Public

createCertainStatus

Create PSI Xrefs from an IntAct cvObject. 
Put Xref(psi-mi, identity) as primaryRef, any other as se

createCvObjectXrefs

createEndCertainStatus

createEndStatus

createNames

createStartCertainStatus

createStartStatus

createStatus

getInstance

Checks if the given CvObject has already been generated as XML content. 
If so, that content is clon

getXmlFromCache

Store in the cache the XML representation related to the given CvObject
instance.

updateCache

createBiologicalRole

createExperimentalRole

hasPsiXref

OutputStreamWriter

Reading from database using SQL prepared statement

The GridBagLayout class is a flexible layout manager that aligns components
vertically and horizonta

java.awt.GridBagLayout

A Rectangle specifies an area in a coordinate space that is enclosed by the 
Rectangle object's top-

java.awt.Rectangle

Produces concatenated messages in language-neutral way. New code should probably
use java.util.Forma

java.text.MessageFormat

An ordered collection (also known as a sequence). The user of this interface has
precise control ove

java.util.List

A Handler object accepts a logging request and exports the desired messages to a
target, for example

java.util.logging.Handler

Defines a general exception a servlet can throw when it encounters difficulty.

javax.servlet.ServletException

putExtra

addToBackStack

scheduleAtFixedRate

/**
     * Generate the XMl content of a proteinParticipant as well as the experimentalForm based on the given component.
     *
     * @param session   the user session.
     * @param parent    the XML Element to which we will attach the proteinParticipant.
     * @param component the component from which we will get the Protein
     *
     * @return the generated XML element
     *
     * @see uk.ac.ebi.intact.model.Interactor
     * @see uk.ac.ebi.intact.model.Protein
     * @see uk.ac.ebi.intact.model.CvComponentRole
     * @see uk.ac.ebi.intact.model.Feature
     */

//    proteinInteractorRef proteinInteractor featureList confidenceList participantRole

// 3. Generating proteinInteractorRef and proteinInteractor...

// add the protein definition to the global list of proteins

// TODO necessary to check the Tags here ?

// TODO export confidence list here ! but from what object ? Component ? in the documentation it is meant to be the confidence of the participant detection

// TODO do we filter on CvComponentRole ? allowed: neutral, bait and prey ?

// That will fall into places when we migrate IntAct to PSI CV v2

//            CvObject2xmlFactory.getInstance( session ).create( session, element, component.getCvComponentRole() );

// 9. Attaching the newly created element to the parent...

/**
     * Generate the XMl content of a participant as well as the experimentalForm based on the given component.
     *
     * @param session   the user session.
     * @param parent    the XML Element to which we will attach the proteinParticipant.
     * @param component the component from which we will get the interactor
     *
     * @return the generated XML element
     *
     * @see uk.ac.ebi.intact.model.Interactor
     * @see uk.ac.ebi.intact.model.Protein
     * @see uk.ac.ebi.intact.model.NucleicAcid
     * @see uk.ac.ebi.intact.model.SmallMolecule
     * @see uk.ac.ebi.intact.model.Polymer
     * @see uk.ac.ebi.intact.model.CvComponentRole
     * @see uk.ac.ebi.intact.model.Feature
     */

//    interactorRef interactor interactionRef

// 3. Generating names ... ( only if we have author-name in the Alias )

// 4. Generating xrefs ... ( will be done when the Component becomes an AnnotatedObject )

// 5. Generating choice of [ interactorRef | interactor | interactionRef ]

// currently we don't have interaction as interactor ... will be implemented later

// we always generate here a interactorRef.

// 7. Generating experimentalRoleList ...

// 8. Generating experimentalFormList ...

//    Dig into the Features and export all 'tagged-protein' Feature.

//        createExperimentalFormList(session, element, component );

// 9. Generating experimentalPreparationList ...

// 10. Generating experimentalInteractorList ...

// leave it for now ... this will be used when we ge tthe facility to distinguish between the interactor

//                      used in the experiment and the one on which we make the interpretation.

// TODO we output all feature here, as well as the tags !!

//                if( ! isTaggedFeature( feature.getCvFeatureType() ) ) {

// tags are exported under experimentalForm so far...

// TODO cache the result of the method : isTaggedFeature

// we have generated at least one feature that was not a tag.

// 14. Attaching the newly created element to the parent...

How to use createBiologicalRolemethodin uk.ac.ebi.intact.application.dataConversion.psiDownload.xmlGenerator.psi2.CvObject2xmlPSI2

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How to use
createBiologicalRole
method
in
uk.ac.ebi.intact.application.dataConversion.psiDownload.xmlGenerator.psi2.CvObject2xmlPSI2