private int[][][] getFullHashes(Sequence seq, int subKmerSize) {
int cutoff =
(int)
((long) Integer.MIN_VALUE
+ ((long) Integer.MAX_VALUE - (long) Integer.MIN_VALUE) / (long) REDUCTION);
// compute just direct hash of sequence
int[] hashes = Utils.computeSequenceHashes(seq.getString(), subKmerSize);
int count = 0;
for (int val : hashes) if (val <= cutoff) count++;
SortableIntPair[] completeHashAsPair = new SortableIntPair[count];
count = 0;
for (int iter = 0; iter < hashes.length; iter++)
if (hashes[iter] <= cutoff) {
completeHashAsPair[count] = new SortableIntPair(hashes[iter], iter);
count++;
}
// sort the results, sort is in place so no need to look at second
Arrays.sort(completeHashAsPair);
return storeAsArray(completeHashAsPair);
}
public OrderKmerHashes(Sequence seq, int kmerSize) {
this.seqLength = seq.length() - kmerSize + 1;
this.orderedHashes = getFullHashes(seq, kmerSize);
}