X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequenceCollectionI.java;h=aa15d1f5fc231fc9b1b9b29ce2e059c3cdaf89fb;hb=c68eb67e2c38d87373b039e0b4d54f7eee7024ea;hp=4203b16a279a42f31844c9dcd69b14613aef986a;hpb=6dda78dd65a8f6f25356d9fe95078afbba4eadcd;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceCollectionI.java b/src/jalview/datamodel/SequenceCollectionI.java
index 4203b16..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);
 
@@ -72,9 +85,10 @@ public interface SequenceCollectionI
   boolean isNucleotide();
 
   /**
-   * Returns all HMM consensus sequences (possibly an empty list)
+   * Returns the (possibly empty) list of HMM consensus sequences in the
+   * collection
    * 
    * @return
    */
-  List<SequenceI> getHMMConsensusSequences();
+  List<SequenceI> getHmmSequences();
 }