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
|
#ifndef _BLASR_WEIGHTED_INTERVAL_HPP_
#define _BLASR_WEIGHTED_INTERVAL_HPP_
#include <set>
#include <vector>
#include <alignment/datastructures/anchoring/MatchPos.hpp>
#include <pbdata/DNASequence.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, const WeightedInterval &wi)
{
out << "[WeightedInterval size=" << wi.size << " start=" << wi.start << " end=" << wi.end
<< " qstart=" << wi.qStart << " qend=" << wi.qEnd << " strand=" << wi.readIndex
<< " pval=" << 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, const WeightedIntervalSet &wis)
{
WeightedIntervalSet::iterator it;
for (it = wis.begin(); it != wis.end(); it++) {
out << *((WeightedInterval *)&(*it)) << std::endl;
}
return out;
}
};
#endif
|
