X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentView.java;h=ebe8301551f10aa01a7ddc099ed07af13b6a6984;hb=bfc02f81d9bd87c62b204d0768b16b3efdca684e;hp=21b5e7f26963750eadc951a5ac7b8ec52965ec21;hpb=1f5616e7db919162a5cc3b25b09ccf95845f03ee;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 21b5e7f..ebe8301 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -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)
           {