Uses of Class
de.isas.mztab2.model.Parameter

Packages that use Parameter

Package	Description
de.isas.lipidomics.mztab2.validation.validators	This package contains custom validators that implement the
de.isas.mztab2.cvmapping	This package contains classes for controlled vocabulary term access, comparison, results and external cv parameter resolution.
de.isas.mztab2.io.serialization	This package contains classes that implement custom Jackson serializers for the mzTab-M model objects.
de.isas.mztab2.model	Base package for the jmztab-m data model, generated from the mzTab_m_swagger.yml specification.
de.isas.mztab2.validation	This package contains interfaces and implementations for the semantic validation via CvTerms.
de.isas.mztab2.validation.handlers	This package contains implementations for the semantic validation controlled vocabulary term rules.
uk.ac.ebi.pride.jmztab2.model	This package contains model classes for mzTab-M structural features like mandatory and optional columns.
uk.ac.ebi.pride.jmztab2.utils.parser	This package contains text file line parser implementations for the mzTab-M document sections.

Uses of Parameter in de.isas.lipidomics.mztab2.validation.validators

Methods in de.isas.lipidomics.mztab2.validation.validators with parameters of type Parameter

Modifier and Type	Method	Description
default boolean	ParameterValidator.isValid(Parameter parameter, javax.validation.ConstraintValidatorContext context)

Uses of Parameter in de.isas.mztab2.cvmapping

Methods in de.isas.mztab2.cvmapping that return Parameter

Modifier and Type	Method	Description
static Parameter	CvMappingUtils.asParameter(CvTerm term)
static Parameter	CvMappingUtils.asParameter(uk.ac.ebi.pride.utilities.ols.web.service.model.Term term)

Methods in de.isas.mztab2.cvmapping that return types with arguments of type Parameter

Modifier and Type	Method	Description
List<org.apache.commons.lang3.tuple.Pair<org.apache.commons.jxpath.Pointer,Parameter>>	RemoveUserParams.handleSelection(List<org.apache.commons.lang3.tuple.Pair<org.apache.commons.jxpath.Pointer,Parameter>> selection)
List<Parameter>	CvParameterLookupService.resolveChildren(Parameter parameter)	Resolve all children of a parameter up to an arbitrary depth.
List<Parameter>	CvParameterLookupService.resolveChildren(Parameter parameter, int levels)	Resolve all children of a parameter up to a given maximum depth (1 meaning immediate children, -1 meaning all).
List<Parameter>	CvParameterLookupService.resolveParents(Parameter parameter)	Resolve all parents of parameter up to an arbitrary depth (actually height, since we go from bottom to top).
List<Parameter>	CvParameterLookupService.resolveParents(Parameter parameter, int levels)	Resolve all parents of a parameter up to a given maximum depth (1 meaning the immediate parents, -1 meaning all).

Methods in de.isas.mztab2.cvmapping with parameters of type Parameter

Modifier and Type	Method	Description
ParameterComparisonResult	CvParameterLookupService.isChildOfOrSame(Parameter parent, Parameter potentialChild)	Compares two parameters for their parent to child relationship.
static boolean	CvMappingUtils.isEqualTo(Parameter one, Parameter two)
static boolean	CvMappingUtils.isEqualTo(uk.ac.ebi.pride.utilities.ols.web.service.model.Term term, Parameter param)
List<Parameter>	CvParameterLookupService.resolveChildren(Parameter parameter)	Resolve all children of a parameter up to an arbitrary depth.
List<Parameter>	CvParameterLookupService.resolveChildren(Parameter parameter, int levels)	Resolve all children of a parameter up to a given maximum depth (1 meaning immediate children, -1 meaning all).
List<Parameter>	CvParameterLookupService.resolveParents(Parameter parameter)	Resolve all parents of parameter up to an arbitrary depth (actually height, since we go from bottom to top).
List<Parameter>	CvParameterLookupService.resolveParents(Parameter parameter, int levels)	Resolve all parents of a parameter up to a given maximum depth (1 meaning the immediate parents, -1 meaning all).

