35 #ifndef OPENMS_FORMAT_PEPXMLFILE_H 36 #define OPENMS_FORMAT_PEPXMLFILE_H 84 void load(
const String& filename,
85 std::vector<ProteinIdentification>& proteins,
86 std::vector<PeptideIdentification>& peptides,
87 const String& experiment_name,
96 void load(
const String& filename,
97 std::vector<ProteinIdentification>& proteins,
98 std::vector<PeptideIdentification>& peptides,
99 const String& experiment_name =
"");
106 void store(
const String& filename, std::vector<ProteinIdentification>& protein_ids,
107 std::vector<PeptideIdentification>& peptide_ids,
const String& mz_file =
"",
108 const String& mz_name =
"",
bool peptideprophet_analyzed =
false);
119 keep_native_name_ = keep;
125 virtual void endElement(
const XMLCh*
const ,
const XMLCh*
const ,
const XMLCh*
const qname);
128 virtual void startElement(
const XMLCh*
const ,
const XMLCh*
const ,
const XMLCh*
const qname,
const xercesc::Attributes& attributes);
136 void readRTMZCharge_(
const xercesc::Attributes& attributes);
150 void matchModification_(
const double mass,
const String& origin,
String& modification_description);
168 aminoacid(rhs.aminoacid),
169 massdiff(rhs.massdiff),
171 variable(rhs.variable),
172 description(rhs.description),
173 terminus(rhs.terminus)
307 #endif // OPENMS_FORMAT_PEPXMLFILE_H AminoAcidModification & operator=(const AminoAcidModification &rhs)
Definition: PepXMLFile.h:181
A more convenient string class.
Definition: String.h:57
std::vector< std::vector< ProteinIdentification >::iterator > current_proteins_
References to currently active ProteinIdentifications.
Definition: PepXMLFile.h:252
double mass
Definition: PepXMLFile.h:156
AminoAcidModification()
Definition: PepXMLFile.h:161
unsigned int UInt
Unsigned integer type.
Definition: Types.h:95
String exp_name_
Name of the associated experiment (filename of the data file, extension will be removed) ...
Definition: PepXMLFile.h:207
std::vector< ProteinIdentification > * proteins_
Pointer to the list of identified proteins.
Definition: PepXMLFile.h:198
Base class for XML handlers.
Definition: XMLHandler.h:110
Element hydrogen_
Hydrogen data (for mass types)
Definition: PepXMLFile.h:225
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
String terminus
Definition: PepXMLFile.h:159
String massdiff
Definition: PepXMLFile.h:155
double rt_
RT and m/z of current PeptideIdentification.
Definition: PepXMLFile.h:273
AminoAcidModification(const AminoAcidModification &rhs)
Definition: PepXMLFile.h:167
std::vector< AminoAcidModification > fixed_modifications_
Fixed aminoacid modifications.
Definition: PepXMLFile.h:294
ProteinIdentification::SearchParameters params_
Search parameters of the current identification run.
Definition: PepXMLFile.h:255
String status_
Definition: PepXMLFile.h:216
Search parameters of the DB search.
Definition: ProteinIdentification.h:104
bool search_score_summary_
Are we currently in an "search_score_summary" element (should be skipped)?
Definition: PepXMLFile.h:234
Used to load and store PepXML files.
Definition: PepXMLFile.h:60
String current_base_name_
current base name
Definition: PepXMLFile.h:249
String current_sequence_
Sequence of the current peptide hit.
Definition: PepXMLFile.h:270
Definition: PepXMLFile.h:152
String description
Definition: PepXMLFile.h:158
bool seen_experiment_
Have we seen the experiment of interest at all?
Definition: PepXMLFile.h:243
bool use_precursor_data_
Get RT and m/z for peptide ID from precursor scan (should only matter for RT)?
Definition: PepXMLFile.h:219
bool search_summary_
Are we currently in an "search_summary" element (should be skipped)?
Definition: PepXMLFile.h:237
Representation of an element.
Definition: Element.h:54
const SpectrumMetaDataLookup * lookup_
Pointer to wrapper for looking up spectrum meta data.
Definition: PepXMLFile.h:204
double hydrogen_mass_
Mass of a hydrogen atom (monoisotopic/average depending on case)
Definition: PepXMLFile.h:288
UInt search_id_
ID of current search result.
Definition: PepXMLFile.h:279
Representation of a peptide hit.
Definition: PeptideHit.h:55
std::map< Size, Size > scan_map_
Mapping between scan number in the pepXML file and index in the corresponding MSExperiment.
Definition: PepXMLFile.h:222
static const double mod_tol_
Definition: PepXMLFile.h:301
String experiment_label_
Definition: PepXMLFile.h:214
std::vector< PeptideIdentification > * peptides_
Pointer to the list of identified peptides.
Definition: PepXMLFile.h:201
bool wrong_experiment_
Do current entries belong to the experiment of interest (for pepXML files that bundle results from di...
Definition: PepXMLFile.h:240
Int charge_
Precursor ion charge.
Definition: PepXMLFile.h:276
DateTime date_
Date the pepXML file was generated.
Definition: PepXMLFile.h:285
Analysis Result (containing search engine / prophet results)
Definition: PeptideHit.h:189
void keepNativeSpectrumName(bool keep)
Whether we should keep the native spectrum name of the pepXML.
Definition: PepXMLFile.h:117
String swath_assay_
Definition: PepXMLFile.h:215
std::vector< std::pair< String, Size > > current_modifications_
The modifications of the current peptide hit (position is 1-based)
Definition: PepXMLFile.h:291
DateTime Class.
Definition: DateTime.h:55
String native_spectrum_name_
Several optional attributes of spectrum_query.
Definition: PepXMLFile.h:213
String prot_id_
Identifier linking PeptideIdentifications and ProteinIdentifications.
Definition: PepXMLFile.h:282
std::vector< AminoAcidModification > variable_modifications_
Variable aminoacid modifications.
Definition: PepXMLFile.h:297
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:49
PeptideHit peptide_hit_
PeptideHit instance currently being processed.
Definition: PepXMLFile.h:267
PeptideIdentification current_peptide_
PeptideIdentification instance currently being processed.
Definition: PepXMLFile.h:261
String aminoacid
Definition: PepXMLFile.h:154
bool checked_base_name_
Have we checked the "base_name" attribute in the "msms_run_summary" element?
Definition: PepXMLFile.h:246
bool analysis_summary_
Are we currently in an "analysis_summary" element (should be skipped)?
Definition: PepXMLFile.h:228
static const double xtandem_artificial_mod_tol_
Definition: PepXMLFile.h:302
String search_engine_
Set name of search engine.
Definition: PepXMLFile.h:210
virtual ~AminoAcidModification()
Definition: PepXMLFile.h:177
int Int
Signed integer type.
Definition: Types.h:103
String enzyme_
Enzyme name associated with the current identification run.
Definition: PepXMLFile.h:258
PeptideHit::PepXMLAnalysisResult current_analysis_result_
Analysis result instance currently being processed.
Definition: PepXMLFile.h:264
bool keep_native_name_
Whether we should keep the native spectrum name of the pepXML.
Definition: PepXMLFile.h:231
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
bool variable
Definition: PepXMLFile.h:157