Package psidev.psi.mi.jami.xml.io.writer.elements

Class PsiXmlElementWriterFactory

java.lang.Object

psidev.psi.mi.jami.xml.io.writer.elements.PsiXmlElementWriterFactory

public class PsiXmlElementWriterFactory
extends Object

Factory to initialise PSI-XML element writers depending on the version and the interaction object category

Since:

23/04/14

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Method Summary

Modifier and Type	Method	Description
static PsiXmlElementWriter<Alias>	createAliasWriter(XMLStreamWriter streamWriter)	createAliasWriter.
static PsiXmlElementWriter<Allostery>	createAllosteryWriter(XMLStreamWriter streamWriter, boolean expanded, PsiXmlObjectCache objectIndex, PsiXmlVariableNameWriter<CvTerm> cvWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlPublicationWriter publicationWriter)	createAllosteryWriter.
static PsiXmlElementWriter<Annotation>	createAnnotationWriter(XMLStreamWriter streamWriter)	createAnnotationWriter.
static PsiXmlElementWriter<String>	createAvailabilityWriter(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex)	createAvailabilityWriter.
static PsiXmlElementWriter<Set<Feature>>	createBindingFeaturesWriter(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex)	createBindingFeaturesWriter.
static PsiXmlCausalRelationshipWriter	createCausalRelationshipWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVariableNameWriter<CvTerm> cvWriter)	createCausalRelationshipWriter.
static PsiXmlElementWriter<Checksum>	createChecksumWriter(XMLStreamWriter streamWriter)	createChecksumWriter.
static PsiXmlElementWriter<Confidence>[]	createConfidenceWriters(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlVariableNameWriter<CvTerm> confidenceTypeWriter, PsiXmlPublicationWriter publicationWriter)	createConfidenceWriters.
static PsiXmlElementWriter<CooperativityEvidence>	createCooperativityEvidenceWriter(XMLStreamWriter streamWriter, boolean expanded, PsiXmlVariableNameWriter<CvTerm> cvWriter, PsiXmlPublicationWriter publicationWriter)	createCooperativityEvidenceWriter.
static PsiXmlVariableNameWriter<CvTerm>	createCvWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlXrefWriter primaryRefWriter)	createCvWriter.
static PsiXmlInteractionWriter[]	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 PsiXmlVariableNameWriter<CvTerm>	createExperimentalCvWriter(XMLStreamWriter streamWriter, PsiXmlVersion version, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlXrefWriter primaryRefWriter)	createExperimentalCvWriter.
static PsiXmlElementWriter<AbstractExperimentalInteractor>	createExperimentalInteractorWriter(XMLStreamWriter streamWriter, PsiXmlVersion version, PsiXmlObjectCache objectIndex, PsiXmlType xmlType)	createExperimentalInteractorWriter.
static PsiXmlExperimentWriter	createExperimentWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVersion version, boolean named, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlPublicationWriter publicationWriter, PsiXmlElementWriter<Organism> nonExperimentalHostOrganismWriter, PsiXmlVariableNameWriter<CvTerm> detectionMethodWriter, PsiXmlElementWriter<Confidence> confidenceWriter)	createExperimentWriter.
static PsiXmlElementWriter<AbstractInferredInteraction>	createExtendedInferredInteractionWriter(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex)	createExtendedInferredInteractionWriter.
static PsiXmlInteractionWriter[]	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 <F extends Feature> PsiXmlElementWriter<F>[]	createFeatureWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVersion version, InteractionCategory category, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlVariableNameWriter<CvTerm> featureTypeWriter, PsiXmlParameterWriter parameterWriter)	createFeatureWriter.
static PsiXmlElementWriter<Organism>	createHostOrganismWriter(XMLStreamWriter streamWriter, PsiXmlVersion version, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> annotationWriter, PsiXmlXrefWriter xrefWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter)	createHostOrganismWriter.
