X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentView.java;h=8e596ceca355d76c01c33a364ebdb45fb6af9145;hb=8c8433dbbca18eb7955537a8756fba92d044dd41;hp=21b5e7f26963750eadc951a5ac7b8ec52965ec21;hpb=1f5616e7db919162a5cc3b25b09ccf95845f03ee;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 21b5e7f..8e596ce 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -107,7 +107,7 @@ public class AlignmentView
     {
       Vector sel = selection.getSequences(null);
       this.selected = new Vector();
-      selseqs = selection.getSequencesInOrder(alignment, false);
+      selseqs = selection.getSequencesInOrder(alignment, selectedRegionOnly);
     }
     else
     {
@@ -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)
           {