Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 58fec17..923d702 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
@@ -36,6 +37,7 @@ import jalview.commands.OrderCommand;
 import jalview.datamodel.*;
 import jalview.io.*;
 import jalview.jbgui.*;
+import jalview.util.MessageManager;
 
 /**
  * DOCUMENT ME!
@@ -273,9 +275,8 @@ public class TreePanel extends GTreePanel
       {
         int start, end;
         SequenceI[] seqs;
-        boolean selview=av
-                .getSelectionGroup() != null && av
-                .getSelectionGroup().getSize()>1;
+        boolean selview = av.getSelectionGroup() != null
+                && av.getSelectionGroup().getSize() > 1;
         AlignmentView seqStrings = av.getAlignmentView(selview);
         if (!selview)
         {
@@ -287,7 +288,8 @@ public class TreePanel extends GTreePanel
         {
           start = av.getSelectionGroup().getStartRes();
           end = av.getSelectionGroup().getEndRes() + 1;
-          seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
+          seqs = av.getSelectionGroup().getSequencesInOrder(
+                  av.getAlignment());
         }
 
         tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
@@ -396,7 +398,7 @@ public class TreePanel extends GTreePanel
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save tree as newick file");
-    chooser.setToolTipText("Save");
+    chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(null);
 
@@ -488,7 +490,7 @@ public class TreePanel extends GTreePanel
         // af.addSortByOrderMenuItem(ServiceName + " Ordering",
         // msaorder);
 
-        Desktop.addInternalFrame(af, "Original Data for " + this.title,
+        Desktop.addInternalFrame(af, MessageManager.formatMessage("label.original_data_for_params", new String[]{this.title}),
                 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
       }
     }
@@ -513,72 +515,76 @@ public class TreePanel extends GTreePanel
    */
   public void sortByTree_actionPerformed(ActionEvent e)
   {
-    
+
     if (treeCanvas.applyToAllViews)
     {
       final ArrayList<CommandI> commands = new ArrayList<CommandI>();
-      for (AlignmentPanel ap: PaintRefresher.getAssociatedPanels(av
+      for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
               .getSequenceSetId()))
       {
         commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
       }
       av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
       {
-        
+
         @Override
         public void undoCommand(AlignmentI[] views)
         {
-          for (CommandI tsort:commands)
+          for (CommandI tsort : commands)
           {
             tsort.undoCommand(views);
-          }          
+          }
         }
-        
+
         @Override
         public int getSize()
         {
           return commands.size();
         }
-        
+
         @Override
         public String getDescription()
         {
           return "Tree Sort (many views)";
         }
-        
+
         @Override
         public void doCommand(AlignmentI[] views)
         {
 
-          for (CommandI tsort:commands)
+          for (CommandI tsort : commands)
           {
             tsort.doCommand(views);
-          }          
+          }
         }
       });
-      for (AlignmentPanel ap: PaintRefresher.getAssociatedPanels(av
+      for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
               .getSequenceSetId()))
       {
         // ensure all the alignFrames refresh their GI after adding an undo item
         ap.alignFrame.updateEditMenuBar();
       }
-    } else {
-      treeCanvas.ap.alignFrame.addHistoryItem(sortAlignmentIn(treeCanvas.ap));
+    }
+    else
+    {
+      treeCanvas.ap.alignFrame
+              .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
     }
 
   }
+
   public CommandI sortAlignmentIn(AlignmentPanel ap)
   {
     AlignViewport av = ap.av;
     SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
     AlignmentSorter.sortByTree(av.getAlignment(), tree);
     CommandI undo;
-    undo=new OrderCommand("Tree Sort", oldOrder,
-          av.getAlignment());
+    undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
 
-    ap.paintAlignment(true);    
+    ap.paintAlignment(true);
     return undo;
   }
+
   /**
    * DOCUMENT ME!
    * 
@@ -686,7 +692,7 @@ public class TreePanel extends GTreePanel
               { "Encapsulated Postscript" }, "Encapsulated Postscript");
       chooser.setFileView(new jalview.io.JalviewFileView());
       chooser.setDialogTitle("Create EPS file from tree");
-      chooser.setToolTipText("Save");
+      chooser.setToolTipText(MessageManager.getString("action.save"));
 
       int value = chooser.showSaveDialog(this);
 
@@ -733,7 +739,7 @@ public class TreePanel extends GTreePanel
 
       chooser.setFileView(new jalview.io.JalviewFileView());
       chooser.setDialogTitle("Create PNG image from tree");
-      chooser.setToolTipText("Save");
+      chooser.setToolTipText(MessageManager.getString("action.save"));
 
       int value = chooser.showSaveDialog(this);