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:

List of all members.

Public Member Functions
std::vector< DataProcessingPtr >	allDataProcessingPtrs () const
	return dataProcessingPtrs augmented by the dataProcessingPtr() set in SpectrumList and/or ChromatogramList
	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

Public Attributes
std::string	accession
	an optional accession number for the mzML document.
std::string	id
	an optional id for the mzML document. It is recommended to use LSIDs when possible.
std::vector< CV >	cvs
	container for one or more controlled vocabulary definitions.
FileDescription	fileDescription
	information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is stored here.
std::vector< ParamGroupPtr >	paramGroupPtrs
	container for a list of referenceableParamGroups
std::vector< SamplePtr >	samplePtrs
	list and descriptions of samples.
std::vector< SoftwarePtr >	softwarePtrs
	list and descriptions of software used to acquire and/or process the data in this mzML file.
std::vector< ScanSettingsPtr >	scanSettingsPtrs
	list with the descriptions of the acquisition settings applied prior to the start of data acquisition.
std::vector < InstrumentConfigurationPtr >	instrumentConfigurationPtrs
	list and descriptions of instrument configurations.
std::vector< DataProcessingPtr >	dataProcessingPtrs
	list and descriptions of data processing applied to this data.
Run	run
	a run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument.

Protected Attributes
std::string	version_

Private Member Functions
	MSData (const MSData &)
MSData &	operator= (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 843 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()().

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

private

Friends And Related Function Documentation

friend struct IO::HandlerMSData

friend

Definition at line 898 of file MSData.hpp.

Member Data Documentation

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

an optional accession number for the mzML document.

Definition at line 846 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 849 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 853 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 856 of file MSData.hpp.

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