Merge branch 'releases/Release_2_10_0_Branch'

[jalview.git] / src / jalview / gui / AlignmentPanel.java

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index f06ca94..3dd581e 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -101,6 +101,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   private boolean dontScrollComplement;
 
+  private PropertyChangeListener propertyChangeListener;
+
   /**
    * Creates a new AlignmentPanel object.
    * 
@@ -135,7 +137,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     vscroll.addAdjustmentListener(this);
 
     final AlignmentPanel ap = this;
-    av.addPropertyChangeListener(new PropertyChangeListener()
+    propertyChangeListener = new PropertyChangeListener()
     {
       @Override
       public void propertyChange(PropertyChangeEvent evt)
@@ -146,7 +148,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
           alignmentChanged();
         }
       }
-    });
+    };
+    av.addPropertyChangeListener(propertyChangeListener);
     fontChanged();
     adjustAnnotationHeight();
     updateLayout();
@@ -1269,6 +1272,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
   {
+    int boarderBottomOffset = 5;
     long pSessionId = System.currentTimeMillis();
     headless = (System.getProperty("java.awt.headless") != null && System
             .getProperty("java.awt.headless").equals("true"));
@@ -1277,7 +1281,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       if (file != null)
       {
         alignFrame.setProgressBar(MessageManager.formatMessage(
-              "status.saving_file", new Object[] { type.getLabel() }),
+                "status.saving_file", new Object[] { type.getLabel() }),
                 pSessionId);
       }
     }
@@ -1305,14 +1309,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
         }
 
         im = new jalview.util.ImageMaker(this, type, imageAction,
-                aDimension.getWidth(), aDimension.getHeight(), file,
-                imageTitle, alignFrame, pSessionId, headless);
+                aDimension.getWidth(), aDimension.getHeight()
+                        + boarderBottomOffset, file, imageTitle,
+                alignFrame, pSessionId, headless);
         if (av.getWrapAlignment())
         {
           if (im.getGraphics() != null)
           {
             printWrappedAlignment(im.getGraphics(), aDimension.getWidth(),
-                    aDimension.getHeight(), 0);
+                    aDimension.getHeight() + boarderBottomOffset, 0);
             im.writeImage();
           }
         }
@@ -1593,8 +1598,18 @@ public class AlignmentPanel extends GAlignmentPanel implements
     PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
     PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
     PaintRefresher.RemoveComponent(this);
+
+    /*
+     * try to ensure references are nulled
+     */
+    if (annotationPanel != null)
+    {
+      annotationPanel.dispose();
+    }
+
     if (av != null)
     {
+      av.removePropertyChangeListener(propertyChangeListener);
       jalview.structure.StructureSelectionManager ssm = av
               .getStructureSelectionManager();
       ssm.removeStructureViewerListener(getSeqPanel(), null);
@@ -1602,7 +1617,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       ssm.removeCommandListener(av);
       ssm.removeStructureViewerListener(getSeqPanel(), null);
       ssm.removeSelectionListener(getSeqPanel());
-      av.setAlignment(null);
+      av.dispose();
       av = null;
     }
     else