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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_ =
"");
73 virtual bool empty()
const;
82 const std::string& name_ =
"");
88 virtual bool empty()
const;
119 Contact(
const std::string& id_ =
"",
120 const std::string& name_ =
"");
123 virtual bool empty()
const;
138 const std::string& name_ =
"");
142 virtual bool empty()
const;
154 Person(
const std::string& id_ =
"",
155 const std::string& name_ =
"");
163 virtual bool empty()
const;
197 Sample(
const std::string& id_ =
"",
198 const std::string& name_ =
"");
214 const std::string& name_ =
"");
225 virtual bool empty()
const;
236 Provider(
const std::string id_ =
"",
237 const std::string name_ =
"");
273 const std::string& name_ =
"");
299 const std::string name_ =
"");
370 Peptide(
const std::string&
id=
"",
371 const std::string& name=
"");
410 Enzyme(
const std::string&
id =
"",
411 const std::string& name =
"");
520 const std::string& name =
"");
548 const std::string& name_ =
"");
575 Measure(
const std::string
id =
"",
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_ =
"");
883 virtual bool empty()
const;
985 namespace IO {
struct HandlerIdentData;}
996 const std::string& creationDate_ =
"");
1029 const std::string& version()
const;
1033 friend struct IO::HandlerIdentData;
1070 #endif // _IDENTDATA_HPP_
std::vector< SearchModificationPtr > modificationParams
Implementation of SpectrumIdentificationItemType from the mzIdentML schema.
PWIZ_API_DECL std::vector< CV > defaultCVList()
returns a default list of CVs used in an IdentData document; currently includes PSI-MS,...
Implementation of PersonType from the mzIdentML schema.
PWIZ_API_DECL void snapModificationsToUnimod(const SpectrumIdentification &si)
sets Unimod CV terms (if possible) for all SearchModifications and Modification elements
std::vector< SpectrumIdentificationItemPtr > spectrumIdentificationItem
std::vector< TranslationTablePtr > translationTable
Implementation of PeptideEvidenceType from the mzIdentML schema.
std::vector< ProteinDetectionProtocolPtr > proteinDetectionProtocol
std::vector< AmbiguousResiduePtr > ambiguousResidue
DBSequencePtr dbSequencePtr
SpectraDataPtr spectraDataPtr
Implementation of ResidueType from the mzIdentML schema.
ParamContainer additionalSearchParams
std::vector< int > msLevel
long numDatabaseSequences
double monoisotopicMassDelta
Implementation of AmbiguousResidueType from the mzIdentML schema.
Implementation of SpectrumIdentificationResultType from the mzIdentML schema.
Implementation of ProteinDetectionHypothesisType from the mzIdentML schema.
Implementation of SpectraDataType from the mzIdentML schema.
Implementation of ProviderType from the mzIdentML schema.
SearchDatabasePtr searchDatabasePtr
std::vector< FragmentArrayPtr > fragmentArray
AnalysisCollection analysisCollection
SpectrumIdentificationProtocolPtr spectrumIdentificationProtocolPtr
std::vector< BibliographicReferencePtr > bibliographicReference
long numSequencesSearched
std::vector< SpectrumIdentificationListPtr > inputSpectrumIdentifications
ParamContainer analysisParams
represents a post-translational modification (PTM) modification formula or masses must be provided at...
Implementation of SubstitutionModificationType from the mzIdentML schema.
Implementation of TranslationTableType from the mzIdentML schema.
std::vector< SamplePtr > samples
std::vector< PeptideHypothesis > peptideHypothesis
std::vector< std::string > externalFormatDocumentation
std::vector< ProteinDetectionHypothesisPtr > proteinDetectionHypothesis
std::vector< MassTablePtr > massTable
ProteinDetectionProtocolPtr proteinDetectionProtocolPtr
PWIZ_API_DECL CVID cleavageAgent(const Enzyme &ez)
returns a cleavage agent CVID for an identdata::Enzyme
Implementation of SourceFileType from the mzIdentML schema.
represents a peptide or polypeptide (a sequence of amino acids)
std::vector< SpectrumIdentificationPtr > spectrumIdentification
double calculatedMassToCharge
TranslationTablePtr translationTablePtr
std::vector< SpectraDataPtr > inputSpectra
Implementation of AbstractOrganizationType from the mzIdentML schema.
Implementation of IonTypeType from the mzIdentML schema.
Implementation of ProteinDetectionType from the mzIdentML schema.
std::vector< EnzymePtr > enzymes
std::vector< FilterPtr > databaseFilters
Implementation of EnzymeType from the mzIdentML schema.
std::vector< ModificationPtr > modification
std::string peptideSequence
virtual ~IdentifiableParamContainer()
AnalysisSoftwarePtr analysisSoftwarePtr
std::vector< PeptideEvidencePtr > peptideEvidence
Parent class representing extensions of the IdentifiableType from the mzIdentML schema.
TYPEDEF_SHARED_PTR(BibliographicReference)
Implementation for the BibliographicReferenceType tag in the mzIdentML schema.
std::vector< SpectrumIdentificationListPtr > spectrumIdentificationList
Implementation of PeptideHypothesisType from the mzIdentML schema.
Implementation of ModificationType from the mzIdentML schema.
