35 #ifndef OPENMS_FORMAT_IDXMLFILE_H 36 #define OPENMS_FORMAT_IDXMLFILE_H 81 void load(
const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids);
92 void load(
const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids,
String& document_id);
101 void store(
String filename,
const std::vector<ProteinIdentification>& protein_ids,
const std::vector<PeptideIdentification>& peptide_ids,
const String& document_id =
"");
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);
111 void addProteinGroups_(
MetaInfoInterface& meta,
const std::vector<ProteinIdentification::ProteinGroup>& groups,
const String& group_name,
const std::map<String, UInt>& accession_to_id);
114 void getProteinGroups_(std::vector<ProteinIdentification::ProteinGroup>& groups,
const String& group_name);
118 std::vector<ProteinIdentification>* prot_ids_;
125 std::map<String, ProteinIdentification::SearchParameters>
parameters_;
151 #endif // OPENMS_FORMAT_IDXMLFILE_H Representation of a protein identification run.
Definition: ProteinIdentification.h:61
A more convenient string class.
Definition: String.h:57
PeptideHit pep_hit_
Temporary peptide hit.
Definition: IdXMLFile.h:137
ProteinIdentification prot_id_
Temporary protein ProteinIdentification.
Definition: IdXMLFile.h:131
std::vector< PeptideIdentification > * pep_ids_
Pointer to fill in peptide identifications.
Definition: IdXMLFile.h:121
bool prot_id_in_run_
true if a prot id is contained in the current run
Definition: IdXMLFile.h:145
String id_
Temporary id.
Definition: IdXMLFile.h:129
Base class for XML handlers.
Definition: XMLHandler.h:99
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
ProteinHit prot_hit_
Temporary protein hit.
Definition: IdXMLFile.h:135
PeptideIdentification pep_id_
Temporary peptide ProteinIdentification.
Definition: IdXMLFile.h:133
Search parameters of the DB search.
Definition: ProteinIdentification.h:117
ProteinIdentification::SearchParameters param_
Temporary search parameters variable.
Definition: IdXMLFile.h:127
std::vector< PeptideEvidence > peptide_evidences_
Temporary peptide evidences.
Definition: IdXMLFile.h:139
Representation of a peptide hit.
Definition: PeptideHit.h:55
std::map< String, ProteinIdentification::SearchParameters > parameters_
Search parameters map (key is the "id")
Definition: IdXMLFile.h:125
String * document_id_
Document identifier.
Definition: IdXMLFile.h:143
Representation of a protein hit.
Definition: ProteinHit.h:54
std::map< String, String > proteinid_to_accession_
Map from protein id to accession.
Definition: IdXMLFile.h:141
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:53
MetaInfoInterface * last_meta_
Pointer to last read object with MetaInfoInterface.
Definition: IdXMLFile.h:123
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
Used to load and store idXML files.
Definition: IdXMLFile.h:63