A run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument. More...

#include <MSData.hpp>

Inheritance diagram for pwiz::msdata::Run:

Public Member Functions
	Run ()
bool	empty () const
	returns true iff the element contains no params or param groups
Public Member Functions inherited from pwiz::data::ParamContainer
CVParam	cvParam (CVID cvid) const
	finds cvid in the container:
CVParam	cvParamChild (CVID cvid) const
	finds child of cvid in the container:
std::vector< CVParam >	cvParamChildren (CVID cvid) const
	finds all children of cvid in the container:
bool	hasCVParam (CVID cvid) const
	returns true iff cvParams contains exact cvid (recursive)
bool	hasCVParamChild (CVID cvid) const
	returns true iff cvParams contains a child (is_a) of cvid (recursive)
UserParam	userParam (const std::string &) const
	finds UserParam with specified name
void	set (CVID cvid, const std::string &value="", CVID units=CVID_Unknown)
	set/add a CVParam (not recursive)
void	set (CVID cvid, double value, CVID units=CVID_Unknown)
	set/add a CVParam (not recursive)
void	set (CVID cvid, int value, CVID units=CVID_Unknown)
	set/add a CVParam (not recursive)
template<typename value_type >
void	set (CVID cvid, value_type value, CVID units=CVID_Unknown)
	set/add a CVParam (not recursive)
void	clear ()
	clears the collections
bool	operator== (const ParamContainer &that) const
	returns true iff this and that have the exact same cvParams and userParams
bool	operator!= (const ParamContainer &that) const
	returns !(this==that)
template<>
void	set (CVID cvid, bool value, CVID units)
	special case for bool (outside the class for gcc 3.4, and inline for msvc)

Public Attributes
std::string	id
	a unique identifier for this run.
InstrumentConfigurationPtr	defaultInstrumentConfigurationPtr
	this attribute MUST reference the 'id' of the default instrument configuration. If a scan does not reference an instrument configuration, it implicitly refers to this configuration.
SamplePtr	samplePtr
	this attribute MUST reference the 'id' of the appropriate sample.
std::string	startTimeStamp
	the optional start timestamp of the run, in UT.
SourceFilePtr	defaultSourceFilePtr
	default source file reference
SpectrumListPtr	spectrumListPtr
	all mass spectra and the acquisitions underlying them are described and attached here. Subsidiary data arrays are also both described and attached here.
ChromatogramListPtr	chromatogramListPtr
	all chromatograms for this run.
Public Attributes inherited from pwiz::data::ParamContainer
std::vector< ParamGroupPtr >	paramGroupPtrs
	a collection of references to ParamGroups
std::vector< CVParam >	cvParams
	a collection of controlled vocabulary terms
std::vector< UserParam >	userParams
	a collection of uncontrolled user terms

Private Member Functions
	Run (const Run &)
Run &	operator= (const Run &)

Detailed Description

A run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument.

Definition at line 803 of file MSData.hpp.

Constructor & Destructor Documentation

pwiz::msdata::Run::Run ( )

inline

Definition at line 826 of file MSData.hpp.

{}

pwiz::msdata::Run::Run ( const Run & )

private

Member Function Documentation

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

returns true iff the element contains no params or param groups

Reimplemented from pwiz::data::ParamContainer.

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

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

private

Member Data Documentation

std::string pwiz::msdata::Run::id

a unique identifier for this run.

Definition at line 806 of file MSData.hpp.

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

InstrumentConfigurationPtr pwiz::msdata::Run::defaultInstrumentConfigurationPtr

this attribute MUST reference the 'id' of the default instrument configuration. If a scan does not reference an instrument configuration, it implicitly refers to this configuration.

Definition at line 809 of file MSData.hpp.

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

SamplePtr pwiz::msdata::Run::samplePtr

this attribute MUST reference the 'id' of the appropriate sample.

Definition at line 812 of file MSData.hpp.

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

std::string pwiz::msdata::Run::startTimeStamp

the optional start timestamp of the run, in UT.

Definition at line 815 of file MSData.hpp.

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

SourceFilePtr pwiz::msdata::Run::defaultSourceFilePtr

default source file reference

Definition at line 818 of file MSData.hpp.

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

SpectrumListPtr pwiz::msdata::Run::spectrumListPtr

all mass spectra and the acquisitions underlying them are described and attached here. Subsidiary data arrays are also both described and attached here.

Definition at line 821 of file MSData.hpp.

Referenced by hackInMemoryMSData(), initialize(), initializeTestData(), initializeTinyMGF(), initializeTinyMS1(), initializeTinyMS2(), pwiz::msdata::TextWriter::operator()(), test(), test5peptideFT(), testAllDataProcessing(), testAutomaticUpdate(), testBinaryDataOnly(), testBombesin(), testDefault(), testFileReads(), testHasBinaryData(), testMaxPrecisionDiff(), testModeBinaryDataOnly(), testModeMetaDataAndBinaryData(), testModeMetaDataOnly(), testMRU(), testMSData(), testMSDataConstruction(), testMSDiffUpdate(), testPrecursorRefine(), testRun(), testSpectrumListSimple(), testUpdateRequest(), testWrap(), testWrapActivation(), testWrapDefaultArrayLength(), testWrapMassAnalyzer(), testWrapMSLevel(), testWrapMZWindow(), testWrapPolarity(), testWrapScanTimeRange(), testWrapSortScanTime(), testWrapTitleMaker(), testWriteRead(), and validateWriteRead().

ChromatogramListPtr pwiz::msdata::Run::chromatogramListPtr

all chromatograms for this run.

Definition at line 824 of file MSData.hpp.

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

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

/Users/parag/_Research/pwiz/svn/trunk/pwiz/pwiz/data/msdata/MSData.hpp

Public Member Functions

Public Attributes

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation