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pwiz::msdata::mz5::ReferenceWrite_mz5 Class Reference

This class is a helper class for converting and writing mz5 files in mz5 format. More...

#include <ReferenceWrite_mz5.hpp>

List of all members.

Public Member Functions

 ReferenceWrite_mz5 (const pwiz::msdata::MSData &msd)
 Default constructor.
unsigned long getCVRefId (const pwiz::cv::CVID cvid) const
 Stores a CVID into internal maps and returns the corresponding index.
unsigned long getParamGroupId (const pwiz::data::ParamGroup &, const ParamGroupMZ5 *pg5=0) const
 Stores a parameter group into internal maps and returns the corresponding index.
void getIndizes (unsigned long &cvstart, unsigned long &cvend, unsigned long &usrstart, unsigned long &usrend, unsigned long &refstart, unsigned long &refend, const std::vector< pwiz::msdata::CVParam > &cvs, const std::vector< pwiz::msdata::UserParam > &usrs, const std::vector< pwiz::msdata::ParamGroupPtr > &groups) const
 Stores a parameter container into internal maps and returns the corresponding index.
unsigned long getSourceFileId (const pwiz::msdata::SourceFile &, const SourceFileMZ5 *sf5=0) const
 Stores a source file into internal maps and returns the corresponding index.
unsigned long getSampleId (const pwiz::msdata::Sample &, const SampleMZ5 *s5=0) const
 Stores a sample into internal maps and returns the corresponding index.
unsigned long getSoftwareId (const pwiz::msdata::Software &, const SoftwareMZ5 *s5=0) const
 Stores a software into internal maps and returns the corresponding index.
unsigned long getScanSettingId (const pwiz::msdata::ScanSettings &, const ScanSettingMZ5 *ss5=0) const
 Stores a scan setting element into internal maps and returns the corresponding index.
unsigned long getInstrumentId (const pwiz::msdata::InstrumentConfiguration &, const InstrumentConfigurationMZ5 *ic5=0) const
 Stores a instrument configuration into internal maps and returns the corresponding index.
unsigned long getDataProcessingId (const pwiz::msdata::DataProcessing &, const DataProcessingMZ5 *dp5=0) const
 Stores a data processing element into internal maps and returns the corresponding index.
void addSpectrumIndexPair (const std::string &, const unsigned long) const
 Stores a spectrum into internal maps and returns the corresponding index.
unsigned long getSpectrumIndex (const std::string &) const
 Resolves a spectrum name and returns the corresponding index.
void writeTo (Connection_mz5 &connection, const pwiz::util::IterationListenerRegistry *iterationListenerRegistry)

Private Member Functions

pwiz::util::IterationListener::Status readAndWriteSpectra (Connection_mz5 &connection, std::vector< BinaryDataMZ5 > &bdl, std::vector< SpectrumMZ5 > &spl, const pwiz::util::IterationListenerRegistry *iterationListenerRegistry)
 Reads and writes all raw spectra using an existing mz5 connection.
pwiz::util::IterationListener::Status readAndWriteChromatograms (Connection_mz5 &connection, std::vector< BinaryDataMZ5 > &bdl, std::vector< ChromatogramMZ5 > &cpl, const pwiz::util::IterationListenerRegistry *iterationListenerRegistry)
 Reads and writes all chromtograms using an existing mz5 connection.