static PsiXmlElementWriter<Set<Feature>>	createInferredInteractionWriter(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex)	createInferredInteractionWriter.
static PsiXmlInteractionWriter[]	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 PsiXmlElementWriter<Interactor>	createInteractorWriter(PsiXmlVersion version, XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlVariableNameWriter<CvTerm> interactorTypeWriter, PsiXmlElementWriter<Organism> organismWriter, PsiXmlElementWriter<Checksum> checksumWriter)	createInteractorWriter.
static PsiXmlInteractionWriter[]	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.
static PsiXmlVariableNameWriter<CvTerm>	createOpenCvWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter)	createOpenCvWriter.
static PsiXmlElementWriter<Organism>	createOrganismWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> annotationWriter, PsiXmlXrefWriter xrefWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter)	createOrganismWriter.
static PsiXmlParameterWriter[]	createParameterWriters(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlPublicationWriter publicationWriter)	createParameterWriters.
static <P extends ParticipantCandidate> PsiXmlElementWriter<P>[]	createParticipantCandidateWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlType xmlType, InteractionCategory category, PsiXmlElementWriter<Interactor> interactorWriter, PsiXmlElementWriter<ModelledFeature> modelledFeatureWriter, PsiXmlElementWriter<FeatureEvidence> featureEvidenceWriter)	createParticipantCandidateWriter.
static <P extends Participant> PsiXmlParticipantWriter<P>[]	createParticipantWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlType xmlType, InteractionCategory category, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlElementWriter<Confidence> confidenceWriter, PsiXmlElementWriter<Interactor> interactorWriter, PsiXmlVariableNameWriter<CvTerm> cvWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter, PsiXmlParameterWriter parameterWriter)	createParticipantWriter.
static PsiXmlElementWriter<Position>[]	createPositionsWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlVariableNameWriter<CvTerm> statusWriter)	createPositionsWriter.
static PsiXmlElementWriter<Preassembly>	createPreassemblyWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVariableNameWriter<CvTerm> cvWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlPublicationWriter publicationWriter)	createPreassemblyWriter.
static PsiXmlPublicationWriter	createPublicationWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlVersion version)	createPublicationWriter.
static PsiXmlElementWriter<Range>	createRangeWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlXrefWriter refWriter, PsiXmlVariableNameWriter<CvTerm> statusWriter)	createRangeWriter.
static PsiXmlElementWriter<ResultingSequence>	createResultingSequenceWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlXrefWriter refWriter)	createResultingSequenceWriter.
static PsiXmlSourceWriter	createSourceWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlVersion version, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlPublicationWriter publicationWriter)	createSourceWriter.
static PsiXmlElementWriter<VariableParameterValueSet>	createVariableParameterValueSetWriter(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex)	createVariableParameterValueSetWriter.
static PsiXmlElementWriter<VariableParameterValue>	createVariableParameterValueWriter(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex)	createVariableParameterValueWriter.
static PsiXmlElementWriter<VariableParameter>	createVariableParameterWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVariableNameWriter<CvTerm> cvWriter)	createVariableParameterWriter.
static PsiXmlXrefWriter	createXrefWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlElementWriter<Annotation> annotationWriter)	createXrefWriter.
static PsiXmlElementWriterFactory	getInstance()	Getter for the field instance.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getInstance

