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

Example 26 with CompartmentSubDomain

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

the class MathDescriptionTreeModel method createBaseTree.

/**
 * Insert the method's description here.
 * Creation date: (11/28/00 1:06:51 PM)
 * @return cbit.vcell.desktop.BioModelNode
 * @param docManager cbit.vcell.clientdb.DocumentManager
 */
private BioModelNode createBaseTree() {
    if (getMathDescription() == null) {
        return new BioModelNode(" ", false);
    }
    // 
    // make root node
    // 
    BioModelNode rootNode = new BioModelNode("math description", true);
    // 
    // create subTree of Constants
    // 
    BioModelNode constantRootNode = new BioModelNode("constants", true);
    Enumeration<Constant> enum1 = getMathDescription().getConstants();
    while (enum1.hasMoreElements()) {
        Constant constant = enum1.nextElement();
        BioModelNode constantNode = new BioModelNode(constant, false);
        constantRootNode.add(constantNode);
    }
    if (constantRootNode.getChildCount() > 0) {
        rootNode.add(constantRootNode);
    }
    // 
    // create subTree of Functions
    // 
    BioModelNode functionRootNode = new BioModelNode("functions", true);
    Enumeration<Function> enum2 = getMathDescription().getFunctions();
    while (enum2.hasMoreElements()) {
        Function function = enum2.nextElement();
        BioModelNode functionNode = new BioModelNode(function, false);
        functionRootNode.add(functionNode);
    }
    if (functionRootNode.getChildCount() > 0) {
        rootNode.add(functionRootNode);
    }
    // 
    // create subTree of VolumeSubDomains and MembraneSubDomains
    // 
    BioModelNode volumeRootNode = new BioModelNode("volume domains", true);
    BioModelNode membraneRootNode = new BioModelNode("membrane domains", true);
    Enumeration<SubDomain> enum3 = getMathDescription().getSubDomains();
    while (enum3.hasMoreElements()) {
        SubDomain subDomain = enum3.nextElement();
        if (subDomain instanceof cbit.vcell.math.CompartmentSubDomain) {
            CompartmentSubDomain volumeSubDomain = (CompartmentSubDomain) subDomain;
            BioModelNode volumeSubDomainNode = new BioModelNode(volumeSubDomain, true);
            if (// stochastic subtree
            getMathDescription().isNonSpatialStoch()) {
                // add stoch variable initial conditions
                BioModelNode varIniConditionNode = new BioModelNode("variable_initial_conditions", true);
                for (VarIniCondition varIni : volumeSubDomain.getVarIniConditions()) {
                    BioModelNode varIniNode = new BioModelNode(varIni, false);
                    varIniConditionNode.add(varIniNode);
                }
                volumeSubDomainNode.add(varIniConditionNode);
                // add jump processes
                for (JumpProcess jp : volumeSubDomain.getJumpProcesses()) {
                    BioModelNode jpNode = new BioModelNode(jp, true);
                    // add probability rate.
                    String probRate = "P_" + jp.getName();
                    BioModelNode prNode = new BioModelNode("probability_rate = " + probRate, false);
                    jpNode.add(prNode);
                    // add Actions
                    Enumeration<Action> actions = Collections.enumeration(jp.getActions());
                    while (actions.hasMoreElements()) {
                        Action action = actions.nextElement();
                        BioModelNode actionNode = new BioModelNode(action, false);
                        jpNode.add(actionNode);
                    }
                    volumeSubDomainNode.add(jpNode);
                }
            } else // non-stochastic subtree
            {
                // 
                // add equation children
                // 
                Enumeration<Equation> eqnEnum = volumeSubDomain.getEquations();
                while (eqnEnum.hasMoreElements()) {
                    Equation equation = eqnEnum.nextElement();
                    BioModelNode equationNode = new BioModelNode(equation, false);
                    volumeSubDomainNode.add(equationNode);
                }
                // 
                // add fast system
                // 
                FastSystem fastSystem = volumeSubDomain.getFastSystem();
                if (fastSystem != null) {
                    BioModelNode fsNode = new BioModelNode(fastSystem, true);
                    Enumeration<FastInvariant> enumFI = fastSystem.getFastInvariants();
                    while (enumFI.hasMoreElements()) {
                        FastInvariant fi = enumFI.nextElement();
                        fsNode.add(new BioModelNode(fi, false));
                    }
                    Enumeration<FastRate> enumFR = fastSystem.getFastRates();
                    while (enumFR.hasMoreElements()) {
                        FastRate fr = enumFR.nextElement();
                        fsNode.add(new BioModelNode(fr, false));
                    }
                    volumeSubDomainNode.add(fsNode);
                }
            }
            volumeRootNode.add(volumeSubDomainNode);
        } else if (subDomain instanceof MembraneSubDomain) {
            MembraneSubDomain membraneSubDomain = (MembraneSubDomain) subDomain;
            BioModelNode membraneSubDomainNode = new BioModelNode(membraneSubDomain, true);
            // 
            // add equation children
            // 
            Enumeration<Equation> eqnEnum = membraneSubDomain.getEquations();
            while (eqnEnum.hasMoreElements()) {
                Equation equation = eqnEnum.nextElement();
                BioModelNode equationNode = new BioModelNode(equation, false);
                membraneSubDomainNode.add(equationNode);
            }
            // 
            // add jump condition children
            // 
            Enumeration<JumpCondition> jcEnum = membraneSubDomain.getJumpConditions();
            while (jcEnum.hasMoreElements()) {
                JumpCondition jumpCondition = jcEnum.nextElement();
                BioModelNode jcNode = new BioModelNode(jumpCondition, false);
                membraneSubDomainNode.add(jcNode);
            }
            // 
            // add fast system
            // 
            FastSystem fastSystem = membraneSubDomain.getFastSystem();
            if (fastSystem != null) {
                BioModelNode fsNode = new BioModelNode(fastSystem, true);
                Enumeration<FastInvariant> enumFI = fastSystem.getFastInvariants();
                while (enumFI.hasMoreElements()) {
                    FastInvariant fi = enumFI.nextElement();
                    fsNode.add(new BioModelNode(fi, false));
                }
                Enumeration<FastRate> enumFR = fastSystem.getFastRates();
                while (enumFR.hasMoreElements()) {
                    FastRate fr = enumFR.nextElement();
                    fsNode.add(new BioModelNode(fr, false));
                }
                membraneSubDomainNode.add(fsNode);
            }
            membraneRootNode.add(membraneSubDomainNode);
        }
    }
    if (volumeRootNode.getChildCount() > 0) {
        rootNode.add(volumeRootNode);
    }
    if (membraneRootNode.getChildCount() > 0) {
        rootNode.add(membraneRootNode);
    }
    return rootNode;
}

Example 27 with CompartmentSubDomain

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

the class StochMathMapping_4_8 method refreshMathDescription.

