Uses of Class
psidev.psi.mi.jami.model.InteractionCategory
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Uses of InteractionCategory in psidev.psi.mi.jami.commons
Methods in psidev.psi.mi.jami.commons with parameters of type InteractionCategory Modifier and Type Method Description Map<String,Object>
MIWriterOptionFactory. getCompactXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, Source defaultSource, XMLGregorianCalendar defaultReleaseDate, Collection<Annotation> defaultEntryAnnotations, PsiXmlVersion version)
Create the options for the compact PSI-XML InteractionWriter.Map<String,Object>
MIWriterOptionFactory. getCompactXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, PsiXmlObjectCache elementCache, Set<Experiment> experimentSet, Set<Interactor> interactorSet, Set<String> availabilitySet, Set<Interaction> interactionSet, boolean writeComplexAsInteractors, boolean extended, PsiXmlVersion version)
Create the options for the compact PSI-XML InteractionWriter.Map<String,Object>
MIWriterOptionFactory. getCompactXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, PsiXmlObjectCache elementCache, Set<Experiment> experimentSet, Set<Interactor> interactorSet, Set<String> availabilitySet, Set<Interaction> interactionSet, Source defaultSource, XMLGregorianCalendar defaultReleaseDate, Collection<Annotation> defaultEntryAnnotations, boolean writeComplexAsInteractors, boolean extended, PsiXmlVersion version)
Create the options for the compact PSI-XML InteractionWriter.Map<String,Object>
MIWriterOptionFactory. getDefaultCompactXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, PsiXmlVersion version)
Create the default options for the compact PSI-XML InteractionWriter.Map<String,Object>
MIWriterOptionFactory. getDefaultExpandedXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, PsiXmlVersion version)
Create the options for the default expanded PSI-XML InteractionWriter.Map<String,Object>
MIWriterOptionFactory. getDefaultXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, PsiXmlType type, PsiXmlVersion version)
getDefaultXmlOptions.Map<String,Object>
MIWriterOptionFactory. getExpandedXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, Source defaultSource, XMLGregorianCalendar defaultReleaseDate, Collection<Annotation> defaultEntryAnnotations, PsiXmlVersion version)
Create the options for the expanded PSI-XML InteractionWriter.Map<String,Object>
MIWriterOptionFactory. getExpandedXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, PsiXmlObjectCache elementCache, Set<Interaction> interactionSet, boolean writeComplexAsInteractors, boolean extended, PsiXmlVersion version)
Create the options for the expanded PSI-XML InteractionWriter.Map<String,Object>
MIWriterOptionFactory. getExpandedXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, PsiXmlObjectCache elementCache, Set<Interaction> interactionSet, Source defaultSource, XMLGregorianCalendar defaultReleaseDate, Collection<Annotation> defaultEntryAnnotations, boolean writeComplexAsInteractors, boolean extended, PsiXmlVersion version)
Create the options for the compact PSI-XML InteractionWriter.Map<String,Object>
MIDataSourceOptionFactory. getMitabOptions(InteractionCategory objectCategory, ComplexType complexType, boolean streaming, MIFileParserListener listener, Object input)
Create the options for the MITAB datasource.Map<String,Object>
MIDataSourceOptionFactory. getMitabOptions(InteractionCategory objectCategory, ComplexType complexType, Object inputData)
Create the options for the MITAB datasource using the provided objectCategory.Map<String,Object>
MIWriterOptionFactory. getMitabOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, ComplexExpansionMethod expansion, boolean writeHeader, MitabVersion version, boolean extended)
Create the options for the MITAB InteractionWriter.Map<String,Object>
MIWriterOptionFactory. getMitabOptions(InteractionCategory objectCategory, ComplexType complexType, File outputFile)
Create the options for a MITAB interaction writer.Map<String,Object>
MIWriterOptionFactory. getMitabOptions(InteractionCategory objectCategory, ComplexType complexType, OutputStream output)
Create the options for a MITAB interaction writer.Map<String,Object>
MIWriterOptionFactory. getMitabOptions(InteractionCategory objectCategory, ComplexType complexType, Writer writer)
Create the options for a MITAB interaction writer.Map<String,Object>
