From 7cf75b5b379dd71b3480726419c7dc55d8e01f0e Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 13 Nov 2006 11:10:24 +0000
Subject: [PATCH] Sequence colour in viewport

---
 src/jalview/gui/TreeCanvas.java |   12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 3a7f05e..57e652c 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -173,14 +173,15 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
             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());
                 }
             }
             else
@@ -419,7 +420,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
             if (node.element() instanceof SequenceI)
             {
-                ((SequenceI) node.element()).setColor(c);
+              av.setSequenceColour((SequenceI) node.element(), c);
             }
         }
         else
@@ -719,7 +720,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         if (highlightNode != null)
         {
           highlightNode = null;
-          setToolTipText("");
+          setToolTipText(null);
           repaint();
         }
       }
@@ -763,6 +764,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
                 av.setSelectionGroup(null);
                 av.alignment.deleteAllGroups();
+                av.sequenceColours.clear();
 
                 colourGroups();
               }
-- 
1.7.10.2