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#ifndef TUPLES_DNA_TUPLE_LIST_H_
#define TUPLES_DNA_TUPLE_LIST_H_
#include <vector>
#include <alignment/tuples/DNATuple.h>
template <typename Sequence>
DNALength StoreTuplePosList(Sequence seq, TupleMetrics &tm,
std::vector<PositionDNATuple> &tupleList)
{
//
// Do this faster later on with a suffix tree -- faster than n log n construction time.
//
DNALength s;
PositionDNATuple tempTuple;
for (s = 0; s < seq.length - tm.tupleSize + 1; s++) {
if (tempTuple.FromStringLR(&(seq.seq[s]), tm)) {
tempTuple.pos = s;
tupleList.push_back(tempTuple);
}
}
std::sort(tupleList.begin(), tupleList.end());
//
// Be nice and leave the pos list in ascending sorted order,
// even though the top of this function does not specify it.
//
return tupleList.size();
}
void WriteTuplePosList(std::vector<PositionDNATuple> &tupleList, int tupleSize, std::ofstream &out)
{
DNALength tupleListLength = tupleList.size();
out.write((char *)&tupleSize, sizeof(tupleSize));
out.write((char *)&tupleListLength, sizeof(DNALength));
out.write((char *)&tupleList[0], sizeof(PositionDNATuple) * tupleList.size());
}
void ReadTuplePosList(std::ifstream &in, std::vector<PositionDNATuple> &tupleList, int &tupleSize)
{
DNALength tupleListLength;
in.read((char *)&tupleSize, sizeof(int));
in.read((char *)&tupleListLength, sizeof(DNALength));
tupleList.resize(tupleListLength);
in.read((char *)&tupleList[0], sizeof(PositionDNATuple) * tupleListLength);
}
#endif
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