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