From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 7 Nov 2006 11:52:14 +0000 (+0000)
Subject: Tidy up group size after alignmentChanged
X-Git-Tag: Release_2_2~172
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f5a39f4861d0f1ffdb3c5b542e00907b2cc18a73;p=jalview.git

Tidy up group size after alignmentChanged
---

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 0161517..b275611 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1536,6 +1536,22 @@ public class AlignViewport
           updateConservation(ap);
         }
 
+        //Reset endRes of groups if beyond alignment width
+        int alWidth = alignment.getWidth();
+        Vector groups = alignment.getGroups();
+        if(groups!=null)
+        {
+          for(int i=0; i<groups.size(); i++)
+          {
+            SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+            if(sg.getEndRes()>alWidth)
+              sg.setEndRes(alWidth-1);
+          }
+        }
+
+        if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)
+          selectionGroup.setEndRes(alWidth-1);
+
         resetAllColourSchemes();
 
         alignment.adjustSequenceAnnotations();