How to use

Xref

in

psidev.psi.mi.jami.model

public String getRefseq() {
  return this.refseq != null ? this.refseq.getId() : null;
}

public void writeIdentifier(Xref identifier) throws IOException {
  if (identifier != null){
    // write db first
    escapeAndWriteString(identifier.getDatabase().getShortName());
    // write xref separator
    writer.write(MitabUtils.XREF_SEPARATOR);
    // write id
    escapeAndWriteString(identifier.getId());
    // write version
    if (identifier.getVersion() != null){
      writer.write(identifier.getVersion());
    }
  }
}

/**
 * Method to know if a Xref is a potential identifier.
 * It can be an identity xref or a secondary xref.
 * @param ref : the Xref
 * @return true if the Xref has a qualifier identity or secondary-ac
 */
public static boolean isXrefAnIdentifier(Xref ref){
  if (ref == null || ref.getQualifier() == null){
    return false;
  }
  String qualifierMI = ref.getQualifier().getMIIdentifier();
  if (qualifierMI != null){
    return (Xref.IDENTITY_MI.equals(qualifierMI) || Xref.SECONDARY_MI.equals(qualifierMI));
  }
  else {
    String qualifier = ref.getQualifier().getShortName();
    return (Xref.IDENTITY.equalsIgnoreCase(qualifier) || Xref.SECONDARY.equalsIgnoreCase(qualifier));
  }
}

CvTerm database = ref.getDatabase();
    return ref.getId().equals(id);
    return ref.getId().equals(id);

CvTerm database1 = xref.getDatabase();
String mi1 = database1.getMIIdentifier();
hashcode = 31 * hashcode + xref.getId().hashCode();
CvTerm qualifier = xref.getQualifier();
if (qualifier != null){
  String qualifierMi = qualifier.getMIIdentifier();

CvTerm database1 = xref.getDatabase();
String mi1 = database1.getMIIdentifier();
hashcode = 31 * hashcode + xref.getId().hashCode();
hashcode = 31 * hashcode + (xref.getVersion() != null ? xref.getVersion().hashCode():0);
CvTerm qualifier = xref.getQualifier();
if (qualifier != null){
  String qualifierMi = qualifier.getMIIdentifier();

if (ref.getDatabase().getMIIdentifier() != null && !dbMiRefs.isEmpty()) {
  if (!dbMiRefs.contains( ref.getDatabase().getMIIdentifier() )){
    continue;
else if (!dbRefs.contains( ref.getDatabase().getShortName() )){
  continue;
if ( ref.getQualifier() == null ) {
  continue;
else if (ref.getQualifier().getMIIdentifier() != null && !typeMiRefs.isEmpty()){
  if ( !typeMiRefs.contains( ref.getQualifier().getMIIdentifier() )){
    continue;
else if (!typeRefs.contains( ref.getQualifier().getShortName() )){
  continue;

/**
 * Return the proper instance of the interactor if the database is recognized (the interactor will be returned on the first database which is recognized). It returns null otherwise.
 * @param xrefs : identifiers
 * @param name : name
 * @return the proper instance of the interactor if the database is recognized (the interactor will be returned on the first database which is recognized). It returns null otherwise.
 */
public Interactor createInteractorFromIdentityXrefs(Collection<? extends Xref> xrefs, String name){
  Interactor interactor = null;
  Iterator<? extends Xref> xrefsIterator = xrefs.iterator();
  while (interactor == null && xrefsIterator.hasNext()){
    interactor = createInteractorFromDatabase(xrefsIterator.next().getDatabase(), name);
  }
  return interactor;
}

CvTerm qualifier = ref.getQualifier();
if (qualifier == null){
  return false;
    return ref.getId().equals(id);
    return ref.getId().equals(id);

String version1 = externalIdentifier1.getVersion();
String version2 = externalIdentifier2.getVersion();

if (xRef.getDatabase() != null){
  String dbAc = xRef.getDatabase().getMIIdentifier();
  String accession = xRef.getId();

