Public

Generate the XMl content of a participant as well as the experimentalForm based
on the given compone

createParticipant

getInstance

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

getParticipantId

Check that the given feature type is a tag.
By definition a Feature is a Tag is its CvFeatureType is

isTaggedFeature

StringBuilder

Reading from database using SQL prepared statement

This class generates cryptographically secure pseudo-random numbers. It is best
to invoke SecureRand

java.security.SecureRandom

Hash table and linked list implementation of the Map interface, with predictable
iteration order. Th

java.util.LinkedHashMap

Factory and utility methods for Executor, ExecutorService,
ScheduledExecutorService, ThreadFactory, 

java.util.concurrent.Executors

Defines the contract between a returned instance and the runtime when an
application needs to provid

javax.ws.rs.core.Response

General file manipulation utilities. Facilities are provided in the following
areas: * writing to a 

org.apache.commons.io.FileUtils

Central representation of an Ant project. This class defines an Ant project with
all of its targets,

org.apache.tools.ant.Project

onCreateOptionsMenu

setContentView

notifyDataSetChanged

/**
     * 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
     */

How to use getParticipantIdmethodin uk.ac.ebi.intact.application.dataConversion.psiDownload.xmlGenerator.psi25.Component2xmlPSI25

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.psiDownload.xmlGenerator.psi25.Component2xmlPSI25.getParticipantId (Showing top 3 results out of 315)

How to use
getParticipantId
method
in
uk.ac.ebi.intact.application.dataConversion.psiDownload.xmlGenerator.psi25.Component2xmlPSI25