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

Example 11 with PathwayModel

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

the class PathwayIOUtil method extractPathwayFromJDOM.

public static PathwayModel extractPathwayFromJDOM(Document jdomDocument, RDFXMLContext context, ClientTaskStatusSupport statusSupport) {
    PathwayModel pathwayModel = null;
    Element rootElement = jdomDocument.getRootElement();
    @SuppressWarnings("unchecked") List<Namespace> namespaces = rootElement.getAdditionalNamespaces();
    boolean itIsLevel3 = false;
    for (Namespace namespace : namespaces) {
        if (namespace != null && namespace.getURI() != null && namespace.getURI().equals(BioPAX3.ns.uri)) {
            itIsLevel3 = true;
            break;
        }
    }
    if (itIsLevel3) {
        PathwayReaderBiopax3 pathwayReader = new PathwayReaderBiopax3(context);
        pathwayModel = pathwayReader.parse(rootElement, true);
    } else {
        // if it's not level3 we assume it to be level2
        // TODO: once biopax version3 becomes dominant change the code to use that as the default
        PathwayReader pathwayReader = new PathwayReader(context);
        pathwayModel = pathwayReader.parse(rootElement, statusSupport);
    }
    pathwayModel.reconcileReferences(statusSupport);
    pathwayModel.refreshParentMap();
    return pathwayModel;
}