How to use

Interactor

in

psidev.psi.mi.jami.model

/***
 * 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());
  }
}

public void writeUniqueIdentifier(P participant) throws IOException {
  if (participant == null){
    writer.write(MitabUtils.EMPTY_COLUMN);
  }
  else {
    Interactor interactor = participant.getInteractor();
    // write first identifier
    if (!interactor.getIdentifiers().isEmpty()){
      writeIdentifier(interactor.getPreferredIdentifier());
    }
    else{
      writer.write(MitabUtils.EMPTY_COLUMN);
    }
  }
}

if (!interactor1.getIdentifiers().isEmpty() || !interactor2.getIdentifiers().isEmpty()){
  Collection<Xref> identifiers1 = interactor1.getIdentifiers();
  Collection<Xref> identifiers2 = interactor2.getIdentifiers();
  return identifierCollectionComparator.compare(identifiers1, identifiers2);
String shortName1 = interactor1.getShortName();
String shortName2 = interactor2.getShortName();
int comp = shortName1.compareTo(shortName2);
String fullName1 = interactor1.getFullName();
String fullName2 = interactor2.getFullName();
if (fullName1 == null && fullName2 == null){
  comp = 0;
Collection<Alias> aliases1 = interactor1.getAliases();
Collection<Alias> aliases2 = interactor2.getAliases();

if (interactor.getOrganism() != null){
  checkOrganism(messages, interactor.getOrganism(), interactor, "interactor");
checkCv(messages, interactor.getInteractorType(), interactor, "interactor");
for (Alias alias : interactor.getAliases()){
  checkAlias(messages, alias, interactor, "interactor");
for (Xref ref : interactor.getIdentifiers()){
  checkXref(messages, ref, interactor, "interactor");
for (Xref ref : interactor.getXrefs()){
  checkXref(messages, ref, interactor, "interactor");
for (Annotation a : interactor.getAnnotations()){
  checkAnnotation(messages, a, interactor, "interactor");
for (Checksum a : interactor.getChecksums()){
  checkChecksum(messages, a, interactor, "interactor");

private void writeInteractorComponent(Interactor object) throws IOException {
  MIJsonUtils.writeStartObject(writer);
  MIJsonUtils.writeProperty("label", JSONValue.escape(object.getShortName()), writer);
  getCvWriter().write(object.getInteractorType());
  if (object.getOrganism() != null){
    MIJsonUtils.writeSeparator(writer);
    MIJsonUtils.writePropertyKey("organism", writer);
    getOrganismWriter().write(object.getOrganism());
  if (object.getPreferredIdentifier() != null){
    MIJsonUtils.writeSeparator(writer);
    MIJsonUtils.writePropertyKey("identifier", writer);
    getIdentifierWriter().write(object.getPreferredIdentifier());

CvTerm type1 = interactor1.getInteractorType();
CvTerm type2 = interactor2.getInteractorType();
Organism organism1 = interactor1.getOrganism();
Organism organism2 = interactor2.getOrganism();

this.ac = (interactor instanceof IntactInteractor) ? ((IntactInteractor)interactor).getAc() : interactor.getShortName();
this.shortName = interactor.getShortName();
for (Xref xref : interactor.getIdentifiers()) {
  if (XrefUtils.isXrefFromDatabase(xref, Xref.UNIPROTKB_MI, Xref.UNIPROTKB)
      && XrefUtils.doesXrefHaveQualifier(xref, Xref.IDENTITY_MI, Xref.IDENTITY)){
for (Alias alias : interactor.getAliases()) {
  if (AliasUtils.doesAliasHaveType(alias, Alias.GENE_NAME_MI, Alias.GENE_NAME)){
    this.shortName = alias.getName();

public void onInteractorTypeUpdate(T protein, CvTerm old) {
  interactorChangeLogger.log(Level.INFO, "The interactor type" + old.toString() + " has been replaced with " + protein.getInteractorType().toString()+ " in the interactor " + protein.toString());
}

escapeAndWriteString(interactor.getShortName());
writer.write("(");
writer.write(MitabUtils.DISPLAY_SHORT);
if (interactor.getFullName() != null){
  writer.write("|");
  writer.write(CvTerm.PSI_MI);
  writer.write(":");
  escapeAndWriteString(interactor.getFullName());
  writer.write("(");
  writer.write(MitabUtils.DISPLAY_LONG);
if (!interactor.getAliases().isEmpty()){
  Iterator<Alias> aliasIterator = interactor.getAliases().iterator();

interactor.setFullName(fullName);
  interactor.getIdentifiers().addAll(uniqueId);
interactor.getChecksums().addAll(checksum);
  interactor.getXrefs().addAll(xref);

public void onShortNameUpdate(T protein, String oldShortName) {
  interactorChangeLogger.log(Level.INFO, "The short name " + oldShortName + " has been updated with " + protein.getShortName() + " in the interactor " + protein.toString());
}