public static PsiXmlElementWriterFactory getInstance()

Getter for the field instance.

Returns:

a PsiXmlElementWriterFactory object.

createInteractionWritersFor

public static PsiXmlInteractionWriter[] 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.

Parameters:

streamWriter - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

version - a PsiXmlVersion object.

xmlType - a PsiXmlType object.

interactionCategory - a InteractionCategory object.

complexType - a ComplexType object.

extended - a boolean.

named - a boolean.

aliasWriter - a PsiXmlElementWriter object.

attributeWriter - a PsiXmlElementWriter object.

primaryRefWriter - a PsiXmlXrefWriter object.

confidenceWriters - an array of PsiXmlElementWriter objects.

checksumWriter - a PsiXmlElementWriter object.

interactionTypeWriter - a PsiXmlVariableNameWriter object.

openCvWriter - a PsiXmlVariableNameWriter object.

experimentWriter - a PsiXmlExperimentWriter object.

availabilityWriter - a PsiXmlElementWriter object.

interactorWriter - a PsiXmlElementWriter object.

publicationWriter - a PsiXmlPublicationWriter object.

Returns:

an array of PsiXmlInteractionWriter objects.

createDefaultPsiXmlInteractionWriters

public static PsiXmlInteractionWriter[] 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.

Parameters:

streamWriter - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

version - a PsiXmlVersion object.

xmlType - a PsiXmlType object.

interactionCategory - a InteractionCategory object.

complexType - a ComplexType object.

aliasWriter - a PsiXmlElementWriter object.

attributeWriter - a PsiXmlElementWriter object.

primaryRefWriter - a PsiXmlXrefWriter object.

confidenceWriters - an array of PsiXmlElementWriter objects.

checksumWriter - a PsiXmlElementWriter object.

interactionTypeWriter - a PsiXmlVariableNameWriter object.

experimentWriter - a PsiXmlExperimentWriter object.

availabilityWriter - a PsiXmlElementWriter object.

parameterWriters - an array of PsiXmlParameterWriter objects.

participantWriters - an array of PsiXmlParticipantWriter objects.

inferredInteractionWriter - a PsiXmlElementWriter object.

publicationWriter - a PsiXmlPublicationWriter object.

openCvWriter - a PsiXmlVariableNameWriter object.

Returns:

an array of PsiXmlInteractionWriter objects.

createNamedPsiXmlInteractionWriters

public static PsiXmlInteractionWriter[] 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.

Parameters:

streamWriter - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

version - a PsiXmlVersion object.

xmlType - a PsiXmlType object.

interactionCategory - a InteractionCategory object.

complexType - a ComplexType object.

aliasWriter - a PsiXmlElementWriter object.

attributeWriter - a PsiXmlElementWriter object.

primaryRefWriter - a PsiXmlXrefWriter object.

confidenceWriters - an array of PsiXmlElementWriter objects.

checksumWriter - a PsiXmlElementWriter object.

interactionTypeWriter - a PsiXmlVariableNameWriter object.

experimentWriter - a PsiXmlExperimentWriter object.

availabilityWriter - a PsiXmlElementWriter object.

parameterWriters - an array of PsiXmlParameterWriter objects.

participantWriters - an array of PsiXmlParticipantWriter objects.

inferredInteractionWriter - a PsiXmlElementWriter object.

publicationWriter - a PsiXmlPublicationWriter object.

openCvWriter - a PsiXmlVariableNameWriter object.

Returns:

an array of PsiXmlInteractionWriter objects.

createExtendedPsiXmlInteractionWriters

public static PsiXmlInteractionWriter[] 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.

Parameters:

streamWriter - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

version - a PsiXmlVersion object.

xmlType - a PsiXmlType object.

interactionCategory - a InteractionCategory object.

complexType - a ComplexType object.

aliasWriter - a PsiXmlElementWriter object.

attributeWriter - a PsiXmlElementWriter object.

primaryRefWriter - a PsiXmlXrefWriter object.

confidenceWriters - an array of PsiXmlElementWriter objects.

checksumWriter - a PsiXmlElementWriter object.

interactionTypeWriter - a PsiXmlVariableNameWriter object.

experimentWriter - a PsiXmlExperimentWriter object.

availabilityWriter - a PsiXmlElementWriter object.

parameterWriters - an array of PsiXmlParameterWriter objects.

participantWriters - an array of PsiXmlParticipantWriter objects.

inferredInteractionWriter - a PsiXmlElementWriter object.

publicationWriter - a PsiXmlPublicationWriter object.

openCvWriter - a PsiXmlVariableNameWriter object.

Returns:

an array of PsiXmlInteractionWriter objects.

createAliasWriter

public static PsiXmlElementWriter<Alias> createAliasWriter(XMLStreamWriter streamWriter)

createAliasWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

Returns:

a PsiXmlElementWriter object.

createAnnotationWriter

public static PsiXmlElementWriter<Annotation> createAnnotationWriter(XMLStreamWriter streamWriter)

createAnnotationWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

Returns:

a PsiXmlElementWriter object.

createXrefWriter

public static PsiXmlXrefWriter createXrefWriter(XMLStreamWriter streamWriter,
                                                boolean extended,
                                                PsiXmlElementWriter<Annotation> annotationWriter)

createXrefWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

extended - a boolean.

annotationWriter - a PsiXmlElementWriter object.

