Index (LIMPOPO MAGE-TAB Parser/Validator 1.1.8 API)

A B C D E F G H I L M N O P Q R S T U V W

A

AbstractADFAttribute - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute: An abstract implementation of an ADF attribute.
AbstractADFAttribute() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.AbstractADFAttribute
AbstractADFNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node: An abstract top-level implementation of an ADFNode.
AbstractADFNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.AbstractADFNode
AbstractConverter<S,T> - Class in uk.ac.ebi.arrayexpress2.magetab.converter: Javadocs go here!
AbstractConverter() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.converter.AbstractConverter
AbstractGraph<S extends Node> - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.graph: An abstract top-level implementation of a MAGE-TAB graph.
AbstractGraph() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractGraph
AbstractHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler: A basic handler implementation that provides some simple functionality common to all handlers.
AbstractHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.AbstractHandler
AbstractNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.graph: An abstract top-level implementation of a Node in the MAGE-TAB graph.
AbstractNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode
AbstractNode(String) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode
AbstractParser<T> - Class in uk.ac.ebi.arrayexpress2.magetab.parser: An abstract basic implementation of a Parser.
AbstractParser() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser
AbstractParser.DefaultHandlerListener - Class in uk.ac.ebi.arrayexpress2.magetab.parser
AbstractParser.DefaultHandlerListener() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser.DefaultHandlerListener
AbstractSDRFAttribute - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute: An abstract implementation of an SDRF attribute.
AbstractSDRFAttribute() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.AbstractSDRFAttribute
AbstractSDRFNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node: An abstract top-level implementation of an SDRFNode.
AbstractSDRFNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.AbstractSDRFNode
AbstractValidator<T> - Class in uk.ac.ebi.arrayexpress2.magetab.validator: An abstract implementation of the Validator interface.
AbstractValidator() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.validator.AbstractValidator
accept(HandlerVisitor) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.AbstractHandler
accept(HandlerVisitor) - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.Handler: Accept a visit from a HandlerVisitor
accession - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
accession - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
AccessionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handles rows in the ADF that describe the arrayaexpress accession number in a comment field.
AccessionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.AccessionHandler
AccessionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler that handles rows in the IDF that describe the arrayaexpress accession number in a comment field.
AccessionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.AccessionHandler
addAttributeLocation(ADFAttribute, Location) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.ADFLayout
addAttributeLocation(SDRFAttribute, Location) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.SDRFLayout
addChildNode(Node) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode
addChildNode(String, String) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode
addChildNode(Node) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node: Adds the child node to this Node.
addChildNode(String, String) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node: Adds a child node to this Node.
addColumn(String) - Method in interface uk.ac.ebi.arrayexpress2.magetab.utils.tab.ITableDataHandler
addColumn(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableDataHandler
addComment(String, String) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF: Add a comment to the array design, keyed by type.
addComment(String, String) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF: Add a comment to the investigation, keyed by type.
addCommentLocation(String, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.IDFLayout: Add a location of an IDF comment type.
addEncounteredException(Exception) - Method in class uk.ac.ebi.arrayexpress2.magetab.listener.ProgressEvent
addErrorItemListener(ErrorItemListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.converter.AbstractConverter
addErrorItemListener(ErrorItemListener) - Method in interface uk.ac.ebi.arrayexpress2.magetab.converter.Converter: Register an ErrorItemListener with this parser.
addErrorItemListener(ErrorItemListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.converter.MAGETABConverter
addErrorItemListener(ErrorItemListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser
addErrorItemListener(ErrorItemListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABArrayParser
addErrorItemListener(ErrorItemListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABParser
addErrorItemListener(ErrorItemListener) - Method in interface uk.ac.ebi.arrayexpress2.magetab.parser.Parser: Register an ErrorItemListener with this parser.
addErrorItemListener(ErrorItemListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.AbstractValidator
addErrorItemListener(ErrorItemListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.MAGETABValidator
addErrorItemListener(ErrorItemListener) - Method in interface uk.ac.ebi.arrayexpress2.magetab.validator.Validator: Register an ErrorItemListener with this parser.
addHandler(Handler, String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser.DefaultHandlerListener: Add a handler that should be tracked to this listener.
addListener(HandlerListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.AbstractHandler
addListener(HandlerListener) - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.Handler: Register a HandlerListener that can listen for handling events.
addLocation(Field, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.IDFLayout: Add a location of a field from IDF.
addNode(S) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractGraph
addNode(S) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Graph: Store a node in the Graph.
addNodeLocation(ADFNode, Location) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.ADFLayout
addNodeLocation(SDRFNode, Location) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.SDRFLayout
addParentNode(Node) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode
addParentNode(String, String) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode
addParentNode(Node) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node: Adds a parent node to this node
addParentNode(String, String) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node: Adds a parent node to this Node.
addPrimitiveLocation(String, String, Location) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.ADFLayout
addPrimitiveLocation(String, String, Location) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.SDRFLayout
addProgressListener(ProgressListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.converter.AbstractConverter
addProgressListener(ProgressListener) - Method in interface uk.ac.ebi.arrayexpress2.magetab.converter.Converter: Register a ProgressListener with this converter.
addProgressListener(ProgressListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser
addProgressListener(ProgressListener) - Method in interface uk.ac.ebi.arrayexpress2.magetab.parser.Parser: Register a ProgressListener with this parser.
addProgressListener(ProgressListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.AbstractValidator
addProgressListener(ProgressListener) - Method in interface uk.ac.ebi.arrayexpress2.magetab.validator.Validator: Register a ProgressListener with this validator.
addRow() - Method in interface uk.ac.ebi.arrayexpress2.magetab.utils.tab.ITableDataHandler
addRow() - Method in class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableDataHandler
addRow() - Method in class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableSectionDataHandler
addRow() - Method in class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableSectionDetectingDataHandler
ADF - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel: A datastructure that models the ADF in the MAGE-TAB spec.
ADF() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
ADF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.MAGETABArrayDesign
ADFAttribute - Interface in uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute: An attribute in the ADF data structure.
ADFAttributeReader - Interface in uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.attribute: An interface that allows ADFGraphReadHandlers to delegate functionality of attribute reading to this interface rather than check all possible attribute combinations themselves.
ADFConversionHandler<O> - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf: An abstract implementation of a ConversionHandler for writing data from an IDF to some external output resource.
ADFConversionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFConversionHandler
ADFGraphReadHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf: An abstract implementation of a ReadHandler for reading from the graph part of an ADF file into a ADF object.
ADFGraphReadHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFGraphReadHandler
ADFHeaderReadHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf: An abstract implementation of ReadHandler for reading from the header part of an ADF file into a MAGETABArrayDesign.
ADFHeaderReadHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFHeaderReadHandler
ADFLayout - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.layout: Javadocs go here!
ADFLayout() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.ADFLayout
ADFNode - Interface in uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node: A node in the ADF data structure.
ADFNodeConversionHandler<D extends ADFNode,O> - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.node: An abstract implementation of a ConversionHandler for writing data from an ADFNode to some external output resource.
ADFNodeConversionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.ADFNodeConversionHandler
ADFParser - Class in uk.ac.ebi.arrayexpress2.magetab.parser: Imports ADF documents into an ADF.
ADFParser() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.parser.ADFParser
ADFValidateHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf: An abstract implementation of a ValidateHandler for writing data from an IDF to some external output resource.
ADFValidateHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFValidateHandler
ADFWriter - Class in uk.ac.ebi.arrayexpress2.magetab.renderer: Writes ADF format output to a Writer.
ADFWriter(Writer) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.ADFWriter
appendAttributeCommentsToGroup(DefaultTabValueGroup, Map<String, String>) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper
appendAttributeToGroup(DefaultTabValueGroup, AbstractSDRFAttribute) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper
appendFactorValuesToGroup(DefaultTabValueGroup) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.AssayNodeWrapper
appendFactorValuesToGroup(DefaultTabValueGroup) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.HybridizationNodeWrapper
appendFactorValuesToGroup(DefaultTabValueGroup) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.ScanNodeWrapper
appendFactorValuesToGroup(DefaultTabValueGroup, SDRFNodeWrapper<T>) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper
appendFactorValuesToGroup(DefaultTabValueGroup) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper
appendNodeCommentsToGroup(DefaultTabValueGroup, Map<String, List<String>>) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper
appendValueToGroup(DefaultTabValueGroup, String, String) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper
ArrayDataHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node: A handler that handles array data nodes in the SDRF graph
Tag: Array Data File
Allowed Attributes: Array Design File/Ref, Comment
ArrayDataHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ArrayDataHandler
ArrayDataMatrixHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node: A handler that handles array data matrix nodes in the SDRF graph
Tag: Array Data Matrix File
Allowed attributes: Array Design File/Ref, Comment
ArrayDataMatrixHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ArrayDataMatrixHandler
ArrayDataMatrixNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node: An array data matrix node in the graph.
ArrayDataMatrixNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ArrayDataMatrixNode
ArrayDataMatrixNodeWrapper - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor
ArrayDataMatrixNodeWrapper(ArrayDataMatrixNode, int, WrapperNodeFactory) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.ArrayDataMatrixNodeWrapper
ArrayDataNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node: An array data node in the graph.
ArrayDataNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ArrayDataNode
ArrayDataNodeWrapper - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor
ArrayDataNodeWrapper(ArrayDataNode, int, WrapperNodeFactory) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.ArrayDataNodeWrapper
ArrayDesignAttribute - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute: An array design node in the graph.
ArrayDesignAttribute() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.ArrayDesignAttribute
ArrayDesignAttributeReader - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute: A handler implementation that will handle Array Design fields in the SDRF.
ArrayDesignAttributeReader() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.ArrayDesignAttributeReader
ArrayDesignFileAttributeReader - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute: Concrete implementation of ArrayDesignAttributeReader dealing with Array Design Files
Tag: Array Design File
ArrayDesignFileAttributeReader() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.ArrayDesignFileAttributeReader
arrayDesignName - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
ArrayDesignNameHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handlers ADF rows describing the array design name.
ArrayDesignNameHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.ArrayDesignNameHandler
ArrayDesignNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node: Deprecated.
since version 1.1
ArrayDesignNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ArrayDesignNode: Deprecated.
ArrayDesignNodeWrapper - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor
ArrayDesignNodeWrapper(ArrayDesignNode, int, WrapperNodeFactory) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.ArrayDesignNodeWrapper
ArrayDesignRefAttributeReader - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute: Concrete implementation of ArrayDesignRefAttributeReader dealing with Array Design Refs
Tag: Array Design Ref
ArrayDesignRefAttributeReader() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.ArrayDesignRefAttributeReader
arrayDesigns - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.HybridizationNode
AssayHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node: A handler that handles Assay nodes in the SDRF graph
Tag: Assay Name
Allowed attributes: Factor Value, Array Design File/Ref, Technology Type, Comment
AssayHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.AssayHandler
AssayNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node: An Assay Node, in the SDRF graph.
AssayNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.AssayNode
AssayNodeWrapper - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor
AssayNodeWrapper(AssayNode, int, WrapperNodeFactory) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.AssayNodeWrapper
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFGraphReadHandler: Return the index of the last header this handler can read from in the supplied header.
assess(String[]) - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.attribute.ADFAttributeReader: Returns an integer representing the number of columns this handler can read forward of the given header.
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.attribute.ControlTypeAttributeReader
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.attribute.ReporterGroupAttributeReader
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.CompositeElementHandler
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.FeatureHandler
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.ReporterHandler
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ArrayDataHandler
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ArrayDataMatrixHandler
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.AssayHandler
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.ArrayDesignAttributeReader
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.CharacteristicsAttributeReader
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.FactorValueAttributeReader
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.LabelAttributeReader
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.MaterialTypeAttributeReader
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.ParameterValueAttributeReader
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.PerformerAttributeReader
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.ProviderAttributeReader
assess(String[]) - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.SDRFAttributeReader: Returns an integer representing the number of columns this handler can read forward of the given header.
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.TechnologyTypeAttributeReader
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.DerivedArrayDataHandler
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.DerivedArrayDataMatrixHandler
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ExtractHandler
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.FactorValueNodeHandler
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.HybridizationHandler
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ImageHandler
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.LabeledExtractHandler
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.NormalizationHandler
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ProtocolHandler
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.SampleHandler
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ScanHandler
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.SourceHandler
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.UnknownHeaderHandler
assess(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadHandler: Return the index of the last header this handler can read from in the supplied header.
assessAttribute(ADFAttributeReader, String[], int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFGraphReadHandler
assessAttribute(SDRFAttributeReader, String[], int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadHandler
assessFrom(String[], int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.FactorValueNodeHandler: A specialised alternate form of the FactorValueNodeHandler.assess(String[]) method, specialised for handling Factor Value "floating" nodes.
assessFrom(String[], int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ProtocolHandler: A specialised alternate form of the SDRFReadInContextHandler.canReadHeader(String[]) method for handling Protocol Application Nodes.
assessFrom(String[], int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadInContextHandler: Return the index of the last header this handler can read from in the supplied header, starting from the given start index.
attributeValue - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.AbstractADFAttribute
attributeValue - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.AbstractSDRFAttribute

B

blockColumn - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.FeatureNode
blockRow - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.FeatureNode

