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MzIdentMLHandler.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Mathias Walzer $
32 // $Authors: Mathias Walzer, Andreas Bertsch $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38
39 #include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
40 #include <OpenMS/FORMAT/ControlledVocabulary.h>
41 #include <OpenMS/METADATA/IdentificationHit.h>
42 #include <OpenMS/METADATA/Identification.h>
43 #include <OpenMS/METADATA/ProteinHit.h>
44 #include <OpenMS/CHEMISTRY/AASequence.h>
45 #include <OpenMS/CHEMISTRY/DigestionEnzymeProtein.h>
46 #include <OpenMS/METADATA/ProteinIdentification.h>
47 #include <OpenMS/METADATA/PeptideIdentification.h>
48
49 #include <OpenMS/CONCEPT/LogStream.h>
50
51 #include <vector>
52
53 namespace OpenMS
54 {
55 class ProgressLogger;
56
57 namespace Internal
58 {
59
69 class OPENMS_DLLAPI MzIdentMLHandler :
70 public XMLHandler
71 {
72 public:
75 MzIdentMLHandler(const Identification& id, const String& filename, const String& version, const ProgressLogger& logger);
78 MzIdentMLHandler(const std::vector<ProteinIdentification>& pro_id, const std::vector<PeptideIdentification>& pep_id, const String& filename, const String& version, const ProgressLogger& logger);
79
81 MzIdentMLHandler(Identification& id, const String& filename, const String& version, const ProgressLogger& logger);
83 MzIdentMLHandler(std::vector<ProteinIdentification>& pro_id, std::vector<PeptideIdentification>& pep_id, const String& filename, const String& version, const ProgressLogger& logger);
84
86 ~MzIdentMLHandler() override;
88
89
90 // Docu in base class
91 void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
92
93 // Docu in base class
94 void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
95
96 // Docu in base class
97 void characters(const XMLCh* const chars, const XMLSize_t length) override;
98
99 //Docu in base class
100 void writeTo(std::ostream& os) override;
101
102 protected:
104 const ProgressLogger& logger_;
105
107 ControlledVocabulary cv_;
109 ControlledVocabulary unimod_;
110
111 //~ PeakMap* ms_exp_;
112
114 String tag_;
115
117 Identification* id_;
119 std::vector<ProteinIdentification>* pro_id_;
121 std::vector<PeptideIdentification>* pep_id_;
122
123 const Identification* cid_;
124 const std::vector<ProteinIdentification>* cpro_id_;
125 const std::vector<PeptideIdentification>* cpep_id_;
126
128 SpectrumIdentification current_spectrum_id_;
129
131 IdentificationHit current_id_hit_;
132
134 void handleCVParam_(const String& parent_parent_tag, const String& parent_tag, const String& accession, /* const String& name, */ /* const String& value, */ const xercesc::Attributes& attributes, const String& cv_ref /* , const String& unit_accession="" */);
135
137 void handleUserParam_(const String& parent_parent_tag, const String& parent_tag, const String& name, const String& type, const String& value);
138
140 void writeMetaInfos_(String& s, const MetaInfoInterface& meta, UInt indent) const;
141
143 ControlledVocabulary::CVTerm getChildWithName_(const String& parent_accession, const String& name) const;
144
146 //void writeSourceFile_(std::ostream& os, const String& id, const SourceFile& software);
147
149 void writeEnzyme_(String& s, DigestionEnzymeProtein enzy, UInt miss, UInt indent) const;
150
152 void writeModParam_(String& s, const std::vector<String>& mod_names, bool fixed, UInt indent) const;
153
155 void writeFragmentAnnotations_(String& s, const std::vector<PeptideHit::PeakAnnotation>& annotations, UInt indent, bool is_ppxl) const;
156
158 String trimOpenMSfileURI(const String file) const;
159
161 void writePeptideHit(const PeptideHit& hit,
162 std::vector<PeptideIdentification>::const_iterator& it,
163 std::map<String, String>& pep_ids,
164 String cv_ns, std::set<String>& sen_set,
165 std::map<String, String>& sen_ids,
166 std::map<String, std::vector<String> >& pep_evis,
167 std::map<String, double>& pp_identifier_2_thresh,
168 String& sidres);
169
171 void writeXLMSPeptideHit(const PeptideHit& hit,
172 std::vector<PeptideIdentification>::const_iterator& it,
173 String ppxl_linkid, std::map<String, String>& pep_ids,
174 String cv_ns, std::set<String>& sen_set,
175 std::map<String, String>& sen_ids,
176 std::map<String, std::vector<String> >& pep_evis,
177 std::map<String, double>& pp_identifier_2_thresh,
178 double ppxl_crosslink_mass,
179 std::map<String, String>& ppxl_specref_2_element,
180 String& sid, bool alpha_peptide);
181
182 private:
183 MzIdentMLHandler();
184 MzIdentMLHandler(const MzIdentMLHandler& rhs);
185 MzIdentMLHandler& operator=(const MzIdentMLHandler& rhs);
186 Map<String, AASequence> pep_sequences_;
187 std::map<String, String> pp_identifier_2_sil_;
188 std::map<String, String> sil_2_sdb_;
189 std::map<String, String> sil_2_sdat_;
190 std::map<String, String> ph_2_sdat_;
191 std::map<String, String> sil_2_sip_;
192 AASequence actual_peptide_;
193 Int current_mod_location_;
194 ProteinHit actual_protein_;
195
196 };
197 } // namespace Internal
198 } // namespace OpenMS
OpenMS::Internal::MzIdentMLHandler::current_id_hit_
IdentificationHit current_id_hit_
IdentificationHit Item.
