X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceCollectionI.java;h=e2bb5a64939182245a646779a1e3594f49fdf727;hb=HEAD;hp=7777dce8a7ba5939c05d0624f92af5750088c27b;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceCollectionI.java b/src/jalview/datamodel/SequenceCollectionI.java
index 7777dce..e2bb5a6 100644
--- a/src/jalview/datamodel/SequenceCollectionI.java
+++ b/src/jalview/datamodel/SequenceCollectionI.java
@@ -25,24 +25,43 @@ 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);
+
   int getWidth();
+
   /**
    * 
    * @return true if getSeqrep doesn't return null
    */
   boolean hasSeqrep();
+
   /**
    * get the reference or representative sequence within this collection
+   * 
    * @return null or the current reference sequence
    */
   SequenceI getSeqrep();
+
   /**
-   * set the reference or representative sequence for this collection. 
-   * Reference is assumed to be present within the collection.
+   * set the reference or representative sequence for this collection. Reference
+   * is assumed to be present within the collection.
+   * 
    * @return
    */
   void setSeqrep(SequenceI refseq);
@@ -58,4 +77,10 @@ public interface SequenceCollectionI
    */
   int getEndRes();
 
+  /**
+   * Answers true if sequence data is nucleotide (according to some heuristic)
+   * 
+   * @return
+   */
+  boolean isNucleotide();
 }