JAL-1793 spike branch updated to latest

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 80f0c73..2727db1 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -55,6 +55,7 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.image.BufferedImage;
 import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
 import java.io.FileOutputStream;
 import java.util.ArrayList;
 import java.util.List;
@@ -63,6 +64,8 @@ import javax.imageio.ImageIO;
 import javax.swing.ButtonGroup;
 import javax.swing.JMenuItem;
 import javax.swing.JRadioButtonMenuItem;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
 
 import org.jibble.epsgraphics.EpsGraphics2D;
 
@@ -141,7 +144,35 @@ public class TreePanel extends GTreePanel
 
     buildAssociatedViewMenu();
 
-    av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+    final PropertyChangeListener listener = addAlignmentListener();
+
+    /*
+     * remove listener when window is closed, so that this
+     * panel can be garbage collected
+     */
+    addInternalFrameListener(new InternalFrameAdapter()
+    {
+      @Override
+      public void internalFrameClosed(InternalFrameEvent evt)
+      {
+        if (av != null)
+        {
+          av.removePropertyChangeListener(listener);
+        }
+      }
+    });
+
+    TreeLoader tl = new TreeLoader(newTree, inputData);
+    tl.start();
+
+  }
+
+  /**
+   * @return
+   */
+  protected PropertyChangeListener addAlignmentListener()
+  {
+    final PropertyChangeListener listener = new PropertyChangeListener()
     {
       @Override
       public void propertyChange(PropertyChangeEvent evt)
@@ -168,11 +199,9 @@ public class TreePanel extends GTreePanel
           repaint();
         }
       }
-    });
-
-    TreeLoader tl = new TreeLoader(newTree, inputData);
-    tl.start();
-
+    };
+    av.addPropertyChangeListener(listener);
+    return listener;
   }
 
   @Override
@@ -493,7 +522,7 @@ public class TreePanel extends GTreePanel
 
     if (treeCanvas.applyToAllViews)
     {
-      final ArrayList<CommandI> commands = new ArrayList<CommandI>();
+      final ArrayList<CommandI> commands = new ArrayList<>();
       for (AlignmentPanel ap : PaintRefresher
               .getAssociatedPanels(av.getSequenceSetId()))
       {
@@ -550,13 +579,14 @@ public class TreePanel extends GTreePanel
 
   public CommandI sortAlignmentIn(AlignmentPanel ap)
   {
+    // TODO: move to alignment view controller
     AlignmentViewport viewport = ap.av;
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
     CommandI undo;
     undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
 
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, false);
     return undo;
   }
 
@@ -793,19 +823,17 @@ public class TreePanel extends GTreePanel
             }
             if (newname == null)
             {
-              SequenceFeature sf[] = sq.getSequenceFeatures();
-              for (int i = 0; sf != null && i < sf.length; i++)
+              List<SequenceFeature> features = sq.getFeatures()
+                      .getPositionalFeatures(labelClass);
+              for (SequenceFeature feature : features)
               {
-                if (sf[i].getType().equals(labelClass))
+                if (newname == null)
+                {
+                  newname = feature.getDescription();
+                }
+                else
                 {
-                  if (newname == null)
-                  {
-                    newname = new String(sf[i].getDescription());
-                  }
-                  else
-                  {
-                    newname = newname + "; " + sf[i].getDescription();
-                  }
+                  newname = newname + "; " + feature.getDescription();
                 }
               }
             }