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
|
#ifndef _BLASR_DNA_TUPLE_HPP_
#define _BLASR_DNA_TUPLE_HPP_
#include <cassert>
#include <cstdint>
#include <ostream>
#include <string>
#include <vector>
#include <alignment/tuples/TupleOperations.h>
#include <pbdata/Types.h>
#include <alignment/tuples/BaseTuple.hpp>
#include <alignment/tuples/TupleList.hpp>
#include <alignment/tuples/TupleMetrics.hpp>
#include <pbdata/DNASequence.hpp>
#include <pbdata/NucConversion.hpp>
#include <pbdata/SeqUtils.hpp>
class DNATuple : public BaseTuple
{
public:
DNALength pos;
DNATuple();
DNATuple(const DNATuple &rhs);
inline int FromStringLR(Nucleotide *strPtr, TupleMetrics &tm);
int FromStringRL(Nucleotide *strPtr, TupleMetrics &tm);
inline int ShiftAddRL(Nucleotide nuc, TupleMetrics &tm);
int MakeRC(DNATuple &dest, TupleMetrics &tm);
std::string ToString(TupleMetrics &tm);
};
class CompareByTuple
{
public:
bool operator()(const DNATuple &lhs, const DNATuple &rhs) const;
};
class CountedDNATuple : public DNATuple
{
public:
int count;
CountedDNATuple(const CountedDNATuple &rhs);
};
class PositionDNATuple : public DNATuple
{
public:
PositionDNATuple();
PositionDNATuple(const PositionDNATuple &tupleP, const DNALength posP);
PositionDNATuple(const PositionDNATuple &rhs);
PositionDNATuple &operator=(const PositionDNATuple &rhs)
{
pos = rhs.pos;
tuple = rhs.tuple;
return *this;
}
int operator<(const PositionDNATuple &pTuple) const
{
if (tuple < pTuple.tuple)
return 1;
else if (tuple == pTuple.tuple)
return pos < pTuple.pos;
else
return 0;
}
int operator==(const PositionDNATuple &pTuple) const
{
return tuple == pTuple.tuple and pos == pTuple.pos;
}
int operator<(const DNATuple &pTuple) const { return (tuple < pTuple.tuple); }
int operator==(const DNATuple &pTuple) const;
int operator!=(const DNATuple &pTuple) const { return tuple != pTuple.tuple; }
};
class OrderPositionDNATuplesByPosition
{
public:
int operator()(const PositionDNATuple &lhs, const PositionDNATuple &rhs) const;
};
class OrderPositionDNATuplesByTuple
{
public:
int operator()(const PositionDNATuple &lhs, const PositionDNATuple &rhs) const;
};
template <typename Sequence>
int SearchSequenceForTuple(Sequence &seq, TupleMetrics &tm, DNATuple &queryTuple);
template <typename Sequence>
int SequenceToTupleList(Sequence &seq, TupleMetrics &tm, TupleList<DNATuple> &tupleList);
template <typename Sequence>
int SequenceToTupleList(Sequence &seq, TupleMetrics &tm, TupleList<PositionDNATuple> &tupleList);
#include "DNATupleImpl.hpp"
#endif // _BLASR_DNA_TUPLE_HPP_
|