CvTerm database1 = xref1.getDatabase();
CvTerm database2 = xref2.getDatabase();
String mi1 = database1.getMIIdentifier();
String mi2 = database2.getMIIdentifier();
String id1 = xref1.getId();
String id2 = xref2.getId();
CvTerm qualifier1 = xref1.getQualifier();
CvTerm qualifier2 = xref2.getQualifier();

/**
 * For each cross reference of this XrefContainer, collects all respective cross reference type(s) and
 * check if the dependencies are correct.
 *
 * @param container to check on.
 * @return a collection of validator messages.
 *         if we fail to retreive the MI Ontology.
 */
public Collection<ValidatorMessage> check( Experiment container) throws ValidatorException {
  Collection<ValidatorMessage> messages = Collections.EMPTY_LIST;
  // Collect the db references
  Collection<Xref> databaseReferences = container.getXrefs();
  if (!databaseReferences.isEmpty()){
    messages = new ArrayList<ValidatorMessage>();
    for ( Xref reference : databaseReferences) {
      MiContext context = RuleUtils.buildContext(reference, "database cross reference");
      context.addAssociatedContext(RuleUtils.buildContext(container, "experiment"));
      // build a context in case of error
      messages.addAll( mapping.check( reference.getDatabase(), reference.getQualifier(), context, this ) );
    }
  }
  return messages;
}

private String buildDbList( Collection<Xref> identities ) {
  StringBuilder sb = new StringBuilder( 128 );
  for ( Iterator<Xref> dbReferenceIterator = identities.iterator(); dbReferenceIterator.hasNext(); ) {
    Xref ref = dbReferenceIterator.next();
    final String db = ref.getDatabase().getShortName();
    final String dbAc = ref.getDatabase().getMIIdentifier();
    if( db != null && db.length() > 0 ) {
      sb.append( db ).append(" ,");
    } else if( dbAc != null && dbAc.length() > 0 ) {
      sb.append( dbAc ).append(" ,");
    }
  }
  int length = sb.length();
  if( length > 0 ) {
    length = length - 2; // gets rid of the last comma
  }
  return sb.substring( 0, length );
}

String version1 = xref1.getVersion();
String version2 = xref2.getVersion();

/**
 *
 * @param ref
 * @param interactor
 * @return an array of String : first the database, then the interactorId
 */
public static String[] extractInteractorId(Xref ref, Interactor interactor){
  String interactorId = null;
  String db = null;
  if (ref != null){
    interactorId = JSONValue.escape(ref.getId());
    db = JSONValue.escape(ref.getDatabase().getShortName());
  }
  else{
    interactorId = Integer.toString(UnambiguousExactInteractorBaseComparator.hashCode(interactor));
    db = "generated";
  }
  return new String[]{db, interactorId};
}

public String getImexId() {
  return this.imexId != null ? this.imexId.getId() : null;
}

CvTerm database1 = xref1.getDatabase();
CvTerm database2 = xref2.getDatabase();
String mi1 = database1.getMIIdentifier();
String mi2 = database2.getMIIdentifier();
String id1 = xref1.getId();
String id2 = xref2.getId();
CvTerm qualifier1 = xref1.getQualifier();
CvTerm qualifier2 = xref2.getQualifier();
if (qualifier1 == null && qualifier2 == null){
  return EQUAL;

CvTerm database1 = externalIdentifier1.getDatabase();
String mi = database1.getMIIdentifier();
String mod = database1.getMODIdentifier();
hashcode = 31 * hashcode + externalIdentifier1.getId().hashCode();
hashcode = 31 * hashcode + (externalIdentifier1.getVersion() != null ? externalIdentifier1.getVersion().hashCode() : 0);

messages.addAll( mapping.check( reference.getDatabase(), reference.getQualifier(), context, this ) );
messages.addAll( mapping.check( reference.getDatabase(), reference.getQualifier(), context, this ) );