Namespaces
namespace	examples
namespace	IO
namespace	References
	functions for resolving references from objects into the internal MSData lists

Classes
class	DefaultReaderList
	default Reader list More...
class	DelimReader
class	DelimWriter
struct	DiffConfig
struct	Identifiable
	Parent class representing extensions of the IdentifiableType from the mzIdentML schema. More...
struct	IdentifiableParamContainer
	Parent class of all Identifiable objects that have ParamGroups. More...
struct	BibliographicReference
	Implementation for the BibliographicReferenceType tag in the mzIdentML schema. More...
struct	Contact
	Implementation of ContactType from mzIdentML. More...
struct	Organization
	Implementation of AbstractOrganizationType from the mzIdentML schema. More...
struct	Person
	Implementation of PersonType from the mzIdentML schema. More...
struct	ContactRole
	Implementation of ContactRoleType from the mzIdentML schema. More...
struct	Sample
	Implementation of the SampleType from the mzIdentML schema. More...
struct	AnalysisSoftware
	Implementation of AnalysisSoftwareType from the mzIdentML schema. More...
struct	Provider
	Implementation of ProviderType from the mzIdentML schema. More...
struct	AnalysisSampleCollection
	Implementation of AnalysisSampleCollectionType from mzIdentML schema. More...
struct	SearchDatabase
	Implementation of SearchDatabaseType from the mzIdentML schema. More...
struct	DBSequence
	Implementation of DBSequenceType from the mzIdentML schema. More...
struct	Modification
	Implementation of ModificationType from the mzIdentML schema. More...
struct	SubstitutionModification
	Implementation of SubstitutionModificationType from the mzIdentML schema. More...
struct	Peptide
	Implementation of PeptideType from the mzIdentML schema. More...
struct	SearchModification
	Implementation of SearchModificationType from the mzIdentML schema. More...
struct	Enzyme
	Implementation of EnzymeType from the mzIdentML schema. More...
struct	Enzymes
	Implementation of EnzymesType from the mzIdentML schema. More...
struct	Residue
	Implementation of ResidueType from the mzIdentML schema. More...
struct	AmbiguousResidue
	Implementation of AmbiguousResidueType from the mzIdentML schema. More...
struct	MassTable
	Implementation of MassTableType from the mzIdentML schema. More...
struct	Filter
	Implementation of FilterType from the mzIdentML schema. More...
struct	TranslationTable
	Implementation of TranslationTableType from the mzIdentML schema. More...
struct	DatabaseTranslation
	Implementation of DatabaseTranslationType from the mzIdentML schema. More...
struct	SpectrumIdentificationProtocol
	Implementation of SpectrumIdentificationProtocolType from the mzIdentML schema. More...
struct	Measure
	Implementation of MeasureType from the mzIdentML schema. More...
struct	FragmentArray
	Implementation of FragmentArrayType from the mzIdentML schema. More...
struct	IonType
	Implementation of IonTypeType from the mzIdentML schema. More...
struct	PeptideEvidence
	Implementation of PeptideEvidenceType from the mzIdentML schema. More...
struct	SequenceCollection
	Implementation of SequenceCollectionType from the mzIdentML schema. More...
struct	SpectrumIdentificationItem
	Implementation of SpectrumIdentificationItemType from the mzIdentML schema. More...
struct	SpectraData
	Implementation of SpectraDataType from the mzIdentML schema. More...
struct	SpectrumIdentificationResult
	Implementation of SpectrumIdentificationResultType from the mzIdentML schema. More...
struct	SpectrumIdentificationList
	Implementation of SpectrumIdentificationListType from the mzIdentML schema. More...
struct	SpectrumIdentification
	Implementation of SpectrumIdentificationType from the mzIdentML schema. More...
struct	ProteinDetectionProtocol
	Implementation of ProteinDetectionProtocolType from the mzIdentML schema. More...
struct	PeptideHypothesis
	Implementation of PeptideHypothesisType from the mzIdentML schema. More...
struct	ProteinDetectionHypothesis
	Implementation of ProteinDetectionHypothesisType from the mzIdentML schema. More...
struct	ProteinAmbiguityGroup
	Implementation of ProteinAmbiguityGroupType from the mzIdentML schema. More...
struct	ProteinDetectionList
	Implementation of ProteinDetectionListType from the mzIdentML schema. More...
struct	ProteinDetection
	Implementation of ProteinDetectionType from the mzIdentML schema. More...
struct	AnalysisCollection
	Implementation of AnalysisCollectionType from the mzIdentML schema. More...
struct	AnalysisProtocolCollection
	Implementation of AnalysisProtocolCollectionType from the mzIdentML schema. More...
struct	SourceFile
	Implementation of SourceFileType from the mzIdentML schema. More...
struct	Inputs
	Implementation of the InputsType from the mzIdentML schema. More...
struct	AnalysisData
	Implementation of AnalysisDataType from the mzIdentML schema. More...
struct	DataCollection
	Implementation of DataCollectionType from the mzIdentML schema. More...
struct	IdentData
	Implementation of the MzIdentMLType from the mzIdentML schema. More...
struct	IdentDataFile
	IdentData object plus file I/O. More...
struct	CVMap
struct	RegexCVMap
struct	StringMatchCVMap
struct	CVIDMatchCVMap
class	MascotReader
struct	id_p
struct	software_p
struct	sequence_p
struct	seq_p
struct	dbsequence_p
struct	organization_p
struct	person_p
class	Pep2MzIdent
	Translates data from a MinimumPepXML object into a IdentData object tree when a translation is known. More...
class	Reader
	interface for file readers More...
class	ReaderFail
class	ReaderList
	Reader container (composite pattern). More...
class	Serializer_mzIdentML
	MZIDData <-> mzIdentML stream serialization. More...
class	Serializer_pepXML
	MZIDData <-> pepXML stream serialization. More...
struct	PepXMLSpecificity
class	Serializer_protXML
	MZIDData <-> pepXML stream serialization. More...
class	Serializer_Text
	Serializer_Text reads in and writes out an id file in tab format. More...
class	TextWriter
struct	Version

