X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=69eb1d43e623c421548fc04907b1cbc4d855db46;hb=e8814cc25a95119c8201007f32035170db2ed299;hp=f1cba43be02b5f2ba384f014f612d996a88b4f67;hpb=23c12388658b08e4bbda2ebfdad286d881689366;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index f1cba43..69eb1d4 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -250,17 +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);
 
@@ -432,7 +435,21 @@ public interface SequenceI extends ASequenceI
    */
   public PDBEntry getPDBEntry(String pdbId);
 
+  /**
+   * Set the distinct source database, and accession number from which a
+   * sequence and its start-end data were derived from. This is very important
+   * for SIFTS mappings and must be set prior to performing SIFTS mapping.
+   * 
+   * @param dbRef
+   *          the source dbRef for the sequence
+   */
   public void setSourceDBRef(DBRefEntryI dbRef);
 
+  /**
+   * Get the distinct source database, and accession number from which a
+   * sequence and its start-end data were derived from.
+   * 
+   * @return
+   */
   public DBRefEntryI getSourceDBRef();
 }