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Public Member Functions | Private Attributes
pwiz::msdata::mz5::ReferenceRead_mz5 Class Reference

This class is a helper class to read and convert a mz5 file to a MSData object. More...

#include <ReferenceRead_mz5.hpp>

List of all members.

Public Member Functions

 ReferenceRead_mz5 (pwiz::msdata::MSData &msd)
 Default constructor.
pwiz::cv::CVID getCVID (const unsigned long) const
 Getter.
pwiz::data::ParamGroupPtr getParamGroupPtr (const unsigned long) const
 Getter.
void fill (std::vector< pwiz::msdata::CVParam > &cv, std::vector< pwiz::msdata::UserParam > &user, std::vector< pwiz::msdata::ParamGroupPtr > &param, const unsigned long &cvstart, const unsigned long &cvend, const unsigned long &usrstart, const unsigned long &usrend, const unsigned long &refstart, const unsigned long &refend) const
pwiz::msdata::SourceFilePtr getSourcefilePtr (const unsigned long) const
 Getter.
pwiz::msdata::SamplePtr getSamplePtr (const unsigned long) const
 Getter.
pwiz::msdata::SoftwarePtr getSoftwarePtr (const unsigned long) const
 Getter.
pwiz::msdata::ScanSettingsPtr getScanSettingPtr (const unsigned long) const
 Getter.
pwiz::msdata::InstrumentConfigurationPtr getInstrumentPtr (const unsigned long) const
 Getter.
pwiz::msdata::DataProcessingPtr getDataProcessingPtr (const unsigned long) const
 Getter.
std::string getSpectrumId (const unsigned long) const
 Getter.
void addSpectrumIndexPair (const std::string &name, const unsigned long index) const
 Adds a spectrum index pair to an internal map.
void setCVRefMZ5 (CVRefMZ5 *, size_t)
 Sets internal controlled vocabulary map.
void fill (boost::shared_ptr< Connection_mz5 > &connection)
 Fills the internal MSData reference with the data from an mz5 file.
pwiz::msdata::DataProcessingPtr getDefaultChromatogramDP (const size_t index)
pwiz::msdata::DataProcessingPtr getDefaultSpectrumDP (const size_t index)

Private Attributes

pwiz::msdata::MSDatamsd_
 Reference to MSData object.
std::vector< CVRefMZ5cvrefs_
 Following are helper maps and lists for reading.
std::map< unsigned long,
pwiz::cv::CVID > 
bbmapping_
std::vector< CVParamMZ5cvParams_
std::vector< UserParamMZ5usrParams_
std::vector< RefMZ5refParms_
std::map< unsigned long,
std::string > 
spectrumIndex_
unsigned long defaultChromatogramDataProcessingRefID_
unsigned long defaultSpectrumDataProcessingRefID_

Detailed Description

This class is a helper class to read and convert a mz5 file to a MSData object.

Definition at line 44 of file ReferenceRead_mz5.hpp.


Constructor & Destructor Documentation

pwiz::msdata::mz5::ReferenceRead_mz5::ReferenceRead_mz5 ( pwiz::msdata::MSData msd)

Default constructor.

Parameters:
msdthis MSData object will be filled

Member Function Documentation

pwiz::cv::CVID pwiz::msdata::mz5::ReferenceRead_mz5::getCVID ( const unsigned  long) const

Getter.

Parameters:
index
Returns:
object with this index. Can throw out_of_range.
pwiz::data::ParamGroupPtr pwiz::msdata::mz5::ReferenceRead_mz5::getParamGroupPtr ( const unsigned  long) const

Getter.

Parameters:
index
Returns:
object with this index. Can throw out_of_range.
void pwiz::msdata::mz5::ReferenceRead_mz5::fill ( std::vector< pwiz::msdata::CVParam > &  cv,
std::vector< pwiz::msdata::UserParam > &  user,
std::vector< pwiz::msdata::ParamGroupPtr > &  param,
const unsigned long &  cvstart,
const unsigned long &  cvend,
const unsigned long &  usrstart,
const unsigned long &  usrend,
const unsigned long &  refstart,
const unsigned long &  refend 
) const
pwiz::msdata::SourceFilePtr pwiz::msdata::mz5::ReferenceRead_mz5::getSourcefilePtr ( const unsigned  long) const

Getter.

