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.classpath

+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry excluding="be/ugent/psb/graphicalmodule/elements/ConditionAnnotationLegend.java|be/ugent/psb/graphicalmodule/elements/ConditionAnnotationMatrix.java|be/ugent/psb/graphicalmodule/actions/ExportToEPSAction.java|be/ugent/psb/graphicalmodule/actions/LoadAracycAction.java|be/ugent/psb/graphicalmodule/actions/LoadBiNGOAction.java|be/ugent/psb/graphicalmodule/actions/LoadConditionAnnotationAction.java|be/ugent/psb/graphicalmodule/actions/LoadGeneCheckListAction.java|be/ugent/psb/graphicalmodule/actions/LoadGeneLinkAction.java|be/ugent/psb/graphicalmodule/actions/LoadGeneMapAction.java|be/ugent/psb/graphicalmodule/actions/LoadMotifFileAction.java|be/ugent/psb/graphicalmodule/actions/LoadTopRegulatorsAction.java|be/ugent/psb/moduleviewer/actions/LoadAracycAction.java|be/ugent/psb/moduleviewer/actions/LoadBiNGOAction.java|be/ugent/psb/moduleviewer/actions/LoadConditionAnnotationAction.java|be/ugent/psb/moduleviewer/actions/LoadGeneCheckListAction.java|be/ugent/psb/moduleviewer/actions/LoadGeneLinkAction.java|be/ugent/psb/moduleviewer/actions/LoadGeneMapAction.java|be/ugent/psb/moduleviewer/actions/LoadMotifFileAction.java|be/ugent/psb/moduleviewer/actions/LoadTopRegulatorsAction.java|be/ugent/psb/moduleviewer/elements/ConditionAnnotationLegend.java|be/ugent/psb/moduleviewer/elements/ConditionAnnotationMatrix.java|docs/|be/ugent/psb/moduleviewer/parsers/LemoneXMLHandler.java|be/ugent/psb/moduleviewer/parsers/ModuleNetworkParser.java|be/ugent/psb/moduleviewer/OldDefaultCanvas.java" kind="src" path=""/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry combineaccessrules="false" kind="src" path="/ModuleGraphics"/>
+	<classpathentry kind="output" path=""/>
+</classpath>

.project

+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>ModuleViewer</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>

.settings/org.eclipse.jdt.core.prefs

+#Fri Apr 01 13:12:30 CEST 2011
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.source=1.6

be/ugent/psb/moduleviewer/DefaultCanvas.java

+package be.ugent.psb.moduleviewer;
+
+import java.awt.Dimension;
+
+import be.ugent.psb.modulegraphics.elements.Canvas;
+import be.ugent.psb.modulegraphics.elements.Spacer;
+import be.ugent.psb.moduleviewer.elements.ConditionLabels;
+import be.ugent.psb.moduleviewer.elements.EnigmaColorizer;
+import be.ugent.psb.moduleviewer.elements.ExpressionMatrix;
+import be.ugent.psb.moduleviewer.elements.GeneNames;
+import be.ugent.psb.moduleviewer.elements.Title;
+import be.ugent.psb.moduleviewer.model.GUIModel;
+import be.ugent.psb.moduleviewer.model.Model;
+import be.ugent.psb.moduleviewer.model.Module;
+import be.ugent.psb.moduleviewer.model.ModuleNetwork;
+
+
+/**
+ * A Default layout for a Canvas that looks up which elements to 
+ * draw in the graphical model of the module.
+ * 
+ * The Module itself is drawn anyway. If topregulators are given, they are drawn as well, together
+ * with the tree structure.
+ * 
+ * @author thpar
+ *
+ */
+public class DefaultCanvas extends Canvas {
+
+	private ModuleNetwork modnet;
+	private Module mod;
+	private GUIModel guiModel;
+	private String title;
+	private Model model;
+
+	public DefaultCanvas(Module mod, Model model, GUIModel guiModel, String title){
+		this.modnet = mod.getModuleNetwork();
+		this.mod = mod;
+		this.model = model;
+		this.guiModel = guiModel;
+		this.title = title;
+		
+		this.composeCanvas();
+
+	}
+
+	private void composeCanvas() {
+		//general settings
+		this.setHorizontalSpacing(5);
+		this.setVerticalSpacing(5);
+		this.setMargin(20);
+		
+		
+		//title
+		if (guiModel.isDrawFileName()){
+			this.add(new Title(title));
+			this.getLastAddedElement().setBottomMargin(10);
+			this.newRow();
+		}
+		
+		if (model.getRegulatorFile()!=null && mod.getRegulatorTree()!=null){
+			ExpressionMatrix regulatorMatrix = new ExpressionMatrix(mod.getRegulatorTree().getColumns(),
+					mod.getConditionTree(),
+					new EnigmaColorizer(modnet.getSigma(),modnet.getMean()),
+					true);
+			this.add(regulatorMatrix);
+
+			GeneNames regNames = new GeneNames(mod.getRegulatorTree().getColumns());
+			this.add(regNames);
+			
+			this.newRow();
+			this.add(new Spacer(new Dimension(0,10)));
+			this.newRow();
+		}
+		
+		ExpressionMatrix expressionMatrix = new ExpressionMatrix(mod.getGeneTree().getColumns(),
+				mod.getConditionTree(),
+				new EnigmaColorizer(modnet.getSigma(),modnet.getMean()),
+				true);
+		this.add(expressionMatrix);
+		
+		GeneNames geneNames = new GeneNames(mod.getGeneTree().getColumns());
+		this.add(geneNames);
+		
+		this.newRow();
+		
+		ConditionLabels condLabels = new ConditionLabels(mod.getConditionTree(), true);
+		this.add(condLabels);
+	}
+
+	
+}

