73 void setId(const std::
string&
id) noexcept;
77 const std::
string& getId() const noexcept;
80 void setCharge(
int charge) noexcept;
83 int getCharge() const noexcept;
86 void setCalculatedMassToCharge(
double mz) noexcept;
89 double getCalculatedMassToCharge() const noexcept;
92 void setExperimentalMassToCharge(
double mz) noexcept;
95 double getExperimentalMassToCharge() const noexcept;
98 void setName(const std::
string& name) noexcept;
101 const std::
string& getName() const noexcept;
104 void setPassThreshold(
bool pass) noexcept;
107 bool getPassThreshold() const noexcept;
110 void setRank(
int rank) noexcept;
113 int getRank() const noexcept;
119 double calculated_mass_to_charge_ = 0.0;
120 double experimental_mass_to_charge_ = 0.0;
122 bool pass_threshold_ = true;
160 void setHits(
const std::vector<IdentificationHit> & hits);
167 const std::vector<IdentificationHit> &
getHits()
const;
173 std::vector<IdentificationHit>
hits_;
213 void setCreationDate(
const DateTime & date);
294 const std::vector<ProteinIdentification>*
cpro_id_;
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,
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);
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
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