From 0616cee67a5fd2f8724f48232873c39d5fa3015a Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 14 Jun 2005 15:06:34 +0000
Subject: [PATCH] update conservation colours after edit

---
 src/jalview/gui/SeqPanel.java |   27 +++++++++++++++++----------
 1 file changed, 17 insertions(+), 10 deletions(-)

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 27cb962..f827fba 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -180,7 +180,7 @@ public class SeqPanel
     editingSeqs = false;
     groupEditing = false;
 
-    seqCanvas.repaint();
+    ap.repaint();
   }
 
   public void doMousePressed(MouseEvent evt)
@@ -485,18 +485,22 @@ public class SeqPanel
     // Y O Y CLUSTALX
     ColourSchemeI cs = av.getGlobalColourScheme();
 
+    if(av.getSelectionGroup()!=null)
+      av.getSelectionGroup().recalcConservation();
+
+
     if (cs instanceof ConservationColourScheme)
     {
       ConservationColourScheme ccs = (ConservationColourScheme) cs;
+      Conservation c = new Conservation("All",
+                                        ResidueProperties.propHash, 3,
+                                        av.alignment.getSequences(), 0,
+                                        av.alignment.getWidth() - 1);
+      c.calculate();
+      c.verdict(false, av.ConsPercGaps);
 
       if (ccs.cs instanceof ClustalxColourScheme)
       {
-        Conservation c = new Conservation("All",
-                                          ResidueProperties.propHash, 3,
-                                          av.alignment.getSequences(), 0,
-                                          av.alignment.getWidth() - 1);
-        c.calculate();
-        c.verdict(false, av.ConsPercGaps);
 
         ClustalxColourScheme cxs = (ClustalxColourScheme) ccs.cs;
         cxs.resetClustalX(av.alignment.getSequences(),
@@ -504,6 +508,11 @@ public class SeqPanel
         ccs = new ConservationColourScheme(c, cxs);
         av.setGlobalColourScheme(ccs);
       }
+      else
+      {
+        ccs = new ConservationColourScheme(c, ccs.cs);
+        av.setGlobalColourScheme(ccs);
+      }
     }
 
     if (cs instanceof ClustalxColourScheme)
@@ -727,8 +736,7 @@ public class SeqPanel
 
       if (stretchGroup.sequences.contains(nextSeq))
       {
-        stretchGroup.deleteSequence(seq, false);
-        stretchGroup.deleteSequence(nextSeq, false);
+          stretchGroup.deleteSequence(seq, false);
       }
       else
       {
@@ -736,7 +744,6 @@ public class SeqPanel
         {
           stretchGroup.addSequence(seq, false);
         }
-
         stretchGroup.addSequence(nextSeq, false);
       }
     }
-- 
1.7.10.2