Method parameters in de.isas.mztab2.cvmapping with type arguments of type Parameter

Modifier and Type	Method	Description
List<org.apache.commons.lang3.tuple.Pair<org.apache.commons.jxpath.Pointer,Parameter>>	RemoveUserParams.handleSelection(List<org.apache.commons.lang3.tuple.Pair<org.apache.commons.jxpath.Pointer,Parameter>> selection)

Uses of Parameter in de.isas.mztab2.io.serialization

Methods in de.isas.mztab2.io.serialization with parameters of type Parameter

Modifier and Type	Method	Description
static void	Serializers.addSubElementParameter(com.fasterxml.jackson.core.JsonGenerator jg, String prefix, Object element, String subElementName, Parameter subElement)	addSubElementParameter.
String	ParameterConverter.convert(Parameter in)

Method parameters in de.isas.mztab2.io.serialization with type arguments of type Parameter

Modifier and Type	Method	Description
static void	Serializers.addLineWithParameters(com.fasterxml.jackson.core.JsonGenerator jg, String prefix, Object element, List<Parameter> parameterList)	addLineWithParameters.
static void	Serializers.addLineWithPropertyParameters(com.fasterxml.jackson.core.JsonGenerator jg, String prefix, String propertyName, Object element, List<Parameter> value)	addLineWithPropertyParameters.
static void	Serializers.addSubElementParameters(com.fasterxml.jackson.core.JsonGenerator jg, String prefix, Object element, String subElementName, List<Parameter> subElements, boolean oneLine)	addSubElementParameters.

Uses of Parameter in de.isas.mztab2.model

Methods in de.isas.mztab2.model that return Parameter

Modifier and Type	Method	Description
Parameter	Parameter.cvAccession(String cvAccession)	Builder method for cvAccession.
Parameter	Parameter.cvLabel(String cvLabel)	Builder method for cvLabel.
Parameter	Parameter.elementType(String elementType)
@Valid Parameter	StudyVariable.getAverageFunction()	The function used to calculate summarised small molecule quantities over the assays referenced by this study variable.
@Valid Parameter	SmallMoleculeSummary.getBestIdConfidenceMeasure()	The approach or database search that identified this small molecule with highest confidence.
@Valid Parameter	SmallMoleculeEvidence.getDerivatizedForm()	If a derivatized form has been analysed by MS, then the functional group attached to the molecule should be reported here using suitable userParam or CV terms as appropriate.
@Valid Parameter	Instrument.getDetector()	The instrument's detector, as defined by the parameter.
@Valid Parameter	MsRun.getFormat()	The msRun's file format.
@Valid Parameter	MsRun.getHashMethod()	The hash method used to calculate the file hash.
@NotNull @Valid Parameter	SmallMoleculeEvidence.getIdentificationMethod()	The database search, search engine or process that was used to identify this small molecule e.g. the name of software, database or manual curation etc.
@Valid Parameter	MsRun.getIdFormat()	The msRun's mass spectra id format.
@Valid Parameter	SmallMoleculeFeature.getIsotopomer()	If de-isotoping has not been performed, then the isotopomer quantified MUST be reported here e.g. “+1”, “+2”, “13C peak” using CV terms, otherwise (i.e. for approaches where SMF rows are de-isotoped features) this MUST be null.
@NotNull @Valid Parameter	SmallMoleculeEvidence.getMsLevel()	The highest MS level used to inform identification e.g.
@Valid Parameter	Instrument.getName()	Get name.
@NotNull @Valid Parameter	ColumnParameterMapping.getParam()	The parameter specifying the unit.
@NotNull @Valid Parameter	Database.getParam()	The parameter to identify this database.
@Valid Parameter	OptColumnMapping.getParam()	The (optional) parameter for this column.
@Valid Parameter	Software.getParameter()	Parameter defining the software being used.
@NotNull @Valid Parameter	Metadata.getQuantificationMethod()	The quantification method used in the experiment reported in the file.
@NotNull @Valid Parameter	Metadata.getSmallMoleculeFeatureQuantificationUnit()	Defines what type of units are reported in the small molecule feature quantification / abundance fields.
@Valid Parameter	Metadata.getSmallMoleculeIdentificationReliability()	The system used for giving reliability / confidence codes to small molecule identifications MUST be specified if not using the default codes.
@NotNull @Valid Parameter	Metadata.getSmallMoleculeQuantificationUnit()	Defines what type of units are reported in the small molecule summary quantification / abundance fields.
@Valid Parameter	Instrument.getSource()	The instrument's source, as defined by the parameter.
@Valid Parameter	StudyVariable.getVariationFunction()	The function used to calculate the variation of small molecule quantities over the assays referenced by this study variable.
Parameter	Parameter.id(Integer id)
Parameter	Parameter.name(String name)	Builder method for name.
Parameter	Parameter.value(String value)	Builder method for value.

