Index (MzTab-M 2.0 reference implementation. 1.0.6 API)

A B C D E F G H I J K L M N O P Q R S T U V W X Z
All Classes All Packages

A

ABUNDANCE_ASSAY - uk.ac.ebi.pride.jmztab2.model.AbundanceColumn.Field
ABUNDANCE_PREFIX - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant ABUNDANCE_PREFIX="abundance_"
ABUNDANCE_STUDY_VARIABLE - uk.ac.ebi.pride.jmztab2.model.AbundanceColumn.Field
ABUNDANCE_VARIATION_STUDY_VARIABLE - uk.ac.ebi.pride.jmztab2.model.AbundanceColumn.Field
abundanceAssay - de.isas.mztab2.model.SmallMoleculeFeature.Properties
abundanceAssay - de.isas.mztab2.model.SmallMoleculeSummary.Properties
abundanceAssay(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Builder method for abundanceAssay.
abundanceAssay(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for abundanceAssay.
AbundanceColumn - Class in uk.ac.ebi.pride.jmztab2.model: If the data exporter wishes to report only final results for 'Summary' files (i.e. following averaging over replicates), then these MUST be reported as quantitative values in the columns associated with the study_variable[1-n] (e.g.
AbundanceColumn - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant AbundanceColumn
AbundanceColumn.Field - Enum in uk.ac.ebi.pride.jmztab2.model
AbundanceColumnSameId - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant AbundanceColumnSameId
AbundanceColumnTogether - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant AbundanceColumnTogether
abundanceStudyVariable - de.isas.mztab2.model.SmallMoleculeSummary.Properties
abundanceStudyVariable(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for abundanceStudyVariable.
abundanceVariationStudyVariable - de.isas.mztab2.model.SmallMoleculeSummary.Properties
abundanceVariationStudyVariable(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for abundanceVariationStudyVariable.
accession - de.isas.mztab2.model.PublicationItem.Properties
accession(String) - Method in class de.isas.mztab2.model.PublicationItem: Builder method for accession.
add(MZTabError) - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: A limit max capacity list, if contains a couple of MZTabError objects.
addAbundanceAssayItem(Double) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Add a single abundanceAssayItem to the abundanceAssay collection.
addAbundanceAssayItem(Double) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single abundanceAssayItem to the abundanceAssay collection.
addAbundanceOptionalColumn(Assay, String) - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory: addAbundanceOptionalColumn.
addAbundanceOptionalColumn(StudyVariable, String, String) - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory: Add an AbundanceColumn into AbundanceColumn, MZTabColumnFactory.optionalColumnMapping and MZTabColumnFactory.columnMapping.
addAbundanceStudyVariableItem(Double) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single abundanceStudyVariableItem to the abundanceStudyVariable collection.
addAbundanceVariationStudyVariableItem(Double) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single abundanceVariationStudyVariableItem to the abundanceVariationStudyVariable collection.
addAdductIonsItem(String) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single adductIonsItem to the adductIons collection.
addAll(List<MZTabError>) - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: A limit max capacity list, if contains a couple of MZTabError objects.
addAnalyzerItem(Parameter) - Method in class de.isas.mztab2.model.Instrument: Add a single analyzerItem to the analyzer collection.
addAssay(Metadata, Assay) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a assay into metadata.
addAssayCustom(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a assay[id]-custom[i] into metadata.
addAssayExternalUri(Metadata, Integer, URI) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a assay[id]-external_uri into metadata.
addAssayItem(Assay) - Method in class de.isas.mztab2.model.Metadata: Add a single assayItem to the assay collection.
addAssayMsRun(Metadata, Integer, MsRun) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add assay[id]-ms_run_ref into metadata.
addAssayRefsItem(Assay) - Method in class de.isas.mztab2.model.StudyVariable: Add a single assayRefsItem to the assayRefs collection.
addAssaySample(Metadata, Integer, Sample) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add assay[id]-sample_ref into metadata.
addCellTypeItem(Parameter) - Method in class de.isas.mztab2.model.Sample: Add a single cellTypeItem to the cellType collection.
addCheckOption(Options) - Static method in class de.isas.mztab2.cli.MZTabCommandLine
addCheckSemanticOption(Options) - Static method in class de.isas.mztab2.cli.MZTabCommandLine
addChemicalFormulaItem(String) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single chemicalFormulaItem to the chemicalFormula collection.
addChemicalNameItem(String) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single chemicalNameItem to the chemicalName collection.
addColunitSmallMoleculeEvidenceItem(ColumnParameterMapping) - Method in class de.isas.mztab2.model.Metadata: Add a single colunitSmallMoleculeEvidenceItem to the colunitSmallMoleculeEvidence collection.
addColunitSmallMoleculeFeatureItem(ColumnParameterMapping) - Method in class de.isas.mztab2.model.Metadata: Add a single colunitSmallMoleculeFeatureItem to the colunitSmallMoleculeFeature collection.
addColunitSmallMoleculeItem(ColumnParameterMapping) - Method in class de.isas.mztab2.model.Metadata: Add a single colunitSmallMoleculeItem to the colunitSmallMolecule collection.
addCommentItem(Comment) - Method in class de.isas.mztab2.model.MzTab: Add a single commentItem to the comment collection.
addCommentItem(Comment) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Add a single commentItem to the comment collection.
addCommentItem(Comment) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Add a single commentItem to the comment collection.
addCommentItem(Comment) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single commentItem to the comment collection.
addConstraintAndValidator(Class<A>, Class<V>, boolean) - Method in class de.isas.mztab2.validation.MzTabBeanValidator: Allows registration of custom constraint / validator pairs on the validation configuration.
addConstraintAndValidator(Class<T>, Class<A>, Class<V>, boolean) - Method in class de.isas.mztab2.validation.MzTabBeanValidator: Allows registration of custom constraint / validator pairs on the validation configuration for a specific (unannotated) type.
addContact(Metadata, Contact) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a contact into metadata.
addContactAffiliation(Metadata, Integer, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add contact[id]-affiliation.
addContactEmail(Metadata, Integer, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add contact[id]-email
addContactItem(Contact) - Method in class de.isas.mztab2.model.Metadata: Add a single contactItem to the contact collection.
addContactName(Metadata, Integer, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add contact[id]-name.
addCustomItem(Parameter) - Method in class de.isas.mztab2.model.Assay: Add a single customItem to the custom collection.
addCustomItem(Parameter) - Method in class de.isas.mztab2.model.Metadata: Add a single customItem to the custom collection.
addCustomItem(Parameter) - Method in class de.isas.mztab2.model.Sample: Add a single customItem to the custom collection.
addCV(Metadata, CV) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a controlled vocabularies/ontologies into metadata.
addCVFullName(Metadata, Integer, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a cv[id]-full_name.
addCvItem(CV) - Method in class de.isas.mztab2.model.Metadata: Add a single cvItem to the cv collection.
addCVLabel(Metadata, Integer, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a cv[id]-label.
addCVURI(Metadata, Integer, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a cv[id]-uri.
addCVVersion(Metadata, Integer, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a cv[id]-version.
addDatabase(Metadata, Database) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: addDatabase.
addDatabaseIdentifierItem(String) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single databaseIdentifierItem to the databaseIdentifier collection.
addDatabaseItem(Database) - Method in class de.isas.mztab2.model.Metadata: Add a single databaseItem to the database collection.
addDatabasePrefix(Metadata, Integer, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: addDatabasePrefix.
addDatabaseUri(Metadata, Integer, URI) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: addDatabaseUri.
addDatabaseVersion(Metadata, Integer, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: addDatabaseVersion.
addDerivatizationAgentItem(Parameter) - Method in class de.isas.mztab2.model.Metadata: Add a single derivatizationAgentItem to the derivatizationAgent collection.
addDeserializeOption(Options) - Static method in class de.isas.mztab2.cli.MZTabCommandLine
addDiseaseItem(Parameter) - Method in class de.isas.mztab2.model.Sample: Add a single diseaseItem to the disease collection.
addExternalStudyUriItem(Uri) - Method in class de.isas.mztab2.model.Metadata: Add a single externalStudyUriItem to the externalStudyUri collection.
addFactorsItem(Parameter) - Method in class de.isas.mztab2.model.StudyVariable: Add a single factorsItem to the factors collection.
addFragmentationMethodItem(Parameter) - Method in class de.isas.mztab2.model.MsRun: Add a single fragmentationMethodItem to the fragmentationMethod collection.
addHelpOption(Options) - Static method in class de.isas.mztab2.cli.MZTabCommandLine
addIdConfidenceMeasureColumn(Parameter, Integer, Class) - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory: addIdConfidenceMeasureColumn.
addIdConfidenceMeasureItem(Parameter) - Method in class de.isas.mztab2.model.Metadata: Add a single idConfidenceMeasureItem to the idConfidenceMeasure collection.
addIdConfidenceMeasureItem(Double) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Add a single idConfidenceMeasureItem to the idConfidenceMeasure collection.
addInchiItem(String) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single inchiItem to the inchi collection.
addIndexedLine(JsonGenerator, SerializerProvider, String, Object, List<T>) - Static method in class de.isas.mztab2.io.serialization.Serializers: addIndexedLine for elements like assay[1] that have an id and a list of additional property elements
addIndexedLine(JsonGenerator, SerializerProvider, String, Object, T) - Static method in class de.isas.mztab2.io.serialization.Serializers: addIndexedLine for elements like assay[1] that have an id and one additional property element
addInstrument(Metadata, Instrument) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a instrument[id] to metadata.
addInstrumentAnalyzer(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a parameter for instrument[id]-analyzer[i]
addInstrumentDetector(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a parameter for instrument[id]-detector
addInstrumentItem(Instrument) - Method in class de.isas.mztab2.model.Metadata: Add a single instrumentItem to the instrument collection.
addInstrumentName(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a parameter for instrument[id]-name
addInstrumentSource(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a parameter for instrument[id]-source
addLevelOption(Options) - Static method in class de.isas.mztab2.cli.MZTabCommandLine
addLine(JsonGenerator, String, Object, Object...) - Static method in class de.isas.mztab2.io.serialization.Serializers: addLine.
addLineWithMetadataProperty(JsonGenerator, String, MetadataProperty, Object, Object...) - Static method in class de.isas.mztab2.io.serialization.Serializers: addLineWithMetadataProperty.
addLineWithNullProperty(JsonGenerator, String, String, Object) - Static method in class de.isas.mztab2.io.serialization.Serializers: addLineWithNullProperty.
addLineWithParameters(JsonGenerator, String, Object, List<Parameter>) - Static method in class de.isas.mztab2.io.serialization.Serializers: addLineWithParameters.
addLineWithProperty(JsonGenerator, String, String, Object, Object...) - Static method in class de.isas.mztab2.io.serialization.Serializers: addLineWithProperty.
addLineWithPropertyParameters(JsonGenerator, String, String, Object, List<Parameter>) - Static method in class de.isas.mztab2.io.serialization.Serializers: addLineWithPropertyParameters.
addMessageOption(Options) - Static method in class de.isas.mztab2.cli.MZTabCommandLine
addMsRun(Metadata, MsRun) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a ms_run[id] into metadata.
addMsRunFormat(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add ms_run[id]-format into metadata.
addMsRunFragmentationMethod(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add ms_run[id]-fragmentation_method into metadata.
addMsRunHash(Metadata, Integer, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: addMsRunHash.
addMsRunHashMethod(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: addMsRunHashMethod.
addMsRunIdFormat(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add ms_run[id]-id_format into metadata.
addMsRunInstrumentRef(Metadata, Integer, Instrument) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add ms_run[id]-instrument_ref into metadata.
addMsRunItem(MsRun) - Method in class de.isas.mztab2.model.Metadata: Add a single msRunItem to the msRun collection.
addMsRunLocation(Metadata, Integer, URI) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add ms_run[id]-location into metadata.
addMsRunRefItem(MsRun) - Method in class de.isas.mztab2.model.Assay: Add a single msRunRefItem to the msRunRef collection.
addMsRunScanPolarity(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: addMsRunScanPolarity.
addOptionalColumn(Parameter, Class) - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory: Add global ParameterOptionColumn into MZTabColumnFactory.optionalColumnMapping and MZTabColumnFactory.columnMapping.
addOptionalColumn(String, Class) - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory: Add global OptionColumn into MZTabColumnFactory.optionalColumnMapping and MZTabColumnFactory.columnMapping.
addOptionalColumn(T, Parameter, Class) - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory: Add ParameterOptionColumn followed by an indexed element (study variable, assay, ms run) into MZTabColumnFactory.optionalColumnMapping and MZTabColumnFactory.columnMapping.
addOptionalColumn(T, String, Class) - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory: Add OptionColumn followed by an indexed element (study variable, assay, ms run) into MZTabColumnFactory.optionalColumnMapping and MZTabColumnFactory.columnMapping.
addOptItem(OptColumnMapping) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Add a single optItem to the opt collection.
addOptItem(OptColumnMapping) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Add a single optItem to the opt collection.
addOptItem(OptColumnMapping) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single optItem to the opt collection.
addOutFileOption(Options) - Static method in class de.isas.mztab2.cli.MZTabCommandLine
addPublication(Metadata, Publication) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a publiction to metadata.
addPublicationItem(Metadata, Integer, PublicationItem.TypeEnum, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a publication item to metadata.
addPublicationItem(Publication) - Method in class de.isas.mztab2.model.Metadata: Add a single publicationItem to the publication collection.
addPublicationItems(Metadata, Integer, Collection<PublicationItem>) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a couple of publication items into publication[id].
addPublicationItemsItem(PublicationItem) - Method in class de.isas.mztab2.model.Publication: Add a single publicationItemsItem to the publicationItems collection.
addSample(Metadata, Sample) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a sample to metadata.
addSampleCellType(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a sample[id]-cell_type into sample.
addSampleCustom(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a sample[id]-custom into sample.
addSampleDescription(Metadata, Integer, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a sample[id]-description into sample.
addSampleDisease(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a sample[id]-disease into sample.
addSampleItem(Sample) - Method in class de.isas.mztab2.model.Metadata: Add a single sampleItem to the sample collection.
addSampleProcessing(Metadata, Integer, List<Parameter>) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a sample_processing[id].
addSampleProcessingItem(Parameter) - Method in class de.isas.mztab2.model.SampleProcessing: Add a single sampleProcessingItem to the sampleProcessing collection.
addSampleProcessingItem(SampleProcessing) - Method in class de.isas.mztab2.model.Metadata: Add a single sampleProcessingItem to the sampleProcessing collection.
addSampleProcessingParameter(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a processing parameter to sample_processing[id]
addSampleSpecies(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a sample[id]-species into sample.
addSampleTissue(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a sample[id]-tissue into sample.
addScanPolarityItem(Parameter) - Method in class de.isas.mztab2.model.MsRun: Add a single scanPolarityItem to the scanPolarity collection.
addSerializeOption(Options) - Static method in class de.isas.mztab2.cli.MZTabCommandLine
addSettingItem(String) - Method in class de.isas.mztab2.model.Software: Add a single settingItem to the setting collection.
addSmallMoleculeColUnit(Metadata, String, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Defines the unit for the data reported in a column of the small molecule section.
addSmallMoleculeEvidenceColUnit(Metadata, String, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Defines the unit for the data reported in a column of the small molecule section.
addSmallMoleculeEvidenceItem(SmallMoleculeEvidence) - Method in class de.isas.mztab2.model.MzTab: Add a single smallMoleculeEvidenceItem to the smallMoleculeEvidence collection.
addSmallMoleculeFeatureColUnit(Metadata, String, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Defines the unit for the data reported in a column of the small molecule section.
addSmallMoleculeFeatureItem(SmallMoleculeFeature) - Method in class de.isas.mztab2.model.MzTab: Add a single smallMoleculeFeatureItem to the smallMoleculeFeature collection.
addSmallMoleculeSummaryItem(SmallMoleculeSummary) - Method in class de.isas.mztab2.model.MzTab: Add a single smallMoleculeSummaryItem to the smallMoleculeSummary collection.
addSmeIdRefsItem(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Add a single smeIdRefsItem to the smeIdRefs collection.
addSmfIdRefsItem(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single smfIdRefsItem to the smfIdRefs collection.
addSmilesItem(String) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single smilesItem to the smiles collection.
addSoftware(Metadata, Software) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a software to metadata, which used to analyze the data and obtain the reported results.
addSoftwareItem(Software) - Method in class de.isas.mztab2.model.Metadata: Add a single softwareItem to the software collection.
addSoftwareParameter(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a software[id] parameter.
addSoftwareSetting(Metadata, Integer, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a software[id]-setting.
addSpeciesItem(Parameter) - Method in class de.isas.mztab2.model.Sample: Add a single speciesItem to the species collection.
addSpectraRefItem(SpectraRef) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Add a single spectraRefItem to the spectraRef collection.
addStudyVariable(Metadata, StudyVariable) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a study variable into metadata.
addStudyVariableAssay(Metadata, Integer, Assay) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a study_variable[id]-assay_refs.
addStudyVariableAverageFunction(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a study_variable[id]-average_function.
addStudyVariableDescription(Metadata, Integer, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a study_variable[id]-description.
addStudyVariableFactors(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a study_variable[id]-factor.
addStudyVariableItem(StudyVariable) - Method in class de.isas.mztab2.model.Metadata: Add a single studyVariableItem to the studyVariable collection.
addStudyVariableVariationFunction(Metadata, Integer, Parameter) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a study_variable[id]-variation_function.
addSubElementParameter(JsonGenerator, String, Object, String, Parameter) - Static method in class de.isas.mztab2.io.serialization.Serializers: addSubElementParameter.
addSubElementParameters(JsonGenerator, String, Object, String, List<Parameter>, boolean) - Static method in class de.isas.mztab2.io.serialization.Serializers: addSubElementParameters.
addSubElementStrings(JsonGenerator, String, Object, String, List<?>, boolean) - Static method in class de.isas.mztab2.io.serialization.Serializers: addSubElementStrings.
addTheoreticalNeutralMassItem(Double) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single theoreticalNeutralMassItem to the theoreticalNeutralMass collection.
addTissueItem(Parameter) - Method in class de.isas.mztab2.model.Sample: Add a single tissueItem to the tissue collection.
ADDUCT_ION - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
ADDUCT_ION - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn.Stable
ADDUCT_IONS - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
adductIon - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
adductIon - de.isas.mztab2.model.SmallMoleculeFeature.Properties
adductIon(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for adductIon.
adductIon(String) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Builder method for adductIon.
adductIons - de.isas.mztab2.model.SmallMoleculeSummary.Properties
adductIons(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for adductIons.
addUriItem(Uri) - Method in class de.isas.mztab2.model.Metadata: Add a single uriItem to the uri collection.
addUriItem(String) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single uriItem to the uri collection.
addVersionOption(Options) - Static method in class de.isas.mztab2.cli.MZTabCommandLine
affiliation - de.isas.mztab2.model.Contact.Properties
affiliation(String) - Method in class de.isas.mztab2.model.Contact: Builder method for affiliation.
after() - Method in class de.isas.mztab2.test.utils.ExtractClassPathFiles
allowChildren - Variable in class info.psidev.cvmapping.CvTerm
AmbiguityMod - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant AmbiguityMod
analyzer - de.isas.mztab2.model.Instrument.Properties
analyzer(List<Parameter>) - Method in class de.isas.mztab2.model.Instrument: Builder method for analyzer.
AND - info.psidev.cvmapping.CvMappingRule.CvTermsCombinationLogic
AndValidationHandler - Class in de.isas.mztab2.validation.handlers: Implements 'AND' logic, meaning all alternative possible terms or term roots for an object must occur.
AndValidationHandler() - Constructor for class de.isas.mztab2.validation.handlers.AndValidationHandler
asMap(Object) - Static method in class de.isas.mztab2.io.serialization.Serializers: asMap.
asParameter(CvTerm) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils
asParameter(Term) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils
assay - de.isas.mztab2.model.Metadata.Properties
assay(List<Assay>) - Method in class de.isas.mztab2.model.Metadata: Builder method for assay.
Assay - Class in de.isas.mztab2.model: Specification of assay.
Assay() - Constructor for class de.isas.mztab2.model.Assay
ASSAY - uk.ac.ebi.pride.jmztab2.model.MetadataElement
ASSAY_CUSTOM - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
ASSAY_EXTERNAL_URI - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
ASSAY_MS_RUN_REF - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
ASSAY_SAMPLE_REF - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
Assay.Properties - Enum in de.isas.mztab2.model: Property enumeration for Assay.
AssayFormat - Class in de.isas.mztab2.io.formats: Format specification for Assay.
AssayFormat() - Constructor for class de.isas.mztab2.io.formats.AssayFormat
AssayNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant AssayNotDefined
assayRefs - de.isas.mztab2.model.StudyVariable.Properties
assayRefs(List<Assay>) - Method in class de.isas.mztab2.model.StudyVariable: Builder method for assayRefs.
AssayRefs - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant AssayRefs
AssaySerializer - Class in de.isas.mztab2.io.serialization: AssaySerializer implementation for Assay.
AssaySerializer() - Constructor for class de.isas.mztab2.io.serialization.AssaySerializer: Constructor for AssaySerializer.
AssaySerializer(Class<Assay>) - Constructor for class de.isas.mztab2.io.serialization.AssaySerializer: Constructor for AssaySerializer.
AssayValidator - Class in de.isas.mztab2.io.validators: Validates that the quantification method section is present in metadata.
AssayValidator() - Constructor for class de.isas.mztab2.io.validators.AssayValidator
averageFunction - de.isas.mztab2.model.StudyVariable.Properties
averageFunction(Parameter) - Method in class de.isas.mztab2.model.StudyVariable: Builder method for averageFunction.

B

BAR - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant BAR='|'
BAR_S - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant BAR='|'
before() - Method in class de.isas.mztab2.test.utils.ExtractClassPathFiles
BEST_ID_CONFIDENCE_MEASURE - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
BEST_ID_CONFIDENCE_VALUE - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
bestIdConfidenceMeasure - de.isas.mztab2.model.SmallMoleculeSummary.Properties
bestIdConfidenceMeasure(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for bestIdConfidenceMeasure.
bestIdConfidenceValue - de.isas.mztab2.model.SmallMoleculeSummary.Properties
bestIdConfidenceValue(Double) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for bestIdConfidenceValue.
build(String) - Method in interface uk.ac.ebi.pride.jmztab2.model.IOptColumnMappingBuilder: Use the current builder state to create an OptColumnMapping with the provided value for e.g. a particular feature (row).
build(String) - Method in class uk.ac.ebi.pride.jmztab2.model.OptColumnMappingBuilder.GlobalOptColumnMappingBuilder
build(String) - Method in class uk.ac.ebi.pride.jmztab2.model.OptColumnMappingBuilder.IndexedElementOptColumnMappingBuilder

