Uses of Class
uk.ac.ebi.arrayexpress2.magetab.datamodel.MAGETABInvestigation

Packages that use MAGETABInvestigation

Package	Description
uk.ac.ebi.arrayexpress2.magetab.converter
uk.ac.ebi.arrayexpress2.magetab.handler	Handler classes, interfaces and utilities for interpreting MAGE-TAB documents and converting to objects in the datamodel and ArrayExpress 2 domain model.
uk.ac.ebi.arrayexpress2.magetab.handler.visitor	Visitor classes that can be used to visit and inspect MAGE-TAB handlers.
uk.ac.ebi.arrayexpress2.magetab.parser	Parser classes for parsing MAGE-TAB aspects.
uk.ac.ebi.arrayexpress2.magetab.utils	Some common utility classes for parsing, validating and interpreting MAGE-TAB files.
uk.ac.ebi.arrayexpress2.magetab.validator	Validator classes for validating the MAGE-TAB datamodel during parsing.

Uses of MAGETABInvestigation in uk.ac.ebi.arrayexpress2.magetab.converter

Methods in uk.ac.ebi.arrayexpress2.magetab.converter with parameters of type MAGETABInvestigation

Modifier and Type	Method and Description
void	MAGETABConverter.convert(MAGETABInvestigation investigation, O outputResource)
void	MAGETABConverter.convert(MAGETABInvestigation investigation, O outputResource, ExecutorService service)

Uses of MAGETABInvestigation in uk.ac.ebi.arrayexpress2.magetab.handler

Methods in uk.ac.ebi.arrayexpress2.magetab.handler with parameters of type MAGETABInvestigation

Modifier and Type	Method and Description
protected abstract boolean	MAGETABValidateHandler.canValidateData(MAGETABInvestigation investigation) Performs specific checks on the MAGETABInvestigation to determine if this handler can validate it.
void	MAGETABValidateHandler.validate(MAGETABInvestigation data) Invoke this validate handler.
protected abstract void	MAGETABValidateHandler.validateData(MAGETABInvestigation data) Performs the unit of work to validate the data.

Uses of MAGETABInvestigation in uk.ac.ebi.arrayexpress2.magetab.handler.visitor

Constructors in uk.ac.ebi.arrayexpress2.magetab.handler.visitor with parameters of type MAGETABInvestigation

Constructor and Description
LocationTracker(MAGETABInvestigation investigation) Deprecated.

Uses of MAGETABInvestigation in uk.ac.ebi.arrayexpress2.magetab.parser

Methods in uk.ac.ebi.arrayexpress2.magetab.parser that return MAGETABInvestigation

Modifier and Type	Method and Description
MAGETABInvestigation	MAGETABParser.parse(File idfFile)
MAGETABInvestigation	MAGETABParser.parse(InputStream idfIn)
MAGETABInvestigation	MAGETABParser.parse(InputStream idfIn, MAGETABInvestigation investigation)
MAGETABInvestigation	MAGETABParser.parse(InputStream idfIn, MAGETABInvestigation investigation, ExecutorService service)
MAGETABInvestigation	MAGETABParser.parse(URL idfURL)

Methods in uk.ac.ebi.arrayexpress2.magetab.parser that return types with arguments of type MAGETABInvestigation

Modifier and Type	Method and Description
Converter<MAGETABInvestigation,O>	MAGETABParser.getConverter() Get the currently configured converter for this parser.
Validator<MAGETABInvestigation>	MAGETABParser.getValidator() Get the currently configured validator for this parser.

Methods in uk.ac.ebi.arrayexpress2.magetab.parser with parameters of type MAGETABInvestigation

Modifier and Type	Method and Description
MAGETABInvestigation	MAGETABParser.parse(InputStream idfIn, MAGETABInvestigation investigation)
MAGETABInvestigation	MAGETABParser.parse(InputStream idfIn, MAGETABInvestigation investigation, ExecutorService service)
protected void	MAGETABParser.readIDF(InputStream idfIn, MAGETABInvestigation investigation, boolean isMerged, ExecutorService service, uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABParser.ProgressFlag flag)

Constructor parameters in uk.ac.ebi.arrayexpress2.magetab.parser with type arguments of type MAGETABInvestigation

Constructor and Description
MAGETABParser(Converter<MAGETABInvestigation,O> converter, O... outputResources) Create a parser that performs conversion using the supplied Converter to convert the MAGETABInvestigation that results from the parse into objects in the given object model.
MAGETABParser(Validator<MAGETABInvestigation> validator) Create a parser that performs validation using the supplied Validator.
MAGETABParser(Validator<MAGETABInvestigation> validator, Converter<MAGETABInvestigation,O> converter, O... outputResources) Create a parser that performs validation using the supplied Validator and conversion using the supplied Converter.
MAGETABParser(Validator<MAGETABInvestigation> validator, Converter<MAGETABInvestigation,O> converter, O... outputResources) Create a parser that performs validation using the supplied Validator and conversion using the supplied Converter.

Uses of MAGETABInvestigation in uk.ac.ebi.arrayexpress2.magetab.utils

Methods in uk.ac.ebi.arrayexpress2.magetab.utils with parameters of type MAGETABInvestigation

Modifier and Type	Method and Description
static Map<String,String>	MAGETABUtils.resolveExperimentFactorTypes(MAGETABInvestigation investigation, HybridizationNode hybNode) Resolves all the factor value types (the typing information in square brackets - so "foo" in Factor Value[foo]) in the provided hybridization node and maps them to the actual experiment factor type declared in the IDF.

Uses of MAGETABInvestigation in uk.ac.ebi.arrayexpress2.magetab.validator

Methods in uk.ac.ebi.arrayexpress2.magetab.validator with parameters of type MAGETABInvestigation

Modifier and Type	Method and Description
void	MAGETABValidator.validate(MAGETABInvestigation investigation)
void	MAGETABValidator.validate(MAGETABInvestigation investigation, ExecutorService service)