X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=d9ffc81d8912c36ea81a33a5bee8fd4cf017a079;hb=30bc1314d4206cafea412dcd9decdea7e318481f;hp=da49a31622403ddda9723910469fec8175c599cd;hpb=45d4eb5f2d3772ac51e2512d49fb0a3a958f2260;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index da49a31..d9ffc81 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -174,6 +174,14 @@ public interface SequenceI
   public int[] gapMap();
 
   /**
+   * Returns an int array where indices correspond to each position in
+   * sequence char array and the element value gives the result of findPosition
+   * for that index in the sequence.
+   * 
+   * @return int[SequenceI.getLength()] 
+   */
+  public int[] findPositionMap();
+  /**
    * Delete a range of aligned sequence columns, creating a new dataset sequence if necessary
    * and adjusting start and end positions accordingly.
    *