C

CALCULATE_ERROR - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant CALCULATE_ERROR="NaN"
camelCaseToUnderscoreLowerCase(String) - Static method in class de.isas.mztab2.io.serialization.Serializers: camelCaseToUnderscoreLowerCase.
category - de.isas.mztab2.model.ValidationMessage.Properties
category(ValidationMessage.CategoryEnum) - Method in class de.isas.mztab2.model.ValidationMessage: Builder method for category.
cellType - de.isas.mztab2.model.Sample.Properties
cellType(List<Parameter>) - Method in class de.isas.mztab2.model.Sample: Builder method for cellType.
charge - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
charge - de.isas.mztab2.model.SmallMoleculeFeature.Properties
charge(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for charge.
charge(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Builder method for charge.
CHARGE - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
CHARGE - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn.Stable
checkAbundanceColumns(int, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabHeaderLineParser: checkAbundanceColumns.
checkAmbiguityMembers(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate target string into parameter list which split by ',' character..
checkBestSearchEngineScore(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: The best search engine score (for this type of score) for the given peptide across all replicates reported.
checkCalcMassToCharge(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate calc_mass_to_charge string into Double.
checkCharge(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate charge string into Integer.
checkChemicalFormula(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check chemical_formula string.
checkColunitMapping(MZTabColumnFactory, Optional<Collection<ColumnParameterMapping>>, Metadata.Properties, MzTab.Properties) - Method in class de.isas.mztab2.io.MzTabFileParser
checkData() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate the columns into mzTab elements.
checkData() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.SMELineParser: Check and translate the columns into mzTab elements.
checkData() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.SMFLineParser: Check and translate the columns into mzTab elements.
checkData() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.SMLLineParser: Check and translate the columns into mzTab elements.
checkData(IMZTabColumn, String, boolean) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: In the table-based sections (protein, peptide, and small molecule) there MUST NOT be any empty cells.
checkDatabase(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check target string.
checkDatabaseVersion(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check target string.
checkDescription(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check target string.
checkDouble(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate target string into Double.
checkDouble(IMZTabColumn, String, boolean) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate target string into Double.
checkDoubleList(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate target string into parameter list which split by splitChar character..
checkEnd(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check target string.
checkExpMassToCharge(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate exp_mass_to_charge string into Double.
checkForNull(Object, List<?>, String) - Static method in class de.isas.mztab2.io.serialization.Serializers: checkForNull.
checkGOTerms(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate target string into string list which split by ',' character..
checkIdentifier(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate identifier string into string list which split by '|' character..
checkInchiKey(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate inchi_key string into parameter list which split by '|' character..
checkIndexedElement(Object) - Static method in class de.isas.mztab2.io.serialization.Serializers
checkInteger(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate target string into Integer.
checkInteger(IMZTabColumn, String, boolean) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate target string into Integer.
checkIntegerList(IMZTabColumn, String, char) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate target string into integer list which split by splitChar character..
checkIntegerList(IMZTabColumn, String, char, boolean) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate target string into integer list which split by splitChar character..
checkItemNumbers(MZTabErrorList, int, List<?>, SmallMoleculeSummary.Properties, List<?>, SmallMoleculeSummary.Properties) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.SMLLineParser
checkMassToCharge(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate mass_to_charge string into Double.
checkMZBoolean(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate target to MZBoolean.
checkNumPeptidesDistinct(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate numPeptidesDistinct string into Integer.
checkNumPeptidesUnique(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate numPeptidesUnique string into Integer.
checkNumPSMs(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate numPSMs string into Integer.
checkOptColumnName(String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabHeaderLineParser: Additional columns can be added to the end of the protein table.
checkParameter(IMZTabColumn, String, boolean) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: checkParameter.
CheckParameter - Annotation Type in de.isas.lipidomics.mztab2.validation.constraints: JAVAX validation compliant annotation.
checkParamList(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate target string into parameter list which split by '|' character..
checkPost(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check target string.
checkPre(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check target string.
checkProteinCoverage(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate protein_coverage string into Double.
checkPSMID(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate psm_id string into Integer.
checkRegexMatches(MZTabErrorList, int, SmallMoleculeFeature.Properties, String, List<String>) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.SMFLineParser
checkRegexMatches(MZTabErrorList, int, SmallMoleculeSummary.Properties, String, List<String>) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.SMLLineParser
checkRetentionTime(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate retention_time string into Double list which split by '|' character..
checkRetentionTimeWindow(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate retention_time_window string into Double list which split by '|' character..
checkSearchEngine(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate searchEngine string into parameter list which split by '|' character..
checkSearchEngineScore(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: The search engine score for the given peptide in the defined ms run.
checkSequence(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate peptide sequence.
checkSmiles(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate smiles string into parameter list which split by '|' character..
checkSpecies(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check target string.
checkSpectraRef(MZTabParserContext, IMZTabColumn, String, boolean) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate spectraRef string into SpectraRef list.
checkStart(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check target string.
checkString(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: In the table-based sections (protein, peptide, and small molecule) there MUST NOT be any empty cells.
checkString(IMZTabColumn, String, boolean) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: In the table-based sections (protein, peptide, and small molecule) there MUST NOT be any empty cells.
checkStringList(IMZTabColumn, String, char) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate target string into parameter list which split by splitChar character..
checkTaxid(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate taxid string into Integer.
checkUnique(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Check and translate unique to MZBoolean.
checkURI(IMZTabColumn, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Checks the provided URI string.
CHEMICAL_FORMULA - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
CHEMICAL_FORMULA - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
CHEMICAL_NAME - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
CHEMICAL_NAME - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
chemicalFormula - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
chemicalFormula - de.isas.mztab2.model.SmallMoleculeSummary.Properties
chemicalFormula(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for chemicalFormula.
chemicalFormula(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for chemicalFormula.
chemicalName - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
chemicalName - de.isas.mztab2.model.SmallMoleculeSummary.Properties
chemicalName(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for chemicalName.
chemicalName(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for chemicalName.
CHEMMODS - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant CHEMMODS
CHEMMODSAccession - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant CHEMMODSAccession
CHILD_OF - de.isas.mztab2.cvmapping.ParameterComparisonResult
ClassPathFile - Enum in de.isas.mztab2.test.utils: Test files enum to configure test files.
clear() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Clear all errors stored in the error list.
clearCaches() - Method in class de.isas.mztab2.cvmapping.CvParameterLookupService: Clears all query result caches (parent and child).
code - de.isas.mztab2.model.Error.Properties
code - de.isas.mztab2.model.ValidationMessage.Properties
code(Integer) - Method in class de.isas.mztab2.model.Error: Builder method for code.
code(String) - Method in class de.isas.mztab2.model.ValidationMessage: Builder method for code.
COLON - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant COLON=':'
columnFor(String) - Static method in enum uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable: Returns a new ISmallMoleculeColumn instance for the given stable column name.
columnFor(String) - Static method in enum uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable: Returns a new ISmallMoleculeEvidenceColumn instance for the given stable column name.
columnFor(String) - Static method in enum uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn.Stable: Returns a new ISmallMoleculeFeatureColumn instance for the given stable column name.
columnFor(SmallMoleculeColumn.Stable) - Static method in enum uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable: Returns a new ISmallMoleculeColumn instance for the given stable column template.
columnFor(SmallMoleculeEvidenceColumn.Stable) - Static method in enum uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable: Returns a new ISmallMoleculeEvidenceColumn instance for the given stable column template.
columnFor(SmallMoleculeFeatureColumn.Stable) - Static method in enum uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn.Stable: Returns a new ISmallMoleculeFeatureColumn instance for the given stable column template.
columnName - de.isas.mztab2.model.ColumnParameterMapping.Properties
columnName(String) - Method in class de.isas.mztab2.model.ColumnParameterMapping: Builder method for columnName.
ColumnNotValid - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant ColumnNotValid
ColumnParameterMapping - Class in de.isas.mztab2.model: Defines the used unit for a column in the mzTab-M file.
ColumnParameterMapping() - Constructor for class de.isas.mztab2.model.ColumnParameterMapping
ColumnParameterMapping.Properties - Enum in de.isas.mztab2.model: Property enumeration for ColumnParameterMapping.
columns() - Static method in enum uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable: Returns all stable ISmallMoleculeColumn templates.
columns() - Static method in enum uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable: Returns all stable SmallMoleculeEvidenceColumn templates.
columns() - Static method in enum uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn.Stable: Returns all stable ISmallMoleculeFeatureColumn templates.
ColUnit - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant ColUnit
COLUNIT - uk.ac.ebi.pride.jmztab2.model.MetadataElement
COLUNIT_SMALL_MOLECULE - uk.ac.ebi.pride.jmztab2.model.MetadataElement
COLUNIT_SMALL_MOLECULE_EVIDENCE - uk.ac.ebi.pride.jmztab2.model.MetadataElement
COLUNIT_SMALL_MOLECULE_FEATURE - uk.ac.ebi.pride.jmztab2.model.MetadataElement
colunitSmallMolecule - de.isas.mztab2.model.Metadata.Properties
colunitSmallMolecule(List<ColumnParameterMapping>) - Method in class de.isas.mztab2.model.Metadata: Builder method for colunitSmallMolecule.
colunitSmallMoleculeEvidence - de.isas.mztab2.model.Metadata.Properties
colunitSmallMoleculeEvidence(List<ColumnParameterMapping>) - Method in class de.isas.mztab2.model.Metadata: Builder method for colunitSmallMoleculeEvidence.
colunitSmallMoleculeFeature - de.isas.mztab2.model.Metadata.Properties
colunitSmallMoleculeFeature(List<ColumnParameterMapping>) - Method in class de.isas.mztab2.model.Metadata: Builder method for colunitSmallMoleculeFeature.
COM - de.isas.mztab2.model.Comment.PrefixEnum
COMLineParser - Class in uk.ac.ebi.pride.jmztab2.utils.parser: Comment line parser.
COMLineParser(MZTabParserContext) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.parser.COMLineParser: Constructor for COMLineParser.
COMMA - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant COMMA=','
comment - de.isas.mztab2.model.MzTab.Properties
comment - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
comment - de.isas.mztab2.model.SmallMoleculeFeature.Properties
comment - de.isas.mztab2.model.SmallMoleculeSummary.Properties
comment(List<Comment>) - Method in class de.isas.mztab2.model.MzTab: Builder method for comment.
comment(List<Comment>) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for comment.
comment(List<Comment>) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Builder method for comment.
comment(List<Comment>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for comment.
Comment - Class in de.isas.mztab2.model: Comment lines can be placed anywhere in an mzTab file.
Comment - uk.ac.ebi.pride.jmztab2.model.Section
Comment() - Constructor for class de.isas.mztab2.model.Comment
Comment.PrefixEnum - Enum in de.isas.mztab2.model: Gets or Sets prefix
Comment.Properties - Enum in de.isas.mztab2.model: Property enumeration for Comment.
complement(Set<T>, Set<T>) - Static method in class de.isas.mztab2.cvmapping.SetOperations: Returns the complement (a without elements also in b) of a and b.
contact - de.isas.mztab2.model.Metadata.Properties
contact(List<Contact>) - Method in class de.isas.mztab2.model.Metadata: Builder method for contact.
Contact - Class in de.isas.mztab2.model: The contact’s name, affiliation and e-mail.
Contact() - Constructor for class de.isas.mztab2.model.Contact
CONTACT - uk.ac.ebi.pride.jmztab2.model.MetadataElement
CONTACT_AFFILIATION - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
CONTACT_EMAIL - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
CONTACT_NAME - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
Contact.Properties - Enum in de.isas.mztab2.model: Property enumeration for Contact.
ContactFormat - Class in de.isas.mztab2.io.formats: Format specification for Contact.
ContactFormat() - Constructor for class de.isas.mztab2.io.formats.ContactFormat
ContactSerializer - Class in de.isas.mztab2.io.serialization: ContactSerializer implementation for Contact.
ContactSerializer() - Constructor for class de.isas.mztab2.io.serialization.ContactSerializer: Constructor for ContactSerializer.
ContactSerializer(Class<Contact>) - Constructor for class de.isas.mztab2.io.serialization.ContactSerializer: Constructor for ContactSerializer.
containsKey(Integer) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.PositionMapping: containsKey.
context - Variable in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabLineParser
convert(Parameter) - Method in class de.isas.mztab2.io.serialization.ParameterConverter
convert(Uri) - Method in class de.isas.mztab2.io.serialization.UriConverter
convertToValidationMessages() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Converts this error list to a list of validation messages.
convertToValidationMessages(MZTabErrorList) - Static method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Converts the provided error list to a list of validation messages.
CountMatch - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant CountMatch
createCvMapping() - Method in class info.psidev.cvmapping.ObjectFactory: Create an instance of CvMapping
createCvMappingCvMappingRuleList() - Method in class info.psidev.cvmapping.ObjectFactory: Create an instance of CvMapping.CvMappingRuleList
createCvMappingCvReferenceList() - Method in class info.psidev.cvmapping.ObjectFactory: Create an instance of CvMapping.CvReferenceList
createCvMappingRule() - Method in class info.psidev.cvmapping.ObjectFactory: Create an instance of CvMappingRule
createCvReference() - Method in class info.psidev.cvmapping.ObjectFactory: Create an instance of CvReference
createCvTerm() - Method in class info.psidev.cvmapping.ObjectFactory: Create an instance of CvTerm
createError(MZTabErrorType.Category, String) - Static method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: Generate a MZTabErrorType.Level.Error by parse keyword.
createInfo(MZTabErrorType.Category, String) - Static method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: Generate a MZTabErrorType.Level.Info by parse keyword.
createOptionalColumn(Section, Assay, int) - Static method in class uk.ac.ebi.pride.jmztab2.model.AbundanceColumn: Generate a abundance optional column as measured in the given assay.The column header like protein_abundance_assay[1-n], the position always stay the most right of the tabled section, and the data type is Double.
createOptionalColumns(Section, StudyVariable, Integer) - Static method in class uk.ac.ebi.pride.jmztab2.model.AbundanceColumn: createOptionalColumns.
createOptionalColumns(Section, StudyVariable, String, String) - Static method in class uk.ac.ebi.pride.jmztab2.model.AbundanceColumn: Generate an abundance optional column as measured in the given study variable.
createWarn(MZTabErrorType.Category, String) - Static method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: Generate a MZTabErrorType.Level.Warn by parse keyword.
CROSS_CHECK - de.isas.mztab2.model.ValidationMessage.CategoryEnum
CrossCheck - uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Category
CrossCheckErrorType - Class in uk.ac.ebi.pride.jmztab2.utils.errors: Provide crosscheck service, that is parse the consistent between current mztab file and some other resource (eg, database, xml file and so on).
custom - de.isas.mztab2.model.Assay.Properties
custom - de.isas.mztab2.model.Metadata.Properties
custom - de.isas.mztab2.model.Sample.Properties
custom(List<Parameter>) - Method in class de.isas.mztab2.model.Assay: Builder method for custom.
custom(List<Parameter>) - Method in class de.isas.mztab2.model.Metadata: Builder method for custom.
custom(List<Parameter>) - Method in class de.isas.mztab2.model.Sample: Builder method for custom.
CUSTOM - uk.ac.ebi.pride.jmztab2.model.MetadataElement
cv - de.isas.mztab2.model.Metadata.Properties
cv(List<CV>) - Method in class de.isas.mztab2.model.Metadata: Builder method for cv.
CV - Class in de.isas.mztab2.model: Specification of controlled vocabularies. label: A string describing the labels of the controlled vocabularies/ontologies used in the mzTab file as a short-hand e.g.
CV - uk.ac.ebi.pride.jmztab2.model.MetadataElement
CV - Static variable in class uk.ac.ebi.pride.jmztab2.model.ParameterOptionColumn: Constant CV="cv_"
CV() - Constructor for class de.isas.mztab2.model.CV
CV_FULL_NAME - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
CV_LABEL - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
CV_PREFIX - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant CV_PREFIX="cv_"
CV_URI - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
CV_VERSION - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
CV.Properties - Enum in de.isas.mztab2.model: Property enumeration for CV.
cvAccession - de.isas.mztab2.model.Parameter.Properties
cvAccession(String) - Method in class de.isas.mztab2.model.Parameter: Builder method for cvAccession.
CvDefinitionValidationHandler - Class in de.isas.mztab2.validation: Validates that controlled vocabularies used by parameters are defined in the metadata CV section.
CvDefinitionValidationHandler() - Constructor for class de.isas.mztab2.validation.CvDefinitionValidationHandler
cvElementPath - Variable in class info.psidev.cvmapping.CvMappingRule
CvFormat - Class in de.isas.mztab2.io.formats: Format specification for CV.
CvFormat() - Constructor for class de.isas.mztab2.io.formats.CvFormat
cvIdentifier - Variable in class info.psidev.cvmapping.CvReference
cvIdentifierRef - Variable in class info.psidev.cvmapping.CvTerm
cvLabel - de.isas.mztab2.model.Parameter.Properties
cvLabel(String) - Method in class de.isas.mztab2.model.Parameter: Builder method for cvLabel.
CvMapping - Class in info.psidev.cvmapping: Java-Klasse für anonymous complex type.
CvMapping() - Constructor for class info.psidev.cvmapping.CvMapping
CvMapping.CvMappingRuleList - Class in info.psidev.cvmapping: Java-Klasse für anonymous complex type.
CvMapping.CvReferenceList - Class in info.psidev.cvmapping: Java-Klasse für anonymous complex type.
cvMappingRule - Variable in class info.psidev.cvmapping.CvMapping.CvMappingRuleList
CvMappingRule - Class in info.psidev.cvmapping: Java-Klasse für anonymous complex type.
CvMappingRule() - Constructor for class info.psidev.cvmapping.CvMappingRule
CvMappingRule.CvTermsCombinationLogic - Enum in info.psidev.cvmapping: Java-Klasse für null.
CvMappingRule.RequirementLevel - Enum in info.psidev.cvmapping: Java-Klasse für null.
cvMappingRuleList - Variable in class info.psidev.cvmapping.CvMapping
CvMappingRuleList() - Constructor for class info.psidev.cvmapping.CvMapping.CvMappingRuleList
CvMappingUtils - Class in de.isas.mztab2.cvmapping: Utility methods for conversion between the mapping file domain and the mzTab domain.
CvMappingUtils() - Constructor for class de.isas.mztab2.cvmapping.CvMappingUtils
CvMappingValidator - Class in de.isas.mztab2.validation: Validator implementation that uses a provided xml mapping file with rules for required, recommended and optional CV parameters to assert that an mzTab follows these rules.
CvMappingValidator() - Constructor for class de.isas.mztab2.validation.CvMappingValidator
cvName - Variable in class info.psidev.cvmapping.CvReference
CvParameterLookupService - Class in de.isas.mztab2.cvmapping: Abstraction over OLSClient to autoconvert Terms to Parameters and to allow easy matching of Parameters against parent terms and their children.
CvParameterLookupService() - Constructor for class de.isas.mztab2.cvmapping.CvParameterLookupService: Create a new instance of the lookup service with default OLS configuration.
CvParameterLookupService(OLSClient) - Constructor for class de.isas.mztab2.cvmapping.CvParameterLookupService: Create a new instance of the lookup service with a custom OLSClient.
CvParameterLookupService(OLSWsConfig) - Constructor for class de.isas.mztab2.cvmapping.CvParameterLookupService: Create a new instance of the lookup service with a custom OLSWsConfig configuration.
cvReference - Variable in class info.psidev.cvmapping.CvMapping.CvReferenceList
CvReference - Class in info.psidev.cvmapping: Java-Klasse für anonymous complex type.
CvReference() - Constructor for class info.psidev.cvmapping.CvReference
cvReferenceList - Variable in class info.psidev.cvmapping.CvMapping
CvReferenceList() - Constructor for class info.psidev.cvmapping.CvMapping.CvReferenceList
CvRuleHandler - Interface in de.isas.mztab2.validation: Interface for rule logic handling implementations.
CvSerializer - Class in de.isas.mztab2.io.serialization: CvSerializer implementation for CV.
CvSerializer() - Constructor for class de.isas.mztab2.io.serialization.CvSerializer: Constructor for CvSerializer.
CvSerializer(Class<CV>) - Constructor for class de.isas.mztab2.io.serialization.CvSerializer: Constructor for CvSerializer.
cvSourceVersion - Variable in class info.psidev.cvmapping.CvMapping.CvReferenceList
cvTerm - Variable in class info.psidev.cvmapping.CvMappingRule
CvTerm - Class in info.psidev.cvmapping: Java-Klasse für anonymous complex type.
CvTerm() - Constructor for class info.psidev.cvmapping.CvTerm
CvTermMalformed - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType: Constant CvTermMalformed
CvTermNotAllowed - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType: Constant CvTermNotAllowed
CvTermNotInRule - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType: Constant CvTermNotInRule
CvTermOptional - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType: Constant CvTermOptional
CvTermRecommended - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType: Constant CvTermRecommended
CvTermRequired - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType: Constant CvTermRequired
cvTermsCombinationLogic - Variable in class info.psidev.cvmapping.CvMappingRule
CvTermSelectionHandler - Interface in de.isas.mztab2.validation: Interface for JxPath subtree selection handling.
CvTermValidationHandler - Interface in de.isas.mztab2.validation: Interface for handling of rule evaluation results.
CvTermXor - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType: Constant CvTermXor
CvUndefinedInMetadata - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType: Constant CvUndefinedInMetadata
CvUnused - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType: Constant CvUnused
CvValidator - Class in de.isas.mztab2.io.validators: Validates that the controlled vocabulary section is present in metadata and that it is correctly populated.
CvValidator() - Constructor for class de.isas.mztab2.io.validators.CvValidator

D

database - de.isas.mztab2.model.Metadata.Properties
database(List<Database>) - Method in class de.isas.mztab2.model.Metadata: Builder method for database.
Database - Class in de.isas.mztab2.model: Specification of databases.
Database() - Constructor for class de.isas.mztab2.model.Database
DATABASE - uk.ac.ebi.pride.jmztab2.model.MetadataElement
DATABASE_IDENTIFIER - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
DATABASE_IDENTIFIER - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
DATABASE_PREFIX - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
DATABASE_URI - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
DATABASE_VERSION - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
Database.Properties - Enum in de.isas.mztab2.model: Property enumeration for Database.
DatabaseFormat - Class in de.isas.mztab2.io.formats: Format specification for Database.
DatabaseFormat() - Constructor for class de.isas.mztab2.io.formats.DatabaseFormat
databaseIdentifier - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
databaseIdentifier - de.isas.mztab2.model.SmallMoleculeSummary.Properties
databaseIdentifier(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for databaseIdentifier.
databaseIdentifier(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for databaseIdentifier.
DatabaseSerializer - Class in de.isas.mztab2.io.serialization: DatabaseSerializer implementation for Database.
DatabaseSerializer() - Constructor for class de.isas.mztab2.io.serialization.DatabaseSerializer: Constructor for DatabaseSerializer.
DatabaseSerializer(Class<Database>) - Constructor for class de.isas.mztab2.io.serialization.DatabaseSerializer: Constructor for DatabaseSerializer.
DatabaseValidator - Class in de.isas.mztab2.io.validators: Validates that the database section is present and correctly populated in metadata.
DatabaseValidator() - Constructor for class de.isas.mztab2.io.validators.DatabaseValidator
de.isas.lipidomics.mztab2.validation - package de.isas.lipidomics.mztab2.validation: This package contains classes that provide the basic validator infrastructure used in the jmztabm-validation module.
de.isas.lipidomics.mztab2.validation.constraints - package de.isas.lipidomics.mztab2.validation.constraints: This package contains custom validation annotations for the javax.validation framework.
de.isas.lipidomics.mztab2.validation.validators - package de.isas.lipidomics.mztab2.validation.validators: This package contains custom validators that implement the
de.isas.mztab2.cli - package de.isas.mztab2.cli: This package contains the command line interface for jmzTab-M validation and conversion.
de.isas.mztab2.cvmapping - package de.isas.mztab2.cvmapping: This package contains classes for controlled vocabulary term access, comparison, results and external cv parameter resolution.
de.isas.mztab2.io - package de.isas.mztab2.io: This package contains implementations for reading and writing of mzTab-M files.
de.isas.mztab2.io.formats - package de.isas.mztab2.io.formats: This package defines formats for Jackson that define, which serializer should be used for a particular object type.
de.isas.mztab2.io.serialization - package de.isas.mztab2.io.serialization: This package contains classes that implement custom Jackson serializers for the mzTab-M model objects.
de.isas.mztab2.io.validators - package de.isas.mztab2.io.validators: This package contains implementations for validation of mzTab-M parts during parsing.
de.isas.mztab2.model - package de.isas.mztab2.model: Base package for the jmztab-m data model, generated from the mzTab_m_swagger.yml specification.
de.isas.mztab2.test.utils - package de.isas.mztab2.test.utils: This package contains custom JUnit Rules for extraction of class path resource files and additional logging for testing.
de.isas.mztab2.validation - package de.isas.mztab2.validation: This package contains interfaces and implementations for the semantic validation via CvTerms.
de.isas.mztab2.validation.handlers - package de.isas.mztab2.validation.handlers: This package contains implementations for the semantic validation controlled vocabulary term rules.
defaultMapper() - Method in class de.isas.mztab2.io.MzTabWriterDefaults: Create a default csv mapper instance.
defaultSchemaForBuilder(CsvSchema.Builder) - Method in class de.isas.mztab2.io.MzTabWriterDefaults: Apply the default csv schema to the provided builder.
DERIVATIZATION_AGENT - uk.ac.ebi.pride.jmztab2.model.MetadataElement
derivatizationAgent - de.isas.mztab2.model.Metadata.Properties
derivatizationAgent(List<Parameter>) - Method in class de.isas.mztab2.model.Metadata: Builder method for derivatizationAgent.
DERIVATIZED_FORM - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
derivatizedForm - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
derivatizedForm(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for derivatizedForm.
description - de.isas.mztab2.model.Metadata.Properties
description - de.isas.mztab2.model.Sample.Properties
description - de.isas.mztab2.model.StudyVariable.Properties
description(String) - Method in class de.isas.mztab2.model.Metadata: Builder method for description.
description(String) - Method in class de.isas.mztab2.model.Sample: Builder method for description.
description(String) - Method in class de.isas.mztab2.model.StudyVariable: Builder method for description.
DESCRIPTION - uk.ac.ebi.pride.jmztab2.model.MetadataElement
detector - de.isas.mztab2.model.Instrument.Properties
detector(Parameter) - Method in class de.isas.mztab2.model.Instrument: Builder method for detector.
disease - de.isas.mztab2.model.Sample.Properties
disease(List<Parameter>) - Method in class de.isas.mztab2.model.Sample: Builder method for disease.
DOI - de.isas.mztab2.model.PublicationItem.TypeEnum
Double - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant Double
DoubleList - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant DoubleList
DuplicationAccession - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant DuplicationAccession
DuplicationDefine - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant DuplicationDefine
DuplicationID - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant DuplicationID

E

ElementNameMappingException - Exception in de.isas.mztab2.io.serialization: ElementNameMappingException should be thrown to indicate that the state of the passed in element did not allow mapping to a proper mzTab name.
ElementNameMappingException(String, Object) - Constructor for exception de.isas.mztab2.io.serialization.ElementNameMappingException: Constructor for ElementNameMappingException.
email - de.isas.mztab2.model.Contact.Properties
email(String) - Method in class de.isas.mztab2.model.Contact: Builder method for email.
Email - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant Email
EmptyRuleHandler - Class in de.isas.mztab2.validation.handlers: Implements handling of rules that have no cv parameter match.
EmptyRuleHandler() - Constructor for class de.isas.mztab2.validation.handlers.EmptyRuleHandler
ENCODE - Static variable in class uk.ac.ebi.pride.jmztab2.utils.MZTabProperties: Constant ENCODE="getProperty(mztab.encode)"
equals(Object) - Method in class de.isas.mztab2.model.Assay
equals(Object) - Method in class de.isas.mztab2.model.ColumnParameterMapping
equals(Object) - Method in class de.isas.mztab2.model.Comment
equals(Object) - Method in class de.isas.mztab2.model.Contact
equals(Object) - Method in class de.isas.mztab2.model.CV
equals(Object) - Method in class de.isas.mztab2.model.Database
equals(Object) - Method in class de.isas.mztab2.model.Error
equals(Object) - Method in class de.isas.mztab2.model.IndexedElementImpl
equals(Object) - Method in class de.isas.mztab2.model.Instrument
equals(Object) - Method in class de.isas.mztab2.model.Metadata
equals(Object) - Method in class de.isas.mztab2.model.MsRun
equals(Object) - Method in class de.isas.mztab2.model.MzTab
equals(Object) - Method in class de.isas.mztab2.model.OptColumnMapping
equals(Object) - Method in class de.isas.mztab2.model.Parameter
equals(Object) - Method in class de.isas.mztab2.model.Publication
equals(Object) - Method in class de.isas.mztab2.model.PublicationItem
equals(Object) - Method in class de.isas.mztab2.model.Sample
equals(Object) - Method in class de.isas.mztab2.model.SampleProcessing
equals(Object) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence
equals(Object) - Method in class de.isas.mztab2.model.SmallMoleculeFeature
equals(Object) - Method in class de.isas.mztab2.model.SmallMoleculeSummary
equals(Object) - Method in class de.isas.mztab2.model.Software
equals(Object) - Method in class de.isas.mztab2.model.SpectraRef
equals(Object) - Method in class de.isas.mztab2.model.StringList
equals(Object) - Method in class de.isas.mztab2.model.StudyVariable
equals(Object) - Method in class de.isas.mztab2.model.Uri
equals(Object) - Method in class de.isas.mztab2.model.ValidationMessage
equals(Object) - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumn
equals(Object) - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType
Error - Class in de.isas.mztab2.model: Error
Error - uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Level
Error() - Constructor for class de.isas.mztab2.model.Error
ERROR - de.isas.mztab2.model.ValidationMessage.MessageTypeEnum
ERROR_AMBIGUITY - Static variable in exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabConversionException: Constant ERROR_AMBIGUITY="mzTab do not support one protein in mor"{trunked}
Error.Properties - Enum in de.isas.mztab2.model: Property enumeration for Error.
errorList - Variable in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabLineParser
EVIDENCE_INPUT_ID - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
evidenceInputId - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
evidenceInputId(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for evidenceInputId.
exchangeMapping - Variable in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser
EXP_MASS_TO_CHARGE - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
EXP_MASS_TO_CHARGE - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn.Stable
expMassToCharge - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
expMassToCharge - de.isas.mztab2.model.SmallMoleculeFeature.Properties
expMassToCharge(Double) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for expMassToCharge.
expMassToCharge(Double) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Builder method for expMassToCharge.
EXTERNAL_STUDY_URI - uk.ac.ebi.pride.jmztab2.model.MetadataElement
ExternalStudyFormatNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant ExternalStudyFormatNotDefined
ExternalStudyIdFormatNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant ExternalStudyIdFormatNotDefined
externalStudyUri - de.isas.mztab2.model.Metadata.Properties
externalStudyUri(List<Uri>) - Method in class de.isas.mztab2.model.Metadata: Builder method for externalStudyUri.
externalUri - de.isas.mztab2.model.Assay.Properties
externalUri(String) - Method in class de.isas.mztab2.model.Assay: Builder method for externalUri.
extract(String, File) - Static method in class de.isas.mztab2.test.utils.ZipResourceExtractor: Extract a JAR resource into the provided destination directory and return that extracted resource's location as a file.
ExtractClassPathFiles - Class in de.isas.mztab2.test.utils: ExtractClassPathFiles class.
ExtractClassPathFiles(ClassPathFile...) - Constructor for class de.isas.mztab2.test.utils.ExtractClassPathFiles: Constructor for ExtractClassPathFiles.
ExtractClassPathFiles(TemporaryFolder, ClassPathFile...) - Constructor for class de.isas.mztab2.test.utils.ExtractClassPathFiles: Constructor for ExtractClassPathFiles.
extractZipArchive(InputStream, File) - Static method in class de.isas.mztab2.test.utils.ZipResourceExtractor: extractZipArchive.
ExtraParametersValidationHandler - Class in de.isas.mztab2.validation.handlers: Implements handling of cv parameters (not user params) that are found at the object.
ExtraParametersValidationHandler() - Constructor for class de.isas.mztab2.validation.handlers.ExtraParametersValidationHandler

F

factors - de.isas.mztab2.model.StudyVariable.Properties
factors(List<Parameter>) - Method in class de.isas.mztab2.model.StudyVariable: Builder method for factors.
factory - Variable in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser
factory - Variable in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabHeaderLineParser
False - uk.ac.ebi.pride.jmztab2.model.MZBoolean
FieldValidator<T> - Interface in de.isas.mztab2.io.validators: Implementations of the field validator are applied to the type object (usually a parsed string element) during the parsing process.
fileName() - Method in enum de.isas.mztab2.test.utils.ClassPathFile
findBoolean(String) - Static method in enum uk.ac.ebi.pride.jmztab2.model.MZBoolean: Find the MZBoolean for the given string representation.
findColumnByHeader(String) - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory: Query the MZTabColumn in factory, based on column header with case-insensitive.
findElement(String) - Static method in enum uk.ac.ebi.pride.jmztab2.model.MetadataElement: Find element by name with case-insensitive match.
findLevel(String) - Static method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: findLevel.
findProperty(MetadataElement, String) - Static method in enum uk.ac.ebi.pride.jmztab2.model.MetadataProperty: Find property by MetadataElement and property name with case-insensitive.
findSection(int) - Static method in enum uk.ac.ebi.pride.jmztab2.model.Section: findSection.
findSection(String) - Static method in enum uk.ac.ebi.pride.jmztab2.model.Section: Query section based on its name or prefix with case-insensitive.
FixedMod - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant FixedMod
forGlobal() - Static method in class uk.ac.ebi.pride.jmztab2.model.OptColumnMappingBuilder: Configure the builder for a global type column.
forIndexedElement(Object) - Static method in class uk.ac.ebi.pride.jmztab2.model.OptColumnMappingBuilder: Configure the builder for an object reference (indexed element) type column.
forLevel(MZTabErrorType.Category, MZTabErrorType.Level, String) - Static method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType
format - de.isas.mztab2.model.MsRun.Properties
format(Parameter) - Method in class de.isas.mztab2.model.MsRun: Builder method for format.
Format - uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Category
FORMAT - de.isas.mztab2.model.ValidationMessage.CategoryEnum
FormatErrorType - Class in uk.ac.ebi.pride.jmztab2.utils.errors: Diagnose different types of format-related (reporting format problems).
forName(String) - Static method in enum uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable: Returns a stable column instance template.
forName(String) - Static method in enum uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable: Returns a stable column instance template.
forName(String) - Static method in enum uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn.Stable: Returns a stable column instance template.
fragmentationMethod - de.isas.mztab2.model.MsRun.Properties
fragmentationMethod(List<Parameter>) - Method in class de.isas.mztab2.model.MsRun: Builder method for fragmentationMethod.
fromIndexToOrder(Integer) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabHeaderLineParser: fromIndexToOrder.
fromValue(String) - Static method in enum de.isas.mztab2.model.Comment.PrefixEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.Metadata.PrefixEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.PublicationItem.TypeEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeEvidence.HeaderPrefixEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeEvidence.PrefixEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeFeature.HeaderPrefixEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeFeature.PrefixEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeSummary.HeaderPrefixEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeSummary.PrefixEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.ValidationMessage.CategoryEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.ValidationMessage.MessageTypeEnum
fromValue(String) - Static method in enum info.psidev.cvmapping.CvMappingRule.CvTermsCombinationLogic
fromValue(String) - Static method in enum info.psidev.cvmapping.CvMappingRule.RequirementLevel
fullName - de.isas.mztab2.model.CV.Properties
fullName(String) - Method in class de.isas.mztab2.model.CV: Builder method for fullName.

