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);