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

Example 1 with TransportImpl

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

the class PathwayReaderBiopax3 method addObjectTransport.

private Transport addObjectTransport(Element element) {
    Transport transport = new TransportImpl();
    addAttributes(transport, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentTransport(transport, element, childElement)) {
                showUnexpected(childElement);
            }
        }
    }
    pathwayModel.add(transport);
    return transport;
}

Example 2 with TransportImpl

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

the class PathwayReader method addObjectTransport.

private Transport addObjectTransport(Element element) {
    Transport transport = new TransportImpl();
    addAttributes(transport, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentTransport(transport, element, childElement)) {
                showUnexpected(childElement, transport);
            }
        }
    }
    pathwayModel.add(transport);
    return transport;
}

Example 3 with TransportImpl

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

the class AnnotationMapping method createInteraction.

private Interaction createInteraction(ReactionStep reactionStep, ArrayList<Xref> xRef, ArrayList<String> name) {
    Interaction interaction = null;
    if (reactionStep instanceof SimpleReaction) {
        interaction = new BiochemicalReactionImpl();
    } else if (reactionStep instanceof FluxReaction) {
        interaction = new TransportImpl();
    }
    interaction.setName(name);
    interaction.setID("BIOMODEL_" + reactionStep.getName());
    for (Xref ref : xRef) {
        interaction.getxRef().add(ref);
    }
    return interaction;
}