Typedefs
typedef boost::shared_ptr< CVMap >	CVMapPtr
typedef boost::shared_ptr < RegexCVMap >	RegexCVMapPtr
typedef boost::shared_ptr < IdentData >	IdentDataPtr
typedef boost::shared_ptr< Reader >	ReaderPtr

Enumerations
enum	SchemaVersion { SchemaVersion_1_1 = 0, SchemaVersion_1_0 }

Functions
PWIZ_API_DECL std::ostream &	operator<< (std::ostream &os, const data::Diff< IdentData, DiffConfig > &diff)
PWIZ_API_DECL std::vector< CV >	defaultCVList ()
	returns a default list of CVs used in an IdentData document; currently includes PSI-MS, Unit Ontology, and UNIMOD
	TYPEDEF_SHARED_PTR (BibliographicReference)
	TYPEDEF_SHARED_PTR (Contact)
	TYPEDEF_SHARED_PTR (Organization)
	TYPEDEF_SHARED_PTR (Person)
	TYPEDEF_SHARED_PTR (ContactRole)
	TYPEDEF_SHARED_PTR (Sample)
	TYPEDEF_SHARED_PTR (AnalysisSoftware)
	TYPEDEF_SHARED_PTR (Provider)
	TYPEDEF_SHARED_PTR (SearchDatabase)
	TYPEDEF_SHARED_PTR (DBSequence)
	TYPEDEF_SHARED_PTR (Modification)
	TYPEDEF_SHARED_PTR (SubstitutionModification)
	TYPEDEF_SHARED_PTR (Peptide)
	TYPEDEF_SHARED_PTR (SearchModification)
	TYPEDEF_SHARED_PTR (Enzyme)
	TYPEDEF_SHARED_PTR (Residue)
	TYPEDEF_SHARED_PTR (AmbiguousResidue)
	TYPEDEF_SHARED_PTR (MassTable)
	TYPEDEF_SHARED_PTR (Filter)
	TYPEDEF_SHARED_PTR (TranslationTable)
	TYPEDEF_SHARED_PTR (DatabaseTranslation)
	TYPEDEF_SHARED_PTR (SpectrumIdentificationProtocol)
	TYPEDEF_SHARED_PTR (Measure)
	TYPEDEF_SHARED_PTR (FragmentArray)
	TYPEDEF_SHARED_PTR (IonType)
	TYPEDEF_SHARED_PTR (PeptideEvidence)
	TYPEDEF_SHARED_PTR (SpectrumIdentificationItem)
	TYPEDEF_SHARED_PTR (SpectraData)
	TYPEDEF_SHARED_PTR (SpectrumIdentificationResult)
	TYPEDEF_SHARED_PTR (SpectrumIdentificationList)
	TYPEDEF_SHARED_PTR (SpectrumIdentification)
	TYPEDEF_SHARED_PTR (ProteinDetectionProtocol)
	TYPEDEF_SHARED_PTR (ProteinDetectionHypothesis)
	TYPEDEF_SHARED_PTR (ProteinAmbiguityGroup)
	TYPEDEF_SHARED_PTR (ProteinDetectionList)
	TYPEDEF_SHARED_PTR (ProteinDetection)
	TYPEDEF_SHARED_PTR (AnalysisProtocolCollection)
	TYPEDEF_SHARED_PTR (SourceFile)
	TYPEDEF_SHARED_PTR (Inputs)
	TYPEDEF_SHARED_PTR (AnalysisData)
	TYPEDEF_SHARED_PTR (DataCollection)
	TYPEDEF_SHARED_PTR (IdentData)
PWIZ_API_DECL proteome::DigestedPeptide	digestedPeptide (const SpectrumIdentificationProtocol &sip, const PeptideEvidence &peptideEvidence)
	given a protocol and a PeptideEvidence instance, returns the PeptideEvidence as a DigestedPeptide instance
PWIZ_API_DECL std::vector < proteome::DigestedPeptide >	digestedPeptides (const SpectrumIdentificationProtocol &sip, const SpectrumIdentificationItem &sii)
	given a protocol and a SpectrumIdentificationItem, builds a set of DigestedPeptides
