X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceCollectionI.java;h=aca79c83f37394812b583491465308e931ac0132;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=991747123f7e2953fc829e1bf7177fcedf7f8d1a;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceCollectionI.java b/src/jalview/datamodel/SequenceCollectionI.java
index 9917471..aca79c8 100644
--- a/src/jalview/datamodel/SequenceCollectionI.java
+++ b/src/jalview/datamodel/SequenceCollectionI.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -33,6 +33,27 @@ public interface SequenceCollectionI
   int getWidth();
 
   /**
+   * 
+   * @return true if getSeqrep doesn't return null
+   */
+  boolean hasSeqrep();
+
+  /**
+   * get the reference or representative sequence within this collection
+   * 
+   * @return null or the current reference sequence
+   */
+  SequenceI getSeqrep();
+
+  /**
+   * set the reference or representative sequence for this collection. Reference
+   * is assumed to be present within the collection.
+   * 
+   * @return
+   */
+  void setSeqrep(SequenceI refseq);
+
+  /**
    * @return the first column included in this collection. Runs from 0<=i<N_cols
    */
   int getStartRes();