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 aca79c8..2dd0ad3 100644 (file)
--- a/src/jalview/datamodel/SequenceCollectionI.java
+++ b/src/jalview/datamodel/SequenceCollectionI.java
@@ -64,4 +64,19 @@ public interface SequenceCollectionI
    */
   int getEndRes();
 
+  /**
+   * Answers true if sequence data is nucleotide (according to some heuristic)
+   * 
+   * @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);
 }