35 #ifndef OPENMS_FORMAT_HANDLERS_MZIDENTMLHANDLER_H
36 #define OPENMS_FORMAT_HANDLERS_MZIDENTMLHANDLER_H
86 virtual void endElement(
const XMLCh *
const ,
const XMLCh *
const ,
const XMLCh *
const qname);
89 virtual void startElement(
const XMLCh *
const ,
const XMLCh *
const ,
const XMLCh *
const qname,
const xercesc::Attributes & attributes);
92 virtual void characters(
const XMLCh *
const chars,
const XMLSize_t length);
95 virtual void writeTo(std::ostream & os);
120 const std::vector<ProteinIdentification> *
cpro_id_;
121 const std::vector<PeptideIdentification> *
cpep_id_;
130 void handleCVParam_(
const String & parent_parent_tag,
const String & parent_tag,
const String & accession,
const xercesc::Attributes & attributes,
const String & cv_ref );
133 void handleUserParam_(
const String & parent_parent_tag,
const String & parent_tag,
const String & name,
const String & type,
const String & value);
SpectrumIdentification current_spectrum_id_
SpectrumIdentification Item.
Definition: MzIdentMLHandler.h:124
std::vector< PeptideIdentification > * pep_id_
Identification Item for peptides.
Definition: MzIdentMLHandler.h:117
Representation of a CV term.
Definition: ControlledVocabulary.h:60
A more convenient string class.
Definition: String.h:56
Map< String, AASequence > pep_sequences_
Definition: MzIdentMLHandler.h:149
IdentificationHit current_id_hit_
IdentificationHit Item.
Definition: MzIdentMLHandler.h:127
Int current_mod_location_
Definition: MzIdentMLHandler.h:151
AASequence actual_peptide_
Definition: MzIdentMLHandler.h:150
Base class for XML handlers.
Definition: XMLHandler.h:89
const ProgressLogger & logger_
Progress logger.
Definition: MzIdentMLHandler.h:100
Representation of a peptide/protein sequence.
Definition: AASequence.h:84
String tag_
XML tag parse element.
Definition: MzIdentMLHandler.h:110
const std::vector< ProteinIdentification > * cpro_id_
Definition: MzIdentMLHandler.h:120
Representation of a controlled vocabulary.
Definition: ControlledVocabulary.h:54
ControlledVocabulary cv_
Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)
Definition: MzIdentMLHandler.h:103
XML handler for MzIdentMLFile.
Definition: MzIdentMLHandler.h:64
Represents a object which can store the information of an analysisXML instance.
Definition: SpectrumIdentification.h:50
Represents a object which can store the information of an analysisXML instance.
Definition: Identification.h:53
ProteinHit actual_protein_
Definition: MzIdentMLHandler.h:152
Identification * id_
Identification Item.
Definition: MzIdentMLHandler.h:113
ControlledVocabulary unimod_
Controlled vocabulary for modifications (unimod from OpenMS/share/OpenMS/CV/unimod.obo)
Definition: MzIdentMLHandler.h:105
Representation of a protein hit.
Definition: ProteinHit.h:54
std::vector< ProteinIdentification > * pro_id_
internal Identification Item for proteins
Definition: MzIdentMLHandler.h:115
Represents a object which can store the information of an analysisXML instance.
Definition: IdentificationHit.h:49
const std::vector< PeptideIdentification > * cpep_id_
Definition: MzIdentMLHandler.h:121
Base class for all classes that want to report their progess.
Definition: ProgressLogger.h:56
const Identification * cid_
Definition: MzIdentMLHandler.h:119
int Int
Signed integer type.
Definition: Types.h:100
Map class based on the STL map (containing serveral convenience functions)
Definition: Map.h:50