MIDataSourceOptionFactory. getOptions(MIFileType type, InteractionCategory objectCategory, ComplexType complexType, boolean streaming, MIFileParserListener listener, Object input)
Create a map of optionsMap<String,Object>
MIDataSourceOptionFactory. getXmlOptions(InteractionCategory objectCategory, ComplexType complexType, boolean streaming, MIFileParserListener listener, Object input, ComplexExpansionMethod expansionMethod, PsiXmlIdCache objectCache)
Create the options for the PSI-XML datasource.Map<String,Object>
MIDataSourceOptionFactory. getXmlOptions(InteractionCategory objectCategory, ComplexType complexType, Object inputData)
Create the options for the Psi-XML datasource using the provided objectCategory.Map<String,Object>
MIWriterOptionFactory. getXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, PsiXmlType xmlType, PsiXmlObjectCache elementCache, Set<Experiment> experimentSet, Set<Interactor> interactorSet, Set<String> availabilitySet, Set<Interaction> interactionSet, Source defaultSource, XMLGregorianCalendar defaultReleaseDate, Collection<Annotation> defaultEntryAnnotations, boolean writeComplexAsInteractors, boolean extended, PsiXmlVersion version)
Create the options for the PSI-XML InteractionWriter. -
Uses of InteractionCategory in psidev.psi.mi.jami.factory
Methods in psidev.psi.mi.jami.factory with parameters of type InteractionCategory Modifier and Type Method Description ComplexExpansionMethod
ComplexExpansionFactory. createBipartiteComplexExpansion(InteractionCategory category)
Create an instance of bipartite complex expansion that suits the interactionCategoryComplexExpansionMethod
DefaultComplexExpansionFactory. createBipartiteComplexExpansion(InteractionCategory category)
Create an instance of bipartite complex expansion that suits the interactionCategoryComplexExpansionMethod
ComplexExpansionFactory. createComplexExpansionMethod(InteractionCategory category, ComplexExpansionType type)
Create an instance of complex expansion that suits the interactionCategory and the ComplexExpansionTypeComplexExpansionMethod
DefaultComplexExpansionFactory. createComplexExpansionMethod(InteractionCategory category, ComplexExpansionType type)
Create an instance of complex expansion that suits the interactionCategory and the ComplexExpansionTypeComplexExpansionMethod
ComplexExpansionFactory. createMatrixComplexExpansion(InteractionCategory category)
Create an instance of matrix complex expansion that suits the interactionCategoryComplexExpansionMethod
DefaultComplexExpansionFactory. createMatrixComplexExpansion(InteractionCategory category)
Create an instance of matrix complex expansion that suits the interactionCategoryComplexExpansionMethod
ComplexExpansionFactory. createSpokeComplexExpansion(InteractionCategory category)
Create an instance of spoke complex expansion that suits the interactionCategoryComplexExpansionMethod
DefaultComplexExpansionFactory. createSpokeComplexExpansion(InteractionCategory category)
Create an instance of spoke complex expansion that suits the interactionCategory -
Uses of InteractionCategory in psidev.psi.mi.jami.html
Methods in psidev.psi.mi.jami.html with parameters of type InteractionCategory Modifier and Type Method Description Map<String,Object>
MIHtmlOptionFactory. getHtmlOptions(Object output, InteractionCategory objectCategory, boolean writeHeader)
Create the options for the HTML InteractionWriter.Map<String,Object>
MIHtmlOptionFactory. getHtmlOptions(InteractionCategory objectCategory, File outputFile)
Create the options for a HTML interaction writer.Map<String,Object>
MIHtmlOptionFactory. getHtmlOptions(InteractionCategory objectCategory, OutputStream output)
Create the options for a HTML interaction writer.Map<String,Object>
MIHtmlOptionFactory. getHtmlOptions(InteractionCategory objectCategory, Writer writer)
Create the options for a HTML interaction writer. -
Uses of InteractionCategory in psidev.psi.mi.jami.json
Methods in psidev.psi.mi.jami.json with parameters of type InteractionCategory Modifier and Type Method Description Map<String,Object>
MIJsonOptionFactory. getJsonOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, MIJsonType type, OntologyTermFetcher ontologyFetcher, ComplexExpansionMethod complexExpansion)
Create the options for the JSON InteractionWriter.Map<String,Object>
MIJsonOptionFactory. getJsonOptions(InteractionCategory objectCategory, File outputFile)
Create the options for a JSON interaction writer.Map<String,Object>
