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OpenMS
2.6.0
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87 void load(
const String& filename,
88 std::vector<ProteinIdentification>& proteins,
89 std::vector<PeptideIdentification>& peptides,
90 const String& experiment_name,
99 void load(
const String& filename,
100 std::vector<ProteinIdentification>& proteins,
101 std::vector<PeptideIdentification>& peptides,
102 const String& experiment_name =
"");
109 void store(
const String& filename, std::vector<ProteinIdentification>& protein_ids,
110 std::vector<PeptideIdentification>& peptide_ids,
const String& mz_file =
"",
111 const String& mz_name =
"",
bool peptideprophet_analyzed =
false,
double rt_tolerance = 0.01);
122 keep_native_name_ = keep;
128 void endElement(
const XMLCh*
const ,
const XMLCh*
const ,
const XMLCh*
const qname)
override;
131 void startElement(
const XMLCh*
const ,
const XMLCh*
const ,
const XMLCh*
const qname,
const xercesc::Attributes& attributes)
override;
139 void readRTMZCharge_(
const xercesc::Attributes& attributes);
173 String toUnimodLikeString()
const;
175 const String& getDescription()
const;
177 bool isVariable()
const;
181 double getMassDiff()
const;
183 double getMass()
const;
185 const String& getTerminus()
const;
187 const String& getAminoAcid()
const;
189 const std::vector<String>& getErrors()
const;
214 bool use_precursor_data_{};
232 bool search_summary_{};
235 bool wrong_experiment_{};
238 bool seen_experiment_{};
241 bool checked_base_name_{};
290 double hydrogen_mass_{};
308 bool lookupAddFromHeader_(
double modification_mass,
309 Size modification_position,
310 std::vector<AminoAcidModification>
const& header_mods);
String native_spectrum_name_
Several optional attributes of spectrum_query.
Definition: PepXMLFile.h:208
String swath_assay_
Definition: PepXMLFile.h:210
const ResidueModification * registered_mod_
Definition: PepXMLFile.h:154
bool analysis_summary_
Are we currently in an "analysis_summary" element (should be skipped)?
Definition: PepXMLFile.h:223
Representation of a modification.
Definition: ResidueModification.h:76
String prot_id_
Identifier linking PeptideIdentifications and ProteinIdentifications.
Definition: PepXMLFile.h:284
Base class for XML handlers.
Definition: XMLHandler.h:151
String enzyme_cuttingsite_
Definition: PepXMLFile.h:260
Representation of an element.
Definition: Element.h:53
bool is_variable_
Definition: PepXMLFile.h:148
Analysis Result (containing search engine / prophet results)
Definition: PeptideHit.h:211
std::map< Size, Size > scan_map_
Mapping between scan number in the pepXML file and index in the corresponding MSExperiment.
Definition: PepXMLFile.h:217
std::vector< std::vector< ProteinIdentification >::iterator > current_proteins_
References to currently active ProteinIdentifications.
Definition: PepXMLFile.h:253
static const double mod_tol_
Definition: PepXMLFile.h:303
A more convenient string class.
Definition: String.h:59
bool is_protein_terminus_
Definition: PepXMLFile.h:151
Element hydrogen_
Hydrogen data (for mass types)
Definition: PepXMLFile.h:220
void keepNativeSpectrumName(bool keep)
Whether we should keep the native spectrum name of the pepXML.
Definition: PepXMLFile.h:120
String enzyme_
Enzyme name associated with the current identification run.
Definition: PepXMLFile.h:259
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
PeptideHit peptide_hit_
PeptideHit instance currently being processed.
Definition: PepXMLFile.h:269
static const double xtandem_artificial_mod_tol_
Definition: PepXMLFile.h:304
Definition: PepXMLFile.h:141
PeptideIdentification current_peptide_
PeptideIdentification instance currently being processed.
Definition: PepXMLFile.h:263
String terminus_
Definition: PepXMLFile.h:150
DateTime date_
Date the pepXML file was generated.
Definition: PepXMLFile.h:287
ProteinIdentification::SearchParameters params_
Search parameters of the current identification run.
Definition: PepXMLFile.h:256
std::vector< ProteinIdentification > * proteins_
Pointer to the list of identified proteins.
Definition: PepXMLFile.h:193
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
String search_engine_
Set name of search engine.
Definition: PepXMLFile.h:205
const SpectrumMetaDataLookup * lookup_
Pointer to wrapper for looking up spectrum meta data.
Definition: PepXMLFile.h:199
std::vector< AminoAcidModification > variable_modifications_
Variable aminoacid modifications.
Definition: PepXMLFile.h:299
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:95
String description_
Definition: PepXMLFile.h:149
double massdiff_
Definition: PepXMLFile.h:146
std::vector< String > errors_
Definition: PepXMLFile.h:153
String decoy_prefix_
In case it has decoys, what is the prefix?
Definition: PepXMLFile.h:247
bool search_score_summary_
Are we currently in an "search_score_summary" element (should be skipped)?
Definition: PepXMLFile.h:229
String status_
Definition: PepXMLFile.h:211
ResidueModification::TermSpecificity term_spec_
Definition: PepXMLFile.h:152
bool keep_native_name_
Whether we should keep the native spectrum name of the pepXML.
Definition: PepXMLFile.h:226
double mass_
Definition: PepXMLFile.h:147
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
std::vector< AminoAcidModification > fixed_modifications_
Fixed aminoacid modifications.
Definition: PepXMLFile.h:296
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
String exp_name_
Name of the associated experiment (filename of the data file, extension will be removed)
Definition: PepXMLFile.h:202
String current_base_name_
current base name
Definition: PepXMLFile.h:250
PeptideHit::PepXMLAnalysisResult current_analysis_result_
Analysis result instance currently being processed.
Definition: PepXMLFile.h:266
String experiment_label_
Definition: PepXMLFile.h:209
String aminoacid_
Definition: PepXMLFile.h:145
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
String current_sequence_
Sequence of the current peptide hit.
Definition: PepXMLFile.h:272
Used to load and store PepXML files.
Definition: PepXMLFile.h:63
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
std::vector< std::pair< const ResidueModification *, Size > > current_modifications_
The modifications of the current peptide hit (position is 1-based)
Definition: PepXMLFile.h:293
DateTime Class.
Definition: DateTime.h:54
std::vector< PeptideIdentification > * peptides_
Pointer to the list of identified peptides.
Definition: PepXMLFile.h:196
Representation of a peptide hit.
Definition: PeptideHit.h:55