Methods in de.isas.mztab2.model that return types with arguments of type Parameter

Modifier and Type	Method	Description
@Valid List<Parameter>	Instrument.getAnalyzer()	The instrument's mass analyzer, as defined by the parameter.
@Valid List<Parameter>	Sample.getCellType()	Biological cell type information on the sample.
@Valid List<Parameter>	Assay.getCustom()	Additional user or cv parameters.
@Valid List<Parameter>	Metadata.getCustom()	Any additional parameters describing the analysis reported.
@Valid List<Parameter>	Sample.getCustom()	Additional user or cv parameters.
@Valid List<Parameter>	Metadata.getDerivatizationAgent()	A description of derivatization agents applied to small molecules, using userParams or CV terms where possible.
@Valid List<Parameter>	Sample.getDisease()	Disease information on the sample.
@Valid List<Parameter>	StudyVariable.getFactors()	Parameters indicating which factors were used for the assays referenced by this study variable, and at which levels.
@Valid List<Parameter>	MsRun.getFragmentationMethod()	The fragmentation methods applied during this msRun.
@NotNull @Valid List<Parameter>	Metadata.getIdConfidenceMeasure()	The type of small molecule confidence measures or scores MUST be reported as a CV parameter [1-n].
@Valid List<Parameter>	SampleProcessing.getSampleProcessing()	Parameters specifiying sample processing that was applied within one step.
@Valid List<Parameter>	MsRun.getScanPolarity()	The scan polarity/polarities used during this msRun.
@Valid List<Parameter>	Sample.getSpecies()	Biological species information on the sample.
@Valid List<Parameter>	Sample.getTissue()	Biological tissue information on the sample.

