* create a new sequence object from start to end of this sequence
*
* @param start
- * int
+ * int index for start position
* @param end
- * int
+ * int index for end position
+ *
* @return SequenceI
+ * @note implementations may use getSequence to get the sequence data
*/
public SequenceI getSubSequence(int start, int end);
* Returns the sequence position for an alignment position
*
* @param i
- * column index in alignment (from 1)
+ * column index in alignment (from 0..<length)
*
* @return residue number for residue (left of and) nearest ith column
*/
public AlignmentAnnotation[] getAnnotation();
+ public boolean hasAnnotation(AlignmentAnnotation ann);
+
public void addAlignmentAnnotation(AlignmentAnnotation annotation);
public void removeAlignmentAnnotation(AlignmentAnnotation annotation);