Returns:

a PsiXmlXrefWriter object.

createPublicationWriter

public static PsiXmlPublicationWriter createPublicationWriter(XMLStreamWriter streamWriter,
                                                              boolean extended,
                                                              PsiXmlElementWriter<Annotation> attributeWriter,
                                                              PsiXmlXrefWriter primaryRefWriter,
                                                              PsiXmlVersion version)

createPublicationWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

extended - a boolean.

attributeWriter - a PsiXmlElementWriter object.

primaryRefWriter - a PsiXmlXrefWriter object.

version - a PsiXmlVersion object.

Returns:

a PsiXmlPublicationWriter object.

createOpenCvWriter

public static PsiXmlVariableNameWriter<CvTerm> createOpenCvWriter(XMLStreamWriter streamWriter,
                                                                  boolean extended,
                                                                  PsiXmlElementWriter<Alias> aliasWriter,
                                                                  PsiXmlElementWriter<Annotation> attributeWriter,
                                                                  PsiXmlXrefWriter primaryRefWriter)

createOpenCvWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

extended - a boolean.

aliasWriter - a PsiXmlElementWriter object.

attributeWriter - a PsiXmlElementWriter object.

primaryRefWriter - a PsiXmlXrefWriter object.

Returns:

a PsiXmlVariableNameWriter object.

createExperimentalCvWriter

public static PsiXmlVariableNameWriter<CvTerm> createExperimentalCvWriter(XMLStreamWriter streamWriter,
                                                                          PsiXmlVersion version,
                                                                          boolean extended,
                                                                          PsiXmlObjectCache objectIndex,
                                                                          PsiXmlElementWriter<Alias> aliasWriter,
                                                                          PsiXmlXrefWriter primaryRefWriter)

createExperimentalCvWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

version - a PsiXmlVersion object.

extended - a boolean.

objectIndex - a PsiXmlObjectCache object.

aliasWriter - a PsiXmlElementWriter object.

primaryRefWriter - a PsiXmlXrefWriter object.

Returns:

a PsiXmlVariableNameWriter object.

createCvWriter

public static PsiXmlVariableNameWriter<CvTerm> createCvWriter(XMLStreamWriter streamWriter,
                                                              boolean extended,
                                                              PsiXmlElementWriter<Alias> aliasWriter,
                                                              PsiXmlXrefWriter primaryRefWriter)

createCvWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

extended - a boolean.

aliasWriter - a PsiXmlElementWriter object.

primaryRefWriter - a PsiXmlXrefWriter object.

Returns:

a PsiXmlVariableNameWriter object.

createHostOrganismWriter

public static PsiXmlElementWriter<Organism> createHostOrganismWriter(XMLStreamWriter streamWriter,
                                                                     PsiXmlVersion version,
                                                                     boolean extended,
                                                                     PsiXmlObjectCache objectIndex,
                                                                     PsiXmlElementWriter<Alias> aliasWriter,
                                                                     PsiXmlElementWriter<Annotation> annotationWriter,
                                                                     PsiXmlXrefWriter xrefWriter,
                                                                     PsiXmlVariableNameWriter<CvTerm> openCvWriter)

createHostOrganismWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

version - a PsiXmlVersion object.

extended - a boolean.

objectIndex - a PsiXmlObjectCache object.

aliasWriter - a PsiXmlElementWriter object.

annotationWriter - a PsiXmlElementWriter object.

xrefWriter - a PsiXmlXrefWriter object.

openCvWriter - a PsiXmlVariableNameWriter object.

Returns:

a PsiXmlElementWriter object.

createOrganismWriter

public static PsiXmlElementWriter<Organism> createOrganismWriter(XMLStreamWriter streamWriter,
                                                                 boolean extended,
                                                                 PsiXmlElementWriter<Alias> aliasWriter,
                                                                 PsiXmlElementWriter<Annotation> annotationWriter,
                                                                 PsiXmlXrefWriter xrefWriter,
                                                                 PsiXmlVariableNameWriter<CvTerm> openCvWriter)

createOrganismWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

extended - a boolean.

aliasWriter - a PsiXmlElementWriter object.

annotationWriter - a PsiXmlElementWriter object.

xrefWriter - a PsiXmlXrefWriter object.

openCvWriter - a PsiXmlVariableNameWriter object.

