverse, "others");
+        damagePlot_three.addData(three_A_to_G_reverse, "3'A>G");
+        damagePlot_three.addData(three_A_to_T_reverse, "3'A>T");
+        damagePlot_three.addData(three_C_to_A_reverse, "3'C>A");
+        damagePlot_three.addData(three_C_to_G_reverse, "3'C>G");
+        damagePlot_three.addData(three_G_to_C_reverse, "3'G>C");
+        damagePlot_three.addData(three_G_to_T_reverse, "3'G>T");
+        damagePlot_three.addData(three_T_to_A_reverse, "3'T>A");
+        damagePlot_three.addData(three_T_to_C_reverse, "3'T>C");
+        damagePlot_three.addData(three_T_to_G_reverse, "3'T>G");
+
+
+
+        LinePlot damagePlot_five  = new LinePlot(threshold, height, LOG, color_DP_C_to_T,
+                color_DP_G_to_A, color_DP_insertions, color_DP_deletions, color_DP_other);
 
           /*
                 add data to plots
@@ -799,48 +882,28 @@ public void plotMisincorporations(String file) throws IOException, DocumentExcep
         damagePlot_five.addData(frequencies.getCount_T_C_5_norm(), "5'T>C" );
         damagePlot_five.addData(frequencies.getCount_T_G_5_norm(), "5'T>G" );
 
-        // three prime end
-        // red
-        damagePlot_three.addData(three_C_to_T_reverse, "3'C>T");
-        // blue
-        damagePlot_three.addData(three_G_to_A_reverse, "3'G>A");
-
-        // purple (insertions)
-        double[] insertions_mean_3 = getMean(frequencies.getCount_0_A_3_norm(),frequencies.getCount_0_C_3_norm(),
-                frequencies.getCount_0_G_3_norm(),frequencies.getCount_0_T_3_norm());
-        damagePlot_three.addData(insertions_mean_3, "insertions");
-
-        // green (deletions)
-        double[] deletions_mean_3 = getMean(frequencies.getCount_A_0_3_norm(), frequencies.getCount_C_0_3_norm() ,
-                frequencies.getCount_G_0_3_norm(), frequencies.getCount_T_0_3_norm());
-        damagePlot_three.addData(deletions_mean_3, "deletions");
-
-
-        // gray
-        damagePlot_three.addData(three_A_to_C_reverse, "others");
-        damagePlot_three.addData(three_A_to_G_reverse, "3'A>G");
-        damagePlot_three.addData(three_A_to_T_reverse, "3'A>T");
-        damagePlot_three.addData(three_C_to_A_reverse, "3'C>A");
-        damagePlot_three.addData(three_C_to_G_reverse, "3'C>G");
-        damagePlot_three.addData(three_G_to_C_reverse, "3'G>C");
-        damagePlot_three.addData(three_G_to_T_reverse, "3'G>T");
-        damagePlot_three.addData(three_T_to_A_reverse, "3'T>A");
-        damagePlot_three.addData(three_T_to_C_reverse, "3'T>C");
-        damagePlot_three.addData(three_T_to_G_reverse, "3'T>G");
-
         // create Dataset
-        XYDataset dataset_three = damagePlot_three.createDataset();
         XYDataset dataset_five = damagePlot_five.createDataset();
 
+        double ymax;
+
         // set equal y axis range
-        double ymax = Math.max(damagePlot_five.getY_max(), damagePlot_three.getY_max());
+        ymax = Math.max(damagePlot_five.getY_max(), damagePlot_three.getY_max());
+
 
+        JFreeChart[] charts;
         // create damage plot five prime
-        JFreeChart chart = damagePlot_five.createChart(dataset_five, ymax, threshold);
+        chart_DP_5prime = damagePlot_five.createChart("5' end", dataset_five, ymax, threshold, ssLibProtocolUsed);
+        XYDataset dataset_three = damagePlot_three.createDataset();
         // create damage plot three prime
-        JFreeChart chart1 = damagePlot_three.createChart(dataset_three, ymax, threshold);
+        chart_DP_3prime = damagePlot_three.createChart("3' end", dataset_three, ymax, threshold, ssLibProtocolUsed);
+        charts = new JFreeChart[]{chart_DP_5prime, chart_DP_3prime};
+        createSVG("/DamagePlot_three_prime.svg", chart_DP_3prime);
+
+
+        createPdf("/DamagePlot.pdf", charts, file);
+        createSVG("/DamagePlot_five_prime.svg", chart_DP_5prime);
 
-        createPdf("/DamagePlot.pdf", new JFreeChart[]{chart, chart1}, file);
     }
 
 
@@ -900,6 +963,24 @@ private double[] getSubArray(double[] array, int n){
     }
 
 
+    /**
+     * Save images sc svg. This is only possible when using JFreeChart library.
+     * @param filename
+     * @param chart
+     * @throws IOException
+     */
+    public void createSVG(String filename, JFreeChart chart) throws IOException {
+
+        int height = (int)(PageSize.A4.getWidth() * (float)0.8);
+        int width = (int)(PageSize.A4.getHeight() / 2);
+
+        SVGGraphics2D g2 = new SVGGraphics2D(width, height);
+        Rectangle r = new Rectangle(0, 0, width, height);
+        chart.draw(g2, r);
+        File f = new File(outpath + "/" + filename);
+        SVGUtils.writeToSVG(f, g2.getSVGElement());
+
+    }
     /**
      * Creates a PDF document.
      *
@@ -918,15 +999,22 @@ public void createPdf(String filename, JFreeChart[] charts, String file) throws
         document.open();
 
         // compute percentage of used reads
-        double ratio_used_reads = damageProfiler.getNumberOfUsedReads() / (double) damageProfiler.getNumberOfAllReads();
+        double ratio_used_reads = damageProfiler.getNumberOfUsedReads() / (double)numberOfRecords;
 
         // draw text
         String[] splitted = file.split("/");
         String title = splitted[splitted.length-1];
         NumberFormat nf = NumberFormat.getNumberInstance(Locale.ENGLISH);
         DecimalFormat df = (DecimalFormat)nf;
-        String read_per = Chunk.NEWLINE + "Number of used reads: " + df.format(damageProfiler.getNumberOfUsedReads()) + " (" +
-                (double)(Math.round(ratio_used_reads*10000))/100 + "% of all input reads) | Specie: " + this.specie;
+
+        String read_per;
+        if(this.species == null){
+            read_per = Chunk.NEWLINE + "Number of used reads: " + df.format(damageProfiler.getNumberOfUsedReads()) + " (" +
+                    (double)(Math.round(ratio_used_reads*10000))/100 + "% of all input reads)";
+        } else{
+            read_per = Chunk.NEWLINE + "Number of used reads: " + df.format(damageProfiler.getNumberOfUsedReads()) + " (" +
+                    (double)(Math.round(ratio_used_reads*10000))/100 + "% of all input reads) | Species: " + this.species;
+        }
 
         Font fontbold = FontFactory.getFont("Times-Roman", 18, Font.BOLD);
         Font font = FontFactory.getFont("Times-Roman", 14);
@@ -963,4 +1051,35 @@ public void createPdf(String filename, JFreeChart[] charts, String file) throws
     }
 
 
+    /*
+            Getter
+     */
+    public JFreeChart[] getDP_chart() {
+        if(chart_DP_3prime!=null){
+            return new JFreeChart[]{chart_DP_5prime, chart_DP_3prime};
+        } else {
+            return new JFreeChart[]{chart_DP_5prime};
+        }
+    }
+
+    public JFreeChart[] getLengthDistPlots() {
+        return new JFreeChart[]{length_chart_all, length_chart_separated};
+
+    }
+    public JFreeChart getEditDist_chart() {
+        return editDist_chart;
+    }
+
+    public JFreeChart getChart_DP_5prime() {
+        return chart_DP_5prime;
+    }
+
+    public JFreeChart getChart_DP_3prime() {
+        return chart_DP_3prime;
+    }
+
+    public JFreeChart getLength_chart_all() {
+        return length_chart_all;
+    }
+
 }
diff --git a/src/main/java/IO/Histogram.java b/src/main/java/org/damageprofiler/IO/PDFoutput/Histogram.java
similarity index 83%
rename from src/main/java/IO/Histogram.java
rename to src/main/java/org/damageprofiler/IO/PDFoutput/Histogram.java
index c36cf7c..7e4079e 100755
--- a/src/main/java/IO/Histogram.java
+++ b/src/main/java/org/damageprofiler/IO/PDFoutput/Histogram.java
@@ -1,4 +1,4 @@
-package IO;
+package org.damageprofiler.IO.PDFoutput;
 
 import org.apache.log4j.Logger;
 import org.jfree.chart.ChartFactory;
@@ -6,8 +6,8 @@
 import org.jfree.chart.axis.ValueAxis;
 import org.jfree.chart.plot.PlotOrientation;
 import org.jfree.chart.plot.XYPlot;
-import org.jfree.chart.renderer.xy.StandardXYBarPainter;
 import org.jfree.chart.renderer.xy.XYBarRenderer;
+import org.jfree.chart.renderer.xy.XYItemRenderer;
 import org.jfree.data.statistics.HistogramDataset;
 import org.jfree.data.statistics.HistogramType;
 
@@ -36,17 +36,16 @@ public void addData(List<Double> data){
         for(int i = 0; i < data.size(); i++){
             d[i] = data.get(i);
         }
-
         data_collected.add(d);
     }
 
 
-    public HistogramDataset createDataset(String[] title, int max){
+    public HistogramDataset createDataset(String[] title, double max){
 
         HistogramDataset dataset = new HistogramDataset();
         dataset.setType(HistogramType.FREQUENCY);
 
-        int bin = max;
+        int bin = (int) max;
 
         for(int i = 0; i < data_collected.size(); i++){
             dataset.addSeries(title[i], data_collected.get(i), bin);
@@ -58,26 +57,26 @@ public HistogramDataset createDataset(String[] title, int max){
 
 
     public JFreeChart createChart(HistogramDataset dataset, String title, String xlab, String ylab,
-                                  double xmin, double xmax){
+                                  double xmin, double xmax, boolean legend){
 
         JFreeChart chart = ChartFactory.createHistogram(
-                title,//"Histogram read length",
+                title,//"Histogram edit distance",
                 xlab, //"Read length",
                 ylab, // "Occurrences",
                 dataset,
                 PlotOrientation.VERTICAL,
-                true,
+                legend,
                 false,
                 false
         );
 
-        chart.setBackgroundPaint(new Color(230,230,230));
         XYPlot xyplot = (XYPlot)chart.getPlot();
         xyplot.setForegroundAlpha(0.7F);
         xyplot.setBackgroundPaint(Color.WHITE);
         xyplot.setDomainGridlinePaint(new Color(150,150,150));
         xyplot.setRangeGridlinePaint(new Color(150,150,150));
 
+
         if(xmin > -1){
             ValueAxis axis = xyplot.getDomainAxis();
             axis.setLowerBound(xmin);
@@ -90,8 +89,6 @@ public JFreeChart createChart(HistogramDataset dataset, String title, String xla
 
         XYBarRenderer xybarrenderer = (XYBarRenderer)xyplot.getRenderer();
         xybarrenderer.setShadowVisible(false);
-        xybarrenderer.setBarPainter(new StandardXYBarPainter());
-        xybarrenderer.setMargin(0.2);
 
         return chart;
 
diff --git a/src/main/java/IO/LinePlot.java b/src/main/java/org/damageprofiler/IO/PDFoutput/LinePlot.java
similarity index 66%
rename from src/main/java/IO/LinePlot.java
rename to src/main/java/org/damageprofiler/IO/PDFoutput/LinePlot.java
index 89caf7f..5ac4db7 100755
--- a/src/main/java/IO/LinePlot.java
+++ b/src/main/java/org/damageprofiler/IO/PDFoutput/LinePlot.java
@@ -1,4 +1,4 @@
-package IO;
+package org.damageprofiler.IO.PDFoutput;
 
 import org.apache.log4j.Logger;
 import org.jfree.chart.ChartFactory;
@@ -27,17 +27,44 @@ public class LinePlot {
     private double y_max=0.0;
     private double y_min=0.0;
     private ArrayList<XYSeries> all_data;
-    private String title;
     private int threshold;
 
