#include "pwiz/utility/misc/Export.hpp"
#include "pwiz/utility/misc/Exception.hpp"
#include "pwiz/data/proteome/Digestion.hpp"
#include "pwiz/data/common/ParamTypes.hpp"
#include "boost/logic/tribool.hpp"
#include <vector>
#include <string>
#include <map>
#include <boost/foreach.hpp>

Classes
struct	pwiz::identdata::Identifiable
	Parent class representing extensions of the IdentifiableType from the mzIdentML schema. More...
struct	pwiz::identdata::IdentifiableParamContainer
	Parent class of all Identifiable objects that have ParamGroups. More...
struct	pwiz::identdata::BibliographicReference
	Implementation for the BibliographicReferenceType tag in the mzIdentML schema. More...
struct	pwiz::identdata::Contact
	Implementation of ContactType from mzIdentML. More...
struct	pwiz::identdata::Organization
	Implementation of AbstractOrganizationType from the mzIdentML schema. More...
struct	pwiz::identdata::Person
	Implementation of PersonType from the mzIdentML schema. More...
struct	pwiz::identdata::ContactRole
	Implementation of ContactRoleType from the mzIdentML schema. More...
struct	pwiz::identdata::Sample
	Implementation of the SampleType from the mzIdentML schema. More...
struct	pwiz::identdata::AnalysisSoftware
	Implementation of AnalysisSoftwareType from the mzIdentML schema. More...
struct	pwiz::identdata::Provider
	Implementation of ProviderType from the mzIdentML schema. More...
struct	pwiz::identdata::AnalysisSampleCollection
	Implementation of AnalysisSampleCollectionType from mzIdentML schema. More...
struct	pwiz::identdata::SearchDatabase
	Implementation of SearchDatabaseType from the mzIdentML schema. More...
struct	pwiz::identdata::DBSequence
	Implementation of DBSequenceType from the mzIdentML schema. More...
struct	pwiz::identdata::Modification
	Implementation of ModificationType from the mzIdentML schema. More...
struct	pwiz::identdata::SubstitutionModification
	Implementation of SubstitutionModificationType from the mzIdentML schema. More...
struct	pwiz::identdata::Peptide
	Implementation of PeptideType from the mzIdentML schema. More...
struct	pwiz::identdata::SearchModification
	Implementation of SearchModificationType from the mzIdentML schema. More...
struct	pwiz::identdata::Enzyme
	Implementation of EnzymeType from the mzIdentML schema. More...
struct	pwiz::identdata::Enzymes
	Implementation of EnzymesType from the mzIdentML schema. More...
struct	pwiz::identdata::Residue
	Implementation of ResidueType from the mzIdentML schema. More...
struct	pwiz::identdata::AmbiguousResidue
	Implementation of AmbiguousResidueType from the mzIdentML schema. More...
struct	pwiz::identdata::MassTable
	Implementation of MassTableType from the mzIdentML schema. More...
struct	pwiz::identdata::Filter
	Implementation of FilterType from the mzIdentML schema. More...
struct	pwiz::identdata::TranslationTable
	Implementation of TranslationTableType from the mzIdentML schema. More...
struct	pwiz::identdata::DatabaseTranslation
	Implementation of DatabaseTranslationType from the mzIdentML schema. More...
struct	pwiz::identdata::SpectrumIdentificationProtocol
	Implementation of SpectrumIdentificationProtocolType from the mzIdentML schema. More...
struct	pwiz::identdata::Measure
	Implementation of MeasureType from the mzIdentML schema. More...
struct	pwiz::identdata::FragmentArray
	Implementation of FragmentArrayType from the mzIdentML schema. More...
struct	pwiz::identdata::IonType
	Implementation of IonTypeType from the mzIdentML schema. More...
struct	pwiz::identdata::PeptideEvidence
	Implementation of PeptideEvidenceType from the mzIdentML schema. More...
struct	pwiz::identdata::SequenceCollection
	Implementation of SequenceCollectionType from the mzIdentML schema. More...
struct	pwiz::identdata::SpectrumIdentificationItem
	Implementation of SpectrumIdentificationItemType from the mzIdentML schema. More...
struct	pwiz::identdata::SpectraData
	Implementation of SpectraDataType from the mzIdentML schema. More...
struct	pwiz::identdata::SpectrumIdentificationResult
	Implementation of SpectrumIdentificationResultType from the mzIdentML schema. More...
struct	pwiz::identdata::SpectrumIdentificationList
	Implementation of SpectrumIdentificationListType from the mzIdentML schema. More...
struct	pwiz::identdata::SpectrumIdentification
	Implementation of SpectrumIdentificationType from the mzIdentML schema. More...
struct	pwiz::identdata::ProteinDetectionProtocol
	Implementation of ProteinDetectionProtocolType from the mzIdentML schema. More...
struct	pwiz::identdata::PeptideHypothesis
	Implementation of PeptideHypothesisType from the mzIdentML schema. More...
struct	pwiz::identdata::ProteinDetectionHypothesis
	Implementation of ProteinDetectionHypothesisType from the mzIdentML schema. More...
struct	pwiz::identdata::ProteinAmbiguityGroup
	Implementation of ProteinAmbiguityGroupType from the mzIdentML schema. More...
struct	pwiz::identdata::ProteinDetectionList
	Implementation of ProteinDetectionListType from the mzIdentML schema. More...
struct	pwiz::identdata::ProteinDetection
	Implementation of ProteinDetectionType from the mzIdentML schema. More...
struct	pwiz::identdata::AnalysisCollection
	Implementation of AnalysisCollectionType from the mzIdentML schema. More...
struct	pwiz::identdata::AnalysisProtocolCollection
	Implementation of AnalysisProtocolCollectionType from the mzIdentML schema. More...
struct	pwiz::identdata::SourceFile
	Implementation of SourceFileType from the mzIdentML schema. More...
struct	pwiz::identdata::Inputs
	Implementation of the InputsType from the mzIdentML schema. More...
struct	pwiz::identdata::AnalysisData
	Implementation of AnalysisDataType from the mzIdentML schema. More...
struct	pwiz::identdata::DataCollection
	Implementation of DataCollectionType from the mzIdentML schema. More...
struct	pwiz::identdata::IdentData
	Implementation of the MzIdentMLType from the mzIdentML schema. More...

Namespaces
namespace	pwiz
	AMTContainer.hpp.
namespace	pwiz::identdata
namespace	pwiz::identdata::IO

Macros
#define	TYPEDEF_SHARED_PTR(type) typedef boost::shared_ptr<type> type##Ptr

Functions
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
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
PWIZ_API_DECL proteome::Peptide	pwiz::identdata::peptide (const Peptide &peptide)
	creates a proteome::Peptide from an identdata::Peptide
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
PWIZ_API_DECL std::vector< CVID >	pwiz::identdata::cleavageAgents (const Enzymes &enzymes)
	returns a list of cleavage agent CVIDs for an identdata::Enzymes instance
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

Macro Definition Documentation

#define TYPEDEF_SHARED_PTR ( type ) typedef boost::shared_ptr<type> type##Ptr

Definition at line 43 of file IdentData.hpp.

Classes

Namespaces

Macros

Functions

Macro Definition Documentation