OpenMS
MzIdentMLHandler.h
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1 // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Mathias Walzer $
6 // $Authors: Mathias Walzer, Andreas Bertsch $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
12 
21 
22 #include <vector>
23 #include <map>
24 
25 namespace OpenMS
26 {
27  class ProgressLogger;
28 
29  namespace Internal
30  {
31 
37  class OPENMS_DLLAPI IdentificationHit :
38  public MetaInfoInterface
39  {
40  public:
42 
43  IdentificationHit() = default;
45 
48 
50  virtual ~IdentificationHit() = default;
51 
53  IdentificationHit(IdentificationHit&&) noexcept = default;
54 
56  IdentificationHit& operator=(const IdentificationHit&) = default;
57 
59  IdentificationHit& operator=(IdentificationHit&&) noexcept = default;
61 
63 
64  bool operator==(const IdentificationHit& rhs) const noexcept;
66 
68  bool operator!=(const IdentificationHit& rhs) const noexcept;
70 
72 
73  void setId(const std::string& id) noexcept;
75 
77  const std::string& getId() const noexcept;
78 
80  void setCharge(int charge) noexcept;
81 
83  int getCharge() const noexcept;
84 
86  void setCalculatedMassToCharge(double mz) noexcept;
87 
89  double getCalculatedMassToCharge() const noexcept;
90 
92  void setExperimentalMassToCharge(double mz) noexcept;
93 
95  double getExperimentalMassToCharge() const noexcept;
96 
98  void setName(const std::string& name) noexcept;
99 
101  const std::string& getName() const noexcept;
102 
104  void setPassThreshold(bool pass) noexcept;
105 
107  bool getPassThreshold() const noexcept;
108 
110  void setRank(int rank) noexcept;
111 
113  int getRank() const noexcept;
115 
116  private:
117  std::string id_;
118  int charge_ = 0;
119  double calculated_mass_to_charge_ = 0.0;
120  double experimental_mass_to_charge_ = 0.0;
121  std::string name_;
122  bool pass_threshold_ = true;
123  int rank_ = 0;
124  };
125 
133  class OPENMS_DLLAPI SpectrumIdentification :
134  public MetaInfoInterface
135  {
136 public:
137 
139 
140  SpectrumIdentification() = default;
153  bool operator==(const SpectrumIdentification & rhs) const;
155  bool operator!=(const SpectrumIdentification & rhs) const;
157 
158  // @name Accessors
160  void setHits(const std::vector<IdentificationHit> & hits);
162 
164  void addHit(const IdentificationHit & hit);
165 
167  const std::vector<IdentificationHit> & getHits() const;
169 
170 protected:
171 
173  std::vector<IdentificationHit> hits_;
174  };
175 
183  class OPENMS_DLLAPI Identification :
184  public MetaInfoInterface
185  {
186  public:
187 
189 
190 
192  Identification() = default;
194  Identification(const Identification & source) = default;
198  virtual ~Identification();
199 
201  Identification & operator=(const Identification & source) = default;
204 
206  bool operator==(const Identification & rhs) const;
208  bool operator!=(const Identification & rhs) const;
210 
212 
213  void setCreationDate(const DateTime & date);
215 
217  const DateTime & getCreationDate() const;
218 
220  void setSpectrumIdentifications(const std::vector<SpectrumIdentification> & ids);
221 
224 
226  const std::vector<SpectrumIdentification> & getSpectrumIdentifications() const;
228  protected:
231  std::vector<SpectrumIdentification> spectrum_identifications_;
232  };
233 
243  class OPENMS_DLLAPI MzIdentMLHandler :
244  public XMLHandler
245  {
246 public:
250  MzIdentMLHandler(const std::vector<ProteinIdentification>& pro_id, const PeptideIdentificationList& pep_id, const String& filename, const String& version, const ProgressLogger& logger);
251 
253  MzIdentMLHandler(std::vector<ProteinIdentification>& pro_id, PeptideIdentificationList& pep_id, const String& filename, const String& version, const ProgressLogger& logger);
254 
256  ~MzIdentMLHandler() override;
258 
259 
260  // Docu in base class
261  void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
262 
263  // Docu in base class
264  void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
265 
266  // Docu in base class
267  void characters(const XMLCh* const chars, const XMLSize_t length) override;
268 
269  //Docu in base class
270  void writeTo(std::ostream& os) override;
271 
272 protected:
275 
280 
281  //~ PeakMap* ms_exp_;
282 
285 
289  std::vector<ProteinIdentification>* pro_id_;
292 
294  const std::vector<ProteinIdentification>* cpro_id_;
296 
299 
302 
304  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="" */);
