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

Example 1 with BiochemicalReactionImpl

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

the class PathwayReader method addObjectBiochemicalReaction.

private BiochemicalReaction addObjectBiochemicalReaction(Element element) {
    BiochemicalReaction biochemicalReaction = new BiochemicalReactionImpl();
    addAttributes(biochemicalReaction, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentBiochemicalReaction(biochemicalReaction, element, (Element) child)) {
                showUnexpected((Element) child, biochemicalReaction);
            }
        }
    }
    pathwayModel.add(biochemicalReaction);
    return biochemicalReaction;
}

Example 2 with BiochemicalReactionImpl

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

the class PathwayReaderBiopax3 method addObjectBiochemicalReaction.

private BiochemicalReaction addObjectBiochemicalReaction(Element element) {
    Namespace bp = Namespace.getNamespace("bp", "http://www.biopax.org/release/biopax-level3.owl#");
    if (element.getChild("TransportWithBiochemicalReaction", bp) != null) {
        return addObjectTransportWithBiochemicalReaction(element.getChild("TransportWithBiochemicalReaction", bp));
    }
    BiochemicalReaction biochemicalReaction = new BiochemicalReactionImpl();
    addAttributes(biochemicalReaction, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentBiochemicalReaction(biochemicalReaction, element, childElement)) {
                showUnexpected(childElement);
            }
        }
    }
    pathwayModel.add(biochemicalReaction);
    return biochemicalReaction;
}

Example 3 with BiochemicalReactionImpl

use of org.vcell.pathway.BiochemicalReactionImpl 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;
}