Private Attributes

const pwiz::msdata::MSDatamsd_
 Internal reference to the MSData object.
std::vector< CVRefMZ5cvrefs_
 Following lists are used as internal storage container.
std::map< pwiz::cv::CVID,
unsigned long > 
cvToIndexMapping_
std::map< unsigned long,
pwiz::cv::CVID > 
cvFromIndexMapping_
std::vector< ParamGroupMZ5paramGroupList_
std::map< std::string,
unsigned long > 
paramGroupMapping_
std::vector< CVParamMZ5cvParams_
std::vector< UserParamMZ5usrParams_
std::vector< RefMZ5refParms_
std::vector< SourceFileMZ5sourceFileList_
std::map< std::string,
unsigned long > 
sourceFileMapping_
std::vector< SampleMZ5sampleList_
std::map< std::string,
unsigned long > 
sampleMapping_
std::vector< SoftwareMZ5softwareList_
std::map< std::string,
unsigned long > 
softwareMapping_
std::vector< ScanSettingMZ5scanSettingList_
std::map< std::string,
unsigned long > 
scanSettingMapping_
std::vector
< InstrumentConfigurationMZ5
instrumentList_
std::map< std::string,
unsigned long > 
instrumentMapping_
std::vector< DataProcessingMZ5dataProcessingList_
std::map< std::string,
unsigned long > 
dataProcessingMapping_
std::map< std::string,
unsigned long > 
spectrumMapping_
std::vector< ContVocabMZ5contvacb_
std::vector< ParamListMZ5fileContent_
std::vector< ParamListMZ5contacts_
std::vector< RunMZ5rl_

Detailed Description

This class is a helper class for converting and writing mz5 files in mz5 format.

Definition at line 44 of file ReferenceWrite_mz5.hpp.


Constructor & Destructor Documentation

pwiz::msdata::mz5::ReferenceWrite_mz5::ReferenceWrite_mz5 ( const pwiz::msdata::MSData msd)

Default constructor.

Parameters:
msdMSData input object

Member Function Documentation

unsigned long pwiz::msdata::mz5::ReferenceWrite_mz5::getCVRefId ( const pwiz::cv::CVID  cvid) const

Stores a CVID into internal maps and returns the corresponding index.

Parameters:
cvidCVID input
Returns:
index in list
unsigned long pwiz::msdata::mz5::ReferenceWrite_mz5::getParamGroupId ( const pwiz::data::ParamGroup ,
const ParamGroupMZ5 pg5 = 0 
) const

Stores a parameter group into internal maps and returns the corresponding index.

Returns:
index in list
void pwiz::msdata::mz5::ReferenceWrite_mz5::getIndizes ( unsigned long &  cvstart,
unsigned long &  cvend,
unsigned long &  usrstart,
unsigned long &  usrend,
unsigned long &  refstart,
unsigned long &  refend,
const std::vector< pwiz::msdata::CVParam > &  cvs,
const std::vector< pwiz::msdata::UserParam > &  usrs,
const std::vector< pwiz::msdata::ParamGroupPtr > &  groups 
) const

Stores a parameter container into internal maps and returns the corresponding index.

Returns:
index in list
unsigned long pwiz::msdata::mz5::ReferenceWrite_mz5::getSourceFileId ( const pwiz::msdata::SourceFile ,
const SourceFileMZ5 sf5 = 0 
) const

Stores a source file into internal maps and returns the corresponding index.

Returns:
index in list
unsigned long pwiz::msdata::mz5::ReferenceWrite_mz5::getSampleId ( const pwiz::msdata::Sample ,
const SampleMZ5 s5 = 0 
) const

Stores a sample into internal maps and returns the corresponding index.

Returns:
index in list
unsigned long pwiz::msdata::mz5::ReferenceWrite_mz5::getSoftwareId ( const pwiz::msdata::Software ,
const SoftwareMZ5 s5 = 0 
) const

Stores a software into internal maps and returns the corresponding index.

Returns:
index in list
unsigned long pwiz::msdata::mz5::ReferenceWrite_mz5::getScanSettingId ( const pwiz::msdata::ScanSettings ,
const ScanSettingMZ5 ss5 = 0 
) const

Stores a scan setting element into internal maps and returns the corresponding index.

Returns:
index in list
unsigned long pwiz::msdata::mz5::ReferenceWrite_mz5::getInstrumentId ( const pwiz::msdata::InstrumentConfiguration ,
const InstrumentConfigurationMZ5 ic5 = 0 
) const

Stores a instrument configuration into internal maps and returns the corresponding index.

