Examples with ModelParameter cbit.vcell.model.Model.ModelParameter used on opensource projects

Example 41 with ModelParameter

use of cbit.vcell.model.Model.ModelParameter in project vcell by virtualcell.

the class Kinetics method convertParameterType.

/**
 * convertParameterType : Used to convert a parameter from model (global) to local or vice versa depending on 'bConvertToLocal'
 * @param param : the parameter to be converted (could be kinetic parameter or kineticProxyParameter)
 * @param bConvertToGlobal : <true> => convert model to local parameter; <false> => convert local to model parameter
 */
public void convertParameterType(Parameter param, boolean bConvertToGlobal) throws PropertyVetoException, ExpressionBindingException {
    Expression expression = param.getExpression();
    if (!bConvertToGlobal) {
        // need to convert model parameter (the proxyparam/global) to local (kinetics) parameter
        if (!(param instanceof KineticsProxyParameter)) {
            throw new RuntimeException("Parameter : \'" + param.getName() + "\' is not a proxy (global) parameter, cannot convert it to a local kinetics parameter.");
        } else {
            // first remove proxy param,
            removeProxyParameter((KineticsProxyParameter) param);
            // then add it as kinetic param
            if (expression != null) {
                Expression newExpr = new Expression(expression);
                newExpr.bindExpression(getReactionStep());
                addKineticsParameter(new KineticsParameter(param.getName(), newExpr, Kinetics.ROLE_UserDefined, param.getUnitDefinition()));
            }
        }
    } else {
        // need to convert local (the kinetics parameter) to model (proxy) parameter
        if (!(param instanceof KineticsParameter)) {
            throw new RuntimeException("Parameter : \'" + param.getName() + "\' is not a local kinetics parameter, cannot convert it to a global (proxy) parameter.");
        } else {
            // else remove kinetic param - should have already been checked in parameterTableModel
            if (((KineticsParameter) param).getRole() != Kinetics.ROLE_UserDefined) {
                throw new RuntimeException("Cannot convert pre-defined kinetic parameter : \'" + param.getName() + "\' to global parameter.");
            }
            // First add param as a model parameter, if it is not already present
            ModelParameter mp = getReactionStep().getModel().getModelParameter(param.getName());
            if (mp == null) {
                Model model = getReactionStep().getModel();
                Expression newExpr = new Expression(expression);
                newExpr.bindExpression(model);
                model.addModelParameter(model.new ModelParameter(param.getName(), newExpr, Model.ROLE_UserDefined, param.getUnitDefinition()));
            }
            // Then remove param as a kinetic param (if 'param' is a model param, it is automatically added as a (proxy/global) param,
            // since it is present in the reaction rate equn.
            removeKineticsParameter((KineticsParameter) param);
        }
    }
}

Example 42 with ModelParameter

use of cbit.vcell.model.Model.ModelParameter in project vcell by virtualcell.

the class ModelOptimizationSpec method getModelParameters.

