How to use

getIdentificationMethods

method

in

psidev.psi.mi.jami.model.ParticipantEvidence

public void writeParticipantIdentificationMethod(ParticipantEvidence participant) throws IOException {
  if (participant != null){
    if (!participant.getIdentificationMethods().isEmpty()){
      Iterator<CvTerm> methodIterator = participant.getIdentificationMethods().iterator();
      while(methodIterator.hasNext()){
        writeCvTerm(methodIterator.next());
        if (methodIterator.hasNext()){
          getWriter().write(MitabUtils.FIELD_SEPARATOR);
        }
      }
    }
    else{
      getWriter().write(MitabUtils.EMPTY_COLUMN);
    }
  }
  else {
    getWriter().write(MitabUtils.EMPTY_COLUMN);
  }
}

/**
 * Make sure that a participant evidence has a valid Participant Identification Method that all the participant identification methods are valid.
 *
 * @param participant an interaction to check on.
 * @return a collection of validator messages.
 */
public Collection<ValidatorMessage> check( ParticipantEvidence participant ) throws ValidatorException {
  // list of messages to return
  Collection<ValidatorMessage> messages = Collections.EMPTY_LIST;
  if (participant.getIdentificationMethods().isEmpty()){
    MiContext context = RuleUtils.buildContext(participant, "participant");
    messages=Collections.singleton(new ValidatorMessage(" The participant does not have a participant identification method and it is required for MIMIx",
        MessageLevel.ERROR,
        context,
        this));
  }
  return messages;
}

for (InteractionEvidence interaction : exp.getInteractionEvidences()){
  for (ParticipantEvidence p : interaction.getParticipants()){
    for (CvTerm identification : p.getIdentificationMethods()){
      if (frequencyMap.containsKey(identification)){
        int frequency = frequencyMap.get(identification)+1;

/**
 * For each experiment associated with this interaction, collect all respective participants and their identification method 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;
  if (participant.getInteraction() != null){
    InteractionEvidence interaction = participant.getInteraction();
    Experiment exp = interaction.getExperiment();
    if (exp != null){
      CvTerm detMethod = exp.getInteractionDetectionMethod();
      if (detMethod != null){
        if (!participant.getIdentificationMethods().isEmpty()){
          messages = new ArrayList<ValidatorMessage>(participant.getIdentificationMethods().size());
          for (CvTerm method : participant.getIdentificationMethods()){
            // build a context in case of error
            MiContext context = RuleUtils.buildContext(participant, "participant");
            context.addAssociatedContext(RuleUtils.buildContext(exp, "experiment"));
            messages.addAll( mapping.check( detMethod, method, context, this ) );
          }
        }
      }
    }
  }
  return messages;
}

target.getParameters().clear();
target.getParameters().addAll(source.getParameters());
target.getIdentificationMethods().clear();
target.getIdentificationMethods().addAll(source.getIdentificationMethods());

if (!object.getIdentificationMethods().isEmpty()){
  MIJsonUtils.writeSeparator(getWriter());
  MIJsonUtils.writePropertyKey("identificationMethods", getWriter());
  MIJsonUtils.writeOpenArray(getWriter());
  Iterator<CvTerm> methodIterator = object.getIdentificationMethods().iterator();
  while (methodIterator.hasNext()){
    getCvWriter().write(methodIterator.next());

Collection<CvTerm> method1 = experimentalParticipant1.getIdentificationMethods();
Collection<CvTerm> method2 = experimentalParticipant2.getIdentificationMethods();

Collection<CvTerm> method1 = experimentalParticipant1.getIdentificationMethods();
Collection<CvTerm> method2 = experimentalParticipant2.getIdentificationMethods();

Collection<CvTerm> method1 = experimentalParticipant1.getIdentificationMethods();
Collection<CvTerm> method2 = experimentalParticipant2.getIdentificationMethods();

for (CvTerm term : p.getIdentificationMethods()){
  checkCv(messages, term, p, "participant");