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MzIdentMLHandler.h
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34 
35 #ifndef OPENMS_FORMAT_HANDLERS_MZIDENTMLHANDLER_H
36 #define OPENMS_FORMAT_HANDLERS_MZIDENTMLHANDLER_H
37 
39 
49 
51 
52 #include <vector>
53 
54 namespace OpenMS
55 {
56  class ProgressLogger;
57 
58  namespace Internal
59  {
60 
70  class OPENMS_DLLAPI MzIdentMLHandler :
71  public XMLHandler
72  {
73 public:
76  MzIdentMLHandler(const Identification& id, const String& filename, const String& version, const ProgressLogger& logger);
79  MzIdentMLHandler(const std::vector<ProteinIdentification>& pro_id, const std::vector<PeptideIdentification>& pep_id, const String& filename, const String& version, const ProgressLogger& logger);
80 
82  MzIdentMLHandler(Identification& id, const String& filename, const String& version, const ProgressLogger& logger);
84  MzIdentMLHandler(std::vector<ProteinIdentification>& pro_id, std::vector<PeptideIdentification>& pep_id, const String& filename, const String& version, const ProgressLogger& logger);
85 
87  virtual ~MzIdentMLHandler();
89 
90 
91  // Docu in base class
92  virtual void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname);
93 
94  // Docu in base class
95  virtual void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes);
96 
97  // Docu in base class
98  virtual void characters(const XMLCh* const chars, const XMLSize_t length);
99 
100  //Docu in base class
101  virtual void writeTo(std::ostream& os);
102 
103 protected:
106 
111 
112  //~ PeakMap* ms_exp_;
113 
116 
120  std::vector<ProteinIdentification>* pro_id_;
122  std::vector<PeptideIdentification>* pep_id_;
123 
125  const std::vector<ProteinIdentification>* cpro_id_;
126  const std::vector<PeptideIdentification>* cpep_id_;
127 
130 
133 
135  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="" */);
136 
138  void handleUserParam_(const String& parent_parent_tag, const String& parent_tag, const String& name, const String& type, const String& value);
139 
141  void writeMetaInfos_(String& s, const MetaInfoInterface& meta, UInt indent) const;
142 
144  ControlledVocabulary::CVTerm getChildWithName_(const String& parent_accession, const String& name) const;
145 
147  //void writeSourceFile_(std::ostream& os, const String& id, const SourceFile& software);
148 
150  void writeEnzyme_(String& s, Enzyme enzy, UInt miss, UInt indent) const;
151 
153  void writeModParam_(String& s, const std::vector<String>& mod_names, bool fixed, UInt indent) const;
154 
156  void writeFragmentAnnotations_(String& s, const std::vector<PeptideHit::PeakAnnotation>& annotations, UInt indent, bool is_ppxl) const;
157 
159  String trimOpenMSfileURI(const String file) const;
160 
161 private:
164  MzIdentMLHandler& operator=(const MzIdentMLHandler& rhs);
166  std::map<String, String> pp_identifier_2_sil_; //mapping peptide/proteinidentification identifier_ to spectrumidentificationlist
167  std::map<String, String> sil_2_sdb_; //mapping spectrumidentificationlist to the search data bases
168  std::map<String, String> sil_2_sdat_; //mapping spectrumidentificationlist to the search input
169  std::map<String, String> ph_2_sdat_; //mapping identification runs (mapping PeptideIdentifications and ProteinIdentifications via .getIdentifier()) to spectra data
170  std::map<String, String> sil_2_sip_; //mapping spectrumidentificationlist to the search protocol (where the params are at)
174 
175  };
176  } // namespace Internal
177 } // namespace OpenMS
178 
179 #endif
SpectrumIdentification current_spectrum_id_
SpectrumIdentification Item.
Definition: MzIdentMLHandler.h:129
std::vector< PeptideIdentification > * pep_id_
Identification Item for peptides.
Definition: MzIdentMLHandler.h:122
Representation of a CV term.
Definition: ControlledVocabulary.h:61
A more convenient string class.
Definition: String.h:57
std::map< String, String > sil_2_sip_
Definition: MzIdentMLHandler.h:170
Map< String, AASequence > pep_sequences_
Definition: MzIdentMLHandler.h:165
IdentificationHit current_id_hit_
IdentificationHit Item.
Definition: MzIdentMLHandler.h:132
std::map< String, String > ph_2_sdat_
Definition: MzIdentMLHandler.h:169
std::map< String, String > pp_identifier_2_sil_
Definition: MzIdentMLHandler.h:166
Int current_mod_location_
Definition: MzIdentMLHandler.h:172
AASequence actual_peptide_
Definition: MzIdentMLHandler.h:171
unsigned int UInt
Unsigned integer type.
Definition: Types.h:95
Base class for XML handlers.
Definition: XMLHandler.h:110
const ProgressLogger & logger_
Progress logger.
Definition: MzIdentMLHandler.h:105
Representation of a peptide/protein sequence.
Definition: AASequence.h:108
String tag_
XML tag parse element.
Definition: MzIdentMLHandler.h:115
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
const std::vector< ProteinIdentification > * cpro_id_
Definition: MzIdentMLHandler.h:125
Representation of a controlled vocabulary.
Definition: ControlledVocabulary.h:55
ControlledVocabulary cv_
Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)
Definition: MzIdentMLHandler.h:108
XML STREAM handler for MzIdentMLFile.
Definition: MzIdentMLHandler.h:70
Represents a object which can store the information of an analysisXML instance.
Definition: SpectrumIdentification.h:50
Represents a object which can store the information of an analysisXML instance.
Definition: Identification.h:53
ProteinHit actual_protein_
Definition: MzIdentMLHandler.h:173
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:56
Identification * id_
Identification Item.
Definition: MzIdentMLHandler.h:118
ControlledVocabulary unimod_
Controlled vocabulary for modifications (unimod from OpenMS/share/OpenMS/CV/unimod.obo)
Definition: MzIdentMLHandler.h:110
Representation of a protein hit.
Definition: ProteinHit.h:54
std::vector< ProteinIdentification > * pro_id_
internal Identification Item for proteins
Definition: MzIdentMLHandler.h:120
Represents a object which can store the information of an analysisXML instance.
Definition: IdentificationHit.h:49
const std::vector< PeptideIdentification > * cpep_id_
Definition: MzIdentMLHandler.h:126
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
const Identification * cid_
Definition: MzIdentMLHandler.h:124
Representation of an enzyme.
Definition: Enzyme.h:56
std::map< String, String > sil_2_sdb_
Definition: MzIdentMLHandler.h:167
std::map< String, String > sil_2_sdat_
Definition: MzIdentMLHandler.h:168
int Int
Signed integer type.
Definition: Types.h:103
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:02 using doxygen 1.8.13