PWIZ_API_DECL proteome::Peptide	peptide (const Peptide &peptide)
	creates a proteome::Peptide from an identdata::Peptide
PWIZ_API_DECL proteome::Modification	modification (const Modification &mod)
	creates a proteome::Modification from an identdata::Modification
PWIZ_API_DECL CVID	cleavageAgent (const Enzyme &ez)
	returns a cleavage agent CVID for an identdata::Enzyme
PWIZ_API_DECL std::vector< CVID >	cleavageAgents (const Enzymes &enzymes)
	returns a list of cleavage agent CVIDs for an identdata::Enzymes instance
PWIZ_API_DECL boost::regex	cleavageAgentRegex (const Enzyme &ez)
	returns a regular expression for an identdata::Enzyme
PWIZ_API_DECL std::vector < boost::regex >	cleavageAgentRegexes (const Enzymes &enzymes)
	returns a list of regular expressions for an identdata::Enzymes instance
PWIZ_API_DECL void	snapModificationsToUnimod (const SpectrumIdentification &si)
	sets Unimod CV terms (if possible) for all SearchModifications and Modification elements
PWIZ_API_DECL std::ostream &	operator<< (std::ostream &os, IdentDataFile::Format format)
PWIZ_API_DECL std::ostream &	operator<< (std::ostream &os, const IdentDataFile::WriteConfig &config)
PWIZ_API_DECL std::ostream &	operator<< (std::ostream &os, const CVMap &cm)
PWIZ_API_DECL std::ostream &	operator<< (std::ostream &os, const CVMapPtr cmp)
PWIZ_API_DECL std::ostream &	operator<< (std::ostream &os, const CVMap *cmp)
PWIZ_API_DECL std::istream &	operator>> (std::istream &is, CVMapPtr &cm)
PWIZ_API_DECL std::ostream &	operator<< (std::ostream &os, const std::vector< CVMapPtr > &cmVec)
PWIZ_API_DECL std::istream &	operator>> (std::istream &is, std::vector< CVMapPtr > &cmVec)
PWIZ_API_DECL ReaderList	operator+ (const ReaderPtr &lhs, const ReaderPtr &rhs)
	returns a list containing the lhs and rhs as readers
PWIZ_API_DECL PepXMLSpecificity	pepXMLSpecificity (const Enzyme &ez)
	converts an identdata::Enzyme into a pepXML cut/no_cut/sense tuple
PWIZ_API_DECL std::string	stripChargeFromConventionalSpectrumId (const std::string &id)
	strips charge state from known conventions of the pepXML spectrum attribute; used to find a unique identifier for a spectrum in order to merge charge states

Typedef Documentation

typedef boost::shared_ptr<CVMap> pwiz::identdata::CVMapPtr

Definition at line 56 of file KwCVMap.hpp.

typedef boost::shared_ptr<RegexCVMap> pwiz::identdata::RegexCVMapPtr

Definition at line 79 of file KwCVMap.hpp.

typedef boost::shared_ptr<IdentData> pwiz::identdata::IdentDataPtr

Definition at line 38 of file Pep2MzIdent.hpp.

typedef boost::shared_ptr< Reader > pwiz::identdata::ReaderPtr

Definition at line 108 of file Reader.hpp.

