X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=76e1884a3016e112524c0008be93b3a74936aa27;hb=d2259df2688d404ac89f6dfed3921280a5038c7b;hp=37b4dac5b5b17f5101e4dcdb21b2e239542aa73f;hpb=3da878124135ff033f42d19d8733891b09e953cd;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 37b4dac..76e1884 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -20,6 +20,26 @@
  */
 package jalview.gui;
 
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Locale;
+
+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;
+
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AverageDistanceTree;
 import jalview.analysis.NJTree;
@@ -28,6 +48,8 @@ import jalview.analysis.TreeModel;
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.commands.CommandI;
 import jalview.commands.OrderCommand;
 import jalview.datamodel.Alignment;
@@ -49,25 +71,6 @@ import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
-import java.awt.Font;
-import java.awt.Graphics;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.util.ArrayList;
-import java.util.List;
-
-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;
-
 /**
  * DOCUMENT ME!
  * 
@@ -102,6 +105,7 @@ public class TreePanel extends GTreePanel
           SimilarityParamsI options)
   {
     super();
+    this.setFrameIcon(null);
     this.similarityParams = options;
     initTreePanel(ap, type, modelName, null, null);
 
@@ -114,6 +118,7 @@ public class TreePanel extends GTreePanel
           String theTitle, AlignmentView inputData)
   {
     super();
+    this.setFrameIcon(null);
     this.treeTitle = theTitle;
     initTreePanel(alignPanel, null, null, newtree, inputData);
   }
@@ -159,6 +164,7 @@ public class TreePanel extends GTreePanel
         {
           av.removePropertyChangeListener(listener);
         }
+        releaseReferences();
       }
     });
 
@@ -168,6 +174,17 @@ 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()
@@ -306,9 +323,8 @@ public class TreePanel extends GTreePanel
       }
       else
       {
-        ScoreModelI sm = ScoreModels.getInstance()
-                .getScoreModel(scoreModelName,
-                        treeCanvas.getAssociatedPanel());
+        ScoreModelI sm = ScoreModels.getInstance().getScoreModel(
+                scoreModelName, treeCanvas.getAssociatedPanel());
         TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
                 ? new NJTree(av, sm, similarityParams)
                 : new AverageDistanceTree(av, sm, similarityParams);
@@ -394,7 +410,7 @@ public class TreePanel extends GTreePanel
   {
     // TODO: JAL-3048 save newick file for Jalview-JS
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(
             MessageManager.getString("label.save_tree_as_newick"));
@@ -405,7 +421,7 @@ public class TreePanel extends GTreePanel
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+      Cache.setProperty("LAST_DIRECTORY",
               chooser.getSelectedFile().getParent());
 
       try
@@ -444,7 +460,7 @@ public class TreePanel extends GTreePanel
     AlignmentView originalData = tree.getOriginalData();
     if (originalData == null)
     {
-      jalview.bin.Cache.log.info(
+      Console.info(
               "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
       return;
     }
@@ -574,9 +590,8 @@ public class TreePanel extends GTreePanel
     }
     else
     {
-      treeCanvas.getAssociatedPanel().alignFrame
-              .addHistoryItem(
-                      sortAlignmentIn(treeCanvas.getAssociatedPanel()));
+      treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem(
+              sortAlignmentIn(treeCanvas.getAssociatedPanel()));
     }
 
   }
@@ -681,7 +696,8 @@ 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));
   }
 
   /**
@@ -711,7 +727,7 @@ public class TreePanel extends GTreePanel
             // search dbrefs, features and annotation
             List<DBRefEntry> refs = jalview.util.DBRefUtils
                     .selectRefs(sq.getDBRefs(), new String[]
-                    { labelClass.toUpperCase() });
+                    { labelClass.toUpperCase(Locale.ROOT) });
             if (refs != null)
             {
               for (int i = 0, ni = refs.size(); i < ni; i++)
@@ -773,8 +789,8 @@ public class TreePanel extends GTreePanel
     /*
      * i18n description of Neighbour Joining or Average Distance method
      */
-    String treecalcnm = MessageManager
-            .getString("label.tree_calc_" + treeType.toLowerCase());
+    String treecalcnm = MessageManager.getString(
+            "label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
 
     /*
      * short score model name (long description can be too long)
@@ -803,8 +819,7 @@ public class TreePanel extends GTreePanel
       int width = treeCanvas.getWidth();
       int height = treeCanvas.getHeight();
 
-      FileOutputStream out = new FileOutputStream(
-              outFile);
+      FileOutputStream out = new FileOutputStream(outFile);
       EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
               height);
       pg.setAccurateTextMode(!textOption);
@@ -818,7 +833,7 @@ public class TreePanel extends GTreePanel
       ex.printStackTrace();
     }
   }
-  
+
   public AlignViewport getViewport()
   {
     return av;