G

GCXGC_MS_EXAMPLE - de.isas.mztab2.test.utils.ClassPathFile
get(Integer) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.PositionMapping: get.
getAbundanceAssay() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: The feature’s abundance in every assay described in the metadata section MUST be reported.
getAbundanceAssay() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: The small molecule’s abundance in every assay described in the metadata section MUST be reported.
getAbundanceFor(Assay, SmallMoleculeFeature) - Method in class de.isas.mztab2.model.MzTabAccess: Retrieves the abundance value for the provided assay and small molecule feature object.
getAbundanceFor(Assay, SmallMoleculeSummary) - Method in class de.isas.mztab2.model.MzTabAccess: Retrieves the abundance value for the provided assay and small molecule summary object.
getAbundanceFor(StudyVariable, SmallMoleculeSummary) - Method in class de.isas.mztab2.model.MzTabAccess: Retrieves the abundance value for the provided study variable and small molecule summary object.
getAbundanceStudyVariable() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: The small molecule’s abundance in all the study variables described in the metadata section (study_variable[1-n]_average_function), calculated using the method as described in the Metadata section (default = arithmetic mean across assays).
getAbundanceVariationFor(StudyVariable, SmallMoleculeSummary) - Method in class de.isas.mztab2.model.MzTabAccess: Retrieves the abundance variation value for the provided study variable and small molecule summary object.
getAbundanceVariationStudyVariable() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: A measure of the variability of the study variable abundance measurement, calculated using the method as described in the metadata section (study_variable[1-n]_average_function), with a default = arithmethic co-efficient of variation of the small molecule’s abundance in the given study variable.
getAccession() - Method in class de.isas.mztab2.model.PublicationItem: The native accession id for this publication item.
getAdductIon() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The assumed classification of this molecule’s adduct ion after detection, following the general style in the 2013 IUPAC recommendations on terms relating to MS e.g.
getAdductIon() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: The assumed classification of this molecule’s adduct ion after detection, following the general style in the 2013 IUPAC recommendations on terms relating to MS e.g.
getAdductIons() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: A “|” separated list of detected adducts for this this molecule, following the general style in the 2013 IUPAC recommendations on terms relating to MS e.g.
getAffiliation() - Method in class de.isas.mztab2.model.Contact: The contact's affiliation.
getAnalyzer() - Method in class de.isas.mztab2.model.Instrument: The instrument's mass analyzer, as defined by the parameter.
getAssay() - Method in class de.isas.mztab2.model.Metadata: Specification of assay.
getAssayFor(OptColumnMapping, Metadata) - Method in class de.isas.mztab2.model.MzTabAccess: Tries to locate the assay referenced by id from the columnMapping identifier.
getAssayFor(Integer, Metadata) - Method in class de.isas.mztab2.model.MzTabAccess: Tries to locate the assay referenced by id from the metadata section.
getAssayRefs() - Method in class de.isas.mztab2.model.StudyVariable: The assays referenced by this study variable.
getAverageFunction() - Method in class de.isas.mztab2.model.StudyVariable: The function used to calculate summarised small molecule quantities over the assays referenced by this study variable.
getBaseDir() - Method in class de.isas.mztab2.test.utils.ExtractClassPathFiles: getBaseDir.
getBestIdConfidenceMeasure() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: The approach or database search that identified this small molecule with highest confidence.
getBestIdConfidenceValue() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: The best confidence measure in identification (for this type of score) for the given small molecule across all assays.
getCategory() - Method in class de.isas.mztab2.model.ValidationMessage: Get category.
getCategory() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: Getter for the field category.
getCause() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: Getter for the field cause.
getCellType() - Method in class de.isas.mztab2.model.Sample: Biological cell type information on the sample.
getCharge() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The small molecule evidence’s charge value using positive integers both for positive and negative polarity modes.
getCharge() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: The feature’s charge value using positive integers both for positive and negative polarity modes.
getChemicalFormula() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The chemical formula of the identified compound e.g. in a database, assumed to match the theoretical mass to charge (in some cases this will be the derivatized form, including adducts and protons).
getChemicalFormula() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: A list of “|” separated potential chemical formulae of the reported compound.
getChemicalName() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The small molecule’s chemical/common name, or general description if a chemical name is unavailable.
getChemicalName() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: A list of “|” separated possible chemical/common names for the small molecule, or general description if a chemical name is unavailable.
getCode() - Method in class de.isas.mztab2.model.Error: Get code.
getCode() - Method in class de.isas.mztab2.model.ValidationMessage: Get code.
getCode() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: Getter for the field code.
getColumnMapping() - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory: Get all columns in the factory.
getColumnName() - Method in class de.isas.mztab2.model.ColumnParameterMapping: The fully qualified target column name.
getColUnitMap() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Defines a method to access the colUnit to help in the transformation from columnName String -> to columnName MZTabColumn
getColunitSmallMolecule() - Method in class de.isas.mztab2.model.Metadata: Defines the used unit for a column in the small molecule section.
getColunitSmallMoleculeEvidence() - Method in class de.isas.mztab2.model.Metadata: Defines the used unit for a column in the small molecule evidence section.
getColunitSmallMoleculeFeature() - Method in class de.isas.mztab2.model.Metadata: Defines the used unit for a column in the small molecule feature section.
getComment() - Method in class de.isas.mztab2.model.MzTab: Comment lines can be placed anywhere in an mzTab file.
getComment() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Get comment.
getComment() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Get comment.
getComment() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Get comment.
getComment() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.COMLineParser: getComment.
getContact() - Method in class de.isas.mztab2.model.Metadata: The contact’s name, affiliation and e-mail.
getCustom() - Method in class de.isas.mztab2.model.Assay: Additional user or cv parameters.
getCustom() - Method in class de.isas.mztab2.model.Metadata: Any additional parameters describing the analysis reported.
getCustom() - Method in class de.isas.mztab2.model.Sample: Additional user or cv parameters.
getCv() - Method in class de.isas.mztab2.model.Metadata: Specification of controlled vocabularies. label: A string describing the labels of the controlled vocabularies/ontologies used in the mzTab file as a short-hand e.g.
getCvAccession() - Method in class de.isas.mztab2.model.Parameter: Get cvAccession.
getCvElementPath() - Method in class info.psidev.cvmapping.CvMappingRule: Ruft den Wert der cvElementPath-Eigenschaft ab.
getCvIdentifier() - Method in class info.psidev.cvmapping.CvReference: Ruft den Wert der cvIdentifier-Eigenschaft ab.
getCvIdentifierRef() - Method in class info.psidev.cvmapping.CvTerm: Ruft den Wert der cvIdentifierRef-Eigenschaft ab.
getCvLabel() - Method in class de.isas.mztab2.model.Parameter: Get cvLabel.
getCvMappingRule() - Method in class info.psidev.cvmapping.CvMapping.CvMappingRuleList: Single mapping rule between a specific elements of the model and to controlled vocabularies listed on the CvTerm element.Gets the value of the cvMappingRule property.
getCvMappingRuleList() - Method in class info.psidev.cvmapping.CvMapping: Ruft den Wert der cvMappingRuleList-Eigenschaft ab.
getCvName() - Method in class info.psidev.cvmapping.CvReference: Ruft den Wert der cvName-Eigenschaft ab.
getCvReference() - Method in class info.psidev.cvmapping.CvMapping.CvReferenceList: Description of a CV or ontology resource.Gets the value of the cvReference property.
getCvReferenceList() - Method in class info.psidev.cvmapping.CvMapping: Ruft den Wert der cvReferenceList-Eigenschaft ab.
getCvSourceVersion() - Method in class info.psidev.cvmapping.CvMapping.CvReferenceList: Ruft den Wert der cvSourceVersion-Eigenschaft ab.
getCvTerm() - Method in class info.psidev.cvmapping.CvMappingRule: One or more terms from a CVsource that are allowed to be associated with the given element of the model.
getCvTermsCombinationLogic() - Method in class info.psidev.cvmapping.CvMappingRule: Ruft den Wert der cvTermsCombinationLogic-Eigenschaft ab.
getDatabase() - Method in class de.isas.mztab2.model.Metadata: Specification of databases.
getDatabaseFor(Integer, Metadata) - Method in class de.isas.mztab2.model.MzTabAccess: Tries to locate the database referenced by id from the metadata section.
getDatabaseIdentifier() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The putative identification for the small molecule sourced from an external database, using the same prefix specified in database[1-n]-prefix.
getDatabaseIdentifier() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: A list of “|” separated possible identifiers for the small molecule; multiple values MUST only be provided to indicate ambiguity in the identification of the molecule and not to demonstrate different identifier types for the same molecule.
getDataType() - Method in interface uk.ac.ebi.pride.jmztab2.model.IMZTabColumn: Get the column data type Class.
getDataType() - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumn: Get the column data type Class.
getDataType() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn: Get the column data type Class.
getDataType() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn: Get the column data type Class.
getDataType() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn: Get the column data type Class.
getDerivatizationAgent() - Method in class de.isas.mztab2.model.Metadata: A description of derivatization agents applied to small molecules, using userParams or CV terms where possible.
getDerivatizedForm() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: 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.
getDescription() - Method in class de.isas.mztab2.model.Metadata: The file’s human readable description.
getDescription() - Method in class de.isas.mztab2.model.Sample: A free form description of the sample.
getDescription() - Method in class de.isas.mztab2.model.StudyVariable: A free-form description of this study variable.
getDetector() - Method in class de.isas.mztab2.model.Instrument: The instrument's detector, as defined by the parameter.
getDisease() - Method in class de.isas.mztab2.model.Sample: Disease information on the sample.
getElement() - Method in interface uk.ac.ebi.pride.jmztab2.model.IMZTabColumn: Indexed element used in optional column header and logical position definition.
getElement() - Method in enum uk.ac.ebi.pride.jmztab2.model.MetadataProperty: Getter for the field element.
getElement() - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumn: Indexed element used in optional column header and logical position definition.
getElement() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn: Indexed element used in optional column header and logical position definition.
getElement() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn: Indexed element used in optional column header and logical position definition.
getElement() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn: Indexed element used in optional column header and logical position definition.
getElementName(Object) - Static method in class de.isas.mztab2.io.serialization.Serializers: getElementName.
getElementType() - Method in class de.isas.mztab2.model.IndexedElementImpl: Returns the element type string.
getEmail() - Method in class de.isas.mztab2.model.Contact: The contact's e-mail address.
getError() - Method in exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException: Getter for the field error.
getError(int) - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Returns the element at the specified position in this list.
getErrorList() - Method in class de.isas.mztab2.io.MzTabFileParser: Getter for the field errorList.
getErrorList() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Unmodifiable list of errors
getEvidenceInputId() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: A within file unique identifier for the input data used to support this identification e.g. fragment spectrum, RT and m/z pair, isotope profile that was used for the identification process, to serve as a grouping mechanism, whereby multiple rows of results from the same input data share the same ID.
getEvidences(SmallMoleculeFeature) - Method in class de.isas.mztab2.model.MzTabAccess: Retrieve all small molecule evidences in order of definition for the provided small molecule feature.
getEvidencesByEvidenceInputId(String) - Method in class de.isas.mztab2.model.MzTabAccess: Retrieve all small molecule evidences for the provided evidence input id.
getExpMassToCharge() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The experimental mass/charge value for the precursor ion.
getExpMassToCharge() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: The experimental mass/charge value for the feature, by default assumed to be the mean across assays or a representative value.
getExternalStudyUri() - Method in class de.isas.mztab2.model.Metadata: A URI pointing to an external file with more details about the study design (e.g., an ISA-TAB file).
getExternalUri() - Method in class de.isas.mztab2.model.Assay: An external URI to further information about this assay.
getFactors() - Method in class de.isas.mztab2.model.StudyVariable: Parameters indicating which factors were used for the assays referenced by this study variable, and at which levels.
getFactory() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabHeaderLineParser: Getter for the field factory.
getFeatures(SmallMoleculeSummary) - Method in class de.isas.mztab2.model.MzTabAccess: Retrieve all small molecule features in order of definition for the provided small molecule summary.
getFiles() - Method in class de.isas.mztab2.test.utils.ExtractClassPathFiles: Getter for the field files.
getFormat() - Method in class de.isas.mztab2.model.MsRun: The msRun's file format.
getFragmentationMethod() - Method in class de.isas.mztab2.model.MsRun: The fragmentation methods applied during this msRun.
getFullName() - Method in class de.isas.mztab2.model.CV: The full name of this CV, for humans.
getHash() - Method in class de.isas.mztab2.model.MsRun: The file hash value of this msRun's data file.
getHashMethod() - Method in class de.isas.mztab2.model.MsRun: The hash method used to calculate the file hash.
getHeader() - Method in interface uk.ac.ebi.pride.jmztab2.model.IMZTabColumn: Get the column name.
getHeader() - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumn: Get the column name.
getHeader() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn: Get the column name.
getHeader() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn: Get the column name.
getHeader() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn: Get the column name.
getHeader(Object, Parameter) - Static method in class uk.ac.ebi.pride.jmztab2.model.ParameterOptionColumn: get column header like: opt_{OBJECT_ID}_cv_{accession}_{parameter name} Spaces within the parameter's name MUST be replaced by '_'.
getHeader(Object, String) - Static method in class uk.ac.ebi.pride.jmztab2.model.OptionColumn: Get the optional column header, which start with the prefix "opt_". the format: opt_{indexedElement[id]}_{name}.
getHeaderPrefix() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The small molecule evidence table header prefix.
getHeaderPrefix() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: The small molecule feature table header prefix.
getHeaderPrefix() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: The small molecule table header prefix.
getId() - Method in class de.isas.mztab2.model.Assay: Get id.
getId() - Method in class de.isas.mztab2.model.Contact: Get id.
getId() - Method in class de.isas.mztab2.model.CV: Get id.
getId() - Method in class de.isas.mztab2.model.Database: Get id.
getId() - Method in interface de.isas.mztab2.model.IndexedElement: Returns the id of the indexed element.
getId() - Method in class de.isas.mztab2.model.IndexedElementImpl
getId() - Method in class de.isas.mztab2.model.Instrument: Get id.
getId() - Method in class de.isas.mztab2.model.MsRun: Get id.
getId() - Method in class de.isas.mztab2.model.Parameter: Get id.
getId() - Method in class de.isas.mztab2.model.Publication: Get id.
getId() - Method in class de.isas.mztab2.model.Sample: Get id.
getId() - Method in class de.isas.mztab2.model.SampleProcessing: Get id.
getId() - Method in class de.isas.mztab2.model.Software: Get id.
getId() - Method in class de.isas.mztab2.model.StudyVariable: Get id.
getId() - Method in class de.isas.mztab2.model.Uri: Get id.
getId() - Method in class info.psidev.cvmapping.CvMappingRule: Ruft den Wert der id-Eigenschaft ab.
getIdConfidenceMeasure() - Method in class de.isas.mztab2.model.Metadata: The type of small molecule confidence measures or scores MUST be reported as a CV parameter [1-n].
getIdConfidenceMeasure() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Any statistical value or score for the identification.
getIdentificationMethod() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: 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.
getIdentifier() - Method in class de.isas.mztab2.model.OptColumnMapping: The fully qualified column name.
getIdFormat() - Method in class de.isas.mztab2.model.MsRun: The msRun's mass spectra id format.
getInchi() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: A standard IUPAC International Chemical Identifier (InChI) for the given substance.
getInchi() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: A list of “|” separated potential standard IUPAC International Chemical Identifier (InChI) of the given substance.
getInstance(Section) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory: Retrieves the MZTabColumnFactory accordingly to the MZTabColumnFactory.section
getInstrument() - Method in class de.isas.mztab2.model.Metadata: The name, source, analyzer and detector of the instruments used in the experiment.
getInstrumentRef() - Method in class de.isas.mztab2.model.MsRun: The instrument on which this msRun was measured.
getIsotopomer() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: 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.
getLabel() - Method in class de.isas.mztab2.model.CV: The abbreviated CV label.
getLevel() - Method in enum uk.ac.ebi.pride.jmztab2.model.Section: Getter for the field level.
getLevel() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Getter for the field level.
getLevel() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: Getter for the field level.
getLineNumber() - Method in class de.isas.mztab2.model.Comment: Get lineNumber.
getLineNumber() - Method in class de.isas.mztab2.model.ValidationMessage: Get lineNumber.
getLineNumber() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError: Getter for the field lineNumber.
getLocation() - Method in class de.isas.mztab2.model.MsRun: The msRun's location URI.
getLogicPosition() - Method in interface uk.ac.ebi.pride.jmztab2.model.IMZTabColumn: Get the column logical position.
getLogicPosition() - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumn: Get the column logical position.
getLogicPosition() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn: Get the column logical position.
getLogicPosition() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn: Get the column logical position.
getLogicPosition() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn: Get the column logical position.
getMaxErrorCount() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Getter for the field maxErrorCount.
getMessage() - Method in class de.isas.mztab2.model.Error: Get message.
getMessage() - Method in class de.isas.mztab2.model.ValidationMessage: Get message.
getMessage() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError: Getter for the field message.
getMessageType() - Method in class de.isas.mztab2.model.ValidationMessage: Get messageType.
getMetadata() - Method in class de.isas.mztab2.model.MzTab: Get metadata.
getMetadata() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser: Getter for the field metadata.
getModelName() - Method in class info.psidev.cvmapping.CvMapping: Ruft den Wert der modelName-Eigenschaft ab.
getModelURI() - Method in class info.psidev.cvmapping.CvMapping: Ruft den Wert der modelURI-Eigenschaft ab.
getModelVersion() - Method in class info.psidev.cvmapping.CvMapping: Ruft den Wert der modelVersion-Eigenschaft ab.
getMsg() - Method in class de.isas.mztab2.model.Comment: Get msg.
getMsLevel() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The highest MS level used to inform identification e.g.
getMsRun() - Method in class de.isas.mztab2.model.Metadata: Specification of ms_run.
getMsRun() - Method in class de.isas.mztab2.model.SpectraRef: The ms run object reference by this spectral reference.
getMsRunFor(Integer, Metadata) - Method in class de.isas.mztab2.model.MzTabAccess: Tries to locate the ms run referenced by id from the metadata section.
getMsRunRef() - Method in class de.isas.mztab2.model.Assay: The ms run(s) referenced by this assay.
getMZTabFile() - Method in class de.isas.mztab2.io.MzTabFileParser: getMZTabFile.
getMzTabID() - Method in class de.isas.mztab2.model.Metadata: The ID of the mzTab file, this could be supplied by the repository from which it is downloaded or a local identifier from the lab producing the file.
getMzTabVersion() - Method in class de.isas.mztab2.model.Metadata: The version of the mzTab file.
getName() - Method in class de.isas.mztab2.model.Assay: The assay name.
getName() - Method in class de.isas.mztab2.model.Contact: The contact's name.
getName() - Method in class de.isas.mztab2.model.Instrument: Get name.
getName() - Method in class de.isas.mztab2.model.MsRun: The msRun's name.
getName() - Method in class de.isas.mztab2.model.Parameter: Get name.
getName() - Method in class de.isas.mztab2.model.Sample: The sample's name.
getName() - Method in class de.isas.mztab2.model.StudyVariable: The study variable name.
getName() - Method in class info.psidev.cvmapping.CvMappingRule: Ruft den Wert der name-Eigenschaft ab.
getName() - Method in interface uk.ac.ebi.pride.jmztab2.model.IMZTabColumn: Get the column name.
getName() - Method in enum uk.ac.ebi.pride.jmztab2.model.MetadataElement: Getter for the field name.
getName() - Method in enum uk.ac.ebi.pride.jmztab2.model.MetadataProperty: Getter for the field name.
getName() - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumn: Get the column name.
getName() - Method in enum uk.ac.ebi.pride.jmztab2.model.Section: Getter for the field name.
getName() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn: Get the column name.
getName() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn: Get the column name.
getName() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn: Get the column name.
getOffsetColumnsMap() - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory: The offset record the position of MZTabColumn in header line.
getOpt() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Additional columns can be added to the end of the small molecule evidence table.
getOpt() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Additional columns can be added to the end of the small molecule feature table.
getOpt() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Additional columns can be added to the end of the small molecule table.
getOptionalColumnMapping() - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory: Get all optional columns, including option column with stable order and name, abundance columns, optional columns and cv param optional columns.
getOrder() - Method in interface uk.ac.ebi.pride.jmztab2.model.IMZTabColumn: Get the column internal order.
getOrder() - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumn: Get the column internal order.
getOrder() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn: Get the column internal order.
getOrder() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn: Get the column internal order.
getOrder() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn: Get the column internal order.
getOriginal() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: Getter for the field original.
getParam() - Method in class de.isas.mztab2.model.ColumnParameterMapping: The parameter specifying the unit.
getParam() - Method in class de.isas.mztab2.model.Database: The parameter to identify this database.
getParam() - Method in class de.isas.mztab2.model.OptColumnMapping: The (optional) parameter for this column.
getParameter() - Method in class de.isas.mztab2.model.Software: Parameter defining the software being used.
getPathLocatorString(ConstraintViolation<?>) - Method in class de.isas.mztab2.validation.MzTabBeanValidator: getPathLocatorString.
getPayload() - Method in class de.isas.mztab2.model.IndexedElementImpl: Returns the wrapped object.
getPrefix() - Method in class de.isas.mztab2.model.Comment: Get prefix.
getPrefix() - Method in class de.isas.mztab2.model.Database: The database prefix.
getPrefix() - Method in class de.isas.mztab2.model.Metadata: The metadata section prefix.
getPrefix() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The small molecule evidence table row prefix.
getPrefix() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: The small molecule feature table row prefix.
getPrefix() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: The small molecule table row prefix.
getPrefix() - Method in enum uk.ac.ebi.pride.jmztab2.model.Section: Getter for the field prefix.
getProperty(String) - Static method in class uk.ac.ebi.pride.jmztab2.utils.MZTabProperties: getProperty.
getPropertyName() - Method in enum de.isas.mztab2.model.Assay.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.ColumnParameterMapping.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Comment.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Contact.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.CV.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Database.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Error.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Instrument.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Metadata.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.MsRun.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.MzTab.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.OptColumnMapping.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Parameter.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Publication.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.PublicationItem.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Sample.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.SampleProcessing.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.SmallMoleculeEvidence.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.SmallMoleculeFeature.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.SmallMoleculeSummary.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Software.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.SpectraRef.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.StudyVariable.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Uri.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.ValidationMessage.Properties
getPropertyNames(Object) - Static method in class de.isas.mztab2.io.serialization.Serializers: getPropertyNames.
getPublication() - Method in class de.isas.mztab2.model.Metadata: A publication associated with this file.
getPublicationItems() - Method in class de.isas.mztab2.model.Publication: The publication item ids referenced by this publication.
getQuantificationMethod() - Method in class de.isas.mztab2.model.Metadata: The quantification method used in the experiment reported in the file.
getRank() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The rank of this identification from this approach as increasing integers from 1 (best ranked identification).
getRecord() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Retrieve the data line to a type mzTab domain object.
getRecord() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.SMELineParser: Retrieve the data line to a type mzTab domain object.
getRecord() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.SMFLineParser: Retrieve the data line to a type mzTab domain object.
getRecord() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.SMLLineParser: getRecord.
getReference() - Method in class de.isas.mztab2.model.SpectraRef: The (vendor-dependendent) reference string to the actual mass spectrum.
getReference(Object, Integer) - Static method in class de.isas.mztab2.io.serialization.Serializers: getReference.
getReliability() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: The reliability of the given small molecule identification.
getRequirementLevel() - Method in class info.psidev.cvmapping.CvMappingRule: Ruft den Wert der requirementLevel-Eigenschaft ab.
getRetentionTimeInSeconds() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: The apex of the feature on the retention time axis, in a Master or aggregate MS run.
getRetentionTimeInSecondsEnd() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: The end time of the feature on the retention time axis, in a Master or aggregate MS run.
getRetentionTimeInSecondsStart() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: The start time of the feature on the retention time axis, in a Master or aggregate MS run.
getSample() - Method in class de.isas.mztab2.model.Metadata: Specification of sample.
getSampleProcessing() - Method in class de.isas.mztab2.model.Metadata: A list of parameters describing a sample processing, preparation or handling step similar to a biological or analytical methods report.
getSampleProcessing() - Method in class de.isas.mztab2.model.SampleProcessing: Parameters specifiying sample processing that was applied within one step.
getSampleRef() - Method in class de.isas.mztab2.model.Assay: The sample referenced by this assay.
getScanPolarity() - Method in class de.isas.mztab2.model.MsRun: The scan polarity/polarities used during this msRun.
getScopePath() - Method in class info.psidev.cvmapping.CvMappingRule: Ruft den Wert der scopePath-Eigenschaft ab.
getSetting() - Method in class de.isas.mztab2.model.Software: A software setting used.
getSmallMoleculeEvidence() - Method in class de.isas.mztab2.model.MzTab: The small molecule evidence section is table-based, representing evidence for identifications of small molecules/features, from database search or any other process used to give putative identifications to molecules.
getSmallMoleculeFeature() - Method in class de.isas.mztab2.model.MzTab: The small molecule feature section is table-based, representing individual MS regions (generally considered to be the elution profile for all isotopomers formed from a single charge state of a molecule), that have been measured/quantified.
getSmallMoleculeFeatureQuantificationUnit() - Method in class de.isas.mztab2.model.Metadata: Defines what type of units are reported in the small molecule feature quantification / abundance fields.
getSmallMoleculeIdentificationReliability() - Method in class de.isas.mztab2.model.Metadata: The system used for giving reliability / confidence codes to small molecule identifications MUST be specified if not using the default codes.
getSmallMoleculeQuantificationUnit() - Method in class de.isas.mztab2.model.Metadata: Defines what type of units are reported in the small molecule summary quantification / abundance fields.
getSmallMoleculeSummary() - Method in class de.isas.mztab2.model.MzTab: The small molecule section is table-based.
getSmeId() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: A within file unique identifier for the small molecule evidence result.
getSmeIdRefAmbiguityCode() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: If multiple values are given under SME_ID_REFS, one of the following codes MUST be provided. 1=Ambiguous identification; 2=Only different evidence streams for the same molecule with no ambiguity; 3=Both ambiguous identification and multiple evidence streams.
getSmeIdRefs() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: References to the identification evidence (SME elements) via referencing SME_ID values.
getSmfId() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: A within file unique identifier for the small molecule feature.
getSmfIdRefs() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: References to all the features on which quantitation has been based (SMF elements) via referencing SMF_ID values.
getSmiles() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The potential molecule’s structure in the simplified molecular-input line-entry system (SMILES) for the small molecule.
getSmiles() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: A list of “|” separated potential molecule structures in the simplified molecular-input line-entry system (SMILES) for the small molecule.
getSmlId() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: A within file unique identifier for the small molecule.
getSoftware() - Method in class de.isas.mztab2.model.Metadata: Software used to analyze the data and obtain the reported results.
getSource() - Method in class de.isas.mztab2.model.Instrument: The instrument's source, as defined by the parameter.
getSpecies() - Method in class de.isas.mztab2.model.Sample: Biological species information on the sample.
getSpectraRef() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Reference to a spectrum in a spectrum file, for example a fragmentation spectrum has been used to support the identification.
getSplitChar() - Method in class uk.ac.ebi.pride.jmztab2.model.SplitList: Getter for the field splitChar.
getStableColumnMapping() - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory: Get stable columns mapping.
getStudyVariable() - Method in class de.isas.mztab2.model.Metadata: Specification of study_variable.
getStudyVariableFor(Integer, Metadata) - Method in class de.isas.mztab2.model.MzTabAccess: Tries to locate the study variable referenced by id from the metadata section.
getTermAccession() - Method in class info.psidev.cvmapping.CvTerm: Ruft den Wert der termAccession-Eigenschaft ab.
getTermName() - Method in class info.psidev.cvmapping.CvTerm: Ruft den Wert der termName-Eigenschaft ab.
getTheoreticalMassToCharge() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The theoretical mass/charge value for the small molecule or the database mass/charge value (for a spectral library match).
getTheoreticalNeutralMass() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: The small molecule’s precursor’s theoretical neutral mass.
getTissue() - Method in class de.isas.mztab2.model.Sample: Biological tissue information on the sample.
getTitle() - Method in class de.isas.mztab2.model.Metadata: The file’s human readable title.
getType() - Method in class de.isas.mztab2.model.PublicationItem: The type qualifier of this publication item.
getType() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError: Getter for the field type.
getType(int) - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorTypeMap: getType.
getTypeMap() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorTypeMap: Getter for the field typeMap.
getUri() - Method in class de.isas.mztab2.model.CV: A URI to the CV definition.
getUri() - Method in class de.isas.mztab2.model.Database: The URI to the online database.
getUri() - Method in class de.isas.mztab2.model.Metadata: A URI pointing to the file’s source data (e.g., a MetaboLights records).
getUri() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: A URI pointing to the small molecule’s entry in a database (e.g., the small molecule’s HMDB, Chebi or KEGG entry).
getUri() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: A URI pointing to the small molecule’s entry in a reference database (e.g., the small molecule’s HMDB or KEGG entry).
getValidationMessagesForLevel(Optional<List<ValidationMessage>>, ValidationMessage.MessageTypeEnum) - Static method in class de.isas.mztab2.io.MzTabValidatingWriter: Returns all validation messages ONLY at the given level.
getValue() - Method in enum de.isas.mztab2.model.Comment.PrefixEnum
getValue() - Method in enum de.isas.mztab2.model.Metadata.PrefixEnum
getValue() - Method in class de.isas.mztab2.model.OptColumnMapping: The value for this column in a particular row.
getValue() - Method in class de.isas.mztab2.model.Parameter: Get value.
getValue() - Method in enum de.isas.mztab2.model.PublicationItem.TypeEnum
getValue() - Method in enum de.isas.mztab2.model.SmallMoleculeEvidence.HeaderPrefixEnum
getValue() - Method in enum de.isas.mztab2.model.SmallMoleculeEvidence.PrefixEnum
getValue() - Method in enum de.isas.mztab2.model.SmallMoleculeFeature.HeaderPrefixEnum
getValue() - Method in enum de.isas.mztab2.model.SmallMoleculeFeature.PrefixEnum
getValue() - Method in enum de.isas.mztab2.model.SmallMoleculeSummary.HeaderPrefixEnum
getValue() - Method in enum de.isas.mztab2.model.SmallMoleculeSummary.PrefixEnum
getValue() - Method in class de.isas.mztab2.model.Uri: The URI pointing to the external resource.
getValue() - Method in enum de.isas.mztab2.model.ValidationMessage.CategoryEnum
getValue() - Method in enum de.isas.mztab2.model.ValidationMessage.MessageTypeEnum
getValues() - Static method in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType
getValues() - Static method in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType
getValues() - Static method in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType
getVariationFunction() - Method in class de.isas.mztab2.model.StudyVariable: The function used to calculate the variation of small molecule quantities over the assays referenced by this study variable.
getVersion() - Method in class de.isas.mztab2.model.CV: The CV version used when the file was generated.
getVersion() - Method in class de.isas.mztab2.model.Database: The database version.
GLOBAL - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant GLOBAL="global"
GLOBAL - Static variable in class uk.ac.ebi.pride.jmztab2.model.OptionColumn: Constant GLOBAL="global"
GlobalOptColumnMappingBuilder() - Constructor for class uk.ac.ebi.pride.jmztab2.model.OptColumnMappingBuilder.GlobalOptColumnMappingBuilder
GOTermList - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant GOTermList
groups() - Method in annotation type de.isas.lipidomics.mztab2.validation.constraints.CheckParameter

