Examples with Domain cbit.vcell.math.Variable.Domain used on opensource projects

Example 41 with Domain

use of cbit.vcell.math.Variable.Domain in project vcell by virtualcell.

the class XmlReader method getMembraneParticalVariable.

private MembraneParticleVariable getMembraneParticalVariable(Element param) {
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    // -- create new VolVariable object
    MembraneParticleVariable var = new MembraneParticleVariable(name, domain);
    transcribeComments(param, var);
    return var;
}

Example 42 with Domain

use of cbit.vcell.math.Variable.Domain in project vcell by virtualcell.

the class XmlReader method getFilamentRegionVariable.

/**
 * This method returns a FilamentRegionVariable object from a XML Element.
 * Creation date: (5/16/2001 2:56:34 PM)
 * @return cbit.vcell.math.FilamentRegionVariable
 * @param param org.jdom.Element
 */
private FilamentRegionVariable getFilamentRegionVariable(Element param) {
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    // -- create new FilamentRegionVariable object
    FilamentRegionVariable filRegVariable = new FilamentRegionVariable(name, domain);
    transcribeComments(param, filRegVariable);
    return filRegVariable;
}

Example 43 with Domain

use of cbit.vcell.math.Variable.Domain in project vcell by virtualcell.

the class XmlReader method getPointVariable.

private PointVariable getPointVariable(Element param) {
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    // Create new memVariable
    PointVariable pointVariable = new PointVariable(name, domain);
    transcribeComments(param, pointVariable);
    return pointVariable;
}

Example 44 with Domain

use of cbit.vcell.math.Variable.Domain in project vcell by virtualcell.

the class XmlReader method getRandomVariable.

private RandomVariable getRandomVariable(Element param) throws XmlParseException {
    // get attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    Element element = param.getChild(XMLTags.RandomVariableSeedTag, vcNamespace);
    Expression seed = null;
    if (element != null) {
        seed = unMangleExpression(element.getText());
    }
    Distribution dist = null;
    element = param.getChild(XMLTags.UniformDistributionTag, vcNamespace);
    if (element != null) {
        dist = getUniformDistribution(element);
    }
    element = param.getChild(XMLTags.GaussianDistributionTag, vcNamespace);
    if (element != null) {
        dist = getGaussianDistribution(element);
    }
    String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    RandomVariable var = null;
    if (param.getName().equals(XMLTags.VolumeRandomVariableTag)) {
        var = new VolumeRandomVariable(name, seed, dist, domain);
    } else if (param.getName().equals(XMLTags.MembraneRandomVariableTag)) {
        var = new MembraneRandomVariable(name, seed, dist, domain);
    } else {
        throw new XmlParseException(param.getName() + " is not supported!");
    }
    transcribeComments(param, var);
    return var;
}

Example 45 with Domain

use of cbit.vcell.math.Variable.Domain in project vcell by virtualcell.

the class XmlReader method getVolVariable.

/**
 * This method returns a VolVariable object from a XML Element.
 * Creation date: (5/16/2001 2:56:34 PM)
 * @return cbit.vcell.math.VolVariable
 * @param param org.jdom.Element
 */
private VolVariable getVolVariable(Element param) {
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    // -- create new VolVariable object
    VolVariable volVariable = new VolVariable(name, domain);
    transcribeComments(param, volVariable);
    return volVariable;
}