X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequenceCollectionI.java;h=aa15d1f5fc231fc9b1b9b29ce2e059c3cdaf89fb;hb=d34b7142d47cab72ca9e0822b4407f3f497f191a;hp=84f5c5d474b51204aed97c1a5fbfc5239d27ec1b;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceCollectionI.java b/src/jalview/datamodel/SequenceCollectionI.java
index 84f5c5d..aa15d1f 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.
  * 
@@ -25,18 +25,51 @@ 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 the first column included in this collection. Runs from 0<=i<N_cols
-  */
+  /**
+   * 
+   * @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();
-  
 
   /**
    * 
@@ -44,4 +77,18 @@ public interface SequenceCollectionI
    */
   int getEndRes();
 
+  /**
+   * Answers true if sequence data is nucleotide (according to some heuristic)
+   * 
+   * @return
+   */
+  boolean isNucleotide();
+
+  /**
+   * Returns the (possibly empty) list of HMM consensus sequences in the
+   * collection
+   * 
+   * @return
+   */
+  List<SequenceI> getHmmSequences();
 }