C

calculateLocations(ADF) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.ADFLayout
calculateLocations(IDF) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.IDFLayout
calculateLocations(T) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.Layout: A factory method for fully calculates the layout of the given datamodel object, using Limpopo's own MAGE-TAB printing algorithms.
calculateLocations(SDRF) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.SDRFLayout
calculateSDRFLayout(SDRF) - Static method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.calc.SDRFLayoutCalculator
calculateUnassignedLocations(ADF) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.ADFLayout
calculateUnassignedLocations(IDF) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.IDFLayout
calculateUnassignedLocations(T) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.Layout: A factory method for calculating the locations of any data items not already assigned.
calculateUnassignedLocations(SDRF) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.SDRFLayout
canConvert(Object, Object) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFConversionHandler
canConvert(Object, Object) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.ADFNodeConversionHandler
canConvert(Object, Object) - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.ConversionHandler: Determine whether this handler can convert the supplied data.
canConvert(Object, Object) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.IDFConversionHandler
canConvert(Object, Object) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.SDRFNodeConversionHandler
canConvert(Object, Object) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFConversionHandler
canConvertData(ADF) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFConversionHandler: Performs specific checks on the ADF to determine if this handler can convert it.
canConvertData(ADFNode) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.ADFNodeConversionHandler: Performs specific checks on the ADFNode to determine if this handler can convert it.
canConvertData(IDF) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.IDFConversionHandler: Performs specific checks on the IDF to determine if this handler can convert it.
canConvertData(SDRFNode) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.SDRFNodeConversionHandler: Performs specific checks on the SDRFNode to determine if this handler can convert it.
canConvertData(SDRF) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFConversionHandler: Performs specific checks on the IDF to determine if this handler can convert it.
canRead(Object) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFGraphReadHandler
canRead(Object) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFHeaderReadHandler
canRead(String) - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.attribute.ADFAttributeReader: Determine whether this reader can read the attributes referenced by this header.
canRead(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.attribute.ControlTypeAttributeReader
canRead(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.attribute.ReporterGroupAttributeReader
canRead(Object) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.IDFReadHandler
canRead(Object) - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.ReadHandler: Determine whether this handler can read the supplied header.
canRead(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.ArrayDesignFileAttributeReader
canRead(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.ArrayDesignRefAttributeReader
canRead(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.CharacteristicsAttributeReader
canRead(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.FactorValueAttributeReader
canRead(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.LabelAttributeReader
canRead(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.MaterialTypeAttributeReader
canRead(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.ParameterValueAttributeReader
canRead(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.PerformerAttributeReader
canRead(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.ProviderAttributeReader
canRead(String) - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.SDRFAttributeReader: Determine whether this reader can read the attributes referenced by this header.
canRead(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.TechnologyTypeAttributeReader
canRead(Object) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadHandler
canReadFrom(String[], int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.FactorValueNodeHandler: A specialised alternate form of the SDRFReadInContextHandler.canReadHeader(String[]) method, specialised for handling Factor Value "floating" nodes.
canReadFrom(String[], int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ProtocolHandler: A specialised alternate form of the SDRFReadInContextHandler.canReadHeader(String[]) method for handling Protocol Application Nodes.
canReadFrom(String[], int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadInContextHandler: Determine whether this handler can read the data referenced by this header, starting from the supplied start index.
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFGraphReadHandler: Determine whether this handler can read the data referenced by this header.
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFHeaderReadHandler: Determine whether this handler can read the data referenced by this header.
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.AccessionHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.ArrayDesignNameHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.CommentHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.PrintingProtocolHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.ProviderHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SequencePolymerTypeHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SequencePolymerTypeTermAccessionHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SequencePolymerTypeTermSourceRefHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SubstrateTypeHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SubstrateTypeTermAccessionHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SubstrateTypeTermSourceRefHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SurfaceTypeHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SurfaceTypeTermAccessionHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SurfaceTypeTermSourceRefHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.TechnologyTypeHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.TechnologyTypeTermAccessionHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.TechnologyTypeTermSourceRefHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.TermSourceFileHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.TermSourceNameHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.TermSourceVersionHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.VersionHandler
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.CompositeElementHandler
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.FeatureHandler
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.ReporterHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.IDFReadHandler: Determine whether this handler can read the data referenced by this header.
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.AccessionHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.CommentHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.DateOfExperimentHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalDesignHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalDesignTermAccessionHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalDesignTermSourceRefHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalFactorNameHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalFactorTermAccessionHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalFactorTermSourceRefHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalFactorTypeHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentDescriptionHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.InvestigationTitleHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.MAGETABVersionHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.NormalizationTermAccessionHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.NormalizationTermSourceRefHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.NormalizationTypeHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonAddressHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonAffiliationHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonEmailHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonFaxHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonFirstNameHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonLastNameHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonMidInitialsHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonPhoneHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonRolesHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonRolesTermAccessionHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonRolesTermSourceRefHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolContactHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolDescriptionHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolHardwareHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolNameHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolParametersHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolSoftwareHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolTermAccessionHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolTermSourceRefHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolTypeHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicationAuthorListHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicationDoiHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicationStatusHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicationStatusTermAccessionHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicationStatusTermSourceRefHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicationTitleHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicReleaseDateHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PubMedIdHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.QualityControlTermAccessionHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.QualityControlTermSourceRefHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.QualityControlTypeHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ReplicateTermAccessionHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ReplicateTermSourceRefHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ReplicateTypeHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.SDRFFileHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.TermSourceFileHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.TermSourceNameHandler
canReadHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.TermSourceVersionHandler
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ArrayDataHandler
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ArrayDataMatrixHandler
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.AssayHandler
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.DerivedArrayDataHandler
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.DerivedArrayDataMatrixHandler
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ExtractHandler
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.HybridizationHandler
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ImageHandler
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.LabeledExtractHandler
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.NormalizationHandler
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.SampleHandler
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ScanHandler
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.SourceHandler
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.UnknownHeaderHandler
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadHandler: Determine whether this handler can read the data referenced by this header.
canReadHeader(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadInContextHandler
canValidate(Object) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFValidateHandler
canValidate(Object) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.IDFValidateHandler
canValidate(Object) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.MAGETABValidateHandler
canValidate(Object) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFValidateHandler
canValidate(Object) - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.ValidateHandler: Determine whether this handler can validate the supplied data.
canValidateData(ADF) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFValidateHandler: Performs specific checks on the ADF to determine if this handler can validate it.
canValidateData(IDF) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.IDFValidateHandler: Performs specific checks on the IDF to determine if this handler can validate it.
canValidateData(MAGETABInvestigation) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.MAGETABValidateHandler: Performs specific checks on the MAGETABInvestigation to determine if this handler can validate it.
canValidateData(SDRF) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFValidateHandler: Performs specific checks on the SDRF to determine if this handler can validate it.
characteristics - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ExtractNode
characteristics - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.LabeledExtractNode
characteristics - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SampleNode
characteristics - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SourceNode
CharacteristicsAttribute - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute: A characteristics attribute node in the graph.
CharacteristicsAttribute() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.CharacteristicsAttribute
CharacteristicsAttributeReader - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute: Handles characteristic attributes in the SDRF graph.
CharacteristicsAttributeReader() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.CharacteristicsAttributeReader
checkForCycles(Node, Node) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractGraph
checkForCycles(Node, Node) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Graph: Assertain whether this graph contains any cycles.
close() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFGraphWriter
close() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.ADFWriter
close() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.IDFWriter
close() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.SDRFWriter
column - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.FeatureNode
CommentHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handles ADF rows describing comments
Tag: Comment[]
CommentHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.CommentHandler
CommentHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler that handles all comments in an arrayexpress IDF document, excluding accession comments
Tag: Comment[*] Cardinality: unlimited
CommentHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.CommentHandler
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.CompositeElementNode
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.FeatureNode
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.ReporterNode
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ArrayDataMatrixNode
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ArrayDataNode
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ArrayDesignNode: Deprecated.
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.ArrayDesignAttribute
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.ParameterValueAttribute
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.PerformerAttribute
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.ProviderAttribute
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.DerivedArrayDataMatrixNode
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.DerivedArrayDataNode
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ExtractNode
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.HybridizationNode
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ImageNode
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.LabeledExtractNode
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.NormalizationNode
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ProtocolApplicationNode
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SampleNode
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ScanNode
comments - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SourceNode
compareTo(Location) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.Location
compareTo(Node) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper
compensateForEscapedNewlines(String, String) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Deprecated.
compositeElementDatabaseEntries - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.CompositeElementNode
CompositeElementHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.node: A handler that handles composite element nodes in the ADF graph.
CompositeElementHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.CompositeElementHandler
CompositeElementNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node: Models "Composite Element" nodes in the ADF graph, according to the MAGE-TAB specification.
CompositeElementNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.CompositeElementNode
containsUnassignedElements(ADF) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.ADFLayout
containsUnassignedElements(IDF) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.IDFLayout
containsUnassignedElements(T) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.Layout: Returns true if the supplied datamodel has elements with no assigned location in this layout.
containsUnassignedElements(SDRF) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.SDRFLayout
ControlTypeAttribute - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute: Models control type attributes in the MAGE-TAB ADF specification.
ControlTypeAttribute() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ControlTypeAttribute
ControlTypeAttributeReader - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.attribute: Handles control type attributes in the ADF graph part.
ControlTypeAttributeReader() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.attribute.ControlTypeAttributeReader
controlTypeAttributes - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.ReporterNode
conversionCompleted(ProgressEvent) - Method in interface uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListener: Invoked whenever a convert operation completes successfully
conversionCompleted(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListenerAdapter
ConversionException - Exception in uk.ac.ebi.arrayexpress2.magetab.exception: A ParseException that gets thrown whenever part of a MAGETABInvestigation or a MAGETABInvestigation fails a conversion process.
ConversionException() - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ConversionException
ConversionException(String) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ConversionException
ConversionException(String, Throwable) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ConversionException
ConversionException(Throwable) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ConversionException
ConversionException(boolean, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ConversionException
ConversionException(boolean, String, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ConversionException
ConversionException(boolean, String, Throwable, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ConversionException
ConversionException(boolean, Throwable, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ConversionException
conversionFailed(ProgressEvent) - Method in interface uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListener: Invoked whenever a convert operation completes, but failed to read some of the document
conversionFailed(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListenerAdapter
ConversionHandler<D,O> - Interface in uk.ac.ebi.arrayexpress2.magetab.handler: A type of Handler that enables convert functionality over a lump of data.
conversionStarted(ProgressEvent) - Method in interface uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListener: Invoked whenever a convert operation commences
conversionStarted(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListenerAdapter
convert(S, T) - Method in interface uk.ac.ebi.arrayexpress2.magetab.converter.Converter: Converts source objects into target objects.
convert(S, T, ExecutorService) - Method in interface uk.ac.ebi.arrayexpress2.magetab.converter.Converter: Perform validation of the supplied validator source, delegating all work to the supplied Executor Service to enable validation in parallel.
convert(IDF, O) - Method in class uk.ac.ebi.arrayexpress2.magetab.converter.IDFConverter
convert(IDF, O, ExecutorService) - Method in class uk.ac.ebi.arrayexpress2.magetab.converter.IDFConverter
convert(MAGETABInvestigation, O) - Method in class uk.ac.ebi.arrayexpress2.magetab.converter.MAGETABConverter
convert(MAGETABInvestigation, O, ExecutorService) - Method in class uk.ac.ebi.arrayexpress2.magetab.converter.MAGETABConverter
convert(SDRF, O) - Method in class uk.ac.ebi.arrayexpress2.magetab.converter.SDRFConverter
convert(SDRF, O, ExecutorService) - Method in class uk.ac.ebi.arrayexpress2.magetab.converter.SDRFConverter
convert(ADF, O) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFConversionHandler: Invoke this convert handler.
convert(D, O) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.ADFNodeConversionHandler: Invoke this convert handler.
convert(D, O) - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.ConversionHandler: Converts data from a data item into some resource.
convert(IDF, O) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.IDFConversionHandler: Invoke this convert handler.
convert(D, O) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.SDRFNodeConversionHandler: Invoke this convert handler.
convert(SDRF, O) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFConversionHandler: Invoke this convert handler.
convertData(ADF, O) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFConversionHandler: Performs the unit of work to convert the data into the given output resource.
convertData(D, O) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.ADFNodeConversionHandler: Performs the unit of work to convert the data into the given output resource.
convertData(IDF, O) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.IDFConversionHandler: Performs the unit of work to convert the data into the given output resource.
convertData(D, O) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.SDRFNodeConversionHandler: Performs the unit of work to convert the data into the given output resource.
convertData(SDRF, O) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFConversionHandler: Performs the unit of work to convert the data into the given output resource.
convertedMore(ProgressEvent) - Method in interface uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListener: Invoked whenever more of a document is convertd.
convertedMore(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListenerAdapter
Converter<S,T> - Interface in uk.ac.ebi.arrayexpress2.magetab.converter: A converter takes objects from the source object model and converts them into something else.
createNewNode(SDRFNode) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.WrapperNodeFactory

D

date - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ProtocolApplicationNode
dateOfExperiment - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
DateOfExperimentHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Date of Experiment fields in the IDF.
DateOfExperimentHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.DateOfExperimentHandler
DEFAULT_ENCODING - Static variable in interface uk.ac.ebi.arrayexpress2.magetab.parser.Parser: The default encoding of the files being parsed.
DerivedArrayDataHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node: A handler that handles Derived Array Data nodes in the SDRF graph
Tag: Derived Array Data File Allowed attributes: Array Design File/Ref, Comment
DerivedArrayDataHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.DerivedArrayDataHandler
DerivedArrayDataMatrixHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node: A handler that handles Derived Array Data Matrix nodes in the SDRF graph
Tag: Derived Array Data Matrix File
Allowed attributes: Array Design File/Ref, Comment
DerivedArrayDataMatrixHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.DerivedArrayDataMatrixHandler
DerivedArrayDataMatrixNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node: A derived array data matrix node in the graph.
DerivedArrayDataMatrixNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.DerivedArrayDataMatrixNode
DerivedArrayDataMatrixNodeWrapper - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor
DerivedArrayDataMatrixNodeWrapper(DerivedArrayDataMatrixNode, int, WrapperNodeFactory) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.DerivedArrayDataMatrixNodeWrapper
DerivedArrayDataNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node: A derived array data node in the graph.
DerivedArrayDataNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.DerivedArrayDataNode
DerivedArrayDataNodeWrapper - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor
DerivedArrayDataNodeWrapper(DerivedArrayDataNode, int, WrapperNodeFactory) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.DerivedArrayDataNodeWrapper
description - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ExtractNode
description - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.LabeledExtractNode
description - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SampleNode
description - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SourceNode
digestHeader(String) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Remove any unescaped or unparenthesised whitespace, and convert to lower case for a single header field
digestHeaders(String[]) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Remove any unescaped or unparenthesised whitespace, and convert to lower case for a row of headers