+    private Color awtColor_DP_C_to_T;
+    private Color awtColor_DP_G_to_A;
+    private Color awtColor_DP_insertions;
+    private Color awtColor_DP_deletions;
+    private Color awtColor_DP_other;
 
-    public LinePlot(String title, int threshold, double height, Logger LOG) {
+
+    public LinePlot(int threshold, double height, Logger LOG, javafx.scene.paint.Color color_DP_C_to_T,
+                    javafx.scene.paint.Color color_DP_G_to_A, javafx.scene.paint.Color color_DP_insertions,
+                    javafx.scene.paint.Color color_DP_deletions, javafx.scene.paint.Color color_DP_other) {
         this.LOG = LOG;
         all_data = new ArrayList<>();
-        this.title = title;
         this.threshold = threshold;
         this.height = height;
 
+        awtColor_DP_C_to_T = new java.awt.Color((float) color_DP_C_to_T.getRed(),
+                (float) color_DP_C_to_T.getGreen(),
+                (float) color_DP_C_to_T.getBlue(),
+                (float) color_DP_C_to_T.getOpacity());
+        awtColor_DP_G_to_A = new java.awt.Color((float) color_DP_G_to_A.getRed(),
+                (float) color_DP_G_to_A.getGreen(),
+                (float) color_DP_G_to_A.getBlue(),
+                (float) color_DP_G_to_A.getOpacity());
+        awtColor_DP_insertions = new java.awt.Color((float) color_DP_insertions.getRed(),
+                (float) color_DP_insertions.getGreen(),
+                (float) color_DP_insertions.getBlue(),
+                (float) color_DP_insertions.getOpacity());
+        awtColor_DP_deletions = new java.awt.Color((float) color_DP_deletions.getRed(),
+                (float) color_DP_deletions.getGreen(),
+                (float) color_DP_deletions.getBlue(),
+                (float) color_DP_deletions.getOpacity());
+        awtColor_DP_other = new java.awt.Color((float) color_DP_other.getRed(),
+                (float) color_DP_other.getGreen(),
+                (float) color_DP_other.getBlue(),
+                (float) color_DP_other.getOpacity());
+
     }
 
 
@@ -51,7 +78,7 @@ public void addData(double[] data, String name){
 
         final XYSeries series = new XYSeries(name);
         for(int i = 0; i < threshold; i++){
-            series.add((double)i, data[i]);
+            series.add(i, data[i]);
         }
         all_data.add(series);
 
@@ -71,7 +98,6 @@ public XYDataset createDataset() {
         for(XYSeries series : all_data){
             dataset.addSeries(series);
             if(series.getMaxY() > y_max){y_max=series.getMaxY();}
-            //if(series.getMinY() < y_min){y_min=series.getMinY();}
         }
 
         y_min = 0.0;
@@ -88,9 +114,10 @@ public XYDataset createDataset() {
      * Creates a chart.
      *
      * @param dataset  the data for the chart.
+     * @param ssLibProtocolUsed
      * @return a chart.
      */
-    public JFreeChart createChart(final XYDataset dataset, double yMax, int threshold) {
+    public JFreeChart createChart(String title, final XYDataset dataset, double yMax, int threshold, boolean ssLibProtocolUsed) {
 
         // create the chart...
         final JFreeChart chart = ChartFactory.createXYLineChart(
@@ -127,26 +154,27 @@ public JFreeChart createChart(final XYDataset dataset, double yMax, int threshol
         legendItemsNew.add(legendItemsOld.get(3));
         legendItemsNew.add(legendItemsOld.get(4));
 
-        legendItemsNew.get(0).setLinePaint(Color.RED);
-        legendItemsNew.get(1).setLinePaint(Color.BLUE);
-        legendItemsNew.get(2).setLinePaint(new Color(255, 0, 255));
-        legendItemsNew.get(3).setLinePaint(Color.GREEN);
-        legendItemsNew.get(4).setLinePaint(Color.GRAY);
+        legendItemsNew.get(0).setLinePaint(this.awtColor_DP_C_to_T);
+        legendItemsNew.get(1).setLinePaint(this.awtColor_DP_G_to_A);
+        legendItemsNew.get(2).setLinePaint(this.awtColor_DP_insertions);
+        legendItemsNew.get(3).setLinePaint(this.awtColor_DP_deletions);
+        legendItemsNew.get(4).setLinePaint(this.awtColor_DP_other);
 
         renderer.setSeriesStroke(0, new BasicStroke(3.0f));
-        renderer.setSeriesStroke(1, new BasicStroke(3.0f));
+        if(!ssLibProtocolUsed)
+            renderer.setSeriesStroke(1, new BasicStroke(3.0f));
         renderer.setAutoPopulateSeriesStroke(false);
 
         plot.setFixedLegendItems(legendItemsNew);
 
         // set colour of line
-        renderer.setSeriesPaint(0, Color.RED);
-        renderer.setSeriesPaint(1, Color.BLUE);
-        renderer.setSeriesPaint(2, new Color(255, 0, 255));
-        renderer.setSeriesPaint(3, Color.GREEN);
-        renderer.setSeriesPaint(4, Color.GRAY);
+        renderer.setSeriesPaint(0, this.awtColor_DP_C_to_T);
+        renderer.setSeriesPaint(1, this.awtColor_DP_G_to_A);
+        renderer.setSeriesPaint(2, this.awtColor_DP_insertions);
+        renderer.setSeriesPaint(3, this.awtColor_DP_deletions);
+        renderer.setSeriesPaint(4, this.awtColor_DP_other);
         for(int i=5; i < all_data.size(); i++){
-            renderer.setSeriesPaint(i, Color.GRAY);
+            renderer.setSeriesPaint(i, this.awtColor_DP_other);
         }
 
         plot.setRenderer(renderer);
@@ -172,13 +200,13 @@ public JFreeChart createChart(final XYDataset dataset, double yMax, int threshol
         }
 
 
-        switch (this.title){
+        switch (title){
             case ("3' end"):
 
                 String[] axis_three_prime =  new String[threshold];
                 int position_three_prime=0;
                 for(int i=threshold; i > 0; i--){
-                    axis_three_prime[position_three_prime] = "-" + String.valueOf(i);
+                    axis_three_prime[position_three_prime] = "-" + i;
                     position_three_prime++;
                 }
 
diff --git a/src/main/java/org/damageprofiler/IO/UserOptionsParser.java b/src/main/java/org/damageprofiler/IO/UserOptionsParser.java
new file mode 100755
index 0000000..05a412a
--- /dev/null
+++ b/src/main/java/org/damageprofiler/IO/UserOptionsParser.java
@@ -0,0 +1,224 @@
+package org.damageprofiler.IO;
+
+import org.apache.commons.cli.*;
+
+
+/**
+ * Created by neukamm on 01.08.16.
+ */
+public class UserOptionsParser {
+
+    private static final String CLASS_NAME = "User option parser";
+    private final String version;
+    private String[] args;
+    private Communicator communicator;
+
+
+    public UserOptionsParser(String[] args, Communicator c, String version){
+        this.args = args;
+        this.communicator = c;
+        this.version = version;
+        parse();
+    }
+
+    private void parse() {
+
+        // create command line parameters
+        Options helpOptions = new Options();
+        helpOptions.addOption("h", "help", false, "show this help page");
+
+        Options options = new Options();
+
+        options.addOption("h", false, "Shows this help page.");
+
+        options.addOption(new Option("version", false,
+                "Shows the version of DamageProfiler."));
+
+        options.addOption(Option.builder("i")
+                .argName("INPUT")
+                .desc("The input sam/bam/cram file.")
+                .hasArg()
+                .build());
+
+        options.addOption(Option.builder("r")
+                .argName("REFERENCE")
+                .desc("The reference file (fasta format).")
+                .hasArg()
+                .build());
+
+        options.addOption(Option.builder("o")
+                .argName("OUTPUT")
+                .desc("The output folder.")
+                .hasArg()
+                .build());
+
+        options.addOption(Option.builder("t")
+                .argName("THRESHOLD")
+                .desc("DamagePlot: Number of bases which are considered for plotting nucleotide misincorporations. Default: 25")
+                .hasArg()
+                .build());
+
+        options.addOption(Option.builder("s")
+                .argName("SPECIES")
+                .desc("Reference sequence name (Reference NAME flag of SAM record). For more details see Documentation.")
+                .hasArg()
+                .build());
+
+        options.addOption(Option.builder("sf")
+                .argName("SPECIES LIST")
+                .desc("List with species for which damage profile has to be calculated. For more details see Documentation.")
+                .hasArg()
+                .build());
+
+        options.addOption(Option.builder("l")
+                .argName("LENGTH")
+                .desc("Number of bases which are considered for frequency computations. Default: 100.")
+                .hasArg()
+                .build());
+
+
+        /*
+                plotting options
+         */
+
+        options.addOption(Option.builder("title")
+                .argName("TITLE")
+                .desc("Title used for all plots. Default: input filename.")
+                .hasArg()
+                .build());
+
+        // damage plot
+
+        options.addOption(Option.builder("yaxis_dp_max")
+                .argName("MAX_VALUE")
+                .desc("DamagePlot: Maximal y-axis value.")
+                .hasArg()
+                .build());
+
+        options.addOption(Option.builder("color_c_t")
+                .argName("COLOR_C_T")
+                .desc("DamagePlot: Color for C to T misincoporation frequency.")
+                .hasArg()
+                .build());
+
+        options.addOption(Option.builder("color_g_a")
+                .argName("COLOR_G_A")
+                .desc("DamagePlot: Color for G to A misincoporation frequency.")
+                .hasArg()
+                .build());
+
+        options.addOption(Option.builder("color_instertions")
+                .argName("COLOR_C_T")
+                .desc("DamagePlot: Color for base insertions.")
+                .hasArg()
+                .build());
+
+        options.addOption(Option.builder("color_deletions")
+                .argName("COLOR_DELETIONS")
+                .desc("DamagePlot: Color for base deletions.")
+                .hasArg()
+                .build());
+
+        options.addOption(Option.builder("color_other")
+                .argName("COLOR_OTHER")
+                .desc("DamagePlot: Color for other bases different to reference.")
+                .hasArg()
+                .build());
+
+
+        // others
+
+        options.addOption(Option.builder("only_merged")
+                .desc("Use only mapped and merged (in case of paired-end sequencing) reads to calculate damage plot " +
+                        "instead of using all mapped reads. The SAM/BAM entry must start with 'M_', otherwise " +
+                        "it will be skipped. Default: false ")
+                .build());
+
+        options.addOption(Option.builder("sslib")
+                .desc("Single-stranded library protocol was used. Default: false")
+                .build());
+
+        String header = "\nDetailed description:\n\n";
+
+        HelpFormatter formatter = new HelpFormatter();
+        formatter.setOptionComparator(null);
+        formatter.setWidth(130);
+        CommandLineParser parser = new BasicParser();
+
+
+// ---------------------------------------------------------------------------------------
+
+
+        try {
+
+            CommandLine cmd = parser.parse(options, args);
+
+            if (cmd.hasOption('h')) {
+                formatter.printHelp("DamageProfiler", header, options, null, true);
+                System.exit(0);
+            }
+
+            if(cmd.hasOption("version")) {
+                System.out.print("DamageProfiler v" + this.version + "\n");
+                System.exit(0);
+            }
+
+            // input files
+
+            if (cmd.hasOption('i')) {
+                communicator.setInput(cmd.getOptionValue('i'));
+            }
+            if (cmd.hasOption('r')) {
+                communicator.setReference(cmd.getOptionValue('r'));
+            }
+            if (cmd.hasOption('o')) {
+                communicator.setOutfolder(cmd.getOptionValue('o'));
+            }
+
+            // damage calculation
+
+            if (cmd.hasOption('s')) {
+                communicator.setSpecies_ref_identifier(cmd.getOptionValue('s'));
+            }
+            if (cmd.hasOption("sf")) {
+                communicator.setSpecieslist_filepath(cmd.getOptionValue("sf"));
+            }
+            if (cmd.hasOption('l')) {
+                communicator.setLength(Integer.parseInt(cmd.getOptionValue('l')));
+            }
+            if(cmd.hasOption("all_mapped_and_merged_reads")) {
+                communicator.setUse_merged_and_mapped_reads(true);
+            }
+
+            if(cmd.hasOption("use_all_reads")) {
+                communicator.setUse_all_reads(false);
+            }
+
+            if(cmd.hasOption("sslib")) {
+                communicator.setSsLibsProtocolUsed(true);
+            }
+
+            // Plotting
+
+            if(cmd.hasOption("title")) {
+                communicator.setTitle_plots(cmd.getOptionValue("title"));
+            }
+
+            if(cmd.hasOption("yaxis_dp_max")) {
+                communicator.setyAxis_damageplot(Double.parseDouble(cmd.getOptionValue("yaxis_dp_max")));
+            }
+
+
+            if (cmd.hasOption('t')) {
+                communicator.setThreshold(Integer.parseInt(cmd.getOptionValue('t')));
+            }
+
+
+        } catch (ParseException e) {
+            formatter.printHelp(CLASS_NAME, options);
+            System.err.println(e.getMessage());
+            System.exit(1);
+        }
+
+    }
+}
diff --git a/src/main/java/calculations/DamageProfiler.java b/src/main/java/org/damageprofiler/calculations/DamageProfiler.java
similarity index 56%
rename from src/main/java/calculations/DamageProfiler.java
rename to src/main/java/org/damageprofiler/calculations/DamageProfiler.java
index 3312e3a..15ab029 100755
--- a/src/main/java/calculations/DamageProfiler.java
+++ b/src/main/java/org/damageprofiler/calculations/DamageProfiler.java
@@ -1,15 +1,12 @@
-package calculations;
+package org.damageprofiler.calculations;
 
