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pwiz::msdata::MSData Struct Reference

This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to capture the use of a mass spectrometer, the data generated, and the initial processing of that data (to the level of the peak list). More...

#include <MSData.hpp>

Inheritance diagram for pwiz::msdata::MSData:
MSDataWithSettableVersion pwiz::msdata::MSDataFile pwiz::msdata::MSDataMerger

Public Member Functions

std::vector< DataProcessingPtrallDataProcessingPtrs () const
 return dataProcessingPtrs augmented by the dataProcessingPtr() set in SpectrumList and/or ChromatogramList More...
 
 MSData ()
 
virtual ~MSData ()
 
bool empty () const
 
const std::string & version () const
 returns the version of this mzML document; for a document created programmatically, the version is the current release version of mzML; for a document created from a file/stream, the version is the schema version read from the file/stream More...
 
void filterApplied ()
 
int countFiltersApplied () const
 

Public Attributes

std::string accession
 an optional accession number for the mzML document. More...
 
std::string id
 an optional id for the mzML document. It is recommended to use LSIDs when possible. More...
 
std::vector< CVcvs
 container for one or more controlled vocabulary definitions. More...
 
FileDescription fileDescription
 information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is stored here. More...
 
std::vector< ParamGroupPtrparamGroupPtrs
 container for a list of referenceableParamGroups More...
 
std::vector< SamplePtrsamplePtrs
 list and descriptions of samples. More...
 
std::vector< SoftwarePtrsoftwarePtrs
 list and descriptions of software used to acquire and/or process the data in this mzML file. More...
 
std::vector< ScanSettingsPtrscanSettingsPtrs
 list with the descriptions of the acquisition settings applied prior to the start of data acquisition. More...
 
std::vector< InstrumentConfigurationPtrinstrumentConfigurationPtrs
 list and descriptions of instrument configurations. More...
 
std::vector< DataProcessingPtrdataProcessingPtrs
 list and descriptions of data processing applied to this data. More...
 
Run run
 a run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument. More...
 

Protected Attributes

std::string version_
 
int nFiltersApplied_
 

Private Member Functions

 MSData (const MSData &)
 
MSDataoperator= (const MSData &)
 

Friends

struct IO::HandlerMSData
 

Detailed Description

This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to capture the use of a mass spectrometer, the data generated, and the initial processing of that data (to the level of the peak list).

Definition at line 845 of file MSData.hpp.

Constructor & Destructor Documentation

§ MSData() [1/2]

pwiz::msdata::MSData::MSData ( )

§ ~MSData()

virtual pwiz::msdata::MSData::~MSData ( )
virtual

§ MSData() [2/2]

pwiz::msdata::MSData::MSData ( const MSData )
private

Member Function Documentation

§ allDataProcessingPtrs()

std::vector<DataProcessingPtr> pwiz::msdata::MSData::allDataProcessingPtrs ( ) const

return dataProcessingPtrs augmented by the dataProcessingPtr() set in SpectrumList and/or ChromatogramList

Referenced by testAllDataProcessing(), and testWrap().

§ empty()

bool pwiz::msdata::MSData::empty ( ) const

§ version()

const std::string& pwiz::msdata::MSData::version ( ) const

returns the version of this mzML document; for a document created programmatically, the version is the current release version of mzML; for a document created from a file/stream, the version is the schema version read from the file/stream

Referenced by pwiz::msdata::TextWriter::operator()().

§ filterApplied()

void pwiz::msdata::MSData::filterApplied ( )
inline

Definition at line 894 of file MSData.hpp.

§ countFiltersApplied()

int pwiz::msdata::MSData::countFiltersApplied ( ) const
inline

Definition at line 895 of file MSData.hpp.

895 {return nFiltersApplied_;};

§ operator=()

MSData& pwiz::msdata::MSData::operator= ( const MSData )
private

Friends And Related Function Documentation

§ IO::HandlerMSData

friend struct IO::HandlerMSData
friend

Definition at line 904 of file MSData.hpp.

