Transparency......

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

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