/usr/include/pbseq/hdf/HDFAtom.hpp is in libpbihdf-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 | #ifndef _BLASR_HDF_ATOM_HPP_
#define _BLASR_HDF_ATOM_HPP_
#include <cassert>
#include <string>
#include <vector>
#include <cstdint>
#include <H5Cpp.h>
#include "HDFConfig.hpp"
#include "HDFGroup.hpp"
#include "HDFData.hpp"
template<typename T>
class HDFAtom : public HDFData {
public:
H5::Attribute attribute;
HDFAtom() {
isInitialized = false;
}
~HDFAtom() {
if (IsInitialized()) {
attribute.close();
}
}
H5::H5Location *GetObject() {
return NULL;
}
int Initialize(H5::H5Location &object, const std::string & attributeName) {
attribute = object.openAttribute(attributeName.c_str());
isInitialized = true;
return 1;
}
int Initialize(HDFGroup &group, const std::string & attributeName) {
return Initialize(group.group, attributeName);
}
int Initialize(HDFData &data, const std::string & attributeName) {
return Initialize(data.dataset, attributeName);
}
int Initialize(H5::Group &object, const std::string & attributeName) {
try {
attribute = object.openAttribute(attributeName.c_str());
}
catch (H5::Exception e) {
cout << "ERROR. Could not open attribute " << attributeName << endl;
exit(1);
}
isInitialized = true;
return 1;
}
int Initialize(H5::H5File &hdfFile, const std::string & groupName, const std::string & attributeName) {
HDFGroup group;
group.Initialize(hdfFile, groupName);
attribute = group.group.openAttribute(attributeName.c_str());
isInitialized = true;
return 1;
}
//
// This handles creation of all non-std::string types. A specialization
// for std::strings is provided below.
//
void Create(H5::H5Location &object, const std::string & atomName) {
hsize_t defaultDims[] = {1};
H5::DataSpace defaultDataSpace(1, defaultDims);
TypedCreate(object, atomName, defaultDataSpace);
}
void Create(H5::H5Location &object, const std::string & name, const std::string & value) {
H5::StrType strType(0, value.size());
attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0,NULL));
isInitialized = true;
attribute.write(strType, value.c_str());
}
void Create(H5::H5Location &object, const std::string & name, std::vector<int> &vect) {
hsize_t length = vect.size();
H5::ArrayType arrayDataType(H5::PredType::NATIVE_INT, 1, &length);
attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, H5::DataSpace(1, &length));
attribute.write(H5::PredType::NATIVE_INT, &((vect)[0]));
}
void Create(H5::H5Location &object, const std::string & name, const std::vector<std::string> &vect) {
hsize_t length = vect.size();
H5::StrType strType(0,H5T_VARIABLE);
H5::ArrayType arrayDataType(strType, 1, &length);
attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length));
attribute.write(strType, &((vect)[0]));
}
void TypedCreate(H5::H5Location &object, const std::string &atomName, H5::DataSpace &dataSpace) {
(void)(object);
(void)(atomName);
(void)(dataSpace);
assert("Calling HDFAtom<T>::typedCreate on an unsupported type" == 0);
}
void Write(T value) {
(void)(value);
assert("Calling HDFAtom<T>::Write on an unsupported type" == 0);
}
void Read(T& value) {
(void)(value);
assert("Calling read on an unsupported type!" == 0);
}
};
//
// Special create for std::strings. Since this uses a H5::StrType for the
// typename rather than specifying a H5::PredType, it mertis its own
// function.
//
template<>
void HDFAtom<std::string>::Create(H5::H5Location &object, const std::string & atomName);
#define DECLARE_TYPED_CREATE_ATOM(T, predtype) template<> \
void HDFAtom<T>::TypedCreate(H5::H5Location &object, const std::string & atomName, H5::DataSpace &defaultDataSpace);
DECLARE_TYPED_CREATE_ATOM(int, H5::PredType::NATIVE_INT)
DECLARE_TYPED_CREATE_ATOM(unsigned int, H5::PredType::NATIVE_UINT)
DECLARE_TYPED_CREATE_ATOM(unsigned char, H5::PredType::NATIVE_UINT8)
DECLARE_TYPED_CREATE_ATOM(char, H5::PredType::NATIVE_INT8)
DECLARE_TYPED_CREATE_ATOM(float, H5::PredType::NATIVE_FLOAT)
DECLARE_TYPED_CREATE_ATOM(uint16_t, H5::PredType::NATIVE_UINT16)
DECLARE_TYPED_CREATE_ATOM(uint64_t, H5::PredType::STD_I64LE)
template<>
void HDFAtom<std::vector<int> >::Write(const std::vector<int> vect);
template<>
void HDFAtom<std::string>::Write(std::string value);
template<>
void HDFAtom<uint64_t>::Write(uint64_t value);
template<>
void HDFAtom<uint16_t>::Write(uint16_t value);
template<>
void HDFAtom<int>::Write(int value);
template<>
void HDFAtom<unsigned int>::Write(unsigned int value);
template<>
void HDFAtom<unsigned char>::Write(unsigned char value);
template<>
void HDFAtom<char>::Write(char value);
template<>
void HDFAtom<float>::Write(float value);
template<>
void HDFAtom<std::string>::Read(std::string &value);
template<>
void HDFAtom<int>::Read(int &value);
template<>
void HDFAtom<uint64_t>::Read(uint64_t &value);
template<>
void HDFAtom<uint16_t>::Read(uint16_t &value);
template<>
void HDFAtom<unsigned int>::Read(unsigned int &value);
template<>
void HDFAtom<float>::Read(float &value);
template<>
void HDFAtom<std::vector<std::string> >::Read(std::vector<std::string> &values);
#endif
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