Moved gmt file check. Fixes #110.

mikekucera · mikekucera · commit f7842489b00e · 2015-06-26T10:41:05.000-04:00
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/CyActivator.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/CyActivator.java
@@ -124,7 +124,7 @@ public void start(BundleContext bc) {
 		//create the Panels
 		BulkEMCreationPanel bulkEmPanel = new BulkEMCreationPanel(cySwingApplicationRef,fileUtil,registrar, sessionManager, streamUtil, cyApplicationManagerRef);		
 		EnrichmentMapInputPanel emPanel = new EnrichmentMapInputPanel(cyNetworkFactoryRef, cyApplicationManagerRef, cyNetworkManagerRef, cyNetworkViewManagerRef, tableFactory, tableManager, cyNetworkViewFactoryRef, visualMappingManagerRef, visualStyleFactoryRef,  continuousMappingFunctionFactoryRef,discreteMappingFunctionFactoryRef, passthroughMappingFunctionFactoryRef, dialogTaskManager, sessionManager, cySwingApplicationRef, openBrowserRef,fileUtil,streamUtil,registrar,layoutManager,mapTableToNetworkTable,bulkEmPanel);				
-		PostAnalysisPanel postEMPanel = new PostAnalysisPanel(cyApplicationManagerRef,cySwingApplicationRef, openBrowserRef,fileUtil,sessionManager, streamUtil,registrar, dialogTaskManager,eventHelper, compilerServiceRef, visualMappingManagerRef, visualStyleFactoryRef, continuousMappingFunctionFactoryRef, discreteMappingFunctionFactoryRef, passthroughMappingFunctionFactoryRef);		
+		PostAnalysisPanel postEMPanel = new PostAnalysisPanel(cyApplicationManagerRef,cySwingApplicationRef, openBrowserRef,fileUtil,sessionManager, streamUtil,registrar, dialogTaskManager, syncTaskManager, eventHelper, compilerServiceRef, visualMappingManagerRef, visualStyleFactoryRef, continuousMappingFunctionFactoryRef, discreteMappingFunctionFactoryRef, passthroughMappingFunctionFactoryRef);		
 		//create two instances of the heatmap panel
 		HeatMapPanel heatMapPanel_node = new HeatMapPanel(true, cySwingApplicationRef, fileUtil, cyApplicationManagerRef, openBrowserRef,dialogTaskManager,streamUtil);
 		HeatMapPanel heatMapPanel_edge = new HeatMapPanel(false, cySwingApplicationRef, fileUtil, cyApplicationManagerRef, openBrowserRef,dialogTaskManager,streamUtil);
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/PostAnalysisParameters.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/PostAnalysisParameters.java
@@ -169,7 +169,7 @@ public FilterParameters getRankTestParameters() {
      */
     public String checkGMTfiles() {
         String signatureGMTFileName = getSignatureGMTFileName();
-		if(signatureGMTFileName.isEmpty() || !EnrichmentMapParameters.checkFile(signatureGMTFileName))
+		if(signatureGMTFileName == null || signatureGMTFileName.isEmpty() || !EnrichmentMapParameters.checkFile(signatureGMTFileName))
             return "Signature GMT file can not be found \n";
         return "";
     }
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/actions/BuildPostAnalysisActionListener.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/actions/BuildPostAnalysisActionListener.java
@@ -117,7 +117,10 @@ public BuildPostAnalysisActionListener (PostAnalysisInputPanel panel,
     }
 
     public void actionPerformed(ActionEvent event) {
-
+    	runPostAnalysis();
+    }
+    
+    public void runPostAnalysis() {
         //make sure that the minimum information is set in the current set of parameters
     	PostAnalysisParameters paParams = inputPanel.getPaParams();
         
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/PostAnalysisInputPanel.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/PostAnalysisInputPanel.java
@@ -87,6 +87,7 @@
 import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
 import org.cytoscape.view.vizmap.VisualMappingManager;
 import org.cytoscape.view.vizmap.VisualStyleFactory;
+import org.cytoscape.work.SynchronousTaskManager;
 import org.cytoscape.work.swing.DialogTaskManager;
 