H

handleAssay(Matcher, String, MetadataElement, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleColunit(String, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleContact(String, Matcher, MetadataElement, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleCustom(String, Matcher, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleCv(String, Matcher, MetadataElement, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleDatabase(String, Matcher, MetadataElement, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleDerivatizationAgent(String, Matcher, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleDescription(String, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleExternalStudyUri(String, Matcher, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleIdConfidenceMeasure(String, Matcher, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleInstrument(String, Matcher, MetadataElement, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleMsgOption(CommandLine, String, MZTabErrorTypeMap) - Static method in class de.isas.mztab2.cli.MZTabCommandLine
handleMsRun(String, Matcher, MetadataElement, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleMzTab(MetadataElement, Matcher, String, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleParam(String, String, MZTabErrorType, int, Consumer<Parameter>) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser: handleParam.
handleParameters(RuleEvaluationResult, boolean) - Method in interface de.isas.mztab2.validation.CvTermValidationHandler: Implementations of this method should take care that they always return a list, even if it is empty.
handleParameters(RuleEvaluationResult, boolean) - Method in class de.isas.mztab2.validation.handlers.AndValidationHandler
handleParameters(RuleEvaluationResult, boolean) - Method in class de.isas.mztab2.validation.handlers.ExtraParametersValidationHandler
handleParameters(RuleEvaluationResult, boolean) - Method in class de.isas.mztab2.validation.handlers.OrValidationHandler
handleParameters(RuleEvaluationResult, boolean) - Method in class de.isas.mztab2.validation.handlers.SharedParametersValidationHandler
handleParameters(RuleEvaluationResult, boolean) - Method in class de.isas.mztab2.validation.handlers.XorValidationHandler
handlePublication(String, Matcher, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleQuantificationMethod(String, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleRule(CvMappingRule, List<Pair<Pointer, Parameter>>) - Method in interface de.isas.mztab2.validation.CvRuleHandler: Handle the provided rule according to the implementor's logic.
handleRule(CvMappingRule, List<Pair<Pointer, Parameter>>) - Method in class de.isas.mztab2.validation.handlers.EmptyRuleHandler
handleRule(CvMappingRule, List<Pair<Pointer, Parameter>>) - Method in class de.isas.mztab2.validation.handlers.ResolvingCvRuleHandler
handleSample(String, Matcher, MetadataElement, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleSampleProcessing(String, Matcher, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleSelection(List<Pair<Pointer, Parameter>>) - Method in class de.isas.mztab2.cvmapping.RemoveUserParams
handleSelection(List<Pair<Pointer, Parameter>>) - Method in interface de.isas.mztab2.validation.CvTermSelectionHandler: Handle the provided selection, e.g. by filtering it or by modifying elements therein.
handleSemanticValidation(CommandLine, String, File, PrintStream, MzTabFileParser, MZTabErrorType.Level) - Static method in class de.isas.mztab2.cli.MZTabCommandLine
handleSmallMolecule(MetadataElement, Matcher, String, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleSmallMoleculeFeature(MetadataElement, Matcher, String, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleSoftware(String, Matcher, MetadataElement, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleStudyVariable(String, Matcher, MetadataElement, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleTitle(String, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleUri(String, Matcher, String, boolean) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser
handleValidation(CommandLine, String, PrintStream, MZTabErrorType.Level, String, boolean, boolean) - Static method in class de.isas.mztab2.cli.MZTabCommandLine
handleValidationOptions(CommandLine, String, String, String, String, String, String) - Static method in class de.isas.mztab2.cli.MZTabCommandLine
hash - de.isas.mztab2.model.MsRun.Properties
hash(String) - Method in class de.isas.mztab2.model.MsRun: Builder method for hash.
hashCode() - Method in class de.isas.mztab2.model.Assay
hashCode() - Method in class de.isas.mztab2.model.ColumnParameterMapping
hashCode() - Method in class de.isas.mztab2.model.Comment
hashCode() - Method in class de.isas.mztab2.model.Contact
hashCode() - Method in class de.isas.mztab2.model.CV
hashCode() - Method in class de.isas.mztab2.model.Database
hashCode() - Method in class de.isas.mztab2.model.Error
hashCode() - Method in class de.isas.mztab2.model.IndexedElementImpl
hashCode() - Method in class de.isas.mztab2.model.Instrument
hashCode() - Method in class de.isas.mztab2.model.Metadata
hashCode() - Method in class de.isas.mztab2.model.MsRun
hashCode() - Method in class de.isas.mztab2.model.MzTab
hashCode() - Method in class de.isas.mztab2.model.OptColumnMapping
hashCode() - Method in class de.isas.mztab2.model.Parameter
hashCode() - Method in class de.isas.mztab2.model.Publication
hashCode() - Method in class de.isas.mztab2.model.PublicationItem
hashCode() - Method in class de.isas.mztab2.model.Sample
hashCode() - Method in class de.isas.mztab2.model.SampleProcessing
hashCode() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence
hashCode() - Method in class de.isas.mztab2.model.SmallMoleculeFeature
hashCode() - Method in class de.isas.mztab2.model.SmallMoleculeSummary
hashCode() - Method in class de.isas.mztab2.model.Software
hashCode() - Method in class de.isas.mztab2.model.SpectraRef
hashCode() - Method in class de.isas.mztab2.model.StringList
hashCode() - Method in class de.isas.mztab2.model.StudyVariable
hashCode() - Method in class de.isas.mztab2.model.Uri
hashCode() - Method in class de.isas.mztab2.model.ValidationMessage
hashCode() - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumn
hashCode() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType
hashMethod - de.isas.mztab2.model.MsRun.Properties
hashMethod(Parameter) - Method in class de.isas.mztab2.model.MsRun: Builder method for hashMethod.
HeaderLine - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant HeaderLine
HeaderNotValid - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant HeaderNotValid
headerPrefix - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
headerPrefix - de.isas.mztab2.model.SmallMoleculeFeature.Properties
headerPrefix - de.isas.mztab2.model.SmallMoleculeSummary.Properties

I

id - de.isas.mztab2.model.Assay.Properties
id - de.isas.mztab2.model.Contact.Properties
id - de.isas.mztab2.model.CV.Properties
id - de.isas.mztab2.model.Database.Properties
id - de.isas.mztab2.model.Instrument.Properties
id - de.isas.mztab2.model.MsRun.Properties
id - de.isas.mztab2.model.Parameter.Properties
id - de.isas.mztab2.model.Publication.Properties
id - de.isas.mztab2.model.Sample.Properties
id - de.isas.mztab2.model.SampleProcessing.Properties
id - de.isas.mztab2.model.Software.Properties
id - de.isas.mztab2.model.StudyVariable.Properties
id - de.isas.mztab2.model.Uri.Properties
id - Variable in class info.psidev.cvmapping.CvMappingRule
id(Integer) - Method in class de.isas.mztab2.model.Assay: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.Contact: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.CV: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.Database: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.Instrument: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.MsRun: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.Parameter: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.Publication: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.Sample: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.SampleProcessing: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.Software: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.StudyVariable: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.Uri: Builder method for id.
ID_CONFIDENCE_MEASURE - uk.ac.ebi.pride.jmztab2.model.MetadataElement
idConfidenceMeasure - de.isas.mztab2.model.Metadata.Properties
idConfidenceMeasure - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
idConfidenceMeasure(List<Parameter>) - Method in class de.isas.mztab2.model.Metadata: Builder method for idConfidenceMeasure.
idConfidenceMeasure(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for idConfidenceMeasure.
IDENTICAL - de.isas.mztab2.cvmapping.ParameterComparisonResult
IDENTIFICATION_METHOD - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
identificationMethod - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
identificationMethod(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for identificationMethod.
identifier - de.isas.mztab2.model.OptColumnMapping.Properties
identifier(String) - Method in class de.isas.mztab2.model.OptColumnMapping: Builder method for identifier.
idFormat - de.isas.mztab2.model.MsRun.Properties
idFormat(Parameter) - Method in class de.isas.mztab2.model.MsRun: Builder method for idFormat.
IdNumber - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant IdNumber
IMZTabColumn - Interface in uk.ac.ebi.pride.jmztab2.model: IMZTabColumn interface.
inchi - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
inchi - de.isas.mztab2.model.SmallMoleculeSummary.Properties
inchi(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for inchi.
inchi(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for inchi.
INCHI - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
INCHI - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
IndexedElement - Interface in de.isas.mztab2.model: Indexed elements (IDs) define a unique ID for a collection of multiple metadata elements of the same type within the mzTab-M document, e.g. for sample, assay, study variable etc.
IndexedElement - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant IndexedElement
IndexedElementImpl - Class in de.isas.mztab2.model: Implementation of IndexedElement where more information is required than just the id.
IndexedElementImpl(Integer, String, Object) - Constructor for class de.isas.mztab2.model.IndexedElementImpl: Create a new indexed element implementation for the provided id, element type and payload.
IndexedElementOptColumnMappingBuilder(Object) - Constructor for class uk.ac.ebi.pride.jmztab2.model.OptColumnMappingBuilder.IndexedElementOptColumnMappingBuilder: Configure this builder to create optional column mapping for an indexed element, such as Assay, StudyVariable, or MsRun.
INFINITY - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant INFINITY="INF"
Info - uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Level
INFO - de.isas.mztab2.model.ValidationMessage.MessageTypeEnum
info.psidev.cvmapping - package info.psidev.cvmapping: This package contains the generated Java objects created via XML binding from the PSI-MS mapping file schema.
instrument - de.isas.mztab2.model.Metadata.Properties
instrument(List<Instrument>) - Method in class de.isas.mztab2.model.Metadata: Builder method for instrument.
Instrument - Class in de.isas.mztab2.model: The name, source, analyzer and detector of the instruments used in the experiment.
Instrument() - Constructor for class de.isas.mztab2.model.Instrument
INSTRUMENT - uk.ac.ebi.pride.jmztab2.model.MetadataElement
INSTRUMENT_ANALYZER - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
INSTRUMENT_DETECTOR - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
INSTRUMENT_NAME - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
INSTRUMENT_SOURCE - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
Instrument.Properties - Enum in de.isas.mztab2.model: Property enumeration for Instrument.
InstrumentFormat - Class in de.isas.mztab2.io.formats: Format specification for Instrument.
InstrumentFormat() - Constructor for class de.isas.mztab2.io.formats.InstrumentFormat
instrumentRef - de.isas.mztab2.model.MsRun.Properties
instrumentRef(Instrument) - Method in class de.isas.mztab2.model.MsRun: Builder method for instrumentRef.
InstrumentSerializer - Class in de.isas.mztab2.io.serialization: InstrumentSerializer implementation for Instrument.
InstrumentSerializer() - Constructor for class de.isas.mztab2.io.serialization.InstrumentSerializer: Constructor for InstrumentSerializer.
InstrumentSerializer(Class<Instrument>) - Constructor for class de.isas.mztab2.io.serialization.InstrumentSerializer: Constructor for InstrumentSerializer.
Integer - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant Integer
IntegerList - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant IntegerList
intersection(Set<T>, Set<T>) - Static method in class de.isas.mztab2.cvmapping.SetOperations: Returns the intersection (a \cap b, all common elements) of a and b.
InvalidColunitFormat - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant InvalidColunitFormat
IOptColumnMappingBuilder - Interface in uk.ac.ebi.pride.jmztab2.model: Interface for optional column mapping builders.
isAllowChildren() - Method in class info.psidev.cvmapping.CvTerm: Ruft den Wert der allowChildren-Eigenschaft ab.
isChildOfOrSame(Parameter, Parameter) - Method in class de.isas.mztab2.cvmapping.CvParameterLookupService: Compares two parameters for their parent to child relationship.
isComment() - Method in enum uk.ac.ebi.pride.jmztab2.model.Section: Judge the section is comment section or not.
isData() - Method in enum uk.ac.ebi.pride.jmztab2.model.Section: Judge the section is protein, peptide, psm, small_molecule, small_molecule_feature or small_molecule_evidence section.
isEmpty() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Returns true if this list contains no elements.
isEmpty() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.PositionMapping: isEmpty.
isEmpty(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabStringUtils: Check the string is null or blank.
isEqualTo(Parameter, Parameter) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils
isEqualTo(Term, Parameter) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils
isHeader() - Method in enum uk.ac.ebi.pride.jmztab2.model.Section: Judge the section is protein_header, peptide_header, psm_header, small_molecule_header, small_molecule_feature_header or small_molecule_evidence_header section.
isIsRepeatable() - Method in class info.psidev.cvmapping.CvTerm: Ruft den Wert der isRepeatable-Eigenschaft ab.
ISmallMoleculeColumn - Interface in uk.ac.ebi.pride.jmztab2.model: ISmallMoleculeColumn interface.
ISmallMoleculeEvidenceColumn - Interface in uk.ac.ebi.pride.jmztab2.model: ISmallMoleculeEvidenceColumn interface.
ISmallMoleculeFeatureColumn - Interface in uk.ac.ebi.pride.jmztab2.model: ISmallMoleculeFeatureColumn interface.
isMetadata() - Method in enum uk.ac.ebi.pride.jmztab2.model.Section: Judge the section is metadata section or not.
isOptional() - Method in interface uk.ac.ebi.pride.jmztab2.model.IMZTabColumn: Judge this column belong to stable column or optional column.
isOptional() - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumn: Judge this column belong to stable column or optional column.
isOptional() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn: Judge this column belong to stable column or optional column.
isOptional() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn: Judge this column belong to stable column or optional column.
isOptional() - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn: Judge this column belong to stable column or optional column.
isotopomer - de.isas.mztab2.model.SmallMoleculeFeature.Properties
isotopomer(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Builder method for isotopomer.
ISOTOPOMER - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn.Stable
isRepeatable - Variable in class info.psidev.cvmapping.CvTerm
isUseTerm() - Method in class info.psidev.cvmapping.CvTerm: Ruft den Wert der useTerm-Eigenschaft ab.
isUseTermName() - Method in class info.psidev.cvmapping.CvTerm: Ruft den Wert der useTermName-Eigenschaft ab.
isValid(Parameter, ConstraintValidatorContext) - Method in interface de.isas.lipidomics.mztab2.validation.validators.ParameterValidator
ItemNumberMismatch - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant ItemNumberMismatch
items - Variable in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabLineParser: based on TAB char to split raw line into String array.

J

JxPathElement - Class in de.isas.mztab2.cvmapping: Utility methods for simpler Java 8 compatible handling of JXPath selections and pointers.
JxPathElement() - Constructor for class de.isas.mztab2.cvmapping.JxPathElement

K

keySet() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.PositionMapping: keySet.

L

label - de.isas.mztab2.model.CV.Properties
label(String) - Method in class de.isas.mztab2.model.CV: Builder method for label.
LEVEL - Static variable in class uk.ac.ebi.pride.jmztab2.utils.MZTabProperties: Constant LEVEL
line - Variable in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabLineParser
lineNumber - de.isas.mztab2.model.Comment.Properties
lineNumber - de.isas.mztab2.model.ValidationMessage.Properties
lineNumber - Variable in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabLineParser
lineNumber(Integer) - Method in class de.isas.mztab2.model.Comment: Builder method for lineNumber.
lineNumber(Long) - Method in class de.isas.mztab2.model.ValidationMessage: Builder method for lineNumber.
LineOrder - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant LineOrder
LinePrefix - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant LinePrefix
LIPIDOMICS_EXAMPLE - de.isas.mztab2.test.utils.ClassPathFile
LIPIDOMICS_EXAMPLE_WRONG_MSSCAN_REF - de.isas.mztab2.test.utils.ClassPathFile
loadBestSearchEngineScoreId(String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: load best_search_engine_score[id], read id value.
loadSearchEngineScoreId(String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: load search_engine_score[id]_ms_run[..], read id value.
location - de.isas.mztab2.model.MsRun.Properties
location(String) - Method in class de.isas.mztab2.model.MsRun: Builder method for location.
Logical - uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Category
LOGICAL - de.isas.mztab2.model.ValidationMessage.CategoryEnum
LogicalErrorType - Class in uk.ac.ebi.pride.jmztab2.utils.errors: Reporting errors related to the logical relationships among the different sections in a file.
LogMethodName - Class in de.isas.mztab2.test.utils: JUnit TestWatcher to LOGGER the executed test method name.
LogMethodName() - Constructor for class de.isas.mztab2.test.utils.LogMethodName

