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

Example 6 with Feature

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

the class XmlReader method getMembrane.

/**
 * This method returns a Membrane object from a XML element.
 * Creation date: (4/4/2001 4:17:32 PM)
 * @return cbit.vcell.model.Membrane
 * @param param org.jdom.Element
 */
private Membrane getMembrane(Model model, Element param, List<Structure> featureList) throws XmlParseException {
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    Membrane newmembrane = null;
    // retrieve the key if there is one
    KeyValue key = null;
    String stringkey = param.getAttributeValue(XMLTags.KeyValueAttrTag);
    if (stringkey != null && stringkey.length() > 0 && this.readKeysFlag) {
        key = new KeyValue(stringkey);
    }
    // try to create new Membrane named "name"
    try {
        newmembrane = new Membrane(key, name);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("An error occurred while trying to create the Membrane object " + name, e);
    }
    // set inside feature
    String infeaturename = unMangle(param.getAttributeValue(XMLTags.InsideFeatureTag));
    String outfeaturename = unMangle(param.getAttributeValue(XMLTags.OutsideFeatureTag));
    String posFeatureName = unMangle(param.getAttributeValue(XMLTags.PositiveFeatureTag));
    String negFeatureName = unMangle(param.getAttributeValue(XMLTags.NegativeFeatureTag));
    Feature infeatureref = null;
    Feature outfeatureref = null;
    Feature posFeature = null;
    Feature negFeature = null;
    for (Structure s : featureList) {
        String sname = s.getName();
        if (sname.equals(infeaturename)) {
            infeatureref = (Feature) s;
        }
        if (sname.equals(outfeaturename)) {
            outfeatureref = (Feature) s;
        }
        if (sname.equals(posFeatureName)) {
            posFeature = (Feature) s;
        }
        if (sname.equals(negFeatureName)) {
            negFeature = (Feature) s;
        }
    }
    // set inside and outside features
    if (infeatureref != null) {
        model.getStructureTopology().setInsideFeature(newmembrane, infeatureref);
    }
    if (outfeatureref != null) {
        model.getStructureTopology().setOutsideFeature(newmembrane, outfeatureref);
    }
    // set positive & negative features
    if (posFeature != null) {
        model.getElectricalTopology().setPositiveFeature(newmembrane, posFeature);
    }
    if (negFeature != null) {
        model.getElectricalTopology().setNegativeFeature(newmembrane, negFeature);
    }
    // set MemVoltName
    if (param.getAttribute(XMLTags.MemVoltNameTag) == null) {
        throw new XmlParseException("Error reading membrane Voltage Name!");
    }
    String memvoltName = unMangle(param.getAttributeValue(XMLTags.MemVoltNameTag));
    try {
        newmembrane.getMembraneVoltage().setName(memvoltName);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("Error setting the membrane Voltage Name", e);
    }
    return newmembrane;
}

Example 7 with Feature

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

the class XmlReader method getFluxReaction.

