JAL-2629 add basic parameter adjustment to hmmsearch/align

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 948fd1b..dd58b31 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -580,16 +580,26 @@ public interface AlignmentI extends AnnotatedCollectionI
    */
   AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
 
+  public void setHiddenColumns(HiddenColumns cols);
+  
   /**
-   * 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.
+   * Returns all HMM consensus sequences.
    * 
-   * @param hiddenCols
+   * @param remove
+   *          If true, remove all HMM consensus sequences from the alignment.
    * @return
    */
-  public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
+  public List<SequenceI> getHMMConsensusSequences(boolean remove);
 
-  public void setHiddenColumns(HiddenColumns cols);
+  /**
+   * Insert a sequence at a position in an alignment
+   * 
+   * @param i
+   *          The idnex of the position.
+   * @param snew
+   *          The new sequence.
+   */
+  void insertSequenceAt(int i, SequenceI snew);