X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=5f0bf6884fc9fabbb7acdec470c31a9e0c50bf10;hb=621a628afc1f6ee7a2778b9d0ae2729b88fe5bfd;hp=daae7c5f7adf538a7cb13650d2587b77b7e5168e;hpb=c16afbb4d0e2672fdc54d32778b6d53f09c5d86c;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index daae7c5..5f0bf68 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -279,19 +279,13 @@ public class Alignment implements AlignmentI
 
 
     /**    */
-    public SequenceGroup findGroup(int i)
-    {
-        return findGroup(getSequenceAt(i));
-    }
-
-    /**    */
     public SequenceGroup findGroup(SequenceI s)
     {
         for (int i = 0; i < this.groups.size(); i++)
         {
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
-            if (sg.sequences.contains(s))
+            if (sg.getSequences(false).contains(s))
             {
                 return sg;
             }
@@ -315,14 +309,14 @@ public class Alignment implements AlignmentI
         for (int i = 0; i < gSize; i++)
         {
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-            if(sg==null || sg.sequences==null)
+            if(sg==null || sg.getSequences(false)==null)
             {
               this.deleteGroup(sg);
               gSize--;
               continue;
             }
 
-            if (sg.sequences.contains(s))
+            if (sg.getSequences(false).contains(s))
             {
                 temp.addElement(sg);
             }
@@ -481,9 +475,9 @@ public class Alignment implements AlignmentI
         for (int i = 0; i < sequences.size(); i++)
         {
             Sequence seq = (Sequence) sequences.elementAt(i);
-            seq.sequence = seq.sequence.replace('.', gc);
-            seq.sequence = seq.sequence.replace('-', gc);
-            seq.sequence = seq.sequence.replace(' ', gc);
+            seq.setSequence( seq.getSequence().replace('.', gc) );
+            seq.setSequence( seq.getSequence().replace('-', gc) );
+            seq.setSequence( seq.getSequence().replace(' ', gc) );
         }
     }