JAL-3949 Complete new abstracted logging framework in jalview.log. Updated log calls...

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index b59d197..e88007a 100755 (executable)
--- 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;
@@ -28,6 +30,7 @@ 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.commands.CommandI;
 import jalview.commands.OrderCommand;
 import jalview.datamodel.Alignment;
@@ -159,6 +162,7 @@ public class TreePanel extends GTreePanel
         {
           av.removePropertyChangeListener(listener);
         }
+        releaseReferences();
       }
     });
 
@@ -168,6 +172,17 @@ 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()
@@ -394,7 +409,7 @@ 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 +420,7 @@ 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 +459,7 @@ public class TreePanel extends GTreePanel
     AlignmentView originalData = tree.getOriginalData();
     if (originalData == null)
     {
-      jalview.bin.Cache.log.info(
+      Cache.info(
               "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
       return;
     }
@@ -681,7 +696,7 @@ 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));
   }
 
   /**
@@ -711,7 +726,7 @@ 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++)
@@ -774,7 +789,7 @@ 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)
@@ -784,7 +799,7 @@ 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;
   }