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std::pair< CVTermList, std::map< String, DataValue > > | parseParamGroup_ (xercesc::DOMNodeList *paramGroup) |
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CVTerm | parseCvParam_ (xercesc::DOMElement *param) |
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std::pair< String, DataValue > | parseUserParam_ (xercesc::DOMElement *param) |
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void | parseAnalysisSoftwareList_ (xercesc::DOMNodeList *analysisSoftwareElements) |
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void | parseDBSequenceElements_ (xercesc::DOMNodeList *dbSequenceElements) |
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void | parsePeptideElements_ (xercesc::DOMNodeList *peptideElements) |
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AASequence | parsePeptideSiblings_ (xercesc::DOMElement *peptide) |
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void | parsePeptideEvidenceElements_ (xercesc::DOMNodeList *peptideEvidenceElements) |
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void | parseSpectrumIdentificationElements_ (xercesc::DOMNodeList *spectrumIdentificationElements) |
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void | parseSpectrumIdentificationProtocolElements_ (xercesc::DOMNodeList *spectrumIdentificationProtocolElements) |
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void | parseInputElements_ (xercesc::DOMNodeList *inputElements) |
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void | parseSpectrumIdentificationListElements_ (xercesc::DOMNodeList *spectrumIdentificationListElements) |
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void | parseSpectrumIdentificationItemSetXLMS (std::set< String >::const_iterator set_it, std::multimap< String, int > xl_val_map, xercesc::DOMElement *element_res, String spectrumID) |
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void | parseSpectrumIdentificationItemElement_ (xercesc::DOMElement *spectrumIdentificationItemElement, PeptideIdentification &spectrum_identification, String &spectrumIdentificationList_ref) |
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void | parseProteinDetectionHypothesisElement_ (xercesc::DOMElement *proteinDetectionHypothesisElement, ProteinIdentification &protein_identification) |
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void | parseProteinAmbiguityGroupElement_ (xercesc::DOMElement *proteinAmbiguityGroupElement, ProteinIdentification &protein_identification) |
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void | parseProteinDetectionListElements_ (xercesc::DOMNodeList *proteinDetectionListElements) |
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static ProteinIdentification::SearchParameters | findSearchParameters_ (std::pair< CVTermList, std::map< String, DataValue > > as_params) |
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XMLCh * | xml_root_tag_ptr_ |
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XMLCh * | xml_cvparam_tag_ptr_ |
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XMLCh * | xml_name_attr_ptr_ |
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xercesc::XercesDOMParser | mzid_parser_ |
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String | search_engine_ |
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String | search_engine_version_ |
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std::map< String, AnalysisSoftware > | as_map_ |
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std::map< String, String > | sr_map_ |
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std::map< String, String > | sd_map_ |
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std::map< String, DatabaseInput > | db_map_ |
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std::map< String, SpectrumIdentification > | si_map_ |
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std::map< String, size_t > | si_pro_map_ |
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std::map< String, SpectrumIdentificationProtocol > | sp_map_ |
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std::map< String, AASequence > | pep_map_ |
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std::map< String, PeptideEvidence > | pe_ev_map_ |
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std::map< String, String > | pv_db_map_ |
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std::multimap< String, String > | p_pv_map_ |
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std::map< String, DBSequence > | db_sq_map_ |
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std::list< std::list< String > > | hit_pev_ |
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bool | xl_ms_search_ |
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std::map< String, String > | xl_id_donor_map_ |
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std::map< String, String > | xl_id_acceptor_map_ |
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std::map< String, SignedSize > | xl_donor_pos_map_ |
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std::map< String, SignedSize > | xl_acceptor_pos_map_ |
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std::map< String, double > | xl_mass_map_ |
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std::map< String, String > | xl_mod_map_ |
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void | buildCvList_ (xercesc::DOMElement *cvElements) |
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void | buildAnalysisSoftwareList_ (xercesc::DOMElement *analysisSoftwareElements) |
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void | buildSequenceCollection_ (xercesc::DOMElement *sequenceCollectionElements) |
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void | buildAnalysisCollection_ (xercesc::DOMElement *analysisCollectionElements) |
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void | buildAnalysisProtocolCollection_ (xercesc::DOMElement *protocolElements) |
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void | buildInputDataCollection_ (xercesc::DOMElement *inputElements) |
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void | buildEnclosedCV_ (xercesc::DOMElement *parentElement, String encel, String acc, String name, String cvref) |
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void | buildAnalysisDataCollection_ (xercesc::DOMElement *analysisElements) |
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| MzIdentMLDOMHandler () |
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| MzIdentMLDOMHandler (const MzIdentMLDOMHandler &rhs) |
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MzIdentMLDOMHandler & | operator= (const MzIdentMLDOMHandler &rhs) |
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XML DOM handler for MzIdentMLFile.
In read-mode, this class will parse an MzIdentML XML file and append the input identifications to the provided PeptideIdentifications and ProteinIdentifications.
- Note
- Do not use this class. It is only needed in MzIdentMLFile.
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DOM and STREAM handler for MzIdentML have the same interface for legacy id structures.
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Only upon destruction of this class it can be guaranteed that all data has been appended to the appropriate containers. Do not try to access the data before that.