35 #ifndef OPENMS_FORMAT_HANDLERS_MZIDENTMLHANDLER_H 36 #define OPENMS_FORMAT_HANDLERS_MZIDENTMLHANDLER_H 91 virtual void endElement(
const XMLCh*
const ,
const XMLCh*
const ,
const XMLCh*
const qname);
94 virtual void startElement(
const XMLCh*
const ,
const XMLCh*
const ,
const XMLCh*
const qname,
const xercesc::Attributes& attributes);
97 virtual void characters(
const XMLCh*
const chars,
const XMLSize_t length);
100 virtual void writeTo(std::ostream& os);
124 const std::vector<ProteinIdentification>*
cpro_id_;
125 const std::vector<PeptideIdentification>*
cpep_id_;
134 void handleCVParam_(
const String& parent_parent_tag,
const String& parent_tag,
const String& accession,
const xercesc::Attributes& attributes,
const String& cv_ref );
152 void writeModParam_(
String& s,
const std::vector<String>& fixed,
const std::vector<String>& variable,
UInt indent)
const;
SpectrumIdentification current_spectrum_id_
SpectrumIdentification Item.
Definition: MzIdentMLHandler.h:128
std::vector< PeptideIdentification > * pep_id_
Identification Item for peptides.
Definition: MzIdentMLHandler.h:121
Representation of a CV term.
Definition: ControlledVocabulary.h:60
A more convenient string class.
Definition: String.h:57
Map< String, AASequence > pep_sequences_
Definition: MzIdentMLHandler.h:158
IdentificationHit current_id_hit_
IdentificationHit Item.
Definition: MzIdentMLHandler.h:131
Int current_mod_location_
Definition: MzIdentMLHandler.h:160
AASequence actual_peptide_
Definition: MzIdentMLHandler.h:159
Base class for XML handlers.
Definition: XMLHandler.h:99
const ProgressLogger & logger_
Progress logger.
Definition: MzIdentMLHandler.h:104
Representation of a peptide/protein sequence.
Definition: AASequence.h:70
String tag_
XML tag parse element.
Definition: MzIdentMLHandler.h:114
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
const std::vector< ProteinIdentification > * cpro_id_
Definition: MzIdentMLHandler.h:124
Representation of a controlled vocabulary.
Definition: ControlledVocabulary.h:54
DigestionEnzyme
Definition: ProteinIdentification.h:103
ControlledVocabulary cv_
Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)
Definition: MzIdentMLHandler.h:107
XML STREAM handler for MzIdentMLFile.
Definition: MzIdentMLHandler.h:69
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:161
Identification * id_
Identification Item.
Definition: MzIdentMLHandler.h:117
ControlledVocabulary unimod_
Controlled vocabulary for modifications (unimod from OpenMS/share/OpenMS/CV/unimod.obo)
Definition: MzIdentMLHandler.h:109
Representation of a protein hit.
Definition: ProteinHit.h:54
std::vector< ProteinIdentification > * pro_id_
internal Identification Item for proteins
Definition: MzIdentMLHandler.h:119
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:125
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
const Identification * cid_
Definition: MzIdentMLHandler.h:123
int Int
Signed integer type.
Definition: Types.h:96
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51