The base class for elements that may contain cvParams, userParams, or paramGroup references. More...

#include <ParamTypes.hpp>

Inheritance diagram for pwiz::data::ParamContainer:

Public Member Functions
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)
bool	empty () const
	returns true iff the element contains no params or param groups
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::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

Detailed Description

The base class for elements that may contain cvParams, userParams, or paramGroup references.

Definition at line 241 of file ParamTypes.hpp.

Member Function Documentation

CVParam pwiz::data::ParamContainer::cvParam ( CVID cvid ) const

finds cvid in the container:

returns first CVParam result such that (result.cvid == cvid);
if not found, returns CVParam(CVID_Unknown)
recursive: looks into paramGroupPtrs

Referenced by EvenMS2Predicate::accept(), checkSpectrumInfo(), MSLevelSorter::less(), testAmbiguousResidue(), testParamContainer(), testPrecursor(), and verifyPrecursorMZ().

CVParam pwiz::data::ParamContainer::cvParamChild ( CVID cvid ) const

finds child of cvid in the container:

returns first CVParam result such that (result.cvid is_a cvid);
if not found, CVParam(CVID_Unknown)
recursive: looks into paramGroupPtrs

Referenced by EvenMS2Predicate::accept(), FTSieve::accept(), doSomething(), and testParamContainer().

std::vector<CVParam> pwiz::data::ParamContainer::cvParamChildren ( CVID cvid ) const

finds all children of cvid in the container:

returns all CVParam results such that (result.cvid is_a cvid);
if not found, empty vector
recursive: looks into paramGroupPtrs

Referenced by testParamContainer().

bool pwiz::data::ParamContainer::hasCVParam ( CVID cvid ) const

returns true iff cvParams contains exact cvid (recursive)

Referenced by test(), testEnzyme(), testFilter(), testMeasure(), testParamContainer(), testPeptideEvidence(), testProteinAmbiguityGroup(), testProteinDetectionHypothesis(), testProteinDetectionList(), testSample(), testSearchDatabase(), and testSourceFile().

bool pwiz::data::ParamContainer::hasCVParamChild ( CVID cvid ) const

returns true iff cvParams contains a child (is_a) of cvid (recursive)

Referenced by testParamContainer().

UserParam pwiz::data::ParamContainer::userParam ( const std::string & ) const

finds UserParam with specified name

returns UserParam() if name not found
not recursive: looks only at local userParams

Referenced by testMaxPrecisionDiff(), and testParamContainer().

void pwiz::data::ParamContainer::set	(	CVID	cvid,
		const std::string &	value = `""`,
		CVID	units = `CVID_Unknown`
	)

set/add a CVParam (not recursive)

Referenced by initializeTestData(), initializeTinyMGF(), initializeTinyMS1(), initializeTinyMS2(), testAmbiguousResidue(), testAnalysisSoftware(), testCleavageAgent(), testContact(), testDBSequence(), testEnzyme(), testEvidence(), testFilter(), testIdentifiableParamContainer(), testInstrumentConfiguration(), testMeasure(), testModification(), testOrganization(), testParamContainer(), testPeptide(), testPeptideEvidence(), testPepXMLSpecificity(), testPerson(), testPrecursor(), testProduct(), testProteinAmbiguityGroup(), testProteinDetectionHypothesis(), testProteinDetectionList(), testProteinDetectionProtocol(), testRetentionTime(), testSample(), testScanList(), testScanSettings(), testSearchDatabase(), testSearchModification(), testSoftware(), testSourceFile(), testSpectrum(), testSpectrumIdentificationItem(), testSpectrumIdentificationProtocol(), testSpectrumIdentificationResult(), testTarget(), testTraData(), testTransition(), and testValidation().

void pwiz::data::ParamContainer::set	(	CVID	cvid,
		double	value,
		CVID	units = `CVID_Unknown`
	)

set/add a CVParam (not recursive)

void pwiz::data::ParamContainer::set	(	CVID	cvid,
		int	value,
		CVID	units = `CVID_Unknown`
	)

set/add a CVParam (not recursive)

template<typename value_type >

void pwiz::data::ParamContainer::set	(	CVID	cvid,
		value_type	value,
		CVID	units = `CVID_Unknown`
	)

inline

set/add a CVParam (not recursive)

Definition at line 292 of file ParamTypes.hpp.

References boost::lexical_cast(), and pwiz::msdata::id::value().

