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OpenMS
2.6.0
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48 #include <xercesc/dom/DOM.hpp>
49 #include <xercesc/dom/DOMDocument.hpp>
50 #include <xercesc/dom/DOMDocumentType.hpp>
51 #include <xercesc/dom/DOMElement.hpp>
52 #include <xercesc/dom/DOMImplementation.hpp>
53 #include <xercesc/dom/DOMImplementationLS.hpp>
54 #include <xercesc/dom/DOMNodeIterator.hpp>
55 #include <xercesc/dom/DOMNodeList.hpp>
56 #include <xercesc/dom/DOMText.hpp>
57 #include <xercesc/util/OutOfMemoryException.hpp>
58 #include <xercesc/util/XMLString.hpp>
59 #include <xercesc/util/PlatformUtils.hpp>
60 #include <xercesc/framework/LocalFileFormatTarget.hpp>
62 #include <xercesc/parsers/XercesDOMParser.hpp>
63 #include <xercesc/util/XMLUni.hpp>
64 #include <xercesc//framework/psvi/XSValue.hpp>
112 void readMzIdentMLFile(
const std::string& mzid_file);
114 void writeMzIdentMLFile(
const std::string& mzid_file);
131 const std::vector<ProteinIdentification>*
cpro_id_;
133 const std::vector<PeptideIdentification>*
cpep_id_;
143 std::pair<CVTermList, std::map<String, DataValue> > parseParamGroup_(xercesc::DOMNodeList* paramGroup);
144 CVTerm parseCvParam_(xercesc::DOMElement* param);
145 std::pair<String, DataValue> parseUserParam_(xercesc::DOMElement* param);
146 void parseAnalysisSoftwareList_(xercesc::DOMNodeList* analysisSoftwareElements);
147 void parseDBSequenceElements_(xercesc::DOMNodeList* dbSequenceElements);
148 void parsePeptideElements_(xercesc::DOMNodeList* peptideElements);
150 AASequence parsePeptideSiblings_(xercesc::DOMElement* peptide);
151 void parsePeptideEvidenceElements_(xercesc::DOMNodeList* peptideEvidenceElements);
152 void parseSpectrumIdentificationElements_(xercesc::DOMNodeList* spectrumIdentificationElements);
153 void parseSpectrumIdentificationProtocolElements_(xercesc::DOMNodeList* spectrumIdentificationProtocolElements);
154 void parseInputElements_(xercesc::DOMNodeList* inputElements);
155 void parseSpectrumIdentificationListElements_(xercesc::DOMNodeList* spectrumIdentificationListElements);
156 void parseSpectrumIdentificationItemSetXLMS(std::set<String>::const_iterator set_it, std::multimap<String, int> xl_val_map, xercesc::DOMElement* element_res,
String spectrumID);
157 void parseSpectrumIdentificationItemElement_(xercesc::DOMElement* spectrumIdentificationItemElement,
PeptideIdentification& spectrum_identification,
String& spectrumIdentificationList_ref);
158 void parseProteinDetectionHypothesisElement_(xercesc::DOMElement* proteinDetectionHypothesisElement,
ProteinIdentification& protein_identification);
159 void parseProteinAmbiguityGroupElement_(xercesc::DOMElement* proteinAmbiguityGroupElement,
ProteinIdentification& protein_identification);
160 void parseProteinDetectionListElements_(xercesc::DOMNodeList* proteinDetectionListElements);
165 void buildCvList_(xercesc::DOMElement* cvElements);
166 void buildAnalysisSoftwareList_(xercesc::DOMElement* analysisSoftwareElements);
167 void buildSequenceCollection_(xercesc::DOMElement* sequenceCollectionElements);
168 void buildAnalysisCollection_(xercesc::DOMElement* analysisCollectionElements);
169 void buildAnalysisProtocolCollection_(xercesc::DOMElement* protocolElements);
170 void buildInputDataCollection_(xercesc::DOMElement* inputElements);
172 void buildAnalysisDataCollection_(xercesc::DOMElement* analysisElements);
262 std::map<String, SpectrumIdentification>
si_map_;
266 std::map<String, SpectrumIdentificationProtocol>
sp_map_;
XMLCh * xml_cvparam_tag_ptr_
Definition: MzIdentMLDOMHandler.h:245
int stop
Definition: MzIdentMLDOMHandler.h:191
String accession
Definition: MzIdentMLDOMHandler.h:201
std::vector< PeptideIdentification > * pep_id_
Internal +w Identification Item for peptides.