MIJsonOptionFactory. getJsonOptions(InteractionCategory objectCategory, OutputStream output)
Create the options for a JSON interaction writer.Map<String,Object>
MIJsonOptionFactory. getJsonOptions(InteractionCategory objectCategory, Writer writer)
Create the options for a JSON interaction writer.Map<String,Object>
MIJsonOptionFactory. getJsonOptions(InteractionCategory objectCategory, ComplexExpansionMethod expansion, File writer)
Create the options for a JSON interaction writer which will be by default of type MIJsonType.binary_only as a complex ecpasnion is provided.Map<String,Object>
MIJsonOptionFactory. getJsonOptions(InteractionCategory objectCategory, ComplexExpansionMethod expansion, OutputStream writer)
Create the options for a JSON interaction writer which will be by default of type MIJsonType.binary_only as a complex ecpasnion is provided.Map<String,Object>
MIJsonOptionFactory. getJsonOptions(InteractionCategory objectCategory, ComplexExpansionMethod expansion, Writer writer)
Create the options for a JSON interaction writer which will be by default of type MIJsonType.binary_only as a complex ecpasnion is provided.Map<String,Object>
MIJsonOptionFactory. getJsonOptions(InteractionCategory objectCategory, ComplexExpansionMethod expansion, OntologyTermFetcher fetcher, File writer)
Create the options for a JSON interaction writer which will be by default of type MIJsonType.binary_only as a complex ecpasnion is provided.Map<String,Object>
MIJsonOptionFactory. getJsonOptions(InteractionCategory objectCategory, ComplexExpansionMethod expansion, OntologyTermFetcher fetcher, OutputStream writer)
Create the options for a JSON interaction writer which will be by default of type MIJsonType.binary_only as a complex ecpasnion is provided.Map<String,Object>
MIJsonOptionFactory. getJsonOptions(InteractionCategory objectCategory, ComplexExpansionMethod expansion, OntologyTermFetcher fetcher, Writer writer)
Create the options for a JSON interaction writer which will be by default of type MIJsonType.binary_only as a complex ecpasnion is provided.Map<String,Object>
MIJsonOptionFactory. getJsonOptions(InteractionCategory objectCategory, OntologyTermFetcher fetcher, File writer)
Create the options for a JSON interaction writer.Map<String,Object>
MIJsonOptionFactory. getJsonOptions(InteractionCategory objectCategory, OntologyTermFetcher fetcher, OutputStream writer)
Create the options for a JSON interaction writer.Map<String,Object>
MIJsonOptionFactory. getJsonOptions(InteractionCategory objectCategory, OntologyTermFetcher fetcher, Writer writer)
Create the options for a JSON interaction writer. -
Uses of InteractionCategory in psidev.psi.mi.jami.model
Methods in psidev.psi.mi.jami.model that return InteractionCategory Modifier and Type Method Description static InteractionCategory
InteractionCategory. valueOf(String name)
Returns the enum constant of this type with the specified name.static InteractionCategory[]
InteractionCategory. values()
Returns an array containing the constants of this enum type, in the order they are declared. -
Uses of InteractionCategory in psidev.psi.mi.jami.tab.extension.datasource
Methods in psidev.psi.mi.jami.tab.extension.datasource with parameters of type InteractionCategory Modifier and Type Method Description protected void
DefaultMitabSource. initialiseDelegate(Map<String,Object> options, MitabDataSourceFactory factory, InteractionCategory category, ComplexType type)
initialiseDelegate.protected void
DefaultMitabStreamSource. initialiseDelegate(Map<String,Object> options, MitabDataSourceFactory factory, InteractionCategory category, ComplexType type)
initialiseDelegate. -
Uses of InteractionCategory in psidev.psi.mi.jami.tab.extension.factory
Methods in psidev.psi.mi.jami.tab.extension.factory with parameters of type InteractionCategory Modifier and Type Method Description MitabStreamSource
MitabDataSourceFactory. createMitabBinaryDataSource(InteractionCategory interactionCategory, boolean streaming)
createMitabBinaryDataSource.InteractionWriter
MitabWriterFactory. createMitabBinaryWriter(InteractionCategory interactionCategory, MitabVersion version, boolean extended)
createMitabBinaryWriter.MitabStreamSource
MitabDataSourceFactory. createMitabDataSource(InteractionCategory interactionCategory, boolean streaming)
createMitabDataSource.MitabStreamSource
MitabDataSourceFactory. createMitabDataSource(InteractionCategory interactionCategory, ComplexType complexType, boolean streaming)
createMitabDataSource.InteractionWriter
