35 #ifndef OPENMS_FORMAT_PEPXMLFILE_H 36 #define OPENMS_FORMAT_PEPXMLFILE_H 85 void load(
const String& filename, std::vector<ProteinIdentification>& proteins, std::vector<PeptideIdentification>& peptides,
const String& experiment_name,
const MSExperiment<>& experiment,
bool use_precursor_data =
false);
93 void load(
const String& filename, std::vector<ProteinIdentification>& proteins, std::vector<PeptideIdentification>& peptides,
const String& experiment_name =
"");
100 void store(
const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids,
const String& mz_file =
"",
const String& mz_name =
"",
bool peptideprophet_analyzed =
false);
105 virtual void endElement(
const XMLCh*
const ,
const XMLCh*
const ,
const XMLCh*
const qname);
108 virtual void startElement(
const XMLCh*
const ,
const XMLCh*
const ,
const XMLCh*
const qname,
const xercesc::Attributes& attributes);
116 void readRTMZCharge_(
const xercesc::Attributes& attributes);
130 void matchModification_(
const double mass,
const String& origin,
String& modification_description);
148 aminoacid(rhs.aminoacid),
149 massdiff(rhs.massdiff),
151 variable(rhs.variable),
152 description(rhs.description),
153 terminus(rhs.terminus)
270 #endif // OPENMS_FORMAT_PEPXMLFILE_H
AminoAcidModification & operator=(const AminoAcidModification &rhs)
Definition: PepXMLFile.h:161
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:220
double mass
Definition: PepXMLFile.h:136
AminoAcidModification()
Definition: PepXMLFile.h:141
String exp_name_
Name of the associated experiment (filename of the data file, extension will be removed) ...
Definition: PepXMLFile.h:187
std::vector< ProteinIdentification > * proteins_
Pointer to the list of identified proteins.
Definition: PepXMLFile.h:178
Base class for XML handlers.
Definition: XMLHandler.h:99
Element hydrogen_
Hydrogen data (for mass types)
Definition: PepXMLFile.h:202
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
String terminus
Definition: PepXMLFile.h:139
String massdiff
Definition: PepXMLFile.h:135
double rt_
RT and m/z of current PeptideIdentification.
Definition: PepXMLFile.h:238
AminoAcidModification(const AminoAcidModification &rhs)
Definition: PepXMLFile.h:147
std::vector< AminoAcidModification > fixed_modifications_
Fixed aminoacid modifications.
Definition: PepXMLFile.h:259
ProteinIdentification::SearchParameters params_
Search parameters of the current identification run.
Definition: PepXMLFile.h:223
Search parameters of the DB search.
Definition: ProteinIdentification.h:117
Used to load and store PepXML files.
Definition: PepXMLFile.h:60
String current_base_name_
current base name
Definition: PepXMLFile.h:217
String current_sequence_
Sequence of the current peptide hit.
Definition: PepXMLFile.h:235
Definition: PepXMLFile.h:132
String description
Definition: PepXMLFile.h:138
bool seen_experiment_
Have we seen the experiment of interest at all?
Definition: PepXMLFile.h:211
bool use_precursor_data_
Get RT and m/z for peptide ID from precursor scan (should only matter for RT)?
Definition: PepXMLFile.h:193
Representation of an element.
Definition: Element.h:54
DigestionEnzyme
Definition: ProteinIdentification.h:103
double hydrogen_mass_
Mass of a hydrogen atom (monoisotopic/average depending on case)
Definition: PepXMLFile.h:253
UInt search_id_
ID of current search result.
Definition: PepXMLFile.h:244
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:196
double rt_tol_
Retention time and mass-to-charge tolerance.
Definition: PepXMLFile.h:199
std::vector< PeptideIdentification > * peptides_
Pointer to the list of identified peptides.
Definition: PepXMLFile.h:181
ProteinIdentification::DigestionEnzyme enzyme_
Enzyme associated with the current identification run.
Definition: PepXMLFile.h:226
bool wrong_experiment_
Do current entries belong to the experiment of interest (for pepXML files that bundle results from di...
Definition: PepXMLFile.h:208
Int charge_
Precursor ion charge.
Definition: PepXMLFile.h:241
DateTime date_
Date the pepXML file was generated.
Definition: PepXMLFile.h:250
std::vector< std::pair< String, Size > > current_modifications_
The modifications of the current peptide hit (position is 1-based)
Definition: PepXMLFile.h:256
DateTime Class.
Definition: DateTime.h:55
String prot_id_
Identifier linking PeptideIdentifications and ProteinIdentifications.
Definition: PepXMLFile.h:247
std::vector< AminoAcidModification > variable_modifications_
Variable aminoacid modifications.
Definition: PepXMLFile.h:262
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:53
PeptideHit peptide_hit_
PeptideHit instance currently being processed.
Definition: PepXMLFile.h:232
PeptideIdentification current_peptide_
PeptideIdentification instance currently being processed.
Definition: PepXMLFile.h:229
String aminoacid
Definition: PepXMLFile.h:134
bool checked_base_name_
Have we checked the "base_name" attribute in the "msms_run_summary" element?
Definition: PepXMLFile.h:214
bool analysis_summary_
Are we currently in an "analysis_summary" element (should be skipped)?
Definition: PepXMLFile.h:205
String search_engine_
Set name of search engine.
Definition: PepXMLFile.h:190
virtual ~AminoAcidModification()
Definition: PepXMLFile.h:157
int Int
Signed integer type.
Definition: Types.h:96
const MSExperiment * experiment_
Pointer to the experiment from which the pepXML file was generated.
Definition: PepXMLFile.h:184
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
bool variable
Definition: PepXMLFile.h:137