/usr/include/blasr/tuples/DNATuple.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 | #ifndef _BLASR_DNA_TUPLE_HPP_
#define _BLASR_DNA_TUPLE_HPP_
#include <cassert>
#include <vector>
#include <stdint.h>
#include <ostream>
#include <string>
#include "Types.h"
#include "SeqUtils.hpp"
#include "DNASequence.hpp"
#include "NucConversion.hpp"
#include "tuples/BaseTuple.hpp"
#include "tuples/TupleMetrics.hpp"
#include "tuples/TupleList.hpp"
#include "tuples/TupleOperations.h"
class DNATuple : public BaseTuple {
public:
DNALength pos;
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;
};
class PositionDNATuple : public DNATuple {
public:
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;
}
PositionDNATuple();
PositionDNATuple(PositionDNATuple &tupleP, DNALength posP);
};
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_
|