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

Example 1 with VolumeParticleObservable

use of cbit.vcell.math.VolumeParticleObservable 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;
}

Example 2 with VolumeParticleObservable

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

the class RulebasedMathMapping method addObservables.

private List<ParticleObservable> addObservables(GeometryClass geometryClass, Domain domain, HashMap<SpeciesPattern, VolumeParticleSpeciesPattern> speciesPatternMap) throws MappingException, MathException {
    ArrayList<ParticleObservable> observables = new ArrayList<>();
    // 
    for (MathMappingParameter mathMappingParameter : getMathMappingParameters()) {
        if (mathMappingParameter instanceof ObservableCountParameter) {
            ObservableCountParameter observableCountParameter = (ObservableCountParameter) mathMappingParameter;
            RbmObservable rbmObservable = observableCountParameter.getObservable();
            ParticleObservable.ObservableType particleObservableType = null;
            if (rbmObservable.getType() == RbmObservable.ObservableType.Molecules) {
                particleObservableType = ParticleObservable.ObservableType.Molecules;
            } else {
                particleObservableType = ParticleObservable.ObservableType.Species;
            }
            ParticleObservable particleObservable = new VolumeParticleObservable(getMathSymbol(observableCountParameter, geometryClass), domain, particleObservableType);
            switch(rbmObservable.getSequence()) {
                case Multimolecular:
                    {
                        particleObservable.setSequence(Sequence.Multimolecular);
                        break;
                    }
                case PolymerLengthEqual:
                    {
                        particleObservable.setSequence(Sequence.PolymerLengthEqual);
                        particleObservable.setQuantity(rbmObservable.getSequenceLength());
                        break;
                    }
                case PolymerLengthGreater:
                    {
                        particleObservable.setSequence(Sequence.PolymerLengthGreater);
                        particleObservable.setQuantity(rbmObservable.getSequenceLength());
                        break;
                    }
                default:
                    {
                        throw new RuntimeException("unexpected sequence " + rbmObservable.getSequence());
                    }
            }
            for (SpeciesPattern speciesPattern : rbmObservable.getSpeciesPatternList()) {
                VolumeParticleSpeciesPattern vpsp = speciesPatternMap.get(speciesPattern);
                particleObservable.addParticleSpeciesPattern(vpsp);
            }
            observables.add(particleObservable);
        }
        if (mathMappingParameter instanceof SpeciesCountParameter) {
            SpeciesCountParameter speciesCountParameter = (SpeciesCountParameter) mathMappingParameter;
            ParticleObservable.ObservableType particleObservableType = ParticleObservable.ObservableType.Species;
            ParticleObservable particleObservable = new VolumeParticleObservable(getMathSymbol(speciesCountParameter, geometryClass), domain, particleObservableType);
            particleObservable.setSequence(Sequence.Multimolecular);
            SpeciesPattern speciesPattern = speciesCountParameter.getSpeciesContext().getSpeciesPattern();
            VolumeParticleSpeciesPattern vpsp = speciesPatternMap.get(speciesPattern);
            particleObservable.addParticleSpeciesPattern(vpsp);
            observables.add(particleObservable);
        }
    }
    return observables;
}

Example 3 with VolumeParticleObservable

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

the class Xmlproducer method getXML.

private Element getXML(ParticleObservable param) {
    Element e = null;
    if (param instanceof VolumeParticleObservable) {
        e = new org.jdom.Element(XMLTags.VolumeParticleObservableTag);
    } else {
        e = new org.jdom.Element(XMLTags.ParticleObservableTag);
    }
    e.setAttribute(XMLTags.NameAttrTag, mangle(param.getName()));
    if (param.getDomain() != null) {
        e.setAttribute(XMLTags.DomainAttrTag, mangle(param.getDomain().getName()));
    }
    e.setAttribute(XMLTags.ParticleMolecularTypePatternTag, mangle(param.getType().name()));
    e.setAttribute(XMLTags.ParticleObservableSequenceTypeAttrTag, mangle(param.getSequence().name()));
    if (param.getSequence() == Sequence.PolymerLengthEqual || param.getSequence() == Sequence.PolymerLengthGreater) {
        e.setAttribute(XMLTags.ParticleObservableSequenceLengthAttrTag, param.getQuantity().toString());
    }
    e.addContent(getVolumeParticleSpeciesPatternList(param));
    return e;
}