63 std::vector<ProteinIdentification>& proteins,
65 const String& experiment_name,
75 std::vector<ProteinIdentification>& proteins,
77 const String& experiment_name =
"");
84 void store(
const String& filename, std::vector<ProteinIdentification>& protein_ids,
86 const String& mz_name =
"",
bool peptideprophet_analyzed =
false,
double rt_tolerance = 0.01);
97 keep_native_name_ = keep;
143 const String& description,
157 const std::vector<const ResidueModification*>& preferred_fixed_mods,
158 const std::vector<const ResidueModification*>& preferred_var_mods,
208 bool use_precursor_data_{};
226 bool search_summary_{};
229 bool wrong_experiment_{};
232 bool seen_experiment_{};
235 bool checked_base_name_{};
241 bool parse_unknown_scores_{};
290 double hydrogen_mass_{};
317 Size modification_position,
318 std::vector<AminoAcidModification>
const& header_mods);
char16_t XMLCh
Definition: ClassTest.h:28
DateTime Class.
Definition: DateTime.h:33
Representation of an element.
Definition: Element.h:32
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:23
Base class for XML handlers.
Definition: XMLHandler.h:328
Used to load and store PepXML files.
Definition: PepXMLFile.h:41
void store(const String &filename, std::vector< ProteinIdentification > &protein_ids, PeptideIdentificationList &peptide_ids, const String &mz_file="", const String &mz_name="", bool peptideprophet_analyzed=false, double rt_tolerance=0.01)
Stores idXML as PepXML file.
static const double xtandem_artificial_mod_tol_
Definition: PepXMLFile.h:312
void load(const String &filename, std::vector< ProteinIdentification > &proteins, PeptideIdentificationList &peptides, const String &experiment_name="")
load function with empty defaults for some parameters (see above)
bool search_score_summary_
Are we currently in an "search_score_summary" element (should be skipped)?
Definition: PepXMLFile.h:223
String exp_name_
Name of the associated experiment (filename of the data file, extension will be removed)
Definition: PepXMLFile.h:196
void setParseUnknownScores(bool parse_unknown_scores)
sets if during load, unknown scores should be parsed
String current_base_name_
current base name
Definition: PepXMLFile.h:247
static const double mod_tol_
Definition: PepXMLFile.h:311
String current_sequence_
Sequence of the current peptide hit.
Definition: PepXMLFile.h:269
PeptideHit peptide_hit_
PeptideHit instance currently being processed.
Definition: PepXMLFile.h:266
std::vector< AminoAcidModification > variable_modifications_
Variable aminoacid modifications as parsed from the header.
Definition: PepXMLFile.h:299
void keepNativeSpectrumName(bool keep)
Whether we should keep the native spectrum name of the pepXML.
Definition: PepXMLFile.h:95
PeptideIdentification current_peptide_
PeptideIdentification instance currently being processed.
Definition: PepXMLFile.h:260
String search_engine_
Set name of search engine.
Definition: PepXMLFile.h:199
std::vector< std::pair< const ResidueModification *, Size > > current_modifications_
The modifications of the current peptide hit (position is 1-based)
Definition: PepXMLFile.h:293
String enzyme_
Enzyme name associated with the current identification run.
Definition: PepXMLFile.h:256
String enzyme_cuttingsite_
Definition: PepXMLFile.h:257
std::vector< std::vector< ProteinIdentification >::iterator > current_proteins_
References to currently active ProteinIdentifications.
Definition: PepXMLFile.h:250
std::vector< const ResidueModification * > preferred_fixed_modifications_
Definition: PepXMLFile.h:303
PeptideIdentificationList * peptides_
Pointer to the list of identified peptides.
Definition: PepXMLFile.h:190
~PepXMLFile() override
Destructor.
void load(const String &filename, std::vector< ProteinIdentification > &proteins, PeptideIdentificationList &peptides, const String &experiment_name, const SpectrumMetaDataLookup &lookup)
Loads peptide sequences with modifications out of a PepXML file.
PeptideHit::PepXMLAnalysisResult current_analysis_result_
Analysis result instance currently being processed.
Definition: PepXMLFile.h:263
std::vector< const ResidueModification * > preferred_variable_modifications_
Definition: PepXMLFile.h:307
bool analysis_summary_
Are we currently in an "analysis_summary" element (should be skipped)?