 
-import IO.FastACacher;
+import org.damageprofiler.IO.FastACacher;
 import htsjdk.samtools.*;
-import htsjdk.samtools.reference.IndexedFastaSequenceFile;
 import htsjdk.samtools.util.SequenceUtil;
 import org.apache.log4j.Logger;
 
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.IOException;
+import java.io.*;
 import java.util.*;
 
 
@@ -18,29 +15,30 @@
  */
 public class  DamageProfiler {
 
+    private final FastACacher cache;
     private SamReader inputSam=null;
     private Functions useful_functions=null;
-    private String specie=null;
+    private String species =null;
     private Logger LOG=null;
-    private IndexedFastaSequenceFile fastaSequenceFile;
     private int numberOfUsedReads;
-    private int numberOfAllReads;
+    private int numberOfRecords;
     private int threshold;
     private int length;
     private Frequencies frequencies;
     private File reference;
-    private FastACacher cache;
     LengthDistribution lengthDistribution;
     private ArrayList<Double> identity;
-    private SpecieHandler specieHandler;
+    private SpeciesHandler speciesHandler;
+    private List<Double> editDistances;
 
     /**
      * constructor
-     * @param specieHandler
+     * @param speciesHandler
+     * @param cache
      */
-    public DamageProfiler(SpecieHandler specieHandler) {
-        this.specieHandler = specieHandler;
-
+    public DamageProfiler(SpeciesHandler speciesHandler, FastACacher cache) {
+        this.speciesHandler = speciesHandler;
+        this.cache = cache;
     }
 
     /**
@@ -53,18 +51,31 @@ public DamageProfiler(SpecieHandler specieHandler) {
      * @param LOG
      */
     public void init(File input, File reference, int threshold, int length, String specie, Logger LOG){
-        // read bam/sam file
+        // read bam/sam/cram file
         if (!input.exists()){
             System.err.println("SAM/BAM file not found. Please check your file path.\nInput: " +
                     input.getAbsolutePath());
             System.exit(0);
         } else {
             try{
+                if(input.getAbsolutePath().endsWith(".sam") || input.getAbsolutePath().endsWith(".bam") ) {
+
+                    inputSam = SamReaderFactory.make().enable(SamReaderFactory.Option.DONT_MEMORY_MAP_INDEX).
+                            validationStringency(ValidationStringency.SILENT).open(input);
+
+                } else if(input.getAbsolutePath().endsWith(".cram")){
+                    if(!reference.isFile()){
+                        System.err.println("Reference file is needed to reads CRAM files.");
+                        System.exit(1);
+                    } else {
+                        inputSam = SamReaderFactory.make().enable(SamReaderFactory.Option.DONT_MEMORY_MAP_INDEX).
+                                referenceSequence(reference).validationStringency(ValidationStringency.SILENT).open(input);
+
+                    }
+                }
 
-                inputSam = SamReaderFactory.make().enable(SamReaderFactory.Option.DONT_MEMORY_MAP_INDEX).
-                        validationStringency(ValidationStringency.LENIENT).open(input);
                 numberOfUsedReads = 0;
-                numberOfAllReads = 0;
+                numberOfRecords = 0;
                 this.LOG = LOG;
                 this.threshold = threshold;
                 this.length = length;
@@ -73,15 +84,16 @@ public void init(File input, File reference, int threshold, int length, String s
                 this.lengthDistribution = new LengthDistribution(this.LOG);
                 this.lengthDistribution.init();
                 this.identity = new ArrayList();
-                this.specie = specie;
-                useful_functions = new Functions(this.LOG);
+                this.editDistances = new ArrayList();
+                this.species = specie;
+                useful_functions = new Functions();
 
 
             } catch (Exception e){
                 System.err.println("Invalid SAM/BAM file. Please check your file.");
                 LOG.error("Invalid SAM/BAM file. Please check your file.");
-                System.out.println(e.toString());
-                System.exit(0);
+                System.err.println(e.toString());
+                System.exit(-1);
             }
         }
     }
@@ -89,7 +101,7 @@ public void init(File input, File reference, int threshold, int length, String s
     /**
      * get all sam records of input sam/bam file,
      * distinguish between mapped and mapped/merged and normalize values
-     * after all calculations
+     * after all org.damageprofiler.calculations
      *
      *
      * @param use_only_merged_reads
@@ -101,43 +113,34 @@ public void extractSAMRecords(boolean use_only_merged_reads, boolean use_all_rea
         if(use_all_reads && use_only_merged_reads){
             LOG.info("-------------------");
             LOG.info("0 reads processed.\nRunning not possible. 'use_only_merged_reads' and 'use_all_reads' was set to 'true'");
-            System.exit(0);
+            System.exit(1);
 
         } else {
+
             for(SAMRecord record : inputSam) {
-                if (this.specie == null) {
+                numberOfRecords++;
 
-                    numberOfAllReads++;
+                if (this.species == null) {
                     handleRecord(use_only_merged_reads, use_all_reads, record);
-
-                    // print number of processed reads
-                    if (numberOfUsedReads % 100 == 0) {
-                        LOG.info(numberOfUsedReads + " Reads processed.");
-                    }
-
                 } else {
-
-                    if (record.getReferenceName().contains(this.specie)) {
-                        numberOfAllReads++;
+                    if (record.getReferenceName().contains(this.species)) {
                         handleRecord(use_only_merged_reads, use_all_reads, record);
-
-                        // print number of processed reads
-                        if (numberOfUsedReads % 100 == 0) {
-                            LOG.info(numberOfUsedReads + " Reads processed.");
-                        }
                     }
                 }
             }
+
             frequencies.normalizeValues();
 
             LOG.info("-------------------");
             LOG.info("# reads used for damage calculation: " + (numberOfUsedReads ));
         }
-
     }
 
 
+
+
     private void handleRecord(boolean use_only_merged_reads, boolean use_all_reads, SAMRecord record) throws Exception {
+
         if(use_all_reads && !use_only_merged_reads){
             // process all reads
             processRecord(record);
@@ -147,12 +150,13 @@ private void handleRecord(boolean use_only_merged_reads, boolean use_all_reads,
             if (!record.getReadUnmappedFlag() && record.getReadName().startsWith("M_")) {
                 processRecord(record);
             }
-        } else if(!use_only_merged_reads && !use_all_reads)
+        } else if(!use_only_merged_reads && !use_all_reads) {
             // process only mapped reads
             if (!record.getReadUnmappedFlag()) {
                 // get all mapped reads
                 processRecord(record);
             }
+        }
     }
 
 
@@ -168,12 +172,12 @@ private void handleRecord(boolean use_only_merged_reads, boolean use_all_reads,
      * @throws IOException
      */
 
-    private void processRecord(SAMRecord record) throws Exception{
+    private void processRecord(SAMRecord record) {
         numberOfUsedReads++;
 
         /*
             If MD value is set, use it to reconstruct reference
-            Otherwise reconstruct reference it based on the CIGAR string
+            Otherwise reconstruct it based on reference.
 
          */
 
@@ -182,98 +186,76 @@ private void processRecord(SAMRecord record) throws Exception{
 
 
         // check if record has MD tag and no reference file is specified
-        if(record.getStringAttribute(SAMTag.MD.name()) == null && this.reference == null){
+        if(record.getStringAttribute(SAMTag.MD.name()) == null && (this.reference == null || !reference.isFile())){
 
-            LOG.error("SAM/BAM file has no MD tag. Please specify reference file ");
-            System.exit(0);
+            LOG.error("SAM/BAM file has no MD tag. Please specify reference file which is needed for MD tag calculations.");
+            System.exit(1);
 
-        } else if (record.getStringAttribute(SAMTag.MD.name()) == null){
+        } else {
 
-            readReferenceInCache();
-            Aligner aligner = new Aligner(LOG);
-            // SAMRecord has 1-based coordinate system -> closed interval [..,..]
-            // normal Array 0-based coordinate system -> interval half-cloded-half-open [...,...)
-            int start = record.getAlignmentStart() - 1;
-            int stop = record.getAlignmentEnd();
+            // MD tag needs to be calculated --> REF needs to be specified
+            if (record.getStringAttribute(SAMTag.MD.name()) == null){
+                SequenceUtil.calculateMdAndNmTags(record, cache.getData().get(record.getReferenceName()), true, true);
+            }
 
-            // get reference sequence
-            byte[] refSeq = Arrays.copyOfRange(cache.getData().get(cache.getKeyName(record.getReferenceName())), start, stop);
-            String reference = new String(refSeq, "UTF-8");
-            // align record and reference
+            try{
+                byte[] ref_seq = SequenceUtil.makeReferenceFromAlignment(record, false);
+                reference_aligned = new String(ref_seq, "UTF-8");
+                record_aligned = record.getReadString();
+                proceed(record, record_aligned, reference_aligned);
 
-            if (record.getReadLength() != reference.length()) {
-                String[] record_reference = aligner.align(record.getReadString(), reference, record);
-                reference_aligned = record_reference[1];
-                record_aligned = record_reference[0];
+            } catch (Exception e){
 
-            } else {
-                reference_aligned = record.getReadString();
-                record_aligned = record.getReadString();
-            }
+                System.err.println(record.getReadName() + "\nMD and NM value will be re-calculated. Error: \n" + e);
+                if(!reference.isFile()){
+                    System.err.println("No MD tag defined. Please specify reference file which is needed for MD tag org.damageprofiler.calculations.");
+                    System.exit(1);
+                }
 
