73 void endElement(
const XMLCh *
const ,
const XMLCh *
const ,
const XMLCh *
const qname)
override;
76 void startElement(
const XMLCh *
const ,
const XMLCh *
const ,
const XMLCh *
const qname,
const xercesc::Attributes & attributes)
override;
79 void characters(
const XMLCh *
const chars,
const XMLSize_t length)
override;
142 std::map<String, ConsensusFeature::Ratio>
r_rtemp_;
144 std::map<String, ConsensusFeature::Ratio>
r_r_obj_;
Representation of a controlled vocabulary.
Definition: ControlledVocabulary.h:55
XML handler for MzQuantMLFile.
Definition: MzQuantMLHandler.h:57
ControlledVocabulary::CVTerm getChildWithName_(const String &parent_accession, const String &name) const
Looks up a child CV term of parent_accession with the name name. If no such term is found,...
std::map< String, std::vector< ExperimentalSettings > > current_files_
1.rawfilesgroup_ref 2.inputfiles for each assay as ExperimentalSettings
Definition: MzQuantMLHandler.h:129
void writeFeature_(String &feature_xml, const std::vector< FeatureMap > &fm, UInt indentation_level)
Helper method that writes the featuremaps.
std::map< String, ConsensusFeature::Ratio > r_rtemp_
Definition: MzQuantMLHandler.h:142
std::map< int, DataProcessing > current_orderedps_
Definition: MzQuantMLHandler.h:148
MSQuantifications::Assay current_assay_
Definition: MzQuantMLHandler.h:136
Size current_count_
Definition: MzQuantMLHandler.h:132
MzQuantMLHandler(const MzQuantMLHandler &rhs)
MSQuantifications * msq_
Definition: MzQuantMLHandler.h:94
~MzQuantMLHandler() override
Destructor.
MzQuantMLHandler(const MSQuantifications &msq, const String &filename, const String &version, const ProgressLogger &logger)
Constructor for a write-only handler.
std::map< String, ConsensusFeature::Ratio > r_r_obj_
Definition: MzQuantMLHandler.h:144
std::vector< double > current_row_
Definition: MzQuantMLHandler.h:154
void writeTo(std::ostream &os) override
Writes the contents to a stream.
MzQuantMLHandler(MSQuantifications &msq, const String &filename, const String &version, const ProgressLogger &logger)
Constructor for a read-only handler.
std::vector< String > current_col_types_
Definition: MzQuantMLHandler.h:152
const ProgressLogger & logger_
Progress logger.
Definition: MzQuantMLHandler.h:87
ControlledVocabulary cv_
Controlled vocabulary (hopefully the psi-pi from OpenMS/share/OpenMS/CV/psi-pi.obo)
Definition: MzQuantMLHandler.h:90
String tag_
Definition: MzQuantMLHandler.h:92
std::multimap< String, String > cm_cf_ids_
Definition: MzQuantMLHandler.h:138
String current_cf_id_
Definition: MzQuantMLHandler.h:131
String current_id_
Definition: MzQuantMLHandler.h:130
std::vector< CVTerm > cvp_stack_
Definition: MzQuantMLHandler.h:135
std::vector< MetaInfo > up_stack_
Definition: MzQuantMLHandler.h:134
std::pair< int, DataProcessing > current_dp_
Definition: MzQuantMLHandler.h:149
MzQuantMLHandler()
Helper method that writes a source file.
std::vector< double > current_dm_values_
Definition: MzQuantMLHandler.h:153
void handleCVParam_(const String &parent_parent_tag, const String &parent_tag, const String &accession, const String &name, const String &value, const xercesc::Attributes &attributes, const String &cv_ref, const String &unit_accession="")
Handles CV terms.
std::map< String, Software > current_sws_
Definition: MzQuantMLHandler.h:147
const MSQuantifications * cmsq_
Definition: MzQuantMLHandler.h:96
void writeUserParams_(std::ostream &os, const MetaInfoInterface &meta, UInt indent)
Writes user terms.
std::map< String, String > numden_r_ids_
Definition: MzQuantMLHandler.h:143
std::map< String, ConsensusFeature > cf_cf_obj_
Definition: MzQuantMLHandler.h:140
void startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
void writeUserParams_(String &s, const MetaInfoInterface &meta, UInt indent)
std::set< DataProcessing::ProcessingAction > current_pas_
Definition: MzQuantMLHandler.h:150
MzQuantMLHandler & operator=(const MzQuantMLHandler &rhs)
void characters(const XMLCh *const chars, const XMLSize_t length) override
void endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override
void handleUserParam_(const String &parent_parent_tag, const String &parent_tag, const String &name, const String &type, const String &value)
Handles user terms.
void writeCVParams_(String &s, const std::map< String, std::vector< CVTerm > > &, UInt indent)
Write CV term.
std::map< String, FeatureHandle > f_f_obj_
Definition: MzQuantMLHandler.h:141
std::map< String, String > f_cf_ids_
Definition: MzQuantMLHandler.h:139
Base class for XML handlers.
Definition: XMLHandler.h:326
Definition: MSQuantifications.h:53
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:53
A more convenient string class.
Definition: String.h:60
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
Representation of a CV term.
Definition: ControlledVocabulary.h:61
Definition: MSQuantifications.h:110