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

Packages that use IDF

Package	Description
uk.ac.ebi.arrayexpress2.magetab.converter
uk.ac.ebi.arrayexpress2.magetab.datamodel	Classes for constructing an in-memory datamodel of the data contained in IDF and SDRF files, as specified by the MAGE-TAB specification.
uk.ac.ebi.arrayexpress2.magetab.datamodel.layout
uk.ac.ebi.arrayexpress2.magetab.handler.idf	IDF specific handler classes.
uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl	Specific, concrete IDF handler implementations.
uk.ac.ebi.arrayexpress2.magetab.parser	Parser classes for parsing MAGE-TAB aspects.
uk.ac.ebi.arrayexpress2.magetab.renderer
uk.ac.ebi.arrayexpress2.magetab.validator	Validator classes for validating the MAGE-TAB datamodel during parsing.

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

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

Modifier and Type	Method and Description
void	IDFConverter.convert(IDF idf, O outputResource)
void	IDFConverter.convert(IDF idf, O outputResource, ExecutorService service)

Uses of IDF in uk.ac.ebi.arrayexpress2.magetab.datamodel

Fields in uk.ac.ebi.arrayexpress2.magetab.datamodel declared as IDF

Modifier and Type	Field and Description
IDF	MAGETABInvestigation.IDF

Uses of IDF in uk.ac.ebi.arrayexpress2.magetab.datamodel.layout

Methods in uk.ac.ebi.arrayexpress2.magetab.datamodel.layout with parameters of type IDF

Modifier and Type	Method and Description
void	IDFLayout.calculateLocations(IDF idf)
void	IDFLayout.calculateUnassignedLocations(IDF idf)
boolean	IDFLayout.containsUnassignedElements(IDF idf)

Uses of IDF in uk.ac.ebi.arrayexpress2.magetab.handler.idf

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

Modifier and Type	Method and Description
protected abstract boolean	IDFConversionHandler.canConvertData(IDF data) Performs specific checks on the IDF to determine if this handler can convert it.
protected abstract boolean	IDFValidateHandler.canValidateData(IDF idf) Performs specific checks on the IDF to determine if this handler can validate it.
void	IDFConversionHandler.convert(IDF data, O out) Invoke this convert handler.
protected abstract void	IDFConversionHandler.convertData(IDF data, O out) Performs the unit of work to convert the data into the given output resource.
void	IDFReadHandler.read(String header, String[] data, IDF idf, int lineNumber, int columnNumber) Invoke this read handler.
protected abstract void	IDFReadHandler.readValue(IDF idf, String value, int lineNumber, String... types) Performs the unit of work to read the data into the internal MAGE-TAB investigation.
void	IDFValidateHandler.validate(IDF data) Invoke this validate handler.
protected abstract void	IDFValidateHandler.validateData(IDF data) Performs the unit of work to validate the data.

Uses of IDF in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl

Methods in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl with parameters of type IDF

Modifier and Type	Method and Description
protected void	ExperimentalDesignTermAccessionHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	ProtocolSoftwareHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	PublicationStatusTermSourceRefHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	ExperimentalFactorTypeHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	ProtocolHardwareHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	QualityControlTypeHandler.readValue(IDF idf, String value, int lineNumber, String... types)
void	AccessionHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	PersonRolesTermSourceRefHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	ReplicateTermSourceRefHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	PublicationDoiHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	TermSourceNameHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	PublicReleaseDateHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	PersonMidInitialsHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	ProtocolDescriptionHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	PublicationAuthorListHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	ExperimentalFactorTermSourceRefHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	PersonAddressHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	PersonFirstNameHandler.readValue(IDF idf, String value, int lineNumber, String... types)
void	CommentHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	PersonEmailHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	ProtocolNameHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	NormalizationTermAccessionHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	ReplicateTermAccessionHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	ProtocolContactHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	QualityControlTermAccessionHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	PublicationStatusTermAccessionHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	ExperimentalDesignTermSourceRefHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	PersonLastNameHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	TermSourceVersionHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	SDRFFileHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	PubMedIdHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	ProtocolTermAccessionHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	ProtocolTypeHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	InvestigationTitleHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	ReplicateTypeHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	NormalizationTypeHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	DateOfExperimentHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	ExperimentDescriptionHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	ExperimentalFactorTermAccessionHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	ProtocolTermSourceRefHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	NormalizationTermSourceRefHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	PersonFaxHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	PersonAffiliationHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	ExperimentalFactorNameHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	ProtocolParametersHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	ExperimentalDesignHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	PersonRolesTermAccessionHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	QualityControlTermSourceRefHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	PublicationStatusHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	PersonRolesHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	TermSourceFileHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	PersonPhoneHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	MAGETABVersionHandler.readValue(IDF idf, String value, int lineNumber, String... types)
protected void	PublicationTitleHandler.readValue(IDF idf, String value, int lineNumber, String... types)

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

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

Modifier and Type	Method and Description
IDF	IDFParser.parse(File idfFile)
IDF	IDFParser.parse(InputStream idfIn) Performs parsing from the specified input stream source, populating an IDF object which is returned.
IDF	IDFParser.parse(InputStream idfIn, IDF idf) Alternate form of the IDFParser.parse(java.io.InputStream) method that allows callers to specify the IDF object they want to be populated.
IDF	IDFParser.parse(InputStream idfIn, IDF idf, ExecutorService service) Alternate form of the IDFParser.parse(java.io.InputStream) method that allows callers to specify both the IDF object they wish to be populated and an executor service that should be used to execute all IDF handler tasks.
IDF	IDFParser.parse(URL idfURL)

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

Modifier and Type	Method and Description
IDF	IDFParser.parse(InputStream idfIn, IDF idf) Alternate form of the IDFParser.parse(java.io.InputStream) method that allows callers to specify the IDF object they want to be populated.
IDF	IDFParser.parse(InputStream idfIn, IDF idf, ExecutorService service) Alternate form of the IDFParser.parse(java.io.InputStream) method that allows callers to specify both the IDF object they wish to be populated and an executor service that should be used to execute all IDF handler tasks.
protected void	IDFParser.read(String[][] idfData, IDF idf, ExecutorService service) Reads tabulated IDF data into the supplied IDF object, delegating the execution of handling tasks to the supplied ExecutorService.

Uses of IDF in uk.ac.ebi.arrayexpress2.magetab.renderer

Methods in uk.ac.ebi.arrayexpress2.magetab.renderer with parameters of type IDF

Modifier and Type	Method and Description
void	IDFWriter.write(IDF idf) Writes the IDF supplied to the underlying writer without printing progress informations to standard out.
void	IDFWriter.write(IDF idf, boolean printStdout) Writes the IDF supplied to the underlying writer, optionally printing progress information to standard out.

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

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

Modifier and Type	Method and Description
void	IDFValidator.validate(IDF idf)
void	IDFValidator.validate(IDF idf, ExecutorService service)