JAL-1911 improvement to bugfix - do not save i18n text in preference file

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 5bedf36..d78350d 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -43,6 +43,7 @@ import jalview.io.NewickFile;
 import jalview.jbgui.GTreePanel;
 import jalview.schemes.ResidueProperties;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Font;
 import java.awt.Graphics;
@@ -138,7 +139,7 @@ public class TreePanel extends GTreePanel
     return treeCanvas.av.getAlignment();
   }
 
-  public AlignViewport getViewPort()
+  public AlignmentViewport getViewPort()
   {
     return treeCanvas.av;
   }
@@ -160,6 +161,7 @@ public class TreePanel extends GTreePanel
 
     av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
     {
+      @Override
       public void propertyChange(PropertyChangeEvent evt)
       {
         if (evt.getPropertyName().equals("alignment"))
@@ -195,6 +197,7 @@ public class TreePanel extends GTreePanel
 
   }
 
+  @Override
   public void viewMenu_menuSelected()
   {
     buildAssociatedViewMenu();
@@ -230,6 +233,7 @@ public class TreePanel extends GTreePanel
       buttonGroup.add(item);
       item.addActionListener(new ActionListener()
       {
+        @Override
         public void actionPerformed(ActionEvent evt)
         {
           treeCanvas.applyToAllViews = false;
@@ -242,11 +246,13 @@ public class TreePanel extends GTreePanel
       associateLeavesMenu.add(item);
     }
 
-    final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
+    final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
+            MessageManager.getString("label.all_views"));
     buttonGroup.add(itemf);
     itemf.setSelected(treeCanvas.applyToAllViews);
     itemf.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent evt)
       {
         treeCanvas.applyToAllViews = itemf.isSelected();
@@ -274,6 +280,7 @@ public class TreePanel extends GTreePanel
       }
     }
 
+    @Override
     public void run()
     {
 
@@ -313,8 +320,26 @@ public class TreePanel extends GTreePanel
           seqs = av.getSelectionGroup().getSequencesInOrder(
                   av.getAlignment());
         }
-
-        tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+        ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
+        if (sm instanceof ViewBasedAnalysisI)
+        {
+          try
+          {
+            sm = sm.getClass().newInstance();
+            ((ViewBasedAnalysisI) sm)
+                    .configureFromAlignmentView(treeCanvas.ap);
+          } catch (Exception q)
+          {
+            Cache.log.error("Couldn't create a scoremodel instance for "
+                    + sm.getName());
+          }
+          tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
+        }
+        else
+        {
+          tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
+                  end);
+        }
         showDistances(true);
       }
 
@@ -325,7 +350,7 @@ public class TreePanel extends GTreePanel
       av.setCurrentTree(tree);
       if (av.getSortByTree())
       {
-        sortByTree_actionPerformed(null);
+        sortByTree_actionPerformed();
       }
     }
   }
@@ -369,6 +394,7 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void textbox_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
@@ -414,12 +440,14 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void saveAsNewick_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick"));
+    chooser.setDialogTitle(MessageManager
+            .getString("label.save_tree_as_newick"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(null);
@@ -453,12 +481,14 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void printMenu_actionPerformed(ActionEvent e)
   {
     // Putting in a thread avoids Swing painting problems
     treeCanvas.startPrinting();
   }
 
+  @Override
   public void originalSeqData_actionPerformed(ActionEvent e)
   {
     if (!tree.hasOriginalSequenceData())
@@ -513,8 +543,8 @@ public class TreePanel extends GTreePanel
         // msaorder);
 
         Desktop.addInternalFrame(af, MessageManager.formatMessage(
-                "label.original_data_for_params", new String[]
-                { this.title }), AlignFrame.DEFAULT_WIDTH,
+                "label.original_data_for_params",
+                new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
       }
     }
@@ -526,6 +556,7 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void fitToWindow_actionPerformed(ActionEvent e)
   {
     treeCanvas.fitToWindow = fitToWindow.isSelected();
@@ -537,7 +568,8 @@ public class TreePanel extends GTreePanel
    * 
    * @param e
    */
-  public void sortByTree_actionPerformed(ActionEvent e)
+  @Override
+  public void sortByTree_actionPerformed()
   {
 
     if (treeCanvas.applyToAllViews)
@@ -599,7 +631,7 @@ public class TreePanel extends GTreePanel
 
   public CommandI sortAlignmentIn(AlignmentPanel ap)
   {
-    AlignViewport av = ap.av;
+    AlignmentViewport av = ap.av;
     SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
     AlignmentSorter.sortByTree(av.getAlignment(), tree);
     CommandI undo;
@@ -615,6 +647,7 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void font_actionPerformed(ActionEvent e)
   {
     if (treeCanvas == null)
@@ -644,6 +677,7 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void distanceMenu_actionPerformed(ActionEvent e)
   {
     treeCanvas.setShowDistances(distanceMenu.isSelected());
@@ -655,6 +689,7 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void bootstrapMenu_actionPerformed(ActionEvent e)
   {
     treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
@@ -666,6 +701,7 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void placeholdersMenu_actionPerformed(ActionEvent e)
   {
     treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
@@ -677,6 +713,7 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void epsTree_actionPerformed(ActionEvent e)
   {
     boolean accurateText = true;
@@ -712,10 +749,11 @@ public class TreePanel extends GTreePanel
     {
       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
               jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-              { "eps" }, new String[]
-              { "Encapsulated Postscript" }, "Encapsulated Postscript");
+              { "eps" }, new String[] { "Encapsulated Postscript" },
+              "Encapsulated Postscript");
       chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle(MessageManager.getString("label.create_eps_from_tree"));
+      chooser.setDialogTitle(MessageManager
+              .getString("label.create_eps_from_tree"));
       chooser.setToolTipText(MessageManager.getString("action.save"));
 
       int value = chooser.showSaveDialog(this);
@@ -749,6 +787,7 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void pngTree_actionPerformed(ActionEvent e)
   {
     int width = treeCanvas.getWidth();
@@ -758,11 +797,12 @@ public class TreePanel extends GTreePanel
     {
       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
               jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-              { "png" }, new String[]
-              { "Portable network graphics" }, "Portable network graphics");
+              { "png" }, new String[] { "Portable network graphics" },
+              "Portable network graphics");
 
       chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle(MessageManager.getString("label.create_png_from_tree"));
+      chooser.setDialogTitle(MessageManager
+              .getString("label.create_png_from_tree"));
       chooser.setToolTipText(MessageManager.getString("action.save"));
 
       int value = chooser.showSaveDialog(this);
@@ -804,6 +844,7 @@ public class TreePanel extends GTreePanel
     tree.applyToNodes(new NodeTransformI()
     {
 
+      @Override
       public void transform(BinaryNode node)
       {
         if (node instanceof SequenceNode
@@ -816,8 +857,8 @@ public class TreePanel extends GTreePanel
           {
             // search dbrefs, features and annotation
             DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
-                    sq.getDBRef(), new String[]
-                    { labelClass.toUpperCase() });
+                    sq.getDBRefs(),
+                    new String[] { labelClass.toUpperCase() });
             if (refs != null)
             {
               for (int i = 0; i < refs.length; i++)