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.model	Base package for the jmztab-m data model, generated from the mzTab_m_swagger.yml specification.

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.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.