M

main(String[]) - Static method in class de.isas.mztab2.cli.MZTabCommandLine: Runs the command line parser for mzTab, including validation.
mapping - Variable in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser
MAX_ERROR_COUNT - Static variable in class uk.ac.ebi.pride.jmztab2.utils.MZTabProperties: Constant MAX_ERROR_COUNT=Integer.parseInt(getProperty("mztab.max_error_count"))
MAY - info.psidev.cvmapping.CvMappingRule.RequirementLevel
message - de.isas.mztab2.model.Error.Properties
message - de.isas.mztab2.model.ValidationMessage.Properties
message() - Method in annotation type de.isas.lipidomics.mztab2.validation.constraints.CheckParameter
message(String) - Method in class de.isas.mztab2.model.Error: Builder method for message.
message(String) - Method in class de.isas.mztab2.model.ValidationMessage: Builder method for message.
messageCode() - Method in annotation type de.isas.lipidomics.mztab2.validation.constraints.CheckParameter
messageType - de.isas.mztab2.model.ValidationMessage.Properties
messageType(ValidationMessage.MessageTypeEnum) - Method in class de.isas.mztab2.model.ValidationMessage: Builder method for messageType.
metadata - de.isas.mztab2.model.MzTab.Properties
metadata - Variable in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser
metadata - Variable in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabHeaderLineParser
metadata(Metadata) - Method in class de.isas.mztab2.model.MzTab: Builder method for metadata.
Metadata - Class in de.isas.mztab2.model: The metadata section provides additional information about the dataset(s) reported in the mzTab file.
Metadata - uk.ac.ebi.pride.jmztab2.model.Section
Metadata() - Constructor for class de.isas.mztab2.model.Metadata
Metadata.PrefixEnum - Enum in de.isas.mztab2.model: The metadata section prefix.
Metadata.Properties - Enum in de.isas.mztab2.model: Property enumeration for Metadata.
MetadataElement - Enum in uk.ac.ebi.pride.jmztab2.model: Define all elements used in metadata.
MetadataFormat - Class in de.isas.mztab2.io.formats: Format specification for Metadata.
MetadataFormat() - Constructor for class de.isas.mztab2.io.formats.MetadataFormat
metadataMapper() - Method in class de.isas.mztab2.io.MzTabWriterDefaults: Create a metadata section csv mapper.
MetadataProperty - Enum in uk.ac.ebi.pride.jmztab2.model: Define a property in metadata, which depend on the MetadataElement.
metaDataSchema(CsvMapper) - Method in class de.isas.mztab2.io.MzTabWriterDefaults: Creates the csv schema for the metadata section (column names, value separators, array element separators, etc.).
MetadataSerializer - Class in de.isas.mztab2.io.serialization: MetadataSerializer class.
MetadataSerializer() - Constructor for class de.isas.mztab2.io.serialization.MetadataSerializer: Constructor for MetadataSerializer.
MetadataSerializer(Class<Metadata>) - Constructor for class de.isas.mztab2.io.serialization.MetadataSerializer: Constructor for MetadataSerializer.
MINIMAL_EXAMPLE - de.isas.mztab2.test.utils.ClassPathFile
MINUS - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant MINUS='-'
modelName - Variable in class info.psidev.cvmapping.CvMapping
modelURI - Variable in class info.psidev.cvmapping.CvMapping
modelVersion - Variable in class info.psidev.cvmapping.CvMapping
ModificationList - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant ModificationList
ModificationPosition - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant ModificationPosition
MOUSELIVER_NEGATIVE - de.isas.mztab2.test.utils.ClassPathFile
MOUSELIVER_NEGATIVE_MZTAB_NULL_COLUNIT - de.isas.mztab2.test.utils.ClassPathFile
MS_LEVEL - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
MS_RUN - uk.ac.ebi.pride.jmztab2.model.MetadataElement
MS_RUN_FORMAT - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
MS_RUN_FRAGMENTATION_METHOD - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
MS_RUN_HASH - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
MS_RUN_HASH_METHOD - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
MS_RUN_ID_FORMAT - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
MS_RUN_INSTRUMENT_REF - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
MS_RUN_LOCATION - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
MS_RUN_SCAN_POLARITY - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
msg - de.isas.mztab2.model.Comment.Properties
msg(String) - Method in class de.isas.mztab2.model.Comment: Builder method for msg.
msLevel - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
msLevel(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for msLevel.
msRun - de.isas.mztab2.model.Metadata.Properties
msRun - de.isas.mztab2.model.SpectraRef.Properties
msRun(MsRun) - Method in class de.isas.mztab2.model.SpectraRef: Builder method for msRun.
msRun(List<MsRun>) - Method in class de.isas.mztab2.model.Metadata: Builder method for msRun.
MsRun - Class in de.isas.mztab2.model: Specification of ms_run.
MsRun() - Constructor for class de.isas.mztab2.model.MsRun
MsRun.Properties - Enum in de.isas.mztab2.model: Property enumeration for MsRun.
MsRunFormat - Class in de.isas.mztab2.io.formats: Format specification for MsRun.
MsRunFormat() - Constructor for class de.isas.mztab2.io.formats.MsRunFormat
MsRunHashMethodNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant MsRunHashMethodNotDefined
MsRunLocation - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant MsRunLocation
MsRunNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant MsRunNotDefined
MsRunOptionalColumn - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant MsRunOptionalColumn
msRunRef - de.isas.mztab2.model.Assay.Properties
msRunRef(List<MsRun>) - Method in class de.isas.mztab2.model.Assay: Builder method for msRunRef.
MsRunSerializer - Class in de.isas.mztab2.io.serialization: MsRunSerializer implementation for MsRun.
MsRunSerializer() - Constructor for class de.isas.mztab2.io.serialization.MsRunSerializer: Constructor for MsRunSerializer.
MsRunSerializer(Class<MsRun>) - Constructor for class de.isas.mztab2.io.serialization.MsRunSerializer: Constructor for MsRunSerializer.
MsRunValidator - Class in de.isas.mztab2.io.validators: Validates that the ms run section is present in metadata.
MsRunValidator() - Constructor for class de.isas.mztab2.io.validators.MsRunValidator
MTBLS263 - de.isas.mztab2.test.utils.ClassPathFile
MTD - de.isas.mztab2.model.Metadata.PrefixEnum
MTDDefineLabel - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant MTDDefineLabel
MTDFILE - de.isas.mztab2.test.utils.ClassPathFile
MTDLine - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant MTDLine
MTDLineParser - Class in uk.ac.ebi.pride.jmztab2.utils.parser: Parse a metadata line into a element.
MTDLineParser(MZTabParserContext) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser: Constructor for MTDLineParser.
MUST - info.psidev.cvmapping.CvMappingRule.RequirementLevel
MZBoolean - Enum in uk.ac.ebi.pride.jmztab2.model: In mzTab, using 0-false, 1-true to express the boolean value.
MZBoolean - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant MZBoolean
MzTab - Class in de.isas.mztab2.model: mzTab-M is intended as a reporting standard for quantitative results from metabolomics/lipodomics approaches.
MzTab() - Constructor for class de.isas.mztab2.model.MzTab
MZTAB - uk.ac.ebi.pride.jmztab2.model.MetadataElement
MZTAB_ERROR_OVERFLOW_EXCEPTION_MESSAGE - Static variable in class uk.ac.ebi.pride.jmztab2.utils.MZTabProperties: Constant MZTAB_ERROR_OVERFLOW_EXCEPTION_MESSAGE="System error queue overflow!
MZTAB_EXCEPTION_MESSAGE - Static variable in class uk.ac.ebi.pride.jmztab2.utils.MZTabProperties: Constant MZTAB_EXCEPTION_MESSAGE="There exist errors in the metadata sect"{trunked}
MZTAB_ID - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
MZTAB_VERSION - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
MzTab.Properties - Enum in de.isas.mztab2.model: Property enumeration for MzTab.
MzTabAccess - Class in de.isas.mztab2.model: Utility class for easier access to linked information within an mztab-M data object.
MzTabAccess(MzTab) - Constructor for class de.isas.mztab2.model.MzTabAccess: Create an MzTabAccess object for the provided mzTab object.
MzTabBeanValidator - Class in de.isas.mztab2.validation: This validator used the HibernateValidator bean validation reference implementation.
MzTabBeanValidator() - Constructor for class de.isas.mztab2.validation.MzTabBeanValidator: Default constructor.
MzTabBeanValidator(boolean) - Constructor for class de.isas.mztab2.validation.MzTabBeanValidator: Constructor setting up the validator configuration and default constraint mapping.
MZTabColumn - Class in uk.ac.ebi.pride.jmztab2.model: Define a column header which used in Section.Protein_Header, Section.Peptide_Header, Section.PSM_Header, or Section.Small_Molecule_Header.
MZTabColumn(String, Class, boolean, String) - Constructor for class uk.ac.ebi.pride.jmztab2.model.MZTabColumn: Create a column header object.
MZTabColumn(String, Class, boolean, String, Integer) - Constructor for class uk.ac.ebi.pride.jmztab2.model.MZTabColumn: Create a column header object.
MZTabColumnFactory - Class in uk.ac.ebi.pride.jmztab2.model: This is a static factory class which used to generate a couple of MZTabColumn objects, and organizes them into "logicalPosition, MZTabColumn" pairs.
MZTabCommandLine - Class in de.isas.mztab2.cli: MZTabCommandLine class.
MZTabCommandLine() - Constructor for class de.isas.mztab2.cli.MZTabCommandLine
MZTabConstants - Class in uk.ac.ebi.pride.jmztab2.model: Define a couple of constants used in the jmzTab API.
MZTabConstants() - Constructor for class uk.ac.ebi.pride.jmztab2.model.MZTabConstants
MZTabConversionException - Exception in uk.ac.ebi.pride.jmztab2.utils.errors: Runtime exception for mzTab conversion
MZTabConversionException() - Constructor for exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabConversionException: Constructor for MZTabConversionException.
MZTabConversionException(String) - Constructor for exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabConversionException: Constructor for MZTabConversionException.
MZTabConversionException(String, Throwable) - Constructor for exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabConversionException: Constructor for MZTabConversionException.
MZTabConversionException(Throwable) - Constructor for exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabConversionException: Constructor for MZTabConversionException.
MZTabDataLineParser<T> - Class in uk.ac.ebi.pride.jmztab2.utils.parser: This class allows the validation and loading of the data into mzTab domain objects.
MZTabDataLineParser(MZTabParserContext) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Constructor for MZTabDataLineParser.
MZTabDataLineParser(MZTabParserContext, MZTabColumnFactory, PositionMapping, Metadata, MZTabErrorList) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser: Generate a mzTab data line parser.
MZTabError - Class in uk.ac.ebi.pride.jmztab2.utils.errors: mzTab files can be validated to ensure that they comply with the latest version of the format specification.
MZTabError(MZTabErrorType, int, String...) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError: System will fill a couple of values one by one, and generate a concrete error message during parse MZTabError.lineNumber line in mzTab file.
MZTabErrorList - Class in uk.ac.ebi.pride.jmztab2.utils.errors: A limit max capacity list, if contains a couple of MZTabError objects.
MZTabErrorList() - Constructor for class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Generate a error list, which max size is MZTabProperties.MAX_ERROR_COUNT, and only allow MZTabErrorType.Level.Error or greater level errors to be added into list.
MZTabErrorList(MZTabErrorType.Level) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Generate a error list, which max size is MZTabProperties.MAX_ERROR_COUNT
MZTabErrorList(MZTabErrorType.Level, int) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Generate a error list, with given error level and maximum error count.
MZTabErrorOverflowException - Exception in uk.ac.ebi.pride.jmztab2.utils.errors: If error count great than MZTabProperties.MAX_ERROR_COUNT System will stop validate and throw overflow exception.
MZTabErrorOverflowException() - Constructor for exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorOverflowException: If error count great than MZTabProperties.MAX_ERROR_COUNT System will stop validate and throw overflow exception.
MZTabErrorType - Class in uk.ac.ebi.pride.jmztab2.utils.errors: MZTabErrorType class.
MZTabErrorType() - Constructor for class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: Constructor for MZTabErrorType.
MZTabErrorType.Category - Enum in uk.ac.ebi.pride.jmztab2.utils.errors
MZTabErrorType.Level - Enum in uk.ac.ebi.pride.jmztab2.utils.errors: We classify diagnosis message types into three levels: Info, Warn and Error, all of them coming from the notational conventions of the specification.
MZTabErrorTypeMap - Class in uk.ac.ebi.pride.jmztab2.utils.errors: This list class used to storage all types of MZTabError, and provide query service based on the error/warn code.
MZTabErrorTypeMap() - Constructor for class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorTypeMap: Constructor for MZTabErrorTypeMap.
MZTabException - Exception in uk.ac.ebi.pride.jmztab2.utils.errors: Wrap a MZTabError.
MZTabException(String) - Constructor for exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException: Constructor for MZTabException.
MZTabException(MZTabError) - Constructor for exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException: Constructor for MZTabException.
MZTabException(MZTabError, Throwable) - Constructor for exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException: Constructor for MZTabException.
MzTabFileParser - Class in de.isas.mztab2.io: MZTabFileParser provides reading functionality of the mzTab file.
MzTabFileParser(File) - Constructor for class de.isas.mztab2.io.MzTabFileParser: Create a new MZTabFileParser for the given file.
MzTabFileParser(URI) - Constructor for class de.isas.mztab2.io.MzTabFileParser: Create a new MZTabFileParser for the given file URI.
MZTabHeaderLineParser - Class in uk.ac.ebi.pride.jmztab2.utils.parser: A couple of common method used to parse a header line into MZTabColumnFactory structure.
MZTabHeaderLineParser(MZTabParserContext, MZTabColumnFactory, Metadata) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabHeaderLineParser: Parse a header line into MZTabColumnFactory structure.
mzTabID - de.isas.mztab2.model.Metadata.Properties
mzTabID(String) - Method in class de.isas.mztab2.model.Metadata: Builder method for mzTabID.
MZTabId - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant MZTabType
MzTabIdValidator - Class in de.isas.mztab2.io.validators: Validates that mzTab-ID is neither null nor empty.
MzTabIdValidator() - Constructor for class de.isas.mztab2.io.validators.MzTabIdValidator
MZTabLineParser - Class in uk.ac.ebi.pride.jmztab2.utils.parser: Common tab split line parser.
MZTabLineParser(MZTabParserContext) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabLineParser: Constructor for MZTabLineParser.
MZTabMode - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant MZTabMode
MzTabNonValidatingWriter - Class in de.isas.mztab2.io: MzTabNonValidatingWriter allows to write MzTab objects without additional validation checks.
MzTabNonValidatingWriter() - Constructor for class de.isas.mztab2.io.MzTabNonValidatingWriter
MzTabNonValidatingWriter(MzTabWriterDefaults) - Constructor for class de.isas.mztab2.io.MzTabNonValidatingWriter
MZTabParserContext - Class in uk.ac.ebi.pride.jmztab2.utils.parser: MZTabParserContext is used to keep track of indexed elements and interrelations during parsing.
MZTabParserContext() - Constructor for class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext
MZTabProperties - Class in uk.ac.ebi.pride.jmztab2.utils: This class will load the properties used by the mzTab-M library for message formatting during validation.
MZTabStringUtils - Class in uk.ac.ebi.pride.jmztab2.model: Provide a couple of functions for translate, parse and print formatted string defined in the mzTab specification.
MZTabType - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant MZTabType
MZTabUtils - Class in uk.ac.ebi.pride.jmztab2.model: Provide a couple of functions for translating, parsing and printing formatted strings defined in the mzTab specification.
MZTabUtils() - Constructor for class uk.ac.ebi.pride.jmztab2.model.MZTabUtils
MzTabValidatingWriter - Class in de.isas.mztab2.io: MzTabValidatingWriter allows to write MzTab objects after validation with a custom or default validator.
MzTabValidatingWriter() - Constructor for class de.isas.mztab2.io.MzTabValidatingWriter: Uses default structural validation based on writing and parsing the written file with the default parsing checks.
MzTabValidatingWriter(Validator<MzTab>, boolean) - Constructor for class de.isas.mztab2.io.MzTabValidatingWriter: Uses the provided validator and default writer configuration.
MzTabValidatingWriter(Validator<MzTab>, MzTabWriterDefaults, boolean) - Constructor for class de.isas.mztab2.io.MzTabValidatingWriter: Uses the provided validator and writerDefaults.
MzTabValidatingWriter.WriteAndParseValidator - Class in de.isas.mztab2.io: A default validator implemenation that first writes and then parses the created temporary file, performing the parser checks.
MzTabValidator - Class in de.isas.lipidomics.mztab2.validation: Delegating validator implementation that forwards validation to the provided validator implementations.
MzTabValidator(Validator<MzTab>...) - Constructor for class de.isas.lipidomics.mztab2.validation.MzTabValidator
mzTabVersion - de.isas.mztab2.model.Metadata.Properties
mzTabVersion(String) - Method in class de.isas.mztab2.model.Metadata: Builder method for mzTabVersion.
MZTabVersion - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant MZTabVersion
MzTabVersionValidator - Class in de.isas.mztab2.io.validators: Validates that mzTab-version is neither null nor empty.
MzTabVersionValidator() - Constructor for class de.isas.mztab2.io.validators.MzTabVersionValidator
MzTabWriter<T> - Interface in de.isas.mztab2.io: Interface for mztab writer implementors.
MzTabWriterDefaults - Class in de.isas.mztab2.io: Default mapper and schema definitions for writing of mzTab files using the Jackson CSV mapper.
MzTabWriterDefaults() - Constructor for class de.isas.mztab2.io.MzTabWriterDefaults





N

name - de.isas.mztab2.model.Assay.Properties
 
name - de.isas.mztab2.model.Contact.Properties
 
name - de.isas.mztab2.model.Instrument.Properties
 
name - de.isas.mztab2.model.MsRun.Properties
 
name - de.isas.mztab2.model.Parameter.Properties
 
name - de.isas.mztab2.model.Sample.Properties
 
name - de.isas.mztab2.model.StudyVariable.Properties
 
name - Variable in class info.psidev.cvmapping.CvMappingRule
 
name(Parameter) - Method in class de.isas.mztab2.model.Instrument

Builder method for name.

name(String) - Method in class de.isas.mztab2.model.Assay

Builder method for name.

name(String) - Method in class de.isas.mztab2.model.Contact

Builder method for name.

name(String) - Method in class de.isas.mztab2.model.MsRun

Builder method for name.

name(String) - Method in class de.isas.mztab2.model.Parameter

Builder method for name.

name(String) - Method in class de.isas.mztab2.model.Sample

Builder method for name.

name(String) - Method in class de.isas.mztab2.model.StudyVariable

Builder method for name.

NEW_LINE - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant NEW_LINE="System.getProperty(line.separator)"

newSet(Collection<? extends T>) - Static method in class de.isas.mztab2.cvmapping.SetOperations

Creates a new typed LinkedHashSet (preserving order of insertion)
 from the given collection.

niceToString(CvMappingRule) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils

Creates a user-friendly string of a mapping rule.

NoDatabaseMustHaveNullPrefix - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NoDatabaseMustHaveNullPrefix

NoHeaderLine - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NoHeaderLine

NoMetadataSection - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NoMetadataSection

NoSmallMoleculeEvidenceSection - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NoSmallMoleculeEvidenceSection

NoSmallMoleculeFeatureQuantificationUnit - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NoSmallMoleculeFeatureQuantificationUnit

NoSmallMoleculeFeatureSection - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NoSmallMoleculeFeatureSection

NoSmallMoleculeIdentificationReliability - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NoSmallMoleculeIdentificationReliability

NoSmallMoleculeQuantificationUnit - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NoSmallMoleculeQuantificationUnit

NoSmallMoleculeSummarySection - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NoSmallMoleculeSummarySection

NOT_RELATED - de.isas.mztab2.cvmapping.ParameterComparisonResult
 
NotDefineInHeader - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NotDefineInHeader

NotDefineInMetadata - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NotDefineInMetadata

NotNULL - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NotNULL

NULL - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant NULL="null"

NULL - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NULL





O

ObjectFactory - Class in info.psidev.cvmapping

This object contains factory methods for each 
 Java content interface and Java element interface 
 generated in the info.psidev.cvmapping package.

ObjectFactory() - Constructor for class info.psidev.cvmapping.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: info.psidev.cvmapping

of(CvMapping, CvParameterLookupService, boolean) - Static method in class de.isas.mztab2.validation.CvMappingValidator

Create a new instance of CvMappingValidator.

of(File, boolean) - Static method in class de.isas.mztab2.validation.CvMappingValidator

Create a new instance of CvMappingValidator.

of(File, CvParameterLookupService, boolean) - Static method in class de.isas.mztab2.validation.CvMappingValidator

Create a new instance of CvMappingValidator.

of(Object) - Static method in interface de.isas.mztab2.model.IndexedElement

Create a new indexed element as a proxy of the provided element.

of(String) - Static method in enum de.isas.mztab2.model.Assay.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.ColumnParameterMapping.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Comment.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Contact.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.CV.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Database.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Error.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Instrument.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Metadata.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.MsRun.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.MzTab.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.OptColumnMapping.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Parameter.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Publication.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.PublicationItem.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Sample.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.SampleProcessing.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Software.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.SpectraRef.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.StudyVariable.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Uri.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.ValidationMessage.Properties
 
of(URL, boolean) - Static method in class de.isas.mztab2.validation.CvMappingValidator

Create a new instance of CvMappingValidator.

of(URL, CvParameterLookupService, boolean) - Static method in class de.isas.mztab2.validation.CvMappingValidator

Create a new instance of CvMappingValidator.

opt - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
opt - de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
opt - de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
opt(List<OptColumnMapping>) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Builder method for opt.

opt(List<OptColumnMapping>) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Builder method for opt.

opt(List<OptColumnMapping>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Builder method for opt.

OPT - Static variable in class uk.ac.ebi.pride.jmztab2.model.OptionColumn

Constant OPT="opt"

OPT_PREFIX - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant OPT_PREFIX="opt_"

OptColumnMapping - Class in de.isas.mztab2.model

Additional columns can be added to the end of the small molecule table.

OptColumnMapping() - Constructor for class de.isas.mztab2.model.OptColumnMapping
 
OptColumnMapping.Properties - Enum in de.isas.mztab2.model

Property enumeration for OptColumnMapping.

OptColumnMappingBuilder - Class in uk.ac.ebi.pride.jmztab2.model

Builder for reusable OptColumnMapping creation for multiple rows.

OptColumnMappingBuilder.GlobalOptColumnMappingBuilder - Class in uk.ac.ebi.pride.jmztab2.model

Create a new OptColumnMappingBuilder for global optional columns.

OptColumnMappingBuilder.IndexedElementOptColumnMappingBuilder - Class in uk.ac.ebi.pride.jmztab2.model

Create a new OptColumnMappingBuilder for IndexedElement.

OptionalCVParamColumn - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant OptionalCVParamColumn

OptionColumn - Class in uk.ac.ebi.pride.jmztab2.model

Additional columns can be added to the end of the protein table.

OptionColumn(Object, String, Class, int) - Constructor for class uk.ac.ebi.pride.jmztab2.model.OptionColumn

Create a optional column.

OR - info.psidev.cvmapping.CvMappingRule.CvTermsCombinationLogic
 
OrValidationHandler - Class in de.isas.mztab2.validation.handlers

Implements 'OR' logic, meaning alternative possible terms or term roots for
 an object may be present.

OrValidationHandler() - Constructor for class de.isas.mztab2.validation.handlers.OrValidationHandler
 




P

param - de.isas.mztab2.model.ColumnParameterMapping.Properties
 
param - de.isas.mztab2.model.Database.Properties
 
param - de.isas.mztab2.model.OptColumnMapping.Properties
 
param(Parameter) - Method in class de.isas.mztab2.model.ColumnParameterMapping

Builder method for param.

param(Parameter) - Method in class de.isas.mztab2.model.Database

Builder method for param.

param(Parameter) - Method in class de.isas.mztab2.model.OptColumnMapping

Builder method for param.

Param - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant Param

ParamAccessionNotNamespaced - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant ParamAccessionNotNamespaced

parameter - de.isas.mztab2.model.Software.Properties
 
parameter(Parameter) - Method in class de.isas.mztab2.model.Software

Builder method for parameter.

Parameter - Class in de.isas.mztab2.model

mzTab makes use of CV parameters.

Parameter() - Constructor for class de.isas.mztab2.model.Parameter
 
Parameter.Properties - Enum in de.isas.mztab2.model

Property enumeration for Parameter.

ParameterComparisonResult - Enum in de.isas.mztab2.cvmapping


 Result of a comparison of a CvTerm T defined in a CvRule against the parameter P
 found via JXPath.

ParameterConverter - Class in de.isas.mztab2.io.serialization


 Parameter to String converter implementation for
 Parameter.

ParameterConverter() - Constructor for class de.isas.mztab2.io.serialization.ParameterConverter
 
ParameterFormat - Class in de.isas.mztab2.io.formats

Format specification for Parameter.

ParameterFormat() - Constructor for class de.isas.mztab2.io.formats.ParameterFormat
 
ParameterOptionColumn - Class in uk.ac.ebi.pride.jmztab2.model

An kind of OptionColumn which use CV parameter accessions in following the format:
 opt_{OBJECT_ID}_cv_{accession}_{parameter name}.

ParameterOptionColumn(Object, Parameter, Class, int) - Constructor for class uk.ac.ebi.pride.jmztab2.model.ParameterOptionColumn

Define a OptionColumn which use CV parameter accessions in following the format:
 opt_{OBJECT_ID}_cv_{accession}_{parameter name}.

ParameterValidator - Interface in de.isas.lipidomics.mztab2.validation.validators

Base interface for parameter validation with default validation method.

ParamList - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant ParamList

parse(int, String, MZTabErrorList) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.COMLineParser

We assume that user before call this method, have parse the raw line
 is not empty line and start with section prefix.

parse(int, String, MZTabErrorList) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser

We assume that user before call this method, have parse the raw line
 is not empty line and start with section prefix.

parse(int, String, MZTabErrorList) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser

We assume that user before call this method, have parse the raw line
 is not empty line and start with section prefix.

parse(int, String, MZTabErrorList) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabHeaderLineParser

We assume that user before call this method, have parse the raw line
 is not empty line and start with section prefix.

parse(int, String, MZTabErrorList) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabLineParser

We assume that user before call this method, have parse the raw line
 is not empty line and start with section prefix.

parse(OutputStream) - Method in class de.isas.mztab2.io.MzTabFileParser

Create a new MZTabParserContext and MZTabErrorList for
 the given file URI.

parse(OutputStream, MZTabErrorType.Level) - Method in class de.isas.mztab2.io.MzTabFileParser

Create a new MZTabParserContext and MZTabErrorList for
 the given file URI.

parse(OutputStream, MZTabErrorType.Level, int) - Method in class de.isas.mztab2.io.MzTabFileParser

Create a new MZTabParserContext and MZTabErrorList for
 the given file URI.

parseColumns() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabHeaderLineParser

This methods delegates to the subclasses the parsing of the columns.

parseColumns() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.SEHLineParser

This methods delegates to the subclasses the parsing of the columns.

parseColumns() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.SFHLineParser

This methods delegates to the subclasses the parsing of the columns.

parseColumns() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.SMHLineParser

This methods delegates to the subclasses the parsing of the columns.

parseDouble(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils

NOTICE: If ratios are included and the denominator is zero, the "INF"
 value MUST be used.

parseDoubleList(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils


 parseDoubleList.

parseEmail(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils

Parse the target string, and check is obey the email format or not.

parseGOTermList(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils

A '|' delimited list of GO accessions

parseIndex(String, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabHeaderLineParser

Parse header to a index id number.

parseIndexedElement(String, MetadataElement) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils

parse the target into a IndexedElement
 object.

parseInteger(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils


 parseInteger.

parseIntegerList(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils


 parseIntegerList.

parseLong(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils


 parseLong.

parseMzTabVersion(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils

Parse the target string, and check it follows the mzTab Version format.

parseParam(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils

Parameters are always reported as [CV label, accession, name, value].

parseParamList(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils

A list of '|' separated parameters

parsePublicationItems(Publication, int, String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils

A publication on this unit.

parseRefList(String, MetadataElement) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils

Parse the target into a IndexedElement list.

parseSpectraRefList(MZTabParserContext, Metadata, String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils

Parse a SpectraRef list.

parseString(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabStringUtils

Pre-process the String object.

parseStringList(char, String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils

Multiple identifiers MUST be separated by splitChar.

parseURI(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils


 parseURI.

payload() - Method in annotation type de.isas.lipidomics.mztab2.validation.constraints.CheckParameter
 
Peptide - uk.ac.ebi.pride.jmztab2.model.Section
 
Peptide_Header - uk.ac.ebi.pride.jmztab2.model.Section
 
PeptideSearchEngineScoreNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant PeptideSearchEngineScoreNotDefined

PeptideSection - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant PeptideSection

positionMapping - Variable in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser
 
PositionMapping - Class in uk.ac.ebi.pride.jmztab2.utils.parser

Create and maintain a couple of mappings between physical position and logical position.

PositionMapping(MZTabColumnFactory, String) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.parser.PositionMapping

Constructor for PositionMapping.

PositionMapping(MZTabColumnFactory, String[]) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.parser.PositionMapping

Constructor for PositionMapping.

prefix - de.isas.mztab2.model.Comment.Properties
 
prefix - de.isas.mztab2.model.Database.Properties
 
prefix - de.isas.mztab2.model.Metadata.Properties
 
prefix - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
prefix - de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
prefix - de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
prefix(Comment.PrefixEnum) - Method in class de.isas.mztab2.model.Comment

Builder method for prefix.

prefix(Metadata.PrefixEnum) - Method in class de.isas.mztab2.model.Metadata

Builder method for prefix.

prefix(String) - Method in class de.isas.mztab2.model.Database

Builder method for prefix.

print(OutputStream) - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList

Print error list to output stream.

printAbundanceAssay(Assay) - Static method in class de.isas.mztab2.io.serialization.Serializers


 printAbundanceAssay.

printAbundanceCoeffVarStudyVar(StudyVariable) - Static method in class de.isas.mztab2.io.serialization.Serializers


 printAbundanceCoeffVarStudyVar.

printAbundanceStudyVar(StudyVariable) - Static method in class de.isas.mztab2.io.serialization.Serializers


 printAbundanceStudyVar.

printDouble(Double) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils

If ratios are included and the denominator is zero, the "INF" value MUST
 be used.

printOptColumnMapping(OptColumnMapping) - Static method in class de.isas.mztab2.io.serialization.Serializers


 printOptColumnMapping.

Protein - uk.ac.ebi.pride.jmztab2.model.Section
 
Protein_Header - uk.ac.ebi.pride.jmztab2.model.Section
 
ProteinCoverage - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant ProteinCoverage

ProteinSearchEngineScoreNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant ProteinSearchEngineScoreNotDefined

PSM - uk.ac.ebi.pride.jmztab2.model.Section
 
PSM_Header - uk.ac.ebi.pride.jmztab2.model.Section
 
PSMSearchEngineScoreNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant PSMSearchEngineScoreNotDefined

publication - de.isas.mztab2.model.Metadata.Properties
 
publication(List<Publication>) - Method in class de.isas.mztab2.model.Metadata

Builder method for publication.

Publication - Class in de.isas.mztab2.model

A publication associated with this file.

Publication - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant Publication

Publication() - Constructor for class de.isas.mztab2.model.Publication
 
PUBLICATION - uk.ac.ebi.pride.jmztab2.model.MetadataElement
 
Publication.Properties - Enum in de.isas.mztab2.model

Property enumeration for Publication.

PublicationFormat - Class in de.isas.mztab2.io.formats

Format specification for Publication.

PublicationFormat() - Constructor for class de.isas.mztab2.io.formats.PublicationFormat
 
PublicationItem - Class in de.isas.mztab2.model

A publication item, defined by a qualifier and a native accession, e.g. pubmed id.

PublicationItem() - Constructor for class de.isas.mztab2.model.PublicationItem
 
PublicationItem.Properties - Enum in de.isas.mztab2.model

Property enumeration for PublicationItem.

