formatting

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index a266412..161937e 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -20,6 +20,8 @@ package jalview.gui;
 import java.beans.*;
 import java.io.*;
 import java.util.*;
+import java.util.List;
+
 import javax.imageio.*;
 
 import java.awt.*;
@@ -152,7 +154,7 @@ 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 +257,11 @@ 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 +273,21 @@ 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 +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.alignment);
+    undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
 
-    ap.paintAlignment(true);    
+    ap.paintAlignment(true);
     return undo;
   }
+
   /**
    * DOCUMENT ME!
    *