protected static Institution getInstitution(AnnotatedObject ao) { if (ao instanceof Institution) { return (Institution)ao; } else { return ao.getOwner(); } }
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); }
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 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 <X extends Xref> void populateWithPsiMi(AnnotatedObject annotatedObject, String psiMi) { this.institution = annotatedObject.getOwner(); Class<? extends Xref> xrefClass = AnnotatedObjectUtils.getXrefClassType(annotatedObject.getClass()); X xref = (X) createPsiMiXref(xrefClass, psiMi); xref.setParent(annotatedObject); if (xref instanceof CvObjectXref) { if (((CvObject)annotatedObject).getIdentifier() == null) { ((CvObjectXref)xref).prepareParentMi(); } } annotatedObject.getXrefs().add(xref); }
public static <A extends Alias> A createAlias(AnnotatedObject<?, A> parent, String name, CvAliasType aliasType) { A alias = (A) newAliasInstanceFor(parent.getClass()); alias.setOwner(parent.getOwner()); alias.setParent(parent); alias.setCvAliasType(aliasType); alias.setName(name); return alias; }
public static <A extends Alias> A createAlias(AnnotatedObject<?, A> parent, String name, CvAliasType aliasType) { A alias = (A) newAliasInstanceFor(parent.getClass()); alias.setOwner(parent.getOwner()); alias.setParent(parent); alias.setCvAliasType(aliasType); alias.setName(name); return alias; }
public static <A extends Alias> A createAlias(AnnotatedObject<?,A> parent, String name, CvAliasType aliasType) { A alias = (A) newAliasInstanceFor(parent.getClass()); alias.setOwner(parent.getOwner()); alias.setParent(parent); alias.setCvAliasType(aliasType); alias.setName(name); return alias; }
public <X extends Xref> X createXref(AnnotatedObject<X,?> parent, String primaryId, CvXrefQualifier cvXrefQualifer, CvDatabase cvDatabase) { X xref = (X) XrefUtils.newXrefInstanceFor(parent.getClass()); xref.setOwner(parent.getOwner()); xref.setParent(parent); xref.setPrimaryId(primaryId); xref.setCvXrefQualifier(cvXrefQualifer); xref.setCvDatabase(cvDatabase); return xref; }
public <X extends Xref> X createXref(AnnotatedObject<X,?> parent, String primaryId, CvXrefQualifier cvXrefQualifer, CvDatabase cvDatabase) { X xref = (X) XrefUtils.newXrefInstanceFor(parent.getClass()); xref.setOwner(parent.getOwner()); xref.setParent(parent); xref.setPrimaryId(primaryId); xref.setCvXrefQualifier(cvXrefQualifer); xref.setCvDatabase(cvDatabase); return xref; }
public <X extends Xref> X createXref(AnnotatedObject<X,?> parent, String primaryId, CvXrefQualifier cvXrefQualifer, CvDatabase cvDatabase) { X xref = (X) XrefUtils.newXrefInstanceFor(parent.getClass()); xref.setOwner(parent.getOwner()); xref.setParent(parent); xref.setPrimaryId(primaryId); xref.setCvXrefQualifier(cvXrefQualifer); xref.setCvDatabase(cvDatabase); return xref; }
private static void populateAttributes( AnnotatedObject<?, ?> annotatedObject, AttributeContainer attributeContainer ) { AnnotationConverter annotationConverter = new AnnotationConverter( annotatedObject.getOwner() ); AnnotationConverterConfig configAnnotation = ConverterContext.getInstance().getAnnotationConfig(); for ( Annotation annotation : IntactCore.ensureInitializedAnnotations(annotatedObject) ) { if (!configAnnotation.isExcluded(annotation.getCvTopic())) { Attribute attribute = annotationConverter.intactToPsi( annotation ); if (!attributeContainer.getAttributes().contains( attribute )) { attributeContainer.getAttributes().add( attribute ); } } } }
protected void traverseAnnotatedObjectCommon(AnnotatedObject ao, IntactVisitor ... visitors) { traverse(ao.getAnnotations(), visitors); traverse(ao.getAliases(), visitors); traverse(ao.getXrefs(), visitors); // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(ao)) { return; } traverse(ao.getOwner(), visitors); }
protected void traverseAnnotatedObjectCommon(AnnotatedObject ao, IntactVisitor ... visitors) { traverse(ao.getAnnotations(), visitors); traverse(ao.getAliases(), visitors); traverse(ao.getXrefs(), visitors); // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(ao)) { return; } traverse(ao.getOwner(), visitors); }