X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=2e8811a9d3d06d73a0c8318124ac0be2ba1d9003;hb=82483c09d45298e6f93a7d3d2b537598cc0451b5;hp=5037a501146653e94b68c1d9a16ccaa93cf5c9a4;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 5037a50..2e8811a 100755
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -27,6 +27,7 @@ import java.awt.*;
 
 import jalview.datamodel.*;
 import jalview.appletgui.PaintRefresher;
+import jalview.commands.*;
 
 public class RedundancyPanel extends SliderPanel implements Runnable, WindowListener
 {
@@ -102,7 +103,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
 
       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();
@@ -142,8 +143,8 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
 
             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
             {
@@ -187,70 +188,84 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
     }
 
     ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
-
-    PaintRefresher.Refresh(null,ap.av.alignment);
+    PaintRefresher.Refresh(this,
+                           ap.av.getSequenceSetId(),
+                           true,
+                           true);
 
     }
   public void applyButton_actionPerformed()
-  {
-    historyList.push(new HistoryItem("Remove redundancy",
-                        ap.av.alignment, HistoryItem.HIDE));
+  {        Vector del = new Vector();
 
-            if ((historyList.size() == 1) ||
-                    !ap.alignFrame.historyList.contains(historyList.firstElement()))
-            {
-                ap.alignFrame.addHistoryItem((HistoryItem) historyList.firstElement());
-                ap.alignFrame.updateEditMenuBar();
-            }
+        undoButton.setEnabled(true);
 
-            Vector del = new Vector();
+        float value = slider.getValue();
+        SequenceGroup sg = ap.av.getSelectionGroup();
 
-            undoButton.setEnabled(true);
+        for (int i = 0; i < redundancy.length; i++)
+        {
+          if (value <= redundancy[i])
+          {
+            del.addElement(originalSequences[i]);
+          }
+        }
 
-            float value = slider.getValue();
-            SequenceGroup sg = ap.av.getSelectionGroup();
+        // This has to be done before the restoreHistoryItem method of alignFrame will
+        // actually restore these sequences.
+        if (del.size() > 0)
+        {
+          SequenceI [] deleted = new SequenceI[del.size()];
 
-            for (int i = 0; i < redundancy.length; i++)
-            {
-              if (value <= redundancy[i])
-              {
-                SequenceI seq = originalSequences[i];
-                ap.av.alignment.deleteSequence(seq);
-                del.addElement(seq);
-                if (sg != null)
-                {
-                  sg.deleteSequence(seq, false);
-                }
-              }
-            }
+          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);
 
-            // This has to be done before the restoreHistoryItem method of alignFrame will
-            // actually restore these sequences.
-            if (del.size() > 0)
+          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)
             {
-                for (int i = 0, j = del.size(); i < j; i++)
-                {
-                    SequenceI sq = (SequenceI) del.elementAt(i);
-                    sq.deleteChars(0, sq.getLength());
-                }
+              sg.deleteSequence(deleted[i], false);
             }
+          }
+
+          historyList.push(cut);
 
-        ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
-        ap.alignFrame.updateEditMenuBar();
+          ap.alignFrame.addHistoryItem(cut);
+
+          ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
+        }
 
   }
 
   public void undoButton_actionPerformed()
   {
-    HistoryItem hi = (HistoryItem) historyList.pop();
-    ap.alignFrame.restoreHistoryItem(hi);
+    CommandI command = (CommandI) historyList.pop();
+    command.undoCommand();
+
+    if (ap.av.historyList.contains(command))
+    {
+      ap.av.historyList.removeElement(command);
+      ap.alignFrame.updateEditMenuBar();
+    }
+
+    ap.repaint();
 
     if (historyList.size() == 0)
     {
       undoButton.setEnabled(false);
-    }
-    ap.alignFrame.updateEditMenuBar();
+      }
   }
 
   public void valueField_actionPerformed(ActionEvent e)