OpenMS  2.8.0
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 
49 #include <vector>
50 
51 namespace OpenMS
52 {
53  class ProgressLogger;
54 
55  namespace Internal
56  {
57 
67  class OPENMS_DLLAPI MzIdentMLHandler :
68  public XMLHandler
69  {
70 public:
74  MzIdentMLHandler(const Identification& id, const String& filename, const String& version, const ProgressLogger& logger);
76  MzIdentMLHandler(const std::vector<ProteinIdentification>& pro_id, const std::vector<PeptideIdentification>& pep_id, const String& filename, const String& version, const ProgressLogger& logger);
77 
79  MzIdentMLHandler(Identification& id, const String& filename, const String& version, const ProgressLogger& logger);
81  MzIdentMLHandler(std::vector<ProteinIdentification>& pro_id, std::vector<PeptideIdentification>& pep_id, const String& filename, const String& version, const ProgressLogger& logger);
82 
84  ~MzIdentMLHandler() override;
86 
87 
88  // Docu in base class
89  void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
90 
91  // Docu in base class
92  void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
93 
94  // Docu in base class
95  void characters(const XMLCh* const chars, const XMLSize_t length) override;
96 
97  //Docu in base class
98  void writeTo(std::ostream& os) override;
99 
100 protected:
103 
108 
109  //~ PeakMap* ms_exp_;
110 
113 
117  std::vector<ProteinIdentification>* pro_id_;
119  std::vector<PeptideIdentification>* pep_id_;
120 
122  const std::vector<ProteinIdentification>* cpro_id_;
123  const std::vector<PeptideIdentification>* cpep_id_;
124 
127 
130 
132  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="" */);
133 
135  void handleUserParam_(const String& parent_parent_tag, const String& parent_tag, const String& name, const String& type, const String& value);
136 
138  void writeMetaInfos_(String& s, const MetaInfoInterface& meta, UInt indent) const;
139 
141  ControlledVocabulary::CVTerm getChildWithName_(const String& parent_accession, const String& name) const;
142 
144  //void writeSourceFile_(std::ostream& os, const String& id, const SourceFile& software);
145 
147  void writeEnzyme_(String& s, DigestionEnzymeProtein enzy, UInt miss, UInt indent) const;
148 
150  void writeModParam_(String& s, const std::vector<String>& mod_names, bool fixed, UInt indent) const;
151 
153  void writeFragmentAnnotations_(String& s, const std::vector<PeptideHit::PeakAnnotation>& annotations, UInt indent, bool is_ppxl) const;
154 
156  String trimOpenMSfileURI(const String file) const;
157 
159  void writePeptideHit(const PeptideHit& hit,
160  std::vector<PeptideIdentification>::const_iterator& it,
161  std::map<String, String>& pep_ids,
162  String cv_ns, std::set<String>& sen_set,
163  std::map<String, String>& sen_ids,
164  std::map<String, std::vector<String> >& pep_evis,
165  std::map<String, double>& pp_identifier_2_thresh,
166  String& sidres);
167 
170  std::vector<PeptideIdentification>::const_iterator& it,
171  String ppxl_linkid, std::map<String, String>& pep_ids,
172  String cv_ns, std::set<String>& sen_set,
173  std::map<String, String>& sen_ids,
174  std::map<String, std::vector<String> >& pep_evis,
175  std::map<String, double>& pp_identifier_2_thresh,
176  double ppxl_crosslink_mass,
177  std::map<String, String>& ppxl_specref_2_element,
178  String& sid, bool alpha_peptide);
179 
180 private:
185  std::map<String, String> pp_identifier_2_sil_;
186  std::map<String, String> sil_2_sdb_;
187  std::map<String, String> sil_2_sdat_;
188  std::map<String, String> ph_2_sdat_;
189  std::map<String, String> sil_2_sip_;
193 
194  };
195  } // namespace Internal
196 } // namespace OpenMS
Representation of a peptide/protein sequence.
Definition: AASequence.h:112
Representation of a controlled vocabulary.
Definition: ControlledVocabulary.h:55
Representation of a digestion enzyme for proteins (protease)
Definition: DigestionEnzymeProtein.h:50
Represents a object which can store the information of an analysisXML instance.
Definition: IdentificationHit.h:50
Represents a object which can store the information of an analysisXML instance.
Definition: Identification.h:54
XML STREAM handler for MzIdentMLFile.
Definition: MzIdentMLHandler.h:69
ControlledVocabulary::CVTerm getChildWithName_(const String &parent_accession, const String &name) const
Looks up a child CV term of parent_accession with the name name. If no such term is found,...
const Identification * cid_
Definition: MzIdentMLHandler.h:121
ProteinHit actual_protein_
Definition: MzIdentMLHandler.h:192
std::map< String, String > sil_2_sdb_
mapping spectrumidentificationlist to the search data bases
Definition: MzIdentMLHandler.h:186
void writeTo(std::ostream &os) override
Writes the contents to a stream.
std::map< String, String > sil_2_sip_
mapping spectrumidentificationlist to the search protocol (where the params are at)
Definition: MzIdentMLHandler.h:189
MzIdentMLHandler(const MzIdentMLHandler &rhs)
void writePeptideHit(const PeptideHit &hit, std::vector< PeptideIdentification >::const_iterator &it, std::map< String, String > &pep_ids, String cv_ns, std::set< String > &sen_set, std::map< String, String > &sen_ids, std::map< String, std::vector< String > > &pep_evis, std::map< String, double > &pp_identifier_2_thresh, String &sidres)
Abstraction of PeptideHit loop for most PeptideHits.