/**
 * This method returns a FluxReaction object from a XML element.
 * Creation date: (3/16/2001 11:52:02 AM)
 * @return cbit.vcell.model.FluxReaction
 * @param param org.jdom.Element
 * @throws XmlParseException
 * @throws PropertyVetoException
 * @throws ModelException
 * @throws Exception
 */
private FluxReaction getFluxReaction(Element param, Model model) throws XmlParseException, PropertyVetoException {
    // retrieve the key if there is one
    KeyValue key = null;
    String keystring = param.getAttributeValue(XMLTags.KeyValueAttrTag);
    if (keystring != null && keystring.length() > 0 && this.readKeysFlag) {
        key = new KeyValue(keystring);
    }
    // resolve reference to the Membrane
    String structureName = unMangle(param.getAttributeValue(XMLTags.StructureAttrTag));
    Membrane structureref = (Membrane) model.getStructure(structureName);
    if (structureref == null) {
        throw new XmlParseException("The membrane " + structureName + " could not be resolved in the dictionnary!");
    }
    // -- Instantiate new FluxReaction --
    FluxReaction fluxreaction = null;
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String reversibleAttributeValue = param.getAttributeValue(XMLTags.ReversibleAttrTag);
    boolean bReversible = true;
    if (reversibleAttributeValue != null) {
        if (Boolean.TRUE.toString().equals(reversibleAttributeValue)) {
            bReversible = true;
        } else if (Boolean.FALSE.toString().equals(reversibleAttributeValue)) {
            bReversible = false;
        } else {
            throw new RuntimeException("unexpected value " + reversibleAttributeValue + " for reversible flag for reaction " + name);
        }
    }
    try {
        fluxreaction = new FluxReaction(model, structureref, key, name, bReversible);
        fluxreaction.setModel(model);
    } catch (Exception e) {
        e.printStackTrace();
        throw new XmlParseException("An exception occurred while trying to create the FluxReaction " + name, e);
    }
    // resolve reference to the fluxCarrier
    if (param.getAttribute(XMLTags.FluxCarrierAttrTag) != null) {
        String speciesname = unMangle(param.getAttributeValue(XMLTags.FluxCarrierAttrTag));
        Species specieref = model.getSpecies(speciesname);
        if (specieref != null) {
            Feature insideFeature = model.getStructureTopology().getInsideFeature(structureref);
            try {
                if (insideFeature != null) {
                    SpeciesContext insideSpeciesContext = model.getSpeciesContext(specieref, insideFeature);
                    fluxreaction.addProduct(insideSpeciesContext, 1);
                }
                Feature outsideFeature = model.getStructureTopology().getOutsideFeature(structureref);
                if (outsideFeature != null) {
                    SpeciesContext outsideSpeciesContext = model.getSpeciesContext(specieref, outsideFeature);
                    fluxreaction.addReactant(outsideSpeciesContext, 1);
                }
            } catch (ModelException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e.getMessage());
            }
        }
    }
    // Annotation
    // String rsAnnotation = null;
    // String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
    // if (annotationText!=null && annotationText.length()>0) {
    // rsAnnotation = unMangle(annotationText);
    // }
    // fluxreaction.setAnnotation(rsAnnotation);
    // set the fluxOption
    String fluxOptionString = null;
    fluxOptionString = param.getAttributeValue(XMLTags.FluxOptionAttrTag);
    if (fluxOptionString != null && fluxOptionString.length() > 0) {
        try {
            if (fluxOptionString.equals(XMLTags.FluxOptionElectricalOnly)) {
                fluxreaction.setPhysicsOptions(FluxReaction.PHYSICS_ELECTRICAL_ONLY);
            } else if (fluxOptionString.equals(XMLTags.FluxOptionMolecularAndElectrical)) {
                fluxreaction.setPhysicsOptions(FluxReaction.PHYSICS_MOLECULAR_AND_ELECTRICAL);
            } else if (fluxOptionString.equals(XMLTags.FluxOptionMolecularOnly)) {
                fluxreaction.setPhysicsOptions(FluxReaction.PHYSICS_MOLECULAR_ONLY);
            }
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("A propertyVetoException was fired when setting the fluxOption to the flux reaction " + name, e);
        }
    }
    // Add Reactants, if any
    try {
        Iterator<Element> iterator = param.getChildren(XMLTags.ReactantTag, vcNamespace).iterator();
        while (iterator.hasNext()) {
            Element temp = iterator.next();
            // Add Reactant to this SimpleReaction
            fluxreaction.addReactionParticipant(getReactant(temp, fluxreaction, model));
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("Error adding a reactant to the reaction " + name + " : " + e.getMessage());
    }
    // Add Products, if any
    try {
        Iterator<Element> iterator = param.getChildren(XMLTags.ProductTag, vcNamespace).iterator();
        while (iterator.hasNext()) {
            Element temp = iterator.next();
            // Add Product to this simplereaction
            fluxreaction.addReactionParticipant(getProduct(temp, fluxreaction, model));
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("Error adding a product to the reaction " + name + " : " + e.getMessage());
    }
    // Add Catalyst(Modifiers) (if there are)
    Iterator<Element> iterator = param.getChildren(XMLTags.CatalystTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element temp = iterator.next();
        fluxreaction.addReactionParticipant(getCatalyst(temp, fluxreaction, model));
    }
    // Add Kinetics
    fluxreaction.setKinetics(getKinetics(param.getChild(XMLTags.KineticsTag, vcNamespace), fluxreaction, model));
    // set the valence (for legacy support for "chargeCarrierValence" stored with reaction).
    String valenceString = null;
    try {
        valenceString = unMangle(param.getAttributeValue(XMLTags.FluxCarrierValenceAttrTag));
        if (valenceString != null && valenceString.length() > 0) {
            KineticsParameter chargeValenceParameter = fluxreaction.getKinetics().getChargeValenceParameter();
            if (chargeValenceParameter != null) {
                chargeValenceParameter.setExpression(new Expression(Integer.parseInt(unMangle(valenceString))));
            }
        }
    } catch (NumberFormatException e) {
        e.printStackTrace();
        throw new XmlParseException("A NumberFormatException was fired when setting the (integer) valence '" + valenceString + "' (integer) to the flux reaction " + name, e);
    }
    return fluxreaction;
}

Example 8 with Feature

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

the class Xmlproducer method getXML.