Definition: MzIdentMLHandler.h:131
OpenMS::IdentificationHit
Represents a object which can store the information of an analysisXML instance.
Definition: IdentificationHit.h:48
ProteinIdentification.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Identification
Represents a object which can store the information of an analysisXML instance.
Definition: Identification.h:52
OpenMS::Internal::MzIdentMLHandler::ph_2_sdat_
std::map< String, String > ph_2_sdat_
mapping identification runs (mapping PeptideIdentifications and ProteinIdentifications via ...
Definition: MzIdentMLHandler.h:190
XMLHandler.h
OpenMS::Internal::MzIdentMLHandler::pep_sequences_
Map< String, AASequence > pep_sequences_
Definition: MzIdentMLHandler.h:186
AASequence.h
OpenMS::Internal::MzIdentMLHandler::cpep_id_
const std::vector< PeptideIdentification > * cpep_id_
Definition: MzIdentMLHandler.h:125
Identification.h
OpenMS::Internal::MzIdentMLHandler::unimod_
ControlledVocabulary unimod_
Controlled vocabulary for modifications (unimod from OpenMS/share/OpenMS/CV/unimod.obo)
Definition: MzIdentMLHandler.h:109
OpenMS::ProteinHit
Representation of a protein hit.
Definition: ProteinHit.h:57
StandardTypes.h
OpenMS::Internal::MzIdentMLHandler::cpro_id_
const std::vector< ProteinIdentification > * cpro_id_
Definition: MzIdentMLHandler.h:124
OpenMS::Internal::MzIdentMLHandler::sil_2_sip_
std::map< String, String > sil_2_sip_
mapping spectrumidentificationlist to the search protocol (where the params are at) ...
Definition: MzIdentMLHandler.h:191
OpenMS::Internal::MzIdentMLHandler::actual_protein_
ProteinHit actual_protein_
Definition: MzIdentMLHandler.h:194
OpenMS::Internal::MzIdentMLHandler::actual_peptide_
AASequence actual_peptide_
Definition: MzIdentMLHandler.h:192
OpenMS::Internal::MzIdentMLHandler::cid_
const Identification * cid_
Definition: MzIdentMLHandler.h:123
ControlledVocabulary.h
OpenMS::DigestionEnzymeProtein
Representation of a digestion enzyme for proteins (protease)
Definition: DigestionEnzymeProtein.h:48
OpenMS::Internal::MzIdentMLHandler::logger_
const ProgressLogger & logger_
Progress logger.
Definition: MzIdentMLHandler.h:104
OpenMS::Internal::MzIdentMLHandler::sil_2_sdb_
std::map< String, String > sil_2_sdb_
mapping spectrumidentificationlist to the search data bases
Definition: MzIdentMLHandler.h:188
OpenMS::SpectrumIdentification
Represents a object which can store the information of an analysisXML instance.
Definition: SpectrumIdentification.h:49
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
ProteinHit.h
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::Internal::MzIdentMLHandler::cv_
ControlledVocabulary cv_
Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)
Definition: MzIdentMLHandler.h:107
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:54
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
LogStream.h
OpenMS::Internal::MzIdentMLHandler::current_spectrum_id_
SpectrumIdentification current_spectrum_id_
SpectrumIdentification Item.
Definition: MzIdentMLHandler.h:128
OpenMS::Internal::MzIdentMLHandler::pro_id_
std::vector< ProteinIdentification > * pro_id_
internal Identification Item for proteins
Definition: MzIdentMLHandler.h:119
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::Internal::MzIdentMLHandler::pep_id_
std::vector< PeptideIdentification > * pep_id_
Identification Item for peptides.
Definition: MzIdentMLHandler.h:121
OpenMS::ControlledVocabulary::CVTerm
Representation of a CV term.
Definition: ControlledVocabulary.h:60
DigestionEnzymeProtein.h
int
OpenMS::Internal::MzIdentMLHandler
XML STREAM handler for MzIdentMLFile.
Definition: MzIdentMLHandler.h:69
IdentificationHit.h
OpenMS::ControlledVocabulary
Representation of a controlled vocabulary.
Definition: ControlledVocabulary.h:54
OpenMS::Internal::MzIdentMLHandler::tag_
String tag_
XML tag parse element.
Definition: MzIdentMLHandler.h:114
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:151
OpenMS::Internal::MzIdentMLHandler::id_
Identification * id_
Identification Item.
Definition: MzIdentMLHandler.h:117
OpenMS::Internal::MzIdentMLHandler::current_mod_location_
Int current_mod_location_
Definition: MzIdentMLHandler.h:193
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
OpenMS::Internal::MzIdentMLHandler::pp_identifier_2_sil_
std::map< String, String > pp_identifier_2_sil_
mapping peptide/proteinidentification identifier_ to spectrumidentificationlist
Definition: MzIdentMLHandler.h:187
OpenMS::Internal::MzIdentMLHandler::sil_2_sdat_
std::map< String, String > sil_2_sdat_
mapping spectrumidentificationlist to the search input
Definition: MzIdentMLHandler.h:189