-        } else if(record.getStringAttribute(SAMTag.MD.name()) != null){
-            // get reference corresponding to the record
-            if(record.getCigar().getReadLength() != 0 && record.getCigar().getReadLength() == record.getReadLength()){
-//                if(record.getCigarString().contains("S")){
-//                    System.out.println("Cigar contains soft clipping");
-//                } else if(record.getCigarString().contains("D")){
-//                    System.out.println("Cigar contains deletion");
-//                } else {
+                try{
+                    SequenceUtil.calculateMdAndNmTags(record, cache.getData().get(record.getReferenceName()), true, true);
                     byte[] ref_seq = SequenceUtil.makeReferenceFromAlignment(record, false);
                     reference_aligned = new String(ref_seq, "UTF-8");
                     record_aligned = record.getReadString();
-               // }
+                    proceed(record, record_aligned, reference_aligned);
+                    System.err.println("Re-calculation was successful!\n");
 
-
-
-            } else {
-                LOG.info("Skipped record (length does not match): " + record.getReadName());
+                } catch (Exception e1){
+                    System.err.println("Re-calculation failed. Record " + record.getReadName() + " will be skipped.\n");
+                }
             }
-
         }
+    }
 
 
+    private void proceed(SAMRecord record, String record_aligned, String reference_aligned) throws Exception {
         // report length distribution
         this.lengthDistribution.fillDistributionTable(record,record_aligned);
-        int hamming = useful_functions.getHammingDistance(record_aligned, reference_aligned);
+
+        // calculate distance between record and reference
+        double hamming = useful_functions.getHammingDistance(record_aligned, reference_aligned);
+
         double id = (double)(record_aligned.length()-hamming) / (double)record_aligned.length();
         this.identity.add(id);
+        this.editDistances.add(hamming);
 
         // calculate frequencies
         frequencies.count(record, record_aligned, reference_aligned);
-        frequencies.calculateMisincorporations(record, record_aligned, reference_aligned);
-
-
-    }
 
-
-    /**
-     * index reference file and put it in cache to get faster
-     * access
-     *
-     * @throws FileNotFoundException
-     */
-
-    private void readReferenceInCache() throws FileNotFoundException{
-        // read reference file as indexed reference
-        fastaSequenceFile = new IndexedFastaSequenceFile(reference);
-        // store reference in cache to get faster access
-        cache = new FastACacher(reference, LOG);
+        // calculate base misincorporations
+        frequencies.calculateMisincorporations(record, record_aligned, reference_aligned);
 
     }
 
-
-
     /*
      * Getter
      */
 
-
     public Frequencies getFrequencies() {
         return frequencies;
     }
-    public HashMap<Integer, Integer> getLength_distribution_map_forward() {return lengthDistribution.getLength_distribution_map_forward(); }
-    public HashMap<Integer, Integer> getLength_distribution_map_reverse() {return lengthDistribution.getLength_distribution_map_reverse(); }
+    public HashMap<Double, Integer> getLength_distribution_map_forward() {return lengthDistribution.getLength_distribution_map_forward(); }
+    public HashMap<Double, Integer> getLength_distribution_map_reverse() {return lengthDistribution.getLength_distribution_map_reverse(); }
     public List<Double> getLength_forward() {
         return lengthDistribution.getLength_forward();
     }
@@ -284,25 +266,32 @@ public List<Double> getLength_all() {
     public int getNumberOfUsedReads() {
         return numberOfUsedReads;
     }
-    public int getNumberOfAllReads() {
-        return numberOfAllReads;
-    }
-    public ArrayList<Double> getIdentity() { return identity; }
 
+    /**
+     * Determines the name of the species based on the NCBI ref ID.
+     *
+     * @param file
+     * @param ref
+     * @return
+     */
     public String getSpeciesname(File file, String ref) {
 
         SamReader input = SamReaderFactory.make().enable(SamReaderFactory.Option.DONT_MEMORY_MAP_INDEX).
-                validationStringency(ValidationStringency.LENIENT).open(file);
+                validationStringency(ValidationStringency.SILENT).open(file);
 
         for(SAMRecord record : input) {
             if(record.getReferenceName().contains(ref)){
-                specieHandler.getSpecie(record.getReferenceName());
-                String spe = specieHandler.getSpecie_name();
+                String spe = speciesHandler.getSpecies(record.getReferenceName());
                 return spe.replace(" ", "_").trim();
             }
         }
         return null;
     }
 
-
+    public int getNumberOfRecords() {
+        return numberOfRecords;
+    }
+    public List<Double> getEditDistances() {
+        return editDistances;
+    }
 }
diff --git a/src/main/java/calculations/Frequencies.java b/src/main/java/org/damageprofiler/calculations/Frequencies.java
similarity index 99%
rename from src/main/java/calculations/Frequencies.java
rename to src/main/java/org/damageprofiler/calculations/Frequencies.java
index ba08833..3858bb6 100755
--- a/src/main/java/calculations/Frequencies.java
+++ b/src/main/java/org/damageprofiler/calculations/Frequencies.java
@@ -1,10 +1,7 @@
-package calculations;
+package org.damageprofiler.calculations;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.util.SequenceUtil;
 import org.apache.log4j.Logger;
-
-import java.util.LinkedList;
-import java.util.List;
 import java.util.stream.IntStream;
 
 /**
@@ -601,7 +598,14 @@ public void count(SAMRecord record, String record_aligned, String ref_aligned){
                     countG_ref_forward_3, countT_ref_forward_3, count0_ref_forward_3, null);
 
         }
+    }
 
+    /**
+     * Count purine bases
+     * @param ref_left bases left of record
+     * @param ref_right bases right of record
+     */
+    public void countRecordFlankingRegions(String ref_left, String ref_right) {
 
     }
 
@@ -693,7 +697,6 @@ public void calculateMisincorporations(SAMRecord record, String record_aligned,
      * compare each position in aligned record with reference to get misincorporations
      * @param seq
      * @param ref
-     * @param mis_positions
      * @param a_c
      * @param a_g
      * @param a_t
diff --git a/src/main/java/org/damageprofiler/calculations/Functions.java b/src/main/java/org/damageprofiler/calculations/Functions.java
new file mode 100755
index 0000000..c3ee1ad
--- /dev/null
+++ b/src/main/java/org/damageprofiler/calculations/Functions.java
@@ -0,0 +1,22 @@
+package org.damageprofiler.calculations;
+
+import org.apache.commons.text.similarity.HammingDistance;
+
+/**
+ * Created by neukamm on 13.03.17.
+ */
+public class Functions {
+
+    /**
+     * Get the hamming distance between two string sequences
+     *
+     * @param sequence1 - the first sequence
+     * @param sequence2 - the second sequence
+     * @return the hamming distance
+     */
+    public int getHammingDistance(String sequence1, String sequence2){
+        HammingDistance hammingDistance = new HammingDistance();
+        return hammingDistance.apply(sequence1, sequence2);
+    }
+
+}
diff --git a/src/main/java/calculations/LengthDistribution.java b/src/main/java/org/damageprofiler/calculations/LengthDistribution.java
similarity index 67%
rename from src/main/java/calculations/LengthDistribution.java
rename to src/main/java/org/damageprofiler/calculations/LengthDistribution.java
index 2780967..f8798e8 100755
--- a/src/main/java/calculations/LengthDistribution.java
+++ b/src/main/java/org/damageprofiler/calculations/LengthDistribution.java
@@ -1,4 +1,4 @@
-package calculations;
+package org.damageprofiler.calculations;
 
 import htsjdk.samtools.SAMRecord;
 import org.apache.log4j.Logger;
@@ -13,8 +13,8 @@
 public class LengthDistribution {
 
     private final Logger LOG;
-    private HashMap<Integer, Integer> length_distribution_map_forward;
-    private HashMap<Integer, Integer> length_distribution_map_reverse;
+    private HashMap<Double, Integer> length_distribution_map_forward;
+    private HashMap<Double, Integer> length_distribution_map_reverse;
     private HashMap<Double, Double> length_distribution_map;
     private List<Double> length_forward;
     private List<Double> length_reverse;
@@ -47,8 +47,8 @@ public void init(){
     public void fillDistributionTable(SAMRecord record, String record_aligned){
 
         // int record_length = record.getReadLength();
-        int record_length = record_aligned.length();
-        length_all.add((double)record_length);
+        double record_length = record_aligned.length();
+        length_all.add(record_length);
 
         // check if record is on forward or reverse strand
         if(record.getReadNegativeStrandFlag()){
@@ -58,7 +58,7 @@ public void fillDistributionTable(SAMRecord record, String record_aligned){
                 int count = length_distribution_map_reverse.get(record_length);
                 length_distribution_map_reverse.put(record_length, count + 1);
             }
-            length_reverse.add((double)record_length);
+            length_reverse.add(record_length);
 
 
 
@@ -69,7 +69,7 @@ public void fillDistributionTable(SAMRecord record, String record_aligned){
                 int count = length_distribution_map_forward.get(record_length);
                 length_distribution_map_forward.put(record_length, count + 1);
             }
-            length_forward.add((double)record_length);
+            length_forward.add(record_length);
 
 
         }
@@ -82,42 +82,18 @@ public void fillDistributionTable(SAMRecord record, String record_aligned){
         }
     }
 
-
     /*
-     *  Getter
-     *
+            Getter
      */
 
-
-    public HashMap<Integer, Integer> getSeqLen(LengthDistribution lengthDistribution) {
-
-        List<Double> length_all = lengthDistribution.getLength_all();
-        HashMap<Integer, Integer> map_length_occurrences_all = new HashMap<>();
-
-        for(double d : length_all){
-            if(!map_length_occurrences_all.containsKey(d)){
-                map_length_occurrences_all.put((int)d, 1);
-            } else {
-                int count = map_length_occurrences_all.get(d);
-                map_length_occurrences_all.put((int)d, count + 1);
-            }
-        }
-        return map_length_occurrences_all;
-    }
-
-
-    public HashMap<Integer, Integer> getLength_distribution_map_forward() {
+    public HashMap<Double, Integer> getLength_distribution_map_forward() {
         return length_distribution_map_forward;
     }
 
-    public HashMap<Integer, Integer> getLength_distribution_map_reverse() {
+    public HashMap<Double, Integer> getLength_distribution_map_reverse() {
         return length_distribution_map_reverse;
     }
 
