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#ifndef TUPLE_H_
#define TUPLE_H_
#include <utility>
#include <vector>
#include <pbdata/Types.h>
#include <alignment/tuples/TupleMetrics.hpp>
template <typename Sequence, typename Tuple>
BuildTupleList(Sequence seq, std::vector<Tuple> &tupleList)
{
BuildTupleList(seq, 0, seq.length, tupleList);
}
template <typename Sequence, typename Tuple>
BuildTupleList(Sequence seq, int seqStart, int length, std::vector<Tuple> &tupleList)
{
}
template <typename Sequence, typename CountedTuple>
BuildCountedTupleList(Sequence seq, int seqStart, int length, TupleMetrics &tm,
std::vector<CountedTuple> &tupleList)
{
int s;
CountedTuple tuple;
for (s = 0; s < seq.length - tm.tupleSize + 1; s++) {
}
}
template <typename Sequence, typename Tuple>
StoreUniqueTuplePosList(Sequence seq, TupleMetrics &tm, std::vector<int> &uniqueTuplePosList)
{
//
// Do this faster later on with a suffix tree -- faster than n log n construction time.
//
int s;
std::vector<pair<Tuple, int> > tuples;
Tuple tempTuple;
for (s = 0; s < seq.length; s++) {
tempTuple.FromStringLR(&(seq.seq[s]), tm);
tuples.push_back(make_pair(tempTuple, s));
}
std::sort(tuples.begin(), tuples.end());
int curUnique = 0, curPos = 0;
//
// Filter out the repetitive tuples.
//
while (curPos < tuples.size()) {
int nextPos = curPos;
while (nextPos < tuples.size() and tuples[nextPos] == tuples[curPos])
nextPos++;
if (nextPos - curPos == 1) {
tuples[curUnique].first == tuples[curPos].first;
uniqueTuplePosList.push_back(tuples[curUnique].second);
++curUnique;
++curPos;
} else {
curPos = nextPos;
}
}
//
// Be nice and leave the pos list in ascending sorted order,
// even though the top of this function does not specify it.
//
std::sort(uniqueTuplePosList.begin(), uniqueTuplePosList.end());
}
#endif
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