/**
 * Insert the method's description here.
 * Creation date: (8/22/2005 10:38:04 AM)
 * @return cbit.vcell.model.Parameter[]
 */
private Parameter[] getModelParameters() {
    java.util.Vector<Parameter> modelParameterList = new java.util.Vector<Parameter>();
    Model model = getSimulationContext().getModel();
    // 
    // get Model (global) parameters
    // 
    ModelParameter[] globalParams = model.getModelParameters();
    for (int i = 0; i < globalParams.length; i++) {
        if (globalParams[i] != null && globalParams[i].getExpression() != null && globalParams[i].getExpression().isNumeric()) {
            modelParameterList.add(globalParams[i]);
        }
    }
    // 
    // get kinetic parameters that are numbers
    // 
    ReactionStep[] reactionSteps = model.getReactionSteps();
    for (int i = 0; i < reactionSteps.length; i++) {
        // 
        // make sure ReactionSteps are "enabled"
        // 
        ReactionSpec reactionSpec = getSimulationContext().getReactionContext().getReactionSpec(reactionSteps[i]);
        if (reactionSpec == null || reactionSpec.isExcluded()) {
            continue;
        }
        Kinetics.KineticsParameter[] kineticsParameters = reactionSteps[i].getKinetics().getKineticsParameters();
        for (int j = 0; j < kineticsParameters.length; j++) {
            if (kineticsParameters[j].getExpression() != null && kineticsParameters[j].getExpression().isNumeric()) {
                if (((kineticsParameters[j].getRole() == Kinetics.ROLE_CurrentDensity) || (kineticsParameters[j].getRole() == Kinetics.ROLE_LumpedCurrent)) && reactionSteps[i].getPhysicsOptions() == ReactionStep.PHYSICS_MOLECULAR_ONLY) {
                    continue;
                }
                if (((kineticsParameters[j].getRole() == Kinetics.ROLE_ReactionRate) || (kineticsParameters[j].getRole() == Kinetics.ROLE_LumpedReactionRate)) && reactionSteps[i].getPhysicsOptions() == ReactionStep.PHYSICS_ELECTRICAL_ONLY) {
                    continue;
                }
                modelParameterList.add(kineticsParameters[j]);
            }
        }
    }
    // 
    // get initial conditions that are numbers
    // 
    SpeciesContextSpec[] speciesContextSpecs = getSimulationContext().getReactionContext().getSpeciesContextSpecs();
    for (int i = 0; i < speciesContextSpecs.length; i++) {
        SpeciesContextSpec.SpeciesContextSpecParameter initParam = speciesContextSpecs[i].getInitialConditionParameter();
        if (initParam != null && initParam.getExpression() != null && initParam.getExpression().isNumeric()) {
            modelParameterList.add(initParam);
        }
    }
    // 
    // get structure parameters
    // 
    StructureMapping[] structureMappings = getSimulationContext().getGeometryContext().getStructureMappings();
    for (int i = 0; i < structureMappings.length; i++) {
        StructureMapping.StructureMappingParameter[] parameters = structureMappings[i].getParameters();
        for (int j = 0; j < parameters.length; j++) {
            if (parameters[j].getRole() == StructureMapping.ROLE_SpecificCapacitance && structureMappings[i] instanceof MembraneMapping && !((MembraneMapping) structureMappings[i]).getCalculateVoltage()) {
                continue;
            }
            if (parameters[j].getExpression() != null && parameters[j].getExpression().isNumeric()) {
                modelParameterList.add(parameters[j]);
            }
        }
    }
    Parameter[] modelParameters = (Parameter[]) BeanUtils.getArray(modelParameterList, Parameter.class);
    return modelParameters;
}

Example 43 with ModelParameter

use of cbit.vcell.model.Model.ModelParameter in project vcell by virtualcell.

the class SBMLExporter method addParameters.

/**
 * addKineticParameterUnits:
 * @throws SbmlException
 */
// private void addKineticAndGlobalParameterUnits() throws SbmlException {
// 
// //
// // Get all kinetic parameters from simple reactions and flux reactions from the Biomodel
// // And all Model (global) parameters from Model.
// // For each parameter,
// //		get its unit (VCunitDefinition)
// //		check if it is part of unitsList - if so, continue
// //		check if it is a base unit - if so, continue
// //		else, get the converted unit (VC -> SBML)
// //		add unit to sbmlModel unit definition
// //
// 
// Vector<Parameter> paramsVector = new Vector<Parameter>();
// // Add globals
// Model vcModel = vcBioModel.getModel();
// ModelParameter[] globalParams = vcModel.getModelParameters();
// for (int i = 0; i < globalParams.length; i++) {
// paramsVector.addElement(globalParams[i]);
// }
// // Add reaction kinetic parameters
// ReactionStep[] vcReactions = vcModel.getReactionSteps();
// for (int i = 0; i < vcReactions.length; i++) {
// Kinetics rxnKinetics = vcReactions[i].getKinetics();
// Parameter[] kineticParams = rxnKinetics.getKineticsParameters();
// for (int j = 0; j < kineticParams.length; j++) {
// paramsVector.addElement(kineticParams[j]);
// }
// }
// 
// for (int i = 0; i < paramsVector.size(); i++){
// Parameter param = (Parameter)paramsVector.elementAt(i);
// VCUnitDefinition paramUnitDefn = param.getUnitDefinition();
// if (paramUnitDefn == null || paramUnitDefn.isTBD()) {
// continue;
// }
// String unitSymbol = org.vcell.util.TokenMangler.mangleToSName(paramUnitDefn.getSymbol());
// if (unitSymbol == null) {
// continue;
// }
// getOrCreateSBMLUnit(paramUnitDefn);
// }
// }
/**
 * At present, the Virtual cell doesn't support global parameters
 * @throws SbmlException
 */
protected void addParameters() throws ExpressionException, SbmlException {
    Model vcModel = getSelectedSimContext().getModel();
    // add VCell global parameters to the SBML listofParameters
    ModelParameter[] vcGlobalParams = vcModel.getModelParameters();
    if (vcGlobalParams != null) {
        for (ModelParameter vcParam : vcGlobalParams) {
            org.sbml.jsbml.Parameter sbmlParam = sbmlModel.createParameter();
            sbmlParam.setId(vcParam.getName());
            sbmlParam.setConstant(vcParam.isConstant());
            Expression paramExpr = new Expression(vcParam.getExpression());
            boolean bParamIsNumeric = true;
            if (paramExpr.isNumeric()) {
                // For a VCell global param, if it is numeric, it has a constant value and is not defined by a rule, hence set Constant = true.
                sbmlParam.setValue(paramExpr.evaluateConstant());
                // the expression for modelParam might be numeric, but modelParam could have a rate rule, if so, set constant attribute to 'false'
                if (getSelectedSimContext().getRateRule(vcParam) != null) {
                    bParamIsNumeric = false;
                }
            } else {
                // non-numeric VCell global parameter will be defined by a (assignment) rule, hence mark Constant = false.
                bParamIsNumeric = false;
                // add assignment rule for param
                ASTNode paramFormulaNode = getFormulaFromExpression(paramExpr);
                AssignmentRule sbmlParamAssignmentRule = sbmlModel.createAssignmentRule();
                sbmlParamAssignmentRule.setVariable(vcParam.getName());
                sbmlParamAssignmentRule.setMath(paramFormulaNode);
            }
            sbmlParam.setConstant(bParamIsNumeric);
            VCUnitDefinition vcParamUnit = vcParam.getUnitDefinition();
            if (!vcParamUnit.isTBD()) {
                sbmlParam.setUnits(getOrCreateSBMLUnit(vcParamUnit));
            }
        }
    }
}

