JAL-3081 new method to get alignment sequence order lookup

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 93a2456..34457fc 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -624,4 +624,12 @@ public interface AlignmentI extends AnnotatedCollectionI
   public HiddenColumns propagateInsertions(SequenceI profileseq,
           AlignmentView input);
 
+  /**
+   * Returns a map whose key is a sequence in the alignment, and value the
+   * position (0, 1, 2...) of the sequence
+   * 
+   * @return
+   */
+  Map<SequenceI, Integer> getSequencePositions();
+
 }