X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=ec896d596f591b07148f892554478e05e3750da8;hb=3e3378e2ccfea39a2b161600c5a2029716acd1b7;hp=50183eb9e2d79d751e8452343aea44ba5be26cfc;hpb=f3bc67915e61855d87866b4a614fe7a953813408;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 50183eb..ec896d5 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -19,15 +19,16 @@
 package jalview.gui;
 
 import jalview.datamodel.*;
-
 import jalview.jbgui.*;
+import jalview.util.Comparison;
+import jalview.commands.*;
 
 import java.awt.event.*;
 
 import java.util.*;
 
 import javax.swing.event.*;
-import jalview.util.Comparison;
+
 import javax.swing.*;
 
 
@@ -223,16 +224,6 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
      */
     public void applyButton_actionPerformed(ActionEvent e)
     {
-        historyList.push(new HistoryItem("Remove redundancy",
-                    ap.av.alignment, HistoryItem.HIDE));
-
-        if ((historyList.size() == 1) ||
-                !af.historyList.contains(historyList.firstElement()))
-        {
-            af.addHistoryItem((HistoryItem) historyList.firstElement());
-            af.updateEditMenuBar();
-        }
-
         Vector del = new Vector();
 
         undoButton.setEnabled(true);
@@ -244,31 +235,48 @@ 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.add(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)
         {
-            for (int i = 0, j = del.size(); i < j; i++)
+          SequenceI [] deleted = new SequenceI[del.size()];
+
+          int width = 0;
+          for (int i = 0; i < del.size(); i++)
+          {
+            deleted[i] = (SequenceI)del.elementAt(i);
+            if(deleted[i].getLength()>width)
+              width = deleted[i].getLength();
+          }
+
+          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)
             {
-                SequenceI sq = (SequenceI) del.elementAt(i);
-                sq.deleteChars(0, sq.getLength());
+              sg.deleteSequence(deleted[i], false);
             }
+          }
+
+          historyList.push(cut);
+
+          ap.alignFrame.addHistoryItem(cut);
+
+          ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
         }
 
-        ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
-        af.updateEditMenuBar();
+
     }
 
 
@@ -279,18 +287,20 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
      */
     public void undoButton_actionPerformed(ActionEvent e)
     {
-      HistoryItem hi = (HistoryItem) historyList.pop();
-      af.restoreHistoryItem(hi);
+      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);
-
-        if (af.historyList.contains(hi))
-        {
-          af.historyList.remove(hi);
-          af.updateEditMenuBar();
-        }
       }
     }