How to use

ensureInitializedXrefs

method

in

uk.ac.ebi.intact.core.persister.IntactCore

public static boolean containSameXrefs(AnnotatedObject ao1, AnnotatedObject ao2) {
  return areCollectionEqual(IntactCore.ensureInitializedXrefs(ao1), IntactCore.ensureInitializedXrefs(ao2));
}

public static boolean containSameXrefs(AnnotatedObject ao1, AnnotatedObject ao2) {
  return areCollectionEqual(IntactCore.ensureInitializedXrefs(ao1), IntactCore.ensureInitializedXrefs(ao2));
}

/**
 * Retrieve the xrefs from an annotated object that comply with the filter.
 *
 * @param ao         The annotated object
 * @param xrefFilter The xref filter
 * @return The collection of filtered xrefs
 * @since 1.9.0
 */
public static <X extends Xref> List<X> searchXrefs(AnnotatedObject<X, ?> ao, XrefCvFilter xrefFilter) {
  List<X> xrefList = new ArrayList<X>();
  CollectionUtils.select(IntactCore.ensureInitializedXrefs(ao), new IntactObjectFilterPredicate(xrefFilter), xrefList);
  return xrefList;
}

/**
 * Retrieve the xrefs from an annotated object that comply with the filter.
 *
 * @param ao         The annotated object
 * @param xrefFilter The xref filter
 * @return The collection of filtered xrefs
 * @since 1.9.0
 */
public static <X extends Xref> List<X> searchXrefs(AnnotatedObject<X, ?> ao, XrefCvFilter xrefFilter) {
  List<X> xrefList = new ArrayList<X>();
  CollectionUtils.select(IntactCore.ensureInitializedXrefs(ao), new IntactObjectFilterPredicate(xrefFilter), xrefList);
  return xrefList;
}

public static boolean containSameAliases(AnnotatedObject ao1, AnnotatedObject ao2) {
  return areCollectionEqual(IntactCore.ensureInitializedAliases(ao1), IntactCore.ensureInitializedXrefs(ao2));
}

public static boolean containSameAliases(AnnotatedObject ao1, AnnotatedObject ao2) {
  return areCollectionEqual(IntactCore.ensureInitializedAliases(ao1), IntactCore.ensureInitializedXrefs(ao2));
}

  protected Collection<Xref> searchXrefs(AnnotatedObject intactObject, String databaseMiRef, String qualifierMiRef, boolean checkInitializedXrefs){
    Collection<Xref> xrefs;
    if (checkInitializedXrefs){
      xrefs = new ArrayList<Xref>(IntactCore.ensureInitializedXrefs(intactObject));
    }
    else {
      xrefs = intactObject.getXrefs();
    }

    if (xrefs.isEmpty()){
       return Collections.EMPTY_LIST;
    }

    Collection<Xref> results = new ArrayList<Xref>(xrefs.size());

    for (Xref xref : xrefs){
      if (xref.getCvDatabase() != null && xref.getCvDatabase().getIdentifier() != null){
         if (xref.getCvDatabase().getIdentifier().equals(databaseMiRef)){
           if (xref.getCvXrefQualifier() != null && xref.getCvXrefQualifier().getIdentifier() != null){
             if (xref.getCvXrefQualifier().getIdentifier().equals(qualifierMiRef)){
                results.add(xref);
             }
           }
         }
      }
    }

    return results;
  }
}

protected Xref getImexXref(Interaction interaction) {
  Collection<? extends Xref> refs;
  if (isCheckInitializedCollections()){
    refs = IntactCore.ensureInitializedXrefs(interaction);
  }
  else {
    refs = interaction.getXrefs();
  }
  for (Xref xref : refs) {
    if (CvDatabase.IMEX_MI_REF.equals(xref.getCvDatabase().getIdentifier())
        && xref.getCvXrefQualifier() != null
        && CvXrefQualifier.IMEX_PRIMARY_MI_REF.equals(xref.getCvXrefQualifier().getIdentifier())) {
      return xref;
    }
  }
  return null;
}

  for ( uk.ac.ebi.intact.model.Xref xref : IntactCore.ensureInitializedXrefs(annotatedObject)) {
    if (annotatedObject.getAc().equals(xref.getPrimaryId())) {
      containsAcXref = true;
Collection<DbReference> dbRefs = toDbReferences( annotatedObject, IntactCore.ensureInitializedXrefs(annotatedObject));

xrefs = IntactCore.ensureInitializedXrefs(annotatedObject);

Collection<? extends Xref> refs = IntactCore.ensureInitializedXrefs(ao);

Collection<? extends Xref> refs = IntactCore.ensureInitializedXrefs(ao);