35 #ifndef OPENMS_FORMAT_HANDLERS_TRAMLHANDLER_H 36 #define OPENMS_FORMAT_HANDLERS_TRAMLHANDLER_H 77 virtual void endElement(
const XMLCh *
const ,
const XMLCh *
const ,
const XMLCh *
const qname);
80 virtual void startElement(
const XMLCh *
const ,
const XMLCh *
const ,
const XMLCh *
const qname,
const xercesc::Attributes & attributes);
83 virtual void characters(
const XMLCh *
const chars,
const XMLSize_t length);
86 virtual void writeTo(std::ostream & os);
137 void handleCVParam_(
const String & parent_parent_tag,
const String & parent_tag,
const CVTerm & cv_term);
140 void handleUserParam_(
const String & parent_parent_tag,
const String & parent_tag,
const String & name,
const String & type,
const String & value);
145 void writeUserParams_(std::ostream & os,
const std::vector<MetaInfoInterface> & meta,
UInt indent)
const;
147 template <
typename CVTList>
150 for (
Map<
String, std::vector<CVTerm> >::const_iterator it = cv_terms.getCVTerms().begin();
151 it != cv_terms.getCVTerms().end(); ++it)
153 for (std::vector<CVTerm>::const_iterator cit = it->second.begin(); cit != it->second.end(); ++cit)
155 os <<
String(2 * indent,
' ') <<
"<cvParam cvRef=\"" << cit->getCVIdentifierRef() <<
"\" accession=\"" << cit->getAccession() <<
"\" name=\"" << cit->getName() <<
"\"";
156 if (cit->hasValue() && !cit->getValue().isEmpty() && !cit->getValue().toString().empty())
158 os <<
" value=\"" << cit->getValue().toString() <<
"\"";
163 os <<
" unitCvRef=\"" << cit->getUnit().cv_ref <<
"\" unitAccession=\"" << cit->getUnit().accession <<
"\" unitName=\"" << cit->getUnit().name <<
"\"";
171 void writeTarget_(std::ostream & os,
const std::vector<IncludeExcludeTarget>::const_iterator & it)
const;
173 void writeProduct_(std::ostream & os,
const std::vector<ReactionMonitoringTransition::Product>::const_iterator & prod_it)
const;
175 void writeConfiguration_(std::ostream & os,
const std::vector<ReactionMonitoringTransition::Configuration>::const_iterator & cit)
const;
192 #endif // OPENMS_FORMAT_HANDLERS_TRAMLHANDLER_H TargetedExperiment::Prediction actual_prediction_
Definition: TraMLHandler.h:108
TargetedExperiment::Peptide actual_peptide_
Definition: TraMLHandler.h:116
Representation of a CV term.
Definition: ControlledVocabulary.h:61
A more convenient string class.
Definition: String.h:57
TargetedExperiment::Protein actual_protein_
Definition: TraMLHandler.h:112
String tag_
Definition: TraMLHandler.h:96
Representation of controlled vocabulary term list.
Definition: CVTermList.h:53
Software actual_software_
Definition: TraMLHandler.h:110
std::vector< ReactionMonitoringTransition::Configuration > ConfigurationListType
Definition: TraMLHandler.h:61
Definition: TargetedExperimentHelper.h:437
void writeCVParams_(std::ostream &os, const CVTList &cv_terms, UInt indent) const
Definition: TraMLHandler.h:148
unsigned int UInt
Unsigned integer type.
Definition: Types.h:95
TargetedExperiment::RetentionTime actual_rt_
Definition: TraMLHandler.h:114
XML handler for TraMLFile.
Definition: TraMLHandler.h:55
Base class for XML handlers.
Definition: XMLHandler.h:110
Description of a file location, used to store the origin of (meta) data.
Definition: SourceFile.h:47
Definition: TargetedExperimentHelper.h:524
Description of the software used for processing.
Definition: Software.h:49
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
TargetedExperiment::Instrument actual_instrument_
Definition: TraMLHandler.h:106
Representation of a controlled vocabulary.
Definition: ControlledVocabulary.h:55
ReactionMonitoringTransition::Product actual_product_
Definition: TraMLHandler.h:130
Definition: TargetedExperimentHelper.h:64
Definition: TargetedExperimentHelper.h:607
TargetedExperiment::Compound actual_compound_
Definition: TraMLHandler.h:118
IncludeExcludeTarget actual_target_
Definition: TraMLHandler.h:122
Representation of controlled vocabulary term.
Definition: CVTerm.h:51
const ProgressLogger & logger_
Progress logger.
Definition: TraMLHandler.h:91
TargetedExperiment::Contact actual_contact_
Definition: TraMLHandler.h:104
Definition: TargetedExperimentHelper.h:181
ControlledVocabulary cv_
Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)
Definition: TraMLHandler.h:94
ReactionMonitoringTransition::Configuration actual_configuration_
Definition: TraMLHandler.h:132
TargetedExperiment::Interpretation actual_interpretation_
Definition: TraMLHandler.h:126
This class stores a SRM/MRM transition.
Definition: IncludeExcludeTarget.h:53
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:62
Definition: TargetedExperimentHelper.h:465
Definition: TargetedExperimentHelper.h:142
Definition: TargetedExperimentHelper.h:493
ReactionMonitoringTransition actual_transition_
Definition: TraMLHandler.h:120
Definition: TargetedExperimentHelper.h:111
TargetedExperiment::Publication actual_publication_
Definition: TraMLHandler.h:102
TargetedExperiment * exp_
Definition: TraMLHandler.h:98
std::vector< ReactionMonitoringTransition::Product > ProductListType
Definition: TraMLHandler.h:60
std::vector< ReactionMonitoringTransition::Product > actual_intermediate_products_
Definition: TraMLHandler.h:128
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51
Definition: TargetedExperimentHelper.h:266
SourceFile actual_sourcefile_
Definition: TraMLHandler.h:134
CVTermList actual_validation_
Definition: TraMLHandler.h:124
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:56
const TargetedExperiment * cexp_
Definition: TraMLHandler.h:100