35 #ifndef OPENMS_FORMAT_HANDLERS_MASCOTXMLHANDLER_H
36 #define OPENMS_FORMAT_HANDLERS_MASCOTXMLHANDLER_H
46 #include <boost/regex.hpp>
64 std::vector<PeptideIdentification>& identifications,
66 std::map<
String, std::vector<AASequence> >& peptides,
67 const RTMapping& rt_mapping = RTMapping(),
68 const String& scan_regex =
"");
74 virtual void endElement(
const XMLCh*
const ,
const XMLCh*
const ,
const XMLCh*
const qname);
77 virtual void startElement(
const XMLCh*
const ,
const XMLCh*
const ,
const XMLCh*
const qname,
const xercesc::Attributes& attributes);
80 virtual void characters(
const XMLCh*
const chars,
const XMLSize_t );
121 #endif // OPENMS_FORMAT_HANDLERS_MASCOTXMLHANDLER_H
Representation of a protein identification run.
Definition: ProteinIdentification.h:61
A more convenient string class.
Definition: String.h:57
String date_time_string_
Definition: MascotXMLHandler.h:95
StringList tags_open_
tracking the current XML tree
Definition: MascotXMLHandler.h:102
String minor_version_
Definition: MascotXMLHandler.h:105
String actual_title_
Definition: MascotXMLHandler.h:99
Base class for XML handlers.
Definition: XMLHandler.h:99
ProteinIdentification & protein_identification_
the protein identifications
Definition: MascotXMLHandler.h:87
ProteinHit actual_protein_hit_
Definition: MascotXMLHandler.h:89
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Handler that is used for parsing MascotXML data.
Definition: MascotXMLHandler.h:55
Search parameters of the DB search.
Definition: ProteinIdentification.h:117
bool no_rt_error_
Error for missing RT information already reported?
Definition: MascotXMLHandler.h:115
String tag_
Definition: MascotXMLHandler.h:93
String major_version_
Definition: MascotXMLHandler.h:104
DateTime date_
Definition: MascotXMLHandler.h:94
PeptideEvidence actual_peptide_evidence_
Definition: MascotXMLHandler.h:91
Representation of a peptide hit.
Definition: PeptideHit.h:55
Representation of a peptide evidence.
Definition: PeptideEvidence.h:51
UInt actual_query_
Definition: MascotXMLHandler.h:96
std::vector< PeptideIdentification > & id_data_
the identifications (storing the peptide hits)
Definition: MascotXMLHandler.h:88
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:74
Representation of a protein hit.
Definition: ProteinHit.h:54
UInt peptide_identification_index_
Definition: MascotXMLHandler.h:92
std::vector< boost::regex > scan_regex_
List of possible Perl-style regular expressions used to extract the scan number (named group "SCAN") ...
Definition: MascotXMLHandler.h:112
DateTime Class.
Definition: DateTime.h:55
String identifier_
Definition: MascotXMLHandler.h:98
const RTMapping & rt_mapping_
Definition: MascotXMLHandler.h:107
PeptideHit actual_peptide_hit_
Definition: MascotXMLHandler.h:90
Map< Size, float > RTMapping
Definition: MascotXMLHandler.h:60
ProteinIdentification::SearchParameters search_parameters_
Definition: MascotXMLHandler.h:97
String character_buffer_
filled by MascotXMLHandler::characters
Definition: MascotXMLHandler.h:103
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51
static const String primary_scan_regex
Definition: MascotXMLHandler.h:83
std::map< String, std::vector< AASequence > > & modified_peptides_
Definition: MascotXMLHandler.h:100