patch for occasional NPE when applet is quit

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index e03f2f4..834b904 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -236,9 +236,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
    * @param type is protocol for accessing data referred to by file\r
    */\r
 \r
-  public void parseFeaturesFile(String file, String type)\r
+  public boolean parseFeaturesFile(String file, String type)\r
   {\r
-    parseFeaturesFile(file, type, true);\r
+    return parseFeaturesFile(file, type, true);\r
   }\r
   \r
   /**\r
@@ -247,9 +247,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
    * @param file file URL, content, or other resolvable path\r
    * @param type is protocol for accessing data referred to by file\r
    * @param autoenabledisplay when true, display features flag will be automatically enabled if features are loaded\r
+   * @return true if data parsed as a features file\r
    */\r
-  public void parseFeaturesFile(String file, String type, boolean autoenabledisplay)\r
+  public boolean parseFeaturesFile(String file, String type, boolean autoenabledisplay)\r
   {    \r
+    // TODO: test if importing a features file onto an alignment which already has features with links overwrites the original links.\r
+    \r
     Hashtable featureLinks = new Hashtable();\r
     boolean featuresFile = false;\r
     try\r
@@ -279,8 +282,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
         viewport.featureSettings.refreshTable();\r
       }\r
       alignPanel.paintAlignment(true);\r
+      statusBar.setText("Successfully added features to alignment.");\r
     }\r
-\r
+    return featuresFile;\r
   }\r
 \r
   public void keyPressed(KeyEvent evt)\r
@@ -753,9 +757,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     {\r
       loadAnnotations();\r
     }\r
-    else if( source == loadScores ) {\r
-       loadScores();\r
-    }\r
     else if (source == outputAnnotations)\r
     {\r
       outputAnnotations(true);\r
@@ -1104,7 +1105,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   public void loadAnnotations()\r
   {\r
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
-    cap.setText("Paste your features / annotations file here.");\r
+    cap.setText("Paste your features / annotations / T-coffee score file here.");\r
     cap.setAnnotationImport();\r
     Frame frame = new Frame();\r
     frame.add(cap);\r
@@ -1112,11 +1113,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 \r
   }\r
   \r
-  public void loadScores() {\r
-         //TODO\r
-         \r
-  }\r
-\r
   public String outputAnnotations(boolean displayTextbox)\r
   {\r
     String annotation = new AnnotationFile().printAnnotations(\r
@@ -1290,8 +1286,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   public void closeMenuItem_actionPerformed()\r
   {\r
     PaintRefresher.RemoveComponent(alignPanel);\r
-    PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
-    PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);\r
+    if (alignPanel.seqPanel!=null && alignPanel.seqPanel.seqCanvas!=null)\r
+    {\r
+      PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
+    }\r
+    if (alignPanel.idPanel!=null && alignPanel.idPanel.idCanvas!=null) {\r
+      PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);\r
+    }\r
 \r
     if (PaintRefresher.components.size() == 0 && viewport.applet == null)\r
     {\r
@@ -2288,11 +2289,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
             overview.getPreferredSize().height + 50);\r
 \r
     frame.pack();\r
+    final AlignmentPanel ap=alignPanel;\r
     frame.addWindowListener(new WindowAdapter()\r
     {\r
       public void windowClosing(WindowEvent e)\r
       {\r
-        alignPanel.setOverviewPanel(null);\r
+        if (ap!=null) {\r
+          ap.setOverviewPanel(null);\r
+        }\r
       };\r
     });\r
 \r
@@ -2795,8 +2799,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 \r
   MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");\r
   \r
-  MenuItem loadScores = new MenuItem("Load Associated T-Coffee scores ...");\r
-\r
   MenuItem outputFeatures = new MenuItem("Export Features ...");\r
 \r
   MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\r
@@ -3003,7 +3005,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 \r
     loadTree.addActionListener(this);\r
     loadAnnotations.addActionListener(this);\r
-    loadScores.addActionListener(this);\r
     outputFeatures.addActionListener(this);\r
     outputAnnotations.addActionListener(this);\r
     selectAllSequenceMenuItem.addActionListener(this);\r
@@ -3221,7 +3222,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     fileMenu.add(inputText);\r
     fileMenu.add(loadTree);\r
     fileMenu.add(loadAnnotations);\r
-    fileMenu.add(loadScores);\r
     \r
     fileMenu.addSeparator();\r
     fileMenu.add(outputTextboxMenu);\r