/**
 * set up a math description based on current simulationContext.
 */
private void refreshMathDescription() throws MappingException, MatrixException, MathException, ExpressionException, ModelException {
    // use local variable instead of using getter all the time.
    SimulationContext simContext = getSimulationContext();
    // local structure mapping list
    StructureMapping[] structureMappings = simContext.getGeometryContext().getStructureMappings();
    // We have to check if all the reactions are able to tranform to stochastic jump processes before generating the math.
    String stochChkMsg = simContext.getModel().isValidForStochApp();
    if (!(stochChkMsg.equals(""))) {
        throw new ModelException("Problem updating math description: " + simContext.getName() + "\n" + stochChkMsg);
    }
    // All sizes must be set for new ODE models and ratios must be set for old ones.
    simContext.checkValidity();
    // 
    // verify that all structures are mapped to subvolumes and all subvolumes are mapped to a structure
    // 
    Structure[] structures = simContext.getGeometryContext().getModel().getStructures();
    for (int i = 0; i < structures.length; i++) {
        StructureMapping sm = simContext.getGeometryContext().getStructureMapping(structures[i]);
        if (sm == null || (sm instanceof FeatureMapping && getSubVolume(((FeatureMapping) sm)) == null)) {
            throw new MappingException("model structure '" + structures[i].getName() + "' not mapped to a geometry subVolume");
        }
        if (sm != null && (sm instanceof MembraneMapping) && ((MembraneMapping) sm).getVolumeFractionParameter() != null) {
            Expression volFractExp = ((MembraneMapping) sm).getVolumeFractionParameter().getExpression();
            try {
                if (volFractExp != null) {
                    double volFract = volFractExp.evaluateConstant();
                    if (volFract >= 1.0) {
                        throw new MappingException("model structure '" + (getSimulationContext().getModel().getStructureTopology().getInsideFeature(((MembraneMapping) sm).getMembrane()).getName() + "' has volume fraction >= 1.0"));
                    }
                }
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
            }
        }
    }
    SubVolume[] subVolumes = simContext.getGeometryContext().getGeometry().getGeometrySpec().getSubVolumes();
    for (int i = 0; i < subVolumes.length; i++) {
        if (getStructures(subVolumes[i]) == null || getStructures(subVolumes[i]).length == 0) {
            throw new MappingException("geometry subVolume '" + subVolumes[i].getName() + "' not mapped from a model structure");
        }
    }
    // 
    // gather only those reactionSteps that are not "excluded"
    // 
    ReactionSpec[] reactionSpecs = simContext.getReactionContext().getReactionSpecs();
    Vector<ReactionStep> rsList = new Vector<ReactionStep>();
    for (int i = 0; i < reactionSpecs.length; i++) {
        if (reactionSpecs[i].isExcluded() == false) {
            rsList.add(reactionSpecs[i].getReactionStep());
        }
    }
    ReactionStep[] reactionSteps = new ReactionStep[rsList.size()];
    rsList.copyInto(reactionSteps);
    // 
    for (int i = 0; i < reactionSteps.length; i++) {
        Kinetics.UnresolvedParameter[] unresolvedParameters = reactionSteps[i].getKinetics().getUnresolvedParameters();
        if (unresolvedParameters != null && unresolvedParameters.length > 0) {
            StringBuffer buffer = new StringBuffer();
            for (int j = 0; j < unresolvedParameters.length; j++) {
                if (j > 0) {
                    buffer.append(", ");
                }
                buffer.append(unresolvedParameters[j].getName());
            }
            throw new MappingException(reactionSteps[i].getDisplayType() + " '" + reactionSteps[i].getName() + "' contains unresolved identifier(s): " + buffer);
        }
    }
    // 
    // create new MathDescription (based on simContext's previous MathDescription if possible)
    // 
    MathDescription oldMathDesc = simContext.getMathDescription();
    mathDesc = null;
    if (oldMathDesc != null) {
        if (oldMathDesc.getVersion() != null) {
            mathDesc = new MathDescription(oldMathDesc.getVersion());
        } else {
            mathDesc = new MathDescription(oldMathDesc.getName());
        }
    } else {
        mathDesc = new MathDescription(simContext.getName() + "_generated");
    }
    // 
    // temporarily place all variables in a hashtable (before binding) and discarding duplicates
    // 
    VariableHash varHash = new VariableHash();
    // 
    // conversion factors
    // 
    Model model = simContext.getModel();
    ModelUnitSystem modelUnitSystem = model.getUnitSystem();
    varHash.addVariable(new Constant(getMathSymbol(model.getKMOLE(), null), getIdentifierSubstitutions(model.getKMOLE().getExpression(), model.getKMOLE().getUnitDefinition(), null)));
    varHash.addVariable(new Constant(getMathSymbol(model.getN_PMOLE(), null), getIdentifierSubstitutions(model.getN_PMOLE().getExpression(), model.getN_PMOLE().getUnitDefinition(), null)));
    varHash.addVariable(new Constant(getMathSymbol(model.getFARADAY_CONSTANT(), null), getIdentifierSubstitutions(model.getFARADAY_CONSTANT().getExpression(), model.getFARADAY_CONSTANT().getUnitDefinition(), null)));
    varHash.addVariable(new Constant(getMathSymbol(model.getFARADAY_CONSTANT_NMOLE(), null), getIdentifierSubstitutions(model.getFARADAY_CONSTANT_NMOLE().getExpression(), model.getFARADAY_CONSTANT_NMOLE().getUnitDefinition(), null)));
    varHash.addVariable(new Constant(getMathSymbol(model.getGAS_CONSTANT(), null), getIdentifierSubstitutions(model.getGAS_CONSTANT().getExpression(), model.getGAS_CONSTANT().getUnitDefinition(), null)));
    varHash.addVariable(new Constant(getMathSymbol(model.getTEMPERATURE(), null), getIdentifierSubstitutions(new Expression(simContext.getTemperatureKelvin()), model.getTEMPERATURE().getUnitDefinition(), null)));
    Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = enum1.nextElement();
        if (scm.getVariable() instanceof StochVolVariable) {
            varHash.addVariable(scm.getVariable());
        }
    }
    // 
    // add rate term for all reactions
    // add current source terms for each reaction step in a membrane
    // 
    /*for (int i = 0; i < reactionSteps.length; i++){
			boolean bAllReactionParticipantsFixed = true;
			ReactionParticipant rp_Array[] = reactionSteps[i].getReactionParticipants();
			for (int j = 0; j < rp_Array.length; j++) {
				SpeciesContextSpec scs = getSimulationContext().getReactionContext().getSpeciesContextSpec(rp_Array[j].getSpeciesContext());
				if (!(rp_Array[j] instanceof Catalyst) && !scs.isConstant()){
					bAllReactionParticipantsFixed = false;  // found at least one reactionParticipant that is not fixed and needs this rate
				}
			}
			StructureMapping sm = simContext.getGeometryContext().getStructureMapping(reactionSteps[i].getStructure());
		}---don't think it's useful, isn't it?*/
    // deals with model parameters
    ModelParameter[] modelParameters = simContext.getModel().getModelParameters();
    for (int j = 0; j < modelParameters.length; j++) {
        Expression expr = getSubstitutedExpr(modelParameters[j].getExpression(), true, false);
