Uses of Interface
uk.ac.ebi.arrayexpress2.magetab.handler.Handler

Packages that use Handler

Package	Description
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	ADF specific handler classes.
uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl	Specific, concrete ADF header handler implementations.
uk.ac.ebi.arrayexpress2.magetab.handler.adf.node	ADF "graph part" specific handler classes.
uk.ac.ebi.arrayexpress2.magetab.handler.idf	IDF specific handler classes.
uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl	Specific, concrete IDF handler implementations.
uk.ac.ebi.arrayexpress2.magetab.handler.listener
uk.ac.ebi.arrayexpress2.magetab.handler.sdrf	SDRF specific handler classes.
uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node	Specific handlers for SDRF node data items, as defined in the MAGE-TAB specification.
uk.ac.ebi.arrayexpress2.magetab.handler.visitor	Visitor classes that can be used to visit and inspect MAGE-TAB handlers.
uk.ac.ebi.arrayexpress2.magetab.parser	Parser classes for parsing MAGE-TAB aspects.

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

Subinterfaces of Handler in uk.ac.ebi.arrayexpress2.magetab.handler

Modifier and Type	Interface and Description
interface	ConversionHandler<D,O> A type of Handler that enables convert functionality over a lump of data.
interface	ReadHandler<H,D,T> A type of Handler that enables read functionality over a section of MAGE-TAB.
interface	ValidateHandler<D> A type of Handler that enables read functionality over a lump of data.

Classes in uk.ac.ebi.arrayexpress2.magetab.handler that implement Handler

Modifier and Type	Class and Description
class	AbstractHandler A basic handler implementation that provides some simple functionality common to all handlers.
class	MAGETABValidateHandler An abstract implementation of a ValidateHandler for validating data from an MAGETABInvestigation#.

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

Classes in uk.ac.ebi.arrayexpress2.magetab.handler.adf that implement Handler

Modifier and Type	Class and Description
class	ADFConversionHandler<O> An abstract implementation of a ConversionHandler for writing data from an IDF to some external output resource.
class	ADFGraphReadHandler An abstract implementation of a ReadHandler for reading from the graph part of an ADF file into a ADF object.
class	ADFHeaderReadHandler An abstract implementation of ReadHandler for reading from the header part of an ADF file into a MAGETABArrayDesign.
class	ADFValidateHandler An abstract implementation of a ValidateHandler for writing data from an IDF to some external output resource.

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

Classes in uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl that implement Handler

Modifier and Type	Class and Description
class	ArrayDesignNameHandler A handler that handlers ADF rows describing the array design name.
class	PrintingProtocolHandler A handler that handlers ADF rows describing the printing protocol Tag: Printing Protocol
class	ProviderHandler A handler that handles ADF rows describing the provider Tag: Provider
class	SequencePolymerTypeHandler A handler that handles ADF rows describing the sequence polymer type Tag: Sequence Polymer Type
class	SequencePolymerTypeTermAccessionHandler A handler that handles ADF rows describing the sequence polymer type term accession Tag: Sequence Polymer Type Term Accession Number
class	SequencePolymerTypeTermSourceRefHandler A handler that handles ADF rows describing the sequence polymer type term source reference Tag: Sequence Polymer Type Term Source REF
class	SubstrateTypeHandler A handler that handles ADF rows describing the substrate type Tag: Substrate Type
class	SubstrateTypeTermAccessionHandler A handler that handles ADF rows describing the substrate type term accession Tag: Substrate Type Term Accession Number
class	SubstrateTypeTermSourceRefHandler A handler that handles ADF rows describing the substrate type term source reference Tag: Substrate Type Term Source REF
class	SurfaceTypeHandler A handler that handles ADF rows describing the surface type Tag: Surface Type
class	SurfaceTypeTermAccessionHandler A handler that handles ADF rows describing the surface type term accession Tag: Surface Type Term Accession Number
class	SurfaceTypeTermSourceRefHandler A handler that handles ADF rows describing the surface type term source reference Tag: Surface Type Term Source REF
class	TechnologyTypeHandler A handler that handles ADF rows describing the technology type Tag: Technology Type
class	TechnologyTypeTermAccessionHandler A handler that handles ADF rows describing the technology type term accession Tag: Technology Type Term Accession Number
class	TechnologyTypeTermSourceRefHandler A handler that handles ADF rows describing the technology type term source reference Tag: Technology Type Term Source REF
class	VersionHandler A handler that handles the version rows of this ADF.

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

Classes in uk.ac.ebi.arrayexpress2.magetab.handler.adf.node that implement Handler

Modifier and Type	Class and Description
class	ADFNodeConversionHandler<D extends ADFNode,O> An abstract implementation of a ConversionHandler for writing data from an ADFNode to some external output resource.
class	CompositeElementHandler A handler that handles composite element nodes in the ADF graph.
class	FeatureHandler A handler that handles feature nodes in the ADF graph.
class	ReporterHandler A handler that handles reporter nodes from the ADF graph.