Returns:
index in list
unsigned long pwiz::msdata::mz5::ReferenceWrite_mz5::getDataProcessingId ( const pwiz::msdata::DataProcessing ,
const DataProcessingMZ5 dp5 = 0 
) const

Stores a data processing element into internal maps and returns the corresponding index.

Returns:
index in list
void pwiz::msdata::mz5::ReferenceWrite_mz5::addSpectrumIndexPair ( const std::string &  ,
const unsigned  long 
) const

Stores a spectrum into internal maps and returns the corresponding index.

Returns:
index in list
unsigned long pwiz::msdata::mz5::ReferenceWrite_mz5::getSpectrumIndex ( const std::string &  ) const

Resolves a spectrum name and returns the corresponding index.

Returns:
index in list
void pwiz::msdata::mz5::ReferenceWrite_mz5::writeTo ( Connection_mz5 connection,
const pwiz::util::IterationListenerRegistry iterationListenerRegistry 
)
pwiz::util::IterationListener::Status pwiz::msdata::mz5::ReferenceWrite_mz5::readAndWriteSpectra ( Connection_mz5 connection,
std::vector< BinaryDataMZ5 > &  bdl,
std::vector< SpectrumMZ5 > &  spl,
const pwiz::util::IterationListenerRegistry iterationListenerRegistry 
)
private

Reads and writes all raw spectra using an existing mz5 connection.

Parameters:
connectionmz5 connection object
bdlbinary data list of a MSData object
splspetrum data list of a MSData object
pwiz::util::IterationListener::Status pwiz::msdata::mz5::ReferenceWrite_mz5::readAndWriteChromatograms ( Connection_mz5 connection,
std::vector< BinaryDataMZ5 > &  bdl,
std::vector< ChromatogramMZ5 > &  cpl,
const pwiz::util::IterationListenerRegistry iterationListenerRegistry 
)
private

Reads and writes all chromtograms using an existing mz5 connection.

Parameters:
connectionmz5 connection object
bdlbinary data list of a MSData object
cplchromatogram list of a MSData object

Member Data Documentation

const pwiz::msdata::MSData& pwiz::msdata::mz5::ReferenceWrite_mz5::msd_
private

Internal reference to the MSData object.

Definition at line 172 of file ReferenceWrite_mz5.hpp.

std::vector<CVRefMZ5> pwiz::msdata::mz5::ReferenceWrite_mz5::cvrefs_
mutableprivate

Following lists are used as internal storage container.

Definition at line 178 of file ReferenceWrite_mz5.hpp.

std::map<pwiz::cv::CVID, unsigned long> pwiz::msdata::mz5::ReferenceWrite_mz5::cvToIndexMapping_
mutableprivate

Definition at line 179 of file ReferenceWrite_mz5.hpp.

std::map<unsigned long, pwiz::cv::CVID> pwiz::msdata::mz5::ReferenceWrite_mz5::cvFromIndexMapping_
mutableprivate

Definition at line 180 of file ReferenceWrite_mz5.hpp.

std::vector<ParamGroupMZ5> pwiz::msdata::mz5::ReferenceWrite_mz5::paramGroupList_
mutableprivate

Definition at line 183 of file ReferenceWrite_mz5.hpp.

std::map<std::string, unsigned long> pwiz::msdata::mz5::ReferenceWrite_mz5::paramGroupMapping_
mutableprivate

Definition at line 184 of file ReferenceWrite_mz5.hpp.

std::vector<CVParamMZ5> pwiz::msdata::mz5::ReferenceWrite_mz5::cvParams_
mutableprivate

Definition at line 186 of file ReferenceWrite_mz5.hpp.

std::vector<UserParamMZ5> pwiz::msdata::mz5::ReferenceWrite_mz5::usrParams_
mutableprivate

