Merge branch 'develop' into features/hmmer

[jalview.git] / src / jalview / datamodel / SequenceI.java

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 12ddf60..20362dd 100755 (executable)
--- 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()