-    public HashMap<Double, Double> getLength_distribution_map() {
-        return length_distribution_map;
-    }
-
     public List<Double> getLength_forward() {
         return length_forward;
     }
diff --git a/src/main/java/org/damageprofiler/calculations/RuntimeEstimator.java b/src/main/java/org/damageprofiler/calculations/RuntimeEstimator.java
new file mode 100755
index 0000000..f5ae95a
--- /dev/null
+++ b/src/main/java/org/damageprofiler/calculations/RuntimeEstimator.java
@@ -0,0 +1,66 @@
+package org.damageprofiler.calculations;
+
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
+import htsjdk.samtools.ValidationStringency;
+
+import java.io.File;
+
+public class RuntimeEstimator {
+
+    private SamReader input;
+    private long numberOfRecords;
+    private double timePer100000RecordsInSeconds = 2;
+    private long estimatedRuntimeInSeconds;
+
+    public RuntimeEstimator(String inputfile){
+        input = SamReaderFactory.make().enable(SamReaderFactory.Option.DONT_MEMORY_MAP_INDEX).
+                validationStringency(ValidationStringency.LENIENT).open(new File(inputfile));
+
+        estimate(inputfile);
+
+    }
+
+    /**
+     * Estimate runtime based on the time needed in previous runs and the number of reads in the
+     * current input file.
+     *
+     * @param inputfile
+     */
+    public void estimate(String inputfile) {
+        // estimate runtime:
+
+        double bytes = new File (inputfile).length();
+        double kilobytes = (bytes / 1024);
+        double megabytes = (kilobytes / 1024);
+        double gigabytes = (megabytes / 1024);
+
+        double sizeSamRecordInBytes = 50;
+
+        double estimatedNumberOfRecords = bytes/sizeSamRecordInBytes;
+        System.out.println("Estimated number of records to process: " + estimatedNumberOfRecords);
+
+//        numberOfRecords = input.iterator().toList().size();
+        numberOfRecords = (long)estimatedNumberOfRecords;
+        System.out.println("Number of records to process: " + numberOfRecords);
+
+        estimatedRuntimeInSeconds = (long) (numberOfRecords/100000 * timePer100000RecordsInSeconds);
+
+        if(estimatedRuntimeInSeconds > 60) {
+            long minutes = estimatedRuntimeInSeconds / 60;
+            long seconds = estimatedRuntimeInSeconds % 60;
+            System.out.println("Estimated Runtime: " + minutes + " minutes, and " + seconds + " seconds.");
+        } else {
+            System.out.println("Estimated Runtime: " + estimatedRuntimeInSeconds + " seconds.");
+        }
+
+    }
+
+    public long getEstimatedRuntimeInSeconds() {
+        return estimatedRuntimeInSeconds;
+    }
+
+    public int getNumberOfRecords() {
+        return (int)numberOfRecords;
+    }
+}
diff --git a/src/main/java/calculations/SpecieHandler.java b/src/main/java/org/damageprofiler/calculations/SpeciesHandler.java
similarity index 83%
rename from src/main/java/calculations/SpecieHandler.java
rename to src/main/java/org/damageprofiler/calculations/SpeciesHandler.java
index 6869d16..cc3c84a 100755
--- a/src/main/java/calculations/SpecieHandler.java
+++ b/src/main/java/org/damageprofiler/calculations/SpeciesHandler.java
@@ -1,32 +1,39 @@
-package calculations;
+package org.damageprofiler.calculations;
 
 import java.io.*;
 import java.util.Random;
 
-import IO.DOMParser;
+import org.damageprofiler.IO.DOMParser;
 import org.apache.log4j.Logger;
 
 
 /**
  * Created by neukamm on 25.07.16.
  */
-public class SpecieHandler {
+public class SpeciesHandler {
 
     private Logger LOG;
     private String gi;
-    private String specie_name;
 
-    public SpecieHandler(){
+    /**
+     * This class accesses NCBI to find the name of a species based on the RefSeqID.
+     */
+    public SpeciesHandler(){
     }
 
 
-    public void getSpecie(String rname){
-        if (rname != null) {
+    /**
+     *
+     * @param ref_name
+     */
+    public String getSpecies(String ref_name){
+        String species_name = "";
+        if (ref_name != null) {
             String tax = "";
 
 
             // get tax id from RNAME string
-            String[] rname_split = rname.split("\\|");
+            String[] rname_split = ref_name.split("\\|");
             for (int i = 0; i < rname_split.length; i++) {
                 switch (rname_split[i]) {
                     case "gi":
@@ -44,10 +51,10 @@ public void getSpecie(String rname){
                         "Please make sure that the SAM/BAM file reference tag contains the tax ID");
             }
             if(!tax.equals("")){
-               specie_name = getSpeciesByID(Integer.parseInt(tax));
-               // specie_name = specie_name.replaceAll(" ", "_");
+               species_name = getSpeciesByID(Integer.parseInt(tax));
             }
         }
+        return species_name;
     }
 
 
@@ -96,16 +103,9 @@ private String getSpeciesByID(int id) {
             System.out.println("'Curl' is not installed. If you would like to use this option, please install it.");
         }
 
-
-
         return species;
     }
 
-
-    public String getSpecie_name() {
-        return specie_name;
-    }
-
     public void setLOG(Logger LOG) {
         this.LOG = LOG;
     }
diff --git a/src/main/java/IO/SpeciesListParser.java b/src/main/java/org/damageprofiler/calculations/SpeciesListParser.java
similarity index 68%
rename from src/main/java/IO/SpeciesListParser.java
rename to src/main/java/org/damageprofiler/calculations/SpeciesListParser.java
index e3ce623..c27ee39 100755
--- a/src/main/java/IO/SpeciesListParser.java
+++ b/src/main/java/org/damageprofiler/calculations/SpeciesListParser.java
@@ -1,6 +1,5 @@
-package IO;
+package org.damageprofiler.calculations;
 
-import calculations.SpecieHandler;
 import org.apache.log4j.Logger;
 
 import java.io.BufferedReader;
@@ -15,26 +14,20 @@ public class SpeciesListParser {
 
     private Logger LOG;
     private String speciesFile;
-    private SpecieHandler specieHandler;
+    private SpeciesHandler speciesHandler;
 
     public SpeciesListParser(String speciesListFile, Logger LOG) {
         this.speciesFile = speciesListFile;
         this.LOG = LOG;
-        specieHandler = new SpecieHandler();
+        speciesHandler = new SpeciesHandler();
     }
 
 
-    public String getSingleSpecie(String rname) {
-
-        specieHandler.getSpecie(rname);
-        return specieHandler.getSpecie_name();
-    }
-
-    public List<String> getList() {
-
-        return readFile();
-    }
-
+    /**
+     * Read file with species listed by the user.
+     *
+     * @return
+     */
     private List<String> readFile() {
 
         try {
@@ -42,15 +35,15 @@ private List<String> readFile() {
             FileReader fileReader = new FileReader(file);
             BufferedReader bufferedReader = new BufferedReader(fileReader);
             String line;
-            List<String> list = new ArrayList<>();
+            List<String> list_species = new ArrayList<>();
 
             while ((line = bufferedReader.readLine()) != null) {
-                list.add(line.trim());
+                list_species.add(line.trim());
             }
 
             fileReader.close();
 
-            return list;
+            return list_species;
         } catch (IOException e) {
             e.printStackTrace();
         }
@@ -60,9 +53,18 @@ private List<String> readFile() {
 
     }
 
+    /*
+        Getter and Setter
+     */
     public void setLOG(Logger LOG) {
         this.LOG = LOG;
-        specieHandler.setLOG(LOG);
+        speciesHandler.setLOG(LOG);
+    }
+
+
+    public List<String> getSpeciesList() {
+
+        return readFile();
     }
 }
 
diff --git a/src/main/java/calculations/StartCalculations.java b/src/main/java/org/damageprofiler/calculations/StartCalculations.java
old mode 100644
new mode 100755
similarity index 59%
rename from src/main/java/calculations/StartCalculations.java
rename to src/main/java/org/damageprofiler/calculations/StartCalculations.java
index c088b1c..c99c728
--- a/src/main/java/calculations/StartCalculations.java
+++ b/src/main/java/org/damageprofiler/calculations/StartCalculations.java
@@ -1,14 +1,18 @@
-package calculations;
-
-import IO.*;
+package org.damageprofiler.calculations;
 
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 
 import com.itextpdf.text.DocumentException;
+import htsjdk.samtools.reference.IndexedFastaSequenceFile;
+import javafx.scene.paint.Color;
 import org.apache.log4j.*;
+import org.damageprofiler.IO.*;
+import org.jfree.chart.JFreeChart;
 
 
 /**
@@ -16,14 +20,12 @@
  */
 public class StartCalculations {
 
-    private final String VERSION;
+    private String VERSION;
     private LogClass logClass;
     private long currtime_prior_execution;  // start time to get overall runtime
-    private boolean calculationsDone = true;
+    private boolean calculationsDone = false;
     private Logger LOG;
     private List<String> specieslist = null;
-    private List<String> species_name_list;
-    private SpeciesListParser speciesListParser;
     private boolean use_only_merged_reads;
     private double height_damageplot; //= 0.4; // set yaxis height to 40% as default
     private int threshold;
@@ -33,22 +35,49 @@ public class StartCalculations {
     private String reference;
     private String outfolder;
     private String input;
-    private SpecieHandler specieHandler;
+    private SpeciesHandler speciesHandler = new SpeciesHandler();
     private boolean use_all_reads;
     private double xaxis_min_id_histogram;
     private double xaxis_max_id_histogram;
     private double xaxis_min_length_histogram;
     private double xaxis_max_length_histogram;
+    private boolean ssLibProtocolUsed;
+    private DamageProfiler damageProfiler;
+    private OutputGenerator outputGenerator;
+    private String inputfileNameWithOutExtension;
+    private Communicator communicator;
+    private IndexedFastaSequenceFile fastaSequenceFile;
+    private FastACacher cache;
+    private HashMap<String, List<JFreeChart>> species_output_summary;
+    private HashMap<String, Integer> number_of_used_reads_summary;
+
+
+    // plot settings
+    private Color color_DP_C_to_T;
+    private Color color_DP_G_to_A;
+    private Color color_DP_insertions;
+    private Color color_DP_deletions;
+    private Color color_DP_other;
+    private String output_folder;
+    private String speciesname = null;
 
 
-    public StartCalculations(String version){
+    public StartCalculations(){
+
+    }
+
+    public void setVERSION(String version){
         VERSION = version;
     }
 
+    /**
+     * Start all calculations.
+     * @param c
+     * @throws Exception
+     */
     public void start(Communicator c) throws Exception {
 
         currtime_prior_execution = System.currentTimeMillis();
-
         input = c.getInput();
         outfolder = c.getOutfolder();
         reference = c.getReference();
@@ -63,9 +92,16 @@ public void start(Communicator c) throws Exception {
         xaxis_max_length_histogram = c.getXaxis_histo_length_max();
         use_only_merged_reads = c.isUse_merged_and_mapped_reads();
         use_all_reads = c.isUse_all_reads();
-        speciesListParser=null;
-        species_name_list=null;
-        specieHandler = new SpecieHandler();
+        ssLibProtocolUsed = c.isSsLibsProtocolUsed();
+
+        color_DP_C_to_T = c.getColor_DP_C_to_T();
+        color_DP_G_to_A = c.getColor_DP_G_to_A();
+        color_DP_insertions = c.getColor_DP_insertions();
+        color_DP_deletions = c.getColor_DP_deletions();
+        color_DP_other = c.getColor_DP_other();
+
+        this.inputfileNameWithOutExtension = input.substring(0, input.lastIndexOf('.'));
+        this.communicator = c;
 
         SpeciesListParser speciesListParser = new SpeciesListParser(
                 specieslist_filepath,
@@ -73,66 +109,46 @@ public void start(Communicator c) throws Exception {
         );
 
 
+        if(!this.reference.equals(""))
+            readReferenceInCache();
+
         if(specieslist_filepath != null){
+            species_output_summary = new HashMap<>();
+            number_of_used_reads_summary = new HashMap<>();
 
+            speciesHandler = new SpeciesHandler();
             /*
                 parse species references (-sf) and run DP for each reference in the file
              */
             specieslist = new ArrayList<>();
-            specieslist.addAll(speciesListParser.getList());
+            specieslist.addAll(speciesListParser.getSpeciesList());
 
 
             for (int i = 0; i < specieslist.size(); i++) {
                 String specie_input_string = specieslist.get(i);
                 //String specie_name = species_real_name_list.get(i);
 
-
-
-                // start DamageProfiler
-                File file = new File(input);
-                DamageProfiler damageProfiler = new DamageProfiler(specieHandler);
-
+               // start DamageProfiler
+                damageProfiler = new DamageProfiler(speciesHandler, cache);
 
                 String ref = specie_input_string.split("\\|")[0].trim();
-                String speciesname = damageProfiler.getSpeciesname(file, ref);
+                speciesname = damageProfiler.getSpeciesname(new File(input), ref);
 