Methods in de.isas.mztab2.model with parameters of type Parameter

Modifier and Type	Method	Description
Instrument	Instrument.addAnalyzerItem(Parameter analyzerItem)	Add a single analyzerItem to the analyzer collection.
Sample	Sample.addCellTypeItem(Parameter cellTypeItem)	Add a single cellTypeItem to the cellType collection.
Assay	Assay.addCustomItem(Parameter customItem)	Add a single customItem to the custom collection.
Metadata	Metadata.addCustomItem(Parameter customItem)	Add a single customItem to the custom collection.
Sample	Sample.addCustomItem(Parameter customItem)	Add a single customItem to the custom collection.
Metadata	Metadata.addDerivatizationAgentItem(Parameter derivatizationAgentItem)	Add a single derivatizationAgentItem to the derivatizationAgent collection.
Sample	Sample.addDiseaseItem(Parameter diseaseItem)	Add a single diseaseItem to the disease collection.
StudyVariable	StudyVariable.addFactorsItem(Parameter factorsItem)	Add a single factorsItem to the factors collection.
MsRun	MsRun.addFragmentationMethodItem(Parameter fragmentationMethodItem)	Add a single fragmentationMethodItem to the fragmentationMethod collection.
Metadata	Metadata.addIdConfidenceMeasureItem(Parameter idConfidenceMeasureItem)	Add a single idConfidenceMeasureItem to the idConfidenceMeasure collection.
SampleProcessing	SampleProcessing.addSampleProcessingItem(Parameter sampleProcessingItem)	Add a single sampleProcessingItem to the sampleProcessing collection.
MsRun	MsRun.addScanPolarityItem(Parameter scanPolarityItem)	Add a single scanPolarityItem to the scanPolarity collection.
Sample	Sample.addSpeciesItem(Parameter speciesItem)	Add a single speciesItem to the species collection.
Sample	Sample.addTissueItem(Parameter tissueItem)	Add a single tissueItem to the tissue collection.
StudyVariable	StudyVariable.averageFunction(Parameter averageFunction)	Builder method for averageFunction.
SmallMoleculeSummary	SmallMoleculeSummary.bestIdConfidenceMeasure(Parameter bestIdConfidenceMeasure)	Builder method for bestIdConfidenceMeasure.
SmallMoleculeEvidence	SmallMoleculeEvidence.derivatizedForm(Parameter derivatizedForm)	Builder method for derivatizedForm.
Instrument	Instrument.detector(Parameter detector)	Builder method for detector.
MsRun	MsRun.format(Parameter format)	Builder method for format.
MsRun	MsRun.hashMethod(Parameter hashMethod)	Builder method for hashMethod.
SmallMoleculeEvidence	SmallMoleculeEvidence.identificationMethod(Parameter identificationMethod)	Builder method for identificationMethod.
MsRun	MsRun.idFormat(Parameter idFormat)	Builder method for idFormat.
SmallMoleculeFeature	SmallMoleculeFeature.isotopomer(Parameter isotopomer)	Builder method for isotopomer.
SmallMoleculeEvidence	SmallMoleculeEvidence.msLevel(Parameter msLevel)	Builder method for msLevel.
Instrument	Instrument.name(Parameter name)	Builder method for name.
ColumnParameterMapping	ColumnParameterMapping.param(Parameter param)	Builder method for param.
Database	Database.param(Parameter param)	Builder method for param.
OptColumnMapping	OptColumnMapping.param(Parameter param)	Builder method for param.
Software	Software.parameter(Parameter parameter)	Builder method for parameter.
Metadata	Metadata.quantificationMethod(Parameter quantificationMethod)	Builder method for quantificationMethod.
void	StudyVariable.setAverageFunction(Parameter averageFunction)	Set averageFunction.
void	SmallMoleculeSummary.setBestIdConfidenceMeasure(Parameter bestIdConfidenceMeasure)	Set bestIdConfidenceMeasure.
void	SmallMoleculeEvidence.setDerivatizedForm(Parameter derivatizedForm)	Set derivatizedForm.
void	Instrument.setDetector(Parameter detector)	Set detector.
void	MsRun.setFormat(Parameter format)	Set format.
void	MsRun.setHashMethod(Parameter hashMethod)	Set hashMethod.
void	SmallMoleculeEvidence.setIdentificationMethod(Parameter identificationMethod)	Set identificationMethod.
void	MsRun.setIdFormat(Parameter idFormat)	Set idFormat.
void	SmallMoleculeFeature.setIsotopomer(Parameter isotopomer)	Set isotopomer.
void	SmallMoleculeEvidence.setMsLevel(Parameter msLevel)	Set msLevel.
void	Instrument.setName(Parameter name)	Set name.
void	ColumnParameterMapping.setParam(Parameter param)	Set param.
void	Database.setParam(Parameter param)	Set param.
void	OptColumnMapping.setParam(Parameter param)	Set param.
void	Software.setParameter(Parameter parameter)	Set parameter.
void	Metadata.setQuantificationMethod(Parameter quantificationMethod)	Set quantificationMethod.
void	Metadata.setSmallMoleculeFeatureQuantificationUnit(Parameter smallMoleculeFeatureQuantificationUnit)	Set smallMoleculeFeatureQuantificationUnit.
void	Metadata.setSmallMoleculeIdentificationReliability(Parameter smallMoleculeIdentificationReliability)	Set smallMoleculeIdentificationReliability.
void	Metadata.setSmallMoleculeQuantificationUnit(Parameter smallMoleculeQuantificationUnit)	Set smallMoleculeQuantificationUnit.
void	Instrument.setSource(Parameter source)	Set source.
void	StudyVariable.setVariationFunction(Parameter variationFunction)	Set variationFunction.
Metadata	Metadata.smallMoleculeFeatureQuantificationUnit(Parameter smallMoleculeFeatureQuantificationUnit)	Builder method for smallMoleculeFeatureQuantificationUnit.
Metadata	Metadata.smallMoleculeIdentificationReliability(Parameter smallMoleculeIdentificationReliability)	Builder method for smallMoleculeIdentificationReliability.
Metadata	Metadata.smallMoleculeQuantificationUnit(Parameter smallMoleculeQuantificationUnit)	Builder method for smallMoleculeQuantificationUnit.
Instrument	Instrument.source(Parameter source)	Builder method for source.
StudyVariable	StudyVariable.variationFunction(Parameter variationFunction)	Builder method for variationFunction.

