/usr/include/blasr/datastructures/anchoring/MatchPos.hpp is in libblasr-dev 0~20151014+gitbe5d1bf-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 | #ifndef _BLASR_MATCH_POS_HPP_
#define _BLASR_MATCH_POS_HPP_
#include <vector>
#include <algorithm>
#include <ostream>
#include "Types.h"
#include "DNASequence.hpp"
class MatchPos {
public:
DNALength t, q;
MatchWeight w;
DNALength l;
int m; // multiplicity
inline MatchPos(DNALength pt, DNALength pq, DNALength pl, int pm = 0);
MatchPos (const MatchPos &rhs);
inline MatchWeight Size();
inline MatchPos();
inline MatchPos& operator=(const MatchPos &rhs);
inline DNALength GetLength() const;
int GetMultiplicity() const;
MatchWeight GetWeight() const;
inline DNALength GetX() const;
inline DNALength GetY() const;
UInt GetT();
UInt GetQ();
UInt GetW();
friend std::ostream& operator<<(std::ostream & out, MatchPos &p);
};
inline MatchPos::MatchPos(DNALength pt, DNALength pq, DNALength pl, int pm) :
t(pt), q(pq), l(pl), m(pm), w(0){ }
inline MatchPos::MatchPos() {
t = q = -1;
l = 0;
w = 0;
m = 0;
}
inline MatchWeight MatchPos::Size() {
return l;
}
inline MatchPos& MatchPos::operator=(const MatchPos &rhs) {
t = rhs.t; q = rhs.q; w = rhs.w;
l = rhs.l;
m = rhs.m;
return *this;
}
inline DNALength MatchPos::GetLength() const {
return l;
}
inline DNALength MatchPos::GetX() const {
return q;
}
inline DNALength MatchPos::GetY() const {
return t;
}
class ChainedMatchPos : public MatchPos {
private:
int score;
ChainedMatchPos *chainPrev;
public:
ChainedMatchPos(DNALength pt, DNALength pq, DNALength pl, int pm);
ChainedMatchPos();
inline ChainedMatchPos(const ChainedMatchPos &rhs);
inline int GetScore();
int SetScore(int _score);
ChainedMatchPos* SetChainPrev(ChainedMatchPos *_chainPrev);
inline ChainedMatchPos* GetChainPrev();
inline ChainedMatchPos &operator=(const ChainedMatchPos &rhs);
friend std::ostream& operator<<(std::ostream & out, ChainedMatchPos &p);
};
inline ChainedMatchPos::ChainedMatchPos(const ChainedMatchPos &rhs) {
(*this) = rhs;
}
inline ChainedMatchPos* ChainedMatchPos::GetChainPrev() {
return chainPrev;
}
inline int ChainedMatchPos::GetScore() {
return score;
}
inline ChainedMatchPos &ChainedMatchPos::operator=(const ChainedMatchPos &rhs) {
((MatchPos&)(*this)) = ((MatchPos&)rhs);
return *this;
}
template<typename T_MatchPos>
class CompareMatchPos {
public:
int operator()(const T_MatchPos &lhs, const T_MatchPos &rhs) const {
if (lhs.t < rhs.t)
return 1;
else if (lhs.t > rhs.t)
return 0;
else {
return lhs.q < rhs.q;
}
}
};
typedef std::vector<MatchPos> MatchPosList;
template<typename T_MatchPos>
class CompareMatchPosByWeight {
public:
int operator()(const T_MatchPos &a, const T_MatchPos &b) const {
return a.l < b.l;
}
};
template<typename T_MatchPos>
class CompareMatchPosIndexByWeight {
public:
std::vector<T_MatchPos> *list;
int operator()(const int i, const int j) const {
return ((*list)[i].w > (*list)[j].w);
}
};
template<typename T_MatchPos>
class CompareMatchPosIndexByTextPos {
public:
std::vector<T_MatchPos> *list;
int operator()(const int i, const int j) const {
return (*list)[i].t < (*list)[j].t;
}
};
template<typename T_MatchPos>
void SortMatchPosList(std::vector<T_MatchPos> &mpl) {
std::sort(mpl.begin(), mpl.end(), CompareMatchPos<T_MatchPos>());
}
template<typename T_MatchPos>
void SortMatchPosListByWeight(std::vector<T_MatchPos> &mpl) {
std::sort(mpl.begin(), mpl.end(), CompareMatchPosByWeight<T_MatchPos>());
}
template<typename T_MatchPos>
void SortMatchPosIndexListByWeight(std::vector<T_MatchPos> &mpl, std::vector<int> &indices) {
CompareMatchPosIndexByWeight<T_MatchPos> cmp;
cmp.list = &mpl;
std::sort(indices.begin(), indices.end(), cmp);
}
template<typename T_MatchPos>
void SortMatchPosIndexListByTextPos(std::vector<T_MatchPos> &mpl, std::vector<int> &indices) {
CompareMatchPosIndexByTextPos<T_MatchPos> cmp;
cmp.list = &mpl;
std::sort(indices.begin(), indices.end(), cmp);
}
#endif // _BLASR_MATCH_POS_HPP_
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