-                String inputfileNameWithOutExtension = input.substring(0, input.lastIndexOf('.'));
-                String output_folder = createOutputFolder(
+                createOutputFolder(
                         outfolder,
                         inputfileNameWithOutExtension.split("/")[inputfileNameWithOutExtension.split("/").length - 1]
                                 + File.separator + ref + "_" + speciesname);
 
-
-
-                if (c.getTitle_plots() == null) {
-                    inputfileNameWithOutExtension = input.substring(0, input.lastIndexOf('.'));
-                } else {
-                    inputfileNameWithOutExtension = c.getTitle_plots();
-                }
-
-
+                initPlot();
 
                 // init Logger
-                logClass = new LogClass();
-                logClass.updateLog4jConfiguration(output_folder + "/DamageProfiler_" + ref + "_" + speciesname +".log");
-                logClass.setUp();
-
-                LOG = logClass.getLogger(this.getClass());
-                System.out.println("DamageProfiler v" + VERSION);
-                LOG.info("DamageProfiler v" + VERSION);
-                LOG.info("Calculate damage profile for species " + ref + " (" + speciesname + ")");
-
-
+                initLogger(output_folder + "/DamageProfiler_" + ref + "_" + speciesname +".log",
+                        "Calculate damage profile for species " + ref + " (" + speciesname + ")");
 
-                // decompress input file if necessary
-                if (input.endsWith(".gz")) {
-                    Unzip unzip = new Unzip(LOG);
-                    input = unzip.decompress(input);
-                }
 
                 // create new output folder
                 // log settings
-                LOG.info("Analysis of file (-i):" + file + "\n"
+                LOG.info("\nAnalysis of file (-i):" + input + "\n"
                         + "Output folder (-o):" + output_folder + "\n"
                         + "Reference (-r, optional) :" + reference + "\n"
                         + "Specie (-s, optional):" + specie_input_string + "\n"
@@ -145,8 +161,7 @@ parse species references (-sf) and run DP for each reference in the file
                         + "x-axis min length histogram (-xaxis_histo_length_min): " + xaxis_min_length_histogram + "\n"
                         + "x-axis max length histogram (-xaxis_histo_length_max): " + xaxis_max_length_histogram + "\n");
 
-
-                damageProfiler.init(file,
+                damageProfiler.init(new File(input),
                         new File(reference),
                         threshold,
                         length,
@@ -154,17 +169,33 @@ parse species references (-sf) and run DP for each reference in the file
                         LOG);
 
                 damageProfiler.extractSAMRecords(use_only_merged_reads, use_all_reads);
-
-                generateOutput(damageProfiler, output_folder, inputfileNameWithOutExtension, speciesname);
+                generateOutput();
+                String spec_no_space = specie_input_string.replace(" ","_");
+                species_output_summary.put(spec_no_space + " (" + speciesname + ")",
+                        List.of(outputGenerator.getChart_DP_5prime(),
+                                outputGenerator.getChart_DP_3prime(),
+                                outputGenerator.getEditDist_chart(),
+                                outputGenerator.getLength_chart_all())
+                );
+
+                number_of_used_reads_summary.put(
+                        spec_no_space + " (" + speciesname + ")",
+                        damageProfiler.getNumberOfUsedReads());
             }
 
+            // generate metagenomic output summary
+            MetagenomicOutput metagenomicOutput = new MetagenomicOutput();
+            String[] splitted = input.split("/");
+            String filename = splitted[splitted.length-1];
+            metagenomicOutput.generate(outfolder + File.separator +
+                    inputfileNameWithOutExtension.split("/")[inputfileNameWithOutExtension.split("/").length - 1],
+                    species_output_summary, filename, number_of_used_reads_summary);
+
 
         } else if(species_ref_identifier != null){
 
             // start DamageProfiler
-            DamageProfiler damageProfiler = new DamageProfiler(
-
-                    specieHandler);
+            damageProfiler = new DamageProfiler(speciesHandler, cache);
 
             /*
                 parse species reference (-s) and run DP
@@ -172,44 +203,23 @@ parse species reference (-s) and run DP
 
             this.specieslist = new ArrayList<>();
             specieslist.add(species_ref_identifier);
-            String speciesname = damageProfiler.getSpeciesname(new File(input), species_ref_identifier);
+            speciesname = damageProfiler.getSpeciesname(new File(input), species_ref_identifier);
 
             String inputfileNameWithOutExtension = input.substring(0, input.lastIndexOf('.'));
 
-            String output_folder = createOutputFolder(
+            createOutputFolder(
                     outfolder,
                     inputfileNameWithOutExtension.split("/")[inputfileNameWithOutExtension.split("/").length - 1] +
                              File.separator + species_ref_identifier + "_" + speciesname);
 
-
-            if (c.getTitle_plots() == null) {
-                inputfileNameWithOutExtension = input.substring(0, input.lastIndexOf('.'));
-            }
-            else {
-                inputfileNameWithOutExtension = c.getTitle_plots();
-            }
-
-
+            initPlot();
 
             // init Logger
-            logClass = new LogClass();
-            logClass.updateLog4jConfiguration(output_folder + "/DamageProfiler.log");
-            logClass.setUp();
-            LOG = logClass.getLogger(this.getClass());
-            System.out.println("DamageProfiler v" + VERSION);
-            LOG.info("DamageProfiler v" + VERSION);
-
-
-            // decompress input file if necessary
-            if (input.endsWith(".gz")) {
-                Unzip unzip = new Unzip(LOG);
-                input = unzip.decompress(input);
-            }
+            initLogger(output_folder + "/DamageProfiler.log", "DamageProfiler v" + VERSION);
+
 
-            // create new output folder
-            File file = new File(input);
             // log settings
-            LOG.info("Analysis of file (-i):" + file + "\n"
+            LOG.info("Analysis of file (-i):" + input + "\n"
                     + "Output folder (-o):" + output_folder + "\n"
                     + "Reference (-r, optional) :" + reference + "\n"
                     + "Specie (-s, optional):" + specieslist + "\n"
@@ -222,10 +232,7 @@ parse species reference (-s) and run DP
                     + "x-axis min length histogram (-xaxis_histo_length_min): " + xaxis_min_length_histogram + "\n"
                     + "x-axis max length histogram (-xaxis_histo_length_max): " + xaxis_max_length_histogram + "\n");
 
-
-
-
-            damageProfiler.init(file,
+            damageProfiler.init(new File(input),
                     new File(reference),
                     threshold,
                     length,
@@ -233,45 +240,29 @@ parse species reference (-s) and run DP
                     LOG);
 
             damageProfiler.extractSAMRecords(use_only_merged_reads, use_all_reads);
-
             speciesListParser.setLOG(LOG);
-            generateOutput(damageProfiler,output_folder, inputfileNameWithOutExtension, null);
+            generateOutput();
+
         } else {
 
             /*
-                    No species specified --> use all (mapping) reads
+                    No species specified --> use all mapped reads
              */
             String inputfileNameWithOutExtension = input.substring(0, input.lastIndexOf('.'));
 
-            String output_folder = createOutputFolder(
+            // create output folder based on file name
+            createOutputFolder(
                     outfolder,
                     inputfileNameWithOutExtension.split("/")[inputfileNameWithOutExtension.split("/").length - 1]);
 
-            if (c.getTitle_plots() == null) {
-                inputfileNameWithOutExtension = input.substring(0, input.lastIndexOf('.'));
-            } else {
-                inputfileNameWithOutExtension = c.getTitle_plots();
-            }
+            initPlot();
 
             // init Logger
-            logClass = new LogClass();
-            logClass.updateLog4jConfiguration(output_folder + "/DamageProfiler.log");
-            logClass.setUp();
-            LOG = logClass.getLogger(this.getClass());
-            System.out.println("DamageProfiler v" + VERSION);
-            LOG.info("DamageProfiler v" + VERSION);
-
-
-            // decompress input file if necessary
-            if (input.endsWith(".gz")) {
-                Unzip unzip = new Unzip(LOG);
-                input = unzip.decompress(input);
-            }
+            initLogger(output_folder + "/DamageProfiler.log", "DamageProfiler v" + VERSION);
+
 
-            // create new output folder
-            File file = new File(input);
             // log settings
-            LOG.info("Analysis of file (-i):" + file + "\n"
+            LOG.info("Analysis of file (-i):" + input + "\n"
                     + "Output folder (-o):" + output_folder + "\n"
                     + "Reference (-r, optional) :" + reference + "\n"
                     + "Specie (-s, optional):" + specieslist + "\n"
@@ -284,52 +275,58 @@ parse species reference (-s) and run DP
                     + "x-axis min length histogram (-xaxis_histo_length_min): " + xaxis_min_length_histogram + "\n"
                     + "x-axis max length histogram (-xaxis_histo_length_max): " + xaxis_max_length_histogram + "\n");
 
-
-
             // start DamageProfiler
-            DamageProfiler damageProfiler = new DamageProfiler(specieHandler);
+            damageProfiler = new DamageProfiler(speciesHandler, cache);
 
-            damageProfiler.init(file,
+            damageProfiler.init(new File(input),
                     new File(reference),
                     threshold,
                     length,
                     null,
                     LOG);
             damageProfiler.extractSAMRecords(use_only_merged_reads, use_all_reads);
-
             speciesListParser.setLOG(LOG);
-
-            generateOutput(damageProfiler, output_folder, inputfileNameWithOutExtension, null);
-
+            generateOutput();
         }
 
+        calculationsDone=true;
+
+    }
 
-        // print runtime
-        long currtime_post_execution = System.currentTimeMillis();
-        long diff = currtime_post_execution - currtime_prior_execution;
-        long runtime_s = diff / 1000;
-        if(runtime_s > 60) {
-            long minutes = runtime_s / 60;
-            long seconds = runtime_s % 60;
-            LOG.info("Runtime of Module was: " + minutes + " minutes, and " + seconds + " seconds.");
+    private void initPlot() {
+        if (communicator.getTitle_plots() == null) {
+            inputfileNameWithOutExtension = input.substring(0, input.lastIndexOf('.'));
         } else {
-            LOG.info("Runtime of Module was: " + runtime_s + " seconds.");
+            inputfileNameWithOutExtension = communicator.getTitle_plots();
         }
+    }
 
-        calculationsDone=true;
+    private void initLogger(String outfolder, String log) {
 
+        logClass = new LogClass();
+        logClass.updateLog4jConfiguration(outfolder);
+        logClass.setUp();
+
+        LOG = logClass.getLogger(this.getClass());
+        System.out.println("DamageProfiler v" + VERSION);
+        LOG.info(log);
 
     }
 
-    private void generateOutput(DamageProfiler damageProfiler, String output_folder, String inputfileNameWithOutExtension, String spe)
-            throws IOException, DocumentException {
+    /**
+     * Generate output files.
+     *
+     * @throws IOException
+     * @throws DocumentException
+     */
+    private void generateOutput() throws IOException, DocumentException {
 
         if (damageProfiler.getNumberOfUsedReads() != 0) {
 
-            OutputGenerator outputGenerator = new OutputGenerator(
+            outputGenerator = new OutputGenerator(
                     output_folder,
                     damageProfiler,
-                    spe,
+                    speciesname,
                     threshold,
                     length,
                     height_damageplot,
@@ -338,7 +335,10 @@ private void generateOutput(DamageProfiler damageProfiler, String output_folder,
                     xaxis_min_length_histogram,
                     xaxis_max_length_histogram,
                     input,
-                    LOG
+                    LOG,
+                    damageProfiler.getNumberOfRecords(),
+                    ssLibProtocolUsed,
+                    color_DP_C_to_T, color_DP_deletions, color_DP_G_to_A, color_DP_insertions, color_DP_other
             );
 
             outputGenerator.writeLengthDistribution();
@@ -367,11 +367,12 @@ private void generateOutput(DamageProfiler damageProfiler, String output_folder,
                     damageProfiler.getLength_reverse(),
                     inputfileNameWithOutExtension
             );
-            outputGenerator.plotIdentitiyHistogram(
-                    damageProfiler.getIdentity(),
+            outputGenerator.plotEditDistanceHistogram(
+                    damageProfiler.getEditDistances(), // damageProfiler.getIdentity(),
                     "Identity distribution",
                     inputfileNameWithOutExtension
             );
+            outputGenerator.writeEditDistance(damageProfiler.getEditDistances());
 