Method parameters in de.isas.mztab2.model with type arguments of type Parameter

Modifier and Type	Method	Description
Instrument	Instrument.analyzer(List<Parameter> analyzer)	Builder method for analyzer.
Sample	Sample.cellType(List<Parameter> cellType)	Builder method for cellType.
Assay	Assay.custom(List<Parameter> custom)	Builder method for custom.
Metadata	Metadata.custom(List<Parameter> custom)	Builder method for custom.
Sample	Sample.custom(List<Parameter> custom)	Builder method for custom.
Metadata	Metadata.derivatizationAgent(List<Parameter> derivatizationAgent)	Builder method for derivatizationAgent.
Sample	Sample.disease(List<Parameter> disease)	Builder method for disease.
StudyVariable	StudyVariable.factors(List<Parameter> factors)	Builder method for factors.
MsRun	MsRun.fragmentationMethod(List<Parameter> fragmentationMethod)	Builder method for fragmentationMethod.
Metadata	Metadata.idConfidenceMeasure(List<Parameter> idConfidenceMeasure)	Builder method for idConfidenceMeasure.
SampleProcessing	SampleProcessing.sampleProcessing(List<Parameter> sampleProcessing)	Builder method for sampleProcessing.
MsRun	MsRun.scanPolarity(List<Parameter> scanPolarity)	Builder method for scanPolarity.
void	Instrument.setAnalyzer(List<Parameter> analyzer)	Set analyzer.
void	Sample.setCellType(List<Parameter> cellType)	Set cellType.
void	Assay.setCustom(List<Parameter> custom)	Set custom.
void	Metadata.setCustom(List<Parameter> custom)	Set custom.
void	Sample.setCustom(List<Parameter> custom)	Set custom.
void	Metadata.setDerivatizationAgent(List<Parameter> derivatizationAgent)	Set derivatizationAgent.
void	Sample.setDisease(List<Parameter> disease)	Set disease.
void	StudyVariable.setFactors(List<Parameter> factors)	Set factors.
void	MsRun.setFragmentationMethod(List<Parameter> fragmentationMethod)	Set fragmentationMethod.
void	Metadata.setIdConfidenceMeasure(List<Parameter> idConfidenceMeasure)	Set idConfidenceMeasure.
void	SampleProcessing.setSampleProcessing(List<Parameter> sampleProcessing)	Set sampleProcessing.
void	MsRun.setScanPolarity(List<Parameter> scanPolarity)	Set scanPolarity.
void	Sample.setSpecies(List<Parameter> species)	Set species.
void	Sample.setTissue(List<Parameter> tissue)	Set tissue.
Sample	Sample.species(List<Parameter> species)	Builder method for species.
Sample	Sample.tissue(List<Parameter> tissue)	Builder method for tissue.

Uses of Parameter in de.isas.mztab2.validation

Methods in de.isas.mztab2.validation that return types with arguments of type Parameter

Modifier and Type	Method	Description
List<org.apache.commons.lang3.tuple.Pair<org.apache.commons.jxpath.Pointer,Parameter>>	CvTermSelectionHandler.handleSelection(List<org.apache.commons.lang3.tuple.Pair<org.apache.commons.jxpath.Pointer,Parameter>> selection)	Handle the provided selection, e.g. by filtering it or by modifying elements therein.

Method parameters in de.isas.mztab2.validation with type arguments of type Parameter

Modifier and Type	Method	Description
RuleEvaluationResult	CvRuleHandler.handleRule(CvMappingRule rule, List<org.apache.commons.lang3.tuple.Pair<org.apache.commons.jxpath.Pointer,Parameter>> filteredSelection)	Handle the provided rule according to the implementor's logic.
List<org.apache.commons.lang3.tuple.Pair<org.apache.commons.jxpath.Pointer,Parameter>>	CvTermSelectionHandler.handleSelection(List<org.apache.commons.lang3.tuple.Pair<org.apache.commons.jxpath.Pointer,Parameter>> selection)	Handle the provided selection, e.g. by filtering it or by modifying elements therein.

