Uses of Class psidev.psi.mi.jami.model.ComplexType (PSI :: JAMI - Java framework for molecular interactions 3.3.0 API)

Packages that use ComplexType
Package	Description
psidev.psi.mi.jami.binary.expansion
psidev.psi.mi.jami.commons
psidev.psi.mi.jami.crosslink
psidev.psi.mi.jami.json
psidev.psi.mi.jami.model
psidev.psi.mi.jami.tab.extension.datasource
psidev.psi.mi.jami.tab.extension.factory
psidev.psi.mi.jami.utils
psidev.psi.mi.jami.xml.io.writer
psidev.psi.mi.jami.xml.io.writer.elements
psidev.psi.mi.jami.xml.model.extension.datasource
psidev.psi.mi.jami.xml.model.extension.factory

Uses of ComplexType in psidev.psi.mi.jami.binary.expansion

Methods in psidev.psi.mi.jami.binary.expansion that return ComplexType
Modifier and Type	Method	Description
`protected ComplexType`	AbstractComplexExpansionMethod.`findInteractionCategory(T interaction)`	findInteractionCategory
`protected ComplexType`	InteractionEvidenceBipartiteExpansion.`findInteractionCategory(InteractionEvidence interaction)`	findInteractionCategory
`protected ComplexType`	InteractionEvidenceMatrixExpansion.`findInteractionCategory(InteractionEvidence interaction)`	findInteractionCategory
`protected ComplexType`	InteractionEvidenceSpokeExpansion.`findInteractionCategory(InteractionEvidence interaction)`	findInteractionCategory
`protected ComplexType`	ModelledInteractionBipartiteExpansion.`findInteractionCategory(ModelledInteraction interaction)`	findInteractionCategory
`protected ComplexType`	ModelledInteractionMatrixExpansion.`findInteractionCategory(ModelledInteraction interaction)`	findInteractionCategory
`protected ComplexType`	ModelledInteractionSpokeExpansion.`findInteractionCategory(ModelledInteraction interaction)`	findInteractionCategory

Uses of ComplexType in psidev.psi.mi.jami.commons

Methods in psidev.psi.mi.jami.commons with parameters of type ComplexType
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 options
`Map<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 ComplexType in psidev.psi.mi.jami.crosslink

Methods in psidev.psi.mi.jami.crosslink with parameters of type ComplexType
Modifier and Type	Method	Description
`Map<String,Object>`	CrossLinkCsvOptionFactory.`getCsvOptions(CsvType csvType, ComplexType complexType, Boolean streaming, MIFileParserListener listener, Object input)`	Create a map of options
`Map<String,Object>`	CrossLinkCsvOptionFactory.`getCsvOptions(CsvType csvType, ComplexType complexType, Object inputData)`	Create the options for the CSV datasource using the provided csvtype.

Uses of ComplexType in psidev.psi.mi.jami.json

Methods in psidev.psi.mi.jami.json with parameters of type ComplexType
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.

Uses of ComplexType in psidev.psi.mi.jami.model

Methods in psidev.psi.mi.jami.model that return ComplexType
Modifier and Type	Method	Description
`static ComplexType`	ComplexType.`valueOf(String name)`	Returns the enum constant of this type with the specified name.
`static ComplexType[]`	ComplexType.`values()`	Returns an array containing the constants of this enum type, in the order they are declared.

Uses of ComplexType in psidev.psi.mi.jami.tab.extension.datasource

Methods in psidev.psi.mi.jami.tab.extension.datasource with parameters of type ComplexType
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 ComplexType in psidev.psi.mi.jami.tab.extension.factory

Methods in psidev.psi.mi.jami.tab.extension.factory with parameters of type ComplexType
Modifier and Type	Method	Description
`MitabStreamSource`	MitabDataSourceFactory.`createMitabDataSource(InteractionCategory interactionCategory, ComplexType complexType, boolean streaming)`	createMitabDataSource.
`InteractionWriter`	MitabWriterFactory.`createMitabWriter(InteractionCategory interactionCategory, ComplexType complexType, MitabVersion version, boolean extended)`	createMitabWriter.