 
@@ -105,7 +106,8 @@ public class PostAnalysisInputPanel extends JPanel {
 	private final CyServiceRegistrar registrar;
 	private final CySessionManager sessionManager;
 	private final StreamUtil streamUtil;
-	private final DialogTaskManager dialog;
+	private final DialogTaskManager dialogTaskManager;
+	private final SynchronousTaskManager syncTaskManager;
 	private final CyEventHelper eventHelper;
 	private final EquationCompiler equationCompiler;
     
@@ -133,7 +135,7 @@ public class PostAnalysisInputPanel extends JPanel {
     public PostAnalysisInputPanel(CyApplicationManager cyApplicationManager, CySwingApplication application, 
     		OpenBrowser browser,FileUtil fileUtil, CySessionManager sessionManager,
     		StreamUtil streamUtil,CyServiceRegistrar registrar,
-    		DialogTaskManager dialog,CyEventHelper eventHelper, EquationCompiler equationCompiler,
+    		DialogTaskManager dialog, SynchronousTaskManager syncTaskManager, CyEventHelper eventHelper, EquationCompiler equationCompiler,
     		VisualMappingManager visualMappingManager, VisualStyleFactory visualStyleFactory,
     		VisualMappingFunctionFactory vmfFactoryContinuous, VisualMappingFunctionFactory vmfFactoryDiscrete, VisualMappingFunctionFactory vmfFactoryPassthrough) {
     	
@@ -144,7 +146,8 @@ public PostAnalysisInputPanel(CyApplicationManager cyApplicationManager, CySwing
         this.registrar = registrar;
         this.sessionManager = sessionManager;
         this.streamUtil = streamUtil;
-        this.dialog = dialog;
+        this.dialogTaskManager = dialog;
+        this.syncTaskManager = syncTaskManager;
         this.eventHelper = eventHelper;
         this.equationCompiler = equationCompiler;
         this.visualMappingManager = visualMappingManager;
@@ -155,7 +158,7 @@ public PostAnalysisInputPanel(CyApplicationManager cyApplicationManager, CySwing
     		
         
         // Create the two main panels, set the default one
-        knownSignaturePanel = new PostAnalysisKnownSignaturePanel(this, cyApplicationManager, application, streamUtil, dialog, fileUtil);
+        knownSignaturePanel = new PostAnalysisKnownSignaturePanel(this, cyApplicationManager, application, streamUtil, syncTaskManager);
         signatureDiscoveryPanel = new PostAnalysisSignatureDiscoveryPanel(this, cyApplicationManager, application, streamUtil, dialog, fileUtil);
        
         userInputPanel = new JPanel(new BorderLayout());
@@ -176,7 +179,7 @@ public PostAnalysisInputPanel(CyApplicationManager cyApplicationManager, CySwing
     }
     
 
-    private void flipPanels(JPanel toRemove, JPanel toAdd){
+    private void flipPanels(JPanel toRemove, JPanel toAdd) {
     	userInputPanel.remove(toRemove);
     	userInputPanel.add(toAdd, BorderLayout.CENTER);
     	userInputPanel.revalidate();
@@ -304,9 +307,19 @@ public void actionPerformed(ActionEvent evt) {
 
         JButton importButton = new JButton();
         importButton.setText("Run");
-        importButton.addActionListener(new BuildPostAnalysisActionListener(this, sessionManager, streamUtil, application, cyApplicationManager, 
-        		                                                           dialog, eventHelper, equationCompiler, visualMappingManager, visualStyleFactory,
-        																   vmfFactoryContinuous, vmfFactoryDiscrete, vmfFactoryPassthrough));
+        importButton.addActionListener(new ActionListener() {
+			public void actionPerformed(ActionEvent e) {
+				boolean okToRun = beforeRun();
+				if(okToRun) {
+					BuildPostAnalysisActionListener action = new BuildPostAnalysisActionListener(PostAnalysisInputPanel.this, sessionManager, streamUtil, application, cyApplicationManager, 
+	                        dialogTaskManager, eventHelper, equationCompiler, visualMappingManager, visualStyleFactory, vmfFactoryContinuous, vmfFactoryDiscrete, vmfFactoryPassthrough);
+					action.runPostAnalysis();
+				}
+			}
+		});
+        		
+        		
+        		
         importButton.setEnabled(true);
 
         panel.add(resetButton);
@@ -323,14 +336,13 @@ protected File chooseGMTFile(JFormattedTextField textField) {
        
