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pwiz::data Namespace Reference

Namespaces

namespace  diff_impl
namespace  unimod
namespace  pepxml
namespace  peakdata
namespace  SampleDatumConstant

Classes

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...
class  CVTranslator
 translates text to CV terms More...
struct  BaseDiffConfig
struct  Diff
 Calculate diffs of objects in a ProteoWizard data model hierarchy. 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  Term
 a single controlled vocabulary term More...
struct  OBO
 Represents a selectively parsed OBO file. More...
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...
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...
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  CalibrationParameters
class  FrequencyData
 Class for binary storage of complex frequency data. More...
struct  SampleDatum

Typedefs

typedef boost::shared_ptr< IndexIndexPtr
typedef boost::shared_ptr
< ParamGroup
ParamGroupPtr
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

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

Definition at line 72 of file Index.hpp.

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

Definition at line 236 of file ParamTypes.hpp.

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

Definition at line 40 of file FrequencyData.hpp.


Function Documentation

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.

References write().

Referenced by testString().

{
std::ostringstream os;
textwriter_type write(os, 1);
if (!diff.a_b.empty())
{
os << "+\n";
write(diff.a_b);
}
if (!diff.b_a.empty())
{
os << "-\n";
write(diff.b_a);
}
return os.str();
}
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.

References diff(), and write().

{
textwriter_type write(os, 1);
if (!diff.a_b.empty())
{
os << "+\n";
write(diff.a_b);
}
if (!diff.b_a.empty())
{
os << "-\n";
write(diff.b_a);
}
return os;
}
PWIZ_API_DECL std::ostream& pwiz::data::operator<< ( std::ostream &  os,
const Term &  term 
)
PWIZ_API_DECL std::ostream& pwiz::data::operator<< ( std::ostream &  os,
const OBO &  obo 
)
PWIZ_API_DECL std::ostream& pwiz::data::operator<< ( std::ostream &  os,
const CVParam &  param 
)
std::ostream& pwiz::data::operator<< ( std::ostream &  os,
const CalibrationParameters &  p 
)
inline

Definition at line 65 of file CalibrationParameters.hpp.

References pwiz::data::CalibrationParameters::A, and pwiz::data::CalibrationParameters::B.

{
os << "(" << p.A << "," << p.B << ")";
return os;
}
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 
)
template<typename abscissa_type , typename ordinate_type >
std::ostream& pwiz::data::operator<< ( std::ostream &  os,
const SampleDatum< abscissa_type, ordinate_type > &  datum 
)
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.

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.

{
std::string buffer;
is >> buffer;
if (!is) return is;
std::istringstream iss(buffer);
char open, separator, close;
abscissa_type x;
ordinate_type y;
iss >> open >> x >> separator >> y >> close;
throw std::runtime_error("[SampleDatum::operator>>] Invalid format.");
datum.x = x;
datum.y = y;
return is;
}

Variable Documentation

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().

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().

const double pwiz::data::thermoA_Orbitrap_ = 4.753e10
const double pwiz::data::thermoB_Orbitrap_ = 0