        expr = getIdentifierSubstitutions(expr, modelParameters[j].getUnitDefinition(), null);
        varHash.addVariable(newFunctionOrConstant(getMathSymbol(modelParameters[j], null), expr));
    }
    // added July 2009, ElectricalStimulusParameter electric mapping tab
    ElectricalStimulus[] elecStimulus = simContext.getElectricalStimuli();
    if (elecStimulus.length > 0) {
        throw new MappingException("Modles with electrophysiology are not supported for stochastic applications.");
    }
    for (int j = 0; j < structureMappings.length; j++) {
        if (structureMappings[j] instanceof MembraneMapping) {
            MembraneMapping memMapping = (MembraneMapping) structureMappings[j];
            Parameter initialVoltageParm = memMapping.getInitialVoltageParameter();
            try {
                Expression exp = initialVoltageParm.getExpression();
                exp.evaluateConstant();
                varHash.addVariable(newFunctionOrConstant(getMathSymbol(memMapping.getMembrane().getMembraneVoltage(), memMapping), getIdentifierSubstitutions(memMapping.getInitialVoltageParameter().getExpression(), memMapping.getInitialVoltageParameter().getUnitDefinition(), memMapping)));
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new MappingException("Membrane initial voltage: " + initialVoltageParm.getName() + " cannot be evaluated as constant.");
            }
        }
    }
    // 
    for (int j = 0; j < reactionSteps.length; j++) {
        ReactionStep rs = reactionSteps[j];
        if (simContext.getReactionContext().getReactionSpec(rs).isExcluded()) {
            continue;
        }
        if (rs.getKinetics() instanceof LumpedKinetics) {
            throw new RuntimeException("Lumped Kinetics not yet supported for Stochastic Math Generation");
        }
        Kinetics.KineticsParameter[] parameters = rs.getKinetics().getKineticsParameters();
        StructureMapping sm = simContext.getGeometryContext().getStructureMapping(rs.getStructure());
        if (parameters != null) {
            for (int i = 0; i < parameters.length; i++) {
                if ((parameters[i].getRole() == Kinetics.ROLE_CurrentDensity) && (parameters[i].getExpression() == null || parameters[i].getExpression().isZero())) {
                    continue;
                }
                // don't add rate, we'll do it later when creating the jump processes
                if (parameters[i].getRole() != Kinetics.ROLE_ReactionRate) {
                    Expression expr = getSubstitutedExpr(parameters[i].getExpression(), true, false);
                    varHash.addVariable(newFunctionOrConstant(getMathSymbol(parameters[i], sm), getIdentifierSubstitutions(expr, parameters[i].getUnitDefinition(), sm)));
                }
            }
        }
    }
    // the parameter "Size" is already put into mathsymbolmapping in refreshSpeciesContextMapping()
    for (int i = 0; i < structureMappings.length; i++) {
        StructureMapping sm = structureMappings[i];
        StructureMapping.StructureMappingParameter parm = sm.getParameterFromRole(StructureMapping.ROLE_Size);
        if (parm.getExpression() != null) {
            try {
                double value = parm.getExpression().evaluateConstant();
                varHash.addVariable(new Constant(getMathSymbol(parm, sm), new Expression(value)));
            } catch (ExpressionException e) {
                // varHash.addVariable(new Function(getMathSymbol0(parm,sm),getIdentifierSubstitutions(parm.getExpression(),parm.getUnitDefinition(),sm)));
                e.printStackTrace(System.out);
                throw new MappingException("Size of structure:" + sm.getNameScope().getName() + " cannot be evaluated as constant.");
            }
        }
    }
    // 
    // species initial values (either function or constant)
    // 
    SpeciesContextSpec[] speciesContextSpecs = simContext.getReactionContext().getSpeciesContextSpecs();
    for (int i = 0; i < speciesContextSpecs.length; i++) {
        // can be concentration or amount
        SpeciesContextSpec.SpeciesContextSpecParameter initParam = null;
        Expression iniExp = null;
        StructureMapping sm = simContext.getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
        if (speciesContextSpecs[i].getInitialConcentrationParameter() != null && speciesContextSpecs[i].getInitialConcentrationParameter().getExpression() != null) {
            // use concentration, need to set up amount functions
            initParam = speciesContextSpecs[i].getInitialConcentrationParameter();
            iniExp = initParam.getExpression();
            iniExp = getSubstitutedExpr(iniExp, true, !speciesContextSpecs[i].isConstant());
            // now create the appropriate function or Constant for the speciesContextSpec.
            varHash.addVariable(newFunctionOrConstant(getMathSymbol(initParam, sm), getIdentifierSubstitutions(iniExp, initParam.getUnitDefinition(), sm)));
            // add function for initial amount
            SpeciesContextSpec.SpeciesContextSpecParameter initAmountParam = speciesContextSpecs[i].getInitialCountParameter();
            Expression iniAmountExp = getExpressionConcToAmt(new Expression(initParam, getNameScope()), speciesContextSpecs[i].getSpeciesContext());
            // iniAmountExp.bindExpression(this);
            varHash.addVariable(new Function(getMathSymbol(initAmountParam, sm), getIdentifierSubstitutions(iniAmountExp, initAmountParam.getUnitDefinition(), sm), nullDomain));
        } else if (speciesContextSpecs[i].getInitialCountParameter() != null && speciesContextSpecs[i].getInitialCountParameter().getExpression() != null) {
            // use amount
            initParam = speciesContextSpecs[i].getInitialCountParameter();
            iniExp = initParam.getExpression();
            iniExp = getSubstitutedExpr(iniExp, false, !speciesContextSpecs[i].isConstant());
            // now create the appropriate function or Constant for the speciesContextSpec.
            varHash.addVariable(newFunctionOrConstant(getMathSymbol(initParam, sm), getIdentifierSubstitutions(iniExp, initParam.getUnitDefinition(), sm)));
        }
        // add spConcentration (concentration of species) to varHash as function or constant
        SpeciesConcentrationParameter spConcParam = getSpeciesConcentrationParameter(speciesContextSpecs[i].getSpeciesContext());
        varHash.addVariable(newFunctionOrConstant(getMathSymbol(spConcParam, sm), getIdentifierSubstitutions(spConcParam.getExpression(), spConcParam.getUnitDefinition(), sm)));
    }
    // 
    // constant species (either function or constant)
    // 
    enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
        if (scm.getVariable() instanceof Constant) {
            varHash.addVariable(scm.getVariable());
        }
    }
    // 
    if (simContext.getGeometryContext().getGeometry() != null) {
        try {
            mathDesc.setGeometry(simContext.getGeometryContext().getGeometry());
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new MappingException("failure setting geometry " + e.getMessage());
        }
    } else {
        throw new MappingException("geometry must be defined");
    }
    // 
    // functions: species which is not a variable, but has dependency expression
    // 
    enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
        if (scm.getVariable() == null && scm.getDependencyExpression() != null) {
            StructureMapping sm = simContext.getGeometryContext().getStructureMapping(scm.getSpeciesContext().getStructure());
            Expression exp = scm.getDependencyExpression();
            exp.bindExpression(this);
            SpeciesCountParameter spCountParam = getSpeciesCountParameter(scm.getSpeciesContext());
            varHash.addVariable(new Function(getMathSymbol(spCountParam, sm), getIdentifierSubstitutions(exp, spCountParam.getUnitDefinition(), sm), nullDomain));
        }
    }
    // 
    // create subDomains
    // 
    SubDomain subDomain = null;
    subVolumes = simContext.getGeometryContext().getGeometry().getGeometrySpec().getSubVolumes();
    for (int j = 0; j < subVolumes.length; j++) {
        SubVolume subVolume = (SubVolume) subVolumes[j];
        // 
        // get priority of subDomain
        // 
        int priority;
        Feature spatialFeature = getResolvedFeature(subVolume);
        if (spatialFeature == null) {
            if (simContext.getGeometryContext().getGeometry().getDimension() > 0) {
                throw new MappingException("no compartment (in Physiology) is mapped to subdomain '" + subVolume.getName() + "' (in Geometry)");
            } else {
                priority = CompartmentSubDomain.NON_SPATIAL_PRIORITY;
            }
        } else {
            // now does not have to match spatial feature, *BUT* needs to be unique
            priority = j;
        }
        subDomain = new CompartmentSubDomain(subVolume.getName(), priority);
        mathDesc.addSubDomain(subDomain);
    }
    // ReactionSpec[] reactionSpecs = simContext.getReactionContext().getReactionSpecs();---need to take a look here!
    for (int i = 0; i < reactionSpecs.length; i++) {
        if (reactionSpecs[i].isExcluded()) {
            continue;
        }
        // get the reaction
        ReactionStep reactionStep = reactionSpecs[i].getReactionStep();
        Kinetics kinetics = reactionStep.getKinetics();
        // the structure where reaction happens
        StructureMapping sm = simContext.getGeometryContext().getStructureMapping(reactionStep.getStructure());
        // create symbol table for jump process based on reactionStep and structure mapping
        // final ReactionStep finalRS = reactionStep;
        // final StructureMapping finalSM = sm;
        // SymbolTable symTable = new SymbolTable(){
        // public SymbolTableEntry getEntry(String identifierString) throws ExpressionBindingException {
        // SymbolTableEntry ste = finalRS.getEntry(identifierString);
        // if(ste == null)
        // {
        // ste = finalSM.getEntry(identifierString);
        // }
        // return ste;
        // }
        // };
        // Different ways to deal with simple reactions and flux reactions
        // probability parameter from modelUnitSystem
        VCUnitDefinition probabilityParamUnit = modelUnitSystem.getStochasticSubstanceUnit().divideBy(modelUnitSystem.getTimeUnit());
        if (// simple reactions
        reactionStep instanceof SimpleReaction) {
            // check the reaction rate law to see if we need to decompose a reaction(reversible) into two jump processes.
            // rate constants are important in calculating the probability rate.
            // for Mass Action, we use KForward and KReverse,
            // for General Kinetics we parse reaction rate J to see if it is in Mass Action form.
            Expression forwardRate = null;
            Expression reverseRate = null;
            if (kinetics.getKineticsDescription().equals(KineticsDescription.MassAction)) {
                forwardRate = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KForward).getExpression();
                reverseRate = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KReverse).getExpression();
            } else if (kinetics.getKineticsDescription().equals(KineticsDescription.General)) {
                Expression rateExp = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate).getExpression();
                MassActionSolver.MassActionFunction maFunc = MassActionSolver.solveMassAction(null, null, rateExp, reactionStep);
                if (maFunc.getForwardRate() == null && maFunc.getReverseRate() == null) {
                    throw new MappingException("Cannot generate stochastic math mapping for the reaction:" + reactionStep.getName() + "\nLooking for the rate function according to the form of k1*Reactant1^Stoir1*Reactant2^Stoir2...-k2*Product1^Stoip1*Product2^Stoip2.");
                } else {
                    if (maFunc.getForwardRate() != null) {
                        forwardRate = maFunc.getForwardRate();
                    }
                    if (maFunc.getReverseRate() != null) {
                        reverseRate = maFunc.getReverseRate();
                    }
                }
            }
            /*else if (kinetics.getKineticsDescription().getName().compareTo(KineticsDescription.HMM_irreversible.getName())==0)
			    {
				    forwardRate = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_Km).getExpression();
				}
			    else if (kinetics.getKineticsDescription().getName().compareTo(KineticsDescription.HMM_reversible.getName())==0)
			    {
					forwardRate = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KmFwd).getExpression();
					reverseRate = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KmRev).getExpression();
				}*/
            boolean isForwardRatePresent = false;
            boolean isReverseRatePresent = false;
            if (forwardRate != null) {
                isForwardRatePresent = true;
            }
            if (reverseRate != null) {
                isReverseRatePresent = true;
            }
            // we process it as forward reaction
            if ((isForwardRatePresent)) /*|| ((forwardRate == null) && (reverseRate == null))*/
            {
                // get jump process name
                String jpName = TokenMangler.mangleToSName(reactionStep.getName());
                // get probability
                Expression exp = null;
                // reactions are mass actions
                exp = getProbabilityRate(reactionStep, true);
                // bind symbol table before substitute identifiers in the reaction step
                exp.bindExpression(this);
                MathMapping_4_8.ProbabilityParameter probParm = null;
                try {
                    probParm = addProbabilityParameter("P_" + jpName, exp, MathMapping_4_8.PARAMETER_ROLE_P, probabilityParamUnit, reactionSpecs[i]);
                } catch (PropertyVetoException pve) {
                    pve.printStackTrace();
                    throw new MappingException(pve.getMessage());
                }
                // add probability to function or constant
                varHash.addVariable(newFunctionOrConstant(getMathSymbol(probParm, sm), getIdentifierSubstitutions(exp, probabilityParamUnit, sm)));
                JumpProcess jp = new JumpProcess(jpName, new Expression(getMathSymbol(probParm, sm)));
                // actions
                ReactionParticipant[] reacPart = reactionStep.getReactionParticipants();
                for (int j = 0; j < reacPart.length; j++) {