if( interactor.getInteractorType() != null && (RuleUtils.isSmallMolecule( ontologyManager, interactor ) || RuleUtils.isPolysaccharide( ontologyManager, interactor ) )) {
  final Set<String> dbRefs = RuleUtils.collectNames( dbs );
  final Collection<Xref> identities = XrefUtils.searchAllXrefsHavingDatabaseAndQualifier(interactor.getIdentifiers(), dbMiRefs, dbRefs, Arrays.asList(Xref.IDENTITY_MI), Arrays.asList(Xref.IDENTITY));
else if( interactor.getInteractorType() != null && RuleUtils.isBiopolymer(ontologyManager, interactor)) {
  final Set<String> dbRefs = RuleUtils.collectNames( dbs );
  final Collection<Xref> identities = XrefUtils.searchAllXrefsHavingDatabaseAndQualifier(interactor.getIdentifiers(), dbMiRefs, dbRefs, Arrays.asList(Xref.IDENTITY_MI), Arrays.asList(Xref.IDENTITY));
  if(identities.isEmpty() ) {

Collection<Xref> identifiers = container.getIdentifiers();
Collection<Xref> databaseReferences = container.getXrefs();

protected void createAliasFromAltId(Interactor interactor, MitabXref ref) {
  // create alias from xref
  MitabAlias alias = new MitabAlias(ref.getDatabase().getShortName(), ref.getQualifier(), ref.getId(), ref.getSourceLocator());
  interactor.getAliases().add(alias);
  if (listener != null){
    listener.onSyntaxWarning(ref, "Found an Alias in the alternative identifiers column. Will load it as a checksum.");
  }
}

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());
  }
}

protected void processInteractorPool(Collection<MitabXref> xref, InteractorPool interactor) {
  InteractorPool pool = (InteractorPool)interactor;
  for (Xref ref : xref){
    // we have a component of the interactor pool
    if (XrefUtils.doesXrefHaveQualifier(ref, Xref.INTERACTOR_SET_QUALIFIER_MI, Xref.INTERACTOR_SET_QUALIFIER)){
      Interactor subInteractor = interactorFactory.createInteractorFromDatabase(ref.getDatabase(), ref.getId().toLowerCase());
      if (subInteractor != null){
        subInteractor.getIdentifiers().add(new MitabXref(ref.getDatabase(), ref.getId(), ref.getVersion(), CvTermUtils.createIdentityQualifier()));
        ((MitabInteractor)subInteractor).setSourceLocator(((MitabXref)ref).getSourceLocator());
      }
      // create a default interactor
      else{
        subInteractor = interactorFactory.createInteractor(ref.getId().toLowerCase(), CvTermUtils.createUnknownInteractorType());
        subInteractor.getIdentifiers().add(new MitabXref(ref.getDatabase(), ref.getId(), ref.getVersion(), CvTermUtils.createIdentityQualifier()));
        ((MitabInteractor)subInteractor).setSourceLocator(((MitabXref)ref).getSourceLocator());
      }
      // add the component to the interactor pool
      pool.add(subInteractor);
    }
    // we have a simple xref
    else{
      pool.getXrefs().add(ref);
    }
  }
}

public void writeParticipantAnnotations(P participant) throws IOException {
  if (participant != null){
    if (!participant.getInteractor().getAnnotations().isEmpty()){
      Iterator<Annotation> interactorAnnotationIterator = participant.getInteractor().getAnnotations().iterator();

if (!participant.getInteractor().getXrefs().isEmpty()){
  Iterator<Xref> interactorXrefIterator = participant.getInteractor().getXrefs().iterator();
    while (interactorIterator.hasNext()){
      Interactor subInteractor = interactorIterator.next();
      Xref preferredId = subInteractor.getPreferredIdentifier();
      if (preferredId != null){
        getWriter().write(MitabUtils.FIELD_SEPARATOR);
    while (interactorIterator.hasNext()){
      Interactor subInteractor = interactorIterator.next();
      Xref preferredId = subInteractor.getPreferredIdentifier();
      if (preferredId != null){
        getWriter().write(MitabUtils.FIELD_SEPARATOR);
    while (interactorIterator.hasNext()){
      Interactor subInteractor = interactorIterator.next();
      Xref preferredId = subInteractor.getPreferredIdentifier();
      if (preferredId != null){
        if (!first){

public void writeParticipantChecksums(P participant) throws IOException {
  if (participant != null){
    if (!participant.getInteractor().getChecksums().isEmpty()){
      Iterator<Checksum> checksumIterator = participant.getInteractor().getChecksums().iterator();
      while(checksumIterator.hasNext()){
        writeChecksum(checksumIterator.next());
        if (checksumIterator.hasNext()){
          getWriter().write(MitabUtils.FIELD_SEPARATOR);
        }
      }
    }
    else{
      getWriter().write(MitabUtils.EMPTY_COLUMN);
    }
  }
  else {
    getWriter().write(MitabUtils.EMPTY_COLUMN);
  }
}

Interactor interactor = object.getInteractor();
keyValues = MIJsonUtils.extractInteractionId(interactor.getPreferredIdentifier(), (Complex)interactor);
keyValues = MIJsonUtils.extractInteractorId(interactor.getPreferredIdentifier(), interactor);