OpenMS  3.0.0
MzIdentMLDOMHandler.h
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31 // $Maintainer: Mathias Walzer $
32 // $Authors: Mathias Walzer$
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34 
35 #pragma once
36 
38 
46 
47 #include <xercesc/dom/DOM.hpp>
48 #include <xercesc/dom/DOMDocument.hpp>
49 #include <xercesc/dom/DOMDocumentType.hpp>
50 #include <xercesc/dom/DOMElement.hpp>
51 #include <xercesc/dom/DOMImplementation.hpp>
52 #include <xercesc/dom/DOMImplementationLS.hpp>
53 #include <xercesc/dom/DOMNodeIterator.hpp>
54 #include <xercesc/dom/DOMNodeList.hpp>
55 #include <xercesc/dom/DOMText.hpp>
56 #include <xercesc/util/OutOfMemoryException.hpp>
57 #include <xercesc/util/XMLString.hpp>
58 #include <xercesc/util/PlatformUtils.hpp>
59 #include <xercesc/framework/LocalFileFormatTarget.hpp>
60 
61 #include <xercesc/parsers/XercesDOMParser.hpp>
62 #include <xercesc/util/XMLUni.hpp>
63 #include <xercesc/framework/psvi/XSValue.hpp>
64 
65 #include <list>
66 #include <string>
67 #include <stdexcept>
68 #include <vector>
69 #include <map>
70 
71 // Error codes
72 //enum {
73 // ERROR_ARGS = 1,
74 // ERROR_XERCES_INIT,
75 // ERROR_PARSE,
76 // ERROR_EMPTY_DOCUMENT
77 //};
78 
79 namespace OpenMS
80 {
81  class ProgressLogger;
82 
83  namespace Internal
84  {
96  class OPENMS_DLLAPI MzIdentMLDOMHandler
97  {
98 public:
101  MzIdentMLDOMHandler(const std::vector<ProteinIdentification>& pro_id, const std::vector<PeptideIdentification>& pep_id, const String& version, const ProgressLogger& logger);
103 
105  MzIdentMLDOMHandler(std::vector<ProteinIdentification>& pro_id, std::vector<PeptideIdentification>& pep_id, const String& version, const ProgressLogger& logger);
106 
108  virtual ~MzIdentMLDOMHandler();
110 
112  void readMzIdentMLFile(const std::string& mzid_file);
114  void writeMzIdentMLFile(const std::string& mzid_file);
115 
116 protected:
119 
124 
126  std::vector<ProteinIdentification>* pro_id_;
128  std::vector<PeptideIdentification>* pep_id_;
129 
131  const std::vector<ProteinIdentification>* cpro_id_;
133  const std::vector<PeptideIdentification>* cpep_id_;
134 
137 
139  ControlledVocabulary::CVTerm getChildWithName_(const String& parent_accession, const String& name) const;
140 
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);
149  //AASequence parsePeptideSiblings_(xercesc::DOMNodeList* peptideSiblings);
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);
161  static ProteinIdentification::SearchParameters findSearchParameters_(std::pair<CVTermList, std::map<String, DataValue> > as_params);
163 
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);
171  void buildEnclosedCV_(xercesc::DOMElement* parentElement, const String& encel, const String& acc, const String& name, const String& cvref);
172  void buildAnalysisDataCollection_(xercesc::DOMElement* analysisElements);
174 
175 
176 private:
179  MzIdentMLDOMHandler& operator=(const MzIdentMLDOMHandler& rhs);
180 
183  {
186  };
189  {
190  int start;
191  int stop;
192  char pre;
193  char post;
194  bool idec;
195  };
197  struct DBSequence
198  {
203  };
206  {
211  };
214  {
216  long double mass_delta;
220  };
223  {
227  std::map<String, DataValue> parameter_ups;