PublicationItem.TypeEnum - Enum in de.isas.mztab2.model

The type qualifier of this publication item.

publicationItems - de.isas.mztab2.model.Publication.Properties
 
publicationItems(List<PublicationItem>) - Method in class de.isas.mztab2.model.Publication

Builder method for publicationItems.

PublicationSerializer - Class in de.isas.mztab2.io.serialization

PublicationSerializer implementation for Publication.

PublicationSerializer() - Constructor for class de.isas.mztab2.io.serialization.PublicationSerializer


 Constructor for PublicationSerializer.

PublicationSerializer(Class<Publication>) - Constructor for class de.isas.mztab2.io.serialization.PublicationSerializer


 Constructor for PublicationSerializer.

PUBMED - de.isas.mztab2.model.PublicationItem.TypeEnum
 
put(Integer, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.PositionMapping

put.





Q

QUANTIFICATION_METHOD - uk.ac.ebi.pride.jmztab2.model.MetadataElement
 
QuantificationAbundance - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant QuantificationAbundance

quantificationMethod - de.isas.mztab2.model.Metadata.Properties
 
quantificationMethod(Parameter) - Method in class de.isas.mztab2.model.Metadata

Builder method for quantificationMethod.

QuantificationMethodValidator - Class in de.isas.mztab2.io.validators

Validates that the quantification method section is present in metadata.

QuantificationMethodValidator() - Constructor for class de.isas.mztab2.io.validators.QuantificationMethodValidator
 




R

rank - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
rank(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Builder method for rank.

RANK - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
 
reference - de.isas.mztab2.model.SpectraRef.Properties
 
reference(String) - Method in class de.isas.mztab2.model.SpectraRef

Builder method for reference.

refine() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabHeaderLineParser

Some validate operation need to be done after the whole MZTabColumnFactory created.

refine() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.SEHLineParser

Some validate operation need to be done after the whole MZTabColumnFactory created.

refine() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.SFHLineParser

Some validate operation need to be done after the whole MZTabColumnFactory created.

refine() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.SMHLineParser

Some validate operation need to be done after the whole MZTabColumnFactory created.

refineNormalMetadata() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser

Refine the metadata, and check whether missing some important
 information. fixed_mode, variable_mode must provide in the Complete file.

refineOptionalColumn(Section, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabHeaderLineParser

Refine optional columns and check, whether they were properly defined.

RefiningValidator<T> - Interface in de.isas.mztab2.io.validators

Implementations of the refining validator are applied to the type object
 after the actual line parsing process, for post-hoc validation.

REGEX_ABUNDANCE_ASSAY_COLUMN_NAME - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_ABUNDANCE_ASSAY_COLUMN_NAME="assay\\[(\\d+)\\]"

REGEX_ABUNDANCE_COLUMN_NAME - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_ABUNDANCE_COLUMN_NAME="abundance_(.+)"

REGEX_ADDUCT - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_ADDUCT="^\[\d*M([+-][\w\d]+)*\]\d*[+-]$"

REGEX_CV_PARAM_OPT_COLUMN_NAME - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_CV_PARAM_OPT_COLUMN_NAME="cv(_([A-Za-z0-9\\-\\[\\]:\\.]+))?


REGEX_DEFAULT_RELIABILITY - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_DEFAULT_RELIABILITY="[1234]{1}"

REGEX_EMAIL - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_EMAIL="[_A-Za-z0-9-]+(\\.


REGEX_INDEXED_VALUE - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_INDEXED_VALUE="\\[(\\d+)\\]"

REGEX_MZTAB_M - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_MZTAB_M="(?<major>[2]{1})\\.(?<minor>\\d{1})\\.(?<micro>\\d{1})-(?<profile>[M]{1})"

REGEX_NORMAL_METADATA - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_NORMAL_METADATA="(\\w+)(\\[(\\w+)\\])?


REGEX_OPT_COLUMN_NAME - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_OPT_COLUMN_NAME="opt_((assay|study_variable|ms_run)\\[(\\w+)\\]|global)_([A-Za-z0-9_\\-\\[\\]:\\.]+)"

REGEX_PARAM_SPLIT - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_PARAM_SPLIT=",(?


REGEX_SPECTRA_REF_FILE - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_SPECTRA_REF_FILE = "file=[\\w]+"

REGEX_SPECTRA_REF_INDEX - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_SPECTRA_REF_INDEX = "index=[\\d]+"

REGEX_SPECTRA_REF_MZML_UNIQUE - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_SPECTRA_REF_MZML_UNIQUE = "[\\w]+"

REGEX_SPECTRA_REF_SCAN - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_SPECTRA_REF_SCAN = "scan=[\\d]+"

REGEX_SPECTRA_REF_SPECTRUM - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_SPECTRA_REF_SPECTRUM = "spectrum=[\\d]+"

REGEX_SPECTRA_REF_THERMO_NATIVE - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_SPECTRA_REF_THERMO_NATIVE = "controllerType=[\\d]+ controllerNumber=[1-9]\\d* scan=[1-9]\\d*"

REGEX_SPECTRA_REF_WATERS_NATIVE - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_SPECTRA_REF_WATERS_NATIVE = "function=[1-9]\\d* process=[\\d]+ scan=[\\d]+"

REGEX_SPECTRA_REF_WIFF_NATIVE - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_SPECTRA_REF_WIFF_NATIVE = "sample=[\\d]+ period=[\\d]+ cycle=[\\d]+ experiment=[\\d]+"

REGEX_STUDY_VARIABLE_COLUMN_NAME - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_STUDY_VARIABLE_COLUMN_NAME="study_variable\\[(\\d+)\\]"

RegexMismatch - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant RegexMismatch

reliability - de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
reliability(String) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Builder method for reliability.

Reliability - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant Reliability

RELIABILITY - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
 
removeDoubleQuotes(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils

If there exists reserved characters in value, like comma, the string need
 to be escape.

RemoveUserParams - Class in de.isas.mztab2.cvmapping

Removes user parameters from the provided selection.

RemoveUserParams() - Constructor for class de.isas.mztab2.cvmapping.RemoveUserParams
 
requirementLevel - Variable in class info.psidev.cvmapping.CvMappingRule
 
resolveChildren(Parameter) - Method in class de.isas.mztab2.cvmapping.CvParameterLookupService

Resolve all children of a parameter up to an arbitrary depth.

resolveChildren(Parameter, int) - Method in class de.isas.mztab2.cvmapping.CvParameterLookupService

Resolve all children of a parameter up to a given maximum depth (1 meaning immediate children, -1 meaning all).

resolveParents(Parameter) - Method in class de.isas.mztab2.cvmapping.CvParameterLookupService

Resolve all parents of parameter up to an arbitrary depth (actually height, since we go from bottom to top).

resolveParents(Parameter, int) - Method in class de.isas.mztab2.cvmapping.CvParameterLookupService

Resolve all parents of a parameter up to a given maximum depth (1 meaning the immediate parents, -1 meaning all).

ResolvingCvRuleHandler - Class in de.isas.mztab2.validation.handlers

Implements resolution of cv parameters using the provided lookup service.

ResolvingCvRuleHandler(CvParameterLookupService) - Constructor for class de.isas.mztab2.validation.handlers.ResolvingCvRuleHandler
 
resourcePath() - Method in enum de.isas.mztab2.test.utils.ClassPathFile
 
RETENTION_TIME_IN_SECONDS - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn.Stable
 
RETENTION_TIME_IN_SECONDS_END - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn.Stable
 
RETENTION_TIME_IN_SECONDS_START - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn.Stable
 
retentionTimeInSeconds - de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
retentionTimeInSeconds(Double) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Builder method for retentionTimeInSeconds.

retentionTimeInSecondsEnd - de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
retentionTimeInSecondsEnd(Double) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Builder method for retentionTimeInSecondsEnd.

retentionTimeInSecondsStart - de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
retentionTimeInSecondsStart(Double) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Builder method for retentionTimeInSecondsStart.

reverse() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.PositionMapping

Exchange key and value to "LogicalPosition, PhysicalPosition".

RuleEvaluationResult - Class in de.isas.mztab2.cvmapping

Captures results of applying a rule to a parameter selection.

RuleEvaluationResult() - Constructor for class de.isas.mztab2.cvmapping.RuleEvaluationResult
 
RulePointerObjectNullOptional - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType

Constant RulePointerObjectNullOptional

RulePointerObjectNullRecommended - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType

Constant RulePointerObjectNullRecommended

RulePointerObjectNullRequired - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType

Constant RulePointerObjectNullRequired





S

sample - de.isas.mztab2.model.Metadata.Properties
 
sample(List<Sample>) - Method in class de.isas.mztab2.model.Metadata

Builder method for sample.

Sample - Class in de.isas.mztab2.model

Specification of sample.

Sample() - Constructor for class de.isas.mztab2.model.Sample
 
SAMPLE - uk.ac.ebi.pride.jmztab2.model.MetadataElement
 
SAMPLE_CELL_TYPE - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
 
SAMPLE_CUSTOM - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
 
SAMPLE_DESCRIPTION - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
 
SAMPLE_DISEASE - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
 
SAMPLE_PROCESSING - uk.ac.ebi.pride.jmztab2.model.MetadataElement
 
SAMPLE_SPECIES - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
 
SAMPLE_TISSUE - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
 
Sample.Properties - Enum in de.isas.mztab2.model

Property enumeration for Sample.

SampleFormat - Class in de.isas.mztab2.io.formats

Format specification for Sample.

SampleFormat() - Constructor for class de.isas.mztab2.io.formats.SampleFormat
 
sampleProcessing - de.isas.mztab2.model.Metadata.Properties
 
sampleProcessing - de.isas.mztab2.model.SampleProcessing.Properties
 
sampleProcessing(List<Parameter>) - Method in class de.isas.mztab2.model.SampleProcessing

Builder method for sampleProcessing.

sampleProcessing(List<SampleProcessing>) - Method in class de.isas.mztab2.model.Metadata

Builder method for sampleProcessing.

SampleProcessing - Class in de.isas.mztab2.model

A list of parameters describing a sample processing, preparation or handling step similar to a biological or analytical methods report.

SampleProcessing() - Constructor for class de.isas.mztab2.model.SampleProcessing
 
SampleProcessing.Properties - Enum in de.isas.mztab2.model

Property enumeration for SampleProcessing.

SampleProcessingFormat - Class in de.isas.mztab2.io.formats

Format specification for SampleProcessing.

SampleProcessingFormat() - Constructor for class de.isas.mztab2.io.formats.SampleProcessingFormat
 
SampleProcessingSerializer - Class in de.isas.mztab2.io.serialization

SampleProcessingSerializer implementation for SampleProcessing.

SampleProcessingSerializer() - Constructor for class de.isas.mztab2.io.serialization.SampleProcessingSerializer

Constructor for SampleProcessingSerializer.

SampleProcessingSerializer(Class<SampleProcessing>) - Constructor for class de.isas.mztab2.io.serialization.SampleProcessingSerializer

Constructor for SampleProcessingSerializer.

sampleRef - de.isas.mztab2.model.Assay.Properties
 
sampleRef(Sample) - Method in class de.isas.mztab2.model.Assay

Builder method for sampleRef.

SampleSerializer - Class in de.isas.mztab2.io.serialization

SampleSerializer implementation for Sample.

SampleSerializer() - Constructor for class de.isas.mztab2.io.serialization.SampleSerializer

Constructor for SampleSerializer.

SampleSerializer(Class<Sample>) - Constructor for class de.isas.mztab2.io.serialization.SampleSerializer

Constructor for SampleSerializer.

scanPolarity - de.isas.mztab2.model.MsRun.Properties
 
scanPolarity(List<Parameter>) - Method in class de.isas.mztab2.model.MsRun

Builder method for scanPolarity.

scopePath - Variable in class info.psidev.cvmapping.CvMappingRule
 
SearchEngineScore - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant SearchEngineScore

section - Variable in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabLineParser
 
Section - Enum in uk.ac.ebi.pride.jmztab2.model

Every line in an mzTab file MUST start with a three letter code identifying the type of line delimited by
 a Tab character.

SEH - de.isas.mztab2.model.SmallMoleculeEvidence.HeaderPrefixEnum
 
SEHLineParser - Class in uk.ac.ebi.pride.jmztab2.utils.parser

Parse and validate Small Molecule Evidence header line into a MZTabColumnFactory.

SEHLineParser(MZTabParserContext, Metadata) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.parser.SEHLineParser

Constructor for SEHLineParser.

SemanticValidationException - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType

Constant SemanticValidationException

Sequence - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant Sequence

serialize(Assay, JsonGenerator, SerializerProvider) - Method in class de.isas.mztab2.io.serialization.AssaySerializer
serialize(Contact, JsonGenerator, SerializerProvider) - Method in class de.isas.mztab2.io.serialization.ContactSerializer
serialize(CV, JsonGenerator, SerializerProvider) - Method in class de.isas.mztab2.io.serialization.CvSerializer
serialize(Database, JsonGenerator, SerializerProvider) - Method in class de.isas.mztab2.io.serialization.DatabaseSerializer
serialize(Instrument, JsonGenerator, SerializerProvider) - Method in class de.isas.mztab2.io.serialization.InstrumentSerializer
serialize(Metadata, JsonGenerator, SerializerProvider) - Method in class de.isas.mztab2.io.serialization.MetadataSerializer
serialize(MsRun, JsonGenerator, SerializerProvider) - Method in class de.isas.mztab2.io.serialization.MsRunSerializer
serialize(Publication, JsonGenerator, SerializerProvider) - Method in class de.isas.mztab2.io.serialization.PublicationSerializer
serialize(SampleProcessing, JsonGenerator, SerializerProvider) - Method in class de.isas.mztab2.io.serialization.SampleProcessingSerializer
serialize(Sample, JsonGenerator, SerializerProvider) - Method in class de.isas.mztab2.io.serialization.SampleSerializer
serialize(SmallMoleculeEvidence, JsonGenerator, SerializerProvider) - Method in class de.isas.mztab2.io.serialization.SmallMoleculeEvidenceSerializer
serialize(SmallMoleculeFeature, JsonGenerator, SerializerProvider) - Method in class de.isas.mztab2.io.serialization.SmallMoleculeFeatureSerializer
serialize(SmallMoleculeSummary, JsonGenerator, SerializerProvider) - Method in class de.isas.mztab2.io.serialization.SmallMoleculeSummarySerializer
serialize(Software, JsonGenerator, SerializerProvider) - Method in class de.isas.mztab2.io.serialization.SoftwareSerializer
serialize(StudyVariable, JsonGenerator, SerializerProvider) - Method in class de.isas.mztab2.io.serialization.StudyVariableSerializer
serialize(Uri, JsonGenerator, SerializerProvider) - Method in class de.isas.mztab2.io.serialization.UriSerializer
serializeList(List<T>, JsonGenerator, SerializerProvider, Comparator<? super T>) - Static method in class de.isas.mztab2.io.serialization.MetadataSerializer


 serializeList.

serializeListWithMetadataElement(List<T>, MetadataElement, JsonGenerator, SerializerProvider, Comparator<? super T>) - Static method in class de.isas.mztab2.io.serialization.MetadataSerializer


 Serialize a list of Parameters for the provided metadata element.

serializeObject(Object, JsonGenerator, SerializerProvider) - Static method in class de.isas.mztab2.io.serialization.MetadataSerializer


 serializeObject.

Serializers - Class in de.isas.mztab2.io.serialization


 Utility class providing helper methods for other serializers.

Serializers() - Constructor for class de.isas.mztab2.io.serialization.Serializers
 
serializeWithType(Assay, JsonGenerator, SerializerProvider, TypeSerializer) - Method in class de.isas.mztab2.io.serialization.AssaySerializer
 
serializeWithType(Contact, JsonGenerator, SerializerProvider, TypeSerializer) - Method in class de.isas.mztab2.io.serialization.ContactSerializer
 
serializeWithType(CV, JsonGenerator, SerializerProvider, TypeSerializer) - Method in class de.isas.mztab2.io.serialization.CvSerializer
 
serializeWithType(Database, JsonGenerator, SerializerProvider, TypeSerializer) - Method in class de.isas.mztab2.io.serialization.DatabaseSerializer
 
serializeWithType(Instrument, JsonGenerator, SerializerProvider, TypeSerializer) - Method in class de.isas.mztab2.io.serialization.InstrumentSerializer
 
serializeWithType(MsRun, JsonGenerator, SerializerProvider, TypeSerializer) - Method in class de.isas.mztab2.io.serialization.MsRunSerializer
 
serializeWithType(Publication, JsonGenerator, SerializerProvider, TypeSerializer) - Method in class de.isas.mztab2.io.serialization.PublicationSerializer
 
serializeWithType(SampleProcessing, JsonGenerator, SerializerProvider, TypeSerializer) - Method in class de.isas.mztab2.io.serialization.SampleProcessingSerializer
 
serializeWithType(Sample, JsonGenerator, SerializerProvider, TypeSerializer) - Method in class de.isas.mztab2.io.serialization.SampleSerializer
 
serializeWithType(SmallMoleculeEvidence, JsonGenerator, SerializerProvider, TypeSerializer) - Method in class de.isas.mztab2.io.serialization.SmallMoleculeEvidenceSerializer
 
serializeWithType(SmallMoleculeFeature, JsonGenerator, SerializerProvider, TypeSerializer) - Method in class de.isas.mztab2.io.serialization.SmallMoleculeFeatureSerializer
 
serializeWithType(SmallMoleculeSummary, JsonGenerator, SerializerProvider, TypeSerializer) - Method in class de.isas.mztab2.io.serialization.SmallMoleculeSummarySerializer
 
serializeWithType(Software, JsonGenerator, SerializerProvider, TypeSerializer) - Method in class de.isas.mztab2.io.serialization.SoftwareSerializer
 
serializeWithType(StudyVariable, JsonGenerator, SerializerProvider, TypeSerializer) - Method in class de.isas.mztab2.io.serialization.StudyVariableSerializer
 
serializeWithType(Uri, JsonGenerator, SerializerProvider, TypeSerializer) - Method in class de.isas.mztab2.io.serialization.UriSerializer
 
setAbundanceAssay(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set abundanceAssay.

setAbundanceAssay(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set abundanceAssay.

setAbundanceStudyVariable(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set abundanceStudyVariable.

setAbundanceVariationStudyVariable(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set abundanceVariationStudyVariable.

setAccession(String) - Method in class de.isas.mztab2.model.PublicationItem

Set accession.

setAdductIon(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set adductIon.

setAdductIon(String) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set adductIon.

setAdductIons(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set adductIons.

setAffiliation(String) - Method in class de.isas.mztab2.model.Contact

Set affiliation.

setAllowChildren(boolean) - Method in class info.psidev.cvmapping.CvTerm

Legt den Wert der allowChildren-Eigenschaft fest.

setAnalyzer(List<Parameter>) - Method in class de.isas.mztab2.model.Instrument

Set analyzer.

setAssay(List<Assay>) - Method in class de.isas.mztab2.model.Metadata

Set assay.

setAssayRefs(List<Assay>) - Method in class de.isas.mztab2.model.StudyVariable

Set assayRefs.

setAverageFunction(Parameter) - Method in class de.isas.mztab2.model.StudyVariable

Set averageFunction.

setBestIdConfidenceMeasure(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set bestIdConfidenceMeasure.

setBestIdConfidenceValue(Double) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set bestIdConfidenceValue.

setCategory(ValidationMessage.CategoryEnum) - Method in class de.isas.mztab2.model.ValidationMessage

Set category.

setCellType(List<Parameter>) - Method in class de.isas.mztab2.model.Sample

Set cellType.

setCharge(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set charge.

setCharge(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set charge.

setChemicalFormula(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set chemicalFormula.

setChemicalFormula(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set chemicalFormula.

setChemicalName(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set chemicalName.

setChemicalName(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set chemicalName.

setCode(Integer) - Method in class de.isas.mztab2.model.Error

Set code.

setCode(String) - Method in class de.isas.mztab2.model.ValidationMessage

Set code.

setColumnName(String) - Method in class de.isas.mztab2.model.ColumnParameterMapping

Set columnName.

setColunitSmallMolecule(List<ColumnParameterMapping>) - Method in class de.isas.mztab2.model.Metadata

Set colunitSmallMolecule.

setColunitSmallMoleculeEvidence(List<ColumnParameterMapping>) - Method in class de.isas.mztab2.model.Metadata

Set colunitSmallMoleculeEvidence.

setColunitSmallMoleculeFeature(List<ColumnParameterMapping>) - Method in class de.isas.mztab2.model.Metadata

Set colunitSmallMoleculeFeature.

setComment(List<Comment>) - Method in class de.isas.mztab2.model.MzTab

Set comment.

setComment(List<Comment>) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set comment.

setComment(List<Comment>) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set comment.

setComment(List<Comment>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set comment.

setContact(List<Contact>) - Method in class de.isas.mztab2.model.Metadata

Set contact.

setCustom(List<Parameter>) - Method in class de.isas.mztab2.model.Assay

Set custom.

setCustom(List<Parameter>) - Method in class de.isas.mztab2.model.Metadata

Set custom.

setCustom(List<Parameter>) - Method in class de.isas.mztab2.model.Sample

Set custom.

setCv(List<CV>) - Method in class de.isas.mztab2.model.Metadata

Set cv.

setCvAccession(String) - Method in class de.isas.mztab2.model.Parameter

Set cvAccession.

setCvElementPath(String) - Method in class info.psidev.cvmapping.CvMappingRule

Legt den Wert der cvElementPath-Eigenschaft fest.

setCvIdentifier(String) - Method in class info.psidev.cvmapping.CvReference

Legt den Wert der cvIdentifier-Eigenschaft fest.

setCvIdentifierRef(CvReference) - Method in class info.psidev.cvmapping.CvTerm

Legt den Wert der cvIdentifierRef-Eigenschaft fest.

setCvLabel(String) - Method in class de.isas.mztab2.model.Parameter

Set cvLabel.

setCvMappingRuleList(CvMapping.CvMappingRuleList) - Method in class info.psidev.cvmapping.CvMapping

Legt den Wert der cvMappingRuleList-Eigenschaft fest.

setCvName(String) - Method in class info.psidev.cvmapping.CvReference

Legt den Wert der cvName-Eigenschaft fest.

setCvReferenceList(CvMapping.CvReferenceList) - Method in class info.psidev.cvmapping.CvMapping

Legt den Wert der cvReferenceList-Eigenschaft fest.

setCvSourceVersion(String) - Method in class info.psidev.cvmapping.CvMapping.CvReferenceList

Legt den Wert der cvSourceVersion-Eigenschaft fest.

setCvTermsCombinationLogic(CvMappingRule.CvTermsCombinationLogic) - Method in class info.psidev.cvmapping.CvMappingRule

Legt den Wert der cvTermsCombinationLogic-Eigenschaft fest.

setDatabase(List<Database>) - Method in class de.isas.mztab2.model.Metadata

Set database.

setDatabaseIdentifier(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set databaseIdentifier.

setDatabaseIdentifier(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set databaseIdentifier.

setDerivatizationAgent(List<Parameter>) - Method in class de.isas.mztab2.model.Metadata

Set derivatizationAgent.

setDerivatizedForm(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set derivatizedForm.

setDescription(String) - Method in class de.isas.mztab2.model.Metadata

Set description.

setDescription(String) - Method in class de.isas.mztab2.model.Sample

Set description.

setDescription(String) - Method in class de.isas.mztab2.model.StudyVariable

Set description.

setDetector(Parameter) - Method in class de.isas.mztab2.model.Instrument

Set detector.

setDisease(List<Parameter>) - Method in class de.isas.mztab2.model.Sample

Set disease.

setElement(Object) - Method in interface uk.ac.ebi.pride.jmztab2.model.IMZTabColumn

Indexed element used in optional column header and logical position
 definition.

setElement(Object) - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumn

Indexed element used in optional column header and logical position
 definition.

setElement(Object) - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn

Indexed element used in optional column header and logical position
 definition.

setElement(Object) - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn

Indexed element used in optional column header and logical position
 definition.

setElement(Object) - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn

Indexed element used in optional column header and logical position
 definition.

setEmail(String) - Method in class de.isas.mztab2.model.Contact

Set email.

setEvidenceInputId(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set evidenceInputId.

setExpMassToCharge(Double) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set expMassToCharge.

setExpMassToCharge(Double) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set expMassToCharge.

setExternalStudyUri(List<Uri>) - Method in class de.isas.mztab2.model.Metadata

Set externalStudyUri.

setExternalUri(String) - Method in class de.isas.mztab2.model.Assay

Set externalUri.

setFactors(List<Parameter>) - Method in class de.isas.mztab2.model.StudyVariable

Set factors.

setFormat(Parameter) - Method in class de.isas.mztab2.model.MsRun

Set format.

setFragmentationMethod(List<Parameter>) - Method in class de.isas.mztab2.model.MsRun

Set fragmentationMethod.

setFullName(String) - Method in class de.isas.mztab2.model.CV

Set fullName.

setHash(String) - Method in class de.isas.mztab2.model.MsRun

Set hash.

setHashMethod(Parameter) - Method in class de.isas.mztab2.model.MsRun

Set hashMethod.

setHeader(String) - Method in interface uk.ac.ebi.pride.jmztab2.model.IMZTabColumn

setHeader.

setHeader(String) - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumn

setHeader.

setHeader(String) - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn

setHeader.

setHeader(String) - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn

setHeader.

setHeader(String) - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn

setHeader.

setId(Integer) - Method in class de.isas.mztab2.model.Assay

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.Contact

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.CV

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.Database

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.Instrument

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.MsRun

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.Parameter

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.Publication

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.Sample

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.SampleProcessing

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.Software

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.StudyVariable

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.Uri

Set id.

setId(String) - Method in class info.psidev.cvmapping.CvMappingRule

Legt den Wert der id-Eigenschaft fest.

setIdConfidenceMeasure(List<Parameter>) - Method in class de.isas.mztab2.model.Metadata

Set idConfidenceMeasure.

setIdConfidenceMeasure(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set idConfidenceMeasure.

setIdentificationMethod(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set identificationMethod.

setIdentifier(String) - Method in class de.isas.mztab2.model.OptColumnMapping

Set identifier.

setIdFormat(Parameter) - Method in class de.isas.mztab2.model.MsRun

Set idFormat.

setInchi(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set inchi.

setInchi(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set inchi.

setInstrument(List<Instrument>) - Method in class de.isas.mztab2.model.Metadata

Set instrument.

setInstrumentRef(Instrument) - Method in class de.isas.mztab2.model.MsRun

Set instrumentRef.

setIsotopomer(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set isotopomer.

setIsRepeatable(Boolean) - Method in class info.psidev.cvmapping.CvTerm

Legt den Wert der isRepeatable-Eigenschaft fest.

setLabel(String) - Method in class de.isas.mztab2.model.CV

Set label.

setLevel(MZTabErrorType.Level) - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList

Define the level of the errors that are going to be store in the list.

setLineNumber(Integer) - Method in class de.isas.mztab2.model.Comment

Set lineNumber.

setLineNumber(Long) - Method in class de.isas.mztab2.model.ValidationMessage

Set lineNumber.

setLocation(String) - Method in class de.isas.mztab2.model.MsRun

Set location.

setLogicPosition(String) - Method in interface uk.ac.ebi.pride.jmztab2.model.IMZTabColumn

setLogicPosition.

setLogicPosition(String) - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumn

setLogicPosition.

setLogicPosition(String) - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn

setLogicPosition.

setLogicPosition(String) - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn

setLogicPosition.

setLogicPosition(String) - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn

setLogicPosition.

setMaxErrorCount(int) - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList

Define the maximum number of errors recorded by this list before an
 MZTabErrorOverflowException
 is thrown

setMessage(String) - Method in class de.isas.mztab2.model.Error

Set message.

setMessage(String) - Method in class de.isas.mztab2.model.ValidationMessage

Set message.

setMessageType(ValidationMessage.MessageTypeEnum) - Method in class de.isas.mztab2.model.ValidationMessage

Set messageType.

setMetadata(Metadata) - Method in class de.isas.mztab2.model.MzTab

Set metadata.

setModelName(String) - Method in class info.psidev.cvmapping.CvMapping

Legt den Wert der modelName-Eigenschaft fest.

setModelURI(String) - Method in class info.psidev.cvmapping.CvMapping

Legt den Wert der modelURI-Eigenschaft fest.

setModelVersion(String) - Method in class info.psidev.cvmapping.CvMapping

Legt den Wert der modelVersion-Eigenschaft fest.

setMsg(String) - Method in class de.isas.mztab2.model.Comment

Set msg.

setMsLevel(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set msLevel.

setMsRun(MsRun) - Method in class de.isas.mztab2.model.SpectraRef

Set msRun.

setMsRun(List<MsRun>) - Method in class de.isas.mztab2.model.Metadata

Set msRun.

setMsRunRef(List<MsRun>) - Method in class de.isas.mztab2.model.Assay

Set msRunRef.

setMzTabID(String) - Method in class de.isas.mztab2.model.Metadata

Set mzTabID.

setMzTabVersion(String) - Method in class de.isas.mztab2.model.Metadata

Set mzTabVersion.

setName(Parameter) - Method in class de.isas.mztab2.model.Instrument

Set name.

setName(String) - Method in class de.isas.mztab2.model.Assay

Set name.

setName(String) - Method in class de.isas.mztab2.model.Contact

Set name.

setName(String) - Method in class de.isas.mztab2.model.MsRun

Set name.

setName(String) - Method in class de.isas.mztab2.model.Parameter

Set name.

setName(String) - Method in class de.isas.mztab2.model.Sample

Set name.

setName(String) - Method in class de.isas.mztab2.model.StudyVariable

Set name.

setName(String) - Method in class info.psidev.cvmapping.CvMappingRule

Legt den Wert der name-Eigenschaft fest.

