OpenMS  2.4.0
MzIdentMLHandler.h
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31 // $Maintainer: Mathias Walzer $
32 // $Authors: Mathias Walzer, Andreas Bertsch $
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34 
35 #pragma once
36 
38 
48 
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:
105 
110 
111  //~ PeakMap* ms_exp_;
112 
115 
119  std::vector<ProteinIdentification>* pro_id_;
121  std::vector<PeptideIdentification>* pep_id_;
122 
124  const std::vector<ProteinIdentification>* cpro_id_;
125  const std::vector<PeptideIdentification>* cpep_id_;
126 
129 
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 
160 private:
163  MzIdentMLHandler& operator=(const MzIdentMLHandler& rhs);
165  std::map<String, String> pp_identifier_2_sil_; //mapping peptide/proteinidentification identifier_ to spectrumidentificationlist
166  std::map<String, String> sil_2_sdb_; //mapping spectrumidentificationlist to the search data bases
167  std::map<String, String> sil_2_sdat_; //mapping spectrumidentificationlist to the search input
168  std::map<String, String> ph_2_sdat_; //mapping identification runs (mapping PeptideIdentifications and ProteinIdentifications via .getIdentifier()) to spectra data
169  std::map<String, String> sil_2_sip_; //mapping spectrumidentificationlist to the search protocol (where the params are at)
173 
174  };
175  } // namespace Internal
176 } // namespace OpenMS
177 
SpectrumIdentification current_spectrum_id_
SpectrumIdentification Item.
Definition: MzIdentMLHandler.h:128
std::vector< PeptideIdentification > * pep_id_
Identification Item for peptides.
Definition: MzIdentMLHandler.h:121
Representation of a CV term.
Definition: ControlledVocabulary.h:60
A more convenient string class.
Definition: String.h:57
std::map< String, String > sil_2_sip_
Definition: MzIdentMLHandler.h:169
Map< String, AASequence > pep_sequences_
Definition: MzIdentMLHandler.h:164
IdentificationHit current_id_hit_
IdentificationHit Item.
Definition: MzIdentMLHandler.h:131
std::map< String, String > ph_2_sdat_
Definition: MzIdentMLHandler.h:168
std::map< String, String > pp_identifier_2_sil_
Definition: MzIdentMLHandler.h:165
Int current_mod_location_
Definition: MzIdentMLHandler.h:171
AASequence actual_peptide_
Definition: MzIdentMLHandler.h:170
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Base class for XML handlers.
Definition: XMLHandler.h:148
const ProgressLogger & logger_
Progress logger.
Definition: MzIdentMLHandler.h:104
Representation of a peptide/protein sequence.
Definition: AASequence.h:107
String tag_
XML tag parse element.
Definition: MzIdentMLHandler.h:114
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
const std::vector< ProteinIdentification > * cpro_id_
Definition: MzIdentMLHandler.h:124
Representation of a controlled vocabulary.
Definition: ControlledVocabulary.h:54
ControlledVocabulary cv_
Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)
Definition: MzIdentMLHandler.h:107
XML STREAM handler for MzIdentMLFile.
Definition: MzIdentMLHandler.h:69
Represents a object which can store the information of an analysisXML instance.
Definition: SpectrumIdentification.h:49
Represents a object which can store the information of an analysisXML instance.
Definition: Identification.h:52
ProteinHit actual_protein_
Definition: MzIdentMLHandler.h:172
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:55
Identification * id_
Identification Item.
Definition: MzIdentMLHandler.h:117
ControlledVocabulary unimod_
Controlled vocabulary for modifications (unimod from OpenMS/share/OpenMS/CV/unimod.obo)
Definition: MzIdentMLHandler.h:109
Representation of a protein hit.
Definition: ProteinHit.h:53
std::vector< ProteinIdentification > * pro_id_
internal Identification Item for proteins
Definition: MzIdentMLHandler.h:119
Represents a object which can store the information of an analysisXML instance.
Definition: IdentificationHit.h:48
const std::vector< PeptideIdentification > * cpep_id_
Definition: MzIdentMLHandler.h:125
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
const Identification * cid_
Definition: MzIdentMLHandler.h:123
std::map< String, String > sil_2_sdb_
Definition: MzIdentMLHandler.h:166
std::map< String, String > sil_2_sdat_
Definition: MzIdentMLHandler.h:167
int Int
Signed integer type.
Definition: Types.h:102
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
Representation of a digestion enzyme for proteins (protease)
Definition: DigestionEnzymeProtein.h:48