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