Examples with Sequence cbit.vcell.math.ParticleObservable.Sequence used on opensource projects

Example 1 with Sequence

use of cbit.vcell.math.ParticleObservable.Sequence in project vcell by virtualcell.

the class XmlReader method getVolumeParticleObservable.

private VolumeParticleObservable getVolumeParticleObservable(Element param, VariableHash varHash) throws XmlParseException {
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    String molecularTypeString = unMangle(param.getAttributeValue(XMLTags.ParticleMolecularTypePatternTag));
    ObservableType observableType = ObservableType.fromString(molecularTypeString);
    VolumeParticleObservable var = new VolumeParticleObservable(name, domain, observableType);
    String sequenceAttr = param.getAttributeValue(XMLTags.ParticleObservableSequenceTypeAttrTag);
    if (sequenceAttr != null) {
        Sequence sequence = Sequence.fromString(sequenceAttr);
        String sequenceLength = param.getAttributeValue(XMLTags.ParticleObservableSequenceLengthAttrTag);
        var.setSequence(sequence);
        if (sequence != Sequence.Multimolecular) {
            var.setQuantity(Integer.parseInt(sequenceLength));
        }
    } else {
        var.setSequence(Sequence.Multimolecular);
    }
    Element volumeParticleSpeciesPatternsElement = param.getChild(XMLTags.VolumeParticleSpeciesPatternsTag, vcNamespace);
    List<Element> volumeParticleSpeciesPatternList = volumeParticleSpeciesPatternsElement.getChildren(XMLTags.VolumeParticleSpeciesPatternTag, vcNamespace);
    for (Element volumeParticleSpeciesPattern : volumeParticleSpeciesPatternList) {
        String volumeParticleSpeciesPatternName = unMangle(volumeParticleSpeciesPattern.getAttributeValue(XMLTags.NameAttrTag));
        Variable v = varHash.getVariable(volumeParticleSpeciesPatternName);
        if (v == null) {
            throw new XmlParseException("failed to find VolumeParticleSpeciesPattern named " + volumeParticleSpeciesPatternName);
        }
        if (v instanceof ParticleSpeciesPattern) {
            var.addParticleSpeciesPattern((ParticleSpeciesPattern) v);
        } else {
            throw new XmlParseException("Variable " + volumeParticleSpeciesPatternName + " is not a ParticleSpeciesPattern");
        }
    }
    return var;
}