Returns:

a PsiXmlElementWriter object.

createChecksumWriter

public static PsiXmlElementWriter<Checksum> createChecksumWriter(XMLStreamWriter streamWriter)

createChecksumWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

Returns:

a PsiXmlElementWriter object.

createConfidenceWriters

public static PsiXmlElementWriter<Confidence>[] createConfidenceWriters(XMLStreamWriter streamWriter,
                                                                        boolean extended,
                                                                        PsiXmlObjectCache objectIndex,
                                                                        PsiXmlVersion version,
                                                                        PsiXmlVariableNameWriter<CvTerm> confidenceTypeWriter,
                                                                        PsiXmlPublicationWriter publicationWriter)

createConfidenceWriters.

Parameters:

streamWriter - a XMLStreamWriter object.

extended - a boolean.

objectIndex - a PsiXmlObjectCache object.

version - a PsiXmlVersion object.

confidenceTypeWriter - a PsiXmlVariableNameWriter object.

publicationWriter - a PsiXmlPublicationWriter object.

Returns:

an array of PsiXmlElementWriter objects.

createResultingSequenceWriter

public static PsiXmlElementWriter<ResultingSequence> createResultingSequenceWriter(XMLStreamWriter streamWriter,
                                                                                   boolean extended,
                                                                                   PsiXmlXrefWriter refWriter)

createResultingSequenceWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

extended - a boolean.

refWriter - a PsiXmlXrefWriter object.

Returns:

a PsiXmlElementWriter object.

createCooperativityEvidenceWriter

public static PsiXmlElementWriter<CooperativityEvidence> createCooperativityEvidenceWriter(XMLStreamWriter streamWriter,
                                                                                           boolean expanded,
                                                                                           PsiXmlVariableNameWriter<CvTerm> cvWriter,
                                                                                           PsiXmlPublicationWriter publicationWriter)

createCooperativityEvidenceWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

expanded - a boolean.

cvWriter - a PsiXmlVariableNameWriter object.

publicationWriter - a PsiXmlPublicationWriter object.

Returns:

a PsiXmlElementWriter object.

createAllosteryWriter

public static PsiXmlElementWriter<Allostery> createAllosteryWriter(XMLStreamWriter streamWriter,
                                                                   boolean expanded,
                                                                   PsiXmlObjectCache objectIndex,
                                                                   PsiXmlVariableNameWriter<CvTerm> cvWriter,
                                                                   PsiXmlElementWriter<Annotation> attributeWriter,
                                                                   PsiXmlPublicationWriter publicationWriter)

createAllosteryWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

expanded - a boolean.

objectIndex - a PsiXmlObjectCache object.

cvWriter - a PsiXmlVariableNameWriter object.

attributeWriter - a PsiXmlElementWriter object.

publicationWriter - a PsiXmlPublicationWriter object.

Returns:

a PsiXmlElementWriter object.

createPreassemblyWriter

public static PsiXmlElementWriter<Preassembly> createPreassemblyWriter(XMLStreamWriter streamWriter,
                                                                       boolean extended,
                                                                       PsiXmlObjectCache objectIndex,
                                                                       PsiXmlVariableNameWriter<CvTerm> cvWriter,
                                                                       PsiXmlElementWriter<Annotation> attributeWriter,
                                                                       PsiXmlPublicationWriter publicationWriter)

createPreassemblyWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

extended - a boolean.

objectIndex - a PsiXmlObjectCache object.

cvWriter - a PsiXmlVariableNameWriter object.

attributeWriter - a PsiXmlElementWriter object.

publicationWriter - a PsiXmlPublicationWriter object.

Returns:

a PsiXmlElementWriter object.

createCausalRelationshipWriter

public static PsiXmlCausalRelationshipWriter createCausalRelationshipWriter(XMLStreamWriter streamWriter,
                                                                            boolean extended,
                                                                            PsiXmlObjectCache objectIndex,
                                                                            PsiXmlVariableNameWriter<CvTerm> cvWriter)

createCausalRelationshipWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

extended - a boolean.

objectIndex - a PsiXmlObjectCache object.

cvWriter - a PsiXmlVariableNameWriter object.

