X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=b730df46207d5c38c689c0fd379283f3b9190d83;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=545010246d84e13f34a3f6111688f34ce0443958;hpb=f9f0b83445a2da848d21614d94a909888484e25e;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 5450102..b730df4 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -20,6 +20,8 @@
  */
 package jalview.gui;
 
+import java.util.Locale;
+
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AverageDistanceTree;
 import jalview.analysis.NJTree;
@@ -84,11 +86,11 @@ public class TreePanel extends GTreePanel
 
   SimilarityParamsI similarityParams;
 
-  TreeCanvas treeCanvas;
+  private TreeCanvas treeCanvas;
 
   TreeModel tree;
 
-  AlignViewport av;
+  private AlignViewport av;
 
   /**
    * Creates a new TreePanel object.
@@ -120,12 +122,13 @@ public class TreePanel extends GTreePanel
 
   public AlignmentI getAlignment()
   {
-    return treeCanvas.av.getAlignment();
+    return getTreeCanvas().getViewport().getAlignment();
   }
 
   public AlignmentViewport getViewPort()
   {
-    return treeCanvas.av;
+    // @Mungo - Why don't we return our own viewport ???
+    return getTreeCanvas().getViewport();
   }
 
   void initTreePanel(AlignmentPanel ap, String type, String modelName,
@@ -158,6 +161,7 @@ public class TreePanel extends GTreePanel
         {
           av.removePropertyChangeListener(listener);
         }
+        releaseReferences();
       }
     });
 
@@ -167,6 +171,17 @@ public class TreePanel extends GTreePanel
   }
 
   /**
+   * Ensure any potentially large object references are nulled
+   */
+  public void releaseReferences()
+  {
+    this.tree = null;
+    this.treeCanvas.tree = null;
+    this.treeCanvas.nodeHash = null;
+    this.treeCanvas.nameHash = null;
+  }
+
+  /**
    * @return
    */
   protected PropertyChangeListener addAlignmentListener()
@@ -213,7 +228,7 @@ public class TreePanel extends GTreePanel
   {
     AlignmentPanel[] aps = PaintRefresher
             .getAssociatedPanels(av.getSequenceSetId());
-    if (aps.length == 1 && treeCanvas.ap == aps[0])
+    if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
     {
       associateLeavesMenu.setVisible(false);
       return;
@@ -236,7 +251,8 @@ public class TreePanel extends GTreePanel
     for (i = 0; i < iSize; i++)
     {
       final AlignmentPanel ap = aps[i];
-      item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
+      item = new JRadioButtonMenuItem(ap.av.getViewName(),
+              ap == treeCanvas.getAssociatedPanel());
       buttonGroup.add(item);
       item.addActionListener(new ActionListener()
       {
@@ -244,8 +260,8 @@ public class TreePanel extends GTreePanel
         public void actionPerformed(ActionEvent evt)
         {
           treeCanvas.applyToAllViews = false;
-          treeCanvas.ap = ap;
-          treeCanvas.av = ap.av;
+          treeCanvas.setAssociatedPanel(ap);
+          treeCanvas.setViewport(ap.av);
           PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
         }
       });
@@ -305,7 +321,8 @@ public class TreePanel extends GTreePanel
       else
       {
         ScoreModelI sm = ScoreModels.getInstance()
-                .getScoreModel(scoreModelName, treeCanvas.ap);
+                .getScoreModel(scoreModelName,
+                        treeCanvas.getAssociatedPanel());
         TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
                 ? new NJTree(av, sm, similarityParams)
                 : new AverageDistanceTree(av, sm, similarityParams);
@@ -571,8 +588,9 @@ public class TreePanel extends GTreePanel
     }
     else
     {
-      treeCanvas.ap.alignFrame
-              .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
+      treeCanvas.getAssociatedPanel().alignFrame
+              .addHistoryItem(
+                      sortAlignmentIn(treeCanvas.getAssociatedPanel()));
     }
 
   }
@@ -677,7 +695,7 @@ public class TreePanel extends GTreePanel
     String tree = MessageManager.getString("label.tree");
     ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
             tree);
-    exporter.doExport(null, this, width, height, tree.toLowerCase());
+    exporter.doExport(null, this, width, height, tree.toLowerCase(Locale.ROOT));
   }
 
   /**
@@ -705,20 +723,20 @@ public class TreePanel extends GTreePanel
           if (sq != null)
           {
             // search dbrefs, features and annotation
-            DBRefEntry[] refs = jalview.util.DBRefUtils
+            List<DBRefEntry> refs = jalview.util.DBRefUtils
                     .selectRefs(sq.getDBRefs(), new String[]
-                    { labelClass.toUpperCase() });
+                    { labelClass.toUpperCase(Locale.ROOT) });
             if (refs != null)
             {
-              for (int i = 0; i < refs.length; i++)
+              for (int i = 0, ni = refs.size(); i < ni; i++)
               {
                 if (newname == null)
                 {
-                  newname = new String(refs[i].getAccessionId());
+                  newname = new String(refs.get(i).getAccessionId());
                 }
                 else
                 {
-                  newname = newname + "; " + refs[i].getAccessionId();
+                  newname += "; " + refs.get(i).getAccessionId();
                 }
               }
             }
@@ -770,7 +788,7 @@ public class TreePanel extends GTreePanel
      * i18n description of Neighbour Joining or Average Distance method
      */
     String treecalcnm = MessageManager
-            .getString("label.tree_calc_" + treeType.toLowerCase());
+            .getString("label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
 
     /*
      * short score model name (long description can be too long)
@@ -780,7 +798,7 @@ public class TreePanel extends GTreePanel
     /*
      * put them together as <method> Using <model>
      */
-    final String ttl = MessageManager.formatMessage("label.treecalc_title",
+    final String ttl = MessageManager.formatMessage("label.calc_title",
             treecalcnm, smn);
     return ttl;
   }
@@ -814,4 +832,19 @@ public class TreePanel extends GTreePanel
       ex.printStackTrace();
     }
   }
+  
+  public AlignViewport getViewport()
+  {
+    return av;
+  }
+
+  public void setViewport(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  public TreeCanvas getTreeCanvas()
+  {
+    return treeCanvas;
+  }
 }