Uses of Class
uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext

Packages that use MZTabParserContext

Package	Description
de.isas.mztab2.io.validators	This package contains implementations for validation of mzTab-M parts during parsing.
uk.ac.ebi.pride.jmztab2.model	This package contains model classes for mzTab-M structural features like mandatory and optional columns.
uk.ac.ebi.pride.jmztab2.utils.parser	This package contains text file line parser implementations for the mzTab-M document sections.

Uses of MZTabParserContext in de.isas.mztab2.io.validators

Methods in de.isas.mztab2.io.validators with parameters of type MZTabParserContext

Modifier and Type	Method	Description
List<uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError>	AssayValidator.validateRefine(de.isas.mztab2.model.Metadata metadata, MZTabParserContext parserContext)
List<uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError>	CvValidator.validateRefine(de.isas.mztab2.model.Metadata metadata, MZTabParserContext parserContext)
List<uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError>	DatabaseValidator.validateRefine(de.isas.mztab2.model.Metadata metadata, MZTabParserContext parserContext)
default List<uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError>	MetadataValidator.validateRefine(T t, MZTabParserContext parserContext)	Validate the given object of type T, using the provided parser context to check state of not yet completely parsed and constructed mzTab hierarchy.
List<uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError>	MsRunValidator.validateRefine(de.isas.mztab2.model.Metadata metadata, MZTabParserContext parserContext)
List<uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError>	MzTabIdValidator.validateRefine(de.isas.mztab2.model.Metadata metadata, MZTabParserContext parserContext)
List<uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError>	MzTabVersionValidator.validateRefine(de.isas.mztab2.model.Metadata metadata, MZTabParserContext parserContext)
List<uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError>	QuantificationMethodValidator.validateRefine(de.isas.mztab2.model.Metadata metadata, MZTabParserContext parserContext)
List<uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError>	SmallMoleculeFeatureQuantificationUnitValidator.validateRefine(de.isas.mztab2.model.Metadata metadata, MZTabParserContext parserContext)
List<uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError>	SmallMoleculeIdConfidenceMeasureValidator.validateRefine(de.isas.mztab2.model.Metadata metadata, MZTabParserContext parserContext)
List<uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError>	SmallMoleculeQuantificationUnitValidator.validateRefine(de.isas.mztab2.model.Metadata metadata, MZTabParserContext parserContext)
List<uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError>	SoftwareValidator.validateRefine(de.isas.mztab2.model.Metadata metadata, MZTabParserContext parserContext)
List<uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError>	StudyVariableValidator.validateRefine(de.isas.mztab2.model.Metadata metadata, MZTabParserContext parserContext)

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

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

Modifier and Type	Method	Description
static List<de.isas.mztab2.model.SpectraRef>	MZTabUtils.parseSpectraRefList(MZTabParserContext context, de.isas.mztab2.model.Metadata metadata, String target)	Parse a SpectraRef list.

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

Fields in uk.ac.ebi.pride.jmztab2.utils.parser declared as MZTabParserContext

Modifier and Type	Field	Description
protected MZTabParserContext	MZTabLineParser.context

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

Modifier and Type	Method	Description
protected List<de.isas.mztab2.model.SpectraRef>	MZTabDataLineParser.checkSpectraRef(MZTabParserContext context, IMZTabColumn column, String spectraRef)	Check and translate spectraRef string into SpectraRef list.
protected List<de.isas.mztab2.model.SpectraRef>	MZTabDataLineParser.checkSpectraRef(MZTabParserContext context, IMZTabColumn column, String spectraRef, boolean allowNull)	Check and translate spectraRef string into SpectraRef list.

Constructors in uk.ac.ebi.pride.jmztab2.utils.parser with parameters of type MZTabParserContext

Constructor	Description
COMLineParser(MZTabParserContext context)	Constructor for COMLineParser.
MTDLineParser(MZTabParserContext context)	Constructor for MTDLineParser.
MZTabDataLineParser(MZTabParserContext context)	Constructor for MZTabDataLineParser.
MZTabDataLineParser(MZTabParserContext context, MZTabColumnFactory factory, PositionMapping positionMapping, de.isas.mztab2.model.Metadata metadata, uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList errorList)	Generate a mzTab data line parser.
MZTabHeaderLineParser(MZTabParserContext context, MZTabColumnFactory factory, de.isas.mztab2.model.Metadata metadata)	Parse a header line into MZTabColumnFactory structure.
MZTabLineParser(MZTabParserContext context)	Constructor for MZTabLineParser.
SEHLineParser(MZTabParserContext context, de.isas.mztab2.model.Metadata metadata)	Constructor for SEHLineParser.
SFHLineParser(MZTabParserContext context, de.isas.mztab2.model.Metadata metadata)	Constructor for SFHLineParser.
SMELineParser(MZTabParserContext context, MZTabColumnFactory factory, PositionMapping positionMapping, de.isas.mztab2.model.Metadata metadata, uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList errorList)	Constructor for SMELineParser.
SMFLineParser(MZTabParserContext context, MZTabColumnFactory factory, PositionMapping positionMapping, de.isas.mztab2.model.Metadata metadata, uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList errorList)	Constructor for SMFLineParser.
SMHLineParser(MZTabParserContext context, de.isas.mztab2.model.Metadata metadata)	Constructor for SMHLineParser.
SMLLineParser(MZTabParserContext context, MZTabColumnFactory factory, PositionMapping positionMapping, de.isas.mztab2.model.Metadata metadata, uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList errorList)	Constructor for SMLLineParser.