From cb52962fdc914e4c1e7fac7afd83dbdf8defec22 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 4 Jun 2010 16:09:48 +0000
Subject: [PATCH] update group annotation for new treegroups (JAL-552)

---
 src/jalview/gui/AlignmentPanel.java |    1 +
 src/jalview/gui/TreeCanvas.java     |    7 ++++++-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 09b7215..72290a7 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1328,6 +1328,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   public void updateAnnotation(boolean applyGlobalSettings)
   {
+    // TODO: this should be merged with other annotation update stuff - that sits on AlignViewport
     boolean updateCalcs = false;
     boolean conv = av.isShowGroupConservation();
     boolean cons = av.isShowGroupConsensus();
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 028552c..c2b9b7f 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -864,6 +864,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
   void colourGroups()
   {
+    AlignmentPanel[] aps = getAssociatedPanels();
     for (int i = 0; i < tree.getGroups().size(); i++)
     {
       Color col = new Color((int) (Math.random() * 255), (int) (Math
@@ -912,7 +913,6 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
       sg.setName("JTreeGroup:" + sg.hashCode());
       sg.setIdColour(col);
-      AlignmentPanel[] aps = getAssociatedPanels();
       for (int a = 0; a < aps.length; a++)
       {
         if (aps[a].av.getGlobalColourScheme() != null
@@ -930,6 +930,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         aps[a].av.alignment.addGroup(sg);
       }
     }
+    // notify the panel to redo any group specific stuff.
+    for (int a=0;a<aps.length;a++)
+    {
+      aps[a].updateAnnotation();
+    }
 
   }
 
-- 
1.7.10.2