X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=12ddf60bac63a24036d813151fbf69d1d20fb2cc;hb=60ee9fb76ea07566ece5c3455a1abedfff467354;hp=92f797ff7757f726e7681a3f3a18ce339fe52809;hpb=dfa35cc477b0d3af4a3cd25472cb6126626c67d3;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 92f797f..12ddf60 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,6 +20,7 @@
  */
 package jalview.datamodel;
 
+import java.util.BitSet;
 import java.util.List;
 import java.util.Vector;
 
@@ -189,12 +190,13 @@ public interface SequenceI extends ASequenceI
   public int findIndex(int pos);
 
   /**
-   * Returns the sequence position for an alignment position
+   * Returns the sequence position for an alignment position.
    * 
    * @param i
    *          column index in alignment (from 0..<length)
    * 
-   * @return residue number for residue (left of and) nearest ith column
+   * @return TODO: JAL-2562 - residue number for residue (left of and) nearest
+   *         ith column
    */
   public int findPosition(int i);
 
@@ -475,4 +477,11 @@ public interface SequenceI extends ASequenceI
    *         list
    */
   public List<DBRefEntry> getPrimaryDBRefs();
+
+  /**
+   * 
+   * @return BitSet corresponding to index [0,length) where Comparison.isGap()
+   *         returns true.
+   */
+  BitSet getInsertionsAsBits();
 }