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#include <alignment/datastructures/anchoring/MatchPos.hpp>
MatchPos::MatchPos(const MatchPos &rhs) { (*this) = rhs; }
int MatchPos::GetMultiplicity() const { return m; }
MatchWeight MatchPos::GetWeight() const
{
if (m > 0) {
return (1.0 * l) / m;
} else {
return 0;
}
}
UInt MatchPos::GetT() { return t; }
UInt MatchPos::GetQ() { return (UInt)q; }
UInt MatchPos::GetW() { return w; }
std::ostream &operator<<(std::ostream &out, MatchPos &p)
{
out << p.q << "\t" << p.t << "\t" << p.l << "\t" << p.m;
return out;
}
ChainedMatchPos::ChainedMatchPos(DNALength pt, DNALength pq, DNALength pl, int pm)
: MatchPos(pt, pq, pl, pm)
{
score = 0;
chainPrev = NULL;
}
ChainedMatchPos::ChainedMatchPos() : MatchPos()
{
score = 0;
chainPrev = NULL;
}
int ChainedMatchPos::SetScore(int _score) { return (score = _score); }
ChainedMatchPos *ChainedMatchPos::SetChainPrev(ChainedMatchPos *_chainPrev)
{
return (chainPrev = _chainPrev);
}
std::ostream &operator<<(std::ostream &out, ChainedMatchPos &p)
{
out << p.q << "\t" << p.t << "\t" << p.l << "\t" << p.m;
return out;
}
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