MitabWriterFactory. createMitabWriter(InteractionCategory interactionCategory, ComplexType complexType, MitabVersion version, boolean extended)
createMitabWriter.InteractionWriter
MitabWriterFactory. createMitabWriter(InteractionCategory interactionCategory, MitabVersion version, boolean extended)
createMitabWriter. -
Uses of InteractionCategory in psidev.psi.mi.jami.xml.cache
Constructors in psidev.psi.mi.jami.xml.cache with parameters of type InteractionCategory Constructor Description PsiXmlFileIndexCache(File file, PsiXmlVersion version, InteractionCategory category)
Constructor for PsiXmlFileIndexCache. -
Uses of InteractionCategory in psidev.psi.mi.jami.xml.io.parser
Methods in psidev.psi.mi.jami.xml.io.parser with parameters of type InteractionCategory Modifier and Type Method Description javax.xml.bind.Unmarshaller
JaxbUnmarshallerFactory. createFullUnmarshaller(PsiXmlVersion version, InteractionCategory category)
createFullUnmarshaller.javax.xml.bind.Unmarshaller
JaxbUnmarshallerFactory. createFullXml253JAXBUnmarshaller(InteractionCategory category)
createFullXml253JAXBUnmarshaller.javax.xml.bind.Unmarshaller
JaxbUnmarshallerFactory. createFullXml254JAXBUnmarshaller(InteractionCategory category)
createFullXml254JAXBUnmarshaller.javax.xml.bind.Unmarshaller
JaxbUnmarshallerFactory. createFullXml300JAXBUnmarshaller(InteractionCategory category)
createFullXml300JAXBUnmarshaller.javax.xml.bind.Unmarshaller
JaxbUnmarshallerFactory. createUnmarshaller(PsiXmlVersion version, InteractionCategory category)
createUnmarshaller.javax.xml.bind.Unmarshaller
JaxbUnmarshallerFactory. createXml253JAXBUnmarshaller(InteractionCategory category)
createXml253JAXBUnmarshaller.javax.xml.bind.Unmarshaller
JaxbUnmarshallerFactory. createXml254JAXBUnmarshaller(InteractionCategory category)
createXml254JAXBUnmarshaller.javax.xml.bind.Unmarshaller
JaxbUnmarshallerFactory. createXml300JAXBUnmarshaller(InteractionCategory category)
createXml300JAXBUnmarshaller. -
Uses of InteractionCategory in psidev.psi.mi.jami.xml.io.writer
Methods in psidev.psi.mi.jami.xml.io.writer with parameters of type InteractionCategory Modifier and Type Method Description protected void
AbstractXmlWriter. initialiseSubWriters(boolean extended, boolean named, PsiXmlType xmlType, InteractionCategory interactionCategory, ComplexType complexType)
initialiseSubWriters. -
Uses of InteractionCategory in psidev.psi.mi.jami.xml.io.writer.elements
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Uses of InteractionCategory in psidev.psi.mi.jami.xml.model.extension.datasource
Methods in psidev.psi.mi.jami.xml.model.extension.datasource with parameters of type InteractionCategory Modifier and Type Method Description protected void
DefaultPsiXmlSource. initialiseDelegate(Map<String,Object> options, PsiXmlDataSourceFactory factory, InteractionCategory category, ComplexType type)
initialiseDelegate.protected void
DefaultPsiXmlStreamSource. initialiseDelegate(Map<String,Object> options, PsiXmlDataSourceFactory factory, InteractionCategory category, ComplexType type)
initialiseDelegate. -
Uses of InteractionCategory in psidev.psi.mi.jami.xml.model.extension.factory
Methods in psidev.psi.mi.jami.xml.model.extension.factory with parameters of type InteractionCategory Modifier and Type Method Description PsiXmlStreamSource
PsiXmlDataSourceFactory. createPsiXmlBinaryDataSource(InteractionCategory interactionCategory, boolean streaming)
createPsiXmlBinaryDataSource.InteractionWriter
PsiXmlWriterFactory. createPsiXmlBinaryWriter(InteractionCategory interactionCategory, PsiXmlVersion version, PsiXmlType type, boolean extended, boolean named)
createPsiXmlBinaryWriter.PsiXmlStreamSource
PsiXmlDataSourceFactory. createPsiXmlDataSource(InteractionCategory interactionCategory, boolean streaming)
createPsiXmlDataSource.PsiXmlStreamSource
PsiXmlDataSourceFactory. createPsiXmlDataSource(InteractionCategory interactionCategory, ComplexType complexType, boolean streaming)
createPsiXmlDataSource.InteractionWriter
PsiXmlWriterFactory. createPsiXmlWriter(InteractionCategory interactionCategory, ComplexType complexType, PsiXmlType type, PsiXmlVersion version, boolean extended, boolean named)
createPsiXmlWriter.InteractionWriter
PsiXmlWriterFactory. createPsiXmlWriter(InteractionCategory interactionCategory, PsiXmlType type, PsiXmlVersion version, boolean extended, boolean named)
createPsiXmlWriter.
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