Definition at line 187 of file ReferenceWrite_mz5.hpp.

std::vector<RefMZ5> pwiz::msdata::mz5::ReferenceWrite_mz5::refParms_
mutableprivate

Definition at line 188 of file ReferenceWrite_mz5.hpp.

std::vector<SourceFileMZ5> pwiz::msdata::mz5::ReferenceWrite_mz5::sourceFileList_
mutableprivate

Definition at line 190 of file ReferenceWrite_mz5.hpp.

std::map<std::string, unsigned long> pwiz::msdata::mz5::ReferenceWrite_mz5::sourceFileMapping_
mutableprivate

Definition at line 191 of file ReferenceWrite_mz5.hpp.

std::vector<SampleMZ5> pwiz::msdata::mz5::ReferenceWrite_mz5::sampleList_
mutableprivate

Definition at line 193 of file ReferenceWrite_mz5.hpp.

std::map<std::string, unsigned long> pwiz::msdata::mz5::ReferenceWrite_mz5::sampleMapping_
mutableprivate

Definition at line 194 of file ReferenceWrite_mz5.hpp.

std::vector<SoftwareMZ5> pwiz::msdata::mz5::ReferenceWrite_mz5::softwareList_
mutableprivate

Definition at line 196 of file ReferenceWrite_mz5.hpp.

std::map<std::string, unsigned long> pwiz::msdata::mz5::ReferenceWrite_mz5::softwareMapping_
mutableprivate

Definition at line 197 of file ReferenceWrite_mz5.hpp.

std::vector<ScanSettingMZ5> pwiz::msdata::mz5::ReferenceWrite_mz5::scanSettingList_
mutableprivate

Definition at line 199 of file ReferenceWrite_mz5.hpp.

std::map<std::string, unsigned long> pwiz::msdata::mz5::ReferenceWrite_mz5::scanSettingMapping_
mutableprivate

Definition at line 200 of file ReferenceWrite_mz5.hpp.

std::vector<InstrumentConfigurationMZ5> pwiz::msdata::mz5::ReferenceWrite_mz5::instrumentList_
mutableprivate

Definition at line 202 of file ReferenceWrite_mz5.hpp.

std::map<std::string, unsigned long> pwiz::msdata::mz5::ReferenceWrite_mz5::instrumentMapping_
mutableprivate

Definition at line 203 of file ReferenceWrite_mz5.hpp.

std::vector<DataProcessingMZ5> pwiz::msdata::mz5::ReferenceWrite_mz5::dataProcessingList_
mutableprivate

Definition at line 205 of file ReferenceWrite_mz5.hpp.

std::map<std::string, unsigned long> pwiz::msdata::mz5::ReferenceWrite_mz5::dataProcessingMapping_
mutableprivate

Definition at line 206 of file ReferenceWrite_mz5.hpp.

std::map<std::string, unsigned long> pwiz::msdata::mz5::ReferenceWrite_mz5::spectrumMapping_
mutableprivate

Definition at line 208 of file ReferenceWrite_mz5.hpp.

std::vector<ContVocabMZ5> pwiz::msdata::mz5::ReferenceWrite_mz5::contvacb_
mutableprivate

Definition at line 210 of file ReferenceWrite_mz5.hpp.

std::vector<ParamListMZ5> pwiz::msdata::mz5::ReferenceWrite_mz5::fileContent_
mutableprivate

Definition at line 211 of file ReferenceWrite_mz5.hpp.

std::vector<ParamListMZ5> pwiz::msdata::mz5::ReferenceWrite_mz5::contacts_
mutableprivate

Definition at line 212 of file ReferenceWrite_mz5.hpp.

std::vector<RunMZ5> pwiz::msdata::mz5::ReferenceWrite_mz5::rl_
mutableprivate

Definition at line 214 of file ReferenceWrite_mz5.hpp.


The documentation for this class was generated from the following file: