35 #ifndef OPENMS_FORMAT_OMSSAXMLFILE_H 
   36 #define OPENMS_FORMAT_OMSSAXMLFILE_H 
   51   class ModificationsDB;
 
   88     void load(
const String & filename, 
ProteinIdentification & protein_identification, std::vector<PeptideIdentification> & id_data, 
bool load_proteins = 
true);
 
   95     void endElement(
const XMLCh * 
const , 
const XMLCh * 
const , 
const XMLCh * 
const qname);
 
   98     void startElement(
const XMLCh * 
const , 
const XMLCh * 
const , 
const XMLCh * 
const qname, 
const xercesc::Attributes & attributes);
 
  101     void characters(
const XMLCh * 
const chars, 
const XMLSize_t );
 
  110     void readMappingFile_();
 
  149 #endif // OPENMS_FORMAT_OMSSAXMLFILE_H 
Representation of a protein identification run. 
Definition: ProteinIdentification.h:61
Map< UInt, std::vector< ResidueModification > > mods_map_
modifications mapping file from OMSSA mod num to UniMod accession 
Definition: OMSSAXMLFile.h:138
A more convenient string class. 
Definition: String.h:56
PeptideIdentification actual_peptide_id_
Definition: OMSSAXMLFile.h:119
ProteinHit actual_protein_hit_
Definition: OMSSAXMLFile.h:115
Base class for XML handlers. 
Definition: XMLHandler.h:89
String actual_mod_type_
type of the modification 
Definition: OMSSAXMLFile.h:129
PeptideHit actual_peptide_hit_
Definition: OMSSAXMLFile.h:117
Representation of a peptide hit. 
Definition: PeptideHit.h:54
Representation of a set of modification definitions. 
Definition: ModificationDefinitionsSet.h:57
Map< String, UInt > mods_to_num_
modification mapping reverse, from the modification to the mod_num 
Definition: OMSSAXMLFile.h:141
Used to load OMSSAXML files. 
Definition: OMSSAXMLFile.h:61
Representation of a protein hit. 
Definition: ProteinHit.h:54
String tag_
Definition: OMSSAXMLFile.h:123
std::vector< PeptideIdentification > * peptide_identifications_
the identifications (storing the peptide hits) 
Definition: OMSSAXMLFile.h:113
ProteinIdentification actual_protein_id_
Definition: OMSSAXMLFile.h:121
Base class for loading/storing XML files that have a handler derived from XMLHandler. 
Definition: XMLFile.h:51
UInt actual_mod_site_
site of the actual modification (simple position in the peptide) 
Definition: OMSSAXMLFile.h:126
ModificationDefinitionsSet mod_def_set_
modification definitions set of the search, needed to annotate fixed modifications ...
Definition: OMSSAXMLFile.h:144
Map class based on the STL map (containing serveral convenience functions) 
Definition: Map.h:50
std::vector< std::pair< UInt, String > > modifications_
modifications of the peptide defined by site and type 
Definition: OMSSAXMLFile.h:132
bool load_proteins_
should protein hits be read from the file? 
Definition: OMSSAXMLFile.h:135
Represents the peptide hits for a spectrum. 
Definition: PeptideIdentification.h:63