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

Example 6 with Evidence

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

the class PathwayReaderBiopax3 method addObjectEvidence.

private Evidence addObjectEvidence(Element element) {
    if (element.getChildren().size() == 0) {
        EvidenceProxy proxy = new EvidenceProxy();
        addAttributes(proxy, element);
        pathwayModel.add(proxy);
        return proxy;
    }
    Evidence evidence = new Evidence();
    addAttributes(evidence, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentEvidence(evidence, element, childElement)) {
                showUnexpected(childElement);
            }
        }
    }
    pathwayModel.add(evidence);
    return evidence;
}

Example 7 with Evidence

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

the class PathwayProducerBiopax3 method addContentEvidence.

private Element addContentEvidence(BioPaxObject bpObject, Element element) {
    element = addContentUtilityClass(bpObject, element);
    Evidence ob = (Evidence) bpObject;
    Element tmpElement = null;
    return element;
}

Example 8 with Evidence

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

the class PathwayProducerBiopax3 method addContentTemplateReactionRegulation.

// evidence 	Evidence 	multiple
private Element addContentTemplateReactionRegulation(BioPaxObject bpObject, Element element) {
    element = addContentControl(bpObject, element);
    TemplateReactionRegulation ob = (TemplateReactionRegulation) bpObject;
    Element tmpElement = null;
    if (ob.getEvidence() != null && ob.getEvidence().size() > 0) {
        List<Evidence> list = ob.getEvidence();
        for (Evidence item : list) {
            tmpElement = new Element("evidence", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    return element;
}