                    Action action = null;
                    SpeciesCountParameter spCountParam = getSpeciesCountParameter(reacPart[j].getSpeciesContext());
                    if (reacPart[j] instanceof Reactant) {
                        // check if the reactant is a constant. If the species is a constant, there will be no action taken on this species
                        if (// not a constant
                        !simContext.getReactionContext().getSpeciesContextSpec(reacPart[j].getSpeciesContext()).isConstant()) {
                            int stoi = ((Reactant) reacPart[j]).getStoichiometry();
                            action = new Action(varHash.getVariable(getMathSymbol(spCountParam, sm)), "inc", new Expression("-" + String.valueOf(stoi)));
                            jp.addAction(action);
                        }
                    } else if (reacPart[j] instanceof Product) {
                        // check if the product is a constant. If the product is a constant, there will be no action taken on this species
                        if (// not a constant
                        !simContext.getReactionContext().getSpeciesContextSpec(reacPart[j].getSpeciesContext()).isConstant()) {
                            int stoi = ((Product) reacPart[j]).getStoichiometry();
                            action = new Action(varHash.getVariable(getMathSymbol(spCountParam, sm)), "inc", new Expression(stoi));
                            jp.addAction(action);
                        }
                    }
                }
                // add jump process to compartment subDomain
                subDomain.addJumpProcess(jp);
            }
            if (// one more jump process for a reversible reaction
            isReverseRatePresent) {
                // get jump process name
                String jpName = TokenMangler.mangleToSName(reactionStep.getName()) + "_reverse";
                Expression exp = null;
                // reactions are mass actions
                exp = getProbabilityRate(reactionStep, false);
                // bind symbol table before substitute identifiers in the reaction step
                exp.bindExpression(this);
                MathMapping_4_8.ProbabilityParameter probRevParm = null;
                try {
                    probRevParm = addProbabilityParameter("P_" + jpName, exp, MathMapping_4_8.PARAMETER_ROLE_P_reverse, probabilityParamUnit, reactionSpecs[i]);
                } catch (PropertyVetoException pve) {
                    pve.printStackTrace();
                    throw new MappingException(pve.getMessage());
                }
                // add probability to function or constant
                varHash.addVariable(newFunctionOrConstant(getMathSymbol(probRevParm, sm), getIdentifierSubstitutions(exp, probabilityParamUnit, sm)));
                JumpProcess jp = new JumpProcess(jpName, new Expression(getMathSymbol(probRevParm, sm)));
                // actions
                ReactionParticipant[] reacPart = reactionStep.getReactionParticipants();
                for (int j = 0; j < reacPart.length; j++) {
                    Action action = null;
                    SpeciesCountParameter spCountParam = getSpeciesCountParameter(reacPart[j].getSpeciesContext());
                    if (reacPart[j] instanceof Reactant) {
                        // check if the reactant is a constant. If the species is a constant, there will be no action taken on this species
                        if (// not a constant
                        !simContext.getReactionContext().getSpeciesContextSpec(reacPart[j].getSpeciesContext()).isConstant()) {
                            int stoi = ((Reactant) reacPart[j]).getStoichiometry();
                            action = new Action(varHash.getVariable(getMathSymbol(spCountParam, sm)), "inc", new Expression(stoi));
                            jp.addAction(action);
                        }
                    } else if (reacPart[j] instanceof Product) {
                        // check if the product is a constant. If the product is a constant, there will be no action taken on this species
                        if (// not a constant
                        !simContext.getReactionContext().getSpeciesContextSpec(reacPart[j].getSpeciesContext()).isConstant()) {
                            int stoi = ((Product) reacPart[j]).getStoichiometry();
                            action = new Action(varHash.getVariable(getMathSymbol(spCountParam, sm)), "inc", new Expression("-" + String.valueOf(stoi)));
                            jp.addAction(action);
                        }
                    }
                }
                // add jump process to compartment subDomain
                subDomain.addJumpProcess(jp);
            }
        // end of if(isForwardRateNonZero), if(isReverseRateNonRate)
        } else if (// flux reactions
        reactionStep instanceof FluxReaction) {
            // we could set jump processes for general flux rate in forms of p1*Sout + p2*Sin
            if (kinetics.getKineticsDescription().equals(KineticsDescription.General)) {
                Expression fluxRate = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate).getExpression();
                // we have to pass the math description para to flux solver, coz somehow math description in simulation context is not updated.
                MassActionSolver.MassActionFunction fluxFunc = MassActionSolver.solveMassAction(null, null, fluxRate, (FluxReaction) reactionStep);
                // create jump process for forward flux if it exists.
                if (fluxFunc.getForwardRate() != null && !fluxFunc.getForwardRate().isZero()) {
                    // jump process name
                    // +"_reverse";
                    String jpName = TokenMangler.mangleToSName(reactionStep.getName());
                    // we do it here instead of fluxsolver, coz we need to use getMathSymbol0(), structuremapping...etc.
                    Expression rate = fluxFunc.getForwardRate();
                    // get species expression (depend on structure, if mem: Species/mem_Size, if vol: species*KMOLE/vol_size)
                    SpeciesContext scOut = fluxFunc.getReactants().get(0).getSpeciesContext();
                    Expression speciesFactor = null;
                    if (scOut.getStructure() instanceof Feature) {
                        Expression exp1 = new Expression(1.0 / 602.0);
                        Expression exp2 = new Expression(scOut.getStructure().getStructureSize(), getNameScope());
                        speciesFactor = Expression.div(Expression.invert(exp1), exp2);
                    } else {
                        throw new MappingException("Species involved in a flux have to be volume species.");
                    }
                    Expression speciesExp = Expression.mult(speciesFactor, new Expression(scOut, getNameScope()));
                    // get probability expression by adding factor to rate (rate: rate*size_mem/KMOLE)
                    Expression expr1 = Expression.mult(rate, speciesExp);
                    Expression numeratorExpr = Expression.mult(expr1, new Expression(sm.getStructure().getStructureSize(), getNameScope()));
                    Expression exp = new Expression(1.0 / 602.0);