Definition: MzIdentMLDOMHandler.h:128
CVTermList modification_parameter
Definition: MzIdentMLDOMHandler.h:229
bool idec
Definition: MzIdentMLDOMHandler.h:194
Struct to hold the PeptideEvidence information.
Definition: MzIdentMLDOMHandler.h:188
std::map< String, String > pv_db_map_
mapping PeptideEvidence id -> DBSequence id
Definition: MzIdentMLDOMHandler.h:271
std::vector< ProteinIdentification > * pro_id_
Internal +w Identification Item for proteins.
Definition: MzIdentMLDOMHandler.h:126
String spectrum_identification_protocol_ref
Definition: MzIdentMLDOMHandler.h:209
Representation of a controlled vocabulary.
Definition: ControlledVocabulary.h:54
String location
Definition: MzIdentMLDOMHandler.h:239
std::map< String, AASequence > pep_map_
mapping Peptide id -> Sequence
Definition: MzIdentMLDOMHandler.h:269
CVTermList modification_param_cvs
Definition: MzIdentMLDOMHandler.h:218
String sequence
Definition: MzIdentMLDOMHandler.h:199
std::map< String, SignedSize > xl_donor_pos_map_
mapping donor value -> cross-link modification location
Definition: MzIdentMLDOMHandler.h:281
A more convenient string class.
Definition: String.h:59
std::map< String, SpectrumIdentification > si_map_
mapping SpectrumIdentification id -> SpectrumIdentification (id refs)
Definition: MzIdentMLDOMHandler.h:262
int start
Definition: MzIdentMLDOMHandler.h:190
String spectrum_identification_list_ref
Definition: MzIdentMLDOMHandler.h:210
String search_database_ref
Definition: MzIdentMLDOMHandler.h:208
DateTime date
Definition: MzIdentMLDOMHandler.h:241
const std::vector< PeptideIdentification > * cpep_id_
Internal -w Identification Item for peptides.
Definition: MzIdentMLDOMHandler.h:133
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
std::map< String, SpectrumIdentificationProtocol > sp_map_
mapping SpectrumIdentificationProtocol id -> SpectrumIdentificationProtocol
Definition: MzIdentMLDOMHandler.h:266
std::map< String, AnalysisSoftware > as_map_
mapping AnalysisSoftware id -> AnalysisSoftware
Definition: MzIdentMLDOMHandler.h:254
String fixed_mod
Definition: MzIdentMLDOMHandler.h:215
const ProgressLogger & logger_
Progress logger.
Definition: MzIdentMLDOMHandler.h:118
CVTermList cvs
Definition: MzIdentMLDOMHandler.h:202
String version
Definition: MzIdentMLDOMHandler.h:185
CVTermList threshold_cvs
Definition: MzIdentMLDOMHandler.h:232
xercesc::XercesDOMParser mzid_parser_
Definition: MzIdentMLDOMHandler.h:248
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Struct to hold the used analysis software for that file.
Definition: MzIdentMLDOMHandler.h:182
String residues
Definition: MzIdentMLDOMHandler.h:217
std::map< String, String > xl_id_donor_map_
mapping Peptide id -> cross-link donor value
Definition: MzIdentMLDOMHandler.h:278
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
CVTerm searchtype
Definition: MzIdentMLDOMHandler.h:224
CVTermList specificities
Definition: MzIdentMLDOMHandler.h:219
String name
Definition: MzIdentMLDOMHandler.h:184
long double mass_delta
Definition: MzIdentMLDOMHandler.h:216
std::map< String, String > sr_map_
mapping sourcefile id -> sourcefile location
Definition: MzIdentMLDOMHandler.h:257
Struct to hold the information from the DBSequence xml tag.