228 // std::vector<ModificationParam> modification_parameter;
230  long double precursor_tolerance;
231  long double fragment_tolerance;
233  std::map<String, DataValue> threshold_ups;
234  };
237  {
242  };
243 
247 
248  xercesc::XercesDOMParser mzid_parser_;
249 
250  //from AnalysisSoftware
253  //mapping from AnalysisSoftware
254  std::map<String, AnalysisSoftware> as_map_;
255 
256  //mapping from DataCollection Inputs
257  std::map<String, String> sr_map_;
258  std::map<String, String> sd_map_;
259  std::map<String, DatabaseInput> db_map_;
260 
261  //mapping from SpectrumIdentification - SpectrumIdentification will be the new IdentificationRuns
262  std::map<String, SpectrumIdentification> si_map_;
263  std::map<String, size_t> si_pro_map_;
264 
265  //mapping from SpectrumIdentificationProtocol
266  std::map<String, SpectrumIdentificationProtocol> sp_map_;
267 
268  //mapping from SequenceCollection
269  std::map<String, AASequence> pep_map_;
270  std::map<String, PeptideEvidence> pe_ev_map_;
271  std::map<String, String> pv_db_map_;
272  std::multimap<String, String> p_pv_map_;
273  std::map<String, DBSequence> db_sq_map_;
274 
275  std::list<std::list<String> > hit_pev_;
276 
278  std::map<String, String> xl_id_donor_map_;
279  //std::map<String, String> xl_id_acceptor_map_; ///< mapping Peptide id -> cross-link acceptor value
280  std::map<String, String> xl_id_acceptor_map_;
281  std::map<String, SignedSize> xl_donor_pos_map_;
282  std::map<String, SignedSize> xl_acceptor_pos_map_;
283  std::map<String, double> xl_mass_map_;
284  std::map<String, String> xl_mod_map_;
285 
286  };
287  } // namespace Internal
288 } // namespace OpenMS
289 
OpenMS::Internal::MzIdentMLDOMHandler::xml_cvparam_tag_ptr_
XMLCh * xml_cvparam_tag_ptr_
Definition: MzIdentMLDOMHandler.h:245
OpenMS::Internal::MzIdentMLDOMHandler::PeptideEvidence::stop
int stop
Definition: MzIdentMLDOMHandler.h:191
OpenMS::Internal::MzIdentMLDOMHandler::DBSequence::accession
String accession
Definition: MzIdentMLDOMHandler.h:201
OpenMS::Internal::MzIdentMLDOMHandler::pep_id_
std::vector< PeptideIdentification > * pep_id_
Internal +w Identification Item for peptides.
Definition: MzIdentMLDOMHandler.h:128
OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentificationProtocol::modification_parameter
CVTermList modification_parameter
Definition: MzIdentMLDOMHandler.h:229
OpenMS::Internal::MzIdentMLDOMHandler::PeptideEvidence::idec
bool idec
Definition: MzIdentMLDOMHandler.h:194
OpenMS::Internal::MzIdentMLDOMHandler::PeptideEvidence
Struct to hold the PeptideEvidence information.
Definition: MzIdentMLDOMHandler.h:188
OpenMS::Internal::MzIdentMLDOMHandler::pv_db_map_
std::map< String, String > pv_db_map_
mapping PeptideEvidence id -> DBSequence id
Definition: MzIdentMLDOMHandler.h:271
OpenMS::Internal::MzIdentMLDOMHandler::pro_id_
std::vector< ProteinIdentification > * pro_id_
Internal +w Identification Item for proteins.
Definition: MzIdentMLDOMHandler.h:126
OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentification::spectrum_identification_protocol_ref
String spectrum_identification_protocol_ref
Definition: MzIdentMLDOMHandler.h:209
OpenMS::ControlledVocabulary
Representation of a controlled vocabulary.
