| 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.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.
|
| Modifier and Type | Method and Description |
|---|---|
<T extends ReadHandler,S> |
HandlerLoader.getReadHandlersOfType(Class<T> superclass,
S header)
Generic method for looking up ReadHandlers that extend the given superclass and can read from the given header.
|
| Modifier and Type | Method and Description |
|---|---|
Collection<ReadHandler<?,?,?>> |
HandlerLoader.getReadHandlers()
Gets the collection of all available
ReadHandlers. |
| Modifier and Type | Class and Description |
|---|---|
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. |
| 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.
|
| Modifier and Type | Class and Description |
|---|---|
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.
|
| Modifier and Type | Class and Description |
|---|---|
class |
IDFReadHandler
An abstract implementation of a ReadHandler for reading data from IDF file into an
MAGETABInvestigation. |
| 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.
|
| Modifier and Type | Class and Description |
|---|---|
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.
|
| 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 |
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.
|
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