JAL-2941 'map hmm to RF' removed pending clarifications

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 9045735..5b3d782 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -499,14 +499,6 @@ public interface SequenceI extends ASequenceI
    */
   public List<DBRefEntry> getPrimaryDBRefs();
 
-  /**
-   * Updates mapping of Hidden Markov Model nodes to aligned sequence positions
-   * (e.g. after an alignment edit). The nodes of the HMM (excluding the first
-   * node, with model average values), are associated in turn with non-gapped
-   * sequence positions.
-   */
-  public void updateHMMMapping();
-
   boolean isHMMConsensusSequence();
 
   void setIsHMMConsensusSequence(boolean isHMMConsensusSequence);
@@ -547,8 +539,6 @@ public interface SequenceI extends ASequenceI
    */
   BitSet getInsertionsAsBits();
 
-  void mapToReference(AlignmentAnnotation rf);
-
   /**
    * Replaces every occurrence of c1 in the sequence with c2 and returns the
    * number of characters changed