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

Classes in uk.ac.ebi.arrayexpress2.magetab.handler.idf that implement Handler

Modifier and Type	Class and Description
class	IDFConversionHandler<O> An abstract implementation of a ConversionHandler for writing data from an IDF to some external output resource.
class	IDFReadHandler An abstract implementation of a ReadHandler for reading data from IDF file into an MAGETABInvestigation.
class	IDFValidateHandler An abstract implementation of a ValidateHandler for writing data from an IDF to some external output resource.

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

Classes in uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl that implement Handler

Modifier and Type	Class and Description
class	AccessionHandler A handler that handles rows in the IDF that describe the arrayaexpress accession number in a comment field.
class	CommentHandler A handler that handles all comments in an arrayexpress IDF document, excluding accession comments Tag: Comment[*] Cardinality: unlimited
class	DateOfExperimentHandler A handler implementation that will handle Date of Experiment fields in the IDF.
class	ExperimentalDesignHandler A handler implementation that will handle Experimental Design fields in the IDF.
class	ExperimentalDesignTermAccessionHandler A handler implementation that will handle Experimental Design Term Accession Number fields in the IDF.
class	ExperimentalDesignTermSourceRefHandler A handler implementation that will handle Experimental Design Term Source Ref fields in the IDF.
class	ExperimentalFactorNameHandler A handler implementation that will handle Experimental Factor Name fields in the IDF.
class	ExperimentalFactorTermAccessionHandler A handler implementation that will handle Experimental Factor Term Accession fields in the IDF.
class	ExperimentalFactorTermSourceRefHandler A handler implementation that will handle Experimental Factor Term Source REF fields in the IDF.
class	ExperimentalFactorTypeHandler A handler implementation that will handle Experimental Factor Type fields in the IDF.
class	ExperimentDescriptionHandler A handler implementation that will handle Experiment Description fields in the IDF.
class	InvestigationTitleHandler A handler implementation that will handle Investigation Title fields in the IDF.
class	MAGETABVersionHandler A handler implementation that will handle MAGE-TAB Version fields in the IDF.
class	NormalizationTermAccessionHandler A handler implementation that will handle Normalization Term Accession fields in the IDF.
class	NormalizationTermSourceRefHandler A handler implementation that will handle Normalization Term Source REF fields in the IDF.
class	NormalizationTypeHandler A handler implementation that will handle Normalization Type fields in the IDF.
class	PersonAddressHandler A handler implementation that will handle Person Address fields in the IDF.
class	PersonAffiliationHandler A handler implementation that will handle Person Affiliation fields in the IDF.
class	PersonEmailHandler A handler implementation that will handle Person Email fields in the IDF.
class	PersonFaxHandler A handler implementation that will handle Person Fax fields in the IDF.
class	PersonFirstNameHandler A handler implementation that will handle Person First Name fields in the IDF.
class	PersonLastNameHandler A handler implementation that will handle Person Last Name fields in the IDF.
class	PersonMidInitialsHandler A handler implementation that will handle Person Mid Initial fields in the IDF.
class	PersonPhoneHandler A handler implementation that will handle Person Phone fields in the IDF.
class	PersonRolesHandler A handler implementation that will handle Person Roles fields in the IDF.
class	PersonRolesTermAccessionHandler A handler implementation that will handle Person Roles Term Accession Number fields in the IDF.
class	PersonRolesTermSourceRefHandler A handler implementation that will handle Person Roles Term Source REF fields in the IDF.
class	ProtocolContactHandler A handler implementation that will handle Protocol Contact fields in the IDF.
class	ProtocolDescriptionHandler A handler implementation that will handle Protocol Description fields in the IDF.
class	ProtocolHardwareHandler A handler implementation that will handle Protocol hardware fields in the IDF.
class	ProtocolNameHandler A handler implementation that will handle Protocol Name fields in the IDF.
class	ProtocolParametersHandler A handler implementation that will handle Protocol Name fields in the IDF.
class	ProtocolSoftwareHandler A handler implementation that will handle Protocol Software fields in the IDF.
class	ProtocolTermAccessionHandler A handler implementation that will handle Protocol Term accession fields in the IDF.
class	ProtocolTermSourceRefHandler A handler implementation that will handle Protocol Term Source Ref fields in the IDF.
class	ProtocolTypeHandler A handler implementation that will handle Protocol Type fields in the IDF.
class	PublicationAuthorListHandler A handler implementation that will handle Publication Author List fields in the IDF.
class	PublicationDoiHandler A handler implementation that will handle Publication DOI Handler fields in the IDF.
class	PublicationStatusHandler A handler implementation that will handle Publication Status fields in the IDF.
class	PublicationStatusTermAccessionHandler A handler implementation that will handle Publication Status Term Accession fields in the IDF.
class	PublicationStatusTermSourceRefHandler A handler implementation that will handle Publication Status Term Source Ref fields in the IDF.
class	PublicationTitleHandler A handler implementation that will handle Publication Title fields in the IDF.
class	PublicReleaseDateHandler A handler implementation that will handle Public Release Date Handler fields in the IDF.
class	PubMedIdHandler A handler implementation that will handle PubMed ID fields in the IDF.
class	QualityControlTermAccessionHandler A handler implementation that will handle Quality Control Term Accession fields in the IDF.
class	QualityControlTermSourceRefHandler A handler implementation that will handle Quality Control Term Source Ref fields in the IDF.
class	QualityControlTypeHandler A handler implementation that will handle Quality Control Type fields in the IDF.
class	ReplicateTermAccessionHandler A handler implementation that will handle Replicate Term Accession fields in the IDF.
class	ReplicateTermSourceRefHandler A handler implementation that will handle Replicate Term Source Ref fields in the IDF.
class	ReplicateTypeHandler A handler implementation that will handle Replicate Types in the IDF.
class	SDRFFileHandler A handler that handles the line in the IDF that references the SDRF file location.
class	TermSourceFileHandler A Handler that handles the IDF rows that point to the file from which term source references are taken from.
class	TermSourceNameHandler A handler that handles the term source name declaration rows in IDF.
class	TermSourceVersionHandler A handler that handles the term source version declaration rows in IDF.

