X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceCollectionI.java;h=aa15d1f5fc231fc9b1b9b29ce2e059c3cdaf89fb;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=2dd0ad33fdb125c93ed3dfa38f5c0b14312c4aa9;hpb=6076783c7a50cc6d318b2478b10800aedb9288c4;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceCollectionI.java b/src/jalview/datamodel/SequenceCollectionI.java
index 2dd0ad3..aa15d1f 100644
--- a/src/jalview/datamodel/SequenceCollectionI.java
+++ b/src/jalview/datamodel/SequenceCollectionI.java
@@ -25,8 +25,21 @@ import java.util.Map;
 
 public interface SequenceCollectionI
 {
+  /**
+   * 
+   * @return (visible) sequences in this collection. This may be a direct
+   *         reference to the collection so not thread safe
+   */
   List<SequenceI> getSequences();
 
+  /**
+   * FIXME: AlignmentI.getSequences(hiddenReps) doesn't actually obey this
+   * contract!
+   * 
+   * @param hiddenReps
+   * @return the full set of sequences in this collection, including any
+   *         sequences represented by sequences in the collection.
+   */
   List<SequenceI> getSequences(
           Map<SequenceI, SequenceCollectionI> hiddenReps);
 
@@ -72,11 +85,10 @@ public interface SequenceCollectionI
   boolean isNucleotide();
 
   /**
-   * Returns all HMM consensus sequences.
+   * Returns the (possibly empty) list of HMM consensus sequences in the
+   * collection
    * 
-   * @param remove
-   *          If true, remove all HMM consensus sequences from the alignment.
    * @return
    */
-  List<SequenceI> getHMMConsensusSequences(boolean remove);
+  List<SequenceI> getHmmSequences();
 }