Example 44 with ModelParameter

use of cbit.vcell.model.Model.ModelParameter in project vcell by virtualcell.

the class SBMLImporter method addInitialAssignments.

protected void addInitialAssignments() {
    if (sbmlModel == null) {
        throw new SBMLImportException("SBML model is NULL");
    }
    ListOf listofInitialAssgns = sbmlModel.getListOfInitialAssignments();
    if (listofInitialAssgns == null) {
        System.out.println("No Initial Assignments specified");
        return;
    }
    Model vcModel = vcBioModel.getSimulationContext(0).getModel();
    for (int i = 0; i < sbmlModel.getNumInitialAssignments(); i++) {
        try {
            InitialAssignment initAssgn = (InitialAssignment) listofInitialAssgns.get(i);
            String initAssgnSymbol = initAssgn.getSymbol();
            Expression initAssignMathExpr = getExpressionFromFormula(initAssgn.getMath());
            // support compartmentSize expressions, warn and bail out.
            if (sbmlModel.getCompartment(initAssgnSymbol) != null) {
                if (!initAssignMathExpr.isNumeric()) {
                    logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.CompartmentError, "compartment '" + initAssgnSymbol + "' size has an initial assignment, cannot handle it at this time.");
                }
            // if init assgn for compartment is numeric, the numeric
            // value for size is set in addCompartments().
            }
            // or other species. Not allowed for species.
            if (!bSpatial && sbmlModel.getSpecies(initAssgnSymbol) != null) {
                if (initAssignMathExpr.hasSymbol(vcModel.getX().getName()) || initAssignMathExpr.hasSymbol(vcModel.getY().getName()) || initAssignMathExpr.hasSymbol(vcModel.getZ().getName())) {
                    logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.SpeciesError, "species '" + initAssgnSymbol + "' initial assignment expression cannot contain 'x', 'y', 'z'.");
                }
            }
            initAssignMathExpr = adjustExpression(initAssignMathExpr, vcModel);
            // set the init assgn expr on VCell species init condn or global
            // parameter expression
            SpeciesContextSpec scs = vcBioModel.getSimulationContext(0).getReactionContext().getSpeciesContextSpec(vcBioModel.getSimulationContext(0).getModel().getSpeciesContext(initAssgnSymbol));
            ModelParameter mp = vcBioModel.getSimulationContext(0).getModel().getModelParameter(initAssgnSymbol);
            if (scs != null) {
                scs.getInitialConditionParameter().setExpression(initAssignMathExpr);
            } else if (mp != null) {
                mp.setExpression(initAssignMathExpr);
            } else {
                localIssueList.add(new Issue(new SBMLIssueSource(initAssgn), issueContext, IssueCategory.SBMLImport_UnsupportedAttributeOrElement, "Symbol '" + initAssgnSymbol + "' not a species or global parameter in VCell; initial assignment ignored.", Issue.SEVERITY_WARNING));
            // logger.sendMessage(VCLogger.Priority.MediumPriority,
            // VCLogger.ErrorType.UnsupportedConstruct,
            // "Symbol '"+initAssgnSymbol+"' not a species or global parameter in VCell; initial assignment ignored..");
            }
        } catch (Exception e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error reading InitialAssignment : " + e.getMessage());
        }
    }
}

