X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=8b68489addf299346baf21d569108ee8d996bbb0;hb=fdaa305572f6d4e0008de3ffa2233444c64b55bf;hp=928d21fb4ad6183ae34140297738b69be11cca5d;hpb=d7d3a412210d013e401a3825eaf425fa55ce8106;p=jalview.git

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 928d21f..8b68489 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -65,7 +65,7 @@ public class TreeCanvas
     addMouseMotionListener(this);
     setLayout(null);
 
-    PaintRefresher.Register(this, av.alignment);
+    PaintRefresher.Register(this, av.getSequenceSetId());
   }
 
   public void treeSelectionChanged(SequenceI sequence)
@@ -133,15 +133,15 @@ public class TreeCanvas
 
       if (node.element() instanceof SequenceI)
       {
-        if ( ( (SequenceI) ( (SequenceNode) node).element()).getColor() ==
-            Color.white)
+        SequenceI seq = (SequenceI) ( (SequenceNode) node).element();
+
+        if (av.getSequenceColour(seq) == Color.white)
         {
           g.setColor(Color.black);
         }
         else
         {
-          g.setColor( ( (SequenceI) ( (SequenceNode) node).element()).getColor().
-                     darker());
+          g.setColor(av.getSequenceColour(seq).darker());
         }
 
       }
@@ -337,7 +337,7 @@ public class TreeCanvas
 
       if (node.element() instanceof SequenceI)
       {
-        ( (SequenceI) node.element()).setColor(c);
+        av.setSequenceColour((SequenceI) node.element(), c);
       }
     }
     else
@@ -472,7 +472,7 @@ public class TreeCanvas
         }
       }
 
-      PaintRefresher.Refresh(this, av.alignment);
+      PaintRefresher.Refresh(this, av.getSequenceSetId());
       repaint();
     }
   }
@@ -514,7 +514,7 @@ public class TreeCanvas
     if (ob instanceof SequenceI)
     {
       treeSelectionChanged( (Sequence) ob);
-      PaintRefresher.Refresh(this, av.alignment);
+      PaintRefresher.Refresh(this, av.getSequenceSetId());
       repaint();
       return;
     }
@@ -533,13 +533,14 @@ public class TreeCanvas
 
         av.setSelectionGroup(null);
         av.alignment.deleteAllGroups();
+        av.sequenceColours=null;
 
         colourGroups();
 
       }
     }
 
-    PaintRefresher.Refresh(this, av.alignment);
+    PaintRefresher.Refresh(this, av.getSequenceSetId());
     repaint();
 
   }