24#ifndef _IDENTDATA_HPP_
25#define _IDENTDATA_HPP_
32#include "boost/logic/tribool.hpp"
39#define TYPEDEF_SHARED_PTR(type) typedef type* type##Ptr
40#define BOOST_FOREACH(a, b) a;
42#include <boost/foreach.hpp>
43#define TYPEDEF_SHARED_PTR(type) typedef boost::shared_ptr<type> type##Ptr
67 const std::string& name_ =
"");
82 const std::string& name_ =
"");
120 const std::string& name_ =
"");
138 const std::string& name_ =
"");
155 const std::string& name_ =
"");
178 const ContactPtr& contactPtr_ = ContactPtr());
198 const std::string& name_ =
"");
214 const std::string& name_ =
"");
237 const std::string name_ =
"");
273 const std::string& name_ =
"");
299 const std::string name_ =
"");
371 const std::string& name=
"");
411 const std::string& name =
"");
520 const std::string& name =
"");
548 const std::string& name_ =
"");
576 const std::string name =
"");
629 const std::string& name =
"");
672 const std::string& name =
"");
700 const std::string name =
"");
725 const std::string& name_ =
"");
746 const std::string& name_ =
"");
767 const std::string& name_ =
"");
789 const std::string& name_ =
"");
822 const std::string& name_ =
"");
842 const std::string& name_ =
"");
858 const std::string& name_ =
"");
875 const std::string name_ =
"");
985namespace IO {
struct HandlerIdentData;}
996 const std::string& creationDate_ =
"");
1033 friend struct IO::HandlerIdentData;
#define TYPEDEF_SHARED_PTR(type)
peptide subclass that contains extra metadata provided by digestion
represents a post-translational modification (PTM) modification formula or masses must be provided at...
represents a peptide or polypeptide (a sequence of amino acids)
PWIZ_API_DECL void snapModificationsToUnimod(const SpectrumIdentification &si)
sets Unimod CV terms (if possible) for all SearchModifications and Modification elements
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 std::vector< std::string > cleavageAgentRegexes(const Enzymes &enzymes)
returns a list of regular expressions for an identdata::Enzymes instance
PWIZ_API_DECL std::string cleavageAgentRegex(const Enzyme &ez)
returns a regular expression for an identdata::Enzyme
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 ins...
PWIZ_API_DECL proteome::Modification modification(const Modification &mod)
creates a proteome::Modification from an identdata::Modification
PWIZ_API_DECL std::vector< CV > defaultCVList()
returns a default list of CVs used in an IdentData document; currently includes PSI-MS,...
PWIZ_API_DECL proteome::Peptide peptide(const Peptide &peptide)
creates a proteome::Peptide from an identdata::Peptide
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 CVID cleavageAgent(const Enzyme &ez)
returns a cleavage agent CVID for an identdata::Enzyme
represents a tag-value pair, where the tag comes from the controlled vocabulary
The base class for elements that may contain cvParams, userParams, or paramGroup references.
Implementation of AmbiguousResidueType from the mzIdentML schema.
Implementation of AnalysisCollectionType from the mzIdentML schema.
std::vector< SpectrumIdentificationPtr > spectrumIdentification
ProteinDetection proteinDetection
Implementation of AnalysisDataType from the mzIdentML schema.
std::vector< SpectrumIdentificationListPtr > spectrumIdentificationList
ProteinDetectionListPtr proteinDetectionListPtr
Implementation of AnalysisProtocolCollectionType from the mzIdentML schema.
std::vector< ProteinDetectionProtocolPtr > proteinDetectionProtocol
std::vector< SpectrumIdentificationProtocolPtr > spectrumIdentificationProtocol
Implementation of AnalysisSampleCollectionType from mzIdentML schema.
std::vector< SamplePtr > samples
Implementation of AnalysisSoftwareType from the mzIdentML schema.
virtual bool empty() const
std::string customizations
ParamContainer softwareName
ContactRolePtr contactRolePtr
AnalysisSoftware(const std::string &id_="", const std::string &name_="")
Implementation for the BibliographicReferenceType tag in the mzIdentML schema.
