* Used to set a particular index of the alignment with the given sequence.
*
* @param i
- * Index of sequence to be updated.
+ * Index of sequence to be updated. if i>length, sequence will be
+ * added to end, with no intervening positions.
* @param seq
- * New sequence to be inserted.
+ * New sequence to be inserted. The existing sequence at position i
+ * will be replaced.
+ * @return existing sequence (or null if i>current length)
*/
- void setSequenceAt(int i, SequenceI seq);
+ SequenceI replaceSequenceAt(int i, SequenceI seq);
/**
* Deletes a sequence from the alignment