X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceCollectionI.java;h=e2bb5a64939182245a646779a1e3594f49fdf727;hb=5a352aa2f3330ae269d9b70c4a7374c2518bfb2e;hp=3af441b896972e9525a399befa842794ce120c57;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceCollectionI.java b/src/jalview/datamodel/SequenceCollectionI.java
index 3af441b..e2bb5a6 100644
--- a/src/jalview/datamodel/SequenceCollectionI.java
+++ b/src/jalview/datamodel/SequenceCollectionI.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -25,14 +25,48 @@ 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.
+   * 
+   * @return
+   */
+  void setSeqrep(SequenceI refseq);
+
+  /**
    * @return the first column included in this collection. Runs from 0<=i<N_cols
    */
   int getStartRes();
@@ -43,4 +77,10 @@ public interface SequenceCollectionI
    */
   int getEndRes();
 
+  /**
+   * Answers true if sequence data is nucleotide (according to some heuristic)
+   * 
+   * @return
+   */
+  boolean isNucleotide();
 }