Uses of Parameter in de.isas.mztab2.validation.handlers

Method parameters in de.isas.mztab2.validation.handlers with type arguments of type Parameter

Modifier and Type	Method	Description
List<ValidationMessage>	EmptyRuleHandler.handleRule(CvMappingRule rule, List<org.apache.commons.lang3.tuple.Pair<org.apache.commons.jxpath.Pointer,Parameter>> selection)
RuleEvaluationResult	ResolvingCvRuleHandler.handleRule(CvMappingRule rule, List<org.apache.commons.lang3.tuple.Pair<org.apache.commons.jxpath.Pointer,Parameter>> filteredSelection)

Uses of Parameter in uk.ac.ebi.pride.jmztab2.model

Methods in uk.ac.ebi.pride.jmztab2.model that return Parameter

Modifier and Type	Method	Description
static Parameter	MZTabUtils.parseParam(String target)	Parameters are always reported as [CV label, accession, name, value].

Methods in uk.ac.ebi.pride.jmztab2.model that return types with arguments of type Parameter

Modifier and Type	Method	Description
static List<Parameter>	MZTabUtils.parseParamList(String target)	A list of '|' separated parameters

Methods in uk.ac.ebi.pride.jmztab2.model with parameters of type Parameter

Modifier and Type	Method	Description
String	MZTabColumnFactory.addIdConfidenceMeasureColumn(Parameter parameter, Integer index, Class columnType)	addIdConfidenceMeasureColumn.
String	MZTabColumnFactory.addOptionalColumn(Parameter param, Class columnType)	Add global ParameterOptionColumn into MZTabColumnFactory.optionalColumnMapping and MZTabColumnFactory.columnMapping.
<T extends IndexedElement> String	MZTabColumnFactory.addOptionalColumn(T columnEntity, Parameter param, Class columnType)	Add ParameterOptionColumn followed by an indexed element (study variable, assay, ms run) into MZTabColumnFactory.optionalColumnMapping and MZTabColumnFactory.columnMapping.
static String	ParameterOptionColumn.getHeader(IndexedElement element, Parameter param)	get column header like: opt_{OBJECT_ID}_cv_{accession}_{parameter name} Spaces within the parameter's name MUST be replaced by '_'.
OptColumnMappingBuilder.GlobalOptColumnMappingBuilder	OptColumnMappingBuilder.GlobalOptColumnMappingBuilder.withParameter(Parameter parameter)
OptColumnMappingBuilder.IndexedElementOptColumnMappingBuilder	OptColumnMappingBuilder.IndexedElementOptColumnMappingBuilder.withParameter(Parameter parameter)

Constructors in uk.ac.ebi.pride.jmztab2.model with parameters of type Parameter

Constructor	Description
ParameterOptionColumn(IndexedElement element, Parameter param, Class columnType, int offset)	Define a OptionColumn which use CV parameter accessions in following the format: opt_{OBJECT_ID}_cv_{accession}_{parameter name}.

Uses of Parameter in uk.ac.ebi.pride.jmztab2.utils.parser

Methods in uk.ac.ebi.pride.jmztab2.utils.parser that return Parameter

Modifier and Type	Method	Description
protected Parameter	MZTabDataLineParser.checkParameter(IMZTabColumn column, String target, boolean allowNull)	checkParameter.

Methods in uk.ac.ebi.pride.jmztab2.utils.parser that return types with arguments of type Parameter

Modifier and Type	Method	Description
protected List<Parameter>	MZTabDataLineParser.checkParamList(IMZTabColumn column, String target)	Check and translate target string into parameter list which split by '|' character..
protected List<Parameter>	MZTabDataLineParser.checkSearchEngine(IMZTabColumn column, String searchEngine)	Check and translate searchEngine string into parameter list which split by '|' character..

