X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=20362dd6b175235c5834f4828c4df3b35c7f98f4;hb=bd4ab013e64863bbbffa93c58953051e11cfb236;hp=12ddf60bac63a24036d813151fbf69d1d20fb2cc;hpb=6568287d7ca9ab336a83e27b9bfbd548a10cf748;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 12ddf60..20362dd 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -42,6 +42,10 @@ public interface SequenceI extends ASequenceI
    */
   public void setName(String name);
 
+  public HiddenMarkovModel getHMM();
+
+  public void setHMM(HiddenMarkovModel hmm);
+
   /**
    * Get the display name
    */
@@ -478,6 +482,20 @@ public interface SequenceI extends ASequenceI
    */
   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()