(JAL-969) refactored alignmentViewport base class to own package and pulled up most...

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

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 77c9691..0b4987c 100755 (executable)
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -28,8 +28,6 @@ import jalview.datamodel.*;
 public class RedundancyPanel extends SliderPanel implements Runnable,
         WindowListener
 {
-  AlignmentPanel ap;
-
   Stack historyList = new Stack(); // simpler than synching with alignFrame.
 
   float[] redundancy;
@@ -109,15 +107,15 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
 
     if ((sg != null) && (sg.getSize() >= 1))
     {
-      originalSequences = sg.getSequencesInOrder(ap.av.alignment);
+      originalSequences = sg.getSequencesInOrder(ap.av.getAlignment());
       start = sg.getStartRes();
       end = sg.getEndRes();
     }
     else
     {
-      originalSequences = ap.av.alignment.getSequencesArray();
+      originalSequences = ap.av.getAlignment().getSequencesArray();
       start = 0;
-      end = ap.av.alignment.getWidth();
+      end = ap.av.getAlignment().getWidth();
     }
 
     height = originalSequences.length;
@@ -241,11 +239,11 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
       }
 
       EditCommand cut = new EditCommand("Remove Redundancy",
-              EditCommand.CUT, deleted, 0, width, ap.av.alignment);
-
+              EditCommand.CUT, deleted, 0, width, ap.av.getAlignment());
+      AlignmentI alignment=ap.av.getAlignment();
       for (int i = 0; i < del.size(); i++)
       {
-        ap.av.alignment.deleteSequence(deleted[i]);
+        alignment.deleteSequence(deleted[i]);
         PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
         if (sg != null)
         {