305 
307  void handleUserParam_(const String& parent_parent_tag, const String& parent_tag, const String& name, const String& type, const String& value);
308 
310  void writeMetaInfos_(String& s, const MetaInfoInterface& meta, UInt indent) const;
311 
313  ControlledVocabulary::CVTerm getChildWithName_(const String& parent_accession, const String& name) const;
314 
316  //void writeSourceFile_(std::ostream& os, const String& id, const SourceFile& software);
317 
319  void writeEnzyme_(String& s, const DigestionEnzymeProtein& enzy, UInt miss, UInt indent) const;
320 
322  void writeModParam_(String& s, const std::vector<String>& mod_names, bool fixed, UInt indent) const;
323 
325  void writeFragmentAnnotations_(String& s, const std::vector<PeptideHit::PeakAnnotation>& annotations, UInt indent, bool is_ppxl) const;
326 
328  String trimOpenMSfileURI(const String& file) const;
329 
331  void writePeptideHit(const PeptideHit& hit,
333  std::map<String, String>& pep_ids,
334  const String& cv_ns, std::set<String>& sen_set,
335  std::map<String, String>& sen_ids,
336  std::map<String, std::vector<String> >& pep_evis,
337  std::map<String, double>& pp_identifier_2_thresh,
338  String& sidres);
339 
343  const String& ppxl_linkid, std::map<String, String>& pep_ids,
344  const String& cv_ns, std::set<String>& sen_set,
345  std::map<String, String>& sen_ids,
346  std::map<String, std::vector<String> >& pep_evis,
347  std::map<String, double>& pp_identifier_2_thresh,
348  double ppxl_crosslink_mass,
349  std::map<String, String>& ppxl_specref_2_element,
350  String& sid, bool alpha_peptide);
351 
352 private:
356  std::map<String, AASequence> pep_sequences_;
357  std::map<String, String> pp_identifier_2_sil_;
358  std::map<String, String> sil_2_sdb_;
359  std::map<String, String> sil_2_sdat_;
360  std::map<String, String> ph_2_sdat_;
361  std::map<String, String> sil_2_sip_;
365 
366  };
367  } // namespace Internal
368 } // namespace OpenMS
char16_t XMLCh
Definition: ClassTest.h:28
Representation of a peptide/protein sequence.
Definition: AASequence.h:86
Definition: ControlledVocabulary.h:29
DateTime Class.
Definition: DateTime.h:33
Representation of a digestion enzyme for proteins (protease)
Definition: DigestionEnzymeProtein.h:24
typename VecMember::const_iterator const_iterator
Definition: ExposedVector.h:69
Represents a object which can store the information of an analysisXML instance.
Definition: MzIdentMLHandler.h:39
virtual ~IdentificationHit()=default
Virtual destructor.
IdentificationHit(const IdentificationHit &)=default
Copy constructor.
IdentificationHit(IdentificationHit &&) noexcept=default
Move constructor.
Definition: MzIdentMLHandler.h:185
void addSpectrumIdentification(const SpectrumIdentification &id)
adds a spectrum identification
DateTime creation_date_
Date and time the search was performed.
Definition: MzIdentMLHandler.h:230
Identification(const Identification &source)=default
Copy constructor.
bool operator==(const Identification &rhs) const
Equality operator.
Identification(Identification &&)=default
Move constructor.
virtual ~Identification()
Destructor.
void setSpectrumIdentifications(const std::vector< SpectrumIdentification > &ids)
sets the spectrum identifications
Identification()=default
Default constructor.
const DateTime & getCreationDate() const
returns the date and time the file was created
std::vector< SpectrumIdentification > spectrum_identifications_
Definition: MzIdentMLHandler.h:231
Identification & operator=(Identification &&) &=default
Move assignment operator.
const std::vector< SpectrumIdentification > & getSpectrumIdentifications() const
returns the spectrum identifications stored
Identification & operator=(const Identification &source)=default
Assignment operator.
String id_
Identifier.
Definition: MzIdentMLHandler.h:229
bool operator!=(const Identification &rhs) const
Inequality operator.
XML STREAM handler for MzIdentMLFile.
Definition: MzIdentMLHandler.h:245
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:293
PeptideIdentificationList * pep_id_
Identification Item for peptides.
Definition: MzIdentMLHandler.h:291
MzIdentMLHandler(const std::vector< ProteinIdentification > &pro_id, const PeptideIdentificationList &pep_id, const String &filename, const String &version, const ProgressLogger &logger)
Constructor for a write-only handler for internal identification structures.