E

endsWithEscapedNewline(String) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Deprecated.
endTable() - Method in interface uk.ac.ebi.arrayexpress2.magetab.utils.tab.ITableDataHandler
endTable() - Method in class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableDataHandler
equals(Object) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.AbstractADFAttribute
equals(Object) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.FeatureNode
equals(Object) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode: Nodes are determined to be equal() if they are of the same class, have the same Node.getNodeType() value and the same AbstractNode.getNodeName() value.
equals(Object) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.Location
equals(Object) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.AbstractSDRFAttribute
equals(Object) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.FactorValueAttribute
ERROR_MARK_UNSUPPORTED - Static variable in exception uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableParserException
ERROR_NULL_READER - Static variable in exception uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableParserException
ErrorItemListener - Interface in uk.ac.ebi.arrayexpress2.magetab.listener: An EventListener interface for making error item callbacks whenever an error item occurs.
errorOccurred(ErrorItem) - Method in interface uk.ac.ebi.arrayexpress2.magetab.listener.ErrorItemListener: Invoked whenever an error item is generated during a parsing operation.
escapeCell(String) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Performs all necessary escaping for cell values using the following rules: - all TAB characters replaced with spaces - cells containing CR and/or LF characters are quoted using double-quotes - existing quoting is preserved - all double-quote characters inside cell will be escaped by pre-pending backslash - existing escaping is preserved
experimentalDesign - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ExperimentalDesignHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Experimental Design fields in the IDF.
ExperimentalDesignHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalDesignHandler
experimentalDesignTermAccession - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ExperimentalDesignTermAccessionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Experimental Design Term Accession Number fields in the IDF.
ExperimentalDesignTermAccessionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalDesignTermAccessionHandler
experimentalDesignTermSourceREF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ExperimentalDesignTermSourceRefHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Experimental Design Term Source Ref fields in the IDF.
ExperimentalDesignTermSourceRefHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalDesignTermSourceRefHandler
experimentalFactorName - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ExperimentalFactorNameHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Experimental Factor Name fields in the IDF.
ExperimentalFactorNameHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalFactorNameHandler
experimentalFactorTermAccession - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ExperimentalFactorTermAccessionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Experimental Factor Term Accession fields in the IDF.
ExperimentalFactorTermAccessionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalFactorTermAccessionHandler
experimentalFactorTermSourceREF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ExperimentalFactorTermSourceRefHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Experimental Factor Term Source REF fields in the IDF.
ExperimentalFactorTermSourceRefHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalFactorTermSourceRefHandler
experimentalFactorType - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ExperimentalFactorTypeHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Experimental Factor Type fields in the IDF.
ExperimentalFactorTypeHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalFactorTypeHandler
experimentDescription - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ExperimentDescriptionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Experiment Description fields in the IDF.
ExperimentDescriptionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentDescriptionHandler
ExtractHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node: A handler that handles Extract nodes in the SDRF graph
Tag: Derived Array Data File
Allowed attributes: Characteristics, Material Type, Description, Comment, Array Design File/Ref
ExtractHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ExtractHandler
ExtractNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node: An extract node in the graph.
ExtractNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ExtractNode
ExtractNodeWrapper - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor
ExtractNodeWrapper(ExtractNode, int, WrapperNodeFactory) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.ExtractNodeWrapper
extractRange(T[], int, int) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Extract a subset of an array from a larger array.
extractRange(T[], int) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Extract a subset of an array from a larger array.
extractSubtype(String) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Extract the subtype given in the header.
extractType(String) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Extract the type given in the header.

F

FactorValueAttribute - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute: A factor value attribute node in the graph.
FactorValueAttribute() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.FactorValueAttribute
FactorValueAttributeReader - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute: Handles factor value attributes in the SDRF graph.
FactorValueAttributeReader(int) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.FactorValueAttributeReader
FactorValueNodeHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node: A special type of 'dummy' handler for handling factor values.
FactorValueNodeHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.FactorValueNodeHandler
factorValues - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.HybridizationNode
factorValues - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ScanNode
FeatureHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.node: A handler that handles feature nodes in the ADF graph.
FeatureHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.FeatureHandler
FeatureNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node: Models "Feature" nodes in the ADF graph, according to the MAGE-TAB specification.
FeatureNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.FeatureNode
fetchUpstreamNode(SDRF, String, Class<T>) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadInContextHandler: Used for adding nodes that are upstream of the current node in the SDRF graph.
finalizeHandlers() - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser.DefaultHandlerListener: Call this when all handlers that are being tracked have been added.
findDownstreamNodes(Node, Class<T>) - Static method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.utils.GraphUtils: Finds nodes downstream of the given node in the graph, searching for nodes of a particular type.
findDownstreamNodes(Node, String) - Static method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.utils.GraphUtils: Finds nodes downstream of the given node in the graph, searching for nodes of a particular type.
findUpstreamNodes(Node, Class<T>) - Static method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.utils.GraphUtils: Finds nodes upstream of the given node in the graph, searching for nodes of a particular type.
findUpstreamNodes(Node, String) - Static method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.utils.GraphUtils: Finds nodes upstream of the given node in the graph, searching for nodes of a particular type.
fireConversionCompletedEvent(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.converter.AbstractConverter
fireConversionEvent(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.converter.AbstractConverter
fireConversionFailedEvent(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.converter.AbstractConverter
fireConversionStartedEvent(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.converter.AbstractConverter
fireErrorItemEvent(ErrorItem) - Method in class uk.ac.ebi.arrayexpress2.magetab.converter.AbstractConverter: Fires an error item notification on any ErrorItemListeners currently configured to listen to this converter.
fireErrorItemEvent(ErrorItem) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser: Fires an error item notification on any ErrorItemListeners currently configured to listen to this parser.
fireErrorItemEvent(ErrorItem) - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.AbstractValidator: Fires an error item notification on any ErrorItemListeners currently configured to listen to this validator.
fireHandlingFailedEvent(HandlerEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.AbstractHandler: Notifies all registered listeners that this handler failed
fireHandlingStartedEvent(HandlerEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.AbstractHandler: Notifies all registered listeners that this handler started
fireHandlingSucceededEvent(HandlerEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.AbstractHandler: Notifies all registered listeners that this handler completed successfully
fireParseEvent(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser
fireParsingCompletedEvent(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser
fireParsingFailedEvent(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser
fireParsingStartedEvent(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser
fireValidationCompletedEvent(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.AbstractValidator
fireValidationEvent(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.AbstractValidator
fireValidationFailedEvent(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.AbstractValidator
fireValidationStartedEvent(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.AbstractValidator
flush() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFGraphWriter
flush() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.ADFWriter
flush() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.IDFWriter
flush() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.SDRFWriter

G

getAccession() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.MAGETABArrayDesign
getAccession() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.MAGETABInvestigation
getADFGraphReadHandlers(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.HandlerLoader: Lookup ADF reading handlers that can read a particular header.
getADFHeaderReadHandlers(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.HandlerLoader: Lookup ADF reading handlers that can read a particular header.
getAllNodes() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractGraph
getAllNodes() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Graph: Lookup all nodes in the SDRF graph
getAllowedLength() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFHeaderReadHandler: Get the legal number of data entries for this type of handler, as specified by the MAGE-TAB specification.
getAllowedLength() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.AccessionHandler
getAllowedLength() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.ArrayDesignNameHandler
getAllowedLength() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.PrintingProtocolHandler
getAllowedLength() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.ProviderHandler
getAllowedLength() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.VersionHandler
getAllowedLength() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.IDFReadHandler: Get the legal number of data entries for this type of handler, as specified by the MAGE-TAB specification.
getAllowedLength() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.AccessionHandler
getAllowedLength() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.DateOfExperimentHandler
getAllowedLength() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentDescriptionHandler
getAllowedLength() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.InvestigationTitleHandler
getAllowedLength() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.MAGETABVersionHandler
getAllowedLength() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicReleaseDateHandler
getAttrColName(SDRFAttribute, String) - Static method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadUtils
getAttribute(Location) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.ADFLayout
getAttribute(Location) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.SDRFLayout
getAttributeType() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ADFAttribute: Get the type of this attribute.
getAttributeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ControlTypeAttribute
getAttributeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ReporterGroupAttribute
getAttributeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.ArrayDesignAttribute
getAttributeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.CharacteristicsAttribute
getAttributeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.FactorValueAttribute
getAttributeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.LabelAttribute
getAttributeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.MaterialTypeAttribute
getAttributeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.ParameterValueAttribute
getAttributeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.PerformerAttribute
getAttributeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.ProviderAttribute
getAttributeType() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.SDRFAttribute: Get the type of this attribute.
getAttributeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.TechnologyTypeAttribute
getAttributeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.UnitAttribute
getAttributeValue() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.AbstractADFAttribute
getAttributeValue() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ADFAttribute: Get the value associated to this attribute in the spreadsheet.
getAttributeValue() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.AbstractSDRFAttribute
getAttributeValue() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.SDRFAttribute: Get the value associated to this attribute in the spreadsheet.
getBase() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper
getChannelMapper() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.WrapperNodeFactory
getChannelNumber(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF: Returns the channel number assigned to any given label.
getChildNodes() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode
getChildNodes() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node: Returns the set of nodes that are children of this node.
getColumn() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.Location
getComments() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF: Get the map of all current comments.
getComments() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF: Get the map of all current comments.
getCommentType(int) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.IDFLayout: Get the comment type on a given line, or null if none exists
getConversionHandlers() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.HandlerLoader: Gets the collection of all available ConversionHandlers.
getConverter() - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABParser: Get the currently configured converter for this parser.
getCurrentChannel() - Method in interface uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.ScannerChannelMapper
getCurrentChannel() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper
getCurrentChannel() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFScannerChannelMapper
getDatatypeName() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.DerivedArrayDataHandler
getDefaultTabValueGroup() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.ArrayDataMatrixNodeWrapper
getDefaultTabValueGroup() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.ArrayDataNodeWrapper
getDefaultTabValueGroup() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.ArrayDesignNodeWrapper
getDefaultTabValueGroup() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.AssayNodeWrapper
getDefaultTabValueGroup() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.DerivedArrayDataMatrixNodeWrapper
getDefaultTabValueGroup() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.DerivedArrayDataNodeWrapper
getDefaultTabValueGroup() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.ExtractNodeWrapper
getDefaultTabValueGroup() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.HybridizationNodeWrapper
getDefaultTabValueGroup() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.ImageNodeWrapper
getDefaultTabValueGroup() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.LabeledExtractNodeWrapper
getDefaultTabValueGroup() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.NormalizationNodeWrapper
getDefaultTabValueGroup() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.ProtocolApplicationNodeWrapper
getDefaultTabValueGroup() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SampleNodeWrapper
getDefaultTabValueGroup() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.ScanNodeWrapper
getDefaultTabValueGroup() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper
getDefaultTabValueGroup() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SourceNodeWrapper
getEncoding() - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser
getEncoding() - Method in interface uk.ac.ebi.arrayexpress2.magetab.parser.Parser: Gets current encoding for the parser.
getErrorItemListeners() - Method in class uk.ac.ebi.arrayexpress2.magetab.converter.AbstractConverter
getErrorItemListeners() - Method in interface uk.ac.ebi.arrayexpress2.magetab.converter.Converter: Get the collection of ErrorItemListeners registered to this parser
getErrorItemListeners() - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser
getErrorItemListeners() - Method in interface uk.ac.ebi.arrayexpress2.magetab.parser.Parser: Get the collection of ErrorItemListeners registered to this parser
getErrorItemListeners() - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.AbstractValidator
getErrorItemListeners() - Method in interface uk.ac.ebi.arrayexpress2.magetab.validator.Validator: Get the current set of ErrorItemListeners registered to this validator
getErrorItems() - Method in exception uk.ac.ebi.arrayexpress2.magetab.exception.ParseException
getField(int) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.IDFLayout: Get the field on the given line, or null if none exists.
getHandledData() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.listener.HandlerEvent
getHandler() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.listener.HandlerEvent
getHandlerLoader() - Static method in class uk.ac.ebi.arrayexpress2.magetab.handler.HandlerLoader
getHeaders() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.ADFLayout
getHeaders() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.SDRFLayout
getIDFLocations(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.visitor.LocationTracker: Deprecated.
since version 1.1, use IDF.getLayout().getLineNumberForHeader() instead
getIDFReadHandlers(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.HandlerLoader: Lookup IDF reading handlers that can read a particular header.
getInputs() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper
getLabelForChannel(int) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF: Returns the label that tags a given channel.
getLastEncounteredException() - Method in class uk.ac.ebi.arrayexpress2.magetab.listener.ProgressEvent
getLayout() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF: Get the layout of this SDRF.
getLayout() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF: Get the layout of this IDF.
getLayout() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF: Get the layout of this SDRF.
getLineCount() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.ADFLayout
getLineCount() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.IDFLayout: Get the number of lines in the serialized IDF.
getLineCount() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.SDRFLayout
getLineNumber() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.Location
getLineNumberForComment(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.IDFLayout: Get the line number assigned to the supplied comment type.
getLineNumberForField(Field) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.IDFLayout: Get the line number assigned to the supplied field.
getLineNumberForHeader(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.IDFLayout
getListeners() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.AbstractHandler
getListeners() - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.Handler: Gets the collection of listeners registered to this handler
getLocation() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF: Get the known location of this SDRF, being the location of the file which was parsed to generate it.
getLocation() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF: Get the known location of this IDF, being the location of the file which was parsed to generate it.
getLocation() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF: Get the known location of this SDRF, being the location of the file which was parsed to generate it.
getLocationsForAttribute(SDRFAttribute) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.SDRFLayout
getLocationsForNode(SDRFNode) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.SDRFLayout
getLocationsForPrimitive(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.SDRFLayout
getLocationTracker() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.MAGETABInvestigation: Deprecated.
since version 1.1, use Layout implementations instead
getLog() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.AbstractADFAttribute
getLog() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractGraph
getLog() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode
getLog() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
getLog() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.ADFLayout
getLog() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.calc.SDRFLayoutCalculator
getLog() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.IDFLayout
getLog() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.SDRFLayout
getLog() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.AbstractSDRFAttribute
getLog() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.AbstractHandler: Gets a logger configured for the current handler class
getLog() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.HandlerLoader
getLog() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.CharacteristicsAttributeReader
getLog() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.FactorValueAttributeReader
getLog() - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser
getLog() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.IDFWriter
getLog() - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.AbstractValidator
getNode(String, Class<T>) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractGraph
getNode(String, String) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractGraph
getNode(String, Class<T>) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Graph: Lookup a node by name and class type in the SDRF graph.
getNode(String, String) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Graph: Lookup a node by name and type in the SDRF graph.
getNode(Location) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.ADFLayout
getNode(Location) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.SDRFLayout
getNodeColName(SDRFNode, String) - Static method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadUtils
getNodeCount() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractGraph
getNodeCount() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Graph: Returns the total number of nodes stored by this SDRF graph.
getNodeName() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.AbstractADFAttribute
getNodeName() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ADFAttribute: Deprecated.
since version 1.1, use ADFAttribute.getAttributeValue() instead. Preserved for backwards compatibility
getNodeName() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode
getNodeName() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node: Get the value associated to this node in the spreadsheet.
getNodeName() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.AbstractSDRFAttribute
getNodeName() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.SDRFAttribute: Deprecated.
since version 1.1, use SDRFAttribute.getAttributeValue() instead. Preserved for backwards compatibility
getNodes(Class<T>) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractGraph
getNodes(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractGraph
getNodes(Class<T>) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Graph: Lookup all nodes of the given class type in the SDRF graph.
getNodes(String) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Graph: Lookup all nodes of the given type (by SDRF spec name) in the SDRF graph.
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.AbstractADFAttribute
getNodeType() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ADFAttribute: Deprecated.
since version 1.1, use ADFAttribute.getAttributeType() instead. Preserved for backwards compatibility
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.CompositeElementNode
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.FeatureNode
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.ReporterNode
getNodeType() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node: Get the type of this node in the graph.
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.UnresolvedPlaceholderNode
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ArrayDataMatrixNode
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ArrayDataNode
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ArrayDesignNode: Deprecated.
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.AssayNode
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.AbstractSDRFAttribute
getNodeType() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.SDRFAttribute: Deprecated.
since version 1.1, use SDRFAttribute.getAttributeType() instead. Preserved for backwards compatibility
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.DerivedArrayDataMatrixNode
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.DerivedArrayDataNode
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ExtractNode
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.HybridizationNode
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ImageNode
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.LabeledExtractNode
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.NormalizationNode
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ProtocolApplicationNode
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SampleNode
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ScanNode
getNodeType() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SourceNode
getNumberOfChannels() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF: Returns the number of channels in this experiment.
getOrder() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper
getOutputResource() - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABArrayParser: Get the currently configured output resource for this parser
getOutputs() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper
getParentNodes() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode
getParentNodes() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node: Returns the set of nodes that are parents of this node.
getPrimitive(Location) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.ADFLayout
getPrimitive(Location) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.SDRFLayout
getProgressListeners() - Method in class uk.ac.ebi.arrayexpress2.magetab.converter.AbstractConverter
getProgressListeners() - Method in interface uk.ac.ebi.arrayexpress2.magetab.converter.Converter: Get the collection of ProgressListeners that are currently registered to this converter.
getProgressListeners() - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser
getProgressListeners() - Method in interface uk.ac.ebi.arrayexpress2.magetab.parser.Parser: Get the collection of ProgressListeners that are currently registered to this parser.
getProgressListeners() - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.AbstractValidator
getProgressListeners() - Method in interface uk.ac.ebi.arrayexpress2.magetab.validator.Validator: Get the collection of ProgressListeners that are currently registered to this validator.
getReadHandlers() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.HandlerLoader: Gets the collection of all available ReadHandlers.
getReadHandlersOfType(Class<T>, S) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.HandlerLoader: Generic method for looking up ReadHandlers that extend the given superclass and can read from the given header.
getRootNodes() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractGraph
getRootNodes() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Graph: Lookup all 'root' nodes in the SDRF graph.
getRow() - Method in class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableDataHandler
getSDRFLocations(SDRFNode) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.visitor.LocationTracker: Deprecated.
since version 1.1, use SDRF.getLayout().getLocationsForNode() instead
getSDRFReadHandlers(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.HandlerLoader: Lookup SDRF reading handlers that can read a particular header.
getTable() - Method in interface uk.ac.ebi.arrayexpress2.magetab.utils.tab.ITableDataHandler
getTable() - Method in class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableDataHandler
getTabValues() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper
getType() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.listener.HandlerEvent
getType() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper
getValidateHandlers() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.HandlerLoader: Gets the collection of all available ValidateHandlers.
getValidator() - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABArrayParser: Get the currently configured validator for this parser.
getValidator() - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABParser: Get the currently configured validator for this parser.
Graph<S extends Node> - Interface in uk.ac.ebi.arrayexpress2.magetab.datamodel.graph: A directed, acyclic graph that can be used to store Nodes that are linked together.
GraphUtils - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.utils: A class containing some useful utility methods for navigating graphs utilising the structures in uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.
GraphUtils() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.utils.GraphUtils

