35 #ifndef OPENMS_FORMAT_OMSSAXMLFILE_H 36 #define OPENMS_FORMAT_OMSSAXMLFILE_H 51 class ModificationsDB;
89 void load(
const String& filename,
91 std::vector<PeptideIdentification>& id_data,
92 bool load_proteins =
true,
93 bool load_empty_hits =
true);
100 void endElement(
const XMLCh*
const ,
const XMLCh*
const ,
const XMLCh*
const qname);
103 void startElement(
const XMLCh*
const ,
const XMLCh*
const ,
const XMLCh*
const qname,
const xercesc::Attributes& attributes);
106 void characters(
const XMLCh*
const chars,
const XMLSize_t );
115 void readMappingFile_();
161 #endif // OPENMS_FORMAT_OMSSAXMLFILE_H Representation of a protein identification run.
Definition: ProteinIdentification.h:62
Map< UInt, std::vector< ResidueModification > > mods_map_
modifications mapping file from OMSSA mod num to UniMod accession
Definition: OMSSAXMLFile.h:150
A more convenient string class.
Definition: String.h:57
bool load_empty_hits_
should empty peptide identifications be loaded or skipped?
Definition: OMSSAXMLFile.h:147
PeptideEvidence actual_peptide_evidence_
Definition: OMSSAXMLFile.h:124
PeptideIdentification actual_peptide_id_
Definition: OMSSAXMLFile.h:128
ProteinHit actual_protein_hit_
Definition: OMSSAXMLFile.h:120
unsigned int UInt
Unsigned integer type.
Definition: Types.h:95
Base class for XML handlers.
Definition: XMLHandler.h:110
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
String actual_mod_type_
type of the modification
Definition: OMSSAXMLFile.h:138
PeptideHit actual_peptide_hit_
Definition: OMSSAXMLFile.h:122
Representation of a peptide hit.
Definition: PeptideHit.h:55
Representation of a set of modification definitions.
Definition: ModificationDefinitionsSet.h:59
Representation of a peptide evidence.
Definition: PeptideEvidence.h:51
std::vector< PeptideEvidence > actual_peptide_evidences_
Definition: OMSSAXMLFile.h:126
Map< String, UInt > mods_to_num_
modification mapping reverse, from the modification to the mod_num
Definition: OMSSAXMLFile.h:153
Used to load OMSSAXML files.
Definition: OMSSAXMLFile.h:61
Representation of a protein hit.
Definition: ProteinHit.h:54
String tag_
Definition: OMSSAXMLFile.h:132
std::vector< PeptideIdentification > * peptide_identifications_
the identifications (storing the peptide hits)
Definition: OMSSAXMLFile.h:118
ProteinIdentification actual_protein_id_
Definition: OMSSAXMLFile.h:130
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:49
UInt actual_mod_site_
site of the actual modification (simple position in the peptide)
Definition: OMSSAXMLFile.h:135
ModificationDefinitionsSet mod_def_set_
modification definitions set of the search, needed to annotate fixed modifications ...
Definition: OMSSAXMLFile.h:156
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51
std::vector< std::pair< UInt, String > > modifications_
modifications of the peptide defined by site and type
Definition: OMSSAXMLFile.h:141
bool load_proteins_
should protein hits be read from the file?
Definition: OMSSAXMLFile.h:144
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63