                    Expression probExp = Expression.mult(numeratorExpr, exp);
                    // bind symbol table before substitute identifiers in the reaction step
                    probExp.bindExpression(reactionStep);
                    MathMapping_4_8.ProbabilityParameter probParm = null;
                    try {
                        probParm = addProbabilityParameter("P_" + jpName, probExp, MathMapping_4_8.PARAMETER_ROLE_P, probabilityParamUnit, reactionSpecs[i]);
                    } catch (PropertyVetoException pve) {
                        pve.printStackTrace();
                        throw new MappingException(pve.getMessage());
                    }
                    // add probability to function or constant
                    varHash.addVariable(newFunctionOrConstant(getMathSymbol(probParm, sm), getIdentifierSubstitutions(probExp, probabilityParamUnit, sm)));
                    JumpProcess jp = new JumpProcess(jpName, new Expression(getMathSymbol(probParm, sm)));
                    // actions
                    Action action = null;
                    SpeciesContext sc = fluxFunc.getReactants().get(0).getSpeciesContext();
                    if (!simContext.getReactionContext().getSpeciesContextSpec(sc).isConstant()) {
                        SpeciesCountParameter spCountParam = getSpeciesCountParameter(sc);
                        action = new Action(varHash.getVariable(getMathSymbol(spCountParam, sm)), "inc", new Expression(-1));
                        jp.addAction(action);
                    }
                    sc = fluxFunc.getProducts().get(0).getSpeciesContext();
                    if (!simContext.getReactionContext().getSpeciesContextSpec(sc).isConstant()) {
                        SpeciesCountParameter spCountParam = getSpeciesCountParameter(sc);
                        action = new Action(varHash.getVariable(getMathSymbol(spCountParam, sm)), "inc", new Expression(1));
                        jp.addAction(action);
                    }
                    subDomain.addJumpProcess(jp);
                }
                if (fluxFunc.getReverseRate() != null && !fluxFunc.getReverseRate().isZero()) {
                    // jump process name
                    String jpName = TokenMangler.mangleToSName(reactionStep.getName()) + "_reverse";
                    Expression rate = fluxFunc.getReverseRate();
                    // get species expression (depend on structure, if mem: Species/mem_Size, if vol: species*KMOLE/vol_size)
                    SpeciesContext scIn = fluxFunc.getProducts().get(0).getSpeciesContext();
                    Expression speciesFactor = null;
                    if (scIn.getStructure() instanceof Feature) {
                        Expression exp1 = new Expression(1.0 / 602.0);
                        Expression exp2 = new Expression(scIn.getStructure().getStructureSize(), getNameScope());
                        speciesFactor = Expression.div(Expression.invert(exp1), exp2);
                    } else {
                        throw new MappingException("Species involved in a flux have to be volume species.");
                    }
                    Expression speciesExp = Expression.mult(speciesFactor, new Expression(scIn, getNameScope()));
                    // get probability expression by adding factor to rate (rate: rate*size_mem/KMOLE)
                    Expression expr1 = Expression.mult(rate, speciesExp);
                    Expression numeratorExpr = Expression.mult(expr1, new Expression(sm.getStructure().getStructureSize(), getNameScope()));
                    Expression exp = new Expression(1.0 / 602.0);
                    Expression probRevExp = Expression.mult(numeratorExpr, exp);
                    // bind symbol table before substitute identifiers in the reaction step
                    probRevExp.bindExpression(reactionStep);
                    MathMapping_4_8.ProbabilityParameter probRevParm = null;
                    try {
                        probRevParm = addProbabilityParameter("P_" + jpName, probRevExp, MathMapping_4_8.PARAMETER_ROLE_P_reverse, probabilityParamUnit, reactionSpecs[i]);
                    } catch (PropertyVetoException pve) {
                        pve.printStackTrace();
                        throw new MappingException(pve.getMessage());
                    }
                    // add probability to function or constant
                    varHash.addVariable(newFunctionOrConstant(getMathSymbol(probRevParm, sm), getIdentifierSubstitutions(probRevExp, probabilityParamUnit, sm)));
                    JumpProcess jp = new JumpProcess(jpName, new Expression(getMathSymbol(probRevParm, sm)));
                    // actions
                    Action action = null;
                    SpeciesContext sc = fluxFunc.getReactants().get(0).getSpeciesContext();
                    if (!simContext.getReactionContext().getSpeciesContextSpec(sc).isConstant()) {
                        SpeciesCountParameter spCountParam = getSpeciesCountParameter(sc);
                        action = new Action(varHash.getVariable(getMathSymbol(spCountParam, sm)), "inc", new Expression(1));
                        jp.addAction(action);
                    }
                    sc = fluxFunc.getProducts().get(0).getSpeciesContext();
                    if (!simContext.getReactionContext().getSpeciesContextSpec(sc).isConstant()) {
                        SpeciesCountParameter spCountParam = getSpeciesCountParameter(sc);
                        action = new Action(varHash.getVariable(getMathSymbol(spCountParam, sm)), "inc", new Expression(-1));
                        jp.addAction(action);
                    }
                    subDomain.addJumpProcess(jp);
                }
            }
        }
    // end of if (simplereaction)...else if(fluxreaction)
    }
    // end of reaction step loop
    // 
    // set Variables to MathDescription all at once with the order resolved by "VariableHash"
    // 
    mathDesc.setAllVariables(varHash.getAlphabeticallyOrderedVariables());
    // set up variable initial conditions in subDomain
    SpeciesContextSpec[] scSpecs = simContext.getReactionContext().getSpeciesContextSpecs();
    for (int i = 0; i < speciesContextSpecs.length; i++) {
        // get stochastic variable by name
        SpeciesCountParameter spCountParam = getSpeciesCountParameter(speciesContextSpecs[i].getSpeciesContext());
        StructureMapping sm = simContext.getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
        String varName = getMathSymbol(spCountParam, sm);
        if (scSpecs[i].isConstant()) {
            continue;
        }
        StochVolVariable var = (StochVolVariable) mathDesc.getVariable(varName);
        // stochastic use initial number of particles
        SpeciesContextSpec.SpeciesContextSpecParameter initParm = scSpecs[i].getInitialCountParameter();
        // stochastic variables initial expression.
        if (initParm != null) {
            VarIniCondition varIni = new VarIniCount(var, new Expression(getMathSymbol(initParm, sm)));
            subDomain.addVarIniCondition(varIni);
        }
    }
    if (!mathDesc.isValid()) {
        throw new MappingException("generated an invalid mathDescription: " + mathDesc.getWarning());
    }
}

