public int[] gapMap();
/**
+ * Returns an int array where indices correspond to each position in
+ * sequence char array and the element value gives the result of findPosition
+ * for that index in the sequence.
+ *
+ * @return int[SequenceI.getLength()]
+ */
+ public int[] findPositionMap();
+ /**
* Delete a range of aligned sequence columns, creating a new dataset sequence if necessary
* and adjusting start and end positions accordingly.
*