Implementation of DBSequenceType from the mzIdentML schema.
SearchDatabasePtr searchDatabasePtr
DBSequence(const std::string id_="", const std::string name_="")
Implementation of DataCollectionType from the mzIdentML schema.
AnalysisData analysisData
Implementation of DatabaseTranslationType from the mzIdentML schema.
std::vector< TranslationTablePtr > translationTable
std::vector< int > frames
Implementation of EnzymeType from the mzIdentML schema.
Enzyme(const std::string &id="", const std::string &name="")
proteome::Digestion::Specificity terminalSpecificity
ParamContainer enzymeName
Implementation of EnzymesType from the mzIdentML schema.
std::vector< EnzymePtr > enzymes
boost::logic::tribool independent
Implementation of FilterType from the mzIdentML schema.
ParamContainer filterType
Implementation of FragmentArrayType from the mzIdentML schema.
std::vector< double > values
Implementation of the MzIdentMLType from the mzIdentML schema.
SequenceCollection sequenceCollection
DataCollection dataCollection
AnalysisProtocolCollection analysisProtocolCollection
std::vector< AnalysisSoftwarePtr > analysisSoftwareList
std::vector< ContactPtr > auditCollection
const std::string & version() const
returns the version of this mzIdentML document; for a document created programmatically,...
IdentData(const std::string &id_="", const std::string &creationDate_="")
std::vector< BibliographicReferencePtr > bibliographicReference
AnalysisSampleCollection analysisSampleCollection
AnalysisCollection analysisCollection
Parent class representing extensions of the IdentifiableType from the mzIdentML schema.
virtual bool empty() const
Identifiable(const std::string &id_="", const std::string &name_="")
Parent class of all Identifiable objects that have ParamGroups.
virtual ~IdentifiableParamContainer()
virtual bool empty() const
IdentifiableParamContainer(const std::string &id_="", const std::string &name_="")
Implementation of IonTypeType from the mzIdentML schema.
std::vector< FragmentArrayPtr > fragmentArray
Implementation of MassTableType from the mzIdentML schema.
std::vector< ResiduePtr > residues
std::vector< AmbiguousResiduePtr > ambiguousResidue
std::vector< int > msLevel
MassTable(const std::string id="")
Implementation of MeasureType from the mzIdentML schema.
Measure(const std::string id="", const std::string name="")
Implementation of ModificationType from the mzIdentML schema.
double monoisotopicMassDelta
std::vector< char > residues
Implementation of AbstractOrganizationType from the mzIdentML schema.
Organization(const std::string &id_="", const std::string &name_="")
boost::shared_ptr< Organization > parent
virtual bool empty() const
Implementation of PeptideEvidenceType from the mzIdentML schema.
DBSequencePtr dbSequencePtr
PeptideEvidence(const std::string &id="", const std::string &name="")
TranslationTablePtr translationTablePtr
Implementation of PeptideType from the mzIdentML schema.
std::vector< ModificationPtr > modification
std::vector< SubstitutionModificationPtr > substitutionModification
Peptide(const std::string &id="", const std::string &name="")
std::string peptideSequence
Implementation of PeptideHypothesisType from the mzIdentML schema.
PeptideEvidencePtr peptideEvidencePtr
std::vector< SpectrumIdentificationItemPtr > spectrumIdentificationItemPtr
Implementation of PersonType from the mzIdentML schema.
Person(const std::string &id_="", const std::string &name_="")
virtual bool empty() const
std::vector< OrganizationPtr > affiliations
Implementation of ProteinAmbiguityGroupType from the mzIdentML schema.
std::vector< ProteinDetectionHypothesisPtr > proteinDetectionHypothesis
ProteinAmbiguityGroup(const std::string &id_="", const std::string &name_="")
Implementation of ProteinDetectionType from the mzIdentML schema.
std::vector< SpectrumIdentificationListPtr > inputSpectrumIdentifications
ProteinDetection(const std::string id_="", const std::string name_="")
ProteinDetectionProtocolPtr proteinDetectionProtocolPtr
ProteinDetectionListPtr proteinDetectionListPtr
virtual bool empty() const
Implementation of ProteinDetectionHypothesisType from the mzIdentML schema.
std::vector< PeptideHypothesis > peptideHypothesis
DBSequencePtr dbSequencePtr
ProteinDetectionHypothesis(const std::string &id_="", const std::string &name_="")
Implementation of ProteinDetectionListType from the mzIdentML schema.
std::vector< ProteinAmbiguityGroupPtr > proteinAmbiguityGroup
ProteinDetectionList(const std::string &id_="", const std::string &name_="")
Implementation of ProteinDetectionProtocolType from the mzIdentML schema.
