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

Example 1 with SBEntityProxy

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

the class PathwayReaderBiopax3 method addObjectSBEntity.

// ---------------- addObject section ---------------------
// 
private SBEntity addObjectSBEntity(Element element) {
    if (element.getChildren().size() == 0) {
        SBEntityProxy proxy = new SBEntityProxy();
        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("SBMeasurable")) {
                SBMeasurable thingie = addObjectSBMeasurable(childElement);
                pathwayModel.add(thingie);
                return thingie;
            } else if (childElement.getName().equals("SBState")) {
                SBState thingie = addObjectSBState(childElement);
                pathwayModel.add(thingie);
                return thingie;
            }
        }
    }
    SBEntity sbSubEntity = new SBEntityImpl();
    if (element.getAttributes().size() > 0) {
        addAttributes(sbSubEntity, element);
    }
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentSBEntity(sbSubEntity, element, childElement)) {
                showUnexpected(childElement);
            }
        }
    }
    pathwayModel.add(sbSubEntity);
    return sbSubEntity;
}