Example 28 with CompartmentSubDomain

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

the class ApplicationConstraintsGenerator method steadyStateFromApplication.

/**
 * Insert the method's description here.
 * Creation date: (6/26/01 8:25:55 AM)
 * @return cbit.vcell.constraints.ConstraintContainerImpl
 */
public static ConstraintContainerImpl steadyStateFromApplication(SimulationContext simContext, double tolerance) {
    try {
        ConstraintContainerImpl ccImpl = new ConstraintContainerImpl();
        // ====================
        // add physical limits
        // ====================
        // 
        // no negative concentrations
        // 
        cbit.vcell.model.Model model = simContext.getModel();
        cbit.vcell.model.SpeciesContext[] speciesContexts = model.getSpeciesContexts();
        for (int i = 0; i < speciesContexts.length; i++) {
            ccImpl.addSimpleBound(new SimpleBounds(speciesContexts[i].getName(), new RealInterval(0, Double.POSITIVE_INFINITY), AbstractConstraint.PHYSICAL_LIMIT, "non-negative concentration"));
        }
        for (int i = 0; i < speciesContexts.length; i++) {
            SpeciesContextSpecParameter initParam = (simContext.getReactionContext().getSpeciesContextSpec(speciesContexts[i])).getInitialConditionParameter();
            if (initParam != null) {
                double initialValue = initParam.getExpression().evaluateConstant();
                double lowInitialValue = Math.min(initialValue / tolerance, initialValue * tolerance);
                double highInitialValue = Math.max(initialValue / tolerance, initialValue * tolerance);
                ccImpl.addSimpleBound(new SimpleBounds(speciesContexts[i].getName(), new RealInterval(lowInitialValue, highInitialValue), AbstractConstraint.MODELING_ASSUMPTION, "close to specified \"initialCondition\""));
            }
        }
        // =========================
        // add modeling assumptions
        // =========================
        // 
        // mass action forward and reverse rates should be non-negative
        // 
        cbit.vcell.model.ReactionStep[] reactionSteps = model.getReactionSteps();
        for (int i = 0; i < reactionSteps.length; i++) {
            Kinetics kinetics = reactionSteps[i].getKinetics();
            if (kinetics instanceof MassActionKinetics) {
                Expression forwardRateConstraintExp = new Expression(((MassActionKinetics) kinetics).getForwardRateParameter().getExpression().infix() + ">=0");
                forwardRateConstraintExp = getSteadyStateExpression(forwardRateConstraintExp);
                if (!forwardRateConstraintExp.compareEqual(new Expression(1.0))) {
                    ccImpl.addGeneralConstraint(new GeneralConstraint(forwardRateConstraintExp, AbstractConstraint.MODELING_ASSUMPTION, "non-negative forward rate"));
                }
                Expression reverseRateConstraintExp = new Expression(((MassActionKinetics) kinetics).getReverseRateParameter().getExpression().infix() + ">=0");
                reverseRateConstraintExp = getSteadyStateExpression(reverseRateConstraintExp);
                if (!reverseRateConstraintExp.compareEqual(new Expression(1.0))) {
                    ccImpl.addGeneralConstraint(new GeneralConstraint(reverseRateConstraintExp, AbstractConstraint.MODELING_ASSUMPTION, "non-negative reverse rate"));
                }
            }
            KineticsParameter authoritativeParameter = kinetics.getAuthoritativeParameter();
            Expression kineticRateConstraintExp = new Expression(authoritativeParameter.getName() + "==" + authoritativeParameter.getExpression().infix());
            kineticRateConstraintExp = getSteadyStateExpression(kineticRateConstraintExp);
            if (!kineticRateConstraintExp.compareEqual(new Expression(1.0))) {
                ccImpl.addGeneralConstraint(new GeneralConstraint(kineticRateConstraintExp, AbstractConstraint.MODELING_ASSUMPTION, "definition"));
            }
        }
        // 
        try {
            simContext.setMathDescription(simContext.createNewMathMapping().getMathDescription());
        } catch (Throwable e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("cannot create mathDescription");
        }
        MathDescription mathDesc = simContext.getMathDescription();
        if (mathDesc.getGeometry().getDimension() > 0) {
            throw new RuntimeException("spatial simulations not yet supported");
        }
        CompartmentSubDomain subDomain = (CompartmentSubDomain) mathDesc.getSubDomains().nextElement();
        java.util.Enumeration<Equation> enumEquations = subDomain.getEquations();
        while (enumEquations.hasMoreElements()) {
            Equation equation = (Equation) enumEquations.nextElement();
            Expression rateConstraintExp = new Expression(equation.getRateExpression().infix() + "==0");
            rateConstraintExp = getSteadyStateExpression(rateConstraintExp);
            if (!rateConstraintExp.compareEqual(new Expression(1.0))) {
                // not a trivial constraint (always true)
                ccImpl.addGeneralConstraint(new GeneralConstraint(rateConstraintExp, AbstractConstraint.PHYSICAL_LIMIT, "definition of steady state"));
            }
        }
        // 
        for (int i = 0; i < reactionSteps.length; i++) {
            Kinetics kinetics = reactionSteps[i].getKinetics();
            Kinetics.KineticsParameter[] parameters = kinetics.getKineticsParameters();
            for (int j = 0; j < parameters.length; j++) {
                Expression exp = parameters[j].getExpression();
                if (exp.getSymbols() == null || exp.getSymbols().length == 0) {
                    // 
                    try {
                        double constantValue = exp.evaluateConstant();
                        double lowValue = Math.min(constantValue / tolerance, constantValue * tolerance);
                        double highValue = Math.max(constantValue / tolerance, constantValue * tolerance);
                        RealInterval interval = new RealInterval(lowValue, highValue);
                        ccImpl.addSimpleBound(new SimpleBounds(parameters[j].getName(), interval, AbstractConstraint.MODELING_ASSUMPTION, "parameter close to model default"));
                    } catch (cbit.vcell.parser.ExpressionException e) {
                        System.out.println("error evaluating parameter " + parameters[j].getName() + " in reaction step " + reactionSteps[i].getName());
                    }
                } else {
                    Expression parameterDefinitionExp = new Expression(parameters[j].getName() + "==" + parameters[j].getExpression().infix());
                    ccImpl.addGeneralConstraint(new GeneralConstraint(getSteadyStateExpression(parameterDefinitionExp), AbstractConstraint.MODELING_ASSUMPTION, "parameter definition"));
                }
            }
        }
        ccImpl.addSimpleBound(new SimpleBounds(model.getFARADAY_CONSTANT().getName(), new RealInterval(model.getFARADAY_CONSTANT().getExpression().evaluateConstant()), AbstractConstraint.PHYSICAL_LIMIT, "Faraday's constant"));
        ccImpl.addSimpleBound(new SimpleBounds(model.getTEMPERATURE().getName(), new RealInterval(300), AbstractConstraint.PHYSICAL_LIMIT, "Absolute Temperature Kelvin"));
        ccImpl.addSimpleBound(new SimpleBounds(model.getGAS_CONSTANT().getName(), new RealInterval(model.getGAS_CONSTANT().getExpression().evaluateConstant()), AbstractConstraint.PHYSICAL_LIMIT, "ideal gas constant"));
        ccImpl.addSimpleBound(new SimpleBounds(model.getKMILLIVOLTS().getName(), new RealInterval(model.getKMILLIVOLTS().getExpression().evaluateConstant()), AbstractConstraint.PHYSICAL_LIMIT, "ideal gas constant"));
        // 
        // add K_fluxs
        // 
        java.util.Enumeration<Variable> enumVars = mathDesc.getVariables();
        while (enumVars.hasMoreElements()) {
            Variable var = (Variable) enumVars.nextElement();
            if (var.getName().startsWith("Kflux_") && var instanceof Function) {
                Expression kfluxExp = new Expression(((Function) var).getExpression());
                kfluxExp.bindExpression(mathDesc);
                kfluxExp = MathUtilities.substituteFunctions(kfluxExp, mathDesc);
                kfluxExp = kfluxExp.flatten();
                ccImpl.addSimpleBound(new SimpleBounds(var.getName(), new RealInterval(kfluxExp.evaluateConstant()), AbstractConstraint.MODELING_ASSUMPTION, "flux conversion factor"));
            }
        }
        return ccImpl;
    } catch (cbit.vcell.parser.ExpressionException e) {
        e.printStackTrace(System.out);
        return null;
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        return null;
    }
}

Example 29 with CompartmentSubDomain

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

the class XmlReader method getCompartmentSubDomain.