be/ugent/psb/moduleviewer/MainMenu.java

+package be.ugent.psb.moduleviewer;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Observable;
+import java.util.Observer;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+
+import be.ugent.psb.moduleviewer.actions.ChangeEpsOutputDirAction;
+import be.ugent.psb.moduleviewer.actions.ExportToEPSAction;
+import be.ugent.psb.moduleviewer.actions.LoadAnnotationAction;
+import be.ugent.psb.moduleviewer.actions.LoadConditionTreeAction;
+import be.ugent.psb.moduleviewer.actions.LoadDataAction;
+import be.ugent.psb.moduleviewer.actions.LoadGeneTreeAction;
+import be.ugent.psb.moduleviewer.actions.LoadRegulatorTreeAction;
+import be.ugent.psb.moduleviewer.actions.LoadSessionAction;
+import be.ugent.psb.moduleviewer.actions.SaveSessionAsAction;
+import be.ugent.psb.moduleviewer.model.GUIModel;
+import be.ugent.psb.moduleviewer.model.Model;
+
+public class MainMenu extends JMenuBar implements Observer{
+
+	
+	private static final long serialVersionUID = 1L;
+	private JMenuItem saveSessionAsItem;
+	private Model model;
+	private GUIModel guiModel;
+	
+	public MainMenu(Model model, final GUIModel guiModel){
+
+		this.model = model;
+		model.addObserver(this);
+
+		this.guiModel = guiModel;
+		
+		JMenu fileMenu = new JMenu("File");
+		JMenuItem loadDataItem = new JMenuItem(new LoadDataAction(model, guiModel));
+		JMenuItem loadGeneTreeItem = new JMenuItem(new LoadGeneTreeAction(model, guiModel));
+		JMenuItem loadConditionTreeItem = new JMenuItem(new LoadConditionTreeAction(model, guiModel));
+		JMenuItem loadRegTreeItem = new JMenuItem(new LoadRegulatorTreeAction(model, guiModel));
+		JMenuItem loadAnnotItem = new JMenuItem(new LoadAnnotationAction(model, guiModel));
+		
+		saveSessionAsItem = new JMenuItem(new SaveSessionAsAction(model, guiModel));
+		saveSessionAsItem.setEnabled(false);
+		JMenuItem loadSessionItem = new JMenuItem(new LoadSessionAction(model, guiModel));
+		
+
+
+		JMenuItem exportItem = new JMenuItem(new ExportToEPSAction(model, guiModel));
+		JMenuItem exitItem = new JMenuItem("Exit");
+		exitItem.addActionListener(new ActionListener(){
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				System.exit(0);
+			}
+		});
+		fileMenu.add(loadDataItem);
+		fileMenu.add(loadGeneTreeItem);
+		fileMenu.add(loadConditionTreeItem);
+		fileMenu.add(loadRegTreeItem);
+		fileMenu.add(loadAnnotItem);
+		
+		fileMenu.addSeparator();
+		
+		fileMenu.add(saveSessionAsItem);
+		fileMenu.add(loadSessionItem);
+		
+		fileMenu.addSeparator();
+		
+		fileMenu.add(exportItem);
+		fileMenu.addSeparator();
+		
+		fileMenu.add(exitItem);
+		
+		
+		JMenu settingsMenu = new JMenu("Settings");
+		JMenuItem epsOutputDirItem = new JMenuItem(new ChangeEpsOutputDirAction(guiModel));
+		settingsMenu.add(epsOutputDirItem);
+		
+		
+
+		JMenu helpMenu = new JMenu("Help");
+		JMenuItem aboutItem = new JMenuItem("About...");
+		aboutItem.addActionListener(new ActionListener() {
+			
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				JOptionPane.showMessageDialog(guiModel.getTopContainer(), "LeMoNe Viewer. Written by thpar");
+			}
+		});
+
+		helpMenu.add(aboutItem);
+		
+		
+		add(fileMenu);
+		add(settingsMenu);
+		add(helpMenu);
+	}
+
+	@Override
+	public void update(Observable o, Object arg) {
+		this.saveSessionAsItem.setEnabled(model.isEssentialsLoaded());
+	}
+}

