X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=ec896d596f591b07148f892554478e05e3750da8;hb=f62b380e6e3cdbce3af5730f682aad99116509c9;hp=2d262452981e25ba73909c1927e3d86fe3f49b38;hpb=4fdeee885a8bca5d4f26d766bd31d86f639f3bc0;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 2d26245..ec896d5 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -235,18 +235,10 @@ 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]);
           }
         }
 
-
         // This has to be done before the restoreHistoryItem method of alignFrame will
         // actually restore these sequences.
         if (del.size() > 0)
@@ -254,8 +246,7 @@ 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)
@@ -265,8 +256,23 @@ 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(),
+                                   true,
+                                   true);
+            if (sg != null)
+            {
+              sg.deleteSequence(deleted[i], false);
+            }
+          }
+
           historyList.push(cut);
 
+          ap.alignFrame.addHistoryItem(cut);
+
           ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
         }
 
@@ -284,6 +290,14 @@ 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)
       {
         undoButton.setEnabled(false);