         // Get the file name
         File file = fileUtil.getFile(SwingUtil.getWindowInstance(this), "Import Signature GMT File", FileUtil.LOAD, all_filters);
-        getPaParams().setSignatureGMTFileName("");
         
         if(file != null) {
-        	textField.setForeground(PostAnalysisInputPanel.checkFile(file.getAbsolutePath()));
-        	textField.setText(file.getAbsolutePath());
-        	textField.setValue(file.getAbsolutePath());
-            getPaParams().setSignatureGMTFileName(file.getAbsolutePath());
-            textField.setToolTipText(file.getAbsolutePath());
+        	String absolutePath = file.getAbsolutePath();
+			textField.setForeground(PostAnalysisInputPanel.checkFile(absolutePath));
+        	textField.setText(absolutePath);
+        	textField.setValue(absolutePath);
+            textField.setToolTipText(absolutePath);
             textField.setCaretPosition(textField.getText().length());
         }
         
@@ -450,4 +462,11 @@ public void setAvSigCount(int avSigCount) {
 		}
 	}
 	
+	public boolean beforeRun() {
+		if(knownSignature.isSelected())
+			return knownSignaturePanel.beforeRun();
+		else
+			return true;
+	}
+	
 }
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/PostAnalysisKnownSignaturePanel.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/PostAnalysisKnownSignaturePanel.java
@@ -2,12 +2,12 @@
 
 import java.awt.BorderLayout;
 import java.awt.Color;
+import java.awt.Font;
 import java.awt.Insets;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
-import java.io.File;
 
 import javax.swing.BoxLayout;
 import javax.swing.JButton;
@@ -25,8 +25,7 @@
 import org.cytoscape.application.CyApplicationManager;
 import org.cytoscape.application.swing.CySwingApplication;
 import org.cytoscape.io.util.StreamUtil;
-import org.cytoscape.util.swing.FileUtil;
-import org.cytoscape.work.swing.DialogTaskManager;
+import org.cytoscape.work.SynchronousTaskManager;
 
 @SuppressWarnings("serial")
 public class PostAnalysisKnownSignaturePanel extends JPanel {
@@ -36,8 +35,7 @@ public class PostAnalysisKnownSignaturePanel extends JPanel {
 	private final CyApplicationManager cyApplicationManager;
     private final CySwingApplication application;
 	private final StreamUtil streamUtil;
-	private final DialogTaskManager dialog;
-	private final FileUtil fileUtil;
+	private final SynchronousTaskManager syncTaskManager;
 	
 	// 'Known Signature Panel' parameters
 	private EnrichmentMap map;
@@ -46,21 +44,20 @@ public class PostAnalysisKnownSignaturePanel extends JPanel {
     private PostAnalysisWeightPanel weightPanel;
     
 	private JFormattedTextField knownSignatureGMTFileNameTextField;
+
 	
 	public PostAnalysisKnownSignaturePanel(
 			PostAnalysisInputPanel parentPanel,
 			CyApplicationManager cyApplicationManager,
 			CySwingApplication application,
 			StreamUtil streamUtil,
-			DialogTaskManager dialog,
-			FileUtil fileUtil) {
+			SynchronousTaskManager syncTaskManager) {
 		
 		this.parentPanel = parentPanel;
 		this.cyApplicationManager = cyApplicationManager;
 		this.application = application;
 		this.streamUtil = streamUtil;
-		this.dialog = dialog;
-		this.fileUtil = fileUtil;
+		this.syncTaskManager = syncTaskManager;
 		
 		createKnownSignatureOptionsPanel();
 	}
@@ -103,20 +100,23 @@ public JToolTip createToolTip() {
         JButton selectSigGMTFileButton = new JButton();
         knownSignatureGMTFileNameTextField = new JFormattedTextField() ;
         knownSignatureGMTFileNameTextField.setColumns(15);
+        final Color textFieldForeground = knownSignatureGMTFileNameTextField.getForeground();
 