Enumeration Type Documentation

enum pwiz::identdata::SchemaVersion

Enumerator:

SchemaVersion_1_1
SchemaVersion_1_0

Definition at line 35 of file IO.hpp.

{ SchemaVersion_1_1 = 0, SchemaVersion_1_0 }; // 0 is the default

Function Documentation

PWIZ_API_DECL std::ostream& pwiz::identdata::operator<<	(	std::ostream &	os,
		const data::Diff< IdentData, DiffConfig > &	diff
	)

PWIZ_API_DECL std::vector<CV> pwiz::identdata::defaultCVList ( )

returns a default list of CVs used in an IdentData document; currently includes PSI-MS, Unit Ontology, and UNIMOD

pwiz::identdata::TYPEDEF_SHARED_PTR ( BibliographicReference )

pwiz::identdata::TYPEDEF_SHARED_PTR ( Contact )

pwiz::identdata::TYPEDEF_SHARED_PTR ( Organization )

pwiz::identdata::TYPEDEF_SHARED_PTR ( Person )

pwiz::identdata::TYPEDEF_SHARED_PTR ( ContactRole )

pwiz::identdata::TYPEDEF_SHARED_PTR ( Sample )

pwiz::identdata::TYPEDEF_SHARED_PTR ( AnalysisSoftware )

pwiz::identdata::TYPEDEF_SHARED_PTR ( Provider )

pwiz::identdata::TYPEDEF_SHARED_PTR ( SearchDatabase )

pwiz::identdata::TYPEDEF_SHARED_PTR ( DBSequence )

pwiz::identdata::TYPEDEF_SHARED_PTR ( Modification )

pwiz::identdata::TYPEDEF_SHARED_PTR ( SubstitutionModification )

pwiz::identdata::TYPEDEF_SHARED_PTR ( Peptide )

pwiz::identdata::TYPEDEF_SHARED_PTR ( SearchModification )

pwiz::identdata::TYPEDEF_SHARED_PTR ( Enzyme )

pwiz::identdata::TYPEDEF_SHARED_PTR ( Residue )

pwiz::identdata::TYPEDEF_SHARED_PTR ( AmbiguousResidue )

pwiz::identdata::TYPEDEF_SHARED_PTR ( MassTable )

pwiz::identdata::TYPEDEF_SHARED_PTR ( Filter )

pwiz::identdata::TYPEDEF_SHARED_PTR ( TranslationTable )

pwiz::identdata::TYPEDEF_SHARED_PTR ( DatabaseTranslation )

pwiz::identdata::TYPEDEF_SHARED_PTR ( SpectrumIdentificationProtocol )

pwiz::identdata::TYPEDEF_SHARED_PTR ( Measure )

pwiz::identdata::TYPEDEF_SHARED_PTR ( FragmentArray )

pwiz::identdata::TYPEDEF_SHARED_PTR ( IonType )

pwiz::identdata::TYPEDEF_SHARED_PTR ( PeptideEvidence )

pwiz::identdata::TYPEDEF_SHARED_PTR ( SpectrumIdentificationItem )

pwiz::identdata::TYPEDEF_SHARED_PTR ( SpectraData )

pwiz::identdata::TYPEDEF_SHARED_PTR ( SpectrumIdentificationResult )

pwiz::identdata::TYPEDEF_SHARED_PTR ( SpectrumIdentificationList )

pwiz::identdata::TYPEDEF_SHARED_PTR ( SpectrumIdentification )

pwiz::identdata::TYPEDEF_SHARED_PTR ( ProteinDetectionProtocol )

pwiz::identdata::TYPEDEF_SHARED_PTR ( ProteinDetectionHypothesis )

pwiz::identdata::TYPEDEF_SHARED_PTR ( ProteinAmbiguityGroup )

pwiz::identdata::TYPEDEF_SHARED_PTR ( ProteinDetectionList )

pwiz::identdata::TYPEDEF_SHARED_PTR ( ProteinDetection )

pwiz::identdata::TYPEDEF_SHARED_PTR ( AnalysisProtocolCollection )

pwiz::identdata::TYPEDEF_SHARED_PTR ( SourceFile )

pwiz::identdata::TYPEDEF_SHARED_PTR ( Inputs )

pwiz::identdata::TYPEDEF_SHARED_PTR ( AnalysisData )

pwiz::identdata::TYPEDEF_SHARED_PTR ( DataCollection )

pwiz::identdata::TYPEDEF_SHARED_PTR ( IdentData )

PWIZ_API_DECL proteome::DigestedPeptide pwiz::identdata::digestedPeptide	(	const SpectrumIdentificationProtocol &	sip,
		const PeptideEvidence &	peptideEvidence
	)

given a protocol and a PeptideEvidence instance, returns the PeptideEvidence as a DigestedPeptide instance

Referenced by testDigestedPeptides().

