How to use

getBiologicalRole

method

in

psidev.psi.mi.jami.model.ParticipantEvidence

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());
}

/**
 * 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) ;
}

/**
 * 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) ;
}

target.setExperimentalRole(source.getExperimentalRole());
target.setExpressedInOrganism(source.getExpressedInOrganism());
target.setBiologicalRole(source.getBiologicalRole());
target.setStoichiometry(source.getStoichiometry());

/**
 * 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;
}

if (p.getBiologicalRole() != null){
  checkCv(messages, p.getBiologicalRole(), p, "participant");