X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=8832bfa94412e6770c141546f3b4a30c70a79c08;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=a266412113e1f5f54a8c262534beeab7efcc7eef;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index a266412..8832bfa 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,25 +1,28 @@
 /*
- * 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 2.8.0b1)
+ * 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;
 
 import java.beans.*;
 import java.io.*;
 import java.util.*;
+import java.util.List;
+
 import javax.imageio.*;
 
 import java.awt.*;
@@ -152,7 +155,7 @@ public class TreePanel extends GTreePanel
                     .println("new alignment sequences vector value is null");
           }
 
-          tree.UpdatePlaceHolders((Vector) evt.getNewValue());
+          tree.UpdatePlaceHolders((List<SequenceI>) evt.getNewValue());
           treeCanvas.nameHash.clear(); // reset the mapping between canvas
           // rectangles and leafnodes
           repaint();
@@ -255,11 +258,11 @@ public class TreePanel extends GTreePanel
       {
         if (odata == null)
         {
-          tree = new NJTree(av.alignment.getSequencesArray(), newtree);
+          tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
         }
         else
         {
-          tree = new NJTree(av.alignment.getSequencesArray(), odata,
+          tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
                   newtree);
         }
         if (!tree.hasOriginalSequenceData())
@@ -271,19 +274,21 @@ public class TreePanel extends GTreePanel
       {
         int start, end;
         SequenceI[] seqs;
-        AlignmentView seqStrings = av.getAlignmentView(av
-                .getSelectionGroup() != null);
-        if (av.getSelectionGroup() == null)
+        boolean selview = av.getSelectionGroup() != null
+                && av.getSelectionGroup().getSize() > 1;
+        AlignmentView seqStrings = av.getAlignmentView(selview);
+        if (!selview)
         {
           start = 0;
-          end = av.alignment.getWidth();
-          seqs = av.alignment.getSequencesArray();
+          end = av.getAlignment().getWidth();
+          seqs = av.getAlignment().getSequencesArray();
         }
         else
         {
           start = av.getSelectionGroup().getStartRes();
           end = av.getSelectionGroup().getEndRes() + 1;
-          seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+          seqs = av.getSelectionGroup().getSequencesInOrder(
+                  av.getAlignment());
         }
 
         tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
@@ -509,72 +514,76 @@ 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.alignment);
+    undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
 
-    ap.paintAlignment(true);    
+    ap.paintAlignment(true);
     return undo;
   }
+
   /**
    * DOCUMENT ME!
    *