How to use

getOrganism

method

in

psidev.psi.mi.jami.model.Interactor

public void onOrganismUpdate(T protein, Organism old) {
  if (old == null){
    interactorChangeLogger.log(Level.INFO, "The organism has been initialised for the interactor " + protein.toString());
  }
  else if (protein.getOrganism() == null){
    interactorChangeLogger.log(Level.INFO, "The organism has been reset for the interactor " + protein.toString());
  }
  else {
    interactorChangeLogger.log(Level.INFO, "The organism " + old.toString() + " has been replaced with " + protein.getOrganism() + " in the interactor " + protein.toString());
  }
}

public void writeInteractorOrganism(P participant) throws IOException {
  if (participant != null){
    Interactor interactor = participant.getInteractor();
    writeOrganism(interactor.getOrganism());
  }
  else{
    writer.write(MitabUtils.EMPTY_COLUMN);
  }
}

@Override
public Collection<ValidatorMessage> check(Interactor interactor) throws ValidatorException {
  Collection<ValidatorMessage> messages = Collections.EMPTY_LIST;
  if (interactor.getInteractorType() != null && RuleUtils.isProtein(ontologyManager, interactor) && interactor.getOrganism() == null){
    MiContext context = RuleUtils.buildContext(interactor, "interactor");
    messages=Collections.singleton(new ValidatorMessage("The protein does not have an organism and it is required for MIMIx.",
        MessageLevel.ERROR,
        context,
        this));
  }
  else if ( InteractorUtils.doesInteractorHaveType(interactor, Gene.GENE_MI, Gene.GENE) && interactor.getOrganism() == null){
    MiContext context = RuleUtils.buildContext(interactor, "interactor");
    messages=Collections.singleton( new ValidatorMessage( "The gene does not have an organism and it is required for MIMIx.",
        MessageLevel.ERROR,
        context,
        this ) );
  }
  return messages;
}

Organism organism1 = interactor1.getOrganism();
Organism organism2 = interactor2.getOrganism();

Organism organism1 = interactor1.getOrganism();
Organism organism2 = interactor2.getOrganism();

  /**
   *
   * @param interactor
   * @return the hashcode consistent with the equals method for this comparator
   */
  public static int hashCode(Interactor interactor){
    if (unambiguousExactInteractorComparator == null){
      unambiguousExactInteractorComparator = new UnambiguousExactInteractorBaseComparator();
    }

    if (interactor == null){
      return 0;
    }

    int hashcode = 31;
    hashcode = 31*hashcode + UnambiguousCvTermComparator.hashCode(interactor.getInteractorType());
    hashcode = 31*hashcode + OrganismTaxIdComparator.hashCode(interactor.getOrganism());
    hashcode = 31*hashcode + UnambiguousInteractorBaseComparator.hashCode(interactor);

    return hashcode;
  }
}

/***
 * This method will copy properties of interactor source in interactor target and will override all the other properties of Target interactor.
 * @param source
 * @param target
 */
public static void copyAndOverrideBasicInteractorProperties(Interactor source, Interactor target){
  if (source != null && target != null){
    target.setShortName(source.getShortName());
    target.setFullName(source.getFullName());
    target.setInteractorType(source.getInteractorType());
    target.setOrganism(source.getOrganism());
    // copy collections
    target.getAnnotations().clear();
    target.getAnnotations().addAll(source.getAnnotations());
    target.getIdentifiers().clear();
    target.getIdentifiers().addAll(source.getIdentifiers());
    target.getAliases().clear();
    target.getAliases().addAll(source.getAliases());
    target.getXrefs().clear();
    target.getXrefs().addAll(source.getXrefs());
    target.getChecksums().clear();
    target.getChecksums().addAll(source.getChecksums());
  }
}

if (interactor.getOrganism() != null){
  checkOrganism(messages, interactor.getOrganism(), interactor, "interactor");

if (object.getOrganism() != null){
  MIJsonUtils.writeSeparator(writer);
  MIJsonUtils.writePropertyKey("organism", writer);
  getOrganismWriter().write(object.getOrganism());

if (object.getOrganism() != null){
  MIJsonUtils.writeSeparator(writer);
  MIJsonUtils.writePropertyKey("organism", writer);
  getOrganismWriter().write(object.getOrganism());