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

Packages that use ADF

Package	Description
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.adf	ADF specific handler classes.
uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl	Specific, concrete ADF header handler implementations.
uk.ac.ebi.arrayexpress2.magetab.handler.adf.node	ADF "graph part" specific handler classes.
uk.ac.ebi.arrayexpress2.magetab.parser	Parser classes for parsing MAGE-TAB aspects.
uk.ac.ebi.arrayexpress2.magetab.renderer

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

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

Modifier and Type	Field and Description
ADF	MAGETABArrayDesign.ADF

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

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

Modifier and Type	Method and Description
void	ADFLayout.calculateLocations(ADF adf)
void	ADFLayout.calculateUnassignedLocations(ADF adf)
boolean	ADFLayout.containsUnassignedElements(ADF adf)

Uses of ADF in uk.ac.ebi.arrayexpress2.magetab.handler.adf

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

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

Uses of ADF in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl

Methods in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl with parameters of type ADF

Modifier and Type	Method and Description
protected void	ProviderHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	SurfaceTypeTermSourceRefHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	SequencePolymerTypeHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	SurfaceTypeHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	AccessionHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	TechnologyTypeHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	TermSourceNameHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	TechnologyTypeTermAccessionHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	SurfaceTypeTermAccessionHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	CommentHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	SequencePolymerTypeTermSourceRefHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	VersionHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	SubstrateTypeTermAccessionHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	SequencePolymerTypeTermAccessionHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	TermSourceVersionHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	SubstrateTypeHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	ArrayDesignNameHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	SubstrateTypeTermSourceRefHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	PrintingProtocolHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	TechnologyTypeTermSourceRefHandler.readValue(ADF adf, String value, int lineNumber, String... types)
protected void	TermSourceFileHandler.readValue(ADF adf, String value, int lineNumber, String... types)

Uses of ADF in uk.ac.ebi.arrayexpress2.magetab.handler.adf.node

Methods in uk.ac.ebi.arrayexpress2.magetab.handler.adf.node with parameters of type ADF

Modifier and Type	Method and Description
protected void	CompositeElementHandler.readData(String[] header, String[] data, ADF adf, int lineNumber, int columnNumber)
protected void	FeatureHandler.readData(String[] header, String[] value, ADF adf, int lineNumber, int columnNumber)
protected void	ReporterHandler.readData(String[] header, String[] data, ADF adf, int lineNumber, int columnNumber)

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

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

Modifier and Type	Method and Description
ADF	ADFParser.parse(InputStream adfIn) Performs parsing from the specified input stream source, populating an ADF object which is returned.
ADF	ADFParser.parse(InputStream adfIn, ADF adf)
ADF	ADFParser.parse(InputStream adfIn, ADF adf, ExecutorService service)

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

Modifier and Type	Method and Description
ADF	ADFParser.parse(InputStream adfIn, ADF adf)
ADF	ADFParser.parse(InputStream adfIn, ADF adf, ExecutorService service)
protected void	ADFParser.read(String[][] adfData, ADF adf, ExecutorService service)
void	ADFParser.validate(ADF adf)
void	ADFParser.validate(ADF adf, ExecutorService service)
void	ADFParser.write(ADF adf)
void	ADFParser.write(ADF adf, ExecutorService service)

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

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

Modifier and Type	Method and Description
void	ADFWriter.write(ADF adf) Writes out the ADF to the underlying writer, without printing any stdout.
void	ADFWriter.write(ADF adf, boolean printStdout) Writes out the ADF to the underlying, specifying whether to convert information about progress to standard out.