Example 45 with ModelParameter

use of cbit.vcell.model.Model.ModelParameter in project vcell by virtualcell.

the class SEDMLExporter method getTargetAttributeXPath.

private XPathTarget getTargetAttributeXPath(SymbolTableEntry ste, Map<Pair<String, String>, String> l2gMap) {
    // to get Xpath string for variables.
    SBMLSupport sbmlSupport = new SBMLSupport();
    XPathTarget targetXpath = null;
    if (ste instanceof SpeciesContext || ste instanceof SpeciesContextSpecParameter) {
        String speciesId = ste.getName();
        // can change species initial concentration or amount
        String speciesAttr = "";
        if (ste instanceof SpeciesContextSpecParameter) {
            SpeciesContextSpecParameter scsp = (SpeciesContextSpecParameter) ste;
            speciesId = (scsp).getSpeciesContext().getName();
            if (scsp.getRole() == SpeciesContextSpec.ROLE_InitialConcentration) {
                speciesAttr = scsp.getName();
            }
            if (scsp.getRole() == SpeciesContextSpec.ROLE_InitialCount) {
                speciesAttr = scsp.getName();
            }
        }
        if (speciesAttr.length() < 1) {
            targetXpath = new XPathTarget(sbmlSupport.getXPathForCompartment(speciesId));
        } else if (speciesAttr.equalsIgnoreCase("initialConcentration") || speciesAttr.equalsIgnoreCase("initConc")) {
            targetXpath = new XPathTarget(sbmlSupport.getXPathForSpecies(speciesId, SpeciesAttribute.initialConcentration));
        } else if (speciesAttr.equalsIgnoreCase("initialCount")) {
            targetXpath = new XPathTarget(sbmlSupport.getXPathForSpecies(speciesId, SpeciesAttribute.initialAmount));
        } else {
            throw new RuntimeException("Unknown species attribute '" + speciesAttr + "'; cannot get xpath target for species '" + speciesId + "'.");
        }
        targetXpath = new XPathTarget(sbmlSupport.getXPathForSpecies(speciesId));
    } else if (ste instanceof ModelParameter) {
        // can only change parameter value.
        targetXpath = new XPathTarget(sbmlSupport.getXPathForGlobalParameter(ste.getName(), ParameterAttribute.value));
    } else if (ste instanceof Structure || ste instanceof Structure.StructureSize || (ste instanceof StructureMappingParameter && ((StructureMappingParameter) ste).getRole() == StructureMapping.ROLE_Size)) {
        String compartmentId = ste.getName();
        // can change compartment size or spatial dimension, but in vcell, we cannot change compartment dimension.
        String compartmentAttr = "";
        if (ste instanceof Structure.StructureSize) {
            compartmentId = ((StructureSize) ste).getStructure().getName();
            compartmentAttr = ((StructureSize) ste).getName();
        }
        if (ste instanceof StructureMappingParameter) {
            StructureMappingParameter smp = (StructureMappingParameter) ste;
            compartmentId = smp.getStructure().getName();
            if (smp.getRole() == StructureMapping.ROLE_Size) {
                compartmentAttr = smp.getName();
            }
        }
        if (compartmentAttr.length() < 1) {
            targetXpath = new XPathTarget(sbmlSupport.getXPathForCompartment(compartmentId));
        } else if (compartmentAttr.equalsIgnoreCase("size")) {
            targetXpath = new XPathTarget(sbmlSupport.getXPathForCompartment(compartmentId, CompartmentAttribute.size));
        } else {
            throw new RuntimeException("Unknown compartment attribute '" + compartmentAttr + "'; cannot get xpath target for compartment '" + compartmentId + "'.");
        }
    } else if (ste instanceof KineticsParameter) {
        KineticsParameter kp = (KineticsParameter) ste;
        String reactionID = kp.getKinetics().getReactionStep().getName();
        String parameterID = kp.getName();
        Pair<String, String> key = new Pair(reactionID, parameterID);
        String value = l2gMap.get(key);
        if (value == null) {
            // stays as local parameter
            targetXpath = new XPathTarget(sbmlSupport.getXPathForKineticLawParameter(reactionID, parameterID, ParameterAttribute.value));
        } else {
            // became a global in SBML, we need to refer to that global
            targetXpath = new XPathTarget(sbmlSupport.getXPathForGlobalParameter(value, ParameterAttribute.value));
        }
    } else {
        System.err.println("Entity should be SpeciesContext, Structure, ModelParameter : " + ste.getClass());
        throw new RuntimeException("Unknown entity in SBML model");
    }
    return targetXpath;
}