H

Handler - Interface in uk.ac.ebi.arrayexpress2.magetab.handler: A class for handling discrete sections of a file that comprises a MAGE-TAB document.
HandlerEvent - Class in uk.ac.ebi.arrayexpress2.magetab.handler.listener: An event generated by Handlers to be passed to a HandlerListener.
HandlerEvent(Handler, HandlerEvent.Type, Object) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.listener.HandlerEvent
HandlerEvent.Type - Enum in uk.ac.ebi.arrayexpress2.magetab.handler.listener
HandlerListener - Interface in uk.ac.ebi.arrayexpress2.magetab.handler.listener: A listener that can be registered to a Handler in order to track events that occur during the parsing of MAGE-TAB documents.
HandlerLoader - Class in uk.ac.ebi.arrayexpress2.magetab.handler: Loads Handler implementations available using service provider discovery (SPI annotations).
HandlerLoader() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.HandlerLoader
HandlerVisitor<T extends Handler> - Interface in uk.ac.ebi.arrayexpress2.magetab.handler.visitor: An visitor interface that can inspect Handlers, and extract useful information about the data that was assigned to it.
handleUpstreamNode(SDRF, String, String, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadInContextHandler: Used for adding nodes that are upstream of the current node in the SDRF graph.
handlingFailed(HandlerEvent) - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.listener.HandlerListener: Invoked whenever a handler fails when handling some data
handlingFailed(HandlerEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser.DefaultHandlerListener
handlingStarted(HandlerEvent) - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.listener.HandlerListener: Invoked whenever a handler starts handling some data
handlingStarted(HandlerEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser.DefaultHandlerListener
handlingSucceeded(HandlerEvent) - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.listener.HandlerListener: Invoked whenever a handler starts succeeds at handling some data
handlingSucceeded(HandlerEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser.DefaultHandlerListener
hasBeenHandled(String, Class<? extends ADFNode>) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF: Determine whether a given node has been handled already, and exists in the graph.
hasBeenHandled(String, Class<? extends SDRFNode>) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF: Determine whether a given node has been handled already, and exists in the graph.
hashCode() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.AbstractADFAttribute
hashCode() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.FeatureNode
hashCode() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode
hashCode() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.Location
hashCode() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.AbstractSDRFAttribute
hashCode() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.FactorValueAttribute
hasSectionDetected(InputStream, String, String...) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableParserRunner
hasSectionDetected() - Method in class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableSectionDetectingDataHandler
headers() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.ADFNode: Returns a string array representing the headers of this node and all it's attributes.
headers() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ADFAttribute: Returns a string array representing the headers of this node and all it's attributes.
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ControlTypeAttribute
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ReporterGroupAttribute
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.CompositeElementNode
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.FeatureNode
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.ReporterNode
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ArrayDataMatrixNode
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ArrayDataNode
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ArrayDesignNode: Deprecated.
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.AssayNode
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.ArrayDesignAttribute
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.CharacteristicsAttribute
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.FactorValueAttribute
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.LabelAttribute
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.MaterialTypeAttribute
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.ParameterValueAttribute
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.PerformerAttribute
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.ProviderAttribute
headers() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.SDRFAttribute: Returns a string array representing the headers of this node and all it's attributes.
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.TechnologyTypeAttribute
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.UnitAttribute
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.DerivedArrayDataMatrixNode
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.DerivedArrayDataNode
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ExtractNode
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.HybridizationNode
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ImageNode
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.LabeledExtractNode
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.NormalizationNode
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ProtocolApplicationNode
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SampleNode
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ScanNode
headers() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SDRFNode: Returns a string array representing the headers of this node and all it's attributes.
headers() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SourceNode
HybridizationHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node: A handler that handles Hybridization nodes in the SDRF graph
Tag: Hybridization Name
Allowed attributes: Factor Value, Comment
HybridizationHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.HybridizationHandler
HybridizationNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node: A hybridization node in the graph.
HybridizationNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.HybridizationNode
HybridizationNodeWrapper - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor
HybridizationNodeWrapper(HybridizationNode, int, WrapperNodeFactory) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.HybridizationNodeWrapper

I

IDF - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel: A datastructure that simply models IDF in the MAGE-TAB spec.
IDF() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
IDF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.MAGETABInvestigation
IDFConversionHandler<O> - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf: An abstract implementation of a ConversionHandler for writing data from an IDF to some external output resource.
IDFConversionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.IDFConversionHandler
IDFConverter<O> - Class in uk.ac.ebi.arrayexpress2.magetab.converter: Javadocs go here!
IDFConverter() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.converter.IDFConverter
IDFField - Annotation Type in uk.ac.ebi.arrayexpress2.magetab.datamodel: Annotation class that adds mapping between fields of IDF.class and fields in IDF object
IDFLayout - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.layout: An object that describes the relationship between an IDF datamodel object and the serialized version of it.
IDFLayout() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.IDFLayout
IDFParser - Class in uk.ac.ebi.arrayexpress2.magetab.parser: Parses IDF documents from the supplied input stream into a IDF object.
IDFParser() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.parser.IDFParser
IDFReadHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf: An abstract implementation of a ReadHandler for reading data from IDF file into an MAGETABInvestigation.
IDFReadHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.IDFReadHandler
IDFValidateHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf: An abstract implementation of a ValidateHandler for writing data from an IDF to some external output resource.
IDFValidateHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.IDFValidateHandler
IDFValidator - Class in uk.ac.ebi.arrayexpress2.magetab.validator: Javadocs go here!
IDFValidator() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.validator.IDFValidator
IDFWriter - Class in uk.ac.ebi.arrayexpress2.magetab.renderer: Javadocs go here!
IDFWriter(Writer) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.IDFWriter
IllegalLineLengthException - Exception in uk.ac.ebi.arrayexpress2.magetab.exception: A ParseException that is thrown whenever a line parsed from a TDT file is an illegal length.
IllegalLineLengthException() - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.IllegalLineLengthException
IllegalLineLengthException(String) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.IllegalLineLengthException
IllegalLineLengthException(String, Throwable) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.IllegalLineLengthException
IllegalLineLengthException(Throwable) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.IllegalLineLengthException
IllegalLineLengthException(boolean, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.IllegalLineLengthException
IllegalLineLengthException(boolean, String, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.IllegalLineLengthException
IllegalLineLengthException(boolean, String, Throwable, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.IllegalLineLengthException
IllegalLineLengthException(boolean, Throwable, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.IllegalLineLengthException
ImageHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node: A handler that handles Image nodes in the SDRF graph
Tag: Image File
Allowed attributes: Array Design File/Ref, Comment
ImageHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ImageHandler
ImageNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node: An image node in the graph.
ImageNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ImageNode
ImageNodeWrapper - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor
ImageNodeWrapper(ImageNode, int, WrapperNodeFactory) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.ImageNodeWrapper
InconsistentEntryCountException - Exception in uk.ac.ebi.arrayexpress2.magetab.exception: A ParseException that is thrown when the number of entries in a spreadsheet is not consistent, for example when an fixed size matrix is expected but column lengths are variable.
InconsistentEntryCountException() - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.InconsistentEntryCountException
InconsistentEntryCountException(String) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.InconsistentEntryCountException
InconsistentEntryCountException(String, Throwable) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.InconsistentEntryCountException
InconsistentEntryCountException(Throwable) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.InconsistentEntryCountException
InconsistentEntryCountException(boolean, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.InconsistentEntryCountException
InconsistentEntryCountException(boolean, String, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.InconsistentEntryCountException
InconsistentEntryCountException(boolean, String, Throwable, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.InconsistentEntryCountException
InconsistentEntryCountException(boolean, Throwable, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.InconsistentEntryCountException
insertColumn(String[][], String, int) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils
investigationTitle - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
InvestigationTitleHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Investigation Title fields in the IDF.
InvestigationTitleHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.InvestigationTitleHandler
isAnchoredAttribute(String, String) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Determines whether the supplied attribute header is anchored to the parent header.
isCompletelyUnassigned() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.ADFLayout
isCompletelyUnassigned() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.IDFLayout
isCompletelyUnassigned() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.Layout: Returns true if there is no layout information contained within this layout
isCompletelyUnassigned() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.SDRFLayout
isCriticalException() - Method in exception uk.ac.ebi.arrayexpress2.magetab.exception.ParseException
isDirectlyDownstream(Node, Node) - Static method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.utils.GraphUtils: Determine whether the query node, "maybeDownstreamNode", is downstream of the current node in the given SDRF graph.
isDirectlyUpstream(Node, Node) - Static method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.utils.GraphUtils: Determine whether the query node, "maybeUpstreamNode", is upstream of the current node in the given graph.
isEndNode() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper
isMergedTabDelimitedInputStream(InputStream, String, String...) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: If possible, checks whether the supplied input stream reads from a merged MAGE-TAB file.
isMultiChannel() - Method in interface uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.ScannerChannelMapper
isMultiChannel() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper
isMultiChannel() - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFScannerChannelMapper
isStrippingEscaping() - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser
ITableDataHandler - Interface in uk.ac.ebi.arrayexpress2.magetab.utils.tab