Definition: ControlledVocabulary.h:54
OpenMS::Internal::MzIdentMLDOMHandler::DatabaseInput::location
String location
Definition: MzIdentMLDOMHandler.h:239
OpenMS::Internal::MzIdentMLDOMHandler::pep_map_
std::map< String, AASequence > pep_map_
mapping Peptide id -> Sequence
Definition: MzIdentMLDOMHandler.h:269
ControlledVocabulary.h
OpenMS::Internal::MzIdentMLDOMHandler::ModificationParam::modification_param_cvs
CVTermList modification_param_cvs
Definition: MzIdentMLDOMHandler.h:218
OpenMS::Internal::MzIdentMLDOMHandler::DBSequence::sequence
String sequence
Definition: MzIdentMLDOMHandler.h:199
OpenMS::Internal::MzIdentMLDOMHandler::xl_donor_pos_map_
std::map< String, SignedSize > xl_donor_pos_map_
mapping donor value -> cross-link modification location
Definition: MzIdentMLDOMHandler.h:281
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Internal::MzIdentMLDOMHandler::si_map_
std::map< String, SpectrumIdentification > si_map_
mapping SpectrumIdentification id -> SpectrumIdentification (id refs)
Definition: MzIdentMLDOMHandler.h:262
OpenMS::Internal::MzIdentMLDOMHandler::PeptideEvidence::start
int start
Definition: MzIdentMLDOMHandler.h:190
OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentification::spectrum_identification_list_ref
String spectrum_identification_list_ref
Definition: MzIdentMLDOMHandler.h:210
OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentification::search_database_ref
String search_database_ref
Definition: MzIdentMLDOMHandler.h:208
OpenMS::Internal::MzIdentMLDOMHandler::DatabaseInput::date
DateTime date
Definition: MzIdentMLDOMHandler.h:241
OpenMS::Internal::MzIdentMLDOMHandler::cpep_id_
const std::vector< PeptideIdentification > * cpep_id_
Internal -w Identification Item for peptides.
Definition: MzIdentMLDOMHandler.h:133
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS::Internal::MzIdentMLDOMHandler::sp_map_
std::map< String, SpectrumIdentificationProtocol > sp_map_
mapping SpectrumIdentificationProtocol id -> SpectrumIdentificationProtocol
Definition: MzIdentMLDOMHandler.h:266
OpenMS::Internal::MzIdentMLDOMHandler::as_map_
std::map< String, AnalysisSoftware > as_map_
mapping AnalysisSoftware id -> AnalysisSoftware
Definition: MzIdentMLDOMHandler.h:254
OpenMS::Internal::MzIdentMLDOMHandler::ModificationParam::fixed_mod
String fixed_mod
Definition: MzIdentMLDOMHandler.h:215
OpenMS::Internal::MzIdentMLDOMHandler::DatabaseInput
Struct to hold the information from the DatabaseInput xml tag.
Definition: MzIdentMLDOMHandler.h:236
OpenMS::Internal::MzIdentMLDOMHandler::logger_
const ProgressLogger & logger_
Progress logger.
Definition: MzIdentMLDOMHandler.h:118
OpenMS::Internal::MzIdentMLDOMHandler::DBSequence::cvs
CVTermList cvs
Definition: MzIdentMLDOMHandler.h:202
OpenMS::Internal::MzIdentMLDOMHandler::AnalysisSoftware::version
String version
Definition: MzIdentMLDOMHandler.h:185
OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentificationProtocol::threshold_cvs
CVTermList threshold_cvs
Definition: MzIdentMLDOMHandler.h:232
OpenMS::Internal::MzIdentMLDOMHandler::mzid_parser_
xercesc::XercesDOMParser mzid_parser_
Definition: MzIdentMLDOMHandler.h:248
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
UniqueIdGenerator.h
OpenMS::Internal::MzIdentMLDOMHandler::AnalysisSoftware
Struct to hold the used analysis software for that file.