-
-        //components needed for the directory load
-        knownSignatureGMTFileNameTextField.setFont(new java.awt.Font("Dialog",1,10));
-        //GMTFileNameTextField.setText(gmt_instruction);
-        knownSignatureGMTFileNameTextField.addPropertyChangeListener("value",new FormattedTextFieldAction());
+        knownSignatureGMTFileNameTextField.setFont(new Font("Dialog",1,10));
+        knownSignatureGMTFileNameTextField.addPropertyChangeListener("value", new PropertyChangeListener() {
+            public void propertyChange(PropertyChangeEvent e) {
+            	// if the text is red set it back to black as soon as the user starts typing
+                knownSignatureGMTFileNameTextField.setForeground(textFieldForeground);
+            }
+        });
 
 
         selectSigGMTFileButton.setText("...");
         selectSigGMTFileButton.setMargin(new Insets(0,0,0,0));
         selectSigGMTFileButton.setActionCommand("Known Signature");
         selectSigGMTFileButton.addActionListener(new ActionListener() {
             public void actionPerformed(ActionEvent evt) {
-                selectSignatureGMTFileButtonActionPerformed(evt);
+            	parentPanel.chooseGMTFile(knownSignatureGMTFileNameTextField);
             }
         });
 
@@ -136,56 +136,29 @@ public void actionPerformed(ActionEvent evt) {
     }
     
     
-    /**
-     * Event Handler for selectSignatureGMTFileButton.<p>
-     * Opens a file browser dialog to select the SignatureGMTFile.
-     */
-    private void selectSignatureGMTFileButtonActionPerformed(ActionEvent evt) {
-    	File file = parentPanel.chooseGMTFile(knownSignatureGMTFileNameTextField);
-    	if(file != null) {
-            //Load in the GMT file
-            //Manually fire the same action listener that is used by the signature discovery panel
-            LoadSignatureSetsActionListener loadAction = new LoadSignatureSetsActionListener(parentPanel, application, cyApplicationManager, dialog, streamUtil);
-            loadAction.setSelectAll(true);
-            loadAction.actionPerformed(evt);
+    public boolean beforeRun() {
+    	String filePath = (String)knownSignatureGMTFileNameTextField.getValue();
+    	
+    	if(filePath == null || PostAnalysisInputPanel.checkFile(filePath).equals(Color.RED)){
+    		String message = "SigGMT file name not valid.\n";
+    		knownSignatureGMTFileNameTextField.setForeground(Color.RED);
+            JOptionPane.showMessageDialog(application.getJFrame(), message, "Post Analysis Known Signature", JOptionPane.WARNING_MESSAGE);
+            return false;
         }
+    	
+    	paParams.setSignatureGMTFileName(filePath);
+    	
+    	// Load in the GMT file
+        // Manually fire the same action listener that is used by the signature discovery panel.
+    	// Use the synchronousTaskManager so that this blocks
+        LoadSignatureSetsActionListener loadAction = new LoadSignatureSetsActionListener(parentPanel, application, cyApplicationManager, syncTaskManager, streamUtil);
+        loadAction.setSelectAll(true);
+        loadAction.actionPerformed(null);
+    	
+        return true;
     }
     
     
-    /**
-     * Handles setting for the text field parameters that are numbers.
-     * Makes sure that the numbers make sense.
-     */
-    private class FormattedTextFieldAction implements PropertyChangeListener {
-        public void propertyChange(PropertyChangeEvent e) {
-            JFormattedTextField source = (JFormattedTextField) e.getSource();
-
-            String message = "The value you have entered is invalid.\n";
-            boolean invalid = false;
-
-            if (source == knownSignatureGMTFileNameTextField) {
-                String value = knownSignatureGMTFileNameTextField.getText();
-                if(value.equalsIgnoreCase("") )
-                    paParams.setSignatureGMTFileName(value);
-                else if(knownSignatureGMTFileNameTextField.getText().equalsIgnoreCase((String)e.getOldValue())){
-                    //do nothing
-                }
-                else if(PostAnalysisInputPanel.checkFile(value).equals(Color.RED)){
-                    JOptionPane.showMessageDialog(application.getJFrame(),message,"File name change entered is not a valid file name",JOptionPane.WARNING_MESSAGE);
-                    knownSignatureGMTFileNameTextField.setForeground(PostAnalysisInputPanel.checkFile(value));
-                }
-                else {
-                    paParams.setSignatureGMTFileName(value);
-                    paParams.getSignatureSetNames().clear();
-                    paParams.getSelectedSignatureSetNames().clear();
-                }
-            } 
-            if (invalid) {
-                JOptionPane.showMessageDialog(application.getJFrame(), message, "Parameter out of bounds", JOptionPane.WARNING_MESSAGE);
-            }
-        }
-    }
-    
     void resetPanel() {
     	paParams.setSignatureGenesets(new SetOfGeneSets());
     	//Gene-Sets Panel
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/PostAnalysisPanel.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/PostAnalysisPanel.java
@@ -25,6 +25,7 @@
 import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
 import org.cytoscape.view.vizmap.VisualMappingManager;
 import org.cytoscape.view.vizmap.VisualStyleFactory;
+import org.cytoscape.work.SynchronousTaskManager;
 import org.cytoscape.work.swing.DialogTaskManager;
 