PWIZ_API_DECL proteome::Peptide peptide(const Peptide &peptide)
creates a proteome::Peptide from an identdata::Peptide
Implementation of DatabaseTranslationType from the mzIdentML schema.
ParamContainer filterType
PWIZ_API_DECL std::vector< std::string > cleavageAgentRegexes(const Enzymes &enzymes)
returns a list of regular expressions for an identdata::Enzymes instance
Implementation of ProteinDetectionListType from the mzIdentML schema.
std::vector< std::string > externalFormatDocumentation
Implementation of FragmentArrayType from the mzIdentML schema.
ContactRolePtr contactRolePtr
Implementation of AnalysisProtocolCollectionType from the mzIdentML schema.
Implementation of ProteinDetectionProtocolType from the mzIdentML schema.
ProteinDetectionListPtr proteinDetectionListPtr
Implementation of AnalysisCollectionType from the mzIdentML schema.
std::vector< ResiduePtr > residues
std::vector< MeasurePtr > fragmentationTable
Implementation of PeptideType from the mzIdentML schema.
Implementation of SpectrumIdentificationProtocolType from the mzIdentML schema.
std::vector< boost::shared_ptr< Sample > > subSamples
boost::shared_ptr< Organization > parent
The base class for elements that may contain cvParams, userParams, or paramGroup references.
boost::shared_ptr< Sample > SamplePtr
Implementation of SearchModificationType from the mzIdentML schema.
PeptideEvidencePtr peptideEvidencePtr
ParamContainer parentTolerance
ProteinDetectionListPtr proteinDetectionListPtr
Implementation of SequenceCollectionType from the mzIdentML schema.
AnalysisSoftwarePtr analysisSoftwarePtr
AnalysisSoftwarePtr analysisSoftwarePtr
Implementation of MassTableType from the mzIdentML schema.
AnalysisSampleCollection analysisSampleCollection
DatabaseTranslationPtr databaseTranslation
std::vector< DBSequencePtr > dbSequences
Implementation of DataCollectionType from the mzIdentML schema.
std::vector< SpectrumIdentificationItemPtr > spectrumIdentificationItemPtr
Implementation of SearchDatabaseType from the mzIdentML schema.
Implementation of the MzIdentMLType from the mzIdentML schema.
std::vector< ProteinAmbiguityGroupPtr > proteinAmbiguityGroup
Implementation of the SampleType from the mzIdentML schema.
double experimentalMassToCharge
SequenceCollection sequenceCollection
std::vector< SearchDatabasePtr > searchDatabase
std::vector< IonTypePtr > fragmentation
proteome::Digestion::Specificity terminalSpecificity
boost::logic::tribool independent
PWIZ_API_DECL std::string cleavageAgentRegex(const Enzyme &ez)
returns a regular expression for an identdata::Enzyme
std::vector< PeptidePtr > peptides
std::vector< double > values
DataCollection dataCollection
Implementation of AnalysisDataType from the mzIdentML schema.
ParamContainer databaseName
Implementation of MeasureType from the mzIdentML schema.
ParamContainer enzymeName
Implementation of DBSequenceType from the mzIdentML schema.
PWIZ_API_DECL proteome::Modification modification(const Modification &mod)
creates a proteome::Modification from an identdata::Modification
std::vector< char > residues
std::vector< SpectrumIdentificationResultPtr > spectrumIdentificationResult
Implementation of AnalysisSoftwareType from the mzIdentML schema.
ParamContainer fragmentTolerance
Implementation of FilterType from the mzIdentML schema.
DBSequencePtr dbSequencePtr
std::vector< char > residues
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< proteome::DigestedPeptide > digestedPeptides(const SpectrumIdentificationProtocol &sip, const SpectrumIdentificationItem &sii)
given a protocol and a SpectrumIdentificationItem, builds a set of DigestedPeptides
Implementation of AnalysisSampleCollectionType from mzIdentML schema.
AnalysisProtocolCollection analysisProtocolCollection
std::vector< int > frames
std::vector< SpectrumIdentificationProtocolPtr > spectrumIdentificationProtocol
ProteinDetection proteinDetection
peptide subclass that contains extra metadata provided by digestion
SpectrumIdentificationListPtr spectrumIdentificationListPtr
AnalysisData analysisData
double monoisotopicMassDelta
Implementation of EnzymesType from the mzIdentML schema.
boost::shared_ptr< Contact > ContactPtr
std::vector< AnalysisSoftwarePtr > analysisSoftwareList
Implementation of SpectrumIdentificationListType from the mzIdentML schema.
Parent class of all Identifiable objects that have ParamGroups.
represents a tag-value pair, where the tag comes from the controlled vocabulary
Implementation of SpectrumIdentificationType from the mzIdentML schema.
std::vector< SubstitutionModificationPtr > substitutionModification
std::vector< ContactRolePtr > contactRole
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...
ParamContainer softwareName
std::vector< PeptideEvidencePtr > peptideEvidencePtr
boost::shared_ptr< Peptide > PeptidePtr
ContactRolePtr contactRolePtr
std::string customizations
Implementation of ProteinAmbiguityGroupType from the mzIdentML schema.
std::vector< ContactPtr > auditCollection
std::vector< OrganizationPtr > affiliations
MassTablePtr massTablePtr