Parameters:
index
Returns:
object with this index. Can throw out_of_range.
pwiz::msdata::SamplePtr pwiz::msdata::mz5::ReferenceRead_mz5::getSamplePtr ( const unsigned  long) const

Getter.

Parameters:
index
Returns:
object with this index. Can throw out_of_range.
pwiz::msdata::SoftwarePtr pwiz::msdata::mz5::ReferenceRead_mz5::getSoftwarePtr ( const unsigned  long) const

Getter.

Parameters:
index
Returns:
object with this index. Can throw out_of_range.
pwiz::msdata::ScanSettingsPtr pwiz::msdata::mz5::ReferenceRead_mz5::getScanSettingPtr ( const unsigned  long) const

Getter.

Parameters:
index
Returns:
object with this index. Can throw out_of_range.
pwiz::msdata::InstrumentConfigurationPtr pwiz::msdata::mz5::ReferenceRead_mz5::getInstrumentPtr ( const unsigned  long) const

Getter.

Parameters:
index
Returns:
object with this index. Can throw out_of_range.
pwiz::msdata::DataProcessingPtr pwiz::msdata::mz5::ReferenceRead_mz5::getDataProcessingPtr ( const unsigned  long) const

Getter.

Parameters:
index
Returns:
object with this index. Can throw out_of_range.
std::string pwiz::msdata::mz5::ReferenceRead_mz5::getSpectrumId ( const unsigned  long) const

Getter.

Parameters:
index
Returns:
object with this index. Can throw out_of_range.
void pwiz::msdata::mz5::ReferenceRead_mz5::addSpectrumIndexPair ( const std::string &  name,
const unsigned long  index 
) const

Adds a spectrum index pair to an internal map.

Parameters:
name
index
void pwiz::msdata::mz5::ReferenceRead_mz5::setCVRefMZ5 ( CVRefMZ5 ,
size_t   
)

Sets internal controlled vocabulary map.

void pwiz::msdata::mz5::ReferenceRead_mz5::fill ( boost::shared_ptr< Connection_mz5 > &  connection)

Fills the internal MSData reference with the data from an mz5 file.

Parameters:
connectionopen mz5 connection to a mz5 file
pwiz::msdata::DataProcessingPtr pwiz::msdata::mz5::ReferenceRead_mz5::getDefaultChromatogramDP ( const size_t  index)
pwiz::msdata::DataProcessingPtr pwiz::msdata::mz5::ReferenceRead_mz5::getDefaultSpectrumDP ( const size_t  index)

Member Data Documentation

pwiz::msdata::MSData& pwiz::msdata::mz5::ReferenceRead_mz5::msd_
private

Reference to MSData object.

Definition at line 153 of file ReferenceRead_mz5.hpp.

std::vector<CVRefMZ5> pwiz::msdata::mz5::ReferenceRead_mz5::cvrefs_
mutableprivate

Following are helper maps and lists for reading.

Definition at line 158 of file ReferenceRead_mz5.hpp.

std::map<unsigned long, pwiz::cv::CVID> pwiz::msdata::mz5::ReferenceRead_mz5::bbmapping_
mutableprivate

Definition at line 159 of file ReferenceRead_mz5.hpp.

std::vector<CVParamMZ5> pwiz::msdata::mz5::ReferenceRead_mz5::cvParams_
mutableprivate

Definition at line 160 of file ReferenceRead_mz5.hpp.

std::vector<UserParamMZ5> pwiz::msdata::mz5::ReferenceRead_mz5::usrParams_
mutableprivate

Definition at line 161 of file ReferenceRead_mz5.hpp.

std::vector<RefMZ5> pwiz::msdata::mz5::ReferenceRead_mz5::refParms_
mutableprivate

Definition at line 162 of file ReferenceRead_mz5.hpp.

std::map<unsigned long, std::string> pwiz::msdata::mz5::ReferenceRead_mz5::spectrumIndex_
mutableprivate

Definition at line 163 of file ReferenceRead_mz5.hpp.

unsigned long pwiz::msdata::mz5::ReferenceRead_mz5::defaultChromatogramDataProcessingRefID_
mutableprivate

Definition at line 165 of file ReferenceRead_mz5.hpp.

unsigned long pwiz::msdata::mz5::ReferenceRead_mz5::defaultSpectrumDataProcessingRefID_
mutableprivate

Definition at line 165 of file ReferenceRead_mz5.hpp.


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