X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=20362dd6b175235c5834f4828c4df3b35c7f98f4;hb=bd4ab013e64863bbbffa93c58953051e11cfb236;hp=329882915eae3573f3fed3c49e04cf51af9dcd03;hpb=e5cba1e6a138feeeb8cf5b5823b3cafc89e71b9f;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 3298829..20362dd 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;
 
@@ -480,4 +481,25 @@ public interface SequenceI extends ASequenceI
    *         list
    */
   public List<DBRefEntry> getPrimaryDBRefs();
+
+  public void updateHMMMapping();
+
+  boolean isHMMConsensusSequence();
+
+  void setIsHMMConsensusSequence(boolean isHMMConsensusSequence);
+
+  boolean hasHMMAnnotation();
+
+  void setHasInfo(boolean status);
+
+  int getPreviousPosition();
+
+  void setPreviousPosition(int previousPosition);
+
+  /**
+   * 
+   * @return BitSet corresponding to index [0,length) where Comparison.isGap()
+   *         returns true.
+   */
+  BitSet getInsertionsAsBits();
 }