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

Creating JSON documents from java classes using gson

Thrown when a program encounters the end of a file or stream during an input
operation.

java.io.EOFException

 KeyStore is responsible for maintaining cryptographic keys and their owners. 
The type of the syste

java.security.KeyStore

 Stack is a Last-In/First-Out(LIFO) data structure which represents a stack of
objects. It enables u

java.util.Stack

Patterns are compiled regular expressions. In many cases, convenience methods
such as String#matches

java.util.regex.Pattern

The exception that is thrown when a handshake could not be completed
successfully.

javax.net.ssl.SSLHandshakeException

javax.swing.BoxLayout

putExtra

getSupportFragmentManager

setRequestProperty

/**
     * 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

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