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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
< InstrumentConfigurationPtr
instrumentConfigurationPtrs
 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 850 of file MSData.hpp.

Constructor & Destructor Documentation

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

Member Function Documentation

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().

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

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

Definition at line 899 of file MSData.hpp.

899 {nFiltersApplied_++;};
int pwiz::msdata::MSData::countFiltersApplied ( ) const
inline

Definition at line 900 of file MSData.hpp.

900 {return nFiltersApplied_;};
MSData& pwiz::msdata::MSData::operator= ( const MSData )
private

Friends And Related Function Documentation

friend struct IO::HandlerMSData
friend

Definition at line 909 of file MSData.hpp.

Member Data Documentation

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

an optional accession number for the mzML document.

Definition at line 853 of file MSData.hpp.

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

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

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

Definition at line 856 of file MSData.hpp.

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

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 860 of file MSData.hpp.

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

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 863 of file MSData.hpp.

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

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

list and descriptions of samples.

Definition at line 869 of file MSData.hpp.

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

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 872 of file MSData.hpp.

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

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 875 of file MSData.hpp.

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

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

list and descriptions of instrument configurations.

Definition at line 878 of file MSData.hpp.

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

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

list and descriptions of data processing applied to this data.

Definition at line 881 of file MSData.hpp.

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

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

Definition at line 908 of file MSData.hpp.

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

Definition at line 910 of file MSData.hpp.


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