fixed issue #109 Display panel retained pointer to auto annotate object even after delete.

Author: risserlin

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/autoannotate/AutoAnnotationManager.java

@@ -293,5 +293,14 @@ public void setClusterTableUpdating(boolean clusterTableUpdating) {
 		this.clusterTableUpdating = clusterTableUpdating;
 	}
 
-	
+	public AutoAnnotationParameters getParams(){
+		//get the current View
+		CyNetworkView selectedView = this.annotationPanel.getCurrentView();
+
+		if (networkViewToAutoAnnotationParameters.containsKey(selectedView)) 
+			
+			return networkViewToAutoAnnotationParameters.get(selectedView);
+		else
+			return null;
+	}
 }

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/autoannotate/task/cluster/DrawClusterLabelTask.java

@@ -39,12 +39,14 @@ public void drawTextLabel() {
 		// Set the text of the label
 		String labelText = cluster.getLabel();
 
-		Map<String, String> ellipseArgs = cluster.getEllipse().getArgMap();
-		double xPos = Double.parseDouble(ellipseArgs.get("x"));
-		double yPos = Double.parseDouble(ellipseArgs.get("y"));
-		double width = Double.parseDouble(ellipseArgs.get("width"));
-		double height = Double.parseDouble(ellipseArgs.get("height"));
-		
+		double xPos= 0.0,yPos= 0.0,width= 0.0,height = 0.0;
+		if(cluster.getEllipse() != null){
+			Map<String, String> ellipseArgs = cluster.getEllipse().getArgMap();
+			xPos = Double.parseDouble(ellipseArgs.get("x"));
+			yPos = Double.parseDouble(ellipseArgs.get("y"));
+			width = Double.parseDouble(ellipseArgs.get("width"));
+			height = Double.parseDouble(ellipseArgs.get("height"));
+		}
 		// Create the text annotation 
 		Integer labelFontSize = null;
 		if (constantFontSize) {

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/autoannotate/view/AutoAnnotationPanel.java

@@ -430,8 +430,8 @@ public void itemStateChanged(ItemEvent itemEvent) {
 				CyGroupFactory groupFactory = autoAnnotationManager.getGroupFactory();
 				if (itemEvent.getStateChange() == ItemEvent.SELECTED) {
 					AnnotationSet annotationSet = (AnnotationSet) itemEvent.getItem();
-					displayOptionsPanel.setSelectedAnnotationSet(annotationSet);
 					params.setSelectedAnnotationSet(annotationSet);
+					displayOptionsPanel.setSelectedAnnotationSet();					
 					// Update the selected annotation set
 					annotationSet.updateCoordinates();
 					String annotationSetName = annotationSet.getName();

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/autoannotate/view/DisplayOptionsPanel.java

@@ -47,7 +47,7 @@ public class DisplayOptionsPanel extends JPanel implements CytoPanelComponent {
 	private JCheckBox showEllipsesCheckBox;
 	private JRadioButton heatmapButton;
 	protected JPanel slidersPanel;
-
+	
 	private static String proportionalSizeButtonString = "Font size by # of nodes";
 	private static String constantSizeButtonString = "Constant font size";
 
@@ -116,8 +116,11 @@ public void actionPerformed(ActionEvent e) {
 		    		if (fontSize <= 0) {
 		    			throw new Exception();
 		    		}
-		    		selectedAnnotationSet.setFontSize(fontSize);
-		    		AutoAnnotationUtils.updateFontSizes();
+		    		setSelectedAnnotationSet();
+					if(selectedAnnotationSet != null){
+						selectedAnnotationSet.setFontSize(fontSize);
+						AutoAnnotationUtils.updateFontSizes();
+					}
 		    	} catch (Exception ex) {
 		            JOptionPane.showMessageDialog(null,
 		                    "Error: Please enter an integer bigger than 0", "Error Message",
@@ -169,6 +172,9 @@ private JPanel createShowAnnotationsCheckBoxPanel() {
 		showEllipsesCheckBox.addActionListener(new ActionListener() {
 			@Override
 			public void actionPerformed(ActionEvent e) {
+				//make sure we are working with the current selected network
+				setSelectedAnnotationSet();
+				
 				if (selectedAnnotationSet != null) {
 					selectedAnnotationSet.setShowEllipses(showEllipsesCheckBox.isSelected());
 					if (selectedAnnotationSet.isShowEllipses()) {
@@ -195,6 +201,9 @@ public void actionPerformed(ActionEvent e) {
 		showTextCheckBox.addActionListener(new ActionListener() {
 			@Override
 			public void actionPerformed(ActionEvent e) {
+				//make sure we are working with the current selected network
+				setSelectedAnnotationSet();
+				
 				if (selectedAnnotationSet != null) {
 					JCheckBox showTextCheckBox = (JCheckBox) e.getSource();
 					selectedAnnotationSet.setShowLabel(showTextCheckBox.isSelected());
@@ -228,6 +237,9 @@ private JPanel createLabelOptionsButtonPanel() {
 		labelOptionsButton.addActionListener(new ActionListener() {
 			@Override
 			public void actionPerformed(ActionEvent e) {
+				//make sure we are working with the current selected network
+				setSelectedAnnotationSet();
+				
 				if (selectedAnnotationSet != null) {
 					LabelOptionsEditor labelOptionsEditor = new LabelOptionsEditor(selectedAnnotationSet);
 					LabelOptions labelOptions = labelOptionsEditor.showDialog();
@@ -384,7 +396,8 @@ public String getTitle() {
 		return "Annotation Display Options Panel";
 	}
 
-	public void setSelectedAnnotationSet(AnnotationSet selectedAnnotationSet) {
-		this.selectedAnnotationSet = selectedAnnotationSet;
+	public void setSelectedAnnotationSet() {		
+			this.selectedAnnotationSet = AutoAnnotationManager.getInstance().getParams().getSelectedAnnotationSet();
+
 	}
 }