ParamContainer analysisParams
ProteinDetectionProtocol(const std::string &id_="", const std::string &name_="")
AnalysisSoftwarePtr analysisSoftwarePtr
Implementation of ProviderType from the mzIdentML schema.
Provider(const std::string id_="", const std::string name_="")
ContactRolePtr contactRolePtr
AnalysisSoftwarePtr analysisSoftwarePtr
Implementation of ResidueType from the mzIdentML schema.
Implementation of the SampleType from the mzIdentML schema.
Sample(const std::string &id_="", const std::string &name_="")
std::vector< boost::shared_ptr< Sample > > subSamples
std::vector< ContactRolePtr > contactRole
Implementation of SearchDatabaseType from the mzIdentML schema.
long numDatabaseSequences
SearchDatabase(const std::string &id_="", const std::string &name_="")
ParamContainer databaseName
Implementation of SearchModificationType from the mzIdentML schema.
std::vector< char > residues
Implementation of SequenceCollectionType from the mzIdentML schema.
std::vector< DBSequencePtr > dbSequences
std::vector< PeptideEvidencePtr > peptideEvidence
std::vector< PeptidePtr > peptides
Implementation of SourceFileType from the mzIdentML schema.
std::vector< std::string > externalFormatDocumentation
Implementation of SpectraDataType from the mzIdentML schema.
SpectraData(const std::string id="", const std::string name="")
std::vector< std::string > externalFormatDocumentation
Implementation of SpectrumIdentificationType from the mzIdentML schema.
std::vector< SpectraDataPtr > inputSpectra
SpectrumIdentification(const std::string &id_="", const std::string &name_="")
SpectrumIdentificationListPtr spectrumIdentificationListPtr
std::vector< SearchDatabasePtr > searchDatabase
SpectrumIdentificationProtocolPtr spectrumIdentificationProtocolPtr
Implementation of SpectrumIdentificationItemType from the mzIdentML schema.
double calculatedMassToCharge
SpectrumIdentificationItem(const std::string &id="", const std::string &name="")
std::vector< PeptideEvidencePtr > peptideEvidencePtr
MassTablePtr massTablePtr
double experimentalMassToCharge
std::vector< IonTypePtr > fragmentation
Implementation of SpectrumIdentificationListType from the mzIdentML schema.
std::vector< SpectrumIdentificationResultPtr > spectrumIdentificationResult
std::vector< MeasurePtr > fragmentationTable
long numSequencesSearched
SpectrumIdentificationList(const std::string &id_="", const std::string &name_="")
Implementation of SpectrumIdentificationProtocolType from the mzIdentML schema.
ParamContainer additionalSearchParams
SpectrumIdentificationProtocol(const std::string &id_="", const std::string &name_="")
std::vector< SearchModificationPtr > modificationParams
ParamContainer fragmentTolerance
DatabaseTranslationPtr databaseTranslation
std::vector< FilterPtr > databaseFilters
std::vector< MassTablePtr > massTable
ParamContainer parentTolerance
AnalysisSoftwarePtr analysisSoftwarePtr
Implementation of SpectrumIdentificationResultType from the mzIdentML schema.
SpectrumIdentificationResult(const std::string &id_="", const std::string &name_="")
SpectraDataPtr spectraDataPtr
std::vector< SpectrumIdentificationItemPtr > spectrumIdentificationItem
Implementation of SubstitutionModificationType from the mzIdentML schema.
double monoisotopicMassDelta
SubstitutionModification()
Implementation of TranslationTableType from the mzIdentML schema.
TranslationTable(const std::string &id="", const std::string &name="")