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

Example 1 with Domain

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

the class XmlReader method getVolumeParticleSpeciesPattern.

private VolumeParticleSpeciesPattern getVolumeParticleSpeciesPattern(Element param, MathDescription mathdes) 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 location = unMangle(param.getAttributeValue(XMLTags.LocationAttrTag));
    VolumeParticleSpeciesPattern var = new VolumeParticleSpeciesPattern(name, domain, location);
    List<Element> molecularTypeList = param.getChildren(XMLTags.ParticleMolecularTypePatternTag, vcNamespace);
    for (Element molecularType : molecularTypeList) {
        ParticleMolecularTypePattern p = getParticleMolecularTypePattern(molecularType, mathdes);
        var.addMolecularTypePattern(p);
    }
    // for (Element levelElement : levelElementList) {
    return var;
}

Example 2 with Domain

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

the class XmlReader method readParameters.

private void readParameters(List<Element> parameterElements, ParameterContext parameterContext, HashMap<String, ParameterRoleEnum> roleHash, ParameterRoleEnum userDefinedRole, HashSet<String> xmlRolesTagsToIgnore, Model model) throws XmlParseException {
    String contextName = parameterContext.getNameScope().getName();
    try {
        // 
        // prepopulate varHash with reserved symbols
        // 
        VariableHash varHash = new VariableHash();
        addResevedSymbols(varHash, model);
        // 
        for (Element xmlParam : parameterElements) {
            String parsedParamName = unMangle(xmlParam.getAttributeValue(XMLTags.NameAttrTag));
            String parsedRoleString = xmlParam.getAttributeValue(XMLTags.ParamRoleAttrTag);
            String parsedExpressionString = xmlParam.getText();
            // 
            if (xmlRolesTagsToIgnore.contains(parsedRoleString)) {
                varHash.removeVariable(parsedParamName);
                continue;
            }
            Expression paramExp = null;
            if (parsedExpressionString.trim().length() > 0) {
                paramExp = unMangleExpression(parsedExpressionString);
            }
            if (varHash.getVariable(parsedParamName) == null) {
                Domain domain = null;
                varHash.addVariable(new Function(parsedParamName, paramExp, domain));
            } else {
                if (model.getReservedSymbolByName(parsedParamName) != null) {
                    varHash.removeVariable(parsedParamName);
                    Domain domain = null;
                    varHash.addVariable(new Function(parsedParamName, paramExp, domain));
                }
            }
            // 
            // get the parameter for this xml role string
            // 
            ParameterRoleEnum paramRole = roleHash.get(parsedRoleString);
            if (paramRole == null) {
                throw new XmlParseException("parameter '" + parsedParamName + "' has unexpected role '" + parsedRoleString + "' in '" + contextName + "'");
            }
            // 
            if (paramRole != userDefinedRole) {
                LocalParameter paramWithSameRole = parameterContext.getLocalParameterFromRole(paramRole);
                if (paramWithSameRole == null) {
                    throw new XmlParseException("can't find parameter with role '" + parsedRoleString + "' in '" + contextName + "'");
                }
                // 
                if (!paramWithSameRole.getName().equals(parsedParamName)) {
                    // 
                    // first rename other parameters with same name
                    // 
                    LocalParameter paramWithSameNameButDifferentRole = parameterContext.getLocalParameterFromName(parsedParamName);
                    if (paramWithSameNameButDifferentRole != null) {
                        // 
                        // find available name
                        // 
                        int n = 0;
                        String newName = parsedParamName + "_" + n++;
                        while (parameterContext.getEntry(newName) != null) {
                            newName = parsedParamName + "_" + n++;
                        }
                        parameterContext.renameLocalParameter(parsedParamName, newName);
                    }
                    // 
                    // then rename parameter with correct role
                    // 
                    parameterContext.renameLocalParameter(paramWithSameRole.getName(), parsedParamName);
                }
            }
        }
        // 
        // create unresolved parameters for all unresolved symbols
        // 
        String unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
        while (unresolvedSymbol != null) {
            try {
                Domain domain = null;
                // will turn into an UnresolvedParameter.
                varHash.addVariable(new Function(unresolvedSymbol, new Expression(0.0), domain));
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e.getMessage());
            }
            parameterContext.addUnresolvedParameter(unresolvedSymbol);
            unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
        }
        // 
        // in topological order, add parameters to model (getting units also).
        // note that all pre-defined parameters already have the correct names
        // here we set expressions on pre-defined parameters and add user-defined parameters
        // 
        Variable[] sortedVariables = varHash.getTopologicallyReorderedVariables();
        ModelUnitSystem modelUnitSystem = model.getUnitSystem();
        for (int i = sortedVariables.length - 1; i >= 0; i--) {
            if (sortedVariables[i] instanceof Function) {
                Function paramFunction = (Function) sortedVariables[i];
                Element xmlParam = null;
                for (int j = 0; j < parameterElements.size(); j++) {
                    Element tempParam = (Element) parameterElements.get(j);
                    if (paramFunction.getName().equals(unMangle(tempParam.getAttributeValue(XMLTags.NameAttrTag)))) {
                        xmlParam = tempParam;
                        break;
                    }
                }
                if (xmlParam == null) {
                    // must have been an unresolved parameter
                    continue;
                }
                String symbol = xmlParam.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
                VCUnitDefinition unit = null;
                if (symbol != null) {
                    unit = modelUnitSystem.getInstance(symbol);
                }
                LocalParameter tempParam = parameterContext.getLocalParameterFromName(paramFunction.getName());
                if (tempParam == null) {
                    tempParam = parameterContext.addLocalParameter(paramFunction.getName(), new Expression(0.0), userDefinedRole, unit, userDefinedRole.getDescription());
                    parameterContext.setParameterValue(tempParam, paramFunction.getExpression(), true);
                } else {
                    if (tempParam.getExpression() != null) {
                        // if the expression is null, it should remain null.
                        parameterContext.setParameterValue(tempParam, paramFunction.getExpression(), true);
                    }
                    tempParam.setUnitDefinition(unit);
                }
            }
        }
    } catch (PropertyVetoException | ExpressionException | MathException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("Exception while setting parameters for '" + contextName + "': " + e.getMessage(), e);
    }
}

Example 3 with Domain

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

the class XmlReader method getVolumeRegionVariable.

/**
 * This method returns a VolumeRegionVariable object from a XML Element.
 * Creation date: (5/16/2001 2:56:34 PM)
 * @return cbit.vcell.math.VolumeRegionVariable
 * @param param org.jdom.Element
 */
private VolumeRegionVariable getVolumeRegionVariable(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 VolumeRegionVariable object
    VolumeRegionVariable volRegVariable = new VolumeRegionVariable(name, domain);
    transcribeComments(param, volRegVariable);
    return volRegVariable;
}

Example 4 with Domain

use of cbit.vcell.math.Variable.Domain 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 5 with Domain

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

the class XmlReader method getVolumeParticalVariable.

private VolumeParticleVariable getVolumeParticalVariable(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
    VolumeParticleVariable var = new VolumeParticleVariable(name, domain);
    transcribeComments(param, var);
    return var;
}