Definition: MzIdentMLDOMHandler.h:197
std::map< String, size_t > si_pro_map_
mapping SpectrumIdentificationList id -> index to ProteinIdentification in pro_id_
Definition: MzIdentMLDOMHandler.h:263
CVTermList parameter_cvs
Definition: MzIdentMLDOMHandler.h:226
bool xl_ms_search_
is true when reading a file containing Cross-Linking MS search results
Definition: MzIdentMLDOMHandler.h:277
long double precursor_tolerance
Definition: MzIdentMLDOMHandler.h:230
std::map< String, PeptideEvidence > pe_ev_map_
mapping PeptideEvidence id -> PeptideEvidence
Definition: MzIdentMLDOMHandler.h:270
const std::vector< ProteinIdentification > * cpro_id_
Internal -w Identification Item for proteins.
Definition: MzIdentMLDOMHandler.h:131
Struct to hold the information from the ModificationParam xml tag.
Definition: MzIdentMLDOMHandler.h:213
Struct to hold the information from the SpectrumIdentificationProtocol xml tag.
Definition: MzIdentMLDOMHandler.h:222
Representation of controlled vocabulary term list.
Definition: CVTermList.h:52
char post
Definition: MzIdentMLDOMHandler.h:193
std::map< String, double > xl_mass_map_
mapping Peptide id -> cross-link mass
Definition: MzIdentMLDOMHandler.h:283
std::map< String, String > sd_map_
mapping spectradata id -> spectradata location
Definition: MzIdentMLDOMHandler.h:258
XMLCh * xml_name_attr_ptr_
Definition: MzIdentMLDOMHandler.h:246
std::map< String, String > xl_id_acceptor_map_
mapping peptide id of acceptor peptide -> cross-link acceptor value
Definition: MzIdentMLDOMHandler.h:280
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
Representation of a CV term.
Definition: ControlledVocabulary.h:60
String enzyme
Definition: MzIdentMLDOMHandler.h:225
Representation of controlled vocabulary term.
Definition: CVTerm.h:52
const String schema_version_
Internal version keeping.
Definition: MzIdentMLDOMHandler.h:136
std::map< String, String > xl_mod_map_
mapping peptide id -> cross-linking reagent name
Definition: MzIdentMLDOMHandler.h:284
std::list< std::list< String > > hit_pev_
writing help only
Definition: MzIdentMLDOMHandler.h:275
std::map< String, DataValue > threshold_ups
Definition: MzIdentMLDOMHandler.h:233
XMLCh * xml_root_tag_ptr_
Definition: MzIdentMLDOMHandler.h:244
String search_engine_version_
Definition: MzIdentMLDOMHandler.h:252
XML DOM handler for MzIdentMLFile.
Definition: MzIdentMLDOMHandler.h:96
std::map< String, DataValue > parameter_ups
Definition: MzIdentMLDOMHandler.h:227
std::map< String, SignedSize > xl_acceptor_pos_map_
mapping acceptor value -> cross-link modification location
Definition: MzIdentMLDOMHandler.h:282
String search_engine_
Definition: MzIdentMLDOMHandler.h:251
ControlledVocabulary cv_
Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)
Definition: MzIdentMLDOMHandler.h:121
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
long double fragment_tolerance
Definition: MzIdentMLDOMHandler.h:231
String spectra_data_ref
Definition: MzIdentMLDOMHandler.h:207
std::multimap< String, String > p_pv_map_
mapping Peptide id -> PeptideEvidence id, multiple PeptideEvidences can have equivalent Peptides.
Definition: MzIdentMLDOMHandler.h:272
Struct to hold the information from the SpectrumIdentification xml tag.
Definition: MzIdentMLDOMHandler.h:205
std::map< String, DatabaseInput > db_map_
mapping database id -> DatabaseInput
Definition: MzIdentMLDOMHandler.h:259
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
char pre
Definition: MzIdentMLDOMHandler.h:192
DateTime Class.
Definition: DateTime.h:54
ControlledVocabulary unimod_
Controlled vocabulary for modifications (unimod from OpenMS/share/OpenMS/CV/unimod....
Definition: MzIdentMLDOMHandler.h:123
String database_ref
Definition: MzIdentMLDOMHandler.h:200
std::map< String, DBSequence > db_sq_map_
mapping DBSequence id -> Sequence
Definition: MzIdentMLDOMHandler.h:273