PaintRefresh changed

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

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 0f74faf..2864eb4 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -65,7 +65,7 @@ public class TreeCanvas
     tree.findHeight(tree.getTopNode());\r
     longestName = label;\r
 \r
-    PaintRefresher.Register(this);\r
+    PaintRefresher.Register(this, av.alignment);\r
   }\r
 \r
   public void TreeSelectionChanged(Sequence sequence)\r
@@ -81,7 +81,7 @@ public class TreeCanvas
     selected.setEndRes(av.alignment.getWidth());\r
     selected.addOrRemove(sequence, true);\r
 \r
-    PaintRefresher.Refresh(this);\r
+    PaintRefresher.Refresh(this, av.alignment);\r
     repaint();\r
   }\r
 \r
@@ -568,11 +568,19 @@ public class TreeCanvas
             sequences.add( (Sequence)((SequenceNode) l.elementAt(j)).element());\r
           }\r
 \r
+          ColourSchemeI cs = ColourSchemeProperty.getColour(sequences, av.alignment.getWidth(),\r
+              ColourSchemeProperty.getColourName(av.getGlobalColourScheme()));\r
+\r
           SequenceGroup sg = new SequenceGroup(sequences, "TreeGroup",\r
-                           av.getGlobalColourScheme(), true, true,\r
+                           cs, true, true,\r
                            false, 0, av.alignment.getWidth());\r
 \r
 \r
+           ( (ResidueColourScheme) sg.cs).setThreshold(25);\r
+\r
+\r
+\r
+\r
           if (av.getGlobalColourScheme() instanceof ConservationColourScheme)\r
           {\r
             ConservationColourScheme ccs = (ConservationColourScheme) av.\r
@@ -594,7 +602,7 @@ public class TreeCanvas
       }\r
     }\r
 \r
-    PaintRefresher.Refresh(this);\r
+    PaintRefresher.Refresh(this, av.alignment);\r
     repaint();\r
   }\r
 \r