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

Packages that use SDRF

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.datamodel.layout.calc
uk.ac.ebi.arrayexpress2.magetab.handler.sdrf	SDRF specific handler classes.
uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node	Specific handlers for SDRF node data items, as defined in the MAGE-TAB specification.
uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute	SDRF Handler implementations that are capable of handling data items that represent attributes attached to a node, as defined by the MAGE-TAB specification.
uk.ac.ebi.arrayexpress2.magetab.parser	Parser classes for parsing MAGE-TAB aspects.
uk.ac.ebi.arrayexpress2.magetab.renderer
uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor
uk.ac.ebi.arrayexpress2.magetab.validator	Validator classes for validating the MAGE-TAB datamodel during parsing.

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

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

Modifier and Type	Method and Description
void	SDRFConverter.convert(SDRF sdrf, O outputResource)
void	SDRFConverter.convert(SDRF sdrf, O outputResource, ExecutorService service)

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

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

Modifier and Type	Field and Description
SDRF	MAGETABInvestigation.SDRF

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

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

Modifier and Type	Method and Description
void	SDRFLayout.calculateLocations(SDRF sdrf)
void	SDRFLayout.calculateUnassignedLocations(SDRF sdrf)
boolean	SDRFLayout.containsUnassignedElements(SDRF sdrf)

Uses of SDRF in uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.calc

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

Modifier and Type	Method and Description
static void	SDRFLayoutCalculator.calculateSDRFLayout(SDRF sdrf)

Uses of SDRF in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf

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

Modifier and Type	Method and Description
protected abstract boolean	SDRFConversionHandler.canConvertData(SDRF data) Performs specific checks on the IDF to determine if this handler can convert it.
protected abstract boolean	SDRFValidateHandler.canValidateData(SDRF sdrf) Performs specific checks on the SDRF to determine if this handler can validate it.
void	SDRFConversionHandler.convert(SDRF data, O out) Invoke this convert handler.
protected abstract void	SDRFConversionHandler.convertData(SDRF data, O out) Performs the unit of work to convert the data into the given output resource.
protected <T extends SDRFNode> T	SDRFReadInContextHandler.fetchUpstreamNode(SDRF sdrf, String nodeName, Class<T> nodeClass) Used for adding nodes that are upstream of the current node in the SDRF graph.
protected SDRFNode	SDRFReadInContextHandler.handleUpstreamNode(SDRF sdrf, String nodeName, String nodeType, int lineNumber, int columnNumber) Used for adding nodes that are upstream of the current node in the SDRF graph.
void	SDRFReadInContextHandler.read(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber)
void	SDRFReadHandler.read(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber)
protected int	SDRFReadHandler.readAttribute(SDRFAttributeReader reader, String[] header, String[] data, SDRF sdrf, SDRFNode parentNode, int lineNumber, int columnNumber, int startIndex)
protected abstract void	SDRFReadHandler.readData(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber) Performs the unit of work to read the data into the internal datamodel.
abstract void	SDRFReadInContextHandler.readDataFrom(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber) Performs the unit of work to read the data into the internal datamodel.
void	SDRFReadInContextHandler.readFrom(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber) Cause the handler to read some of the supplied data (usually starting from startIndex) into the supplied target object, using additional context information where appropriate.
void	SDRFValidateHandler.validate(SDRF data) Invoke this validate handler.
protected abstract void	SDRFValidateHandler.validateData(SDRF data) Performs the unit of work to validate the data.