ProteinHit actual_protein_
Definition: MzIdentMLHandler.h:364
String trimOpenMSfileURI(const String &file) const
Convenience method to remove the [] from OpenMS internal file uri representation.
std::map< String, String > sil_2_sdb_
mapping spectrumidentificationlist to the search data bases
Definition: MzIdentMLHandler.h:358
void writeXLMSPeptideHit(const PeptideHit &hit, PeptideIdentificationList::const_iterator &it, const String &ppxl_linkid, std::map< String, String > &pep_ids, const 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.
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:361
MzIdentMLHandler(const MzIdentMLHandler &rhs)
IdentificationHit current_id_hit_
IdentificationHit Item.
Definition: MzIdentMLHandler.h:301
const std::vector< ProteinIdentification > * cpro_id_
Definition: MzIdentMLHandler.h:294
const ProgressLogger & logger_
Progress logger.
Definition: MzIdentMLHandler.h:274
ControlledVocabulary cv_
Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)
Definition: MzIdentMLHandler.h:277
String tag_
XML tag parse element.
Definition: MzIdentMLHandler.h:284
std::map< String, String > ph_2_sdat_
mapping identification runs (mapping PeptideIdentifications and ProteinIdentifications via ....
Definition: MzIdentMLHandler.h:360
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:298
void writePeptideHit(const PeptideHit &hit, PeptideIdentificationList::const_iterator &it, std::map< String, String > &pep_ids, const 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.
MzIdentMLHandler & operator=(const MzIdentMLHandler &rhs)
MzIdentMLHandler(std::vector< ProteinIdentification > &pro_id, PeptideIdentificationList &pep_id, const String &filename, const String &version, const ProgressLogger &logger)
Constructor for a read-only handler for internal identification structures.
std::vector< ProteinIdentification > * pro_id_
internal Identification Item for proteins
Definition: MzIdentMLHandler.h:289
std::map< String, AASequence > pep_sequences_
Definition: MzIdentMLHandler.h:356
Identification * id_
Identification Item.
Definition: MzIdentMLHandler.h:287
ControlledVocabulary unimod_
Controlled vocabulary for modifications (unimod from OpenMS/share/OpenMS/CV/unimod....
Definition: MzIdentMLHandler.h:279
std::map< String, String > pp_identifier_2_sil_
mapping peptide/proteinidentification identifier_ to spectrumidentificationlist
Definition: MzIdentMLHandler.h:357
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:359
AASequence actual_peptide_
Definition: MzIdentMLHandler.h:362
~MzIdentMLHandler() override
Destructor.
void writeMetaInfos_(String &s, const MetaInfoInterface &meta, UInt indent) const
Writes user terms.
Int current_mod_location_
Definition: MzIdentMLHandler.h:363
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 writeEnzyme_(String &s, const DigestionEnzymeProtein &enzy, UInt miss, UInt indent) const
Helper method that writes a source file.
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)
const PeptideIdentificationList * cpep_id_
Definition: MzIdentMLHandler.h:295
Definition: MzIdentMLHandler.h:135
bool operator==(const SpectrumIdentification &rhs) const
Equality operator.
SpectrumIdentification & operator=(const SpectrumIdentification &)=default
Assignment operator.
bool operator!=(const SpectrumIdentification &rhs) const
Inequality operator.
const std::vector< IdentificationHit > & getHits() const
returns the identification hits of this spectrum identification
SpectrumIdentification & operator=(SpectrumIdentification &&) &=default
Move assignment operator.
virtual ~SpectrumIdentification()
Destructor.
std::vector< IdentificationHit > hits_
Single peptide hits.
Definition: MzIdentMLHandler.h:173
void addHit(const IdentificationHit &hit)
adds a single identification hit to the hits
SpectrumIdentification(SpectrumIdentification &&)=default
Move constructor.
String id_
Identifier.
Definition: MzIdentMLHandler.h:172
SpectrumIdentification(const SpectrumIdentification &)=default
Copy constructor.
Base class for XML handlers.
Definition: XMLHandler.h:328
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:35
Represents a single spectrum match (candidate) for a specific tandem mass spectrum (MS/MS).
Definition: PeptideHit.h:50
Container for peptide identifications from multiple spectra.
Definition: PeptideIdentificationList.h:66
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:27
Representation of a protein hit.
Definition: ProteinHit.h:34
A more convenient string class.
Definition: String.h:34
int Int
Signed integer type.
Definition: Types.h:72
unsigned int UInt
Unsigned integer type.
Definition: Types.h:64
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
PeptideIdentification SpectrumIdentification
Definition: PeptideIdentification.h:24
Representation of a CV term.
Definition: ControlledVocabulary.h:50