Public

Generated an interactor out of an IntAct Experiment.

create

createAttributeList

Generates an interactorRef out of an IntAct interactor.

createInteractorReference

createNames

Generate the xref tag of the given interactor. That content is attached to the
given parent Element.

createXrefs

getInstance

get the value what will be used as ID of the protein.

getInteractorId

Interactor2xmlPSI25

Running tasks concurrently on multiple threads

java.awt.image.Kernel

An exception that indicates a failed JDBC operation. It provides the following
information about pro

java.sql.SQLException

Java representation of an SQL TIME value. Provides utilities to format and parse
the time's represen

java.sql.Time

Formats or parses dates and times.This class provides factories for obtaining
instances configured f

java.text.DateFormat

Formats and parses dates in a locale-sensitive manner. Formatting turns a Date
into a String, and pa

java.text.SimpleDateFormat

javax.swing.JTable

notifyDataSetChanged

Schedules the specified task for repeated fixed-rate execution, beginning after
the specified delay.

scheduleAtFixedRate

startActivity

/**
     * 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...

/**
     * 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.CvExperimentalRole
     * @see uk.ac.ebi.intact.model.CvBiologicalRole
     * @see uk.ac.ebi.intact.model.Feature
     */

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uk.ac.ebi.intact.application.dataConversion.psiDownload.xmlGenerator.psi25.Interactor2xmlPSI25