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#ifndef _BLASR_WEIGHTED_INTERVAL_HPP_
#define _BLASR_WEIGHTED_INTERVAL_HPP_
#include <vector>
#include <set>
#include "../../../pbdata/DNASequence.hpp"
#include "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:
size_t maxSize;
WeightedIntervalSet();
WeightedIntervalSet(const size_t 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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