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

Example 1 with InteractionVocabularyProxy

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

the class PathwayReaderBiopax3 method addObjectInteractionVocabulary.

private InteractionVocabulary addObjectInteractionVocabulary(Element element) {
    if (element.getChildren().size() == 0) {
        InteractionVocabularyProxy proxy = new InteractionVocabularyProxy();
        addAttributes(proxy, element);
        pathwayModel.add(proxy);
        return proxy;
    }
    InteractionVocabulary interactionVocabulary = new InteractionVocabulary();
    addAttributes(interactionVocabulary, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentControlledVocabulary(interactionVocabulary, element, childElement)) {
                showUnexpected(childElement);
            }
        }
    }
    pathwayModel.add(interactionVocabulary);
    return interactionVocabulary;
}