Uses of SDRF in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node

Methods in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node with parameters of type SDRF

Modifier and Type	Method and Description
void	DerivedArrayDataHandler.readData(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber)
void	LabeledExtractHandler.readData(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber)
void	NormalizationHandler.readData(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber)
void	ScanHandler.readData(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber)
void	ImageHandler.readData(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber)
void	ArrayDataMatrixHandler.readData(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber)
void	ProtocolHandler.readData(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber)
void	AssayHandler.readData(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber)
void	FactorValueNodeHandler.readData(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber)
void	ExtractHandler.readData(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber)
void	DerivedArrayDataMatrixHandler.readData(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber)
protected void	ArrayDataHandler.readData(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber)
protected void	UnknownHeaderHandler.readData(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber)
void	SourceHandler.readData(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber)
void	SampleHandler.readData(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber)
void	HybridizationHandler.readData(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber)
void	ProtocolHandler.readDataFrom(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber) A specialised alternate form of the SDRFReadInContextHandler.canReadHeader(String[]) method for handling Protocol Application Nodes.
void	FactorValueNodeHandler.readDataFrom(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber) A specialised alternate form of the SDRFReadHandler.readData(String[], String[], uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF, int, int) method, specialised for handling Factor Value "floating" nodes.

Uses of SDRF in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute

Methods in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute with parameters of type SDRF

Modifier and Type	Method and Description
void	PerformerAttributeReader.readAttributes(String[] header, String[] data, SDRF sdrf, SDRFNode sdrfNode, int lineNumber, int columnNumber)
void	MaterialTypeAttributeReader.readAttributes(String[] header, String[] data, SDRF sdrf, SDRFNode sdrfNode, int lineNumber, int columnNumber)
void	TechnologyTypeAttributeReader.readAttributes(String[] header, String[] data, SDRF sdrf, SDRFNode sdrfNode, int lineNumber, int columnNumber)
void	LabelAttributeReader.readAttributes(String[] header, String[] data, SDRF sdrf, SDRFNode sdrfNode, int lineNumber, int columnNumber)
void	ArrayDesignAttributeReader.readAttributes(String[] header, String[] data, SDRF sdrf, SDRFNode parentNode, int lineNumber, int columnNumber)
void	ParameterValueAttributeReader.readAttributes(String[] header, String[] data, SDRF sdrf, SDRFNode sdrfNode, int lineNumber, int columnNumber)
void	ProviderAttributeReader.readAttributes(String[] header, String[] data, SDRF sdrf, SDRFNode sdrfNode, int lineNumber, int columnNumber)
void	SDRFAttributeReader.readAttributes(String[] header, String[] data, SDRF sdrf, SDRFNode sdrfNode, int lineNumber, int columnNumber) Reads the attributes from the data and sets them on the supplied SDRFNode
void	FactorValueAttributeReader.readAttributes(String[] header, String[] data, SDRF sdrf, SDRFNode sdrfNode, int lineNumber, int columnNumber)
void	CharacteristicsAttributeReader.readAttributes(String[] header, String[] data, SDRF sdrf, SDRFNode parentNode, int lineNumber, int columnNumber)

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

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

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

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

Modifier and Type	Method and Description
SDRF	SDRFParser.parse(InputStream sdrfIn, SDRF sdrf) Alternate form of the SDRFParser.parse(java.io.InputStream) method that allows callers to specify the SDRF object they want to be populated.
SDRF	SDRFParser.parse(InputStream sdrfIn, SDRF sdrf, ExecutorService service) Alternate form of the SDRFParser.parse(java.io.InputStream) method that allows callers to specify both the SDRF object they wish to be populated and an executor service that should be used to execute all SDRF handler tasks.
protected void	SDRFParser.read(String[][] sdrfData, SDRF sdrf, ExecutorService service) Reads tabulated SDRF data into the supplied SDRF object, delegating the execution of handling tasks to the supplied ExecutorService.
protected void	MAGETABParser.readSDRF(InputStream sdrfIn, SDRF sdrf, ExecutorService service, uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABParser.ProgressFlag flag)

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

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

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

Uses of SDRF in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor

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

Modifier and Type	Method and Description
void	SDRFGraphWriter.write(SDRF sdrf)

Constructors in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor with parameters of type SDRF

Constructor and Description
SDRFScannerChannelMapper(SDRF sdrf)
WrapperNodeFactory(SDRF sdrf)

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

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

Modifier and Type	Method and Description
void	SDRFValidator.validate(SDRF sdrf)
void	SDRFValidator.validate(SDRF sdrf, ExecutorService service)