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ParticipantEvidence.getBiologicalRole
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How to use
getBiologicalRole
method
in
psidev.psi.mi.jami.model.ParticipantEvidence

Best Java code snippets using psidev.psi.mi.jami.model.ParticipantEvidence.getBiologicalRole (Showing top 6 results out of 315)

origin: psidev.psi.mi.jami/jami-core

public void onExperimentalRoleUpdate(T entity, CvTerm oldTerm) {
  experimentalEntityChangeLogger.log(Level.INFO, "The experimental role " + oldTerm + " has been updated with " + entity.getBiologicalRole() + " in the experimental entity " + entity.toString());
}
origin: psidev.psi.mi.jami/jami-core

/**
 * Method to know if a participant evidence has a putative self experimental or biological role
 * @param p
 * @return
 */
public static boolean isPutativeSelfParticipantEvidence(ParticipantEvidence p){
  if (p == null){
    return false;
  }
  CvTerm experimentalRole = p.getExperimentalRole();
  CvTerm biologicalRole = p.getBiologicalRole();
  return DefaultCvTermComparator.areEquals(CvTermUtils.getPutativeSelf(), experimentalRole)
      || DefaultCvTermComparator.areEquals(CvTermUtils.getPutativeSelf(), biologicalRole) ;
}
origin: psidev.psi.mi.jami/jami-core

/**
 * Method to know if a participant evidence has a self experimental or biological role
 * @param p
 * @return
 */
public static boolean isSelfParticipantEvidence(ParticipantEvidence p){
  if (p == null){
    return false;
  }
  CvTerm experimentalRole = p.getExperimentalRole();
  CvTerm biologicalRole = p.getBiologicalRole();
  return DefaultCvTermComparator.areEquals(CvTermUtils.getSelf(), experimentalRole)
      || DefaultCvTermComparator.areEquals(CvTermUtils.getSelf(), biologicalRole) ;
}
origin: psidev.psi.mi.jami/jami-core

target.setExperimentalRole(source.getExperimentalRole());
target.setExpressedInOrganism(source.getExpressedInOrganism());
target.setBiologicalRole(source.getBiologicalRole());
target.setStoichiometry(source.getStoichiometry());
origin: psidev.psi.mi/psimi-schema-validator

/**
 * For each experiment associated with this interaction, collect all respective participants and their biological roles and
 * check if the dependencies are correct.
 *
 * @param participant a participant to check on.
 * @return a collection of validator messages.
 *         if we fail to retreive the MI Ontology.
 */
public Collection<ValidatorMessage> check( ParticipantEvidence participant ) throws ValidatorException {
  Collection<ValidatorMessage> messages = Collections.EMPTY_LIST;
  CvTerm biolRole = participant.getBiologicalRole();
  if (participant.getInteraction() != null){
    InteractionEvidence interaction = participant.getInteraction();
    Experiment exp = interaction.getExperiment();
    if (exp != null){
      CvTerm method = exp.getInteractionDetectionMethod();
      // build a context in case of error
      MiContext context = RuleUtils.buildContext(participant, "participant");
      context.addAssociatedContext(RuleUtils.buildContext(exp, "experiment"));
      messages=mapping.check( method, biolRole, context, this );
    }
  }
  return messages;
}
origin: psidev.psi.mi/psimi-schema-validator

if (p.getBiologicalRole() != null){
  checkCv(messages, p.getBiologicalRole(), p, "participant");
psidev.psi.mi.jami.modelParticipantEvidencegetBiologicalRole

Popular methods of ParticipantEvidence

  • getExperimentalRole
    The experimental role of the participant. It is a controlled vocabulary term and cannot be null. It
  • getIdentificationMethods
    The identification methods for this participant. Each identification method is a controlled vocabula
  • getAnnotations
  • getConfidences
    The confidences for this participant. The Collection cannot be null. If the participant does not hav
  • getExpressedInOrganism
    The organisms in which the participant has been expressed. It can be null if not relevant or same as
  • getInteractor
  • getParameters
    Numerical parameters associated with this participant. The Collection cannot be null. If the partici
  • getAliases
  • getExperimentalPreparations
    The experimental preparations for this participant. Each experimental preparation is a controlled vo
  • getFeatures
  • getInteraction
  • getXrefs
  • getInteraction,
  • getXrefs,
  • addFeature,
  • getCausalRelationships,
  • getStoichiometry,
  • setBiologicalRole,
  • setExperimentalRole,
  • setExpressedInOrganism,
  • setInteraction

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