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pwiz::data Namespace Reference

Namespaces

namespace  diff_impl
 
namespace  peakdata
 
namespace  pepxml
 
namespace  SampleDatumConstant
 
namespace  unimod
 

Classes

struct  BaseDiffConfig
 
class  BinaryIndexStream
 index implementation in a stream (intended for fstreams but any iostream works); find(string id) is O(logN); find(ordinal index) is O(1); memory footprint is negligible More...
 
struct  CalibrationParameters
 
struct  CVParam
 represents a tag-value pair, where the tag comes from the controlled vocabulary More...
 
struct  CVParamIs
 functor for finding CVParam with specified exact CVID in a collection of CVParams: More...
 
struct  CVParamIsChildOf
 functor for finding children of a specified CVID in a collection of CVParams: More...
 
class  CVTranslator
 translates text to CV terms More...
 
struct  Diff
 Calculate diffs of objects in a ProteoWizard data model hierarchy. More...
 
class  FrequencyData
 Class for binary storage of complex frequency data. More...
 
class  Index
 generic interface for creating and using an index on a stream of serialized objects More...
 
class  MemoryIndex
 index implementation in memory; find(string id) is O(logN); find(ordinal index) is O(1); memory footprint is basically (number of entries * 2) More...
 
struct  OBO
 Represents a selectively parsed OBO file. More...
 
struct  ParamContainer
 The base class for elements that may contain cvParams, userParams, or paramGroup references. More...
 
struct  ParamGroup
 A collection of CVParam and UserParam elements that can be referenced from elsewhere in this mzML document by using the 'paramGroupRef' element in that location to reference the 'id' attribute value of this element. More...
 
struct  SampleDatum
 
struct  Term
 a single controlled vocabulary term More...
 
struct  UserParam
 Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead. More...
 

Typedefs

typedef boost::shared_ptr< IndexIndexPtr
 
typedef boost::shared_ptr< ParamGroupParamGroupPtr
 
typedef SampleDatum< double, std::complex< double > > FrequencyDatum
 

Functions

template<typename textwriter_type , typename diff_type >
std::string diff_string (const diff_type &diff)
 
template<typename textwriter_type , typename object_type , typename config_type >
std::ostream & operator<< (std::ostream &os, const Diff< object_type, config_type > &diff)
 stream insertion of Diff results
 
PWIZ_API_DECL std::ostream & operator<< (std::ostream &os, const Term &term)
 
PWIZ_API_DECL std::ostream & operator<< (std::ostream &os, const OBO &obo)
 
PWIZ_API_DECL std::ostream & operator<< (std::ostream &os, const CVParam &param)
 
std::ostream & operator<< (std::ostream &os, const CalibrationParameters &p)
 
template<typename abscissa_type , typename ordinate_type >
bool operator== (const SampleDatum< abscissa_type, ordinate_type > &a, const SampleDatum< abscissa_type, ordinate_type > &b)
 
template<typename abscissa_type , typename ordinate_type >
std::ostream & operator<< (std::ostream &os, const SampleDatum< abscissa_type, ordinate_type > &datum)
 
template<typename abscissa_type , typename ordinate_type >
std::istream & operator>> (std::istream &is, SampleDatum< abscissa_type, ordinate_type > &datum)
 

Variables

const double thermoA_FT_ = 1.075e8
 
const double thermoB_FT_ = -3.455e8
 
const double thermoA_Orbitrap_ = 4.753e10
 
const double thermoB_Orbitrap_ = 0
 

Typedef Documentation

◆ IndexPtr

typedef boost::shared_ptr<Index> pwiz::data::IndexPtr

Definition at line 72 of file Index.hpp.

◆ ParamGroupPtr

typedef boost::shared_ptr<ParamGroup> pwiz::data::ParamGroupPtr

Definition at line 240 of file ParamTypes.hpp.

◆ FrequencyDatum

typedef SampleDatum< double, std::complex<double> > pwiz::data::FrequencyDatum

Definition at line 40 of file FrequencyData.hpp.

Function Documentation

◆ diff_string()

template<typename textwriter_type , typename diff_type >
std::string pwiz::data::diff_string ( const diff_type &  diff)

Definition at line 177 of file diff_std.hpp.

178{
179 std::ostringstream os;
180 textwriter_type write(os, 1);
181
182 if (!diff.a_b.empty())
183 {
184 os << "+\n";
185 write(diff.a_b);
186 }
187
188 if (!diff.b_a.empty())
189 {
190 os << "-\n";
191 write(diff.b_a);
192 }
193
194 return os.str();
195}
void diff(const string &filename1, const string &filename2)

References diff().

