From 0b2b9b7570d68da631d657d05e6c7cff019d9a3f Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 1 Apr 2005 16:44:16 +0000
Subject: [PATCH] update conservation and consensus

---
 src/jalview/gui/SeqPanel.java |   23 ++++++-----------------
 1 file changed, 6 insertions(+), 17 deletions(-)

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 8e7141b..9f05887 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -250,7 +250,9 @@ public class SeqPanel extends JPanel
 	// Group editing
 	if (evt.isAltDown() || evt.isControlDown())
         {
-	  SequenceGroup sg = av.getAlignment().findGroup(startseq);
+	  SequenceGroup sg = av.getSelectionGroup();
+          if(sg==null)
+            av.getAlignment().findGroup(startseq);
           if (sg != null)
           {
             boolean deleteAllowed = false;
@@ -360,21 +362,8 @@ public class SeqPanel extends JPanel
 
   void updateConservation(int i)
   {
-  /*  Alignment al = (Alignment) av.getAlignment();
-    SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));
-    if(sg==null || !(sg.cs instanceof ConservationColourScheme))
-      return;
-
-    Conservation c = sg.getConservation();
-
-    c = new Conservation("All", al.cons,
-                         ResidueProperties.propHash, 3, sg.sequences, 0,
-                         al.getWidth());
-    c.calculate();
-    c.verdict(false, 100);
-    sg.setConservation(c);
-    ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-    ccs.conserve = c;*/
+    av.updateConservation();
+    av.updateConsensus();
   }
 
 //////////////////////////////////////////
@@ -397,7 +386,7 @@ public class SeqPanel extends JPanel
     if(stretchGroup == null)
      {
        stretchGroup = av.alignment.findGroup( sequence );
-       if(res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())
+       if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())
          av.setSelectionGroup(stretchGroup);
        else
          stretchGroup = null;
-- 
1.7.10.2