Returns:

a PsiXmlCausalRelationshipWriter object.

createVariableParameterValueSetWriter

public static PsiXmlElementWriter<VariableParameterValueSet> createVariableParameterValueSetWriter(XMLStreamWriter streamWriter,
                                                                                                   PsiXmlObjectCache objectIndex)

createVariableParameterValueSetWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Returns:

a PsiXmlElementWriter object.

createVariableParameterValueWriter

public static PsiXmlElementWriter<VariableParameterValue> createVariableParameterValueWriter(XMLStreamWriter streamWriter,
                                                                                             PsiXmlObjectCache objectIndex)

createVariableParameterValueWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Returns:

a PsiXmlElementWriter object.

createVariableParameterWriter

public static PsiXmlElementWriter<VariableParameter> createVariableParameterWriter(XMLStreamWriter streamWriter,
                                                                                   boolean extended,
                                                                                   PsiXmlObjectCache objectIndex,
                                                                                   PsiXmlVariableNameWriter<CvTerm> cvWriter)

createVariableParameterWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

extended - a boolean.

objectIndex - a PsiXmlObjectCache object.

cvWriter - a PsiXmlVariableNameWriter object.

Returns:

a PsiXmlElementWriter object.

createPositionsWriter

public static PsiXmlElementWriter<Position>[] createPositionsWriter(XMLStreamWriter streamWriter,
                                                                    boolean extended,
                                                                    PsiXmlVariableNameWriter<CvTerm> statusWriter)

createPositionsWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

extended - a boolean.

statusWriter - a PsiXmlVariableNameWriter object.

Returns:

an array of PsiXmlElementWriter objects.

createRangeWriter

public static PsiXmlElementWriter<Range> createRangeWriter(XMLStreamWriter streamWriter,
                                                           boolean extended,
                                                           PsiXmlObjectCache objectIndex,
                                                           PsiXmlVersion version,
                                                           PsiXmlXrefWriter refWriter,
                                                           PsiXmlVariableNameWriter<CvTerm> statusWriter)

createRangeWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

extended - a boolean.

objectIndex - a PsiXmlObjectCache object.

version - a PsiXmlVersion object.

refWriter - a PsiXmlXrefWriter object.

statusWriter - a PsiXmlVariableNameWriter object.

Returns:

a PsiXmlElementWriter object.

createParameterWriters

public static PsiXmlParameterWriter[] createParameterWriters(XMLStreamWriter streamWriter,
                                                             boolean extended,
                                                             PsiXmlObjectCache objectIndex,
                                                             PsiXmlVersion version,
                                                             PsiXmlPublicationWriter publicationWriter)

createParameterWriters.

Parameters:

streamWriter - a XMLStreamWriter object.

extended - a boolean.

objectIndex - a PsiXmlObjectCache object.

version - a PsiXmlVersion object.

publicationWriter - a PsiXmlPublicationWriter object.

Returns:

an array of PsiXmlParameterWriter objects.

createAvailabilityWriter

public static PsiXmlElementWriter<String> createAvailabilityWriter(XMLStreamWriter streamWriter,
                                                                   PsiXmlObjectCache objectIndex)

createAvailabilityWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Returns:

a PsiXmlElementWriter object.

createInferredInteractionWriter

public static PsiXmlElementWriter<Set<Feature>> createInferredInteractionWriter(XMLStreamWriter streamWriter,
                                                                                PsiXmlObjectCache objectIndex)

createInferredInteractionWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Returns:

a PsiXmlElementWriter object.

createExtendedInferredInteractionWriter

public static PsiXmlElementWriter<AbstractInferredInteraction> createExtendedInferredInteractionWriter(XMLStreamWriter streamWriter,
                                                                                                       PsiXmlObjectCache objectIndex)

createExtendedInferredInteractionWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Returns:

a PsiXmlElementWriter object.

createBindingFeaturesWriter

public static PsiXmlElementWriter<Set<Feature>> createBindingFeaturesWriter(XMLStreamWriter streamWriter,
                                                                            PsiXmlObjectCache objectIndex)

createBindingFeaturesWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

objectIndex - a PsiXmlObjectCache object.