Referenced by testString().

◆ operator<<() [1/6]

template<typename textwriter_type , typename object_type , typename config_type >
std::ostream & pwiz::data::operator<< ( std::ostream &  os,
const Diff< object_type, config_type > &  diff 
)

stream insertion of Diff results

Definition at line 200 of file diff_std.hpp.

201{
202 textwriter_type write(os, 1);
203
204 if (!diff.a_b.empty())
205 {
206 os << "+\n";
207 write(diff.a_b);
208 }
209
210 if (!diff.b_a.empty())
211 {
212 os << "-\n";
213 write(diff.b_a);
214 }
215
216 return os;
217}

References diff().

◆ operator<<() [2/6]

PWIZ_API_DECL std::ostream & pwiz::data::operator<< ( std::ostream &  os,
const Term term 
)

◆ operator<<() [3/6]

PWIZ_API_DECL std::ostream & pwiz::data::operator<< ( std::ostream &  os,
const OBO obo 
)

◆ operator<<() [4/6]

PWIZ_API_DECL std::ostream & pwiz::data::operator<< ( std::ostream &  os,
const CVParam param 
)

◆ operator<<() [5/6]

std::ostream & pwiz::data::operator<< ( std::ostream &  os,
const CalibrationParameters p 
)
inline

◆ operator==()

template<typename abscissa_type , typename ordinate_type >
bool pwiz::data::operator== ( const SampleDatum< abscissa_type, ordinate_type > &  a,
const SampleDatum< abscissa_type, ordinate_type > &  b 
)

◆ operator<<() [6/6]

template<typename abscissa_type , typename ordinate_type >
std::ostream & pwiz::data::operator<< ( std::ostream &  os,
const SampleDatum< abscissa_type, ordinate_type > &  datum 
)

Definition at line 68 of file SampleDatum.hpp.

69{
70 os << SampleDatumConstant::open_
71 << datum.x
72 << SampleDatumConstant::separator_
73 << datum.y
74 << SampleDatumConstant::close_;
75
76 return os;
77}

References pwiz::data::SampleDatumConstant::close_, pwiz::data::SampleDatumConstant::open_, pwiz::data::SampleDatumConstant::separator_, pwiz::data::SampleDatum< abscissa_type, ordinate_type >::x, and pwiz::data::SampleDatum< abscissa_type, ordinate_type >::y.

◆ operator>>()

template<typename abscissa_type , typename ordinate_type >
std::istream & pwiz::data::operator>> ( std::istream &  is,
SampleDatum< abscissa_type, ordinate_type > &  datum 
)

Definition at line 81 of file SampleDatum.hpp.

82{
83 std::string buffer;
84 is >> buffer;
85 if (!is) return is;
86
87 std::istringstream iss(buffer);
88
89 char open, separator, close;
90 abscissa_type x;
91 ordinate_type y;
92 iss >> open >> x >> separator >> y >> close;
93
94 if (open != SampleDatumConstant::open_ ||
95 separator != SampleDatumConstant::separator_ ||
96 close != SampleDatumConstant::close_)
97 throw std::runtime_error("[SampleDatum::operator>>] Invalid format.");
98
99 datum.x = x;
100 datum.y = y;
101
102 return is;
103}
KernelTraitsBase< Kernel >::space_type::abscissa_type x
KernelTraitsBase< Kernel >::space_type::ordinate_type y

References pwiz::data::SampleDatumConstant::close_, pwiz::data::SampleDatumConstant::open_, pwiz::data::SampleDatumConstant::separator_, pwiz::data::SampleDatum< abscissa_type, ordinate_type >::x, x, pwiz::data::SampleDatum< abscissa_type, ordinate_type >::y, and y.

Variable Documentation

◆ thermoA_FT_

const double pwiz::data::thermoA_FT_ = 1.075e8

Definition at line 38 of file CalibrationParameters.hpp.

Referenced by test(), and pwiz::data::CalibrationParameters::thermo_FT().

◆ thermoB_FT_

const double pwiz::data::thermoB_FT_ = -3.455e8

Definition at line 39 of file CalibrationParameters.hpp.

Referenced by test(), and pwiz::data::CalibrationParameters::thermo_FT().

◆ thermoA_Orbitrap_

const double pwiz::data::thermoA_Orbitrap_ = 4.753e10

◆ thermoB_Orbitrap_

const double pwiz::data::thermoB_Orbitrap_ = 0