Examples with Complex org.vcell.pathway.Complex used on opensource projects

Example 11 with Complex

use of org.vcell.pathway.Complex in project vcell by virtualcell.

the class PathwayReaderBiopax3 method addObjectComplex.

private Complex addObjectComplex(Element element) {
    Complex complex = new Complex();
    addAttributes(complex, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentComplex(complex, element, childElement)) {
                showUnexpected(childElement);
            }
        }
    }
    pathwayModel.add(complex);
    return complex;
}

Example 12 with Complex

use of org.vcell.pathway.Complex in project vcell by virtualcell.

the class PathwayProducerBiopax3 method addContentComplex.

// componentStoichiometry 	Stoichiometry 		multiple
// component 				PhysicalEntity 		multiple
private Element addContentComplex(BioPaxObject bpObject, Element element) {
    element = addContentPhysicalEntity(bpObject, element);
    Complex ob = (Complex) bpObject;
    Element tmpElement = null;
    if (ob.getComponentStoichiometry() != null && ob.getComponentStoichiometry().size() > 0) {
        List<Stoichiometry> list = ob.getComponentStoichiometry();
        for (Stoichiometry item : list) {
            tmpElement = new Element("componentStoichiometry", bp);
            // if(item instanceof RdfObjectProxy) {
            // tmpElement.setAttribute("resource", ((RdfObjectProxy)item).getResource(), rdf);
            // } else {
            // tmpElement.setAttribute("resource", item.resourceFromID(), rdf);
            // }
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getComponents() != null && ob.getComponents().size() > 0) {
        List<PhysicalEntity> list = ob.getComponents();
        for (PhysicalEntity item : list) {
            tmpElement = new Element("component", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    return element;
}