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 f129a4c..34457fc 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -595,11 +595,13 @@ public interface AlignmentI extends AnnotatedCollectionI
   AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
 
   /**
-   * Set the hidden columns collection on the alignment
+   * Set the hidden columns collection on the alignment. Answers true if the
+   * hidden column selection changed, else false.
    * 
    * @param cols
+   * @return
    */
-  public void setHiddenColumns(HiddenColumns cols);
+  public boolean setHiddenColumns(HiddenColumns cols);
 
   /**
    * Set the first sequence as representative and hide its insertions. Typically
@@ -622,4 +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();
+
 }