be/ugent/psb/moduleviewer/ModuleLabel.java

+package be.ugent.psb.moduleviewer;
+
+import java.awt.Dimension;
+import java.util.Observable;
+import java.util.Observer;
+
+import javax.swing.ImageIcon;
+
+import be.ugent.psb.modulegraphics.display.CanvasLabel;
+import be.ugent.psb.modulegraphics.elements.Element;
+import be.ugent.psb.moduleviewer.model.ConditionNode;
+import be.ugent.psb.moduleviewer.model.GUIModel;
+import be.ugent.psb.moduleviewer.model.Model;
+import be.ugent.psb.moduleviewer.model.Module;
+import be.ugent.psb.moduleviewer.model.ModuleNetwork;
+import be.ugent.psb.moduleviewer.model.UnknownItemException;
+
+
+
+public class ModuleLabel extends CanvasLabel implements Observer{
+
+	private static final long serialVersionUID = 1L;
+	private GUIModel guiModel;
+
+//	private int currentPaintedModule = -1;
+	private ModuleNetwork modnet;
+	
+	private Dimension currentCanvasSize = new Dimension();
+	//FIXME DONT DO THIS HARD CODED!
+	private final String GENEFETCH = "http://bioinformatics.psb.ugent.be/webtools/genefetch/search.html";
+	private Model model; 
+		
+		
+	public ModuleLabel(Model model, GUIModel guiModel){
+		this.model = model;
+		this.modnet = model.getModnet();
+		this.guiModel = guiModel;
+		this.guiModel.addObserver(this);
+		this.setSplash(new ImageIcon(this.getClass().getResource("/icons/lemone.png")));
+	}
+	
+	
+	public Element initCanvas() {
+		//don't even start if we don't have the essential data loaded
+		if (!model.isEssentialsLoaded()) return null;
+		
+		
+		int displayedModule = guiModel.getDisplayedModule();
+		Module mod = null;
+		try {
+			mod = modnet.getModule(displayedModule);
+		} catch (UnknownItemException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		
+		ConditionNode n = mod.getConditionTree();
+//		mod.hierarchicalTree = n;
+		
+//		for (TreeNode node : mod.hierarchicalTree.getInternalNodes()){
+//			Collections.sort(node.testSplits);
+//			node.regulationSplit = node.testSplits.get(0);
+//		}
+		
+		DefaultCanvas canvas = new DefaultCanvas(mod, model, guiModel, "Module "+displayedModule);
+		setCanvas(canvas);
+		
+//		addCanvasListeners(canvas);
+		
+				
+		currentCanvasSize = canvas.getDimension(this.getGraphics());
+		setPreferredSize(currentCanvasSize);
+		revalidate();
+		
+//		this.currentPaintedModule = displayedModule;
+		return canvas;
+	}
+
+
+
+//	private void addCanvasListeners(DefaultCanvas canvas) {
+//		canvas.getGeneNames().addMouseListener(new MouseAdapter(){
+//			@Override
+//			public void mouseClicked(MouseEvent e) {
+//				GeneNames gn = (GeneNames)e.getSource();
+//				String gnString = gn.getHitGeneName(e.getX(), e.getY());
+//				if (Desktop.isDesktopSupported()){
+//					guiModel.setStateString("GeneFetching: "+gnString);
+//					Desktop desktop = Desktop.getDesktop();
