updated version to 2.6.1

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index e77134e..6bcfd25 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -364,16 +364,16 @@ public class TreePanel extends GTreePanel
       buffer.append("PID");
     }
 
-
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
-            .getTopNode());
-    try {
+    jalview.io.NewickFile fout = new jalview.io.NewickFile(
+            tree.getTopNode());
+    try
+    {
       cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
-            tree.isHasRootDistance()));
+              tree.isHasRootDistance()));
       Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
     } catch (OutOfMemoryError oom)
     {
-      new OOMWarning("generating newick tree file",oom);
+      new OOMWarning("generating newick tree file", oom);
       cap.dispose();
     }
 
@@ -387,8 +387,8 @@ 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");
@@ -403,10 +403,10 @@ 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);
@@ -725,9 +725,9 @@ 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++)