Methods in uk.ac.ebi.pride.jmztab2.utils.parser with parameters of type Parameter

Modifier and Type	Method	Description
Assay	MZTabParserContext.addAssayCustom(Metadata metadata, Integer id, Parameter param)	Add a assay[id]-custom[i] into metadata.
Instrument	MZTabParserContext.addInstrumentAnalyzer(Metadata metadata, Integer id, Parameter analyzer)	Add a parameter for instrument[id]-analyzer[i]
Instrument	MZTabParserContext.addInstrumentDetector(Metadata metadata, Integer id, Parameter detector)	Add a parameter for instrument[id]-detector
Instrument	MZTabParserContext.addInstrumentName(Metadata metadata, Integer id, Parameter name)	Add a parameter for instrument[id]-name
Instrument	MZTabParserContext.addInstrumentSource(Metadata metadata, Integer id, Parameter source)	Add a parameter for instrument[id]-source
MsRun	MZTabParserContext.addMsRunFormat(Metadata metadata, Integer id, Parameter format)	Add ms_run[id]-format into metadata.
MsRun	MZTabParserContext.addMsRunFragmentationMethod(Metadata metadata, Integer id, Parameter fragmentationMethod)	Add ms_run[id]-fragmentation_method into metadata.
MsRun	MZTabParserContext.addMsRunHashMethod(Metadata metadata, Integer id, Parameter hashMethod)	addMsRunHashMethod.
MsRun	MZTabParserContext.addMsRunIdFormat(Metadata metadata, Integer id, Parameter idFormat)	Add ms_run[id]-id_format into metadata.
MsRun	MZTabParserContext.addMsRunScanPolarity(Metadata metadata, Integer id, Parameter scanPolarity)	addMsRunScanPolarity.
Sample	MZTabParserContext.addSampleCellType(Metadata metadata, Integer id, Parameter cellType)	Add a sample[id]-cell_type into sample.
Sample	MZTabParserContext.addSampleCustom(Metadata metadata, Integer id, Parameter custom)	Add a sample[id]-custom into sample.
Sample	MZTabParserContext.addSampleDisease(Metadata metadata, Integer id, Parameter disease)	Add a sample[id]-disease into sample.
SampleProcessing	MZTabParserContext.addSampleProcessingParameter(Metadata metadata, Integer id, Parameter param)	Add a processing parameter to sample_processing[id]
Sample	MZTabParserContext.addSampleSpecies(Metadata metadata, Integer id, Parameter species)	Add a sample[id]-species into sample.
Sample	MZTabParserContext.addSampleTissue(Metadata metadata, Integer id, Parameter tissue)	Add a sample[id]-tissue into sample.
void	MZTabParserContext.addSmallMoleculeColUnit(Metadata metadata, String columnName, Parameter param)	Defines the unit for the data reported in a column of the small molecule section.
void	MZTabParserContext.addSmallMoleculeEvidenceColUnit(Metadata metadata, String columnName, Parameter param)	Defines the unit for the data reported in a column of the small molecule section.
void	MZTabParserContext.addSmallMoleculeFeatureColUnit(Metadata metadata, String columnName, Parameter param)	Defines the unit for the data reported in a column of the small molecule section.
Software	MZTabParserContext.addSoftwareParameter(Metadata metadata, Integer id, Parameter param)	Add a software[id] parameter.
StudyVariable	MZTabParserContext.addStudyVariableAverageFunction(Metadata metadata, Integer id, Parameter checkParameter)	Add a study_variable[id]-average_function.
StudyVariable	MZTabParserContext.addStudyVariableFactors(Metadata metadata, Integer id, Parameter checkParameter)	Add a study_variable[id]-factor.
StudyVariable	MZTabParserContext.addStudyVariableVariationFunction(Metadata metadata, Integer id, Parameter checkParameter)	Add a study_variable[id]-variation_function.

Method parameters in uk.ac.ebi.pride.jmztab2.utils.parser with type arguments of type Parameter

Modifier and Type	Method	Description
SampleProcessing	MZTabParserContext.addSampleProcessing(Metadata metadata, Integer id, List<Parameter> sampleProcessing)	Add a sample_processing[id].
void	MTDLineParser.handleParam(String defineLabel, String valueLabel, MZTabErrorType errorType, int lineNumber, Consumer<Parameter> consumer)	handleParam.