- * Attach the annotation to seqRef, starting from startRes position.
+ * Attach the annotation to seqRef, starting from startRes position. If alreadyMapped is true then the indices of the annotation[] array are sequence positions rather than alignment column positions.
* @param seqRef
* @param startRes
* @param seqRef
* @param startRes
+ * @param alreadyMapped
*/
*/
- public void createSequenceMapping(SequenceI seqRef, int startRes)
+ public void createSequenceMapping(SequenceI seqRef,