X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=5423dc96e02598a42b843b47256bee816224958c;hb=c9c74c082bdd9323850a864144dc8a9b36399157;hp=b2482948bd9edc602be41b5fa7ff73e09371b7b1;hpb=7c05496d1da22f21ce5ae1a199afb9b16c8777ea;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index b248294..5423dc9 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -44,8 +44,8 @@ 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 +53,11 @@ 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 +70,7 @@ 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 +85,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
             {
               public void internalFrameClosing(InternalFrameEvent evt)
               {
-                resetColours();
+               ap.idPanel.idCanvas.setHighlighted(null);
               }
             }
             );
@@ -121,7 +122,6 @@ 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))
@@ -147,7 +147,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
         if (ap.av.hasHiddenColumns)
         {
-          omitHidden = ap.av.getSelectionAsString();
+          omitHidden = ap.av.getViewAsString(sg!=null);
         }
 
 
@@ -157,8 +157,6 @@ 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 +207,13 @@ 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);
     }
 
     /**
@@ -272,16 +270,6 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         af.updateEditMenuBar();
     }
 
-    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!