Definition: PepXMLFile.h:217
const SpectrumMetaDataLookup * lookup_
Pointer to wrapper for looking up spectrum meta data.
Definition: PepXMLFile.h:193
String native_spectrum_name_
Several optional attributes of spectrum_query.
Definition: PepXMLFile.h:202
String prot_id_
Identifier linking PeptideIdentifications and ProteinIdentifications.
Definition: PepXMLFile.h:284
void startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
Docu in base class.
bool keep_native_name_
Whether we should keep the native spectrum name of the pepXML.
Definition: PepXMLFile.h:220
std::vector< ProteinIdentification > * proteins_
Pointer to the list of identified proteins.
Definition: PepXMLFile.h:187
DateTime date_
Date the pepXML file was generated.
Definition: PepXMLFile.h:287
std::vector< AminoAcidModification > fixed_modifications_
Fixed aminoacid modifications as parsed from the header.
Definition: PepXMLFile.h:296
String decoy_prefix_
In case it has decoys, what is the prefix?
Definition: PepXMLFile.h:244
String swath_assay_
Definition: PepXMLFile.h:204
bool lookupAddFromHeader_(double modification_mass, Size modification_position, std::vector< AminoAcidModification > const &header_mods)
Element hydrogen_
Hydrogen data (for mass types)
Definition: PepXMLFile.h:214
String experiment_label_
Definition: PepXMLFile.h:203
ProteinIdentification::SearchParameters params_
Search parameters of the current identification run.
Definition: PepXMLFile.h:253
String status_
Definition: PepXMLFile.h:205
void readRTMZCharge_(const xercesc::Attributes &attributes)
Read RT, m/z, charge information from attributes of "spectrum_query".
void setPreferredFixedModifications(const std::vector< const ResidueModification * > &mods)
sets the preferred fixed modifications
void endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override
Docu in base class.
std::map< Size, Size > scan_map_
Mapping between scan number in the pepXML file and index in the corresponding MSExperiment.
Definition: PepXMLFile.h:211
void setPreferredVariableModifications(const std::vector< const ResidueModification * > &mods)
sets the preferred variable modifications
void makeScanMap_()
Fill scan_map_.
Analysis Result (containing search engine / prophet results)
Definition: PeptideHit.h:168
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
Represents the set of candidates (SpectrumMatches) identified for a single precursor spectrum.
Definition: PeptideIdentification.h:63
Representation of a modification on an amino acid residue.
Definition: ResidueModification.h:53
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:72
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
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:97
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
Definition: PepXMLFile.h:126
std::vector< String > errors_
Definition: PepXMLFile.h:137
double massdiff_
Definition: PepXMLFile.h:130
String toUnimodLikeString() const
double mass_
Definition: PepXMLFile.h:131
String aminoacid_
Definition: PepXMLFile.h:129
bool is_protein_terminus_
Definition: PepXMLFile.h:135
double getMassDiff() const
virtual ~AminoAcidModification()=default
String description_
Definition: PepXMLFile.h:133
const ResidueModification * registered_mod_
Definition: PepXMLFile.h:138
AminoAcidModification(const String &aminoacid, const String &massdiff, const String &mass, String variable, const String &description, String terminus, const String &protein_terminus, const std::vector< const ResidueModification * > &preferred_fixed_mods, const std::vector< const ResidueModification * > &preferred_var_mods, double tolerance)
AminoAcidModification(const AminoAcidModification &rhs)=default
ResidueModification::TermSpecificity term_spec_
Definition: PepXMLFile.h:136
const ResidueModification * lookupModInPreferredMods_(const std::vector< const ResidueModification * > &preferred_fixed_mods, const String &aminoacid, double massdiff, const String &description, const ResidueModification::TermSpecificity term_spec, double tolerance)
const std::vector< String > & getErrors() const
const String & getDescription() const
AminoAcidModification()=delete
const ResidueModification * getRegisteredMod() const
AminoAcidModification & operator=(const AminoAcidModification &rhs)=default
bool is_variable_
Definition: PepXMLFile.h:132
String terminus_
Definition: PepXMLFile.h:134
const String & getTerminus() const
const String & getAminoAcid() const
Search parameters of the DB search.
Definition: ProteinIdentification.h:248