SetOperations - Class in de.isas.mztab2.cvmapping

Utility methods for sets with common names.

SetOperations() - Constructor for class de.isas.mztab2.cvmapping.SetOperations
 
setOpt(List<OptColumnMapping>) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set opt.

setOpt(List<OptColumnMapping>) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set opt.

setOpt(List<OptColumnMapping>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set opt.

setOrder(String) - Method in interface uk.ac.ebi.pride.jmztab2.model.IMZTabColumn

setOrder.

setOrder(String) - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumn

setOrder.

setOrder(String) - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn

setOrder.

setOrder(String) - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn

setOrder.

setOrder(String) - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn

setOrder.

setParam(Parameter) - Method in class de.isas.mztab2.model.ColumnParameterMapping

Set param.

setParam(Parameter) - Method in class de.isas.mztab2.model.Database

Set param.

setParam(Parameter) - Method in class de.isas.mztab2.model.OptColumnMapping

Set param.

setParameter(Parameter) - Method in class de.isas.mztab2.model.Software

Set parameter.

setPrefix(Comment.PrefixEnum) - Method in class de.isas.mztab2.model.Comment

Set prefix.

setPrefix(Metadata.PrefixEnum) - Method in class de.isas.mztab2.model.Metadata

Set prefix.

setPrefix(String) - Method in class de.isas.mztab2.model.Database

Set prefix.

setPublication(List<Publication>) - Method in class de.isas.mztab2.model.Metadata

Set publication.

setPublicationItems(List<PublicationItem>) - Method in class de.isas.mztab2.model.Publication

Set publicationItems.

setQuantificationMethod(Parameter) - Method in class de.isas.mztab2.model.Metadata

Set quantificationMethod.

setRank(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set rank.

setReference(String) - Method in class de.isas.mztab2.model.SpectraRef

Set reference.

setReliability(String) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set reliability.

setRequirementLevel(CvMappingRule.RequirementLevel) - Method in class info.psidev.cvmapping.CvMappingRule

Legt den Wert der requirementLevel-Eigenschaft fest.

setRetentionTimeInSeconds(Double) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set retentionTimeInSeconds.

setRetentionTimeInSecondsEnd(Double) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set retentionTimeInSecondsEnd.

setRetentionTimeInSecondsStart(Double) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set retentionTimeInSecondsStart.

setSample(List<Sample>) - Method in class de.isas.mztab2.model.Metadata

Set sample.

setSampleProcessing(List<Parameter>) - Method in class de.isas.mztab2.model.SampleProcessing

Set sampleProcessing.

setSampleProcessing(List<SampleProcessing>) - Method in class de.isas.mztab2.model.Metadata

Set sampleProcessing.

setSampleRef(Sample) - Method in class de.isas.mztab2.model.Assay

Set sampleRef.

setScanPolarity(List<Parameter>) - Method in class de.isas.mztab2.model.MsRun

Set scanPolarity.

setScopePath(String) - Method in class info.psidev.cvmapping.CvMappingRule

Legt den Wert der scopePath-Eigenschaft fest.

setSetting(List<String>) - Method in class de.isas.mztab2.model.Software

Set setting.

setSmallMoleculeEvidence(List<SmallMoleculeEvidence>) - Method in class de.isas.mztab2.model.MzTab

Set smallMoleculeEvidence.

setSmallMoleculeFeature(List<SmallMoleculeFeature>) - Method in class de.isas.mztab2.model.MzTab

Set smallMoleculeFeature.

setSmallMoleculeFeatureQuantificationUnit(Parameter) - Method in class de.isas.mztab2.model.Metadata

Set smallMoleculeFeatureQuantificationUnit.

setSmallMoleculeIdentificationReliability(Parameter) - Method in class de.isas.mztab2.model.Metadata

Set smallMoleculeIdentificationReliability.

setSmallMoleculeQuantificationUnit(Parameter) - Method in class de.isas.mztab2.model.Metadata

Set smallMoleculeQuantificationUnit.

setSmallMoleculeSummary(List<SmallMoleculeSummary>) - Method in class de.isas.mztab2.model.MzTab

Set smallMoleculeSummary.

setSmeId(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set smeId.

setSmeIdRefAmbiguityCode(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set smeIdRefAmbiguityCode.

setSmeIdRefs(List<Integer>) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set smeIdRefs.

setSmfId(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set smfId.

setSmfIdRefs(List<Integer>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set smfIdRefs.

setSmiles(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set smiles.

setSmiles(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set smiles.

setSmlId(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set smlId.

setSoftware(List<Software>) - Method in class de.isas.mztab2.model.Metadata

Set software.

setSource(Parameter) - Method in class de.isas.mztab2.model.Instrument

Set source.

setSpecies(List<Parameter>) - Method in class de.isas.mztab2.model.Sample

Set species.

setSpectraRef(List<SpectraRef>) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set spectraRef.

setSplitChar(char) - Method in class uk.ac.ebi.pride.jmztab2.model.SplitList

Setter for the field splitChar.

setStudyVariable(List<StudyVariable>) - Method in class de.isas.mztab2.model.Metadata

Set studyVariable.

setTermAccession(String) - Method in class info.psidev.cvmapping.CvTerm

Legt den Wert der termAccession-Eigenschaft fest.

setTermName(String) - Method in class info.psidev.cvmapping.CvTerm

Legt den Wert der termName-Eigenschaft fest.

setTheoreticalMassToCharge(Double) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set theoreticalMassToCharge.

setTheoreticalNeutralMass(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set theoreticalNeutralMass.

setting - de.isas.mztab2.model.Software.Properties
 
setting(List<String>) - Method in class de.isas.mztab2.model.Software

Builder method for setting.

setTissue(List<Parameter>) - Method in class de.isas.mztab2.model.Sample

Set tissue.

setTitle(String) - Method in class de.isas.mztab2.model.Metadata

Set title.

setType(PublicationItem.TypeEnum) - Method in class de.isas.mztab2.model.PublicationItem

Set type.

setUri(String) - Method in class de.isas.mztab2.model.CV

Set uri.

setUri(String) - Method in class de.isas.mztab2.model.Database

Set uri.

setUri(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set uri.

setUri(List<Uri>) - Method in class de.isas.mztab2.model.Metadata

Set uri.

setUri(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set uri.

setUseTerm(boolean) - Method in class info.psidev.cvmapping.CvTerm

Legt den Wert der useTerm-Eigenschaft fest.

setUseTermName(Boolean) - Method in class info.psidev.cvmapping.CvTerm

Legt den Wert der useTermName-Eigenschaft fest.

setValue(String) - Method in class de.isas.mztab2.model.OptColumnMapping

Set value.

setValue(String) - Method in class de.isas.mztab2.model.Parameter

Set value.

setValue(String) - Method in class de.isas.mztab2.model.Uri

Set value.

setVariationFunction(Parameter) - Method in class de.isas.mztab2.model.StudyVariable

Set variationFunction.

setVersion(String) - Method in class de.isas.mztab2.model.CV

Set version.

setVersion(String) - Method in class de.isas.mztab2.model.Database

Set version.

SFH - de.isas.mztab2.model.SmallMoleculeFeature.HeaderPrefixEnum
 
SFHLineParser - Class in uk.ac.ebi.pride.jmztab2.utils.parser

Parse and validate Small Molecule Feature header line into a MZTabColumnFactory.

SFHLineParser(MZTabParserContext, Metadata) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.parser.SFHLineParser

Constructor for SFHLineParser.

SharedParametersValidationHandler - Class in de.isas.mztab2.validation.handlers

Implements support for validating multiple parameters and the intersection
 between terms as described by the rule and the actually found ones.

SharedParametersValidationHandler() - Constructor for class de.isas.mztab2.validation.handlers.SharedParametersValidationHandler
 
SHOULD - info.psidev.cvmapping.CvMappingRule.RequirementLevel
 
SingleStudyVariableName - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant SingleStudyVariableName

size() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList

Returns the number of elements in this list.

size() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.PositionMapping

size.

Small_Molecule - uk.ac.ebi.pride.jmztab2.model.Section
 
SMALL_MOLECULE - uk.ac.ebi.pride.jmztab2.model.MetadataElement
 
Small_Molecule_Evidence - uk.ac.ebi.pride.jmztab2.model.Section
 
Small_Molecule_Evidence_Header - uk.ac.ebi.pride.jmztab2.model.Section
 
Small_Molecule_Feature - uk.ac.ebi.pride.jmztab2.model.Section
 
SMALL_MOLECULE_FEATURE - uk.ac.ebi.pride.jmztab2.model.MetadataElement
 
Small_Molecule_Feature_Header - uk.ac.ebi.pride.jmztab2.model.Section
 
SMALL_MOLECULE_FEATURE_QUANTIFICATION_UNIT - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
 
Small_Molecule_Header - uk.ac.ebi.pride.jmztab2.model.Section
 
SMALL_MOLECULE_IDENTIFICATION_RELIABILITY - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
 
SMALL_MOLECULE_QUANTIFICATION_UNIT - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
 
SMALLMOLECULE_FEATURE_QUANTIFICATION_UNIT - uk.ac.ebi.pride.jmztab2.model.MetadataElement
 
SMALLMOLECULE_IDENTIFICATION_RELIABILITY - uk.ac.ebi.pride.jmztab2.model.MetadataElement
 
SMALLMOLECULE_QUANTIFICATION_UNIT - uk.ac.ebi.pride.jmztab2.model.MetadataElement
 
SmallMoleculeColumn - Class in uk.ac.ebi.pride.jmztab2.model

Define the stable columns which have stable order in the small molecule header
 line

SmallMoleculeColumn.Stable - Enum in uk.ac.ebi.pride.jmztab2.model

Stable SmallMoleculeColumn definition templates.

smallMoleculeEvidence - de.isas.mztab2.model.MzTab.Properties
 
smallMoleculeEvidence(List<SmallMoleculeEvidence>) - Method in class de.isas.mztab2.model.MzTab

Builder method for smallMoleculeEvidence.

SmallMoleculeEvidence - Class in de.isas.mztab2.model

The small molecule evidence section is table-based, representing evidence for identifications of small molecules/features, from database search or any other process used to give putative identifications to molecules.

SmallMoleculeEvidence() - Constructor for class de.isas.mztab2.model.SmallMoleculeEvidence
 
SmallMoleculeEvidence.HeaderPrefixEnum - Enum in de.isas.mztab2.model

The small molecule evidence table header prefix.

SmallMoleculeEvidence.PrefixEnum - Enum in de.isas.mztab2.model

The small molecule evidence table row prefix.

SmallMoleculeEvidence.Properties - Enum in de.isas.mztab2.model

Property enumeration for SmallMoleculeEvidence.

SmallMoleculeEvidenceColumn - Class in uk.ac.ebi.pride.jmztab2.model

Define the stable columns which have stable order in the small molecule
 evidence header line.

SmallMoleculeEvidenceColumn.Stable - Enum in uk.ac.ebi.pride.jmztab2.model

Stable SmallMoleculeEvidenceColumn definition templates.

SmallMoleculeEvidenceFormat - Class in de.isas.mztab2.io.formats

Format specification for SmallMoleculeEvidence.

SmallMoleculeEvidenceFormat() - Constructor for class de.isas.mztab2.io.formats.SmallMoleculeEvidenceFormat
 
smallMoleculeEvidenceMapper() - Method in class de.isas.mztab2.io.MzTabWriterDefaults

Create a small molecule evidence section csv mapper.

smallMoleculeEvidenceSchema(CsvMapper, MzTab) - Method in class de.isas.mztab2.io.MzTabWriterDefaults

Creates the csv schema (column names and types) for the small molecule feature section.

SmallMoleculeEvidenceSerializer - Class in de.isas.mztab2.io.serialization

SmallMoleculeEvidenceSerializer implementation for SmallMoleculeEvidence.

SmallMoleculeEvidenceSerializer() - Constructor for class de.isas.mztab2.io.serialization.SmallMoleculeEvidenceSerializer


 Constructor for SmallMoleculeEvidenceSerializer.

SmallMoleculeEvidenceSerializer(Class<SmallMoleculeEvidence>) - Constructor for class de.isas.mztab2.io.serialization.SmallMoleculeEvidenceSerializer


 Constructor for SmallMoleculeEvidenceSerializer.

smallMoleculeFeature - de.isas.mztab2.model.MzTab.Properties
 
smallMoleculeFeature(List<SmallMoleculeFeature>) - Method in class de.isas.mztab2.model.MzTab

Builder method for smallMoleculeFeature.

SmallMoleculeFeature - Class in de.isas.mztab2.model

The small molecule feature section is table-based, representing individual MS regions (generally considered to be the elution profile for all isotopomers formed from a single charge state of a molecule), that have been measured/quantified.

SmallMoleculeFeature() - Constructor for class de.isas.mztab2.model.SmallMoleculeFeature
 
SmallMoleculeFeature.HeaderPrefixEnum - Enum in de.isas.mztab2.model

The small molecule feature table header prefix.

SmallMoleculeFeature.PrefixEnum - Enum in de.isas.mztab2.model

The small molecule feature table row prefix.

SmallMoleculeFeature.Properties - Enum in de.isas.mztab2.model

Property enumeration for SmallMoleculeFeature.

SmallMoleculeFeatureColumn - Class in uk.ac.ebi.pride.jmztab2.model

Define the stable columns which have stable order in the small molecule
 feature header line.

SmallMoleculeFeatureColumn.Stable - Enum in uk.ac.ebi.pride.jmztab2.model

Stable SmallMoleculeFeatureColumn definition templates.

SmallMoleculeFeatureFormat - Class in de.isas.mztab2.io.formats

Format specification for SmallMoleculeFeature.

SmallMoleculeFeatureFormat() - Constructor for class de.isas.mztab2.io.formats.SmallMoleculeFeatureFormat
 
smallMoleculeFeatureMapper() - Method in class de.isas.mztab2.io.MzTabWriterDefaults

Create a small molecule feature section csv mapper.

smallMoleculeFeatureQuantificationUnit - de.isas.mztab2.model.Metadata.Properties
 
smallMoleculeFeatureQuantificationUnit(Parameter) - Method in class de.isas.mztab2.model.Metadata

Builder method for smallMoleculeFeatureQuantificationUnit.

SmallMoleculeFeatureQuantificationUnitValidator - Class in de.isas.mztab2.io.validators

Validates that smallMoleculeFeatureQuantificationUnit is neither null nor
 empty.

SmallMoleculeFeatureQuantificationUnitValidator() - Constructor for class de.isas.mztab2.io.validators.SmallMoleculeFeatureQuantificationUnitValidator
 
smallMoleculeFeatureSchema(CsvMapper, MzTab) - Method in class de.isas.mztab2.io.MzTabWriterDefaults

Creates the csv schema (column names and types) for the small molecule feature section.

SmallMoleculeFeatureSerializer - Class in de.isas.mztab2.io.serialization

SmallMoleculeFeatureSerializer implementation for SmallMoleculeFeature.

SmallMoleculeFeatureSerializer() - Constructor for class de.isas.mztab2.io.serialization.SmallMoleculeFeatureSerializer


 Constructor for SmallMoleculeFeatureSerializer.

SmallMoleculeFeatureSerializer(Class<SmallMoleculeFeature>) - Constructor for class de.isas.mztab2.io.serialization.SmallMoleculeFeatureSerializer


 Constructor for SmallMoleculeFeatureSerializer.

SmallMoleculeIdConfidenceMeasureValidator - Class in de.isas.mztab2.io.validators

Validates that smallMolecule identification confidence measure is neither
 null nor empty.

SmallMoleculeIdConfidenceMeasureValidator() - Constructor for class de.isas.mztab2.io.validators.SmallMoleculeIdConfidenceMeasureValidator
 
smallMoleculeIdentificationReliability - de.isas.mztab2.model.Metadata.Properties
 
smallMoleculeIdentificationReliability(Parameter) - Method in class de.isas.mztab2.model.Metadata

Builder method for smallMoleculeIdentificationReliability.

smallMoleculeQuantificationUnit - de.isas.mztab2.model.Metadata.Properties
 
smallMoleculeQuantificationUnit(Parameter) - Method in class de.isas.mztab2.model.Metadata

Builder method for smallMoleculeQuantificationUnit.

SmallMoleculeQuantificationUnitValidator - Class in de.isas.mztab2.io.validators

Validates that smallMoleculeQuantificationUnit is neither null nor empty.

SmallMoleculeQuantificationUnitValidator() - Constructor for class de.isas.mztab2.io.validators.SmallMoleculeQuantificationUnitValidator
 
SmallMoleculeSearchEngineScoreNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant SmallMoleculeSearchEngineScoreNotDefined

smallMoleculeSummary - de.isas.mztab2.model.MzTab.Properties
 
smallMoleculeSummary(List<SmallMoleculeSummary>) - Method in class de.isas.mztab2.model.MzTab

Builder method for smallMoleculeSummary.

SmallMoleculeSummary - Class in de.isas.mztab2.model

The small molecule summary section is table-based, represented summarized quantitative information across assays and study variables, grouped by identification in rows.

SmallMoleculeSummary() - Constructor for class de.isas.mztab2.model.SmallMoleculeSummary
 
SmallMoleculeSummary.HeaderPrefixEnum - Enum in de.isas.mztab2.model

The small molecule table header prefix.

SmallMoleculeSummary.PrefixEnum - Enum in de.isas.mztab2.model

The small molecule table row prefix.

SmallMoleculeSummary.Properties - Enum in de.isas.mztab2.model

Property enumeration for SmallMoleculeSummary.

SmallMoleculeSummaryFormat - Class in de.isas.mztab2.io.formats

Format specification for SmallMoleculeSummary.

SmallMoleculeSummaryFormat() - Constructor for class de.isas.mztab2.io.formats.SmallMoleculeSummaryFormat
 
smallMoleculeSummaryMapper() - Method in class de.isas.mztab2.io.MzTabWriterDefaults

Create a small molecule summary section csv mapper.

smallMoleculeSummarySchema(CsvMapper, MzTab) - Method in class de.isas.mztab2.io.MzTabWriterDefaults

Creates the csv schema (column names and types) for the small molecule summary section.

SmallMoleculeSummarySerializer - Class in de.isas.mztab2.io.serialization

SmallMoleculeSummarySerializer implementation for SmallMoleculeSummary.

SmallMoleculeSummarySerializer() - Constructor for class de.isas.mztab2.io.serialization.SmallMoleculeSummarySerializer


 Constructor for SmallMoleculeSummarySerializer.

SmallMoleculeSummarySerializer(Class<SmallMoleculeSummary>) - Constructor for class de.isas.mztab2.io.serialization.SmallMoleculeSummarySerializer


 Constructor for SmallMoleculeSummarySerializer.

SME - de.isas.mztab2.model.SmallMoleculeEvidence.PrefixEnum
 
SME_ID - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
 
SME_ID_REF_AMBIGUITY_CODE - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn.Stable
 
SME_ID_REFS - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn.Stable
 
smeId - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
smeId(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Builder method for smeId.

smeIdRefAmbiguityCode - de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
smeIdRefAmbiguityCode(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Builder method for smeIdRefAmbiguityCode.

smeIdRefs - de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
smeIdRefs(List<Integer>) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Builder method for smeIdRefs.

SMELineParser - Class in uk.ac.ebi.pride.jmztab2.utils.parser

SMELineParser class.

SMELineParser(MZTabParserContext, MZTabColumnFactory, PositionMapping, Metadata, MZTabErrorList) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.parser.SMELineParser

Constructor for SMELineParser.

SMF - de.isas.mztab2.model.SmallMoleculeFeature.PrefixEnum
 
SMF_ID - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn.Stable
 
SMF_ID_REFS - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
 
smfId - de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
smfId(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Builder method for smfId.

smfIdRefs - de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
smfIdRefs(List<Integer>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Builder method for smfIdRefs.

SMFLineParser - Class in uk.ac.ebi.pride.jmztab2.utils.parser


 SMFLineParser class.

SMFLineParser(MZTabParserContext, MZTabColumnFactory, PositionMapping, Metadata, MZTabErrorList) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.parser.SMFLineParser


 Constructor for SMFLineParser.

SMH - de.isas.mztab2.model.SmallMoleculeSummary.HeaderPrefixEnum
 
SMHLineParser - Class in uk.ac.ebi.pride.jmztab2.utils.parser

Parse and validate Small Molecule header line into a MZTabColumnFactory.

SMHLineParser(MZTabParserContext, Metadata) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.parser.SMHLineParser

Constructor for SMHLineParser.

smiles - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
smiles - de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
smiles(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Builder method for smiles.

smiles(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Builder method for smiles.

SMILES - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
 
SMILES - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
 
SML - de.isas.mztab2.model.SmallMoleculeSummary.PrefixEnum
 
SML_ID - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
 
smlId - de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
smlId(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Builder method for smlId.

SMLLineParser - Class in uk.ac.ebi.pride.jmztab2.utils.parser


 SMLLineParser class.

SMLLineParser(MZTabParserContext, MZTabColumnFactory, PositionMapping, Metadata, MZTabErrorList) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.parser.SMLLineParser


 Constructor for SMLLineParser.

software - de.isas.mztab2.model.Metadata.Properties
 
software(List<Software>) - Method in class de.isas.mztab2.model.Metadata

Builder method for software.

Software - Class in de.isas.mztab2.model

Software used to analyze the data and obtain the reported results.

Software() - Constructor for class de.isas.mztab2.model.Software
 
SOFTWARE - uk.ac.ebi.pride.jmztab2.model.MetadataElement
 
SOFTWARE_SETTING - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
 
Software.Properties - Enum in de.isas.mztab2.model

Property enumeration for Software.

SoftwareFormat - Class in de.isas.mztab2.io.formats

Format specification for Software.

SoftwareFormat() - Constructor for class de.isas.mztab2.io.formats.SoftwareFormat
 
SoftwareSerializer - Class in de.isas.mztab2.io.serialization

SoftwareSerializer implementation for Software.

SoftwareSerializer() - Constructor for class de.isas.mztab2.io.serialization.SoftwareSerializer


 Constructor for SoftwareSerializer.

SoftwareSerializer(Class<Software>) - Constructor for class de.isas.mztab2.io.serialization.SoftwareSerializer


 Constructor for SoftwareSerializer.

SoftwareValidator - Class in de.isas.mztab2.io.validators

Validates that the software section is present in metadata and contains at
 least one item.

SoftwareValidator() - Constructor for class de.isas.mztab2.io.validators.SoftwareValidator
 
SoftwareVersion - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant SoftwareVersion

source - de.isas.mztab2.model.Instrument.Properties
 
source(Parameter) - Method in class de.isas.mztab2.model.Instrument

Builder method for source.

species - de.isas.mztab2.model.Sample.Properties
 
species(List<Parameter>) - Method in class de.isas.mztab2.model.Sample

Builder method for species.

Species - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType

Constant Species

SPECTRA_REF - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
 
SpectraIdFormatNotSupported - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant SpectraIdFormatNotSupported

SpectraIdFormatNotValid - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant SpectraIdFormatNotValid

spectraRef - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
spectraRef(List<SpectraRef>) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Builder method for spectraRef.

SpectraRef - Class in de.isas.mztab2.model

Reference to a spectrum in a spectrum file, for example a fragmentation spectrum has been used to support the identification.

SpectraRef - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant SpectraRef

SpectraRef - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant SpectraRef

SpectraRef() - Constructor for class de.isas.mztab2.model.SpectraRef
 
SpectraRef.Properties - Enum in de.isas.mztab2.model

Property enumeration for SpectraRef.

SpectraRefValidator - Class in de.isas.mztab2.io.validators
 
SpectraRefValidator() - Constructor for class de.isas.mztab2.io.validators.SpectraRefValidator
 
SplitList<E> - Class in uk.ac.ebi.pride.jmztab2.model

This is list which each item split by a split char.

SplitList(char) - Constructor for class uk.ac.ebi.pride.jmztab2.model.SplitList

Constructor for SplitList.

StableColumn - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant StableColumn

STANDARDMIX_NEGATIVE_EXPORTPOSITIONLEVEL - de.isas.mztab2.test.utils.ClassPathFile
 
STANDARDMIX_NEGATIVE_EXPORTSPECIESLEVEL - de.isas.mztab2.test.utils.ClassPathFile
 
STANDARDMIX_POSITIVE_EXPORTPOSITIONLEVEL - de.isas.mztab2.test.utils.ClassPathFile
 
STANDARDMIX_POSITIVE_EXPORTSPECIESLEVEL - de.isas.mztab2.test.utils.ClassPathFile
 
starting(Description) - Method in class de.isas.mztab2.test.utils.LogMethodName

Called when JUnit is about to execute the provided method.

StringList - Class in de.isas.mztab2.model

A typed list of strings.

StringList - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant StringList

StringList() - Constructor for class de.isas.mztab2.model.StringList
 
STUDY_VARIABLE - uk.ac.ebi.pride.jmztab2.model.MetadataElement
 
STUDY_VARIABLE_ASSAY_REFS - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
 
STUDY_VARIABLE_AVERAGE_FUNCTION - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
 
STUDY_VARIABLE_DESCRIPTION - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
 
STUDY_VARIABLE_FACTORS - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
 
STUDY_VARIABLE_VARIATION_FUNCTION - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
 
studyVariable - de.isas.mztab2.model.Metadata.Properties
 
studyVariable(List<StudyVariable>) - Method in class de.isas.mztab2.model.Metadata

Builder method for studyVariable.

StudyVariable - Class in de.isas.mztab2.model

Specification of study_variable.

StudyVariable() - Constructor for class de.isas.mztab2.model.StudyVariable
 
StudyVariable.Properties - Enum in de.isas.mztab2.model

Property enumeration for StudyVariable.

StudyVariableFormat - Class in de.isas.mztab2.io.formats

Format specification for StudyVariable.