Uses of Handler in uk.ac.ebi.arrayexpress2.magetab.handler.listener

Methods in uk.ac.ebi.arrayexpress2.magetab.handler.listener that return Handler

Modifier and Type	Method and Description
Handler	HandlerEvent.getHandler()

Constructors in uk.ac.ebi.arrayexpress2.magetab.handler.listener with parameters of type Handler

Constructor and Description
HandlerEvent(Handler handler, HandlerEvent.Type handlerEventType, Object handledData)

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

Classes in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf that implement Handler

Modifier and Type	Class and Description
class	SDRFConversionHandler<O> An abstract implementation of a ConversionHandler for writing data from an SDRF to some external output resource.
class	SDRFReadHandler An abstract implementation of a ReadHandler for reading data from an SDRF file into a MAGETABInvestigation.
class	SDRFReadInContextHandler An implementation of an SDRFReadHandler that defines two extra methods that allow extra contextual data to be passed to concrete implementations.
class	SDRFValidateHandler An abstract implementation of a ValidateHandler for writing data from an IDF to some external output resource.

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

Classes in uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node that implement Handler

Modifier and Type	Class and Description
class	ArrayDataHandler A handler that handles array data nodes in the SDRF graph Tag: Array Data File Allowed Attributes: Array Design File/Ref, Comment
class	ArrayDataMatrixHandler A handler that handles array data matrix nodes in the SDRF graph Tag: Array Data Matrix File Allowed attributes: Array Design File/Ref, Comment
class	AssayHandler A handler that handles Assay nodes in the SDRF graph Tag: Assay Name Allowed attributes: Factor Value, Array Design File/Ref, Technology Type, Comment
class	DerivedArrayDataHandler A handler that handles Derived Array Data nodes in the SDRF graph Tag: Derived Array Data File Allowed attributes: Array Design File/Ref, Comment
class	DerivedArrayDataMatrixHandler 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
class	ExtractHandler 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
class	FactorValueNodeHandler A special type of 'dummy' handler for handling factor values.
class	HybridizationHandler A handler that handles Hybridization nodes in the SDRF graph Tag: Hybridization Name Allowed attributes: Factor Value, Comment
class	ImageHandler A handler that handles Image nodes in the SDRF graph Tag: Image File Allowed attributes: Array Design File/Ref, Comment
class	LabeledExtractHandler 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
class	NormalizationHandler A handler that handles Normalization nodes in the SDRF graph Tag: Normalization Name Allowed attributes: Array Design File/Ref, Comment
class	ProtocolHandler A handler that handles Protocol edges in the SDRF graph.
class	SampleHandler A handler that handles Sample nodes in the SDRF graph Tag: Sample Name Allowed attributes: Characteristics, Material Type, Description, Comment, Array Design File/Ref
class	ScanHandler A handler that handles Scan nodes in the SDRF graph Tag: Scan Name Allowed attributes: Factor Value, Array Design File/Ref, Comment
class	SDRFNodeConversionHandler<D extends SDRFNode,O> An abstract implementation of a ConversionHandler for writing data from an SDRFNode to some external output resource.
class	SourceHandler 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
class	UnknownHeaderHandler A handler that can handle any node in the graph, to allow SDRFs to be parsed even when they contain unrecognised headings.

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

Classes in uk.ac.ebi.arrayexpress2.magetab.handler.visitor with type parameters of type Handler

Modifier and Type	Interface and Description
interface	HandlerVisitor<T extends Handler> An visitor interface that can inspect Handlers, and extract useful information about the data that was assigned to it.

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

Modifier and Type	Method and Description
void	LocationTracker.trackLocation(Handler handler, Point p) Deprecated. since version 1.1

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

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

Modifier and Type	Method and Description
void	AbstractParser.DefaultHandlerListener.addHandler(Handler handler, String[] data) Add a handler that should be tracked to this listener.