X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=01d3d8d626f1eb53767631146123f43687d57bdd;hb=b948e764c92b0954100f216927114b2c9720b76c;hp=9c5914fde4f7df716a59206f4cea468719484d1c;hpb=b5d61763044c1d72f06ce0e50da2171422a3774b;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 9c5914f..01d3d8d 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1571,6 +1571,39 @@ public class Alignment implements AlignmentI
     }
   }
 
+
+ private SequenceI seqrep=null;
+
+ /**
+  * 
+  * @return the representative sequence for this group
+  */
+ public SequenceI getSeqrep()
+ {
+   return seqrep;
+ }
+
+ /**
+  * set the representative sequence for this group. Note - this affects the
+  * interpretation of the Hidereps attribute.
+  * 
+  * @param seqrep
+  *          the seqrep to set (null means no sequence representative)
+  */
+ public void setSeqrep(SequenceI seqrep)
+ {
+   this.seqrep = seqrep;
+ }
+
+ /**
+  * 
+  * @return true if group has a sequence representative
+  */
+ public boolean hasSeqrep()
+ {
+   return seqrep != null;
+ }
+
   @Override
   public int getEndRes()
   {