X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=759075a46a1b723a133a69bc0879f81f9a1f49b5;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=70306374540c6bbad68feb559544884f985535df;hpb=ca812007f560910bab66a186420d8fde7cb461cf;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 7030637..759075a 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * 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.
  * 
@@ -601,6 +601,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       viewport.autocalculateConsensus = autoCalculate.getState();
     }
+    else if (evt.getSource() == sortByTree)
+    {
+      viewport.sortByTree = sortByTree.getState();
+    }
     else if (evt.getSource() == this.centreColumnLabelFlag)
     {
       centreColumnLabelFlag_stateChanged();
@@ -2551,7 +2555,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         sortByTree(treePanel, title); // treePanel.getTitle());
       }
     });
-
+    
     treePanel.addWindowListener(new WindowAdapter()
     {
       public void windowOpened(WindowEvent e)
@@ -2585,6 +2589,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     alignPanel.paintAlignment(true);
     return true;
   }
+
   protected void documentation_actionPerformed()
   {
     alignPanel.av.applet.openJalviewHelpUrl();
@@ -2818,6 +2823,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
           "Autocalculate Consensus", true);
 
+  CheckboxMenuItem sortByTree = new CheckboxMenuItem(
+          "Sort Alignment With New Tree", true);
+
   Menu sortByTreeMenu = new Menu();
 
   Menu sort = new Menu();
@@ -3013,6 +3021,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     sort.setLabel("Sort");
     calculate.setLabel("Calculate Tree");
     autoCalculate.addItemListener(this);
+    sortByTree.addItemListener(this);
     inputText.setLabel("Input from textbox");
     inputText.addActionListener(this);
     centreColumnLabelFlag.setLabel("Centre column labels");
@@ -3157,6 +3166,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     calculateMenu.add(pairwiseAlignmentMenuItem);
     calculateMenu.add(PCAMenuItem);
     calculateMenu.add(autoCalculate);
+    calculateMenu.add(sortByTree);
     this.add(statusBar, BorderLayout.SOUTH);
     pasteMenu.add(pasteNew);
     pasteMenu.add(pasteThis);