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#include "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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