X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=3df55c1455deb87a51cabcc46cc97f4fcd651443;hb=d1a58585358deed317674daeeac5fb5be66637ab;hp=3d1bfb7f1f5a5a5bc5b2df460e1cf2cbce16c65b;hpb=ef6555067c63693c06f0b6335a1c9f5761d712c6;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 3d1bfb7..3df55c1 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -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.*;
 
 
@@ -44,8 +45,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     Stack historyList = new Stack(); // simpler than synching with alignFrame.
     float [] redundancy;
     SequenceI [] originalSequences;
-    Hashtable originalColours;
     JInternalFrame frame;
+    Vector redundantSeqs;
 
     /**
      * Creates a new RedundancyPanel object.
@@ -53,10 +54,11 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
      * @param ap DOCUMENT ME!
      * @param af DOCUMENT ME!
      */
-    public RedundancyPanel(AlignmentPanel ap, AlignFrame af)
+    public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)
     {
         this.ap = ap;
         this.af = af;
+        redundantSeqs = new Vector();
 
         slider.addChangeListener(new ChangeListener()
             {
@@ -69,7 +71,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
         applyButton.setText("Remove");
         allGroupsCheck.setVisible(false);
-        slider.setMinimum(60);
+        slider.setMinimum(0);
         slider.setMaximum(100);
         slider.setValue(100);
 
@@ -84,7 +86,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
             {
               public void internalFrameClosing(InternalFrameEvent evt)
               {
-                resetColours();
+               ap.idPanel.idCanvas.setHighlighted(null);
               }
             }
             );
@@ -121,7 +123,6 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         SequenceGroup sg = ap.av.getSelectionGroup();
         int height;
 
-        originalColours = new Hashtable();
         int start, end;
 
         if ( (sg != null) && (sg.getSize(false) >= 1))
@@ -157,8 +158,6 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         String seqi, seqj;
         for (int i = 0; i < height; i++)
         {
-            originalColours.put(originalSequences[i],
-                               originalSequences[i].getColor());
 
             for (int j = 0; j < i; j++)
             {
@@ -209,13 +208,13 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       for(int i=0; i<redundancy.length; i++)
       {
         if (value > redundancy[i])
-           originalSequences[i].setColor(java.awt.Color.white);
-        else
-          originalSequences[i].setColor(java.awt.Color.red);
-      }
+          redundantSeqs.remove(originalSequences[i]);
+        else if(!redundantSeqs.contains(originalSequences[i]))
+          redundantSeqs.add(originalSequences[i]);
 
-      PaintRefresher.Refresh(null,ap.av.alignment);
+      }
 
+      ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
     }
 
     /**
@@ -225,16 +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);
@@ -246,43 +235,50 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         {
           if (value <= redundancy[i])
           {
-            SequenceI seq = originalSequences[i];
-            ap.av.alignment.deleteSequence(seq);
-            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(),
+                                   deleted[i], null);
+            if (sg != null)
             {
-                SequenceI sq = (SequenceI) del.elementAt(i);
-                sq.deleteChars(0, sq.getLength());
+              sg.deleteSequence(deleted[i], false);
             }
-        }
+          }
 
-        ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
-        af.updateEditMenuBar();
-    }
+          historyList.push(cut);
+
+          ap.alignFrame.addHistoryItem(cut);
+
+          ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
+        }
 
-    void resetColours()
-    {
-      for(int i=0; i<originalSequences.length; i++)
-      {
-        SequenceI seq = originalSequences[i];
-        seq.setColor( (java.awt.Color)originalColours.get(seq));
-      }
 
-      PaintRefresher.Refresh(ap.av.alignment);
     }
 
+
     /**
      * DOCUMENT ME!
      *
@@ -290,18 +286,20 @@ 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 (af.historyList.contains(command))
+      {
+        af.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();
-        }
       }
     }