24 class ModificationsDB;
65 bool load_proteins =
true,
66 bool load_empty_hits =
true);
123 std::map<UInt, std::vector<const ResidueModification*> >
mods_map_;
char16_t XMLCh
Definition: ClassTest.h:28
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:23
Base class for XML handlers.
Definition: XMLHandler.h:328
Definition: ModificationDefinitionsSet.h:34
Used to load OMSSAXML files.
Definition: OMSSAXMLFile.h:37
OMSSAXMLFile & operator=(const OMSSAXMLFile &rhs)
std::vector< PeptideEvidence > actual_peptide_evidences_
Definition: OMSSAXMLFile.h:99
PeptideEvidence actual_peptide_evidence_
Definition: OMSSAXMLFile.h:97
void readMappingFile_()
reads the mapping file needed for modifications
ProteinIdentification actual_protein_id_
Definition: OMSSAXMLFile.h:103
PeptideIdentification actual_peptide_id_
Definition: OMSSAXMLFile.h:101
std::map< UInt, std::vector< const ResidueModification * > > mods_map_
modifications mapping file from OMSSA mod num to UniMod accession
Definition: OMSSAXMLFile.h:123
PeptideHit actual_peptide_hit_
Definition: OMSSAXMLFile.h:95
String tag_
Definition: OMSSAXMLFile.h:105
ModificationDefinitionsSet mod_def_set_
modification definitions set of the search, needed to annotate fixed modifications
Definition: OMSSAXMLFile.h:129
std::map< String, UInt > mods_to_num_
modification mapping reverse, from the modification to the mod_num
Definition: OMSSAXMLFile.h:126
OMSSAXMLFile()
Default constructor.
OMSSAXMLFile(const OMSSAXMLFile &rhs)
ProteinHit actual_protein_hit_
Definition: OMSSAXMLFile.h:93
bool load_empty_hits_
should empty peptide identifications be loaded or skipped?
Definition: OMSSAXMLFile.h:120
void startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
String actual_mod_type_
type of the modification
Definition: OMSSAXMLFile.h:111
void setModificationDefinitionsSet(const ModificationDefinitionsSet &rhs)
sets the valid modifications
bool load_proteins_
should protein hits be read from the file?
Definition: OMSSAXMLFile.h:117
void characters(const XMLCh *const chars, const XMLSize_t) override
std::vector< std::pair< UInt, String > > modifications_
modifications of the peptide defined by site and type
Definition: OMSSAXMLFile.h:114
~OMSSAXMLFile() override
Destructor.
void endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override
UInt actual_mod_site_
site of the actual modification (simple position in the peptide)
Definition: OMSSAXMLFile.h:108
PeptideIdentificationList * peptide_identifications_
the identifications (storing the peptide hits)
Definition: OMSSAXMLFile.h:91
Representation of a peptide evidence.
Definition: PeptideEvidence.h:25
Represents a single spectrum match (candidate) for a specific tandem mass spectrum (MS/MS).
Definition: PeptideHit.h:50
Container for peptide identifications from multiple spectra.
Definition: PeptideIdentificationList.h:66
Represents the set of candidates (SpectrumMatches) identified for a single precursor spectrum.
Definition: PeptideIdentification.h:63
Representation of a protein hit.
Definition: ProteinHit.h:34
Representation of a protein identification run.
Definition: ProteinIdentification.h:51
A more convenient string class.
Definition: String.h:34
unsigned int UInt
Unsigned integer type.
Definition: Types.h:64
void load(const String &filename, ProteinIdentification &protein_identification, PeptideIdentificationList &id_data, bool load_proteins=true, bool load_empty_hits=true)
loads data from a OMSSAXML file
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19