+//					 if (desktop.isSupported(Desktop.Action.BROWSE)) {
+//						 try {
+//							URI uri = new URI(GENEFETCH+"?gene="+gnString);
+//							 desktop.browse(uri);
+//						} catch (URISyntaxException e1) {
+//							// TODO Auto-generated catch block
+//							e1.printStackTrace();
+//						} catch (IOException e1) {
+//							// TODO Auto-generated catch block
+//							e1.printStackTrace();
+//						}
+//
+//				     } else {
+//				    	 System.err.println("Can't identify web browser");
+//				     }
+//				} else {
+//					System.err.println("No Desktop operations supported!");
+//				}
+//			}
+//		});
+//		
+//		canvas.getMatrix().addMouseListener(new MouseAdapter(){
+//			@Override
+//			public void mouseClicked(MouseEvent e) {
+//				ExpressionMatrix matrix = (ExpressionMatrix)e.getSource();
+//				double data = matrix.getHitData(e.getX(), e.getY());
+//				guiModel.setStateString(String.valueOf(data));
+//			}
+//		});
+//		
+//		ExpressionMatrix topRegMatrix = canvas.getTopRegMatrix();
+//		if (topRegMatrix!=null){
+//			topRegMatrix.addMouseListener(new MouseAdapter(){
+//				@Override
+//				public void mouseClicked(MouseEvent e) {
+//					ExpressionMatrix matrix = (ExpressionMatrix)e.getSource();
+//					double data = matrix.getHitData(e.getX(), e.getY());
+//					guiModel.setStateString(String.valueOf(data));
+//				}
+//			});
+//		}
+//		
+//		GeneNames topRegGeneNames = canvas.getTopRegGeneNames();
+//		if (topRegGeneNames!=null){
+//			canvas.getTopRegGeneNames().addMouseListener(new MouseAdapter(){
+//				@Override
+//				public void mouseClicked(MouseEvent e) {
+//					GeneNames gn = (GeneNames)e.getSource();
+//					String gnString = gn.getHitGeneName(e.getX(), e.getY());
+//					guiModel.setStateString(gnString);
+//				}
+//			});
+//		}
+//		canvas.getConditionLabels().addMouseListener(new MouseAdapter(){
+//			@Override
+//			public void mouseClicked(MouseEvent e) {
+//				ConditionLabels cl = (ConditionLabels)e.getSource();
+//				String cnString = cl.getHitConditionName(e.getX(), e.getY());
+//				guiModel.setStateString(cnString);
+//			}
+//		});
+////		ConditionAnnotationMatrix condAnnotMatrix = canvas.getConditionAnnotationMatrix();
+////		if (condAnnotMatrix!=null){
+////			canvas.getConditionAnnotationMatrix().addMouseListener(new MouseAdapter(){
+////				@Override
+////				public void mouseClicked(MouseEvent e) {
+////					ConditionAnnotationMatrix cam = (ConditionAnnotationMatrix)e.getSource();
+////					String cnString = cam.getHitAnnotation(e.getX(), e.getY());
+////					guiModel.setStateString(cnString);
+////				}
+////			});
+////		}
+//	}
+
+
+	@Override
+	public void update(Observable o, Object arg) {
+		initCanvas();
+		repaint();
+	}
+
+	public Dimension getCurrentCanvasSize() {
+		return currentCanvasSize;
+	}
+	
+	
+	
+	
+}

