Index (jmztabm-io 1.0.5 API)

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

A

ABUNDANCE_ASSAY - uk.ac.ebi.pride.jmztab2.model.AbundanceColumn.Field
ABUNDANCE_STUDY_VARIABLE - uk.ac.ebi.pride.jmztab2.model.AbundanceColumn.Field
ABUNDANCE_VARIATION_STUDY_VARIABLE - uk.ac.ebi.pride.jmztab2.model.AbundanceColumn.Field
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.Field - Enum in uk.ac.ebi.pride.jmztab2.model
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, optionalColumnMapping and columnMapping.
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.
addAssayMsRun(Metadata, Integer, MsRun) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add assay[id]-ms_run_ref into metadata.
addAssaySample(Metadata, Integer, Sample) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add assay[id]-sample_ref into metadata.
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
addContactName(Metadata, Integer, String) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add contact[id]-name.
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.
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.
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.
addIdConfidenceMeasureColumn(Parameter, Integer, Class) - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory: addIdConfidenceMeasureColumn.
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
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
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.
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.
addMsRunLocation(Metadata, Integer, URI) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add ms_run[id]-location into metadata.
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 optionalColumnMapping and columnMapping.
addOptionalColumn(String, Class) - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory: Add global OptionColumn into optionalColumnMapping and 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 optionalColumnMapping and 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 optionalColumnMapping and columnMapping.
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.
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].
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.
addSampleProcessing(Metadata, Integer, List<Parameter>) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext: Add a sample_processing[id].
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.
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.
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.
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.
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.
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.
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.
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
asMap(Object) - Static method in class de.isas.mztab2.io.serialization.Serializers: asMap.
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
AssayFormat - Class in de.isas.mztab2.io.formats: Format specification for Assay.
AssayFormat() - Constructor for class de.isas.mztab2.io.formats.AssayFormat
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

B

BEST_ID_CONFIDENCE_MEASURE - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
BEST_ID_CONFIDENCE_VALUE - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
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

camelCaseToUnderscoreLowerCase(String) - Static method in class de.isas.mztab2.io.serialization.Serializers: camelCaseToUnderscoreLowerCase.
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(IndexedElement) - 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.
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
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.
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 - 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
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.
Comment - uk.ac.ebi.pride.jmztab2.model.Section
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
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
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.
CUSTOM - uk.ac.ebi.pride.jmztab2.model.MetadataElement
CV - uk.ac.ebi.pride.jmztab2.model.MetadataElement
CV - Static variable in class uk.ac.ebi.pride.jmztab2.model.ParameterOptionColumn: Constant CV="cv_"
CV_FULL_NAME - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
CV_LABEL - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
CV_URI - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
CV_VERSION - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
CvFormat - Class in de.isas.mztab2.io.formats: Format specification for CV.
CvFormat() - Constructor for class de.isas.mztab2.io.formats.CvFormat
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.
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 - 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
DatabaseFormat - Class in de.isas.mztab2.io.formats: Format specification for Database.
DatabaseFormat() - Constructor for class de.isas.mztab2.io.formats.DatabaseFormat
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.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.
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
DERIVATIZED_FORM - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
DESCRIPTION - uk.ac.ebi.pride.jmztab2.model.MetadataElement

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.
equals(Object) - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumn
errorList - Variable in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabLineParser
EVIDENCE_INPUT_ID - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
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
EXTERNAL_STUDY_URI - uk.ac.ebi.pride.jmztab2.model.MetadataElement

F

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.
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.
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.
forGlobal() - Static method in class uk.ac.ebi.pride.jmztab2.model.OptColumnMappingBuilder: Configure the builder for a global type column.
forIndexedElement(IndexedElement) - Static method in class uk.ac.ebi.pride.jmztab2.model.OptColumnMappingBuilder: Configure the builder for an object reference (indexed element) type column.
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.
fromIndexToOrder(Integer) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabHeaderLineParser: fromIndexToOrder.

G

get(Integer) - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.PositionMapping: get.
getColumnMapping() - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory: Get all columns in the factory.
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
getComment() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.COMLineParser: getComment.
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.
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.
getErrorList() - Method in class de.isas.mztab2.io.MzTabFileParser: Getter for the field errorList.
getFactory() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabHeaderLineParser: Getter for the field factory.
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(IndexedElement, 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(IndexedElement, 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}.
getInstance(Section) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory: Retrieves the MZTabColumnFactory accordingly to the section
getLevel() - Method in enum uk.ac.ebi.pride.jmztab2.model.Section: Getter for the field level.
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.
getMetadata() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.MTDLineParser: Getter for the field metadata.
getMZTabFile() - Method in class de.isas.mztab2.io.MzTabFileParser: getMZTabFile.
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.
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.
getPrefix() - Method in enum uk.ac.ebi.pride.jmztab2.model.Section: Getter for the field prefix.
getPropertyNames(Object) - Static method in class de.isas.mztab2.io.serialization.Serializers: getPropertyNames.
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(Object, Integer) - Static method in class de.isas.mztab2.io.serialization.Serializers: getReference.
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.
getValidationMessagesForLevel(Optional<List<ValidationMessage>>, ValidationMessage.MessageTypeEnum) - Static method in class de.isas.mztab2.io.MzTabValidatingWriter: Returns all validation messages ONLY at the given level.
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

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

I

ID_CONFIDENCE_MEASURE - uk.ac.ebi.pride.jmztab2.model.MetadataElement
IDENTIFICATION_METHOD - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
IMZTabColumn - Interface in uk.ac.ebi.pride.jmztab2.model: IMZTabColumn interface.
INCHI - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
INCHI - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
IndexedElementOptColumnMappingBuilder(IndexedElement) - 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.
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
InstrumentFormat - Class in de.isas.mztab2.io.formats: Format specification for Instrument.
InstrumentFormat() - Constructor for class de.isas.mztab2.io.formats.InstrumentFormat
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.
IOptColumnMappingBuilder - Interface in uk.ac.ebi.pride.jmztab2.model: Interface for optional column mapping builders.
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.parser.PositionMapping: isEmpty.
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.
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 - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn.Stable
items - Variable in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabLineParser: based on TAB char to split raw line into String array.