IdentificationHit current_id_hit_
IdentificationHit Item.
Definition: MzIdentMLHandler.h:129
const std::vector< ProteinIdentification > * cpro_id_
Definition: MzIdentMLHandler.h:122
const ProgressLogger & logger_
Progress logger.
Definition: MzIdentMLHandler.h:102
ControlledVocabulary cv_
Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)
Definition: MzIdentMLHandler.h:105
String tag_
XML tag parse element.
Definition: MzIdentMLHandler.h:112
std::map< String, String > ph_2_sdat_
mapping identification runs (mapping PeptideIdentifications and ProteinIdentifications via ....
Definition: MzIdentMLHandler.h:188
MzIdentMLHandler(Identification &id, const String &filename, const String &version, const ProgressLogger &logger)
Constructor for a read-only handler.
void writeFragmentAnnotations_(String &s, const std::vector< PeptideHit::PeakAnnotation > &annotations, UInt indent, bool is_ppxl) const
Helper method that writes the FragmentAnnotations section of a spectrum identification.
SpectrumIdentification current_spectrum_id_
SpectrumIdentification Item.
Definition: MzIdentMLHandler.h:126
MzIdentMLHandler & operator=(const MzIdentMLHandler &rhs)
std::vector< ProteinIdentification > * pro_id_
internal Identification Item for proteins
Definition: MzIdentMLHandler.h:117
Identification * id_
Identification Item.
Definition: MzIdentMLHandler.h:115
std::vector< PeptideIdentification > * pep_id_
Identification Item for peptides.
Definition: MzIdentMLHandler.h:119
MzIdentMLHandler(const std::vector< ProteinIdentification > &pro_id, const std::vector< PeptideIdentification > &pep_id, const String &filename, const String &version, const ProgressLogger &logger)
Constructor for a write-only handler for internal identification structures.
ControlledVocabulary unimod_
Controlled vocabulary for modifications (unimod from OpenMS/share/OpenMS/CV/unimod....
Definition: MzIdentMLHandler.h:107
std::map< String, String > pp_identifier_2_sil_
mapping peptide/proteinidentification identifier_ to spectrumidentificationlist
Definition: MzIdentMLHandler.h:185
void startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
std::map< String, String > sil_2_sdat_
mapping spectrumidentificationlist to the search input
Definition: MzIdentMLHandler.h:187
AASequence actual_peptide_
Definition: MzIdentMLHandler.h:190
~MzIdentMLHandler() override
Destructor.
MzIdentMLHandler(const Identification &id, const String &filename, const String &version, const ProgressLogger &logger)
Constructor for a write-only handler.
const std::vector< PeptideIdentification > * cpep_id_
Definition: MzIdentMLHandler.h:123
void writeMetaInfos_(String &s, const MetaInfoInterface &meta, UInt indent) const
Writes user terms.
void writeEnzyme_(String &s, DigestionEnzymeProtein enzy, UInt miss, UInt indent) const
Helper method that writes a source file.
Int current_mod_location_
Definition: MzIdentMLHandler.h:191
void characters(const XMLCh *const chars, const XMLSize_t length) override
void endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override
void handleUserParam_(const String &parent_parent_tag, const String &parent_tag, const String &name, const String &type, const String &value)
Handles user terms.
void handleCVParam_(const String &parent_parent_tag, const String &parent_tag, const String &accession, const xercesc::Attributes &attributes, const String &cv_ref)
Handles CV terms.
void writeModParam_(String &s, const std::vector< String > &mod_names, bool fixed, UInt indent) const
Helper method that writes the modification search params (fixed or variable)
String trimOpenMSfileURI(const String file) const
Convenience method to remove the [] from OpenMS internal file uri representation.
void writeXLMSPeptideHit(const PeptideHit &hit, std::vector< PeptideIdentification >::const_iterator &it, String ppxl_linkid, std::map< String, String > &pep_ids, String cv_ns, std::set< String > &sen_set, std::map< String, String > &sen_ids, std::map< String, std::vector< String > > &pep_evis, std::map< String, double > &pp_identifier_2_thresh, double ppxl_crosslink_mass, std::map< String, String > &ppxl_specref_2_element, String &sid, bool alpha_peptide)
Abstraction of PeptideHit loop for XL-MS data from OpenPepXL.
MzIdentMLHandler(std::vector< ProteinIdentification > &pro_id, std::vector< PeptideIdentification > &pep_id, const String &filename, const String &version, const ProgressLogger &logger)
Constructor for a read-only handler for internal identification structures.
Map< String, AASequence > pep_sequences_
Definition: MzIdentMLHandler.h:184
Base class for XML handlers.
Definition: XMLHandler.h:325
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:52
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:61
Representation of a peptide hit.
Definition: PeptideHit.h:57
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:53
Representation of a protein hit.
Definition: ProteinHit.h:60
Represents a object which can store the information of an analysisXML instance.
Definition: SpectrumIdentification.h:51
A more convenient string class.
Definition: String.h:60
int Int
Signed integer type.
Definition: Types.h:102
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Representation of a CV term.
Definition: ControlledVocabulary.h:61