From d426f538337d32aad42cedd555446dff7e8cffc2 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 24 Oct 2006 12:05:01 +0000
Subject: [PATCH] Must set alignIndex before delete takes place

---
 src/jalview/gui/RedundancyPanel.java |   26 ++++++++++++++++----------
 1 file changed, 16 insertions(+), 10 deletions(-)

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 2d26245..2e136e0 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -235,14 +235,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         {
           if (value <= redundancy[i])
           {
-            SequenceI seq = originalSequences[i];
-            ap.av.alignment.deleteSequence(seq);
-            PaintRefresher.Refresh(this,ap.av.getSequenceSetId(),seq,null);
-            del.addElement(seq);
-            if (sg != null)
-            {
-              sg.deleteSequence(seq, false);
-            }
+            del.addElement(originalSequences[i]);
           }
         }
 
@@ -254,8 +247,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
           SequenceI [] deleted = new SequenceI[del.size()];
 
           int width = 0;
-
-          for (int i = 0, j = del.size(); i < j; i++)
+          for (int i = 0; i < del.size(); i++)
           {
             deleted[i] = (SequenceI)del.elementAt(i);
             if(deleted[i].getLength()>width)
@@ -265,6 +257,18 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
           EditCommand cut = new EditCommand("Remove Redundancy",
               EditCommand.CUT, deleted,0,width,ap.av.alignment);
 
+          for (int i = 0; i < del.size(); i++)
+          {
+            ap.av.alignment.deleteSequence( deleted[i] );
+            PaintRefresher.Refresh(this,
+                                   ap.av.getSequenceSetId(),
+                                   deleted[i], null);
+            if (sg != null)
+            {
+              sg.deleteSequence(deleted[i], false);
+            }
+          }
+
           historyList.push(cut);
 
           ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
@@ -284,6 +288,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       CommandI command = (CommandI) historyList.pop();
       command.undoCommand();
 
+      ap.repaint();
+
       if (historyList.size() == 0)
       {
         undoButton.setEnabled(false);
-- 
1.7.10.2