/**
* @param gas_seq The sequence which we wish to map it against other sequence(s)
* @param gas_targetSeqs The target sequence
*/
private HashMap<Integer, Integer> doMapSeq2Seq(
GappedAlignmentString gas_seq, GappedAlignmentString[] gas_targetSeqs) {
int N = gas_seq.gappedLength();
// making map allocation more efficient
int initCapacity = (int) Math.ceil(1.5 * N);
HashMap<Integer, Integer> map = new HashMap<Integer, Integer>(initCapacity);
// When a gap position corresponds to a gap remove it from seq
HashMap<Integer, Integer> gapped2UngappedMap_seq = gas_seq.getGapped2UngappedMap();
Integer[] gapPositions_seq = gas_seq.determineGapPositions();
for (Integer e : gapPositions_seq) gapped2UngappedMap_seq.remove(e);
// When a gap position corresponds to a gap, put -1 as its value
HashMap<Integer, Integer> gapped2UngappedMap_targetSeq =
gas_targetSeqs[0].getGapped2UngappedMap();
Integer[] gapPositions_targetSeq = gas_targetSeqs[0].determineGapPositions();
for (Integer e : gapPositions_targetSeq) gapped2UngappedMap_targetSeq.put(e, -1);
Integer[] gappedPositionsNoGaps_seq =
gapped2UngappedMap_seq.keySet().toArray(new Integer[gapped2UngappedMap_seq.size()]);
for (Integer gappedPosNoGaps : gappedPositionsNoGaps_seq) {
Integer ungappedPos = gapped2UngappedMap_targetSeq.get(gappedPosNoGaps);
if (ungappedPos.equals(null)) {
ungappedPos = -1;
}
map.put(gapped2UngappedMap_seq.get(gappedPosNoGaps), ungappedPos);
}
return map;
} // end of doMapSeq2Seq method