L

label - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.LabeledExtractNode
LabelAttribute - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute: A label attribute node in the graph.
LabelAttribute() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.LabelAttribute
LabelAttributeReader - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute: Handles label attributes in the SDRF graph.
LabelAttributeReader() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.LabelAttributeReader
LabeledExtractHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node: A handler that handles Labeled Extract nodes in the SDRF graph
Tag: Labeled Extract Name
Allowed attributes: Characteristics, Material Type, Description, Label, Array Design File/Ref, Comment
LabeledExtractHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.LabeledExtractHandler
LabeledExtractNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node: A labeled extract node in the graph.
LabeledExtractNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.LabeledExtractNode
LabeledExtractNodeWrapper - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor
LabeledExtractNodeWrapper(LabeledExtractNode, int, WrapperNodeFactory) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.LabeledExtractNodeWrapper
Layout<T> - Interface in uk.ac.ebi.arrayexpress2.magetab.datamodel.layout: An object that describes the relationship between a datamodel object and the serialized version of it.
listeners - Variable in class uk.ac.ebi.arrayexpress2.magetab.handler.AbstractHandler
loadHandlers() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.HandlerLoader: Loads all handlers available.
locateIDF(File) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Given a directory that represents a MAGE-TAB document, locate the IDF file it contains
locateSDRF(File) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Given a directory that represents a MAGE-TAB document, locate the SDRF file it contains
Location - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.layout: An object representing a location within a tab delimited text file.
Location(int, int) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.Location
LocationTracker - Class in uk.ac.ebi.arrayexpress2.magetab.handler.visitor: Deprecated.
since version 1.1, use Layout implementations instead
LocationTracker(MAGETABInvestigation) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.visitor.LocationTracker: Deprecated.
lookupNode(String, Class<T>) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF: Deprecated.
since version 1.1, use AbstractGraph.getNode(String, Class) instead
lookupNode(String, String) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF: Deprecated.
since version 1.1, use AbstractGraph.getNode(String, String) instead
lookupNode(String, Class<T>) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF: Deprecated.
since version 1.1, use AbstractGraph.getNode(String, Class) instead
lookupNode(String, String) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF: Deprecated.
since version 1.1, use AbstractGraph.getNode(String, String) instead
lookupNodes(Class<T>) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF: Deprecated.
since version 1.1, use AbstractGraph.getNodes(Class) instead
lookupNodes(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF: Deprecated.
since version 1.1, use AbstractGraph.getNodes(String) instead
lookupNodes(Class<T>) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF: Deprecated.
since version 1.1, use AbstractGraph.getNodes(Class) instead
lookupNodes(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF: Deprecated.
since version 1.1, use AbstractGraph.getNodes(String) instead
lookupProtocols() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF: Lookup all named protocols references in this SDRF.

M

MAGETABArrayDesign - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel: An object that models a MAGE-TAB representation of an array design, with a single ADF element that corresponds to the MAGE-TAB specification.
MAGETABArrayDesign() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.MAGETABArrayDesign
MAGETABArrayParser<O> - Class in uk.ac.ebi.arrayexpress2.magetab.parser: Imports MAGETAB Array Design documents into a MAGETABArrayDesign.
MAGETABArrayParser() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABArrayParser
MAGETABConverter<O> - Class in uk.ac.ebi.arrayexpress2.magetab.converter: Performs conversion of a MAGE-TAB object model using any ConversionHandlers available.
MAGETABConverter() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.converter.MAGETABConverter
MAGETABInvestigation - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel: An object that models a MAGE-TAB document, with elements for each type of structure within the MAGE-TAB specification.
MAGETABInvestigation() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.MAGETABInvestigation
MAGETABParser<O> - Class in uk.ac.ebi.arrayexpress2.magetab.parser: Imports MAGETAB documents into a MAGETABInvestigation.
MAGETABParser() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABParser: Create a default parser.
MAGETABParser(O...) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABParser: Create a default parser.
MAGETABParser(Validator<MAGETABInvestigation>) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABParser: Create a parser that performs validation using the supplied Validator.
MAGETABParser(Converter<MAGETABInvestigation, O>, O...) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABParser: 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>, Converter<MAGETABInvestigation, O>, O...) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABParser: Create a parser that performs validation using the supplied Validator and conversion using the supplied Converter.
MAGETABUtils - Class in uk.ac.ebi.arrayexpress2.magetab.utils: Some common utilities for working with MAGE-TAB files.
MAGETABUtils() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils
MAGETABValidateHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler: An abstract implementation of a ValidateHandler for validating data from an MAGETABInvestigation#.
MAGETABValidateHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.MAGETABValidateHandler
MAGETABValidator - Class in uk.ac.ebi.arrayexpress2.magetab.validator: Performs validation of a MAGE-TAB object model using any ValidateHandlers available.
MAGETABValidator() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.validator.MAGETABValidator
magetabVersion - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
magetabVersion - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
MAGETABVersionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle MAGE-TAB Version fields in the IDF.
MAGETABVersionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.MAGETABVersionHandler
materialType - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ExtractNode
materialType - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.LabeledExtractNode
materialType - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SampleNode
materialType - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SourceNode
MaterialTypeAttribute - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute: A material type attribute node in the graph.
MaterialTypeAttribute() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.MaterialTypeAttribute
MaterialTypeAttributeReader - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute: Handles material type attributes in the SDRF graph.
MaterialTypeAttributeReader() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.MaterialTypeAttributeReader
ModelTableBuilder - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor: Class needed for graph2tab algorithm
Creates instances for SDRF graph node's wrappers from SDRF graph nodes
ModelTableBuilder(Collection<? extends SDRFNode>, WrapperNodeFactory) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.ModelTableBuilder

N

needsData() - Method in interface uk.ac.ebi.arrayexpress2.magetab.utils.tab.ITableDataHandler
needsData() - Method in class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableDataHandler
needsData() - Method in class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableSectionDataHandler
needsData() - Method in class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableSectionDetectingDataHandler
Node - Interface in uk.ac.ebi.arrayexpress2.magetab.datamodel.graph: A node in a MAGETAB graph data structure (either ADF or SDRF).
nodeName - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode
NormalizationHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node: A handler that handles Normalization nodes in the SDRF graph
Tag: Normalization Name
Allowed attributes: Array Design File/Ref, Comment
NormalizationHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.NormalizationHandler
NormalizationNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node: A normalization node in the graph.
NormalizationNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.NormalizationNode
NormalizationNodeWrapper - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor
NormalizationNodeWrapper(NormalizationNode, int, WrapperNodeFactory) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.NormalizationNodeWrapper
normalizationTermAccession - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
NormalizationTermAccessionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Normalization Term Accession fields in the IDF.
NormalizationTermAccessionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.NormalizationTermAccessionHandler
normalizationTermSourceREF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
NormalizationTermSourceRefHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Normalization Term Source REF fields in the IDF.
NormalizationTermSourceRefHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.NormalizationTermSourceRefHandler
normalizationType - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
NormalizationTypeHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Normalization Type fields in the IDF.
NormalizationTypeHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.NormalizationTypeHandler

O

optionalType - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.FactorValueAttribute

P

ParameterValueAttribute - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute: A parameter value attribute node in the graph.
ParameterValueAttribute() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.ParameterValueAttribute
ParameterValueAttributeReader - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute: Handles parameter value attributes in the SDRF graph.
ParameterValueAttributeReader() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.ParameterValueAttributeReader
parameterValues - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ProtocolApplicationNode
parse(InputStream) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.ADFParser: Performs parsing from the specified input stream source, populating an ADF object which is returned.
parse(InputStream, ADF) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.ADFParser
parse(InputStream, ADF, ExecutorService) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.ADFParser
parse(File) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.IDFParser
parse(URL) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.IDFParser
parse(InputStream) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.IDFParser: Performs parsing from the specified input stream source, populating an IDF object which is returned.
parse(InputStream, IDF) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.IDFParser: Alternate form of the IDFParser.parse(java.io.InputStream) method that allows callers to specify the IDF object they want to be populated.
parse(InputStream, IDF, ExecutorService) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.IDFParser: 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.
parse(File) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABArrayParser
parse(URL) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABArrayParser
parse(InputStream) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABArrayParser
parse(InputStream, MAGETABArrayDesign) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABArrayParser
parse(InputStream, MAGETABArrayDesign, ExecutorService) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABArrayParser
parse(File) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABParser
parse(URL) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABParser
parse(InputStream) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABParser
parse(InputStream, MAGETABInvestigation) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABParser
parse(InputStream, MAGETABInvestigation, ExecutorService) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABParser
parse(InputStream) - Method in interface uk.ac.ebi.arrayexpress2.magetab.parser.Parser: Perform parsing from the supplied input stream to a new data model instance.
parse(InputStream, T) - Method in interface uk.ac.ebi.arrayexpress2.magetab.parser.Parser: Perform parsing from the supplied input stream to a new data model instance.
parse(InputStream, T, ExecutorService) - Method in interface uk.ac.ebi.arrayexpress2.magetab.parser.Parser: Perform parsing from the supplied input stream to a new data model instance, delegating all work to the supplied Executor Service to enable parsing in parallel.
parse(File) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.SDRFParser
parse(URL) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.SDRFParser
parse(InputStream) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.SDRFParser: Performs parsing from the specified input stream source, populating an SDRF object which is returned.
parse(InputStream, SDRF) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.SDRFParser: Alternate form of the SDRFParser.parse(java.io.InputStream) method that allows callers to specify the SDRF object they want to be populated.
parse(InputStream, SDRF, ExecutorService) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.SDRFParser: 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.
parse(InputStream, String) - Method in class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableParser
parse(InputStream, String, TableParser.Option...) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableParserRunner
parsedMore(ProgressEvent) - Method in interface uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListener: Invoked whenever more of a document is parsed.
parsedMore(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListenerAdapter
ParseException - Exception in uk.ac.ebi.arrayexpress2.magetab.exception: An exception thrown whenever there was a problem parsing a native MAGE-TAB file.
ParseException() - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ParseException
ParseException(String) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ParseException
ParseException(String, Throwable) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ParseException
ParseException(Throwable) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ParseException
ParseException(boolean, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ParseException
ParseException(boolean, String, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ParseException
ParseException(boolean, String, Throwable, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ParseException
ParseException(boolean, Throwable, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ParseException
Parser<T> - Interface in uk.ac.ebi.arrayexpress2.magetab.parser: A parser that reads from a given URL and populates a data model.
parseSection(InputStream, String, String, String, TableParser.Option...) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableParserRunner
parsingCompleted(ProgressEvent) - Method in interface uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListener: Invoked whenever a parse operation completes successfully
parsingCompleted(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListenerAdapter
parsingFailed(ProgressEvent) - Method in interface uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListener: Invoked whenever a parse operation completes, but failed to read some of the document
parsingFailed(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListenerAdapter
parsingStarted(ProgressEvent) - Method in interface uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListener: Invoked whenever a parse operation commences
parsingStarted(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListenerAdapter
performer - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ProtocolApplicationNode
PerformerAttribute - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute: A performer attribute node in the graph.
PerformerAttribute() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.PerformerAttribute
PerformerAttributeReader - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute: Handles performer attributes in the SDRF graph.
PerformerAttributeReader() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.PerformerAttributeReader
personAddress - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
PersonAddressHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Person Address fields in the IDF.
PersonAddressHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonAddressHandler
personAffiliation - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
PersonAffiliationHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Person Affiliation fields in the IDF.
PersonAffiliationHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonAffiliationHandler
personEmail - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
PersonEmailHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Person Email fields in the IDF.
PersonEmailHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonEmailHandler
personFax - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
PersonFaxHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Person Fax fields in the IDF.
PersonFaxHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonFaxHandler
personFirstName - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
PersonFirstNameHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Person First Name fields in the IDF.
PersonFirstNameHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonFirstNameHandler
personLastName - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
PersonLastNameHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Person Last Name fields in the IDF.
PersonLastNameHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonLastNameHandler
personMidInitials - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
PersonMidInitialsHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Person Mid Initial fields in the IDF.
PersonMidInitialsHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonMidInitialsHandler
personPhone - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
PersonPhoneHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Person Phone fields in the IDF.
PersonPhoneHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonPhoneHandler
personRoles - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
PersonRolesHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Person Roles fields in the IDF.
PersonRolesHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonRolesHandler
personRolesTermAccession - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
PersonRolesTermAccessionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Person Roles Term Accession Number fields in the IDF.
PersonRolesTermAccessionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonRolesTermAccessionHandler
personRolesTermSourceREF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
PersonRolesTermSourceRefHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Person Roles Term Source REF fields in the IDF.
PersonRolesTermSourceRefHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonRolesTermSourceRefHandler
printingProtocol - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
PrintingProtocolHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handlers ADF rows describing the printing protocol
Tag: Printing Protocol
PrintingProtocolHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.PrintingProtocolHandler
ProgressEvent - Class in uk.ac.ebi.arrayexpress2.magetab.listener: An event that indicates parser progress
ProgressEvent() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.listener.ProgressEvent
ProgressListener - Interface in uk.ac.ebi.arrayexpress2.magetab.listener: A listener used by Parser implementations to report on the progress of a parse operation
ProgressListenerAdapter - Class in uk.ac.ebi.arrayexpress2.magetab.listener: An empty implementation of the ProgressListener interface, provided as a convenience to simplify the task of creating listeners, by extending and implementing only the methods of interest.
ProgressListenerAdapter() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListenerAdapter
protocol - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ProtocolApplicationNode
PROTOCOL_DELIMITER - Static variable in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadHandler
ProtocolApplicationNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node: A protocol "node" in the graph.
ProtocolApplicationNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ProtocolApplicationNode
ProtocolApplicationNodeWrapper - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor
ProtocolApplicationNodeWrapper(ProtocolApplicationNode, int, WrapperNodeFactory) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.ProtocolApplicationNodeWrapper
protocolContact - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ProtocolContactHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Protocol Contact fields in the IDF.
ProtocolContactHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolContactHandler
protocolDescription - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ProtocolDescriptionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Protocol Description fields in the IDF.
ProtocolDescriptionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolDescriptionHandler
ProtocolHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node: A handler that handles Protocol edges in the SDRF graph.
ProtocolHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ProtocolHandler
protocolHardware - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ProtocolHardwareHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Protocol hardware fields in the IDF.
ProtocolHardwareHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolHardwareHandler
protocolName - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ProtocolNameHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Protocol Name fields in the IDF.
ProtocolNameHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolNameHandler
protocolParameters - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ProtocolParametersHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Protocol Name fields in the IDF.
ProtocolParametersHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolParametersHandler
protocolSoftware - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ProtocolSoftwareHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Protocol Software fields in the IDF.
ProtocolSoftwareHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolSoftwareHandler
protocolTermAccession - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ProtocolTermAccessionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Protocol Term accession fields in the IDF.
ProtocolTermAccessionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolTermAccessionHandler
protocolTermSourceREF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ProtocolTermSourceRefHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Protocol Term Source Ref fields in the IDF.
ProtocolTermSourceRefHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolTermSourceRefHandler
protocolType - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ProtocolTypeHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Protocol Type fields in the IDF.
ProtocolTypeHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolTypeHandler
provider - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
provider - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SourceNode
ProviderAttribute - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute: A provider attribute node in the graph.
ProviderAttribute() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.ProviderAttribute
ProviderAttributeReader - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute: Handles provider attributes in the SDRF graph.
ProviderAttributeReader() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.ProviderAttributeReader
ProviderHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handles ADF rows describing the provider
Tag: Provider
ProviderHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.ProviderHandler
publicationAuthorList - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
PublicationAuthorListHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Publication Author List fields in the IDF.
PublicationAuthorListHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicationAuthorListHandler
publicationDOI - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
PublicationDoiHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Publication DOI Handler fields in the IDF.
PublicationDoiHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicationDoiHandler
publicationStatus - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
PublicationStatusHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Publication Status fields in the IDF.
PublicationStatusHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicationStatusHandler
publicationStatusTermAccession - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
PublicationStatusTermAccessionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Publication Status Term Accession fields in the IDF.
PublicationStatusTermAccessionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicationStatusTermAccessionHandler
publicationStatusTermSourceREF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
PublicationStatusTermSourceRefHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Publication Status Term Source Ref fields in the IDF.
PublicationStatusTermSourceRefHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicationStatusTermSourceRefHandler
publicationTitle - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
PublicationTitleHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Publication Title fields in the IDF.
PublicationTitleHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicationTitleHandler
publicReleaseDate - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
PublicReleaseDateHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Public Release Date Handler fields in the IDF.
PublicReleaseDateHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicReleaseDateHandler
pubMedId - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
PubMedIdHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle PubMed ID fields in the IDF.
PubMedIdHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PubMedIdHandler

