/usr/include/pbdata/reads/RegionAnnotation.hpp is in libpbdata-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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 | // Copyright (c) 2014-2015, Pacific Biosciences of California, Inc. //
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted (subject to the limitations in the
// disclaimer below) provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
//
// * Neither the name of Pacific Biosciences nor the names of its
// contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
// SUCH DAMAGE.
// 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;
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_
|