JAL-2629 add multiple options for running hmmbuild on alignment/groups

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

diff --git a/src/jalview/datamodel/SequenceCollectionI.java b/src/jalview/datamodel/SequenceCollectionI.java
index f681f11..2dd0ad3 100644 (file)
--- a/src/jalview/datamodel/SequenceCollectionI.java
+++ b/src/jalview/datamodel/SequenceCollectionI.java
@@ -70,4 +70,13 @@ public interface SequenceCollectionI
    * @return
    */
   boolean isNucleotide();
+
+  /**
+   * Returns all HMM consensus sequences.
+   * 
+   * @param remove
+   *          If true, remove all HMM consensus sequences from the alignment.
+   * @return
+   */
+  List<SequenceI> getHMMConsensusSequences(boolean remove);
 }