Member Data Documentation

§ accession

std::string pwiz::msdata::MSData::accession

an optional accession number for the mzML document.

Definition at line 848 of file MSData.hpp.

Referenced by initializeTestData(), pwiz::msdata::TextWriter::operator()(), and testMSData().

§ id

std::string pwiz::msdata::MSData::id

an optional id for the mzML document. It is recommended to use LSIDs when possible.

Definition at line 851 of file MSData.hpp.

Referenced by initializeTestData(), pwiz::msdata::TextWriter::operator()(), test(), testMSData(), and testMSDiffUpdate().

§ cvs

std::vector<CV> pwiz::msdata::MSData::cvs

container for one or more controlled vocabulary definitions.

note: one of the <cv> elements in this list MUST be the PSI MS controlled vocabulary. All <cvParam> elements in the document MUST refer to one of the <cv> elements in this list.

Definition at line 855 of file MSData.hpp.

Referenced by initializeTestData(), pwiz::msdata::TextWriter::operator()(), and testMSData().

§ fileDescription

FileDescription pwiz::msdata::MSData::fileDescription

information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is stored here.

Definition at line 858 of file MSData.hpp.

Referenced by hackInMemoryMSData(), initializeTestData(), initializeTinyMGF(), initializeTinyMS1(), initializeTinyMS2(), pwiz::msdata::TextWriter::operator()(), test(), testMSData(), testRun(), testScanSettings(), testSHA1(), and testSpectrum().

§ paramGroupPtrs

std::vector<ParamGroupPtr> pwiz::msdata::MSData::paramGroupPtrs

§ samplePtrs

std::vector<SamplePtr> pwiz::msdata::MSData::samplePtrs

list and descriptions of samples.

Definition at line 864 of file MSData.hpp.

Referenced by initializeTestData(), pwiz::msdata::TextWriter::operator()(), testMSData(), and testRun().

§ softwarePtrs

std::vector<SoftwarePtr> pwiz::msdata::MSData::softwarePtrs

list and descriptions of software used to acquire and/or process the data in this mzML file.

Definition at line 867 of file MSData.hpp.

Referenced by hackInMemoryMSData(), initializeTestData(), pwiz::msdata::TextWriter::operator()(), test(), testDataProcessing(), testInstrumentConfiguration(), and testMSData().

§ scanSettingsPtrs

std::vector<ScanSettingsPtr> pwiz::msdata::MSData::scanSettingsPtrs

list with the descriptions of the acquisition settings applied prior to the start of data acquisition.

Definition at line 870 of file MSData.hpp.

Referenced by initializeTestData(), pwiz::msdata::TextWriter::operator()(), and testMSData().

§ instrumentConfigurationPtrs

std::vector<InstrumentConfigurationPtr> pwiz::msdata::MSData::instrumentConfigurationPtrs

list and descriptions of instrument configurations.

Definition at line 873 of file MSData.hpp.

Referenced by initializeTestData(), main(), pwiz::msdata::TextWriter::operator()(), test(), testMSData(), testRun(), and testScan().

§ dataProcessingPtrs

std::vector<DataProcessingPtr> pwiz::msdata::MSData::dataProcessingPtrs

list and descriptions of data processing applied to this data.

Definition at line 876 of file MSData.hpp.

Referenced by initializeTestData(), pwiz::msdata::TextWriter::operator()(), test(), testAllDataProcessing(), testBinaryDataArray(), testChromatogram(), testMSData(), and testSpectrum().

§ run

Run pwiz::msdata::MSData::run

§ version_

std::string pwiz::msdata::MSData::version_
protected

Definition at line 903 of file MSData.hpp.

§ nFiltersApplied_

int pwiz::msdata::MSData::nFiltersApplied_
protected

Definition at line 905 of file MSData.hpp.


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