PWIZ_API_DECL std::vector<proteome::DigestedPeptide> pwiz::identdata::digestedPeptides	(	const SpectrumIdentificationProtocol &	sip,
		const SpectrumIdentificationItem &	sii
	)

given a protocol and a SpectrumIdentificationItem, builds a set of DigestedPeptides

Referenced by testDigestedPeptides().

PWIZ_API_DECL proteome::Peptide pwiz::identdata::peptide ( const Peptide & peptide )

creates a proteome::Peptide from an identdata::Peptide

Referenced by fragmentTest(), modificationTest(), pwiz::tradata::TextWriter::operator()(), peptideTest(), stripUnmappedMetadata(), testConversion(), testNontrypticBSA(), testSemitrypticBSA(), testSemitrypticMethionineClippingBSA(), and testTrypticBSA().

PWIZ_API_DECL proteome::Modification pwiz::identdata::modification ( const Modification & mod )

creates a proteome::Modification from an identdata::Modification

PWIZ_API_DECL CVID pwiz::identdata::cleavageAgent ( const Enzyme & ez )

returns a cleavage agent CVID for an identdata::Enzyme

Referenced by testCleavageAgent(), and testPepXMLSpecificity().

PWIZ_API_DECL std::vector<CVID> pwiz::identdata::cleavageAgents ( const Enzymes & enzymes )

returns a list of cleavage agent CVIDs for an identdata::Enzymes instance

Referenced by testCleavageAgents().

PWIZ_API_DECL boost::regex pwiz::identdata::cleavageAgentRegex ( const Enzyme & ez )

returns a regular expression for an identdata::Enzyme

PWIZ_API_DECL std::vector<boost::regex> pwiz::identdata::cleavageAgentRegexes ( const Enzymes & enzymes )

returns a list of regular expressions for an identdata::Enzymes instance

PWIZ_API_DECL void pwiz::identdata::snapModificationsToUnimod ( const SpectrumIdentification & si )

sets Unimod CV terms (if possible) for all SearchModifications and Modification elements

Referenced by testSnapModifications().

PWIZ_API_DECL std::ostream& pwiz::identdata::operator<<	(	std::ostream &	os,
		IdentDataFile::Format	format
	)

PWIZ_API_DECL std::ostream& pwiz::identdata::operator<<	(	std::ostream &	os,
		const IdentDataFile::WriteConfig &	config
	)

PWIZ_API_DECL std::ostream& pwiz::identdata::operator<<	(	std::ostream &	os,
		const CVMap &	cm
	)

PWIZ_API_DECL std::ostream& pwiz::identdata::operator<<	(	std::ostream &	os,
		const CVMapPtr	cmp
	)

PWIZ_API_DECL std::ostream& pwiz::identdata::operator<<	(	std::ostream &	os,
		const CVMap *	cmp
	)

PWIZ_API_DECL std::istream& pwiz::identdata::operator>>	(	std::istream &	is,
		CVMapPtr &	cm
	)

PWIZ_API_DECL std::ostream& pwiz::identdata::operator<<	(	std::ostream &	os,
		const std::vector< CVMapPtr > &	cmVec
	)

PWIZ_API_DECL std::istream& pwiz::identdata::operator>>	(	std::istream &	is,
		std::vector< CVMapPtr > &	cmVec
	)

PWIZ_API_DECL ReaderList pwiz::identdata::operator+	(	const ReaderPtr &	lhs,
		const ReaderPtr &	rhs
	)

returns a list containing the lhs and rhs as readers

PWIZ_API_DECL PepXMLSpecificity pwiz::identdata::pepXMLSpecificity ( const Enzyme & ez )

converts an identdata::Enzyme into a pepXML cut/no_cut/sense tuple

Referenced by testPepXMLSpecificity().

PWIZ_API_DECL std::string pwiz::identdata::stripChargeFromConventionalSpectrumId ( const std::string & id )

strips charge state from known conventions of the pepXML spectrum attribute; used to find a unique identifier for a spectrum in order to merge charge states

Referenced by testStripChargeFromConventionalSpectrumId().

Namespaces

Classes

Typedefs

Enumerations

Functions

Typedef Documentation

Enumeration Type Documentation

Function Documentation