X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=161937e2c4dec85eb350b397c9be0446cdbffc13;hp=58fec178f726b8ce55ad7561626a2b48d1ac8cf3;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hpb=1cc81e06ac2faa5ee4b8879e9fa019956e34259f

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 58fec17..161937e 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -273,9 +273,8 @@ 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 +286,8 @@ 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);
@@ -513,72 +513,76 @@ 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!
    *