 /**
@@ -43,6 +44,7 @@ public class PostAnalysisPanel extends JPanel implements CytoPanelComponent {
 	private final CySessionManager sessionManager;
 	private final StreamUtil streamUtil;
 	private final DialogTaskManager dialog;
+	private final SynchronousTaskManager syncTaskManager;
 	private final CyEventHelper eventHelper;
 	private final EquationCompiler equationCompiler;
     
@@ -61,7 +63,7 @@ public class PostAnalysisPanel extends JPanel implements CytoPanelComponent {
     public PostAnalysisPanel(CyApplicationManager cyApplicationManager, CySwingApplication application, 
     		OpenBrowser browser,FileUtil fileUtil, CySessionManager sessionManager,
     		StreamUtil streamUtil,CyServiceRegistrar registrar,
-    		DialogTaskManager dialog,CyEventHelper eventHelper, EquationCompiler equationCompiler,
+    		DialogTaskManager dialog, SynchronousTaskManager syncTaskManager, CyEventHelper eventHelper, EquationCompiler equationCompiler,
     		VisualMappingManager visualMappingManager, VisualStyleFactory visualStyleFactory,
     		VisualMappingFunctionFactory vmfFactoryContinuous, VisualMappingFunctionFactory vmfFactoryDiscrete, VisualMappingFunctionFactory vmfFactoryPassthrough) {
     	
@@ -73,6 +75,7 @@ public PostAnalysisPanel(CyApplicationManager cyApplicationManager, CySwingAppli
         this.sessionManager = sessionManager;
         this.streamUtil = streamUtil;
         this.dialog = dialog;
+        this.syncTaskManager = syncTaskManager;
         this.eventHelper = eventHelper;
         this.equationCompiler = equationCompiler;
         this.visualMappingManager = visualMappingManager;
@@ -113,7 +116,7 @@ public void removeEnrichmentMap(EnrichmentMap map) {
     }    
     
     private PostAnalysisInputPanel newPostAnalysisInputPanel() {
-    	return new PostAnalysisInputPanel(cyApplicationManager, application, browser, fileUtil, sessionManager, streamUtil, registrar, dialog, 
+    	return new PostAnalysisInputPanel(cyApplicationManager, application, browser, fileUtil, sessionManager, streamUtil, registrar, dialog, syncTaskManager, 
     			eventHelper, equationCompiler, visualMappingManager, visualStyleFactory, vmfFactoryContinuous, vmfFactoryDiscrete, vmfFactoryPassthrough);
     }
     
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/PostAnalysisSignatureDiscoveryPanel.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/PostAnalysisSignatureDiscoveryPanel.java

Original file line number	Diff line number	Diff line change
`@@ -169,7 +169,7 @@ public FilterParameters getRankTestParameters() {`
`169`	`169`	`*/`
`170`	`170`	`public String checkGMTfiles() {`
`171`	`171`	`String signatureGMTFileName = getSignatureGMTFileName();`
`172`		`- if(signatureGMTFileName.isEmpty() \|\| !EnrichmentMapParameters.checkFile(signatureGMTFileName))`
	`172`	`+ if(signatureGMTFileName == null \|\| signatureGMTFileName.isEmpty() \|\| !EnrichmentMapParameters.checkFile(signatureGMTFileName))`
`173`	`173`	`return "Signature GMT file can not be found \n";`
`174`	`174`	`return "";`
`175`	`175`	`}`