Merge branch 'feature_29/JAL-1372_referenceseq' into develop

[jalview.git] / src / jalview / datamodel / SequenceCollectionI.java

diff --git a/src/jalview/datamodel/SequenceCollectionI.java b/src/jalview/datamodel/SequenceCollectionI.java
index 3af441b..ee216a4 100644 (file)
--- a/src/jalview/datamodel/SequenceCollectionI.java
+++ b/src/jalview/datamodel/SequenceCollectionI.java
@@ -29,8 +29,23 @@ public interface SequenceCollectionI
 
   List<SequenceI> getSequences(
           Map<SequenceI, SequenceCollectionI> hiddenReps);
-
   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