/usr/include/pbseq/pbdata/reads/RegionAnnotation.hpp is in libpbdata-dev 0~20161219-2.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 | // Author: Mark Chaisson
#ifndef _BLASR_REGION_ANNOTATION_HPP_
#define _BLASR_REGION_ANNOTATION_HPP_
#include <cassert>
#include <cstring>
#include <string>
#include <iostream>
#include <vector>
#include <map>
#include <ostream>
#include "../Types.h"
#include "../Enumerations.h"
#include "../PacBioDefs.h"
#include "RegionTypeMap.hpp"
class HDFRegionTableReader;
class HDFRegionTableWriter;
class HDFRegionsWriter;
class RegionAnnotation {
friend class HDFRegionTableReader;
friend class HDFRegionTableWriter;
friend class HDFRegionsWriter;
public:
static const int HOLENUMBERCOL = 0;
static const int REGIONTYPEINDEXCOL = 1;
static const int REGIONSTARTCOL = 2;
static const int REGIONENDCOL = 3;
static const int REGIONSCORECOL = 4;
static const int NCOLS=5;
// Notice the discrepencies between Region and other hdf datasets!!
// Region annotation is defined as int32_t * 5, while
// holeNumber is defined as type UInt in other datasets (e.g., majorly ZMW),
// start and end are defined as type DNALength in other datasets.
int row[NCOLS];
public:
// FIXME: use regionType as a member varaible instead of regionTypeIndex
inline RegionAnnotation(UInt holeNumber = 0,
int typeIndex = 0,
int start = 0, int end = 0,
int score = -1);
inline bool operator<(const RegionAnnotation &rhs) const;
inline bool operator<(int holeNumber) const;
inline RegionAnnotation& operator=(const RegionAnnotation &rhs);
inline bool operator==(const RegionAnnotation &rhs) const;
inline int GetHoleNumber(void) const;
inline RegionAnnotation & SetHoleNumber(int holeNumber);
inline int GetTypeIndex(void) const;
inline std::string GetTypeString(const std::vector<RegionType> & types) const;
inline RegionAnnotation & SetTypeIndex(int typeIndex);
inline int GetStart(void) const;
inline RegionAnnotation & SetStart(int start);
inline int GetEnd(void) const;
inline RegionAnnotation & SetEnd(int end);
inline int GetScore(void) const;
inline RegionAnnotation & SetScore(int score);
public:
friend std::ostream & operator << (std::ostream & os, const RegionAnnotation& ra);
};
inline
bool compare_region_annotation_by_type(const RegionAnnotation & lhs,
const RegionAnnotation & rhs);
inline
RegionAnnotation::RegionAnnotation(UInt holeNumber,
int typeIndex, int start, int end, int score) {
SetHoleNumber(static_cast<int>(holeNumber));
SetTypeIndex(typeIndex);
SetStart(start);
SetEnd(end);
SetScore(score);
}
inline
bool RegionAnnotation::operator<(const RegionAnnotation &rhs) const
{
if (GetHoleNumber() == rhs.GetHoleNumber())
if (GetStart() == rhs.GetStart()) {
if (GetEnd() == rhs.GetEnd())
return GetScore() < rhs.GetScore();
else
return GetEnd() > rhs.GetEnd();
} else {
return GetStart() < rhs.GetStart();
}
else
return GetHoleNumber() < rhs.GetHoleNumber();
}
inline
bool RegionAnnotation::operator<(int holeNumber) const
{ return GetHoleNumber() < holeNumber; }
inline
RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation &rhs) {
memcpy(row, rhs.row, sizeof(int)*NCOLS);
return *this;
}
inline
bool RegionAnnotation::operator==(const RegionAnnotation &rhs) const {
return (GetHoleNumber() == rhs.GetHoleNumber() and
GetTypeIndex() == rhs.GetTypeIndex() and
GetStart() == rhs.GetStart() and
GetEnd() == rhs.GetEnd() and
GetScore() == rhs.GetScore());
}
inline
int RegionAnnotation::GetHoleNumber(void) const {
return row[HOLENUMBERCOL];
}
inline
RegionAnnotation & RegionAnnotation::SetHoleNumber(int holeNumber) {
row[HOLENUMBERCOL] = holeNumber;
return *this;
}
inline
int RegionAnnotation::GetTypeIndex(void) const {
return row[REGIONTYPEINDEXCOL];
}
inline std::string RegionAnnotation::GetTypeString(const std::vector<RegionType> & typesTable) const {
assert(GetTypeIndex() >= 0 and GetTypeIndex() < static_cast<int>(typesTable.size()));
return RegionTypeMap::ToString(typesTable[GetTypeIndex()]);
}
inline
RegionAnnotation & RegionAnnotation::SetTypeIndex(int regionTypeIndex) {
row[REGIONTYPEINDEXCOL] = regionTypeIndex;
return *this;
}
inline
int RegionAnnotation::GetStart(void) const {
return row[REGIONSTARTCOL];
}
inline
RegionAnnotation & RegionAnnotation::SetStart(int start) {
row[REGIONSTARTCOL] = start;
return *this;
}
inline
int RegionAnnotation::GetEnd(void) const {
return row[REGIONENDCOL];
}
inline
RegionAnnotation & RegionAnnotation::SetEnd(int end) {
row[REGIONENDCOL] = end;
return *this;
}
inline
int RegionAnnotation::GetScore(void) const {
return row[REGIONSCORECOL];
}
inline
RegionAnnotation & RegionAnnotation::SetScore(int score) {
row[REGIONSCORECOL] = score;
return *this;
}
inline
bool compare_region_annotation_by_type(const RegionAnnotation & lhs,
const RegionAnnotation & rhs)
{
if (lhs.GetHoleNumber() == rhs.GetHoleNumber()) {
if (lhs.GetTypeIndex() == rhs.GetTypeIndex()) {
if (lhs.GetStart() == rhs.GetStart()) {
if (lhs.GetEnd() == rhs.GetEnd())
return lhs.GetScore() < rhs.GetScore();
else return lhs.GetEnd() > rhs.GetEnd();
} else return lhs.GetStart() < rhs.GetStart();
} else return lhs.GetTypeIndex() < rhs.GetTypeIndex();
} else {
return lhs.GetHoleNumber() < rhs.GetHoleNumber();
}
}
#endif // _BLASR_REGION_ANNOTATION_HPP_
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