Examples with DistributedKinetics cbit.vcell.model.DistributedKinetics used on opensource projects

Example 11 with DistributedKinetics

use of cbit.vcell.model.DistributedKinetics in project vcell by virtualcell.

the class SBMLExporter method getAnnotationElement.

/**
 * 	getAnnotationElement :
 *	For a flux reaction, we need to add an annotation specifying the structure, flux carrier, carrier valence and fluxOption.
 *  For a simple reaction, we need to add a annotation specifying the structure (useful for import)
 *  Using XML JDOM elements, so that it is convenient for libSBML setAnnotation (requires the annotation to be provided as an xml string).
 */
private Element getAnnotationElement(ReactionStep reactionStep) throws cbit.vcell.xml.XmlParseException {
    Element sbmlImportRelatedElement = new Element(XMLTags.VCellRelatedInfoTag, sbml_vcml_ns);
    Element rxnElement = null;
    if (reactionStep instanceof FluxReaction) {
        FluxReaction fluxRxn = (FluxReaction) reactionStep;
        // Element for flux reaction. Write out the structure and flux carrier name.
        rxnElement = new Element(XMLTags.FluxStepTag, sbml_vcml_ns);
        rxnElement.setAttribute(XMLTags.StructureAttrTag, fluxRxn.getStructure().getName());
        // Get the physics option value.
        if (fluxRxn.getPhysicsOptions() == ReactionStep.PHYSICS_ELECTRICAL_ONLY) {
            rxnElement.setAttribute(XMLTags.FluxOptionAttrTag, XMLTags.FluxOptionElectricalOnly);
        } else if (fluxRxn.getPhysicsOptions() == ReactionStep.PHYSICS_MOLECULAR_AND_ELECTRICAL) {
            rxnElement.setAttribute(XMLTags.FluxOptionAttrTag, XMLTags.FluxOptionMolecularAndElectrical);
        } else if (fluxRxn.getPhysicsOptions() == ReactionStep.PHYSICS_MOLECULAR_ONLY) {
            rxnElement.setAttribute(XMLTags.FluxOptionAttrTag, XMLTags.FluxOptionMolecularOnly);
        }
    } else if (reactionStep instanceof cbit.vcell.model.SimpleReaction) {
        // Element for a simple reaction - just store structure name - will be useful while importing.
        cbit.vcell.model.SimpleReaction simpleRxn = (cbit.vcell.model.SimpleReaction) reactionStep;
        rxnElement = new org.jdom.Element(cbit.vcell.xml.XMLTags.SimpleReactionTag, sbml_vcml_ns);
        rxnElement.setAttribute(cbit.vcell.xml.XMLTags.StructureAttrTag, simpleRxn.getStructure().getName());
    }
    // Add rate name as an element of annotation - this is especially useful when roundtripping VCell models, when the reaction
    // rate parameters have been renamed by user.
    Element rateElement = new Element(XMLTags.ReactionRateTag, sbml_vcml_ns);
    if (reactionStep.getKinetics() instanceof DistributedKinetics) {
        rateElement.setAttribute(XMLTags.NameAttrTag, ((DistributedKinetics) reactionStep.getKinetics()).getReactionRateParameter().getName());
    } else if (reactionStep.getKinetics() instanceof LumpedKinetics) {
        rateElement.setAttribute(XMLTags.NameAttrTag, ((LumpedKinetics) reactionStep.getKinetics()).getLumpedReactionRateParameter().getName());
    } else {
        throw new RuntimeException("unexpected kinetic type " + reactionStep.getKinetics().getClass().getName());
    }
    sbmlImportRelatedElement.addContent(rxnElement);
    sbmlImportRelatedElement.addContent(rateElement);
    return sbmlImportRelatedElement;
}

Example 12 with DistributedKinetics

use of cbit.vcell.model.DistributedKinetics in project vcell by virtualcell.

the class KineticsAdapter method create.

/**
 * @param k not null
 * @return adapter for type
 * @throws SbmlException if type not recognized
 * @throws {@link NullPointerException} if k null
 */
public static KineticsAdapter create(Kinetics k) throws SbmlException {
    DistributedKinetics dk = BeanUtils.downcast(DistributedKinetics.class, k);
    if (dk != null) {
        return new Distributed(dk);
    }
    LumpedKinetics lk = BeanUtils.downcast(LumpedKinetics.class, k);
    if (lk != null) {
        return new Lumped(lk);
    }
    throw new SbmlException("Unknown Kinetics subclass " + k.getClass().getName());
}