Merge branch 'develop' into features/hmmer

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 1b5207f..dd58b31 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -581,5 +581,26 @@ public interface AlignmentI extends AnnotatedCollectionI
   AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
 
   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
+   * 
+   * @param i
+   *          The idnex of the position.
+   * @param snew
+   *          The new sequence.
+   */
+  void insertSequenceAt(int i, SequenceI snew);
+
+  
 
 }