Examples with EntityReferenceProxy org.vcell.pathway.persistence.BiopaxProxy.EntityReferenceProxy used on opensource projects

Example 1 with EntityReferenceProxy

use of org.vcell.pathway.persistence.BiopaxProxy.EntityReferenceProxy in project vcell by virtualcell.

the class PathwayReaderBiopax3 method addObjectEntityReference.

private EntityReference addObjectEntityReference(Element element) {
    if (element.getChildren().size() == 0) {
        EntityReferenceProxy proxy = new EntityReferenceProxy();
        addAttributes(proxy, element);
        pathwayModel.add(proxy);
        return proxy;
    }
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (childElement.getName().equals("DnaReference")) {
                DnaReference thingie = addObjectDnaReference(childElement);
                pathwayModel.add(thingie);
                return thingie;
            } else if (childElement.getName().equals("DnaRegionReference")) {
                DnaRegionReference thingie = addObjectDnaRegionReference(childElement);
                pathwayModel.add(thingie);
                return thingie;
            } else if (childElement.getName().equals("ProteinReference")) {
                ProteinReference thingie = addObjectProteinReference(childElement);
                pathwayModel.add(thingie);
                return thingie;
            } else if (childElement.getName().equals("RnaReference")) {
                RnaReference thingie = addObjectRnaReference(childElement);
                pathwayModel.add(thingie);
                return thingie;
            } else if (childElement.getName().equals("RnaRegionReference")) {
                RnaRegionReference thingie = addObjectRnaRegionReference(childElement);
                pathwayModel.add(thingie);
                return thingie;
            } else if (childElement.getName().equals("SmallMoleculeReference")) {
                SmallMoleculeReference thingie = addObjectSmallMoleculeReference(childElement);
                pathwayModel.add(thingie);
                return thingie;
            }
        }
    }
    EntityReference entityReference = new EntityReference();
    addAttributes(entityReference, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentEntityReference(entityReference, element, childElement)) {
                // to self ??
                showUnexpected(childElement);
            }
        }
    }
    pathwayModel.add(entityReference);
    return entityReference;
}