public int findIndex(int pos);
/**
- * DOCUMENT ME!
+ * Returns the sequence position for an alignment position
*
- * @param i DOCUMENT ME!
+ * @param i column index in alignment (from 1)
*
- * @return DOCUMENT ME!
+ * @return residue number for residue (left of and) nearest ith column
*/
public int findPosition(int i);
/**
- * DOCUMENT ME!
+ * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment
*
- * @return DOCUMENT ME!
+ * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object
*/
public int[] gapMap();