Definition: MzIdentMLDOMHandler.h:182
OpenMS::Internal::MzIdentMLDOMHandler::ModificationParam::residues
String residues
Definition: MzIdentMLDOMHandler.h:217
OpenMS::Internal::MzIdentMLDOMHandler::xl_id_donor_map_
std::map< String, String > xl_id_donor_map_
mapping Peptide id -> cross-link donor value
Definition: MzIdentMLDOMHandler.h:278
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentificationProtocol::searchtype
CVTerm searchtype
Definition: MzIdentMLDOMHandler.h:224
OpenMS::Internal::MzIdentMLDOMHandler::ModificationParam::specificities
CVTermList specificities
Definition: MzIdentMLDOMHandler.h:219
OpenMS::Internal::MzIdentMLDOMHandler::AnalysisSoftware::name
String name
Definition: MzIdentMLDOMHandler.h:184
OpenMS::Internal::MzIdentMLDOMHandler::ModificationParam::mass_delta
long double mass_delta
Definition: MzIdentMLDOMHandler.h:216
OpenMS::Internal::MzIdentMLDOMHandler::sr_map_
std::map< String, String > sr_map_
mapping sourcefile id -> sourcefile location
Definition: MzIdentMLDOMHandler.h:257
ProteinHit.h
OpenMS::Internal::MzIdentMLDOMHandler::DBSequence
Struct to hold the information from the DBSequence xml tag.
Definition: MzIdentMLDOMHandler.h:197
OpenMS::Internal::MzIdentMLDOMHandler::si_pro_map_
std::map< String, size_t > si_pro_map_
mapping SpectrumIdentificationList id -> index to ProteinIdentification in pro_id_
Definition: MzIdentMLDOMHandler.h:263
ProteinIdentification.h
OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentificationProtocol::parameter_cvs
CVTermList parameter_cvs
Definition: MzIdentMLDOMHandler.h:226
OpenMS::Internal::MzIdentMLDOMHandler::xl_ms_search_
bool xl_ms_search_
is true when reading a file containing Cross-Linking MS search results
Definition: MzIdentMLDOMHandler.h:277
OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentificationProtocol::precursor_tolerance
long double precursor_tolerance
Definition: MzIdentMLDOMHandler.h:230
OpenMS::Internal::MzIdentMLDOMHandler::pe_ev_map_
std::map< String, PeptideEvidence > pe_ev_map_
mapping PeptideEvidence id -> PeptideEvidence
Definition: MzIdentMLDOMHandler.h:270
OpenMS::Internal::MzIdentMLDOMHandler::cpro_id_
const std::vector< ProteinIdentification > * cpro_id_
Internal -w Identification Item for proteins.
Definition: MzIdentMLDOMHandler.h:131
OpenMS::Internal::MzIdentMLDOMHandler::ModificationParam
Struct to hold the information from the ModificationParam xml tag.
Definition: MzIdentMLDOMHandler.h:213
OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentificationProtocol
Struct to hold the information from the SpectrumIdentificationProtocol xml tag.
Definition: MzIdentMLDOMHandler.h:222
OpenMS::CVTermList
Representation of controlled vocabulary term list.
Definition: CVTermList.h:52
OpenMS::Internal::MzIdentMLDOMHandler::PeptideEvidence::post
char post
Definition: MzIdentMLDOMHandler.h:193
OpenMS::Internal::MzIdentMLDOMHandler::xl_mass_map_
std::map< String, double > xl_mass_map_
mapping Peptide id -> cross-link mass
Definition: MzIdentMLDOMHandler.h:283
OpenMS::Internal::MzIdentMLDOMHandler::sd_map_
std::map< String, String > sd_map_
mapping spectradata id -> spectradata location
Definition: MzIdentMLDOMHandler.h:258
OpenMS::Internal::MzIdentMLDOMHandler::xml_name_attr_ptr_
XMLCh * xml_name_attr_ptr_
Definition: MzIdentMLDOMHandler.h:246
OpenMS::Internal::MzIdentMLDOMHandler::xl_id_acceptor_map_
std::map< String, String > xl_id_acceptor_map_
mapping peptide id of acceptor peptide -> cross-link acceptor value
Definition: MzIdentMLDOMHandler.h:280
CVTermList.h
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
AASequence.h
OpenMS::ControlledVocabulary::CVTerm
Representation of a CV term.
Definition: ControlledVocabulary.h:60
OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentificationProtocol::enzyme
String enzyme
Definition: MzIdentMLDOMHandler.h:225
OpenMS::CVTerm
Representation of controlled vocabulary term.
