How to use

getOwner

method

in

uk.ac.ebi.intact.model.AnnotatedObject

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);
}