From a3df398bea1970500d44f0e6adc45c9d4bf4a295 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 5 Jan 2011 15:36:30 +0000
Subject: [PATCH] propagated groups trimmed to correct region on viscontig

---
 src/jalview/datamodel/AlignmentView.java |   12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 21b5e7f..2a93861 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -351,9 +351,14 @@ public class AlignmentView
                 continue;
               }
             }
+
+            // clone group properties
+            nsg[g] = new SequenceGroup(sg);
+
             // may need to shift/trim start and end ?
             if (r && !viscontigs)
             {
+              // Not fully tested code - routine not yet called with viscontigs==false
               if (nsg[g].getStartRes() < gstart)
               {
                 nsg[g].setStartRes(0);
@@ -363,14 +368,11 @@ public class AlignmentView
                 nsg[g].setStartRes(nsg[g].getStartRes() - gstart);
                 nsg[g].setEndRes(nsg[g].getEndRes() - gstart);
               }
-              if (nsg[g].getEndRes() > gend)
+              if (nsg[g].getEndRes() > (gend-gstart))
               {
-                nsg[g].setEndRes(gend);
+                nsg[g].setEndRes(gend-gstart);
               }
             }
-
-            // clone group properties
-            nsg[g] = new SequenceGroup(sg);
           }
           if (viscontigs)
           {
-- 
1.7.10.2