Q

qualityControlTermAccession - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
QualityControlTermAccessionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Quality Control Term Accession fields in the IDF.
QualityControlTermAccessionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.QualityControlTermAccessionHandler
qualityControlTermSourceREF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
QualityControlTermSourceRefHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Quality Control Term Source Ref fields in the IDF.
QualityControlTermSourceRefHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.QualityControlTermSourceRefHandler
qualityControlType - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
QualityControlTypeHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Quality Control Type fields in the IDF.
QualityControlTypeHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.QualityControlTypeHandler

R

read(String[], String[], ADF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFGraphReadHandler
read(String, String[], ADF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFHeaderReadHandler: Invoke this read handler.
read(String, String[], IDF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.IDFReadHandler: Invoke this read handler.
read(H, D, T, int, int) - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.ReadHandler: Cause the handler to read the supplied data into the supplied target object.
read(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadHandler
read(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadInContextHandler
read(String[][], ADF, ExecutorService) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.ADFParser
read(String[][], IDF, ExecutorService) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.IDFParser: Reads tabulated IDF data into the supplied IDF object, delegating the execution of handling tasks to the supplied ExecutorService.
read(String[][], SDRF, ExecutorService) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.SDRFParser: Reads tabulated SDRF data into the supplied SDRF object, delegating the execution of handling tasks to the supplied ExecutorService.
readAttribute(ADFAttributeReader, String[], String[], ADFNode, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFGraphReadHandler
readAttribute(SDRFAttributeReader, String[], String[], SDRF, SDRFNode, int, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadHandler
readAttributes(String[], String[], ADFNode) - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.attribute.ADFAttributeReader: Reads the attributes from the data and sets them on the supplied SDRFNode
readAttributes(String[], String[], ADFNode) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.attribute.ControlTypeAttributeReader
readAttributes(String[], String[], ADFNode) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.attribute.ReporterGroupAttributeReader
readAttributes(String[], String[], SDRF, SDRFNode, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.ArrayDesignAttributeReader
readAttributes(String[], String[], SDRF, SDRFNode, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.CharacteristicsAttributeReader
readAttributes(String[], String[], SDRF, SDRFNode, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.FactorValueAttributeReader
readAttributes(String[], String[], SDRF, SDRFNode, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.LabelAttributeReader
readAttributes(String[], String[], SDRF, SDRFNode, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.MaterialTypeAttributeReader
readAttributes(String[], String[], SDRF, SDRFNode, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.ParameterValueAttributeReader
readAttributes(String[], String[], SDRF, SDRFNode, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.PerformerAttributeReader
readAttributes(String[], String[], SDRF, SDRFNode, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.ProviderAttributeReader
readAttributes(String[], String[], SDRF, SDRFNode, int, int) - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.SDRFAttributeReader: Reads the attributes from the data and sets them on the supplied SDRFNode
readAttributes(String[], String[], SDRF, SDRFNode, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.TechnologyTypeAttributeReader
readData(String[], String[], ADF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFGraphReadHandler: Performs the unit of work to read the data into the internal datamodel.
readData(String[], String[], ADF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.CompositeElementHandler
readData(String[], String[], ADF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.FeatureHandler
readData(String[], String[], ADF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.ReporterHandler
readData(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ArrayDataHandler
readData(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ArrayDataMatrixHandler
readData(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.AssayHandler
readData(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.DerivedArrayDataHandler
readData(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.DerivedArrayDataMatrixHandler
readData(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ExtractHandler
readData(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.FactorValueNodeHandler
readData(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.HybridizationHandler
readData(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ImageHandler
readData(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.LabeledExtractHandler
readData(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.NormalizationHandler
readData(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ProtocolHandler
readData(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.SampleHandler
readData(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ScanHandler
readData(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.SourceHandler
readData(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.UnknownHeaderHandler
readData(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadHandler: Performs the unit of work to read the data into the internal datamodel.
readDataFrom(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.FactorValueNodeHandler: 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.
readDataFrom(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ProtocolHandler: A specialised alternate form of the SDRFReadInContextHandler.canReadHeader(String[]) method for handling Protocol Application Nodes.
readDataFrom(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadInContextHandler: Performs the unit of work to read the data into the internal datamodel.
readFrom(String[], String[], SDRF, int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadInContextHandler: 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.
ReadHandler<H,D,T> - Interface in uk.ac.ebi.arrayexpress2.magetab.handler: A type of Handler that enables read functionality over a section of MAGE-TAB.
readIDF(InputStream, MAGETABInvestigation, boolean, ExecutorService, MAGETABParser<O>.ProgressFlag) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABParser
readMergedTabDelimitedInputStream(InputStream, String, boolean, String...) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Deprecated.
readMergedTabDelimitedInputStream(InputStream, String, boolean, boolean, String...) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Deprecated.
readSDRF(InputStream, SDRF, ExecutorService, MAGETABParser<O>.ProgressFlag) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABParser
readTabDelimitedInputStream(InputStream, String, boolean, boolean) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Deprecated.
readTabDelimitedInputStream(InputStream, String, boolean) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Deprecated.
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFHeaderReadHandler: Performs the unit of work to read the data into the internal MAGE-TAB investigation.
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.AccessionHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.ArrayDesignNameHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.CommentHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.PrintingProtocolHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.ProviderHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SequencePolymerTypeHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SequencePolymerTypeTermAccessionHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SequencePolymerTypeTermSourceRefHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SubstrateTypeHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SubstrateTypeTermAccessionHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SubstrateTypeTermSourceRefHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SurfaceTypeHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SurfaceTypeTermAccessionHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SurfaceTypeTermSourceRefHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.TechnologyTypeHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.TechnologyTypeTermAccessionHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.TechnologyTypeTermSourceRefHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.TermSourceFileHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.TermSourceNameHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.TermSourceVersionHandler
readValue(ADF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.VersionHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.IDFReadHandler: Performs the unit of work to read the data into the internal MAGE-TAB investigation.
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.AccessionHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.CommentHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.DateOfExperimentHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalDesignHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalDesignTermAccessionHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalDesignTermSourceRefHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalFactorNameHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalFactorTermAccessionHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalFactorTermSourceRefHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalFactorTypeHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentDescriptionHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.InvestigationTitleHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.MAGETABVersionHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.NormalizationTermAccessionHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.NormalizationTermSourceRefHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.NormalizationTypeHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonAddressHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonAffiliationHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonEmailHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonFaxHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonFirstNameHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonLastNameHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonMidInitialsHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonPhoneHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonRolesHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonRolesTermAccessionHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PersonRolesTermSourceRefHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolContactHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolDescriptionHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolHardwareHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolNameHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolParametersHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolSoftwareHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolTermAccessionHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolTermSourceRefHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ProtocolTypeHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicationAuthorListHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicationDoiHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicationStatusHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicationStatusTermAccessionHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicationStatusTermSourceRefHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicationTitleHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PublicReleaseDateHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.PubMedIdHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.QualityControlTermAccessionHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.QualityControlTermSourceRefHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.QualityControlTypeHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ReplicateTermAccessionHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ReplicateTermSourceRefHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ReplicateTypeHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.SDRFFileHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.TermSourceFileHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.TermSourceNameHandler
readValue(IDF, String, int, String...) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.TermSourceVersionHandler
reloadHandlers() - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.HandlerLoader: Clears any currently loaded handlers and reloads handlers available on the classpath.
removeChildNode(Node) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode
removeChildNode(Node) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node: Removes the reference to the child from this node
removeErrorItemListener(ErrorItemListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.converter.AbstractConverter
removeErrorItemListener(ErrorItemListener) - Method in interface uk.ac.ebi.arrayexpress2.magetab.converter.Converter: Deregister an ErrorItemListener with this parser.
removeErrorItemListener(ErrorItemListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser
removeErrorItemListener(ErrorItemListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABArrayParser
removeErrorItemListener(ErrorItemListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABParser
removeErrorItemListener(ErrorItemListener) - Method in interface uk.ac.ebi.arrayexpress2.magetab.parser.Parser: Deregister an ErrorItemListener with this parser.
removeErrorItemListener(ErrorItemListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.AbstractValidator
removeErrorItemListener(ErrorItemListener) - Method in interface uk.ac.ebi.arrayexpress2.magetab.validator.Validator: Deregister an ErrorItemListener with this parser.
removeEscaping(String) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Deprecated.
removeEscaping(String, boolean) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Deprecated.
removeEscaping(String[]) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Deprecated.
removeEscaping(String[], boolean) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Deprecated.
removeListener(HandlerListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.AbstractHandler
removeListener(HandlerListener) - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.Handler: Deregister a HandlerListener that can listen for handling events.
removeNode(Node) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractGraph
removeNode(S) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Graph: Remove a node that was previously stored in the Graph.
removeNodeFromGraph(ADFNode) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF: Deprecated.
since version 1.1, use AbstractGraph.removeNode(uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node) instead
removeNodeFromGraph(SDRFNode) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF: Deprecated.
since version 1.1, use AbstractGraph.removeNode(uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node) instead
removeParentNode(Node) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode
removeParentNode(Node) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node: Removes the reference to the parent from this node
removeProgressListener(ProgressListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.converter.AbstractConverter
removeProgressListener(ProgressListener) - Method in interface uk.ac.ebi.arrayexpress2.magetab.converter.Converter: Deregister a ProgressListener from this converter.
removeProgressListener(ProgressListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser
removeProgressListener(ProgressListener) - Method in interface uk.ac.ebi.arrayexpress2.magetab.parser.Parser: Deregister a ProgressListener from this parser.
removeProgressListener(ProgressListener) - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.AbstractValidator
removeProgressListener(ProgressListener) - Method in interface uk.ac.ebi.arrayexpress2.magetab.validator.Validator: Deregister a ProgressListener from this validator.
removeTrailingEmptyCells(String[]) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Deprecated.
removeWhitespace(String[]) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Deprecated.
replicateTermAccession - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ReplicateTermAccessionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Replicate Term Accession fields in the IDF.
ReplicateTermAccessionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ReplicateTermAccessionHandler
replicateTermSourceREF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ReplicateTermSourceRefHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Replicate Term Source Ref fields in the IDF.
ReplicateTermSourceRefHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ReplicateTermSourceRefHandler
replicateType - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
ReplicateTypeHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler implementation that will handle Replicate Types in the IDF.
ReplicateTypeHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ReplicateTypeHandler
reporterDatabaseEntries - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.ReporterNode
ReporterGroupAttribute - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute: Models a reporter group attribute in the MAGE-TAB SDRF specification.
ReporterGroupAttribute() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ReporterGroupAttribute
ReporterGroupAttributeReader - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.attribute: Handles reporter group attributes in the ADF graph part.
ReporterGroupAttributeReader() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.attribute.ReporterGroupAttributeReader
reporterGroupAttributes - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.ReporterNode
ReporterHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.node: A handler that handles reporter nodes from the ADF graph.
ReporterHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.ReporterHandler
ReporterNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node: Models "Reporter" nodes in the ADF graph, according to the MAGE-TAB specification.
ReporterNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.ReporterNode
reporterSequence - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.ReporterNode
resolveExperimentFactorTypes(MAGETABInvestigation, HybridizationNode) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: 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.
resolveGraphStructure(S) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractGraph
resolveGraphStructure(S) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Graph: Update this node being stored with appropriate references to it's parents and update any child node references that are already present in the graph.
resolveRelativeLocation(URL, String) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Convenience method for obtaining the URL for a file given only a relative path and the URL of the document the relative path is declared in.
row - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.FeatureNode