Returns:

a PsiXmlElementWriter object.

createExperimentalInteractorWriter

public static PsiXmlElementWriter<AbstractExperimentalInteractor> createExperimentalInteractorWriter(XMLStreamWriter streamWriter,
                                                                                                     PsiXmlVersion version,
                                                                                                     PsiXmlObjectCache objectIndex,
                                                                                                     PsiXmlType xmlType)

createExperimentalInteractorWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

version - a PsiXmlVersion object.

objectIndex - a PsiXmlObjectCache object.

xmlType - a PsiXmlType object.

Returns:

a PsiXmlElementWriter object.

createSourceWriter

public static PsiXmlSourceWriter createSourceWriter(XMLStreamWriter streamWriter,
                                                    boolean extended,
                                                    PsiXmlVersion version,
                                                    PsiXmlElementWriter<Alias> aliasWriter,
                                                    PsiXmlElementWriter<Annotation> attributeWriter,
                                                    PsiXmlXrefWriter primaryRefWriter,
                                                    PsiXmlPublicationWriter publicationWriter)

createSourceWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

extended - a boolean.

version - a PsiXmlVersion object.

aliasWriter - a PsiXmlElementWriter object.

attributeWriter - a PsiXmlElementWriter object.

primaryRefWriter - a PsiXmlXrefWriter object.

publicationWriter - a PsiXmlPublicationWriter object.

Returns:

a PsiXmlSourceWriter object.

createExperimentWriter

public static PsiXmlExperimentWriter createExperimentWriter(XMLStreamWriter streamWriter,
                                                            boolean extended,
                                                            PsiXmlObjectCache objectIndex,
                                                            PsiXmlVersion version,
                                                            boolean named,
                                                            PsiXmlElementWriter<Alias> aliasWriter,
                                                            PsiXmlElementWriter<Annotation> attributeWriter,
                                                            PsiXmlXrefWriter primaryRefWriter,
                                                            PsiXmlPublicationWriter publicationWriter,
                                                            PsiXmlElementWriter<Organism> nonExperimentalHostOrganismWriter,
                                                            PsiXmlVariableNameWriter<CvTerm> detectionMethodWriter,
                                                            PsiXmlElementWriter<Confidence> confidenceWriter)

createExperimentWriter.

Parameters:

streamWriter - a XMLStreamWriter object.

extended - a boolean.

objectIndex - a PsiXmlObjectCache object.

version - a PsiXmlVersion object.

named - a boolean.

aliasWriter - a PsiXmlElementWriter object.

attributeWriter - a PsiXmlElementWriter object.

primaryRefWriter - a PsiXmlXrefWriter object.

publicationWriter - a PsiXmlPublicationWriter object.

nonExperimentalHostOrganismWriter - a PsiXmlElementWriter object.

detectionMethodWriter - a PsiXmlVariableNameWriter object.

confidenceWriter - a PsiXmlElementWriter object.

Returns:

a PsiXmlExperimentWriter object.

createInteractorWriter

public static PsiXmlElementWriter<Interactor> createInteractorWriter(PsiXmlVersion version,
                                                                     XMLStreamWriter streamWriter,
                                                                     boolean extended,
                                                                     PsiXmlObjectCache objectIndex,
                                                                     PsiXmlElementWriter<Alias> aliasWriter,
                                                                     PsiXmlElementWriter<Annotation> attributeWriter,
                                                                     PsiXmlXrefWriter primaryRefWriter,
                                                                     PsiXmlVariableNameWriter<CvTerm> interactorTypeWriter,
                                                                     PsiXmlElementWriter<Organism> organismWriter,
                                                                     PsiXmlElementWriter<Checksum> checksumWriter)

createInteractorWriter.

Parameters:

version - a PsiXmlVersion object.

streamWriter - a XMLStreamWriter object.

extended - a boolean.

objectIndex - a PsiXmlObjectCache object.

aliasWriter - a PsiXmlElementWriter object.

attributeWriter - a PsiXmlElementWriter object.

primaryRefWriter - a PsiXmlXrefWriter object.

interactorTypeWriter - a PsiXmlVariableNameWriter object.

organismWriter - a PsiXmlElementWriter object.

checksumWriter - a PsiXmlElementWriter object.