Definition: CVTerm.h:52
OpenMS::Internal::MzIdentMLDOMHandler::schema_version_
const String schema_version_
Internal version keeping.
Definition: MzIdentMLDOMHandler.h:136
OpenMS::Internal::MzIdentMLDOMHandler::xl_mod_map_
std::map< String, String > xl_mod_map_
mapping peptide id -> cross-linking reagent name
Definition: MzIdentMLDOMHandler.h:284
OpenMS::Internal::MzIdentMLDOMHandler::hit_pev_
std::list< std::list< String > > hit_pev_
writing help only
Definition: MzIdentMLDOMHandler.h:275
OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentificationProtocol::threshold_ups
std::map< String, DataValue > threshold_ups
Definition: MzIdentMLDOMHandler.h:233
OpenMS::Internal::MzIdentMLDOMHandler::xml_root_tag_ptr_
XMLCh * xml_root_tag_ptr_
Definition: MzIdentMLDOMHandler.h:244
OpenMS::Internal::MzIdentMLDOMHandler::search_engine_version_
String search_engine_version_
Definition: MzIdentMLDOMHandler.h:252
OpenMS::Internal::MzIdentMLDOMHandler
XML DOM handler for MzIdentMLFile.
Definition: MzIdentMLDOMHandler.h:96
OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentificationProtocol::parameter_ups
std::map< String, DataValue > parameter_ups
Definition: MzIdentMLDOMHandler.h:227
OpenMS::Internal::MzIdentMLDOMHandler::xl_acceptor_pos_map_
std::map< String, SignedSize > xl_acceptor_pos_map_
mapping acceptor value -> cross-link modification location
Definition: MzIdentMLDOMHandler.h:282
OpenMS::Internal::MzIdentMLDOMHandler::search_engine_
String search_engine_
Definition: MzIdentMLDOMHandler.h:251
OpenMS::Internal::MzIdentMLDOMHandler::cv_
ControlledVocabulary cv_
Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)
Definition: MzIdentMLDOMHandler.h:121
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentificationProtocol::fragment_tolerance
long double fragment_tolerance
Definition: MzIdentMLDOMHandler.h:231
OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentification::spectra_data_ref
String spectra_data_ref
Definition: MzIdentMLDOMHandler.h:207
OpenMS::Internal::MzIdentMLDOMHandler::p_pv_map_
std::multimap< String, String > p_pv_map_
mapping Peptide id -> PeptideEvidence id, multiple PeptideEvidences can have equivalent Peptides.
Definition: MzIdentMLDOMHandler.h:272
OpenMS::Internal::MzIdentMLDOMHandler::SpectrumIdentification
Struct to hold the information from the SpectrumIdentification xml tag.
Definition: MzIdentMLDOMHandler.h:205
OpenMS::Internal::MzIdentMLDOMHandler::db_map_
std::map< String, DatabaseInput > db_map_
mapping database id -> DatabaseInput
Definition: MzIdentMLDOMHandler.h:259
PeptideIdentification.h
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
OpenMS::Internal::MzIdentMLDOMHandler::PeptideEvidence::pre
char pre
Definition: MzIdentMLDOMHandler.h:192
StandardTypes.h
OpenMS::DateTime
DateTime Class.
Definition: DateTime.h:58
OpenMS::Internal::MzIdentMLDOMHandler::unimod_
ControlledVocabulary unimod_
Controlled vocabulary for modifications (unimod from OpenMS/share/OpenMS/CV/unimod....
Definition: MzIdentMLDOMHandler.h:123
OpenMS::Internal::MzIdentMLDOMHandler::DBSequence::database_ref
String database_ref
Definition: MzIdentMLDOMHandler.h:200
OpenMS::Internal::MzIdentMLDOMHandler::db_sq_map_
std::map< String, DBSequence > db_sq_map_
mapping DBSequence id -> Sequence
Definition: MzIdentMLDOMHandler.h:273