public <X extends Xref> X createIdentityXref(AnnotatedObject<X,?> parent, String primaryId, CvDatabase cvDatabase) { return XrefUtils.createIdentityXref(parent, primaryId, getIdentityQualifier(), cvDatabase); }
public <X extends Xref> X createIdentityXref(AnnotatedObject<X,?> parent, String primaryId, CvDatabase cvDatabase) { return XrefUtils.createIdentityXref(parent, primaryId, getIdentityQualifier(), cvDatabase); }
public <X extends Xref> X createIdentityXref(AnnotatedObject<X,?> parent, String primaryId, CvDatabase cvDatabase) { return XrefUtils.createIdentityXref(parent, primaryId, getIdentityQualifier(), cvDatabase); }
public static <X extends Xref> X createIdentityXref(AnnotatedObject<X, ?> parent, String primaryId, CvDatabase cvDatabase) { CvObjectBuilder builder = new CvObjectBuilder(); return createIdentityXref(parent, primaryId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXref(AnnotatedObject<X, ?> parent, String primaryId, CvDatabase cvDatabase) { CvObjectBuilder builder = new CvObjectBuilder(); return createIdentityXref(parent, primaryId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXrefEmblGenbankDdbj(AnnotatedObject<X, ?> parent, String emblGenbankDdbjId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.DDBG_MI_REF, CvDatabase.DDBG); return createIdentityXref(parent, emblGenbankDdbjId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXrefUniprot(AnnotatedObject<X, ?> parent, String primaryId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.UNIPROT_MI_REF, CvDatabase.UNIPROT); return createIdentityXref(parent, primaryId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXrefUniprot(AnnotatedObject<X, ?> parent, String primaryId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.UNIPROT_MI_REF, CvDatabase.UNIPROT); return createIdentityXref(parent, primaryId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXrefUniprot(AnnotatedObject<X,?> parent, String primaryId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.UNIPROT_MI_REF, CvDatabase.UNIPROT); return createIdentityXref(parent, primaryId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXrefIntact(AnnotatedObject<X, ?> parent, String intactId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.INTACT_MI_REF, CvDatabase.INTACT); return createIdentityXref(parent, intactId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
protected InteractorXref createImexXref(Interaction interaction, String imexId) { CvDatabase cvImex = CvObjectUtils.createCvObject(interaction.getOwner(), CvDatabase.class, CvDatabase.IMEX_MI_REF, CvDatabase.IMEX); cvImex.setFullName(CvDatabase.IMEX); CvXrefQualifier imexPrimary = CvObjectUtils.createCvObject(interaction.getOwner(), CvXrefQualifier.class, CvXrefQualifier.IMEX_PRIMARY_MI_REF, CvXrefQualifier.IMEX_PRIMARY); return XrefUtils.createIdentityXref(interaction, imexId, imexPrimary, cvImex); }
public static <X extends Xref> X createIdentityXrefEmblGenbankDdbj(AnnotatedObject<X, ?> parent, String emblGenbankDdbjId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.DDBG_MI_REF, CvDatabase.DDBG); return createIdentityXref(parent, emblGenbankDdbjId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXrefPsiMi(AnnotatedObject<X,?> parent, String primaryId) { CvObjectBuilder builder = new CvObjectBuilder(); return createIdentityXref(parent, primaryId, builder.createIdentityCvXrefQualifier(parent.getOwner()), builder.createPsiMiCvDatabase(parent.getOwner())); }
public static <X extends Xref> X createIdentityXrefPsiMi(AnnotatedObject<X, ?> parent, String primaryId) { CvObjectBuilder builder = new CvObjectBuilder(); return createIdentityXref(parent, primaryId, builder.createIdentityCvXrefQualifier(parent.getOwner()), builder.createPsiMiCvDatabase(parent.getOwner())); }
public static <X extends Xref> X createIdentityXrefIntact(AnnotatedObject<X, ?> parent, String intactId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.INTACT_MI_REF, CvDatabase.INTACT); return createIdentityXref(parent, intactId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXrefChebi(AnnotatedObject<X, ?> parent, String chebiId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.CHEBI_MI_REF, CvDatabase.CHEBI); return createIdentityXref(parent, chebiId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXrefChebi(AnnotatedObject<X, ?> parent, String chebiId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.CHEBI_MI_REF, CvDatabase.CHEBI); return createIdentityXref(parent, chebiId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXrefPsiMi(AnnotatedObject<X, ?> parent, String primaryId) { CvObjectBuilder builder = new CvObjectBuilder(); return createIdentityXref(parent, primaryId, builder.createIdentityCvXrefQualifier(parent.getOwner()), builder.createPsiMiCvDatabase(parent.getOwner())); }
public static CvObjectXref createIdentityXref(CvDagObject term, String database, String identifier) { DaoFactory factory = IntactContext.getCurrentInstance().getDaoFactory(); CvObjectXref cvXref; CvXrefQualifier identity = factory.getCvObjectDao(CvXrefQualifier.class).getByPsiMiRef(CvXrefQualifier.IDENTITY_MI_REF); CvDatabase db = factory.getCvObjectDao(CvDatabase.class).getByPsiMiRef(database); if (identity == null){ identity = CvObjectUtils.createCvObject(IntactContext.getCurrentInstance().getInstitution(), CvXrefQualifier.class, CvXrefQualifier.IDENTITY_MI_REF, CvXrefQualifier.IDENTITY); IntactContext.getCurrentInstance().getCorePersister().saveOrUpdate(identity); } if (db == null){ db = CvObjectUtils.createCvObject(IntactContext.getCurrentInstance().getInstitution(), CvDatabase.class, database, database); IntactContext.getCurrentInstance().getCorePersister().saveOrUpdate(db); } // create identity xref cvXref = XrefUtils.createIdentityXref(term, identifier, identity, db); term.addXref(cvXref); return cvXref; }
public static CvObjectXref createSecondaryXref(CvDagObject term, String database, String identifier) { DaoFactory factory = IntactContext.getCurrentInstance().getDaoFactory(); CvObjectXref cvXref; CvXrefQualifier secondary = factory.getCvObjectDao(CvXrefQualifier.class).getByPsiMiRef(CvXrefQualifier.SECONDARY_AC_MI_REF); CvDatabase db = factory.getCvObjectDao(CvDatabase.class).getByPsiMiRef(database); if (secondary == null){ secondary = CvObjectUtils.createCvObject(IntactContext.getCurrentInstance().getInstitution(), CvXrefQualifier.class, CvXrefQualifier.SECONDARY_AC_MI_REF, CvXrefQualifier.SECONDARY_AC); IntactContext.getCurrentInstance().getCorePersister().saveOrUpdate(secondary); } if (db == null){ db = CvObjectUtils.createCvObject(IntactContext.getCurrentInstance().getInstitution(), CvDatabase.class, database, database); IntactContext.getCurrentInstance().getCorePersister().saveOrUpdate(db); } // create identity xref cvXref = XrefUtils.createIdentityXref(term, identifier, secondary, db); term.addXref(cvXref); return cvXref; }