/usr/include/blasr/datastructures/anchoring/WeightedInterval.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 | #ifndef _BLASR_WEIGHTED_INTERVAL_HPP_
#define _BLASR_WEIGHTED_INTERVAL_HPP_
#include <vector>
#include <set>
#include "DNASequence.hpp"
#include "datastructures/anchoring/MatchPos.hpp"
class WeightedInterval {
public:
DNALength size; // not necessarily end - start + 1
DNALength start;
DNALength end;
DNALength qStart, qEnd;
int readIndex;
float pValue;
std::vector<int> positions;
std::vector<ChainedMatchPos> matches;
float pValueVariance, pValueNStdDev;
float sizeVariance, sizeNStdDev;
int nAnchors;
int totalAnchorSize;
bool isOverlapping;
WeightedInterval();
WeightedInterval(int _size, int _start, int _end,
int _readIndex, float _pValue =0.0);
WeightedInterval(int _size, int _start, int _end,
int _readIndex, float _pValue, int _qStart, int _qEnd);
WeightedInterval(int _size, unsigned int _nAnchors,
unsigned int _totalAnchorSize, int _start, int _end,
int _readIndex, float _pValue, int _qStart, int _qEnd,
std::vector<ChainedMatchPos> &_matches);
void Init(int _size, int _start, int _end,
int _readIndex, float _pValue);
int GetStrandIndex() const;
void SetPValueVariance(float v);
void SetPValueNStdDev(float v);
void SetSizeVariance(float v);
void SetSizeNStdDev(float v);
int operator<(const WeightedInterval &intv) const;
int operator==(const WeightedInterval &intv) const;
friend std::ostream & operator << (std::ostream & out, WeightedInterval & wi) {
out << wi.size << " " << wi.start << " " << wi.end
<< " " << wi.qStart << " " << wi.qEnd << " " << wi.readIndex
<< " " << wi.pValue ;
return out;
}
float PValue() const;
int Size() const;
};
class CompareWeightedIntervalByPValue {
public:
int operator()(const WeightedInterval& a, const WeightedInterval& b) const;
};
typedef std::vector<WeightedInterval> WeightedIntervalVector;
typedef std::multiset<WeightedInterval, CompareWeightedIntervalByPValue>
T_WeightedIntervalMultiSet;
class WeightedIntervalSet: public T_WeightedIntervalMultiSet {
public:
int maxSize;
WeightedIntervalSet();
WeightedIntervalSet(int maxSizeP);
bool insert(WeightedInterval &intv);
friend std::ostream & operator << (std::ostream & out, WeightedIntervalSet & wis) {
WeightedIntervalSet::iterator it;
for (it = wis.begin(); it != wis.end(); it++) {
out << *((WeightedInterval*)&(*it)) << std::endl;
}
return out;
}
};
#endif
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