             LOG.info("Output files generated");
 
@@ -380,6 +381,7 @@ private void generateOutput(DamageProfiler damageProfiler, String output_folder,
         }
     }
 
+
     /**
      * create output folder.
      * Save all files in subfolder, which has the same name as the input file
@@ -388,7 +390,7 @@ private void generateOutput(DamageProfiler damageProfiler, String output_folder,
      * @param path
      * @throws IOException
      */
-    private static String createOutputFolder(String path, String inputfileNameWithOutExtension) {
+    private void createOutputFolder(String path, String inputfileNameWithOutExtension) {
 
         // use Pattern.quote(File.separator) to split file path
         File f = new File(path + File.separator + inputfileNameWithOutExtension);
@@ -398,11 +400,33 @@ private static String createOutputFolder(String path, String inputfileNameWithOu
             f.mkdirs();
         }
 
-        return f.getAbsolutePath();
+        this.output_folder = f.getAbsolutePath();
     }
 
+    /**
+     * index reference file and put it in cache to get faster
+     * access
+     *
+     * @throws FileNotFoundException
+     */
+
+    private void readReferenceInCache() throws FileNotFoundException{
+        // read reference file as indexed reference
+        fastaSequenceFile = new IndexedFastaSequenceFile(new File(this.reference));
+        // store reference in cache to get faster access
+        cache = new FastACacher(new File(reference), LOG);
+
+    }
 