    {
        set(cvid, boost::lexical_cast<std::string>(value), units);
    }

bool pwiz::data::ParamContainer::empty ( ) const

returns true iff the element contains no params or param groups

Reimplemented in pwiz::identdata::SourceFile, pwiz::identdata::ProteinDetectionList, pwiz::identdata::ProteinAmbiguityGroup, pwiz::identdata::ProteinDetectionHypothesis, pwiz::msdata::Run, pwiz::identdata::SpectrumIdentificationResult, pwiz::identdata::SpectrumIdentificationItem, pwiz::identdata::PeptideEvidence, pwiz::msdata::Chromatogram, pwiz::identdata::Measure, pwiz::msdata::Spectrum, pwiz::identdata::AmbiguousResidue, pwiz::msdata::BinaryDataArray, pwiz::identdata::SearchModification, pwiz::msdata::ScanList, pwiz::msdata::Scan, pwiz::identdata::Peptide, pwiz::tradata::TargetList, pwiz::msdata::Precursor, pwiz::identdata::Modification, pwiz::data::ParamGroup, pwiz::tradata::Target, pwiz::identdata::DBSequence, pwiz::tradata::Transition, pwiz::identdata::SearchDatabase, pwiz::tradata::Product, pwiz::msdata::ProcessingMethod, pwiz::tradata::Precursor, pwiz::tradata::Compound, pwiz::msdata::InstrumentConfiguration, pwiz::tradata::Peptide, pwiz::tradata::Modification, pwiz::identdata::Sample, pwiz::msdata::Software, pwiz::tradata::Protein, pwiz::tradata::Interpretation, pwiz::identdata::Person, pwiz::tradata::Configuration, pwiz::msdata::Component, pwiz::identdata::Organization, pwiz::tradata::Instrument, pwiz::tradata::Validation, pwiz::identdata::Contact, pwiz::tradata::Evidence, pwiz::msdata::Sample, pwiz::tradata::Prediction, pwiz::tradata::RetentionTime, pwiz::identdata::IdentifiableParamContainer, pwiz::tradata::Software, pwiz::msdata::SourceFile, pwiz::tradata::Publication, and pwiz::tradata::Contact.

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

void pwiz::data::ParamContainer::clear ( )

clears the collections

Referenced by stripUnmappedMetadata(), testFilter(), and testPepXMLSpecificity().

bool pwiz::data::ParamContainer::operator== ( const ParamContainer & that ) const

returns true iff this and that have the exact same cvParams and userParams

recursive: looks into paramGroupPtrs

bool pwiz::data::ParamContainer::operator!= ( const ParamContainer & that ) const

returns !(this==that)

template<>

void pwiz::data::ParamContainer::set	(	CVID	cvid,
		bool	value,
		CVID	units
	)

inline

special case for bool (outside the class for gcc 3.4, and inline for msvc)

Definition at line 314 of file ParamTypes.hpp.

References pwiz::msdata::id::value().

{
    set(cvid, (value ? "true" : "false"), units);
}

Member Data Documentation

std::vector<ParamGroupPtr> pwiz::data::ParamContainer::paramGroupPtrs

a collection of references to ParamGroups

Definition at line 244 of file ParamTypes.hpp.

Referenced by initializeTestData(), pwiz::msdata::TextWriter::operator()(), spectrumHasMetadata(), testBinaryDataArray(), testChromatogram(), testComponent(), testComponentList(), testFileDescription(), testInstrumentConfiguration(), testMSData(), testParamContainer(), testParamGroup(), testPrecursor(), testProduct(), testRun(), testSample(), testScan(), testScanList(), testSourceFile(), and testSpectrum().

std::vector<CVParam> pwiz::data::ParamContainer::cvParams

a collection of controlled vocabulary terms

Definition at line 247 of file ParamTypes.hpp.

Referenced by checkSpectrumInfo(), initializeTestData(), pwiz::tradata::TextWriter::operator()(), pwiz::identdata::TextWriter::operator()(), pwiz::msdata::TextWriter::operator()(), spectrumHasMetadata(), test_v3(), testAnalyzer(), testChromatogram(), testComponent(), testCompound(), testConfiguration(), testContact(), testDataProcessing(), testDetector(), testEnzyme(), testEvidence(), testFileDescription(), testInstrument(), testInstrumentConfiguration(), testIonisation(), testMeasure(), testModelAndManufacturer(), testMSData(), testParamContainer(), testParamGroup(), testPeptideEvidence(), testPrecursor(), testPrediction(), testProcessingMethod(), testProduct(), testProteinAmbiguityGroup(), testProteinDetectionHypothesis(), testProteinDetectionList(), testRetentionTime(), testSample(), testScan(), testScanList(), testSearchDatabase(), testSearchModification(), testSourceFile(), testSpectrum(), and testValidation().

std::vector<UserParam> pwiz::data::ParamContainer::userParams

a collection of uncontrolled user terms

Definition at line 250 of file ParamTypes.hpp.

Referenced by initializeTestData(), pwiz::tradata::TextWriter::operator()(), pwiz::identdata::TextWriter::operator()(), pwiz::msdata::TextWriter::operator()(), spectrumHasMetadata(), testAnalyzer(), testCleavageAgent(), testComponent(), testCompound(), testConfiguration(), testContact(), testDataProcessing(), testDetector(), testEvidence(), testFileContent(), testFileDescription(), testIdentifiableParamContainer(), testInstrument(), testIonisation(), testMaxPrecisionDiff(), testModelAndManufacturer(), testParamContainer(), testParamGroup(), testPepXMLSpecificity(), testPrecursor(), testPrediction(), testProcessingMethod(), testRetentionTime(), testSample(), testScanSettings(), testSearchDatabase(), testSource(), testSourceFile(), and testValidation().

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

/Users/parag/_Research/pwiz/svn/trunk/pwiz/pwiz/data/common/ParamTypes.hpp

Public Member Functions

Public Attributes

Detailed Description

Member Function Documentation

Member Data Documentation