How to use

getExperimentalRole

method

in

psidev.psi.mi.jami.model.ParticipantEvidence

/**
 *
 * @param participants
 * @param roleMi
 * @param roleName
 * @return the number of participants with a specific experimental role
 */
private int getNumberOfParticipantWithExperimentalRole(Collection<? extends ParticipantEvidence> participants, String roleMi, String roleName){
  int num = 0;
  for (ParticipantEvidence p : participants){
    CvTerm experimentRole = p.getExperimentalRole();
    if (checkParticipantRole(experimentRole, roleMi, roleName)){
      num++;
    }
  }
  return num;
}

public void writeExperimentalRole(ParticipantEvidence participant) throws IOException {
  if (participant != null){
    writeCvTerm(participant.getExperimentalRole());
  }
  else {
    getWriter().write(MitabUtils.EMPTY_COLUMN);
  }
}

@Override
protected boolean isParticipantBait(Participant component) {
  return getBaitMi().contains(((ParticipantEvidence) component)
      .getExperimentalRole().getMIIdentifier());
}

@Override
protected boolean isParticipantPrey(Participant component) {
  return getPreyMi().contains(((ParticipantEvidence) component)
      .getExperimentalRole().getMIIdentifier());
}

/**
 * To know if the participant evidence does have a specific experimental role
 * @param participant
 * @param roleId
 * @param roleName
 * @return true if the participant has the experimental role with given name/identifier
 */
public static boolean doesParticipantHaveExperimentalRole(ParticipantEvidence participant, String roleId, String roleName){
  if (participant == null || (roleName == null && roleId == null)){
    return false;
  }
  CvTerm role = participant.getExperimentalRole();
  // we can compare identifiers
  if (roleId != null && role.getMIIdentifier() != null){
    // we have the same topic id
    return role.getMIIdentifier().equals(roleId);
  }
  // we need to compare topic names
  else if (roleName != null) {
    return roleName.equalsIgnoreCase(role.getShortName());
  }
  return false;
}

/**
 * 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) ;
}

/**
 * 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 has a putative self biological role.
 * If checkParticipantEvidence is set to true, it will check if the given p is a ParticipantEvidence and look at the experimental role
 * @param p
 * @param checkParticipantEvidence
 * @return
 */
public static boolean isPutativeSelfParticipant(Participant p, boolean checkParticipantEvidence){
  if (p == null){
    return false;
  }
  CvTerm biologicalRole = p.getBiologicalRole();
  if (DefaultCvTermComparator.areEquals(CvTermUtils.getPutativeSelf(), biologicalRole)){
    return true;
  }
  if (checkParticipantEvidence){
    if (p instanceof ParticipantEvidence){
      CvTerm expRole = ((ParticipantEvidence)p).getExperimentalRole();
      return DefaultCvTermComparator.areEquals(CvTermUtils.getPutativeSelf(), expRole) ;
    }
  }
  return false;
}

/**
 * Method to know if a participant has a self biological role
 * If checkParticipantEvidence is set to true, it will check if the given p is a ParticipantEvidence and look at the experimental role
 * @param p
 * @param checkParticipantEvidence
 * @return
 */
public static boolean isSelfParticipant(Participant p, boolean checkParticipantEvidence){
  if (p == null){
    return false;
  }
  CvTerm biologicalRole = p.getBiologicalRole();
  if (DefaultCvTermComparator.areEquals(CvTermUtils.getSelf(), biologicalRole)){
    return true;
  }
  if (checkParticipantEvidence){
    if (p instanceof ParticipantEvidence){
      CvTerm expRole = ((ParticipantEvidence)p).getExperimentalRole();
      return DefaultCvTermComparator.areEquals(CvTermUtils.getSelf(), expRole) ;
    }
  }
  return false;
}

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

/**
 * For each experiment associated with this interaction, collect all respective participants and their experimental 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 role = participant.getExperimentalRole();
  if (participant.getInteraction() != null){
    InteractionEvidence interaction = participant.getInteraction();
    Experiment exp = interaction.getExperiment();
    if (exp != null){
      // build a context in case of error
      MiContext context = RuleUtils.buildContext(participant, "participant");
      context.addAssociatedContext(RuleUtils.buildContext(exp, "experiment"));
      final CvTerm method = exp.getInteractionDetectionMethod();
      messages=mapping.check( method, role, context, this );
    }
  }
  return messages;
}

getCvWriter().write(object.getExperimentalRole());

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

CvTerm expRoles1 = experimentalParticipant1.getExperimentalRole();
CvTerm expRoles2 = experimentalParticipant2.getExperimentalRole();

CvTerm expRoles1 = experimentalParticipant1.getExperimentalRole();
CvTerm expRoles2 = experimentalParticipant2.getExperimentalRole();

CvTerm expRoles1 = experimentalParticipant1.getExperimentalRole();
CvTerm expRoles2 = experimentalParticipant2.getExperimentalRole();