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_
AnalysisProtocolCollection analysisProtocolCollection
SpectrumIdentificationProtocolPtr spectrumIdentificationProtocolPtr
std::vector< OrganizationPtr > affiliations
ParamContainer analysisParams
PWIZ_API_DECL proteome::Modification modification(const Modification &mod)
creates a proteome::Modification from an identdata::Modification
std::vector< SpectrumIdentificationItemPtr > spectrumIdentificationItemPtr
boost::logic::tribool independent
Implementation of AnalysisCollectionType from the mzIdentML schema.
Implementation of AnalysisSampleCollectionType from mzIdentML schema.
std::vector< PeptideEvidencePtr > peptideEvidence
Implementation of PeptideEvidenceType from the mzIdentML schema.
Implementation of MeasureType from the mzIdentML schema.
Implementation of TranslationTableType from the mzIdentML schema.
SpectraDataPtr spectraDataPtr
SearchDatabasePtr searchDatabasePtr
double monoisotopicMassDelta
std::vector< PeptideEvidencePtr > peptideEvidencePtr
AnalysisCollection analysisCollection
Implementation of EnzymeType from the mzIdentML schema.
TYPEDEF_SHARED_PTR(BibliographicReference)
Implementation of AmbiguousResidueType from the mzIdentML schema.
Implementation of SpectraDataType from the mzIdentML schema.
std::vector< TranslationTablePtr > translationTable
PWIZ_API_DECL proteome::Peptide peptide(const Peptide &peptide)
creates a proteome::Peptide from an identdata::Peptide
std::vector< SpectrumIdentificationResultPtr > spectrumIdentificationResult
Parent class representing extensions of the IdentifiableType 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, Unit Ontology, and UNIMOD
Implementation of DatabaseTranslationType from the mzIdentML schema.
std::string customizations
Implementation of PersonType from the mzIdentML schema.
std::vector< SpectrumIdentificationListPtr > spectrumIdentificationList
std::string peptideSequence
ParamContainer parentTolerance
std::vector< IonTypePtr > fragmentation
Implementation of SpectrumIdentificationResultType from the mzIdentML schema.
Implementation of ProteinDetectionHypothesisType from the mzIdentML schema.
std::vector< SpectrumIdentificationProtocolPtr > spectrumIdentificationProtocol
std::vector< PeptideHypothesis > peptideHypothesis
long numDatabaseSequences
std::vector< ProteinDetectionProtocolPtr > proteinDetectionProtocol
Implementation of ProteinDetectionProtocolType from the mzIdentML schema.
ParamContainer filterType
std::vector< ResiduePtr > residues
std::vector< SpectraDataPtr > inputSpectra
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 ...
represents a post-translational modification (PTM) modification formula or masses must be provided at...
Implementation of FilterType from the mzIdentML schema.
Implementation of PeptideType from the mzIdentML schema.
PWIZ_API_DECL std::vector< CVID > cleavageAgents(const Enzymes &enzymes)
returns a list of cleavage agent CVIDs for an identdata::Enzymes instance
Implementation of AnalysisDataType from the mzIdentML schema.
double experimentalMassToCharge
DataCollection dataCollection
std::vector< EnzymePtr > enzymes
TranslationTablePtr translationTablePtr
std::vector< double > values
boost::shared_ptr< Organization > parent
represents a peptide or polypeptide (a sequence of amino acids)
std::vector< SearchDatabasePtr > searchDatabase
Implementation of ProviderType from the mzIdentML schema.
std::vector< PeptidePtr > peptides
std::vector< int > frames
Implementation of ProteinAmbiguityGroupType from the mzIdentML schema.
std::vector< MassTablePtr > massTable
std::vector< SubstitutionModificationPtr > substitutionModification
Implementation of MassTableType from the mzIdentML schema.
std::vector< std::string > externalFormatDocumentation
AnalysisSoftwarePtr analysisSoftwarePtr
ProteinDetection proteinDetection
AnalysisSampleCollection analysisSampleCollection
std::vector< boost::shared_ptr< Sample > > subSamples
The base class for elements that may contain cvParams, userParams, or paramGroup references.
Implementation of SequenceCollectionType from the mzIdentML schema.
boost::shared_ptr< Contact > ContactPtr
Implementation of the MzIdentMLType from the mzIdentML schema.
std::vector< int > msLevel
AnalysisSoftwarePtr analysisSoftwarePtr
PWIZ_API_DECL std::vector< std::string > cleavageAgentRegexes(const Enzymes &enzymes)
returns a list of regular expressions for an identdata::Enzymes instance
DBSequencePtr dbSequencePtr
Implementation of EnzymesType from the mzIdentML schema.
