X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=90bdcae2ee318ae29b290bbb5ea1e5a145b2389a;hb=d2177decb24a93432ad55175b2123741bb3d8ac7;hp=bd7882730794699965bb12d96069b1b98bb230f9;hpb=52402128d98c6744eb6348dd788fe6e8cd34575c;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index bd78827..90bdcae 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -366,17 +366,18 @@ public class Alignment implements AlignmentI
    * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
    */
   @Override
-  public SequenceGroup findGroup(SequenceI s)
+  public SequenceGroup findGroup(SequenceI seq, int position)
   {
     synchronized (groups)
     {
-      for (int i = 0; i < this.groups.size(); i++)
+      for (SequenceGroup sg : groups)
       {
-        SequenceGroup sg = groups.get(i);
-
-        if (sg.getSequences(null).contains(s))
+        if (sg.getSequences(null).contains(seq))
         {
-          return sg;
+          if (position >= sg.getStartRes() && position <= sg.getEndRes())
+          {
+            return sg;
+          }
         }
       }
     }
@@ -1837,7 +1838,7 @@ public class Alignment implements AlignmentI
   @Override
   public String toString()
   {
-    return new FastaFile().print(getSequencesArray());
+    return new FastaFile().print(getSequencesArray(), true);
   }
 
   /**