X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FRotatableCanvas.java;h=36e0859114bac2960e20ff99c40e307610b07842;hb=bad9b1c3e957e44c2fa5ad3a0717ea2a40c1bc12;hp=370de5f9cdbc95c8fb2b7021fa67e671520cfa1e;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java
index 370de5f..36e0859 100755
--- a/src/jalview/appletgui/RotatableCanvas.java
+++ b/src/jalview/appletgui/RotatableCanvas.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
@@ -99,7 +99,7 @@ public class RotatableCanvas
   {
     this.points = points;
     this.npoint = npoint;
-    PaintRefresher.Register(this, av.alignment);
+    PaintRefresher.Register(this, av.getSequenceSetId());
 
     prefsize = getPreferredSize();
     orig = new float[npoint][3];
@@ -371,18 +371,18 @@ public class RotatableCanvas
       int y = (int) ( (float) (sp.coord[1] - centre[1]) * scale) + halfheight;
       float z = sp.coord[1] - centre[2];
 
-      if (sp.sequence.getColor() == Color.black)
+      if (av.getSequenceColour(sp.sequence) == Color.black)
       {
         g.setColor(Color.white);
       }
       else
       {
-        g.setColor(sp.sequence.getColor());
+        g.setColor(av.getSequenceColour(sp.sequence));
       }
 
       if (av.getSelectionGroup() != null)
       {
-        if (av.getSelectionGroup().sequences.contains( ( (SequencePoint) points.
+        if (av.getSelectionGroup().getSequences(null).contains( ( (SequencePoint) points.
             elementAt(i)).sequence))
         {
           g.setColor(Color.gray);
@@ -498,7 +498,7 @@ public class RotatableCanvas
       {
         av.getSelectionGroup().addOrRemove(found, true);
         av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1);
-        PaintRefresher.Refresh(this, av.alignment);
+        PaintRefresher.Refresh(this, av.getSequenceSetId());
       }
       else
       {
@@ -577,7 +577,7 @@ public class RotatableCanvas
       {
         if (av != null)
         {
-          if (!av.getSelectionGroup().sequences.contains(sp.sequence))
+          if (!av.getSelectionGroup().getSequences(null).contains(sp.sequence))
           {
             av.getSelectionGroup().addSequence(sp.sequence, true);
           }