ProteoWizard
Namespaces | Classes | Typedefs | Functions | Variables
pwiz::data Namespace Reference

Namespaces

 diff_impl
 
 peakdata
 
 pepxml
 
 SampleDatumConstant
 
 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 More...
 
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 239 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.

References pwiz::identdata::IO::write().

Referenced by testString().

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)
PWIZ_API_DECL void write(minimxml::XMLWriter &writer, const CV &cv)

§ 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.

References diff(), and pwiz::identdata::IO::write().

Referenced by pwiz::data::OBO::OBO(), and pwiz::data::CVParam::valueAs().

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 }
void diff(const string &filename1, const string &filename2)
PWIZ_API_DECL void write(minimxml::XMLWriter &writer, const CV &cv)

§ 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

Definition at line 65 of file CalibrationParameters.hpp.

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

66 {
67  os << "(" << p.A << "," << p.B << ")";
68  return os;
69 }

§ 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 
)

§ 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.

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.

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_ ||
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

Variable Documentation

§ thermoA_FT_

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

Definition at line 38 of file CalibrationParameters.hpp.

Referenced by test().

§ thermoB_FT_

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

Definition at line 39 of file CalibrationParameters.hpp.

Referenced by test().

§ thermoA_Orbitrap_

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

Definition at line 40 of file CalibrationParameters.hpp.

§ thermoB_Orbitrap_

const double pwiz::data::thermoB_Orbitrap_ = 0

Definition at line 41 of file CalibrationParameters.hpp.