X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=efabb9b0b7bd2e972363f12ecf4ae0bc2d19d2b6;hb=a02b6ca8444260bee8a15204345fa3cddf54df0e;hp=7608cb9bbdeac91a8c7c6f6027d1b0b6196aadad;hpb=0c0f58648af5512096275b634158c37c87989eaa;p=jalview.git

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 7608cb9..efabb9b 100755
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -35,13 +35,14 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
   Stack historyList = new Stack(); // simpler than synching with alignFrame.
   float [] redundancy;
   SequenceI [] originalSequences;
-  Hashtable originalColours;
   Frame frame;
+  Vector redundantSeqs;
 
   public RedundancyPanel(AlignmentPanel ap)
   {
     super(ap, 0, false, null);
 
+    redundantSeqs = new Vector();
     this.ap = ap;
     undoButton.setVisible(true);
     applyButton.setVisible(true);
@@ -51,7 +52,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
     valueField.setText("100");
 
     slider.setVisibleAmount(1);
-    slider.setMinimum(40);
+    slider.setMinimum(0);
     slider.setMaximum(100+slider.getVisibleAmount());
     slider.setValue(100);
 
@@ -99,7 +100,6 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
       SequenceGroup sg = ap.av.getSelectionGroup();
       int height;
 
-      originalColours = new Hashtable();
       int start, end;
 
       if ( (sg != null) && (sg.getSize(false) >= 1))
@@ -135,9 +135,6 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
       String seqi, seqj;
       for (int i = 0; i < height; i++)
       {
-          originalColours.put(originalSequences[i],
-                             originalSequences[i].getColor());
-
           for (int j = 0; j < i; j++)
           {
             if(i==j)
@@ -184,11 +181,13 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
     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.removeElement(originalSequences[i]);
+      else if(!redundantSeqs.contains(originalSequences[i]))
+         redundantSeqs.addElement(originalSequences[i]);
     }
 
+    ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
+
     PaintRefresher.Refresh(null,ap.av.alignment);
 
     }
@@ -273,13 +272,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
 
   public void windowClosing(WindowEvent evt)
   {
-    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);
+    ap.idPanel.idCanvas.setHighlighted(null);
   }
 
   public void windowClosed(WindowEvent evt)