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

Example 1 with StoichiometryProxy

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

the class PathwayReaderBiopax3 method addObjectStoichiometry.

private Stoichiometry addObjectStoichiometry(Element element) {
    if (element.getChildren().size() == 0) {
        // if there are no children it must be a resource inside another object
        StoichiometryProxy proxy = new StoichiometryProxy();
        addAttributes(proxy, element);
        pathwayModel.add(proxy);
        return proxy;
    }
    Stoichiometry stoichiometry = new Stoichiometry();
    addAttributes(stoichiometry, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentStoichiometry(stoichiometry, element, childElement)) {
                showUnexpected(childElement);
            }
        }
    }
    pathwayModel.add(stoichiometry);
    return stoichiometry;
}