Multiple Views

[jalview.git] / src / jalview / gui / RedundancyPanel.java

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index b248294..50183eb 100755 (executable)
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -44,8 +44,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
     float [] redundancy;\r
     SequenceI [] originalSequences;\r
-    Hashtable originalColours;\r
     JInternalFrame frame;\r
+    Vector redundantSeqs;\r
 \r
     /**\r
      * Creates a new RedundancyPanel object.\r
@@ -53,10 +53,11 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
      * @param ap DOCUMENT ME!\r
      * @param af DOCUMENT ME!\r
      */\r
-    public RedundancyPanel(AlignmentPanel ap, AlignFrame af)\r
+    public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)\r
     {\r
         this.ap = ap;\r
         this.af = af;\r
+        redundantSeqs = new Vector();\r
 \r
         slider.addChangeListener(new ChangeListener()\r
             {\r
@@ -69,7 +70,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 \r
         applyButton.setText("Remove");\r
         allGroupsCheck.setVisible(false);\r
-        slider.setMinimum(60);\r
+        slider.setMinimum(0);\r
         slider.setMaximum(100);\r
         slider.setValue(100);\r
 \r
@@ -84,7 +85,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
             {\r
               public void internalFrameClosing(InternalFrameEvent evt)\r
               {\r
-                resetColours();\r
+               ap.idPanel.idCanvas.setHighlighted(null);\r
               }\r
             }\r
             );\r
@@ -121,7 +122,6 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         SequenceGroup sg = ap.av.getSelectionGroup();\r
         int height;\r
 \r
-        originalColours = new Hashtable();\r
         int start, end;\r
 \r
         if ( (sg != null) && (sg.getSize(false) >= 1))\r
@@ -147,7 +147,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 \r
         if (ap.av.hasHiddenColumns)\r
         {\r
-          omitHidden = ap.av.getSelectionAsString();\r
+          omitHidden = ap.av.getViewAsString(sg!=null);\r
         }\r
 \r
 \r
@@ -157,8 +157,6 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         String seqi, seqj;\r
         for (int i = 0; i < height; i++)\r
         {\r
-            originalColours.put(originalSequences[i],\r
-                               originalSequences[i].getColor());\r
 \r
             for (int j = 0; j < i; j++)\r
             {\r
@@ -209,13 +207,13 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       for(int i=0; i<redundancy.length; i++)\r
       {\r
         if (value > redundancy[i])\r
-           originalSequences[i].setColor(java.awt.Color.white);\r
-        else\r
-          originalSequences[i].setColor(java.awt.Color.red);\r
-      }\r
+          redundantSeqs.remove(originalSequences[i]);\r
+        else if(!redundantSeqs.contains(originalSequences[i]))\r
+          redundantSeqs.add(originalSequences[i]);\r
 \r
-      PaintRefresher.Refresh(null,ap.av.alignment);\r
+      }\r
 \r
+      ap.idPanel.idCanvas.setHighlighted(redundantSeqs);\r
     }\r
 \r
     /**\r
@@ -248,6 +246,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
           {\r
             SequenceI seq = originalSequences[i];\r
             ap.av.alignment.deleteSequence(seq);\r
+            PaintRefresher.Refresh(this,ap.av.getSequenceSetId(),seq,null);\r
             del.add(seq);\r
             if (sg != null)\r
             {\r
@@ -272,16 +271,6 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         af.updateEditMenuBar();\r
     }\r
 \r
-    void resetColours()\r
-    {\r
-      for(int i=0; i<originalSequences.length; i++)\r
-      {\r
-        SequenceI seq = originalSequences[i];\r
-        seq.setColor( (java.awt.Color)originalColours.get(seq));\r
-      }\r
-\r
-      PaintRefresher.Refresh(ap.av.alignment);\r
-    }\r
 \r
     /**\r
      * DOCUMENT ME!\r