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Example 1 with InteractionVocabularyProxy

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

the class PathwayReaderBiopax3 method addObjectInteractionVocabulary.

private InteractionVocabulary addObjectInteractionVocabulary(Element element) {
    if (element.getChildren().size() == 0) {
        InteractionVocabularyProxy proxy = new InteractionVocabularyProxy();
        addAttributes(proxy, element);
        pathwayModel.add(proxy);
        return proxy;
    }
    InteractionVocabulary interactionVocabulary = new InteractionVocabulary();
    addAttributes(interactionVocabulary, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentControlledVocabulary(interactionVocabulary, element, childElement)) {
                showUnexpected(childElement);
            }
        }
    }
    pathwayModel.add(interactionVocabulary);
    return interactionVocabulary;
}
Also used : InteractionVocabulary(org.vcell.pathway.InteractionVocabulary) Element(org.jdom.Element) GroupObject(org.vcell.pathway.GroupObject) BioPaxObject(org.vcell.pathway.BioPaxObject) InteractionVocabularyProxy(org.vcell.pathway.persistence.BiopaxProxy.InteractionVocabularyProxy)

Aggregations

Element (org.jdom.Element)1 BioPaxObject (org.vcell.pathway.BioPaxObject)1 GroupObject (org.vcell.pathway.GroupObject)1 InteractionVocabulary (org.vcell.pathway.InteractionVocabulary)1 InteractionVocabularyProxy (org.vcell.pathway.persistence.BiopaxProxy.InteractionVocabularyProxy)1