JAL-4133 update validChar width when font is changed so characters are suppressed...

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 5450102..76e1884 100755 (executable)
--- 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!
  * 
@@ -84,11 +87,11 @@ public class TreePanel extends GTreePanel
 
   SimilarityParamsI similarityParams;
 
-  TreeCanvas treeCanvas;
+  private TreeCanvas treeCanvas;
 
   TreeModel tree;
 
-  AlignViewport av;
+  private AlignViewport av;
 
   /**
    * Creates a new TreePanel object.
@@ -102,6 +105,7 @@ public class TreePanel extends GTreePanel
           SimilarityParamsI options)
   {
     super();
+    this.setFrameIcon(null);
     this.similarityParams = options;
     initTreePanel(ap, type, modelName, null, null);
 
@@ -114,18 +118,20 @@ public class TreePanel extends GTreePanel
           String theTitle, AlignmentView inputData)
   {
     super();
+    this.setFrameIcon(null);
     this.treeTitle = theTitle;
     initTreePanel(alignPanel, null, null, newtree, inputData);
   }
 
   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 +164,7 @@ public class TreePanel extends GTreePanel
         {
           av.removePropertyChangeListener(listener);
         }
+        releaseReferences();
       }
     });
 
@@ -167,6 +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()
@@ -213,7 +231,7 @@ 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 +254,8 @@ 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 +263,8 @@ 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());
         }
       });
@@ -304,8 +323,8 @@ public class TreePanel extends GTreePanel
       }
       else
       {
-        ScoreModelI sm = ScoreModels.getInstance()
-                .getScoreModel(scoreModelName, treeCanvas.ap);
+        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);
@@ -391,7 +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"));
@@ -402,7 +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
@@ -441,7 +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;
     }
@@ -571,8 +590,8 @@ public class TreePanel extends GTreePanel
     }
     else
     {
-      treeCanvas.ap.alignFrame
-              .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
+      treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem(
+              sortAlignmentIn(treeCanvas.getAssociatedPanel()));
     }
 
   }
@@ -677,7 +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));
   }
 
   /**
@@ -705,20 +725,20 @@ 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();
                 }
               }
             }
@@ -769,8 +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)
@@ -780,7 +800,7 @@ 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;
   }
@@ -799,8 +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);
@@ -814,4 +833,19 @@ 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;
+  }
 }