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

Example 6 with Dna

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

the class PathwayProducerBiopax3 method addContentDna.

// entityReference 	EntityReference 	single
private Element addContentDna(BioPaxObject bpObject, Element element) {
    element = addContentPhysicalEntity(bpObject, element);
    Dna ob = (Dna) bpObject;
    Element tmpElement = null;
    if (ob.getEntityReference() != null) {
        tmpElement = new Element("entityReference", bp);
        addIDToProperty(tmpElement, ob.getEntityReference());
        mustPrintObject(ob.getEntityReference());
        element.addContent(tmpElement);
    }
    return element;
}

Example 7 with Dna

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

the class PathwayReader method addObjectDna.

private Dna addObjectDna(Element element) {
    Dna dna = new Dna();
    addAttributes(dna, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentDna(dna, element, childElement)) {
                showUnexpected(childElement, dna);
            }
        }
    }
    pathwayModel.add(dna);
    return dna;
}