Examples with ParticleMolecularType cbit.vcell.math.ParticleMolecularType used on opensource projects

Example 6 with ParticleMolecularType

use of cbit.vcell.math.ParticleMolecularType in project vcell by virtualcell.

the class XmlReader method getParticleMolecularTypePattern.

private ParticleMolecularTypePattern getParticleMolecularTypePattern(Element param, MathDescription mathDescription) throws XmlParseException {
    String molecularTypeName = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String matchLabel = unMangle(param.getAttributeValue(XMLTags.ParticleMolecularTypePatternMatchLabelAttrTag));
    ParticleMolecularType particleMolecularType = mathDescription.getParticleMolecularType(molecularTypeName);
    if (particleMolecularType != null) {
        ParticleMolecularTypePattern var = new ParticleMolecularTypePattern(particleMolecularType);
        if (matchLabel != null) {
            var.setMatchLabel(matchLabel);
        }
        List<Element> componentPatternList = param.getChildren(XMLTags.ParticleMolecularComponentPatternTag, vcNamespace);
        for (Element componentPattern : componentPatternList) {
            ParticleMolecularComponentPattern p = getParticleMolecularComponentPattern(componentPattern, particleMolecularType);
            var.addMolecularComponentPattern(p);
        }
        return var;
    } else {
        throw new XmlParseException("failed to find ParticleMolecularType named " + molecularTypeName);
    }
}