/**
* Get the suffix array value at a given sequence.
*
* @param index Index at which to retrieve the suffix array vaule.
* @return The suffix array value at that entry.
*/
public long get(long index) {
int iterations = 0;
while (index % sequenceInterval != 0) {
// The inverseSA0 ('$') doesn't have a usable ASCII representation; it must be treated as a
// special case.
if (index == inverseSA0) index = 0;
else {
byte base = bwt.getBase(index);
index = bwt.counts(base) + bwt.occurrences(base, index);
}
iterations++;
}
return (sequence[(int) (index / sequenceInterval)] + iterations) % length();
}
/**
* Retrieves the length of the sequence array.
*
* @return Length of the suffix array.
*/
public long length() {
if (bwt != null) return bwt.length() + 1;
else return sequence.length;
}