JAL-2629 add StringParameter

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 88c165f..f4ee3a2 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -580,25 +580,7 @@ public interface AlignmentI extends AnnotatedCollectionI
    */
   AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
 
-  /**
-   * Calculate the visible start and end index of an alignment. The result is
-   * returned an int array where: int[0] = startIndex, and int[1] = endIndex.
-   * 
-   * @param hiddenCols
-   * @return
-   */
-  public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
-
   public void setHiddenColumns(HiddenColumns cols);
-  
-  /**
-   * Returns all HMM consensus sequences.
-   * 
-   * @param remove
-   *          If true, remove all HMM consensus sequences from the alignment.
-   * @return
-   */
-  public List<SequenceI> getHMMConsensusSequences(boolean remove);
 
   /**
    * Insert a sequence at a position in an alignment