ProteoWizard
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This class is a helper class for converting and writing mz5 files in mz5 format. More...
#include <ReferenceWrite_mz5.hpp>
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::MSData & | msd_ |
Internal reference to the MSData object. | |
std::vector< CVRefMZ5 > | cvrefs_ |
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< ParamGroupMZ5 > | paramGroupList_ |
std::map< std::string, unsigned long > | paramGroupMapping_ |
std::vector< CVParamMZ5 > | cvParams_ |
std::vector< UserParamMZ5 > | usrParams_ |
std::vector< RefMZ5 > | refParms_ |
std::vector< SourceFileMZ5 > | sourceFileList_ |
std::map< std::string, unsigned long > | sourceFileMapping_ |
std::vector< SampleMZ5 > | sampleList_ |
std::map< std::string, unsigned long > | sampleMapping_ |
std::vector< SoftwareMZ5 > | softwareList_ |
std::map< std::string, unsigned long > | softwareMapping_ |
std::vector< ScanSettingMZ5 > | scanSettingList_ |
std::map< std::string, unsigned long > | scanSettingMapping_ |
std::vector < InstrumentConfigurationMZ5 > | instrumentList_ |
std::map< std::string, unsigned long > | instrumentMapping_ |
std::vector< DataProcessingMZ5 > | dataProcessingList_ |
std::map< std::string, unsigned long > | dataProcessingMapping_ |
std::map< std::string, unsigned long > | spectrumMapping_ |
std::vector< ContVocabMZ5 > | contvacb_ |
std::vector< ParamListMZ5 > | fileContent_ |
std::vector< ParamListMZ5 > | contacts_ |
std::vector< RunMZ5 > | rl_ |
This class is a helper class for converting and writing mz5 files in mz5 format.
Definition at line 44 of file ReferenceWrite_mz5.hpp.
pwiz::msdata::mz5::ReferenceWrite_mz5::ReferenceWrite_mz5 | ( | const pwiz::msdata::MSData & | msd | ) |
Default constructor.
msd | MSData input object |
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.
cvid | CVID input |
unsigned long pwiz::msdata::mz5::ReferenceWrite_mz5::getParamGroupId | ( | const pwiz::data::ParamGroup & | , |
const ParamGroupMZ5 * | pg5 = 0 |
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) | const |
Stores a parameter group into internal maps and returns the corresponding index.
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.
unsigned long pwiz::msdata::mz5::ReferenceWrite_mz5::getSourceFileId | ( | const pwiz::msdata::SourceFile & | , |
const SourceFileMZ5 * | sf5 = 0 |
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) | const |
Stores a source file into internal maps and returns the corresponding index.
unsigned long pwiz::msdata::mz5::ReferenceWrite_mz5::getSampleId | ( | const pwiz::msdata::Sample & | , |
const SampleMZ5 * | s5 = 0 |
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) | const |
Stores a sample into internal maps and returns the corresponding index.
unsigned long pwiz::msdata::mz5::ReferenceWrite_mz5::getSoftwareId | ( | const pwiz::msdata::Software & | , |
const SoftwareMZ5 * | s5 = 0 |
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) | const |
Stores a software into internal maps and returns the corresponding index.
unsigned long pwiz::msdata::mz5::ReferenceWrite_mz5::getScanSettingId | ( | const pwiz::msdata::ScanSettings & | , |
const ScanSettingMZ5 * | ss5 = 0 |
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) | const |
Stores a scan setting element into internal maps and returns the corresponding index.
unsigned long pwiz::msdata::mz5::ReferenceWrite_mz5::getInstrumentId | ( | const pwiz::msdata::InstrumentConfiguration & | , |
const InstrumentConfigurationMZ5 * | ic5 = 0 |
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) | const |
Stores a instrument configuration into internal maps and returns the corresponding index.
unsigned long pwiz::msdata::mz5::ReferenceWrite_mz5::getDataProcessingId | ( | const pwiz::msdata::DataProcessing & | , |
const DataProcessingMZ5 * | dp5 = 0 |
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) | const |
Stores a data processing element into internal maps and returns the corresponding index.
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.
unsigned long pwiz::msdata::mz5::ReferenceWrite_mz5::getSpectrumIndex | ( | const std::string & | ) | const |
Resolves a spectrum name and returns the corresponding index.
void pwiz::msdata::mz5::ReferenceWrite_mz5::writeTo | ( | Connection_mz5 & | connection, |
const pwiz::util::IterationListenerRegistry * | iterationListenerRegistry | ||
) |
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Internal reference to the MSData object.
Definition at line 172 of file ReferenceWrite_mz5.hpp.
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Following lists are used as internal storage container.
Definition at line 178 of file ReferenceWrite_mz5.hpp.
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