StudyVariableFormat() - Constructor for class de.isas.mztab2.io.formats.StudyVariableFormat
 
StudyVariableNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant StudyVariableNotDefined

StudyVariableSerializer - Class in de.isas.mztab2.io.serialization

StudyVariableSerializer implementation for StudyVariable.

StudyVariableSerializer() - Constructor for class de.isas.mztab2.io.serialization.StudyVariableSerializer


 Constructor for StudyVariableSerializer.

StudyVariableSerializer(Class<StudyVariable>) - Constructor for class de.isas.mztab2.io.serialization.StudyVariableSerializer


 Constructor for StudyVariableSerializer.

StudyVariableValidator - Class in de.isas.mztab2.io.validators

Validates that the study variable section is present in metadata and is
 linked to all assays and ms runs.

StudyVariableValidator() - Constructor for class de.isas.mztab2.io.validators.StudyVariableValidator
 
SubstituteIdentifier - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant SubstituteIdentifier

symmetricDifference(Set<T>, Set<T>) - Static method in class de.isas.mztab2.cvmapping.SetOperations

Returns the symmetric set difference
 (union(complement(a,b),complement(b,a))) on a
 and b.





T

TAB - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant TAB='   '

TAB_STRING - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant TABs=""+'       '

termAccession - Variable in class info.psidev.cvmapping.CvTerm
 
termName - Variable in class info.psidev.cvmapping.CvTerm
 
THEOR_NEUTRAL_MASS - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
 
THEORETICAL_MASS_TO_CHARGE - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
 
theoreticalMassToCharge - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
theoreticalMassToCharge(Double) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Builder method for theoreticalMassToCharge.

theoreticalNeutralMass - de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
theoreticalNeutralMass(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Builder method for theoreticalNeutralMass.

tissue - de.isas.mztab2.model.Sample.Properties
 
tissue(List<Parameter>) - Method in class de.isas.mztab2.model.Sample

Builder method for tissue.

title - de.isas.mztab2.model.Metadata.Properties
 
title(String) - Method in class de.isas.mztab2.model.Metadata

Builder method for title.

TITLE - uk.ac.ebi.pride.jmztab2.model.MetadataElement
 
toBoolean() - Method in enum uk.ac.ebi.pride.jmztab2.model.MZBoolean

Convert to a native Boolean.

toCapital(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabStringUtils

Translate the string to the first char is upper case, others are lower case.

toDataSection(Section) - Static method in enum uk.ac.ebi.pride.jmztab2.model.Section

Translate the section to corresponding data section.

toErrorLevel(CvMappingRule.RequirementLevel) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils

Maps the provided requirement level to the corresponding MZTabErrorType.Level.

toHeaderSection(Section) - Static method in enum uk.ac.ebi.pride.jmztab2.model.Section

Translate the section to corresponding header section.

toList(JXPathContext, String, Class<? extends T>) - Static method in class de.isas.mztab2.cvmapping.JxPathElement

Returns the elements selected by the xpath expression from the provided JXPathContext as a list of the given object type.

toList(Pointer, Class<? extends T>) - Static method in class de.isas.mztab2.cvmapping.JxPathElement

Wrap the provided pointer as a list of the given object type.

toStream(Iterator<? extends T>) - Static method in class de.isas.mztab2.cvmapping.JxPathElement

Wraps the provided typed iterator into a stream, based on Spliterators.

toStream(Iterator, Class<? extends T>) - Static method in class de.isas.mztab2.cvmapping.JxPathElement

Creates a typed stream from an untyped (pre Java 6) iterator.

toStream(Pointer, Class<? extends T>) - Static method in class de.isas.mztab2.cvmapping.JxPathElement

Wrap the provided pointer as a stream of the given object type.

toString() - Method in enum de.isas.mztab2.model.Assay.Properties
 
toString() - Method in class de.isas.mztab2.model.Assay
 
toString() - Method in enum de.isas.mztab2.model.ColumnParameterMapping.Properties
 
toString() - Method in class de.isas.mztab2.model.ColumnParameterMapping
 
toString() - Method in enum de.isas.mztab2.model.Comment.PrefixEnum
 
toString() - Method in enum de.isas.mztab2.model.Comment.Properties
 
toString() - Method in class de.isas.mztab2.model.Comment
 
toString() - Method in enum de.isas.mztab2.model.Contact.Properties
 
toString() - Method in class de.isas.mztab2.model.Contact
 
toString() - Method in enum de.isas.mztab2.model.CV.Properties
 
toString() - Method in class de.isas.mztab2.model.CV
 
toString() - Method in enum de.isas.mztab2.model.Database.Properties
 
toString() - Method in class de.isas.mztab2.model.Database
 
toString() - Method in enum de.isas.mztab2.model.Error.Properties
 
toString() - Method in class de.isas.mztab2.model.Error
 
toString() - Method in class de.isas.mztab2.model.IndexedElementImpl
 
toString() - Method in enum de.isas.mztab2.model.Instrument.Properties
 
toString() - Method in class de.isas.mztab2.model.Instrument
 
toString() - Method in enum de.isas.mztab2.model.Metadata.PrefixEnum
 
toString() - Method in enum de.isas.mztab2.model.Metadata.Properties
 
toString() - Method in class de.isas.mztab2.model.Metadata
 
toString() - Method in enum de.isas.mztab2.model.MsRun.Properties
 
toString() - Method in class de.isas.mztab2.model.MsRun
 
toString() - Method in enum de.isas.mztab2.model.MzTab.Properties
 
toString() - Method in class de.isas.mztab2.model.MzTab
 
toString() - Method in enum de.isas.mztab2.model.OptColumnMapping.Properties
 
toString() - Method in class de.isas.mztab2.model.OptColumnMapping
 
toString() - Method in enum de.isas.mztab2.model.Parameter.Properties
 
toString() - Method in class de.isas.mztab2.model.Parameter
 
toString() - Method in enum de.isas.mztab2.model.Publication.Properties
 
toString() - Method in class de.isas.mztab2.model.Publication
 
toString() - Method in enum de.isas.mztab2.model.PublicationItem.Properties
 
toString() - Method in class de.isas.mztab2.model.PublicationItem
 
toString() - Method in enum de.isas.mztab2.model.PublicationItem.TypeEnum
 
toString() - Method in enum de.isas.mztab2.model.Sample.Properties
 
toString() - Method in class de.isas.mztab2.model.Sample
 
toString() - Method in enum de.isas.mztab2.model.SampleProcessing.Properties
 
toString() - Method in class de.isas.mztab2.model.SampleProcessing
 
toString() - Method in enum de.isas.mztab2.model.SmallMoleculeEvidence.HeaderPrefixEnum
 
toString() - Method in enum de.isas.mztab2.model.SmallMoleculeEvidence.PrefixEnum
 
toString() - Method in enum de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
toString() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence
 
toString() - Method in enum de.isas.mztab2.model.SmallMoleculeFeature.HeaderPrefixEnum
 
toString() - Method in enum de.isas.mztab2.model.SmallMoleculeFeature.PrefixEnum
 
toString() - Method in enum de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
toString() - Method in class de.isas.mztab2.model.SmallMoleculeFeature
 
toString() - Method in enum de.isas.mztab2.model.SmallMoleculeSummary.HeaderPrefixEnum
 
toString() - Method in enum de.isas.mztab2.model.SmallMoleculeSummary.PrefixEnum
 
toString() - Method in enum de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
toString() - Method in class de.isas.mztab2.model.SmallMoleculeSummary
 
toString() - Method in enum de.isas.mztab2.model.Software.Properties
 
toString() - Method in class de.isas.mztab2.model.Software
 
toString() - Method in enum de.isas.mztab2.model.SpectraRef.Properties
 
toString() - Method in class de.isas.mztab2.model.SpectraRef
 
toString() - Method in class de.isas.mztab2.model.StringList
 
toString() - Method in enum de.isas.mztab2.model.StudyVariable.Properties
 
toString() - Method in class de.isas.mztab2.model.StudyVariable
 
toString() - Method in enum de.isas.mztab2.model.Uri.Properties
 
toString() - Method in class de.isas.mztab2.model.Uri
 
toString() - Method in enum de.isas.mztab2.model.ValidationMessage.CategoryEnum
 
toString() - Method in enum de.isas.mztab2.model.ValidationMessage.MessageTypeEnum
 
toString() - Method in enum de.isas.mztab2.model.ValidationMessage.Properties
 
toString() - Method in class de.isas.mztab2.model.ValidationMessage
 
toString() - Method in enum uk.ac.ebi.pride.jmztab2.model.AbundanceColumn.Field
 
toString() - Method in enum uk.ac.ebi.pride.jmztab2.model.MetadataElement
toString() - Method in enum uk.ac.ebi.pride.jmztab2.model.MetadataProperty
toString() - Method in enum uk.ac.ebi.pride.jmztab2.model.MZBoolean
toString() - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumn
toString() - Method in class uk.ac.ebi.pride.jmztab2.model.SplitList
toString() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError



 Code: Unique number for error/warn Category: Currently, there are three
 types of messages: Format, Logical Original: Message expression pattern.
 "{?}"

toString() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList

Print error list to string.

toString() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType

Code: Unique number for error/warn
 Category: Currently, there are three types of messages: Format, Logical
 Original: Message expression pattern. "{?}"

toString(CvMappingRule) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils

Creates a string representation of a mapping rule.

toString(List<CvTerm>) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils
 
toUpper() - Method in enum de.isas.mztab2.model.Assay.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.ColumnParameterMapping.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Comment.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Contact.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.CV.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Database.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Error.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Instrument.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Metadata.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.MsRun.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.MzTab.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.OptColumnMapping.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Parameter.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Publication.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.PublicationItem.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Sample.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.SampleProcessing.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Software.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.SpectraRef.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.StudyVariable.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Uri.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.ValidationMessage.Properties
 
toValidationMessage() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError
 
translateCommaToTab(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils

locate param label [label, accession, name, value], translate ',' to '\t'

translateLastToTab(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils


 translateLastToTab.

translateMinusInCVtoUnicode(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils


 translateMinusInCVtoUnicode.

translateMinusToTab(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils


 translateMinusToTab.

translateMinusToUnicode(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils

Solve the conflict about minus char between modification position and
 CHEMMOD charge.

translateTabToComma(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils

solve the conflict about comma char which used in split modification and
 split cv param components.

translateTabToMinus(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils

solve the conflict about comma char which used in split modification and
 split cv param components.

translateUnicodeCVTermMinus(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils


 translateUnicodeCVTermMinus.

translateUnicodeToMinus(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabUtils

Solve the conflict about minus char between modification position and
 CHEMMOD charge.

True - uk.ac.ebi.pride.jmztab2.model.MZBoolean
 
type - de.isas.mztab2.model.PublicationItem.Properties
 
type(PublicationItem.TypeEnum) - Method in class de.isas.mztab2.model.PublicationItem

Builder method for type.

typedIter(Iterator, Class<? extends T>) - Static method in class de.isas.mztab2.cvmapping.JxPathElement

Creates a typed iterator from an untyped (pre Java 6) iterator.





U

uk.ac.ebi.pride.jmztab2 - package uk.ac.ebi.pride.jmztab2

This package contains jmzTab-M model and utility classes that were adapted from the original jmzTab implementation.

uk.ac.ebi.pride.jmztab2.model - package 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 - package uk.ac.ebi.pride.jmztab2.utils

This package contains the property file mapping for mzTab-M's validation messages.

uk.ac.ebi.pride.jmztab2.utils.errors - package uk.ac.ebi.pride.jmztab2.utils.errors

This package contains error type definitions and related classes used during mzTab validation.

uk.ac.ebi.pride.jmztab2.utils.parser - package uk.ac.ebi.pride.jmztab2.utils.parser

This package contains text file line parser implementations for the mzTab-M document sections.

UndefinedStudyVariableNameOnceOnly - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant UndefinedStudyVariableNameOnceOnly

union(Set<T>, Set<T>) - Static method in class de.isas.mztab2.cvmapping.SetOperations

Returns the union (a+b) of a and b.

UnknownRefId - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant UnknownRefId

uri - de.isas.mztab2.model.CV.Properties
 
uri - de.isas.mztab2.model.Database.Properties
 
uri - de.isas.mztab2.model.Metadata.Properties
 
uri - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
uri - de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
uri(String) - Method in class de.isas.mztab2.model.CV

Builder method for uri.

uri(String) - Method in class de.isas.mztab2.model.Database

Builder method for uri.

uri(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Builder method for uri.

uri(List<Uri>) - Method in class de.isas.mztab2.model.Metadata

Builder method for uri.

uri(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Builder method for uri.

Uri - Class in de.isas.mztab2.model

A URI pointing to the file’s source data (e.g., a MetaboLights records) or an external file with more details about the study design.

Uri() - Constructor for class de.isas.mztab2.model.Uri
 
URI - de.isas.mztab2.model.PublicationItem.TypeEnum
 
URI - uk.ac.ebi.pride.jmztab2.model.MetadataElement
 
URI - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
 
URI - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
 
URI - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant URI

Uri.Properties - Enum in de.isas.mztab2.model

Property enumeration for Uri.

UriConverter - Class in de.isas.mztab2.io.serialization

Converter from Uri to String.

UriConverter() - Constructor for class de.isas.mztab2.io.serialization.UriConverter
 
UriFormat - Class in de.isas.mztab2.io.formats

Format specification for Uri.

UriFormat() - Constructor for class de.isas.mztab2.io.formats.UriFormat
 
UriSerializer - Class in de.isas.mztab2.io.serialization


 UriSerializer implementation for Uri.

UriSerializer() - Constructor for class de.isas.mztab2.io.serialization.UriSerializer


 Constructor for UriSerializer.

UriSerializer(Class<Uri>) - Constructor for class de.isas.mztab2.io.serialization.UriSerializer


 Constructor for UriSerializer.

URL - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant URL

useTerm - Variable in class info.psidev.cvmapping.CvTerm
 
useTermName - Variable in class info.psidev.cvmapping.CvTerm
 




V

validate(MzTab) - Method in class de.isas.lipidomics.mztab2.validation.MzTabValidator
 
validate(MzTab) - Method in class de.isas.mztab2.io.MzTabValidatingWriter.WriteAndParseValidator
 
validate(MzTab) - Method in class de.isas.mztab2.validation.CvDefinitionValidationHandler
 
validate(MzTab) - Method in class de.isas.mztab2.validation.CvMappingValidator
 
validate(MzTab) - Method in class de.isas.mztab2.validation.MzTabBeanValidator


 validate.

validate(MzTab, ValidationMessage.MessageTypeEnum, Validator<MzTab>...) - Static method in class de.isas.lipidomics.mztab2.validation.MzTabValidator

Validate the given mzTab object, filtering messages that are of a lower
 level than the given one.

validate(T) - Method in interface de.isas.lipidomics.mztab2.validation.Validator


 validate.

validateLine(int, MZTabParserContext, IMZTabColumn, String, List<SpectraRef>) - Method in class de.isas.mztab2.io.validators.SpectraRefValidator
 
validateLine(int, MZTabParserContext, IMZTabColumn, String, T) - Method in interface de.isas.mztab2.io.validators.FieldValidator

Validate the given object of type T, using the provided parser context and column to
 check the state of not yet completely parsed and constructed mzTab hierarchy.

validatePattern(Pattern, String, int, IMZTabColumn, String, MsRun) - Method in class de.isas.mztab2.io.validators.SpectraRefValidator
 
validateRefine(Metadata, MZTabParserContext) - Method in class de.isas.mztab2.io.validators.AssayValidator
 
validateRefine(Metadata, MZTabParserContext) - Method in class de.isas.mztab2.io.validators.CvValidator
 
validateRefine(Metadata, MZTabParserContext) - Method in class de.isas.mztab2.io.validators.DatabaseValidator
 
validateRefine(Metadata, MZTabParserContext) - Method in class de.isas.mztab2.io.validators.MsRunValidator
 
validateRefine(Metadata, MZTabParserContext) - Method in class de.isas.mztab2.io.validators.MzTabIdValidator
 
validateRefine(Metadata, MZTabParserContext) - Method in class de.isas.mztab2.io.validators.MzTabVersionValidator
 
validateRefine(Metadata, MZTabParserContext) - Method in class de.isas.mztab2.io.validators.QuantificationMethodValidator
 
validateRefine(Metadata, MZTabParserContext) - Method in class de.isas.mztab2.io.validators.SmallMoleculeFeatureQuantificationUnitValidator
 
validateRefine(Metadata, MZTabParserContext) - Method in class de.isas.mztab2.io.validators.SmallMoleculeIdConfidenceMeasureValidator
 
validateRefine(Metadata, MZTabParserContext) - Method in class de.isas.mztab2.io.validators.SmallMoleculeQuantificationUnitValidator
 
validateRefine(Metadata, MZTabParserContext) - Method in class de.isas.mztab2.io.validators.SoftwareValidator
 
validateRefine(Metadata, MZTabParserContext) - Method in class de.isas.mztab2.io.validators.StudyVariableValidator
 
validateRefine(T, MZTabParserContext) - Method in interface de.isas.mztab2.io.validators.RefiningValidator

Validate the given object of type T, using the provided parser context to
 check state of not yet completely parsed and constructed mzTab hierarchy.

ValidationMessage - Class in de.isas.mztab2.model

ValidationMessage

ValidationMessage() - Constructor for class de.isas.mztab2.model.ValidationMessage
 
ValidationMessage.CategoryEnum - Enum in de.isas.mztab2.model

Gets or Sets category

ValidationMessage.MessageTypeEnum - Enum in de.isas.mztab2.model

Gets or Sets messageType

ValidationMessage.Properties - Enum in de.isas.mztab2.model

Property enumeration for ValidationMessage.

Validator<T> - Interface in de.isas.lipidomics.mztab2.validation


 Validator interface.

value - de.isas.mztab2.model.OptColumnMapping.Properties
 
value - de.isas.mztab2.model.Parameter.Properties
 
value - de.isas.mztab2.model.Uri.Properties
 
value() - Method in enum info.psidev.cvmapping.CvMappingRule.CvTermsCombinationLogic
 
value() - Method in enum info.psidev.cvmapping.CvMappingRule.RequirementLevel
 
value(String) - Method in class de.isas.mztab2.model.OptColumnMapping

Builder method for value.

value(String) - Method in class de.isas.mztab2.model.Parameter

Builder method for value.

value(String) - Method in class de.isas.mztab2.model.Uri

Builder method for value.

valueOf(String) - Static method in enum de.isas.mztab2.cvmapping.ParameterComparisonResult

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Assay.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.ColumnParameterMapping.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Comment.PrefixEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Comment.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Contact.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.CV.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Database.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Error.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Instrument.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Metadata.PrefixEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Metadata.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.MsRun.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.MzTab.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.OptColumnMapping.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Parameter.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Publication.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.PublicationItem.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.PublicationItem.TypeEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Sample.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SampleProcessing.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeEvidence.HeaderPrefixEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeEvidence.PrefixEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeEvidence.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeFeature.HeaderPrefixEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeFeature.PrefixEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeFeature.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeSummary.HeaderPrefixEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeSummary.PrefixEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeSummary.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Software.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SpectraRef.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.StudyVariable.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Uri.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.ValidationMessage.CategoryEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.ValidationMessage.MessageTypeEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.ValidationMessage.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.test.utils.ClassPathFile

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum info.psidev.cvmapping.CvMappingRule.CvTermsCombinationLogic

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum info.psidev.cvmapping.CvMappingRule.RequirementLevel

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pride.jmztab2.model.AbundanceColumn.Field

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pride.jmztab2.model.MetadataElement

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pride.jmztab2.model.MetadataProperty

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pride.jmztab2.model.MZBoolean

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pride.jmztab2.model.Section

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn.Stable

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Category

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Level

Returns the enum constant of this type with the specified name.

values() - Static method in enum de.isas.mztab2.cvmapping.ParameterComparisonResult

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Assay.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.ColumnParameterMapping.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Comment.PrefixEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Comment.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Contact.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.CV.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Database.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Error.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Instrument.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Metadata.PrefixEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Metadata.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.MsRun.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.MzTab.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.OptColumnMapping.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Parameter.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Publication.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.PublicationItem.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.PublicationItem.TypeEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Sample.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SampleProcessing.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SmallMoleculeEvidence.HeaderPrefixEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SmallMoleculeEvidence.PrefixEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SmallMoleculeEvidence.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SmallMoleculeFeature.HeaderPrefixEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SmallMoleculeFeature.PrefixEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SmallMoleculeFeature.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SmallMoleculeSummary.HeaderPrefixEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SmallMoleculeSummary.PrefixEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SmallMoleculeSummary.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Software.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SpectraRef.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.StudyVariable.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Uri.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.ValidationMessage.CategoryEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.ValidationMessage.MessageTypeEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.ValidationMessage.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.test.utils.ClassPathFile

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum info.psidev.cvmapping.CvMappingRule.CvTermsCombinationLogic

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum info.psidev.cvmapping.CvMappingRule.RequirementLevel

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum uk.ac.ebi.pride.jmztab2.model.AbundanceColumn.Field

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum uk.ac.ebi.pride.jmztab2.model.MetadataElement

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum uk.ac.ebi.pride.jmztab2.model.MetadataProperty

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum uk.ac.ebi.pride.jmztab2.model.MZBoolean

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum uk.ac.ebi.pride.jmztab2.model.Section

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn.Stable

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Category

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Level

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.PositionMapping

values.

VariableMod - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant VariableMod

variationFunction - de.isas.mztab2.model.StudyVariable.Properties
 
variationFunction(Parameter) - Method in class de.isas.mztab2.model.StudyVariable

Builder method for variationFunction.

version - de.isas.mztab2.model.CV.Properties
 
version - de.isas.mztab2.model.Database.Properties
 
version(String) - Method in class de.isas.mztab2.model.CV

Builder method for version.

version(String) - Method in class de.isas.mztab2.model.Database

Builder method for version.

VERSION_MZTAB_M - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant VERSION="2.0.0-M"





W

Warn - uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Level
 
WARN - de.isas.mztab2.model.ValidationMessage.MessageTypeEnum
 
withName(String) - Method in class uk.ac.ebi.pride.jmztab2.model.OptColumnMappingBuilder.GlobalOptColumnMappingBuilder
 
withName(String) - Method in class uk.ac.ebi.pride.jmztab2.model.OptColumnMappingBuilder.IndexedElementOptColumnMappingBuilder
 
withParameter(Parameter) - Method in class uk.ac.ebi.pride.jmztab2.model.OptColumnMappingBuilder.GlobalOptColumnMappingBuilder
 
withParameter(Parameter) - Method in class uk.ac.ebi.pride.jmztab2.model.OptColumnMappingBuilder.IndexedElementOptColumnMappingBuilder
 
withPostValidator(Validator<MzTab>) - Method in class de.isas.mztab2.validation.CvMappingValidator

Add the provided validator implementation to the list of validators that run last.

withPreValidator(Validator<MzTab>) - Method in class de.isas.mztab2.validation.CvMappingValidator

Add the provided validator implementation to the list of validators that run first.

write(OutputStreamWriter, MzTab) - Method in class de.isas.mztab2.io.MzTabNonValidatingWriter


 Write the mzTab object to the provided output stream writer.

write(OutputStreamWriter, MzTab) - Method in class de.isas.mztab2.io.MzTabValidatingWriter
 
write(OutputStreamWriter, MzTab) - Method in interface de.isas.mztab2.io.MzTabWriter


 Write the mzTab object to the provided output stream writer.

write(Path, MzTab) - Method in class de.isas.mztab2.io.MzTabNonValidatingWriter


 Write the mzTab object to the provided path.

write(Path, MzTab) - Method in class de.isas.mztab2.io.MzTabValidatingWriter
 
write(Path, MzTab) - Method in interface de.isas.mztab2.io.MzTabWriter


 Write the mzTab object to the provided path file.

WriteAndParseValidator(OutputStream, MZTabErrorType.Level, int) - Constructor for class de.isas.mztab2.io.MzTabValidatingWriter.WriteAndParseValidator

Create a new instance of this validator.

writeAsNumberArray(String, JsonGenerator, List<? extends Number>) - Static method in class de.isas.mztab2.io.serialization.Serializers


 writeAsNumberArray.

writeAsNumberArray(IMZTabColumn, JsonGenerator, List<? extends Number>) - Static method in class de.isas.mztab2.io.serialization.Serializers


 writeAsNumberArray.

writeAsStringArray(JsonGenerator, List<String>) - Static method in class de.isas.mztab2.io.serialization.Serializers


 writeAsStringArray.

writeAsStringArray(String, JsonGenerator, List<String>) - Static method in class de.isas.mztab2.io.serialization.Serializers


 writeAsStringArray.

writeAsStringArray(IMZTabColumn, JsonGenerator, List<String>) - Static method in class de.isas.mztab2.io.serialization.Serializers


 writeAsStringArray.

writeIndexedDoubles(String, JsonGenerator, List<Double>) - Static method in class de.isas.mztab2.io.serialization.Serializers


 writeIndexedValues.

writeNumber(JsonGenerator, Double) - Static method in class de.isas.mztab2.io.serialization.Serializers


 writeNumber.

writeNumber(JsonGenerator, Integer) - Static method in class de.isas.mztab2.io.serialization.Serializers


 writeNumber.

writeNumber(String, JsonGenerator, Double) - Static method in class de.isas.mztab2.io.serialization.Serializers


 writeNumber.

writeNumber(String, JsonGenerator, Integer) - Static method in class de.isas.mztab2.io.serialization.Serializers


 writeNumber.

writeNumber(IMZTabColumn, JsonGenerator, Double) - Static method in class de.isas.mztab2.io.serialization.Serializers


 writeNumber.

writeNumber(IMZTabColumn, JsonGenerator, Integer) - Static method in class de.isas.mztab2.io.serialization.Serializers


 writeNumber.

writeObject(String, JsonGenerator, SerializerProvider, Object) - Static method in class de.isas.mztab2.io.serialization.Serializers


 writeObject.

writeObject(IMZTabColumn, JsonGenerator, SerializerProvider, Object) - Static method in class de.isas.mztab2.io.serialization.Serializers


 writeObject.

writeOptColumnMappings(List<OptColumnMapping>, JsonGenerator, SerializerProvider) - Static method in class de.isas.mztab2.io.serialization.Serializers


 writeOptColumnMappings.

writeString(String, JsonGenerator, String) - Static method in class de.isas.mztab2.io.serialization.Serializers


 writeString.

writeString(IMZTabColumn, JsonGenerator, String) - Static method in class de.isas.mztab2.io.serialization.Serializers


 writeString.





X

XOR - info.psidev.cvmapping.CvMappingRule.CvTermsCombinationLogic
 
XorValidationHandler - Class in de.isas.mztab2.validation.handlers

Implements 'XOR' logic, meaning mutually exclusive alternative possible terms or term roots for
 an object are allowed.

XorValidationHandler() - Constructor for class de.isas.mztab2.validation.handlers.XorValidationHandler
 




Z

ZipResourceExtractionException - Exception in de.isas.mztab2.test.utils

This runtime exception is thrown when IO exceptions are encountered within
 the ZipResourceExtractor test rule.

ZipResourceExtractionException() - Constructor for exception de.isas.mztab2.test.utils.ZipResourceExtractionException
 
ZipResourceExtractionException(String) - Constructor for exception de.isas.mztab2.test.utils.ZipResourceExtractionException
 
ZipResourceExtractionException(String, Throwable) - Constructor for exception de.isas.mztab2.test.utils.ZipResourceExtractionException
 
ZipResourceExtractionException(String, Throwable, boolean, boolean) - Constructor for exception de.isas.mztab2.test.utils.ZipResourceExtractionException
 
ZipResourceExtractionException(Throwable) - Constructor for exception de.isas.mztab2.test.utils.ZipResourceExtractionException
 
ZipResourceExtractor - Class in de.isas.mztab2.test.utils


 ZipResourceExtractor class.


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