K

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

L

line - Variable in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabLineParser
lineNumber - Variable in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabLineParser
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.

M

mapping - Variable in class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser
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 - uk.ac.ebi.pride.jmztab2.model.Section
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.
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
MsRunFormat - Class in de.isas.mztab2.io.formats: Format specification for MsRun.
MsRunFormat() - Constructor for class de.isas.mztab2.io.formats.MsRunFormat
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
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.
MZBoolean - Enum in uk.ac.ebi.pride.jmztab2.model: In mzTab, using 0-false, 1-true to express the boolean value.
MZTAB - uk.ac.ebi.pride.jmztab2.model.MetadataElement
MZTAB_ID - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
MZTAB_VERSION - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
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.
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.
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.
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.
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
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.
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

O

OPT - Static variable in class uk.ac.ebi.pride.jmztab2.model.OptionColumn: Constant OPT="opt"
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.
OptionColumn - Class in uk.ac.ebi.pride.jmztab2.model: Additional columns can be added to the end of the protein table.
OptionColumn(IndexedElement, String, Class, int) - Constructor for class uk.ac.ebi.pride.jmztab2.model.OptionColumn: Create a optional column.

P

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(IndexedElement, 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}.
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.
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.
Peptide - uk.ac.ebi.pride.jmztab2.model.Section
Peptide_Header - uk.ac.ebi.pride.jmztab2.model.Section
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.
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
PSM - uk.ac.ebi.pride.jmztab2.model.Section
PSM_Header - uk.ac.ebi.pride.jmztab2.model.Section
PUBLICATION - uk.ac.ebi.pride.jmztab2.model.MetadataElement
PublicationFormat - Class in de.isas.mztab2.io.formats: Format specification for Publication.
PublicationFormat() - Constructor for class de.isas.mztab2.io.formats.PublicationFormat
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.
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
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 - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
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.
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.
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
reverse() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.PositionMapping: Exchange key and value to "LogicalPosition, PhysicalPosition".

S

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
SampleFormat - Class in de.isas.mztab2.io.formats: Format specification for Sample.
SampleFormat() - Constructor for class de.isas.mztab2.io.formats.SampleFormat
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.
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.
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.
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.
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
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
setElement(IndexedElement) - Method in interface uk.ac.ebi.pride.jmztab2.model.IMZTabColumn: Indexed element used in optional column header and logical position definition.
setElement(IndexedElement) - Method in class uk.ac.ebi.pride.jmztab2.model.MZTabColumn: Indexed element used in optional column header and logical position definition.
setElement(IndexedElement) - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn: Indexed element used in optional column header and logical position definition.
setElement(IndexedElement) - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn: Indexed element used in optional column header and logical position definition.
setElement(IndexedElement) - Method in class uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn: Indexed element used in optional column header and logical position definition.
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.
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.
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.
setSplitChar(char) - Method in class uk.ac.ebi.pride.jmztab2.model.SplitList: Setter for the field splitChar.
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.
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.
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.
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.
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
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
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_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
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_ID - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeFeatureColumn.Stable
SMF_ID_REFS - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
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.
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 - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
SMILES - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
SML_ID - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
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 - uk.ac.ebi.pride.jmztab2.model.MetadataElement
SOFTWARE_SETTING - uk.ac.ebi.pride.jmztab2.model.MetadataProperty
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
SPECTRA_REF - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
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.
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
StudyVariableFormat - Class in de.isas.mztab2.io.formats: Format specification for StudyVariable.
StudyVariableFormat() - Constructor for class de.isas.mztab2.io.formats.StudyVariableFormat
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

T

THEOR_NEUTRAL_MASS - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeColumn.Stable
THEORETICAL_MASS_TO_CHARGE - uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn.Stable
TITLE - uk.ac.ebi.pride.jmztab2.model.MetadataElement
toBoolean() - Method in enum uk.ac.ebi.pride.jmztab2.model.MZBoolean: Convert to a native Boolean.
toDataSection(Section) - Static method in enum uk.ac.ebi.pride.jmztab2.model.Section: Translate the section to corresponding data section.
toHeaderSection(Section) - Static method in enum uk.ac.ebi.pride.jmztab2.model.Section: Translate the section to corresponding header section.
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
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

U

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.parser - package uk.ac.ebi.pride.jmztab2.utils.parser: This package contains text file line parser implementations for the mzTab-M document sections.
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
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

V

validate(MzTab) - Method in class de.isas.mztab2.io.MzTabValidatingWriter.WriteAndParseValidator
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.
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.
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() - Method in class uk.ac.ebi.pride.jmztab2.utils.parser.PositionMapping: values.

W

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
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.

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