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_;
 
  149 #endif // OPENMS_FORMAT_IDXMLFILE_H 
Representation of a protein identification run. 
Definition: ProteinIdentification.h:61
A more convenient string class. 
Definition: String.h:56
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:143
String id_
Temporary id. 
Definition: IdXMLFile.h:129
Base class for XML handlers. 
Definition: XMLHandler.h:89
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:115
ProteinIdentification::SearchParameters param_
Temporary search parameters variable. 
Definition: IdXMLFile.h:127
Representation of a peptide hit. 
Definition: PeptideHit.h:54
std::map< String, ProteinIdentification::SearchParameters > parameters_
Search parameters map (key is the "id") 
Definition: IdXMLFile.h:125
String * document_id_
Document identitifier. 
Definition: IdXMLFile.h:141
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:139
Base class for loading/storing XML files that have a handler derived from XMLHandler. 
Definition: XMLFile.h:51
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