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

Updating database using SQL prepared statement

The Color class is used encapsulate colors in the default sRGB color space or
colors in arbitrary co

java.awt.Color

A writable sink for bytes.Most clients will use output streams that write data
to the file system ( 

java.io.OutputStream

The abstract base class for all number formats. This class provides the
interface for formatting and

java.text.NumberFormat

Thrown when trying to retrieve an element past the end of an Enumeration or
Iterator.

java.util.NoSuchElementException

A java.util.Queue that additionally supports operations that wait for the queue
to become non-empty 

java.util.concurrent.BlockingQueue

javax.swing.JButton

setScale

orElseThrow

getSharedPreferences

/**
     * 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 proteinExperimentalForm (ie. experimentalFormList).
     * @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
     */

//    experimentRef proteinParticipantRef isTagged isOverexpressed experimentalForm experimentalRole

// TODO we may have to loop over experiment + Feature in order to produce all experimentalForm (experiment/protein/tag)

// to write the experimentRef we need the interaction again !

// 2. generating proteinParticipantRef...

// TODO do we create that expermentalForm if this is not a tag ?

// TODO if no, how do we do if there is no Tags

// TODO what feature do we declare in participant/feature and in experimentalForm

// TODO how do I find out if the protein is over expressed ?

//            CvObject2xmlFactory.getInstance( session ).create( session,

//                                                               proteinExperimentalFormElement,

//                                                               component.getCvComponentRole() );

/**
     * 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.

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

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

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

// 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.

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

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

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

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