Sequence colour in viewport

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