S

SampleHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node: A handler that handles Sample nodes in the SDRF graph
Tag: Sample Name
Allowed attributes: Characteristics, Material Type, Description, Comment, Array Design File/Ref
SampleHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.SampleHandler
SampleNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node: A sample node in the graph.
SampleNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SampleNode
SampleNodeWrapper - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor
SampleNodeWrapper(SampleNode, int, WrapperNodeFactory) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SampleNodeWrapper
ScanHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node: A handler that handles Scan nodes in the SDRF graph
Tag: Scan Name
Allowed attributes: Factor Value, Array Design File/Ref, Comment
ScanHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.ScanHandler
scannerChannel - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.FactorValueAttribute: Scanner channel attribute allows factors to be detected on a specific channel.
ScannerChannelMapper - Interface in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor
ScanNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node: A scan node in the graph.
ScanNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ScanNode
ScanNodeWrapper - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor
ScanNodeWrapper(ScanNode, int, WrapperNodeFactory) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.ScanNodeWrapper
SDRF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.MAGETABInvestigation
SDRF - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel: A datastructure that simply models SDRF in the MAGE-TAB spec.
SDRF() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF
SDRFAttribute - Interface in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute: An attribute in the SDRF data structure.
SDRFAttributeReader - Interface in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute: An interface that allows SDRFReadHandlers to delegate functionality of attribute reading to this interface rather than check all possible attribute combinations themselves.
SDRFConversionHandler<O> - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf: An abstract implementation of a ConversionHandler for writing data from an SDRF to some external output resource.
SDRFConversionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFConversionHandler
SDRFConverter<O> - Class in uk.ac.ebi.arrayexpress2.magetab.converter: Javadocs go here!
SDRFConverter() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.converter.SDRFConverter
sdrfFile - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
SDRFFileHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler that handles the line in the IDF that references the SDRF file location.
SDRFFileHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.SDRFFileHandler
SDRFGraphWriter - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor: An adaptor class to convert between a Limpopo SDRF and a generic Graph2tab graph interface.
SDRFGraphWriter(Writer) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFGraphWriter
SDRFLayout - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.layout: An object that describes the relationship between an SDRF datamodel object and the serialized version of it.
SDRFLayout() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.SDRFLayout
SDRFLayoutCalculator - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.calc: A class that provides layout calculation functionality for graphs according to the MAGE-TAB graph layout heuristic defined in the MAGE-TAB specification.
SDRFLayoutCalculator() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.calc.SDRFLayoutCalculator
SDRFNode - Interface in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node: A node in the SDRF data structure.
SDRFNodeConversionHandler<D extends SDRFNode,O> - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node: An abstract implementation of a ConversionHandler for writing data from an SDRFNode to some external output resource.
SDRFNodeConversionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.SDRFNodeConversionHandler
SDRFNodeWrapper<T extends SDRFNode> - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor: Class needed for graph2tab algorithm
Creates wrappers for the SDRF graph's nodes
SDRFNodeWrapper(T, int, WrapperNodeFactory) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper
SDRFParser - Class in uk.ac.ebi.arrayexpress2.magetab.parser: Imports SDRF documents into an SDRF.
SDRFParser() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.parser.SDRFParser
SDRFReadHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf: An abstract implementation of a ReadHandler for reading data from an SDRF file into a MAGETABInvestigation.
SDRFReadHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadHandler
SDRFReadInContextHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf: An implementation of an SDRFReadHandler that defines two extra methods that allow extra contextual data to be passed to concrete implementations.
SDRFReadInContextHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadInContextHandler
SDRFReadUtils - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf
SDRFReadUtils() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadUtils
SDRFScannerChannelMapper - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor
SDRFScannerChannelMapper(SDRF) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFScannerChannelMapper
SDRFValidateHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf: An abstract implementation of a ValidateHandler for writing data from an IDF to some external output resource.
SDRFValidateHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFValidateHandler
SDRFValidator - Class in uk.ac.ebi.arrayexpress2.magetab.validator: Javadocs go here!
SDRFValidator() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.validator.SDRFValidator
SDRFWriter - Class in uk.ac.ebi.arrayexpress2.magetab.renderer: Writes SDRF objects to a character output stream, formatted according to the MAGE-TAB SDRF serialization specification.
SDRFWriter(Writer) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.SDRFWriter
sequencePolymerType - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
SequencePolymerTypeHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handles ADF rows describing the sequence polymer type
Tag: Sequence Polymer Type
SequencePolymerTypeHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SequencePolymerTypeHandler
sequencePolymerTypeTermAccession - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
SequencePolymerTypeTermAccessionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handles ADF rows describing the sequence polymer type term accession
Tag: Sequence Polymer Type Term Accession Number
SequencePolymerTypeTermAccessionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SequencePolymerTypeTermAccessionHandler
sequencePolymerTypeTermSourceRef - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
SequencePolymerTypeTermSourceRefHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handles ADF rows describing the sequence polymer type term source reference
Tag: Sequence Polymer Type Term Source REF
SequencePolymerTypeTermSourceRefHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SequencePolymerTypeTermSourceRefHandler
setAttributeValue(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.AbstractADFAttribute
setAttributeValue(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.AbstractSDRFAttribute
setCurrentChannel(String) - Method in interface uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.ScannerChannelMapper
setCurrentChannel(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper
setCurrentChannel(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFScannerChannelMapper
setEncoding(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser
setEncoding(String) - Method in interface uk.ac.ebi.arrayexpress2.magetab.parser.Parser: Sets an alternative encoding for the parser.
setLocation(URL) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF: Get the known location of this SDRF, being the location of the file which was parsed to generate it.
setLocation(URL) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF: Get the known location of this IDF, being the location of the file which was parsed to generate it.
setLocation(URL) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF: Get the known location of this SDRF, being the location of the file which was parsed to generate it.
setNodeName(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode
setNodeName(String) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node: Set the value associated to this node in the spreadsheet.
setNodeType(String) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.UnresolvedPlaceholderNode
setOptions(Set<TableParser.Option>) - Method in interface uk.ac.ebi.arrayexpress2.magetab.utils.tab.ITableDataHandler
setOptions(Set<TableParser.Option>) - Method in class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableDataHandler
setOutputResource(O) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABArrayParser: Configure this parser with an output resource to convert data to.
setStripEscaping(boolean) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser
setStripEscaping(boolean) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABArrayParser
setStripEscaping(boolean) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABParser
setValidator(Validator<MAGETABArrayDesign>) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABArrayParser: Configure this parser with a Validator.
SourceHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node: A handler that handles Source nodes in the SDRF graph
Tag: Source Name
Allowed attributes: Characteristics, Provider, Material Type, Description, Comment, Array Design File/Ref
SourceHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.SourceHandler
SourceNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node: A source node in the graph.
SourceNode() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SourceNode
SourceNodeWrapper - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor
SourceNodeWrapper(SourceNode, int, WrapperNodeFactory) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SourceNodeWrapper
splitLine(String) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Deprecated.
splitLine(String, boolean) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Deprecated.
splitLine(String, boolean, boolean) - Static method in class uk.ac.ebi.arrayexpress2.magetab.utils.MAGETABUtils: Deprecated.
startTable() - Method in interface uk.ac.ebi.arrayexpress2.magetab.utils.tab.ITableDataHandler
startTable() - Method in class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableDataHandler
startTable() - Method in class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableSectionDataHandler
startTable() - Method in class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableSectionDetectingDataHandler
storeHeaders(String[]) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.SDRFLayout
storeNode(ADFNode) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF: Deprecated.
since version 1.1, use AbstractGraph.addNode(uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node) instead
storeNode(SDRFNode) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF: Deprecated.
since version 1.1, use AbstractGraph.addNode(uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node) instead
substrateType - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
SubstrateTypeHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handles ADF rows describing the substrate type
Tag: Substrate Type
SubstrateTypeHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SubstrateTypeHandler
substrateTypeTermAccession - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
SubstrateTypeTermAccessionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handles ADF rows describing the substrate type term accession
Tag: Substrate Type Term Accession Number
SubstrateTypeTermAccessionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SubstrateTypeTermAccessionHandler
substrateTypeTermSourceRef - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
SubstrateTypeTermSourceRefHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handles ADF rows describing the substrate type term source reference
Tag: Substrate Type Term Source REF
SubstrateTypeTermSourceRefHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SubstrateTypeTermSourceRefHandler
surfaceType - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
SurfaceTypeHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handles ADF rows describing the surface type
Tag: Surface Type
SurfaceTypeHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SurfaceTypeHandler
surfaceTypeTermAccession - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
SurfaceTypeTermAccessionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handles ADF rows describing the surface type term accession
Tag: Surface Type Term Accession Number
SurfaceTypeTermAccessionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SurfaceTypeTermAccessionHandler
surfaceTypeTermSourceRef - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
SurfaceTypeTermSourceRefHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handles ADF rows describing the surface type term source reference
Tag: Surface Type Term Source REF
SurfaceTypeTermSourceRefHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.SurfaceTypeTermSourceRefHandler

T

TableDataHandler - Class in uk.ac.ebi.arrayexpress2.magetab.utils.tab: Generic table data handler for finite state machine based parser
TableDataHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableDataHandler
TableParser - Class in uk.ac.ebi.arrayexpress2.magetab.utils.tab: Finite state machine based parser for tab-delimited files Main features: - accepts all common line separators (CR, LF, CR+LF) - stripping of quote and escape characters, trimming of column whitespace and removal of empty trailing columns and rows are configurable options - warning: NOT THREAD SAFE!
TableParser(ITableDataHandler, TableParser.Option...) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableParser
TableParser(TableParser.Option...) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableParser
TableParser.Option - Enum in uk.ac.ebi.arrayexpress2.magetab.utils.tab
TableParserException - Exception in uk.ac.ebi.arrayexpress2.magetab.utils.tab
TableParserException(String) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableParserException
TableParserRunner - Class in uk.ac.ebi.arrayexpress2.magetab.utils.tab: Runner class for finite state machine based parser for tab-delimited files
TableParserRunner() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableParserRunner
TableSectionDataHandler - Class in uk.ac.ebi.arrayexpress2.magetab.utils.tab: Table section data handler for finite state machine based parser
TableSectionDataHandler(String, String) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableSectionDataHandler
TableSectionDetectingDataHandler - Class in uk.ac.ebi.arrayexpress2.magetab.utils.tab: Table section detecting data handler
TableSectionDetectingDataHandler(String...) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableSectionDetectingDataHandler
technologyType - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
technologyType - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.AssayNode
TechnologyTypeAttribute - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute: A technology type attribute node in the SDRF graph.
TechnologyTypeAttribute() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.TechnologyTypeAttribute
TechnologyTypeAttributeReader - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute: Handles technology type attributes in the SDRF graph.
TechnologyTypeAttributeReader() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute.TechnologyTypeAttributeReader
TechnologyTypeHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handles ADF rows describing the technology type
Tag: Technology Type
TechnologyTypeHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.TechnologyTypeHandler
technologyTypeTermAccession - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
TechnologyTypeTermAccessionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handles ADF rows describing the technology type term accession
Tag: Technology Type Term Accession Number
TechnologyTypeTermAccessionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.TechnologyTypeTermAccessionHandler
technologyTypeTermSourceRef - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
TechnologyTypeTermSourceRefHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handles ADF rows describing the technology type term source reference
Tag: Technology Type Term Source REF
TechnologyTypeTermSourceRefHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.TechnologyTypeTermSourceRefHandler
termAccessionNumber - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ControlTypeAttribute
termAccessionNumber - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ReporterGroupAttribute
termAccessionNumber - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ArrayDesignNode: Deprecated.
termAccessionNumber - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.ArrayDesignAttribute
termAccessionNumber - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.CharacteristicsAttribute
termAccessionNumber - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.FactorValueAttribute
termAccessionNumber - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.LabelAttribute
termAccessionNumber - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.MaterialTypeAttribute
termAccessionNumber - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.TechnologyTypeAttribute
termAccessionNumber - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.UnitAttribute
termAccessionNumber - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ProtocolApplicationNode
termSourceFile - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
termSourceFile - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
TermSourceFileHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A Handler that handles the ADF rows that point to the file from which term source references are taken from.
TermSourceFileHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.TermSourceFileHandler
TermSourceFileHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A Handler that handles the IDF rows that point to the file from which term source references are taken from.
TermSourceFileHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.TermSourceFileHandler
termSourceName - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
termSourceName - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
TermSourceNameHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handles the term source name declaration rows in ADF.
TermSourceNameHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.TermSourceNameHandler
TermSourceNameHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler that handles the term source name declaration rows in IDF.
TermSourceNameHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.TermSourceNameHandler
termSourceREF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ControlTypeAttribute
termSourceREF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ReporterGroupAttribute
termSourceREF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ArrayDesignNode: Deprecated.
termSourceREF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.ArrayDesignAttribute
termSourceREF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.CharacteristicsAttribute
termSourceREF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.FactorValueAttribute
termSourceREF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.LabelAttribute
termSourceREF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.MaterialTypeAttribute
termSourceREF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.TechnologyTypeAttribute
termSourceREF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.UnitAttribute
termSourceREF - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ProtocolApplicationNode
termSourceVersion - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
termSourceVersion - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF
TermSourceVersionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handles the term source version declaration rows in ADF.
TermSourceVersionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.TermSourceVersionHandler
TermSourceVersionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: A handler that handles the term source version declaration rows in IDF.
TermSourceVersionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.TermSourceVersionHandler
toString() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode
toString() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.Location
toString() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.MAGETABArrayDesign
toString() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.MAGETABInvestigation
toString() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.AbstractSDRFNode
trackLocation(Handler, Point) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.visitor.LocationTracker: Deprecated.
since version 1.1
type - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ControlTypeAttribute
type - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ReporterGroupAttribute
type - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.CharacteristicsAttribute
type - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.FactorValueAttribute
type - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.ParameterValueAttribute
type - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.UnitAttribute

