JAL-2629 removed SequenceI.get/setLastPosition and related code

[jalview.git] / src / jalview / hmmer / HmmerCommand.java

diff --git a/src/jalview/hmmer/HmmerCommand.java b/src/jalview/hmmer/HmmerCommand.java
index 0f45184..a9d7018 100644 (file)
--- a/src/jalview/hmmer/HmmerCommand.java
+++ b/src/jalview/hmmer/HmmerCommand.java
@@ -182,30 +182,6 @@ public class HmmerCommand
   }
 
   /**
-   * Adds any HMM sequences removed before submitting the alignment as a job
-   * back into the alignment.
-   * 
-   * @param af
-   */
-  public void addHMMConsensusSequences(AlignFrame af)
-  {
-    AlignmentI al = af.getViewport().getAlignment();
-    if (hmmSeqs == null || hmmSeqs.size() < 1)
-    {
-      return;
-    }
-    for (SequenceI seq : hmmSeqs)
-    {
-      Integer position = seq.getPreviousPosition();
-      al.getSequences().add(position, seq);
-    }
-    af.getViewport().setAlignment(al);
-    af.alignPanel.adjustAnnotationHeight();
-    af.getViewport().updateSequenceIdColours();
-    af.buildSortByAnnotationScoresMenu();
-  }
-
-  /**
    * Returns the list of HMM sequences removed
    * 
    * @return