be/ugent/psb/moduleviewer/ModuleViewer.java

+package be.ugent.psb.moduleviewer;
+
+
+public class ModuleViewer {
+
+	public static void main(String[] args) {
+
+		ViewerGUI gui = new ViewerGUI();
+		gui.startGUI();
+
+
+	}
+
+}
+

be/ugent/psb/moduleviewer/NavigationToolBar.java

+package be.ugent.psb.moduleviewer;
+
+import java.awt.Dimension;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.util.Observable;
+import java.util.Observer;
+
+import javax.swing.BoxLayout;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JLabel;
+import javax.swing.JTextField;
+import javax.swing.JToolBar;
+
+import be.ugent.psb.moduleviewer.actions.ExportToEPSAction;
+import be.ugent.psb.moduleviewer.actions.NavModuleAction;
+import be.ugent.psb.moduleviewer.model.GUIModel;
+import be.ugent.psb.moduleviewer.model.Model;
+import be.ugent.psb.moduleviewer.model.ModuleNetwork;
+
+public class NavigationToolBar extends JToolBar implements Observer, FocusListener, KeyListener{
+
+	private static final long serialVersionUID = 1L;
+	private JLabel totalLabel;
+	private GUIModel guiModel;
+	private JTextField locationField;
+	private Model model;	
+	
+	public NavigationToolBar(Model model, GUIModel guiModel){
+		super("LeMoNe Navigation");
+
+		this.model = model;
+		this.guiModel = guiModel;
+		guiModel.addObserver(this);
+		
+		locationField = new JTextField();
+		locationField.setColumns(4);
+		locationField.setMaximumSize(new Dimension(30, 50));
+		locationField.addFocusListener(this);
+		locationField.addKeyListener(this);
+		totalLabel = new JLabel();
+		
+		JButton nextButton = new JButton();
+		JButton prevButton = new JButton();
+		JButton exportButton = new JButton();
+		
+		nextButton.setAction(new NavModuleAction(new ImageIcon(getClass().getResource("/icons/next.png")),+1, guiModel));
+		prevButton.setAction(new NavModuleAction(new ImageIcon(getClass().getResource("/icons/prev.png")),-1, guiModel));
+		exportButton.setAction(new ExportToEPSAction(new ImageIcon(getClass().getResource("/icons/eps_icon.jpg")),model, guiModel));
+		
+		setLayout(new BoxLayout(this, BoxLayout.X_AXIS));
+		
+		add(locationField);
+		add(totalLabel);
+		add(prevButton);
+		add(nextButton);
+		
+		add(new JToolBar.Separator());
+		add(exportButton);
+		
+		this.update(null, null);
+	}
+
+
+	@Override
+	public void update(Observable o, Object arg) {
+		int modnr = guiModel.getDisplayedModule();
+		ModuleNetwork modnet = model.getModnet();
+		locationField.setText(String.valueOf(modnr));
+		int totalModnr = 0;
+		String totalString;
+		if (modnet.getModules() != null){
+			totalModnr=	modnet.getModules().size();
+			totalString = new String("/"+totalModnr);
+		} else {
+			totalString = new String("--");
+		}
+		totalLabel.setText(totalString);
+	}
+
+
+	@Override
+	public void focusGained(FocusEvent e) {
+		// TODO Auto-generated method stub
+		
+	}
+
+
+	@Override
+	public void focusLost(FocusEvent e) {
+		goToModule();
+	}
+
+	private void goToModule(){
+		String content = locationField.getText();
+		try {
+			int contNr = Integer.parseInt(content);
+			guiModel.setDisplayedModule(contNr);
+		} catch (NumberFormatException e1) {
+			locationField.setText(String.valueOf(guiModel.getDisplayedModule()));
+		}		
+	}
+
+	@Override
+	public void keyPressed(KeyEvent e) {
+		if (e.getKeyChar()=='\n'){
+			goToModule();
+		}
+	}
+
+
+	@Override
+	public void keyReleased(KeyEvent e) {
+		// TODO Auto-generated method stub
+		
+	}
+
+
+	@Override
+	public void keyTyped(KeyEvent e) {
+		// TODO Auto-generated method stub
+		
+	}
+
+
+	
+}

be/ugent/psb/moduleviewer/OldDefaultCanvas.java

+package be.ugent.psb.moduleviewer;
+
+import be.ugent.psb.modulegraphics.elements.Canvas;
+import be.ugent.psb.modulegraphics.elements.Element;
+import be.ugent.psb.moduleviewer.elements.ConditionLabels;
+import be.ugent.psb.moduleviewer.elements.ExpressionMatrix;
+import be.ugent.psb.moduleviewer.elements.GeneNames;
+import be.ugent.psb.moduleviewer.elements.Title;
+import be.ugent.psb.moduleviewer.model.GUIModel;
+import be.ugent.psb.moduleviewer.model.Module;
+import be.ugent.psb.moduleviewer.model.ModuleNetwork;
+
+/**
+ * A Default layout for a Canvas that looks up which elements to 
+ * draw in the graphical model of the module.
+ * 
+ * The Module itself is drawn anyway. If topregulators are given, they are drawn as well, together
+ * with the tree structure.
+ * 
+ * @author thpar
+ *
+ */
+public class OldDefaultCanvas extends Canvas {
+	
+	ModuleNetwork modnet;
+	
+	private ExpressionMatrix matrix;
+	private GeneNames geneNames;
+	private ExpressionMatrix topRegMatrix;
+	private GeneNames topRegGeneNames;
+//	private ConditionAnnotationMatrix conditionAnnotationMatrix;
+	private Element conditionLabels;
+	
+	public OldDefaultCanvas(Module mod, GUIModel guiModel, String title){
+
+		this.modnet = mod.getModuleNetwork();
+