U

uk.ac.ebi.arrayexpress2.magetab.converter - package uk.ac.ebi.arrayexpress2.magetab.converter
uk.ac.ebi.arrayexpress2.magetab.datamodel - package 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.adf.node - package uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node: Classes that model the nodes in the ADF graph datastructure, as described by the MAGE-TAB specification.
uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute - package uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute: Classes that model attributes of nodes in the ADF graph datastructure, as described by the MAGE-TAB specification.
uk.ac.ebi.arrayexpress2.magetab.datamodel.graph - package uk.ac.ebi.arrayexpress2.magetab.datamodel.graph: Some high-level graph modelling classes, for representing abstract graphs.
uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.utils - package uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.utils
uk.ac.ebi.arrayexpress2.magetab.datamodel.layout - package uk.ac.ebi.arrayexpress2.magetab.datamodel.layout
uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.calc - package uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.calc
uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node - package uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node: Classes that model nodes in the SDRF graph datastructure, as described by the MAGE-TAB specification.
uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute - package uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute: Classes that model attributes of nodes in the SDRF graph datastructure, as described by the MAGE-TAB specification.
uk.ac.ebi.arrayexpress2.magetab.exception - package uk.ac.ebi.arrayexpress2.magetab.exception: All defined exceptions thrown anywhere in the suite of tools and utilities for working with MAGE-TAB documents and datastructures.
uk.ac.ebi.arrayexpress2.magetab.handler - package 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.adf - package uk.ac.ebi.arrayexpress2.magetab.handler.adf: ADF specific handler classes.
uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl - package uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: Specific, concrete ADF header handler implementations.
uk.ac.ebi.arrayexpress2.magetab.handler.adf.node - package uk.ac.ebi.arrayexpress2.magetab.handler.adf.node: ADF "graph part" specific handler classes.
uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.attribute - package uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.attribute: ADF graph handler implementations that are capable of handling data items that represent attributes attached to a node in the ADF, as defined by the MAGE-TAB specification.
uk.ac.ebi.arrayexpress2.magetab.handler.idf - package uk.ac.ebi.arrayexpress2.magetab.handler.idf: IDF specific handler classes.
uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl - package uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl: Specific, concrete IDF handler implementations.
uk.ac.ebi.arrayexpress2.magetab.handler.listener - package uk.ac.ebi.arrayexpress2.magetab.handler.listener
uk.ac.ebi.arrayexpress2.magetab.handler.sdrf - package uk.ac.ebi.arrayexpress2.magetab.handler.sdrf: SDRF specific handler classes.
uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node - package 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 - package 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.handler.visitor - package 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.listener - package uk.ac.ebi.arrayexpress2.magetab.listener
uk.ac.ebi.arrayexpress2.magetab.parser - package uk.ac.ebi.arrayexpress2.magetab.parser: Parser classes for parsing MAGE-TAB aspects.
uk.ac.ebi.arrayexpress2.magetab.renderer - package uk.ac.ebi.arrayexpress2.magetab.renderer
uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor - package uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor
uk.ac.ebi.arrayexpress2.magetab.utils - package uk.ac.ebi.arrayexpress2.magetab.utils: Some common utility classes for parsing, validating and interpreting MAGE-TAB files.
uk.ac.ebi.arrayexpress2.magetab.utils.tab - package uk.ac.ebi.arrayexpress2.magetab.utils.tab
uk.ac.ebi.arrayexpress2.magetab.validator - package uk.ac.ebi.arrayexpress2.magetab.validator: Validator classes for validating the MAGE-TAB datamodel during parsing.
UNASSIGNED - Static variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.Location
unit - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.CharacteristicsAttribute
unit - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.FactorValueAttribute
unit - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.ParameterValueAttribute
UnitAttribute - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute: A unit attribute node in the graph.
UnitAttribute() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.UnitAttribute
UnknownHeaderHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node: A handler that can handle any node in the graph, to allow SDRFs to be parsed even when they contain unrecognised headings.
UnknownHeaderHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.UnknownHeaderHandler
UnmatchedTagException - Exception in uk.ac.ebi.arrayexpress2.magetab.exception: A ParseException that gets thrown whenever a tag in a TDT file is mismatched when compared to the expected one, or if the content type is wrong for the header.
UnmatchedTagException() - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.UnmatchedTagException
UnmatchedTagException(String) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.UnmatchedTagException
UnmatchedTagException(String, Throwable) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.UnmatchedTagException
UnmatchedTagException(Throwable) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.UnmatchedTagException
UnmatchedTagException(boolean, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.UnmatchedTagException
UnmatchedTagException(boolean, String, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.UnmatchedTagException
UnmatchedTagException(boolean, String, Throwable, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.UnmatchedTagException
UnmatchedTagException(boolean, Throwable, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.UnmatchedTagException
UnresolvedPlaceholderNode - Class in uk.ac.ebi.arrayexpress2.magetab.datamodel.graph: A dedicated type of graph node that serves as a simple placeholder in lieu of the node being fully parsed.
UnresolvedPlaceholderNode(String, String) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.UnresolvedPlaceholderNode
updateChildNode(Node) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode
updateChildNode(Node) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node: Updates a child node equal to the supplied node with a new object reference.
updateChildNode(String[], String[], ADFNode, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFGraphReadHandler
updateChildNode(String[], String[], SDRFNode, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadHandler
updateNode(S) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractGraph
updateNode(S) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Graph: Updates an node in the SDRF graph, on the assumption that its position in the graph, or its children, have been altered.
updateParentNode(Node) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode
updateParentNode(Node) - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node: Updates a parent node equal to the supplied node with a new object reference.

V

validate(ADF) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFValidateHandler: Invoke this validate handler.
validate(IDF) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.IDFValidateHandler: Invoke this validate handler.
validate(MAGETABInvestigation) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.MAGETABValidateHandler: Invoke this validate handler.
validate(SDRF) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFValidateHandler: Invoke this validate handler.
validate(D) - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.ValidateHandler: Causes this handler to validate some data that has been read into a MAGETABInvestigation.
validate(ADF) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.ADFParser
validate(ADF, ExecutorService) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.ADFParser
validate(T, ExecutorService) - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.AbstractValidator: This default implementation ignored the supplied service and executes tasks in a linear manner, This is retained to preserve backwards compatibility with the 1.0 release.
validate(IDF) - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.IDFValidator
validate(IDF, ExecutorService) - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.IDFValidator
validate(MAGETABInvestigation) - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.MAGETABValidator
validate(MAGETABInvestigation, ExecutorService) - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.MAGETABValidator
validate(SDRF) - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.SDRFValidator
validate(SDRF, ExecutorService) - Method in class uk.ac.ebi.arrayexpress2.magetab.validator.SDRFValidator
validate(T) - Method in interface uk.ac.ebi.arrayexpress2.magetab.validator.Validator: Perform validation of the supplied validator source.
validate(T, ExecutorService) - Method in interface uk.ac.ebi.arrayexpress2.magetab.validator.Validator: Perform validation of the supplied validator source, delegating all work to the supplied Executor Service to enable validation in parallel.
validateData(ADF) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFValidateHandler: Performs the unit of work to validate the data.
validateData(IDF) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.idf.IDFValidateHandler: Performs the unit of work to validate the data.
validateData(MAGETABInvestigation) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.MAGETABValidateHandler: Performs the unit of work to validate the data.
validateData(SDRF) - Method in class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFValidateHandler: Performs the unit of work to validate the data.
validatedMore(ProgressEvent) - Method in interface uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListener: Invoked whenever more of a document is validated.
validatedMore(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListenerAdapter
ValidateException - Exception in uk.ac.ebi.arrayexpress2.magetab.exception: A ParseException that gets thrown whenever part of a MAGETABInvestigation or a MAGETABInvestigation fails a validation process.
ValidateException() - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ValidateException
ValidateException(String) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ValidateException
ValidateException(String, Throwable) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ValidateException
ValidateException(Throwable) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ValidateException
ValidateException(boolean, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ValidateException
ValidateException(boolean, String, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ValidateException
ValidateException(boolean, String, Throwable, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ValidateException
ValidateException(boolean, Throwable, ErrorItem...) - Constructor for exception uk.ac.ebi.arrayexpress2.magetab.exception.ValidateException
ValidateHandler<D> - Interface in uk.ac.ebi.arrayexpress2.magetab.handler: A type of Handler that enables read functionality over a lump of data.
validationCompleted(ProgressEvent) - Method in interface uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListener: Invoked whenever a validate operation completes successfully
validationCompleted(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListenerAdapter
validationFailed(ProgressEvent) - Method in interface uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListener: Invoked whenever a validate operation completes, but failed to read some of the document
validationFailed(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListenerAdapter
validationStarted(ProgressEvent) - Method in interface uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListener: Invoked whenever a validate operation commences
validationStarted(ProgressEvent) - Method in class uk.ac.ebi.arrayexpress2.magetab.listener.ProgressListenerAdapter
Validator<T> - Interface in uk.ac.ebi.arrayexpress2.magetab.validator: A semantic validator process, distinct from syntactic validation which is handled by a Parser.
valueOf(String) - Static method in enum uk.ac.ebi.arrayexpress2.magetab.handler.listener.HandlerEvent.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableParser.Option: Returns the enum constant of this type with the specified name.
values() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.ADFNode: Returns the strings representing the values of this node and all it's attributes, indexed by the matching headers.
values() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ADFAttribute: Returns the strings representing the values of this node and all it's attributes, indexed by the matching headers.
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ControlTypeAttribute
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.attribute.ReporterGroupAttribute
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.CompositeElementNode
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.FeatureNode
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.adf.node.ReporterNode
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ArrayDataMatrixNode
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ArrayDataNode
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ArrayDesignNode: Deprecated.
values(int) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.AssayNode: Request values by factor value attribute scanner channel.
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.ArrayDesignAttribute
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.CharacteristicsAttribute
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.FactorValueAttribute
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.LabelAttribute
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.MaterialTypeAttribute
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.ParameterValueAttribute
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.PerformerAttribute
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.ProviderAttribute
values() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.SDRFAttribute: Returns the strings representing the values of this node and all it's attributes, indexed by the matching headers.
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.TechnologyTypeAttribute
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.UnitAttribute
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.DerivedArrayDataMatrixNode
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.DerivedArrayDataNode
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ExtractNode
values(int) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.HybridizationNode: Request values by factor value attribute scanner channel.
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.HybridizationNode: Delegates to HybridizationNode.values(int) using the channel labeled as channel one.
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ImageNode
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.LabeledExtractNode
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.NormalizationNode
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ProtocolApplicationNode
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SampleNode
values(int) - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ScanNode: Request values by factor value attribute scanner channel.
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.ScanNode: Delegates to ScanNode.values(int), using the channel labeled as channel one.
values() - Method in interface uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SDRFNode: Returns the strings representing the values of this node and all it's attributes, indexed by the matching headers.
values() - Method in class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SourceNode
values() - Static method in enum uk.ac.ebi.arrayexpress2.magetab.handler.listener.HandlerEvent.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.ebi.arrayexpress2.magetab.utils.tab.TableParser.Option: Returns an array containing the constants of this enum type, in the order they are declared.
version - Variable in class uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF
VersionHandler - Class in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl: A handler that handles the version rows of this ADF.
VersionHandler() - Constructor for class uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.VersionHandler
visit(T) - Method in interface uk.ac.ebi.arrayexpress2.magetab.handler.visitor.HandlerVisitor: Visit a Handler and extract relevant information

W

WrapperNodeFactory - Class in uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor: Factory to create wrapper classes needed for graph2tab algorithm
WrapperNodeFactory(SDRF) - Constructor for class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.WrapperNodeFactory
write(ADF) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.ADFParser
write(ADF, ExecutorService) - Method in class uk.ac.ebi.arrayexpress2.magetab.parser.ADFParser
write(SDRF) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFGraphWriter
write(char[], int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFGraphWriter
write(char[], int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.ADFWriter
write(ADF) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.ADFWriter: Writes out the ADF to the underlying writer, without printing any stdout.
write(ADF, boolean) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.ADFWriter: Writes out the ADF to the underlying, specifying whether to convert information about progress to standard out.
write(char[], int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.IDFWriter
write(IDF) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.IDFWriter: Writes the IDF supplied to the underlying writer without printing progress informations to standard out.
write(IDF, boolean) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.IDFWriter: Writes the IDF supplied to the underlying writer, optionally printing progress information to standard out.
write(char[], int, int) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.SDRFWriter
write(SDRF) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.SDRFWriter: Writes out the SDRF to the underlying writer, without printing any stdout.
write(SDRF, boolean) - Method in class uk.ac.ebi.arrayexpress2.magetab.renderer.SDRFWriter: Writes out the SDRF to the underlying, specifying whether to convert information about progress to standard out.

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