/**
 * This method identifies if the structure as a parameter is a Feature or a Membrane, and then calls the respective getXML method.
 * Creation date: (2/22/2001 6:31:04 PM)
 * @return Element
 * @param param cbit.vcell.model.Structure
 * @param model cbit.vcell.model.Model
 */
private Element getXML(Structure structure, Model model) throws XmlParseException {
    Element structureElement = null;
    StructureTopology structTopology = model.getStructureTopology();
    if (structure instanceof Feature) {
        // This is a Feature
        structureElement = new Element(XMLTags.FeatureTag);
    } else if (structure instanceof Membrane) {
        // process a Membrane
        structureElement = new Element(XMLTags.MembraneTag);
        // add specific attributes
        Feature insideFeature = structTopology.getInsideFeature((Membrane) structure);
        if (insideFeature != null) {
            structureElement.setAttribute(XMLTags.InsideFeatureTag, mangle(insideFeature.getName()));
        }
        Feature outsideFeature = structTopology.getOutsideFeature((Membrane) structure);
        if (outsideFeature != null) {
            structureElement.setAttribute(XMLTags.OutsideFeatureTag, mangle(outsideFeature.getName()));
        }
        // positive & negative features for electrical topology
        ElectricalTopology electricalTopology = model.getElectricalTopology();
        Feature positiveFeature = electricalTopology.getPositiveFeature((Membrane) structure);
        if (positiveFeature != null) {
            structureElement.setAttribute(XMLTags.PositiveFeatureTag, mangle(positiveFeature.getName()));
        }
        Feature negativeFeature = electricalTopology.getNegativeFeature((Membrane) structure);
        if (negativeFeature != null) {
            structureElement.setAttribute(XMLTags.NegativeFeatureTag, mangle(negativeFeature.getName()));
        }
        structureElement.setAttribute(XMLTags.MemVoltNameTag, mangle(((Membrane) structure).getMembraneVoltage().getName()));
    } else {
        throw new XmlParseException("An unknown type of structure was found:" + structure.getClass().getName());
    }
    // add attributes
    structureElement.setAttribute(XMLTags.NameAttrTag, mangle(structure.getName()));
    // If the keyFlag is on, print Keys
    if (structure.getKey() != null && this.printKeysFlag) {
        structureElement.setAttribute(XMLTags.KeyValueAttrTag, structure.getKey().toString());
    }
    return structureElement;
}

Example 9 with Feature

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

the class SpeciesContextSpec method initializeForSpatial.

public void initializeForSpatial() {
    if (getDiffusionParameter() != null && getDiffusionParameter().getExpression() != null && getDiffusionParameter().getExpression().isZero()) {
        Expression e = null;
        ModelUnitSystem modelUnitSystem = getSimulationContext().getModel().getUnitSystem();
        VCUnitDefinition micronsqpersecond = modelUnitSystem.getInstance("um2.s-1");
        if (speciesContext.getStructure() instanceof Feature) {
            RationalNumber rn = RationalNumber.getApproximateFraction(micronsqpersecond.convertTo(10, getDiffusionParameter().getUnitDefinition()));
            e = new Expression(rn.doubleValue());
        } else if (speciesContext.getStructure() instanceof Membrane) {
            RationalNumber rn = RationalNumber.getApproximateFraction(micronsqpersecond.convertTo(0.1, getDiffusionParameter().getUnitDefinition()));
            e = new Expression(rn.doubleValue());
        } else {
            RationalNumber rn = RationalNumber.getApproximateFraction(micronsqpersecond.convertTo(1.0, getDiffusionParameter().getUnitDefinition()));
            e = new Expression(rn.doubleValue());
        }
        try {
            getDiffusionParameter().setExpression(e);
        } catch (ExpressionBindingException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Error while initializing diffusion rate, " + e1.getMessage());
        }
    }
}

Example 10 with Feature

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

the class SpeciesContextSpec method hasTransport.

public boolean hasTransport() {
    if (isConstant() || isWellMixed() || simulationContext == null || simulationContext.getGeometry() == null || simulationContext.getGeometry().getDimension() == 0) {
        return false;
    }
    int dimension = simulationContext.getGeometry().getDimension();
    SpeciesContext speciesContext = getSpeciesContext();
    if (speciesContext.getStructure() instanceof Membrane) {
        if (dimension > 1 && !getDiffusionParameter().getExpression().isZero()) {
            return true;
        }
    } else if (speciesContext.getStructure() instanceof Feature) {
        if (!getDiffusionParameter().getExpression().isZero()) {
            return true;
        }
        if (getVelocityXParameter().getExpression() != null && !getVelocityXParameter().getExpression().isZero()) {
            return true;
        }
        SpatialQuantity[] velX_quantities = getVelocityQuantities(QuantityComponent.X);
        if (velX_quantities.length > 0) {
            return true;
        }
        if (dimension > 1) {
            if (getVelocityYParameter().getExpression() != null && !getVelocityYParameter().getExpression().isZero()) {
                return true;
            }
            if (dimension > 2) {
                if (getVelocityZParameter().getExpression() != null && !getVelocityZParameter().getExpression().isZero()) {
                    return true;
                }
            }
        }
    }
    return false;
}