public int[] gapMap();
/**
- * DOCUMENT ME!
+ * Delete a range of aligned sequence columns, creating a new dataset sequence if necessary
+ * and adjusting start and end positions accordingly.
*
- * @param i DOCUMENT ME!
- * @param j DOCUMENT ME!
+ * @param i first column in range to delete
+ * @param j last column in range to delete
*/
public void deleteChars(int i, int j);
public DBRefEntry[] getDBRef();
+ /**
+ * add the given entry to the list of DBRefs for this sequence,
+ * or replace a similar one if entry contains a map object
+ * and the existing one doesnt.
+ * @param entry
+ */
public void addDBRef(DBRefEntry entry);
public void addSequenceFeature(SequenceFeature sf);
* @param revealed
*/
public void setAlignmentAnnotation(AlignmentAnnotation[] annotation);
+ /**
+ * Get one or more alignment annotations with a particular label.
+ * @param label string which each returned annotation must have as a label.
+ * @return null or array of annotations.
+ */
+ public AlignmentAnnotation[] getAnnotation(String label);
}