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

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index dc0fe88..755abbb 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1916,50 +1916,6 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   @Override
-  public void updateHMMMapping()
-  {
-    if (hmm == null)
-    {
-      return;
-    }
-    hmm.updateMapping(sequence);
-  }
-
-  /**
-   * Maps the HMM sequence to the reference annotation.
-   * 
-   * @param rf
-   */
-  @Override
-  public void mapToReference(AlignmentAnnotation rf)
-  {
-    if (this.isHMMConsensusSequence)
-    {
-      int node = 1;
-      hmm.clearNodeLookup();
-      for (int i = 0; i < getLength(); i++)
-      {
-        if (rf.annotations[i].displayCharacter.equalsIgnoreCase("x"))
-        {
-          if (i < hmm.getNodeAlignmentColumn(node))
-          {
-            this.deleteChars(i, hmm.getNodeAlignmentColumn(node));
-            updateHMMMapping();
-          }
-          else if (i > hmm.getNodeAlignmentColumn(node))
-          {
-            int length = i - hmm.getNodeAlignmentColumn(node);
-            this.insertCharAt(hmm.getNodeAlignmentColumn(node), length,
-                    '-');
-            updateHMMMapping();
-          }
-          node++;
-        }
-      }
-    }
-  }
-
-  @Override
   public boolean isHMMConsensusSequence()
   {
     return isHMMConsensusSequence;