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

Uses a one-way hash function to turn an arbitrary number of bytes into a
fixed-length byte sequence.

java.security.MessageDigest

A Java representation of the SQL TIMESTAMP type. It provides the capability of
representing the SQL 

java.sql.Timestamp

The Modifier class provides static methods and constants to decode class and
member access modifiers

javassist.Modifier

Provides an abstract class to be subclassed to create an HTTP servlet suitable
for a Web site. A sub

javax.servlet.http.HttpServlet

javax.swing.JTextField

Provides Base64 encoding and decoding as defined by RFC 2045.This class
implements section 6.8. Base

org.apache.commons.codec.binary.Base64

startActivity

compareTo

getApplicationContext

/**
     * 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