Implementation of ProteinDetectionListType from the mzIdentML schema.
boost::shared_ptr< Peptide > PeptidePtr
std::vector< SearchModificationPtr > modificationParams
long numSequencesSearched
Implementation of IonTypeType from the mzIdentML schema.
double monoisotopicMassDelta
ParamContainer enzymeName
Implementation of SearchModificationType from the mzIdentML schema.
Implementation of the SampleType from the mzIdentML schema.
std::vector< SamplePtr > samples
proteome::Digestion::Specificity terminalSpecificity
Implementation of PeptideHypothesisType from the mzIdentML schema.
std::vector< SpectrumIdentificationPtr > spectrumIdentification
Implementation of AbstractOrganizationType from the mzIdentML schema.
ParamContainer softwareName
std::vector< MeasurePtr > fragmentationTable
Implementation of DataCollectionType from the mzIdentML schema.
std::vector< FilterPtr > databaseFilters
ParamContainer databaseName
ParamContainer fragmentTolerance
std::vector< SpectrumIdentificationListPtr > inputSpectrumIdentifications
Implementation of SourceFileType from the mzIdentML schema.
std::vector< BibliographicReferencePtr > bibliographicReference
std::vector< char > residues
Implementation of SpectrumIdentificationProtocolType from the mzIdentML schema.
std::vector< ContactPtr > auditCollection
AnalysisSoftwarePtr analysisSoftwarePtr
std::vector< DBSequencePtr > dbSequences
Implementation of FragmentArrayType from the mzIdentML schema.
SequenceCollection sequenceCollection
PWIZ_API_DECL void snapModificationsToUnimod(const SpectrumIdentification &si)
sets Unimod CV terms (if possible) for all SearchModifications and Modification elements ...
Implementation of SubstitutionModificationType from the mzIdentML schema.
std::vector< std::string > externalFormatDocumentation
std::vector< ModificationPtr > modification
Implementation of ModificationType from the mzIdentML schema.
ProteinDetectionProtocolPtr proteinDetectionProtocolPtr
PWIZ_API_DECL std::string cleavageAgentRegex(const Enzyme &ez)
returns a regular expression for an identdata::Enzyme
Implementation of SearchDatabaseType from the mzIdentML schema.
ContactRolePtr contactRolePtr
ContactRolePtr contactRolePtr
PWIZ_API_DECL CVID cleavageAgent(const Enzyme &ez)
returns a cleavage agent CVID for an identdata::Enzyme
Implementation of AnalysisSoftwareType from the mzIdentML schema.
ParamContainer additionalSearchParams
PeptideEvidencePtr peptideEvidencePtr
Implementation of SpectrumIdentificationType from the mzIdentML schema.
Implementation of ResidueType from the mzIdentML schema.
std::vector< AnalysisSoftwarePtr > analysisSoftwareList
std::vector< ProteinDetectionHypothesisPtr > proteinDetectionHypothesis
boost::shared_ptr< Sample > SamplePtr
virtual ~IdentifiableParamContainer()
Implementation of AnalysisProtocolCollectionType from the mzIdentML schema.
std::vector< ProteinAmbiguityGroupPtr > proteinAmbiguityGroup
DBSequencePtr dbSequencePtr
Implementation of DBSequenceType from the mzIdentML schema.
Implementation for the BibliographicReferenceType tag in the mzIdentML schema.
std::vector< FragmentArrayPtr > fragmentArray
double calculatedMassToCharge
peptide subclass that contains extra metadata provided by digestion
SpectrumIdentificationListPtr spectrumIdentificationListPtr
DatabaseTranslationPtr databaseTranslation
ProteinDetectionListPtr proteinDetectionListPtr
std::vector< char > residues
Implementation of SpectrumIdentificationItemType from the mzIdentML schema.
MassTablePtr massTablePtr
AnalysisData analysisData
std::vector< AmbiguousResiduePtr > ambiguousResidue
ProteinDetectionListPtr proteinDetectionListPtr
Implementation of SpectrumIdentificationListType from the mzIdentML schema.
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...
Parent class of all Identifiable objects that have ParamGroups.
std::vector< SpectrumIdentificationItemPtr > spectrumIdentificationItem
std::vector< ContactRolePtr > contactRole
represents a tag-value pair, where the tag comes from the controlled vocabulary
Implementation of ProteinDetectionType from the mzIdentML schema.