Uses of ComplexType in psidev.psi.mi.jami.utils

Methods in psidev.psi.mi.jami.utils that return ComplexType
Modifier and Type	Method	Description
`static ComplexType`	InteractionUtils.`findInteractionCategoryOf(Interaction interaction, boolean checkExperimentalRoleIfInteractionEvidence)`	The method will find the interactionCategory (binary, self, etc.)
`static ComplexType`	InteractionUtils.`findInteractionEvidenceCategoryOf(InteractionEvidence interaction)`	The method will find the interactionCategory (binary, self, etc.)
`static ComplexType`	InteractionUtils.`findModelledInteractionCategoryOf(ModelledInteraction interaction)`	The method will find the interactionCategory (binary, self, etc.)

Uses of ComplexType in psidev.psi.mi.jami.xml.io.writer

Methods in psidev.psi.mi.jami.xml.io.writer with parameters of type ComplexType
Modifier and Type	Method	Description
`protected void`	AbstractXmlWriter.`initialiseSubWriters(boolean extended, boolean named, PsiXmlType xmlType, InteractionCategory interactionCategory, ComplexType complexType)`	initialiseSubWriters.

Uses of ComplexType in psidev.psi.mi.jami.xml.io.writer.elements

Methods in psidev.psi.mi.jami.xml.io.writer.elements with parameters of type ComplexType
Modifier and Type	Method	Description
`static PsiXmlInteractionWriter[]`	PsiXmlElementWriterFactory.createDefaultPsiXmlInteractionWriters(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlType xmlType, InteractionCategory interactionCategory, ComplexType complexType, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlElementWriter[] confidenceWriters, PsiXmlElementWriter<Checksum> checksumWriter, PsiXmlVariableNameWriter<CvTerm> interactionTypeWriter, PsiXmlExperimentWriter experimentWriter, PsiXmlElementWriter<String> availabilityWriter, PsiXmlParameterWriter[] parameterWriters, PsiXmlParticipantWriter[] participantWriters, PsiXmlElementWriter inferredInteractionWriter, PsiXmlPublicationWriter publicationWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter)	createDefaultPsiXmlInteractionWriters.
`static PsiXmlInteractionWriter[]`	PsiXmlElementWriterFactory.createExtendedPsiXmlInteractionWriters(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlType xmlType, InteractionCategory interactionCategory, ComplexType complexType, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlElementWriter[] confidenceWriters, PsiXmlElementWriter<Checksum> checksumWriter, PsiXmlVariableNameWriter<CvTerm> interactionTypeWriter, PsiXmlExperimentWriter experimentWriter, PsiXmlElementWriter<String> availabilityWriter, PsiXmlParameterWriter[] parameterWriters, PsiXmlParticipantWriter[] participantWriters, PsiXmlElementWriter inferredInteractionWriter, PsiXmlPublicationWriter publicationWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter)	createExtendedPsiXmlInteractionWriters.
`static PsiXmlInteractionWriter[]`	PsiXmlElementWriterFactory.createInteractionWritersFor(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlType xmlType, InteractionCategory interactionCategory, ComplexType complexType, boolean extended, boolean named, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlElementWriter[] confidenceWriters, PsiXmlElementWriter<Checksum> checksumWriter, PsiXmlVariableNameWriter<CvTerm> interactionTypeWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter, PsiXmlExperimentWriter experimentWriter, PsiXmlElementWriter<String> availabilityWriter, PsiXmlElementWriter<Interactor> interactorWriter, PsiXmlPublicationWriter publicationWriter)	createInteractionWritersFor.
`static PsiXmlInteractionWriter[]`	PsiXmlElementWriterFactory.createNamedPsiXmlInteractionWriters(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlType xmlType, InteractionCategory interactionCategory, ComplexType complexType, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlElementWriter[] confidenceWriters, PsiXmlElementWriter<Checksum> checksumWriter, PsiXmlVariableNameWriter<CvTerm> interactionTypeWriter, PsiXmlExperimentWriter experimentWriter, PsiXmlElementWriter<String> availabilityWriter, PsiXmlParameterWriter[] parameterWriters, PsiXmlParticipantWriter[] participantWriters, PsiXmlElementWriter inferredInteractionWriter, PsiXmlPublicationWriter publicationWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter)	createNamedPsiXmlInteractionWriters.

Uses of ComplexType in psidev.psi.mi.jami.xml.model.extension.datasource

Methods in psidev.psi.mi.jami.xml.model.extension.datasource with parameters of type ComplexType
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 ComplexType in psidev.psi.mi.jami.xml.model.extension.factory

Methods in psidev.psi.mi.jami.xml.model.extension.factory with parameters of type ComplexType
Modifier and Type	Method	Description
`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.