X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=4ca114dbba6ae7528c81c9503375251e5cb6d7f5;hb=ad35f232acd499d9457056ca24b663866a09edd2;hp=2e136e0c9b4f8045241f7e702d36e5cee93edd47;hpb=d426f538337d32aad42cedd555446dff7e8cffc2;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 2e136e0..4ca114d 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -125,7 +125,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
         int start, end;
 
-        if ( (sg != null) && (sg.getSize(false) >= 1))
+        if ( (sg != null) && (sg.getSize() >= 1))
         {
            originalSequences = sg.getSequencesInOrder(ap.av.alignment);
            start = sg.getStartRes();
@@ -166,8 +166,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
               if(omitHidden==null)
               {
-                seqi = originalSequences[i].getSequence(start, end);
-                seqj = originalSequences[j].getSequence(start, end);
+                seqi = originalSequences[i].getSequenceAsString(start, end);
+                seqj = originalSequences[j].getSequenceAsString(start, end);
               }
               else
               {
@@ -239,7 +239,6 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
           }
         }
 
-
         // This has to be done before the restoreHistoryItem method of alignFrame will
         // actually restore these sequences.
         if (del.size() > 0)
@@ -262,7 +261,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
             ap.av.alignment.deleteSequence( deleted[i] );
             PaintRefresher.Refresh(this,
                                    ap.av.getSequenceSetId(),
-                                   deleted[i], null);
+                                   true,
+                                   true);
             if (sg != null)
             {
               sg.deleteSequence(deleted[i], false);
@@ -271,6 +271,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
           historyList.push(cut);
 
+          ap.alignFrame.addHistoryItem(cut);
+
           ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
         }
 
@@ -288,6 +290,12 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       CommandI command = (CommandI) historyList.pop();
       command.undoCommand();
 
+      if (ap.av.historyList.contains(command))
+      {
+        ap.av.historyList.remove(command);
+        af.updateEditMenuBar();
+      }
+
       ap.repaint();
 
       if (historyList.size() == 0)