apply version 2.7 copyright

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 45fc0df..d8253db 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 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -29,6 +29,7 @@ import javax.swing.*;
 
 import org.jibble.epsgraphics.*;
 import jalview.analysis.*;
+import jalview.commands.CommandI;
 import jalview.commands.OrderCommand;
 import jalview.datamodel.*;
 import jalview.io.*;
@@ -364,12 +365,19 @@ public class TreePanel extends GTreePanel
       buffer.append("PID");
     }
 
-    Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+    jalview.io.NewickFile fout = new jalview.io.NewickFile(
+            tree.getTopNode());
+    try
+    {
+      cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
+              tree.isHasRootDistance()));
+      Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+    } catch (OutOfMemoryError oom)
+    {
+      new OOMWarning("generating newick tree file", oom);
+      cap.dispose();
+    }
 
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
-            .getTopNode());
-    cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
-            tree.isHasRootDistance()));
   }
 
   /**
@@ -380,8 +388,8 @@ public class TreePanel extends GTreePanel
    */
   public void saveAsNewick_actionPerformed(ActionEvent e)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
-            .getProperty("LAST_DIRECTORY"));
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save tree as newick file");
     chooser.setToolTipText("Save");
@@ -396,10 +404,10 @@ public class TreePanel extends GTreePanel
 
       try
       {
-        jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
-                .getTopNode());
-        String output = fout.print(tree.isHasBootstrap(), tree
-                .isHasDistances(), tree.isHasRootDistance());
+        jalview.io.NewickFile fout = new jalview.io.NewickFile(
+                tree.getTopNode());
+        String output = fout.print(tree.isHasBootstrap(),
+                tree.isHasDistances(), tree.isHasRootDistance());
         java.io.PrintWriter out = new java.io.PrintWriter(
                 new java.io.FileWriter(choice));
         out.println(output);
@@ -501,17 +509,72 @@ public class TreePanel extends GTreePanel
    */
   public void sortByTree_actionPerformed(ActionEvent e)
   {
-    AlignmentPanel ap = av.getAlignPanel();
-    SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
-    AlignmentSorter.sortByTree(av.getAlignment(), tree);
-
-    ap.alignFrame.addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
-            av.alignment));
+    
+    if (treeCanvas.applyToAllViews)
+    {
+      final ArrayList<CommandI> commands = new ArrayList<CommandI>();
+      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)
+          {
+            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)
+        {
 
-    ap.paintAlignment(true);
+          for (CommandI tsort:commands)
+          {
+            tsort.doCommand(views);
+          }          
+        }
+      });
+      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));
+    }
 
   }
+  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);
 
+    ap.paintAlignment(true);    
+    return undo;
+  }
   /**
    * DOCUMENT ME!
    * 
@@ -718,9 +781,9 @@ public class TreePanel extends GTreePanel
           if (sq != null)
           {
             // search dbrefs, features and annotation
-            DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(sq
-                    .getDBRef(), new String[]
-            { labelClass.toUpperCase() });
+            DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
+                    sq.getDBRef(), new String[]
+                    { labelClass.toUpperCase() });
             if (refs != null)
             {
               for (int i = 0; i < refs.length; i++)