JAL-2046 explicit contract for get/set SequenceFeatures on SequenceI

[jalview.git] / src / jalview / datamodel / SequenceI.java

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 0e649c0..60040d8 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,6 +20,8 @@
  */
 package jalview.datamodel;
 
+import jalview.api.DBRefEntryI;
+
 import java.util.List;
 import java.util.Vector;
 
@@ -248,17 +250,20 @@ public interface SequenceI extends ASequenceI
   public void insertCharAt(int position, int count, char ch);
 
   /**
-   * DOCUMENT ME!
+   * Gets array holding sequence features associated with this sequence. The
+   * array may be held by the sequence's dataset sequence if that is defined.
    * 
-   * @return DOCUMENT ME!
+   * @return hard reference to array
    */
   public SequenceFeature[] getSequenceFeatures();
 
   /**
-   * DOCUMENT ME!
+   * Replaces the array of sequence features associated with this sequence with
+   * a new array reference. If this sequence has a dataset sequence, then this
+   * method will update the dataset sequence's feature array
    * 
-   * @param v
-   *          DOCUMENT ME!
+   * @param features
+   *          New array of sequence features
    */
   public void setSequenceFeatures(SequenceFeature[] features);
 
@@ -296,9 +301,9 @@ public interface SequenceI extends ASequenceI
 
   public void setVamsasId(String id);
 
-  public void setDBRef(DBRefEntry[] dbs);
+  public void setDBRefs(DBRefEntry[] dbs);
 
-  public DBRefEntry[] getDBRef();
+  public DBRefEntry[] getDBRefs();
 
   /**
    * add the given entry to the list of DBRefs for this sequence, or replace a
@@ -429,4 +434,8 @@ public interface SequenceI extends ASequenceI
    * @return
    */
   public PDBEntry getPDBEntry(String pdbId);
+
+  public void setSourceDBRef(DBRefEntryI dbRef);
+
+  public DBRefEntryI getSourceDBRef();
 }