     public boolean isCalculationsDone() {
         return calculationsDone;
     }
+
+    public void setCalculationsDone(boolean calculationsDone) {
+        this.calculationsDone = calculationsDone;
+    }
+
+    public OutputGenerator getOutputGenerator() {
+        return outputGenerator;
+    }
 }
diff --git a/src/main/java/org/damageprofiler/controller/DamageProfilerMainController.java b/src/main/java/org/damageprofiler/controller/DamageProfilerMainController.java
new file mode 100755
index 0000000..f65e7c7
--- /dev/null
+++ b/src/main/java/org/damageprofiler/controller/DamageProfilerMainController.java
@@ -0,0 +1,431 @@
+package org.damageprofiler.controller;
+
+import org.damageprofiler.GUI.*;
+import org.damageprofiler.GUI.Dialogues.AdvancedPlottingOptionsDialogue;
+import org.damageprofiler.GUI.Dialogues.HelpDialogue;
+import org.damageprofiler.GUI.Dialogues.RunInfoDialogue;
+import org.damageprofiler.GUI.Dialogues.RuntimeEstimatorDialogue;
+import org.damageprofiler.calculations.RuntimeEstimator;
+import org.damageprofiler.calculations.StartCalculations;
+import org.damageprofiler.IO.Communicator;
+import javafx.concurrent.Task;
+import javafx.event.Event;
+import javafx.event.EventHandler;
+import javafx.scene.control.*;
+import javafx.scene.paint.Color;
+import org.jfree.chart.JFreeChart;
+import org.jfree.chart.fx.ChartViewer;
+
+public class DamageProfilerMainController {
+
+    private final Button btn_leftpane_run_config;
+    private final Button btn_leftpane_identityDist;
+    private final Button btn_leftpane_damageProfile;
+    private final Button btn_leftpane_lengthDist;
+    private final ProgressBarController progressBarController;
+    private final Button btn_estimate_runtime;
+    private final Button btn_help;
+    private final HelpDialogue help_dialogue;
+    private final AdvancedPlottingOptionsDialogue advancedPlottingOptionsDialogue;
+    private final PlottingSettingController plottingSettingController;
+    private RunInfoDialogue runInfoDialogue;
+    private Communicator communicator;
+    private Button btn_inputfile;
+    private Button btn_reference;
+    private Button btn_output;
+    private Button btn_run;
+    private Button btn_speciesList;
+    private TextField textfield_threshold;
+    private TextField textfield_length;
+    private TextField textfield_species;
+    private CheckBox checkbox_use_merged_reads;
+    private CheckBox checkbox_ssLibs_protocol;
+    private TextField textfield_title;
+    private TextField textfield_y_axis_height;
+    private StartCalculations starter = new StartCalculations();
+    private DamageProfilerMainGUI mainGUI;
+    private RuntimeEstimatorDialogue runtimeInfoDialogue;
+    /**
+     * Constructor
+     * @param damageProfilerMainGUI
+     * @param progressBarController
+     * @param plottingSettingController
+     */
+    public DamageProfilerMainController(DamageProfilerMainGUI damageProfilerMainGUI,
+                                        ProgressBarController progressBarController,
+                                        PlottingSettingController plottingSettingController){
+
+        this.mainGUI = damageProfilerMainGUI;
+        this.progressBarController = progressBarController;
+        this.communicator = mainGUI.getCommunicator();
+        runInfoDialogue = new RunInfoDialogue("Run configuration", communicator);
+        starter.setVERSION(damageProfilerMainGUI.getVersion());
+        this.help_dialogue = new HelpDialogue();
+
+        this.btn_inputfile = mainGUI.getConfig_dialogue().getBtn_inputfile();
+        this.btn_reference = mainGUI.getConfig_dialogue().getBtn_reference();
+        this.btn_output = mainGUI.getConfig_dialogue().getBtn_output();
+        this.btn_run = mainGUI.getConfig_dialogue().getBtn_run();
+        this.btn_estimate_runtime = mainGUI.getConfig_dialogue().getBtn_estimate_runtime();
+        this.btn_speciesList = mainGUI.getConfig_dialogue().getBtn_speciesList();
+        this.btn_leftpane_identityDist = mainGUI.getBtn_leftpane_identityDist();
+        this.btn_leftpane_run_config = mainGUI.getBtn_leftpane_info();
+        this.btn_help = mainGUI.getBtn_help();
+        this.btn_leftpane_damageProfile = mainGUI.getBtn_leftpane_damageProfile();
+        this.btn_leftpane_lengthDist = mainGUI.getBtn_leftpane_lengthDist();
+
+        this.textfield_threshold = mainGUI.getConfig_dialogue().getTextfield_threshold();
+        this.textfield_length = mainGUI.getConfig_dialogue().getTextfield_length();
+        this.textfield_species = mainGUI.getConfig_dialogue().getTextfield_species();
+        this.textfield_title = mainGUI.getConfig_dialogue().getTextfield_title();
+        this.textfield_y_axis_height = mainGUI.getConfig_dialogue().getTextfield_y_axis_height();
+
+        this.checkbox_use_merged_reads = mainGUI.getConfig_dialogue().getCheckbox_use_merged_reads();
+        this.checkbox_ssLibs_protocol = mainGUI.getConfig_dialogue().getCheckbox_ssLibs_protocol();
+
+
+        // attributes of advanced plotting settings
+        this.plottingSettingController = plottingSettingController;
+        this.advancedPlottingOptionsDialogue = this.mainGUI.getConfig_dialogue().getAdvancedPlottingOptionsDialogue();
+        this.plottingSettingController.addListener(this.advancedPlottingOptionsDialogue);
+
+
+        runtimeInfoDialogue = new RuntimeEstimatorDialogue("Runtime information",
+                "This gives you an estimate of the runtime. For large files with a long runtime,\n" +
+                        "it's recommended to use the command line version of DamageProfiler.");
+
+        setColorsPlotting();
+        addListener();
+
+    }
+
+    private void setColorsPlotting() {
+
+        communicator.setColor_DP_C_to_T(this.advancedPlottingOptionsDialogue.getTabAdvancedSettingsDamagePlot().getColorPicker_C_to_T().getValue());
+        communicator.setColor_DP_G_to_A(this.advancedPlottingOptionsDialogue.getTabAdvancedSettingsDamagePlot().getColorPicker_G_to_A().getValue());
+        communicator.setColor_DP_insertions(this.advancedPlottingOptionsDialogue.getTabAdvancedSettingsDamagePlot().getColorPicker_insertions().getValue());
+        communicator.setColor_DP_deletions(this.advancedPlottingOptionsDialogue.getTabAdvancedSettingsDamagePlot().getColorPicker_deletions().getValue());
+        communicator.setColor_DP_other(this.advancedPlottingOptionsDialogue.getTabAdvancedSettingsDamagePlot().getColorPicker_others().getValue());
+
+    }
+
+    private void addListener() {
+
+        btn_inputfile.setOnAction(e -> {
+
+            BamFileChooser fqfc = new BamFileChooser(communicator);
+            if (communicator.getInput() != null){
+                Tooltip tooltip_input = new Tooltip(communicator.getInput());
+                //setTooltipDelay(tooltip_input);
+                btn_inputfile.setTooltip(tooltip_input);
+
+                String filepath = communicator.getInput().substring(0, communicator.getInput().lastIndexOf('.'));
+                String filename = filepath.split("/")[filepath.split("/").length-1];
+                mainGUI.getConfig_dialogue().setTextfield_title(filename);
+
+                if (checkIfInputWasSelected()) {
+                    btn_run.setDisable(false);
+                    btn_estimate_runtime.setDisable(false);
+
+                } else {
+                    btn_run.setDisable(true);
+                    btn_estimate_runtime.setDisable(true);
+                }
+            }
+
+
+        });
+
+        btn_help.setOnAction(e -> {
+            mainGUI.getRoot().setCenter(new ScrollPane(this.help_dialogue.getGridPane()));
+        });
+
+        btn_reference.setOnAction(e -> {
+
+            ReferenceFileChooser rfc = new ReferenceFileChooser(communicator);
+            Tooltip tooltip_ref = new Tooltip(communicator.getReference());
+            //setTooltipDelay(tooltip_ref);
+            btn_reference.setTooltip(tooltip_ref);
+
+            if (checkIfInputWasSelected()) {
+                btn_run.setDisable(false);
+                btn_estimate_runtime.setDisable(false);
+            } else {
+                btn_run.setDisable(true);
+                btn_estimate_runtime.setDisable(true);
+            }
+
+        });
+
+
+
+        btn_output.setOnAction(e -> {
+
+            OutputDirChooser rfc = new OutputDirChooser(communicator);
+            Tooltip tooltip_output = new Tooltip(communicator.getOutfolder());
+            //setTooltipDelay(tooltip_output);
+            btn_output.setTooltip(tooltip_output);
+
+            if (checkIfInputWasSelected()) {
+                btn_run.setDisable(false);
+                btn_estimate_runtime.setDisable(false);
+
+            } else {
+                btn_run.setDisable(true);
+                btn_estimate_runtime.setDisable(true);
+            }
+
+        });
+
+
+
+        btn_estimate_runtime.setOnAction(e -> {
+
+            RuntimeEstimator runtimeEstimator = new RuntimeEstimator(communicator.getInput());
+            long estimatedRuntimeInSeconds = runtimeEstimator.getEstimatedRuntimeInSeconds();
+            String text_estimatedRuntime;
+
+
+            if(estimatedRuntimeInSeconds > 60) {
+                long minutes = estimatedRuntimeInSeconds / 60;
+                long seconds = estimatedRuntimeInSeconds % 60;
+                text_estimatedRuntime = "Estimated Runtime: " + minutes + " minutes, and " + seconds + " seconds.";
+            } else {
+                if(estimatedRuntimeInSeconds == 0 ){
+                    text_estimatedRuntime = "Estimated Runtime: Insignificant";
+                } else {
+                    text_estimatedRuntime = "Estimated Runtime: " + estimatedRuntimeInSeconds + " seconds.";
+                }
+
+            }
+
+            runtimeInfoDialogue.setNumberOfRecords(runtimeEstimator.getNumberOfRecords());
+            runtimeInfoDialogue.setResultText(text_estimatedRuntime);
+            runtimeInfoDialogue.addComponents();
+            runtimeInfoDialogue.show();
+        });
+
+        runtimeInfoDialogue.getBtn_proceed().setOnAction(e_start -> {
+            runtimeInfoDialogue.close();
+            runDamageProfiler();
+        });
+
+        runtimeInfoDialogue.getBtn_cancel().setOnAction(e_cancel -> runtimeInfoDialogue.close());
+
+        btn_run.setOnAction(e -> {
+            runDamageProfiler();
+        });
+
+        btn_speciesList.setOnAction(e -> {
+
+            SpeciesListFileChooser slfc = new SpeciesListFileChooser(communicator);
+            if (checkIfInputWasSelected()) {
+                btn_speciesList.setDisable(false);
+            } else {
+                btn_speciesList.setDisable(true);
+            }
+
+        });
+
+//        btn_loadSpecies.setOnAction(e -> {
+//            LoadSpeciesDialogue loadSpeciesDialogue = new LoadSpeciesDialogue(communicator.getInput());
+//
+//
+//        });
+
+
+        btn_leftpane_damageProfile.setOnAction(e -> {
+            if(starter.isCalculationsDone()){
+                // generate plot
+                generateDamageProfile();
+            }
+        });
+
+
+        btn_leftpane_identityDist.setOnAction(e -> {
+
+            if(starter.isCalculationsDone()){
+                // generate plot
+                generateIdentityDist();
+            }
+
+        });
+
+        btn_leftpane_lengthDist.setOnAction(e -> {
+
+
+            if(starter.isCalculationsDone()){
+                // generate plot
+                generateLengthDist();
+            }
+
+        });
+
+        btn_leftpane_run_config.setOnAction(e -> {
+            if(starter.isCalculationsDone()){
+                mainGUI.getRoot().setCenter(runInfoDialogue.getGridPane());
+                // show info (parameter / input / output / ...)
+                // ask for new configuration
+            } else {
+                mainGUI.getRoot().setCenter(mainGUI.getConfig_dialogue().getConfig_gridpane());
+            }
+        });
+
+        runInfoDialogue.getBtn_new_config().setOnAction(e -> {
+            mainGUI.getRoot().setCenter(mainGUI.getConfig_dialogue().getConfig_gridpane());
+            clear();
+        });
+
+
+    }
+
+    private void clear() {
+        btn_leftpane_lengthDist.setDisable(true);
+        btn_leftpane_identityDist.setDisable(true);
+        btn_leftpane_damageProfile.setDisable(true);
+        starter.setCalculationsDone(false);
+        btn_inputfile.setTooltip(null);
+        btn_output.setTooltip(null);
+        btn_reference.setTooltip(null);
+    }
+
+    private void runDamageProfiler() {
+
+        // set all user options
+        communicator.setLength(Integer.parseInt(textfield_length.getText()));
+        communicator.setThreshold(Integer.parseInt(textfield_threshold.getText()));
+        communicator.setSsLibsProtocolUsed(checkbox_ssLibs_protocol.isSelected());
+        communicator.setUse_merged_and_mapped_reads(checkbox_use_merged_reads.isSelected());
+        communicator.setyAxis_damageplot(Double.parseDouble(textfield_y_axis_height.getText()));
+        communicator.setTitle_plots(textfield_title.getText());
+
+        // set colors
+        communicator.setColor_DP_C_to_T(this.advancedPlottingOptionsDialogue.getTabAdvancedSettingsDamagePlot().getColorPicker_C_to_T().getValue());
+        communicator.setColor_DP_G_to_A(this.advancedPlottingOptionsDialogue.getTabAdvancedSettingsDamagePlot().getColorPicker_G_to_A().getValue());
+        communicator.setColor_DP_insertions(this.advancedPlottingOptionsDialogue.getTabAdvancedSettingsDamagePlot().getColorPicker_insertions().getValue());
+        communicator.setColor_DP_deletions(this.advancedPlottingOptionsDialogue.getTabAdvancedSettingsDamagePlot().getColorPicker_deletions().getValue());
+        communicator.setColor_DP_other(this.advancedPlottingOptionsDialogue.getTabAdvancedSettingsDamagePlot().getColorPicker_others().getValue());
+
+
+        if(textfield_species.getText().equals(""))
+            communicator.setSpecies_ref_identifier(null);
+        else
+            communicator.setSpecies_ref_identifier(textfield_species.getText());
+
+        if(!textfield_title.getText().equals("")){
+            communicator.setTitle_plots(textfield_title.getText());
+        }
+
+
+        try {
+            // add progress indicator
+            Task startCalculuations = new Task() {
+                @Override
+                protected Object call() throws Exception {
+                    starter.start(communicator);
+                    runInfoDialogue.updateParameters();
+                    return true;
+                }
+            };
+
+            progressBarController.activate(startCalculuations);
+
+            startCalculuations.setOnSucceeded((EventHandler<Event>) event -> {
+                // replace config with result org.damageprofiler.GUI
+                btn_leftpane_lengthDist.setDisable(false);
+                btn_leftpane_identityDist.setDisable(false);
+                btn_leftpane_damageProfile.setDisable(false);
+                generateDamageProfile();
+                progressBarController.stop();
+            });
+
+            new Thread(startCalculuations).start();
+
+        } catch (Exception e1) {
+            e1.printStackTrace();
+        }
+
+    }
+
+    /**
+     * The following methods generate the result plots after successful damage profile calculations.
+     *    todo: if plot already created, just reload
+     */
+
+    private void generateLengthDist() {
+
+        JFreeChart[] lengthCharts = starter.getOutputGenerator().getLengthDistPlots();
+
+        TabPane tabPane_lengthDist = new TabPane();
+        Tab allData = new Tab("All data");
+        Tab splitData = new Tab("Forward vs. Reverse");
+
+        ChartViewer viewerLengthAll = new ChartViewer(lengthCharts[0]);
+        ChartViewer viewerLengthSep = new ChartViewer(lengthCharts[1]);
+
+        // disable zoom on x-axis
+        viewerLengthAll.getCanvas().setDomainZoomable(false);
+        viewerLengthAll.getCanvas().setDomainZoomable(false);
+
+        allData.setContent(viewerLengthAll);
+        splitData.setContent(viewerLengthSep);
+
+        tabPane_lengthDist.getTabs().addAll(allData, splitData);
+
+        mainGUI.getRoot().setCenter(tabPane_lengthDist);
+
+    }
+
+    private void generateIdentityDist() {
+        ChartViewer viewerEditDistance = new ChartViewer(starter.getOutputGenerator().getEditDist_chart());
+        mainGUI.getRoot().setCenter(viewerEditDistance);
+
+    }
+
+    private void generateDamageProfile() {
+
+        JFreeChart[] dpCharts = starter.getOutputGenerator().getDP_chart();
+        if(dpCharts.length==1){
+            ChartViewer viewer5prime = new ChartViewer(dpCharts[0]);
+            viewer5prime.getCanvas().setDomainZoomable(false);
+            mainGUI.getRoot().setCenter(viewer5prime);
+        } else if(dpCharts.length == 2){
+
+            TabPane tabPane_damagePlot = new TabPane();
+            Tab fivePrime = new Tab("5'end");
+            Tab threePrime = new Tab("3'end");
+
+            ChartViewer viewer5prime = new ChartViewer(dpCharts[0]);
+            ChartViewer viewer3prime = new ChartViewer(dpCharts[1]);
+
+            // disable zoom on x-axis
+            viewer5prime.getCanvas().setDomainZoomable(false);
+            viewer3prime.getCanvas().setDomainZoomable(false);
+
+            fivePrime.setContent(viewer5prime);
+            threePrime.setContent(viewer3prime);
+
+            tabPane_damagePlot.getTabs().addAll(fivePrime, threePrime);
+
+            mainGUI.getRoot().setCenter(tabPane_damagePlot);
+        }
+    }
+
+
+    /**
+     * This method checks if all mandatory fields are set. Otherwise, it's not possible to run the tool.
+     * @return
+     */
+    private boolean checkIfInputWasSelected() {
+        boolean tmp = false;
+        if (communicator.getInput() != null && communicator.getReference() != null && communicator.getOutfolder() != null) {
+            if (communicator.getInput().length() != 0) {
+                tmp = true;
+            }
+        }
+        return tmp;
+    }
+
+
+
+}
diff --git a/src/main/java/org/damageprofiler/controller/PlottingSettingController.java b/src/main/java/org/damageprofiler/controller/PlottingSettingController.java
new file mode 100644
index 0000000..43dcda7
--- /dev/null
+++ b/src/main/java/org/damageprofiler/controller/PlottingSettingController.java
@@ -0,0 +1,25 @@
+package org.damageprofiler.controller;
+
+import org.damageprofiler.GUI.Dialogues.AdvancedPlottingOptionsDialogue;
+import org.damageprofiler.GUI.Dialogues.TabAdvancedSettingsDamagePlot;
+
+public class PlottingSettingController {
+
+    public PlottingSettingController(){
+
+    }
+
+    /**
+     * Adding all listener to advancedPlottingOptionsDialogue
+     *
+     * @param advancedPlottingOptionsDialogue
+     */
+    public void addListener(AdvancedPlottingOptionsDialogue advancedPlottingOptionsDialogue) {
+        TabAdvancedSettingsDamagePlot dp_settings_pane = advancedPlottingOptionsDialogue.getTabAdvancedSettingsDamagePlot();
+        dp_settings_pane.getBtn_reset().setOnAction(e ->{
+            dp_settings_pane.reset();
+
+        });
+
+    }
+}
diff --git a/src/main/java/org/damageprofiler/controller/ProgressBarController.java b/src/main/java/org/damageprofiler/controller/ProgressBarController.java
new file mode 100755
index 0000000..e1d04e4
--- /dev/null
+++ b/src/main/java/org/damageprofiler/controller/ProgressBarController.java
@@ -0,0 +1,34 @@
+package org.damageprofiler.controller;
+
+import javafx.concurrent.Task;
+import javafx.geometry.Insets;
+import javafx.scene.control.ProgressBar;
+
+public class ProgressBarController {
+
+    private ProgressBar progressBar;
+
+
+    public void create(){
+        progressBar = new ProgressBar(0);
+        progressBar.setDisable(true);
+        progressBar.setPadding(new Insets(5,5,5,5));
+    }
+
+    public void activate(Task task){
+        progressBar.progressProperty().unbind();
+        progressBar.setProgress(0);
+        progressBar.progressProperty().bind(task.progressProperty());
+
+    }
+
+    public void stop(){
+        progressBar.progressProperty().unbind();
+        progressBar.setProgress(0);
+        progressBar.setDisable(true);
+    }
+
+    public ProgressBar getProgressBar() {
+        return progressBar;
+    }
+}
diff --git a/src/main/java/org/damageprofiler/controller/TabPaneAdvPlottingController.java b/src/main/java/org/damageprofiler/controller/TabPaneAdvPlottingController.java
new file mode 100755
index 0000000..4f85de9
--- /dev/null
+++ b/src/main/java/org/damageprofiler/controller/TabPaneAdvPlottingController.java
@@ -0,0 +1,4 @@
+package org.damageprofiler.controller;
+
+public class TabPaneAdvPlottingController {
+}
diff --git a/src/main/resources/logo.png b/src/main/resources/logo.png
new file mode 100755
index 0000000..7c839a9
Binary files /dev/null and b/src/main/resources/logo.png differ