Returns:

a PsiXmlElementWriter object.

createFeatureWriter

public static <F extends Feature> PsiXmlElementWriter<F>[] createFeatureWriter(XMLStreamWriter streamWriter,
                                                                               boolean extended,
                                                                               PsiXmlObjectCache objectIndex,
                                                                               PsiXmlVersion version,
                                                                               InteractionCategory category,
                                                                               PsiXmlElementWriter<Alias> aliasWriter,
                                                                               PsiXmlElementWriter<Annotation> attributeWriter,
                                                                               PsiXmlXrefWriter primaryRefWriter,
                                                                               PsiXmlVariableNameWriter<CvTerm> featureTypeWriter,
                                                                               PsiXmlParameterWriter parameterWriter)

createFeatureWriter.

Type Parameters:

F - a F object.

Parameters:

streamWriter - a XMLStreamWriter object.

extended - a boolean.

objectIndex - a PsiXmlObjectCache object.

version - a PsiXmlVersion object.

category - a InteractionCategory object.

aliasWriter - a PsiXmlElementWriter object.

attributeWriter - a PsiXmlElementWriter object.

primaryRefWriter - a PsiXmlXrefWriter object.

featureTypeWriter - a PsiXmlVariableNameWriter object.

parameterWriter - a PsiXmlParameterWriter object.

Returns:

an array of PsiXmlElementWriter objects.

createParticipantWriter

public static <P extends Participant> PsiXmlParticipantWriter<P>[] createParticipantWriter(XMLStreamWriter streamWriter,
                                                                                           boolean extended,
                                                                                           PsiXmlObjectCache objectIndex,
                                                                                           PsiXmlVersion version,
                                                                                           PsiXmlType xmlType,
                                                                                           InteractionCategory category,
                                                                                           PsiXmlElementWriter<Alias> aliasWriter,
                                                                                           PsiXmlElementWriter<Annotation> attributeWriter,
                                                                                           PsiXmlXrefWriter primaryRefWriter,
                                                                                           PsiXmlElementWriter<Confidence> confidenceWriter,
                                                                                           PsiXmlElementWriter<Interactor> interactorWriter,
                                                                                           PsiXmlVariableNameWriter<CvTerm> cvWriter,
                                                                                           PsiXmlVariableNameWriter<CvTerm> openCvWriter,
                                                                                           PsiXmlParameterWriter parameterWriter)

createParticipantWriter.

Type Parameters:

P - a P object.

Parameters:

streamWriter - a XMLStreamWriter object.

extended - a boolean.

objectIndex - a PsiXmlObjectCache object.

version - a PsiXmlVersion object.

xmlType - a PsiXmlType object.

category - a InteractionCategory object.

aliasWriter - a PsiXmlElementWriter object.

attributeWriter - a PsiXmlElementWriter object.

primaryRefWriter - a PsiXmlXrefWriter object.

confidenceWriter - a PsiXmlElementWriter object.

interactorWriter - a PsiXmlElementWriter object.

cvWriter - a PsiXmlVariableNameWriter object.

openCvWriter - a PsiXmlVariableNameWriter object.

parameterWriter - a PsiXmlParameterWriter object.

Returns:

an array of PsiXmlParticipantWriter objects.

createParticipantCandidateWriter

public static <P extends ParticipantCandidate> PsiXmlElementWriter<P>[] createParticipantCandidateWriter(XMLStreamWriter streamWriter,
                                                                                                         boolean extended,
                                                                                                         PsiXmlObjectCache objectIndex,
                                                                                                         PsiXmlVersion version,
                                                                                                         PsiXmlType xmlType,
                                                                                                         InteractionCategory category,
                                                                                                         PsiXmlElementWriter<Interactor> interactorWriter,
                                                                                                         PsiXmlElementWriter<ModelledFeature> modelledFeatureWriter,
                                                                                                         PsiXmlElementWriter<FeatureEvidence> featureEvidenceWriter)

createParticipantCandidateWriter.

Type Parameters:

P - a P object.

Parameters:

streamWriter - a XMLStreamWriter object.

extended - a boolean.

objectIndex - a PsiXmlObjectCache object.

version - a PsiXmlVersion object.

xmlType - a PsiXmlType object.

category - a InteractionCategory object.

interactorWriter - a PsiXmlElementWriter object.

modelledFeatureWriter - a PsiXmlElementWriter object.

featureEvidenceWriter - a PsiXmlElementWriter object.

Returns:

an array of PsiXmlElementWriter objects.