/**
 * This method returns a CompartmentSubDomain objecy from a XML element.
 * Creation date: (5/17/2001 11:59:45 AM)
 * @return cbit.vcell.math.CompartmentSubDomain
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private CompartmentSubDomain getCompartmentSubDomain(Element param, MathDescription mathDesc) throws XmlParseException {
    // get attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    int priority = -1;
    String temp = param.getAttributeValue(XMLTags.PriorityAttrTag);
    if (temp != null) {
        priority = Integer.parseInt(temp);
    }
    // --- create new CompartmentSubDomain ---
    CompartmentSubDomain subDomain = new CompartmentSubDomain(name, priority);
    transcribeComments(param, subDomain);
    // Process BoundaryConditions
    Iterator<Element> iterator = param.getChildren(XMLTags.BoundaryTypeTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        // create BoundaryConditionType
        temp = tempelement.getAttributeValue(XMLTags.BoundaryTypeAttrTag);
        BoundaryConditionType bType = new BoundaryConditionType(temp);
        // Process Xm
        if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueXm)) {
            subDomain.setBoundaryConditionXm(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueXp)) {
            // Process Xp
            subDomain.setBoundaryConditionXp(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueYm)) {
            // Process Ym
            subDomain.setBoundaryConditionYm(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueYp)) {
            // Process Yp
            subDomain.setBoundaryConditionYp(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueZm)) {
            // Process Zm
            subDomain.setBoundaryConditionZm(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueZp)) {
            // Process Zp
            subDomain.setBoundaryConditionZp(bType);
        } else {
            // If not indentified throw an exception!!
            throw new XmlParseException("Unknown BoundaryConditionType: " + tempelement.getAttributeValue(XMLTags.BoundaryAttrTag));
        }
    }
    // process BoundaryConditionSpecs
    iterator = param.getChildren(XMLTags.BoundaryConditionSpecTag, vcNamespace).iterator();
    if (iterator != null) {
        while (iterator.hasNext()) {
            Element tempelement = (Element) iterator.next();
            try {
                subDomain.addBoundaryConditionSpec(getBoundaryConditionSpec(tempelement));
            } catch (MathException e) {
                e.printStackTrace();
                throw new XmlParseException("A MathException was fired when adding a BoundaryConditionSpec to the compartmentSubDomain " + name, e);
            }
        }
    }
    // process OdeEquations
    iterator = param.getChildren(XMLTags.OdeEquationTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addEquation(getOdeEquation(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding an OdeEquation to the compartmentSubDomain " + name, e);
        }
    }
    // process PdeEquations
    iterator = param.getChildren(XMLTags.PdeEquationTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addEquation(getPdeEquation(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding an PdeEquation to the compartmentSubDomain " + name, e);
        }
    }
    // Process VolumeRegionEquation
    iterator = param.getChildren(XMLTags.VolumeRegionEquationTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addEquation(getVolumeRegionEquation(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding a VolumeRegionEquation to the compartmentSubDomain " + name, e);
        }
    }
    // Process Variable initial conditions (added for stochastic algos)
    iterator = param.getChildren(XMLTags.VarIniCount_OldTag, vcNamespace).iterator();
    if (iterator != null) {
        while (iterator.hasNext()) {
            Element tempelement = (Element) iterator.next();
            try {
                subDomain.addVarIniCondition(getVarIniCount(tempelement, mathDesc));
            } catch (MathException e) {
                e.printStackTrace();
                throw new XmlParseException("A MathException was fired when adding a variable initial condition to the compartmentSubDomain " + name, e);
            } catch (ExpressionException e) {
                e.printStackTrace();
            }
        }
    }
    iterator = param.getChildren(XMLTags.VarIniCountTag, vcNamespace).iterator();
    if (iterator != null) {
        while (iterator.hasNext()) {
            Element tempelement = (Element) iterator.next();
            try {
                subDomain.addVarIniCondition(getVarIniCount(tempelement, mathDesc));
            } catch (MathException e) {
                e.printStackTrace();
                throw new XmlParseException("A MathException was fired when adding a variable initial condition to the compartmentSubDomain " + name, e);
            } catch (ExpressionException e) {
                e.printStackTrace();
            }
        }
    }
    iterator = param.getChildren(XMLTags.VarIniPoissonExpectedCountTag, vcNamespace).iterator();
    if (iterator != null) {
        while (iterator.hasNext()) {
            Element tempelement = (Element) iterator.next();
            try {
                subDomain.addVarIniCondition(getVarIniPoissonExpectedCount(tempelement, mathDesc));
            } catch (MathException e) {
                e.printStackTrace();
                throw new XmlParseException("A MathException was fired when adding a variable initial condition to the compartmentSubDomain " + name, e);
            } catch (ExpressionException e) {
                e.printStackTrace();
            }
        }
    }
    // 
    // Process JumpProcesses (added for stochastic algos)
    iterator = param.getChildren(XMLTags.JumpProcessTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addJumpProcess(getJumpProcess(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding a jump process to the compartmentSubDomain " + name, e);
        }
    }
    iterator = param.getChildren(XMLTags.ParticleJumpProcessTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addParticleJumpProcess(getParticleJumpProcess(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding a jump process to the compartmentSubDomain " + name, e);
        }
    }
    iterator = param.getChildren(XMLTags.ParticlePropertiesTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addParticleProperties(getParticleProperties(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding a jump process to the compartmentSubDomain " + name, e);
        }
    }
    // process ComputeCentroid "equations"
    iterator = param.getChildren(XMLTags.ComputeCentroidTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addEquation(getComputeCentroid(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding an ComputeCentroid 'equation' to the compartmentSubDomain " + name, e);
        }
    }
    // process ComputeMembraneMetric "equations"
    iterator = param.getChildren(XMLTags.ComputeMembraneMetricTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addEquation(getComputeMembraneMetric(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding an ComputeMembraneMetric 'equation' to the compartmentSubDomain " + name, e);
        }
    }
    // Process the FastSystem (if thre is)
    Element tempelement = param.getChild(XMLTags.FastSystemTag, vcNamespace);
    if (tempelement != null) {
        subDomain.setFastSystem(getFastSystem(tempelement, mathDesc));
    }
    return subDomain;
}

Example 30 with CompartmentSubDomain

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

the class XmlReader method getFilamentSubDomain.

/**
 * This method returns a FilamentSubDomain object from a XMl element.
 * Creation date: (5/18/2001 4:27:22 PM)
 * @return cbit.vcell.math.FilamentSubDomain
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private FilamentSubDomain getFilamentSubDomain(Element param, MathDescription mathDesc) throws XmlParseException {
    // get name
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    // get outside Compartment ref
    String outsideName = unMangle(param.getAttributeValue(XMLTags.OutsideCompartmentTag));
    CompartmentSubDomain outsideRef = (CompartmentSubDomain) mathDesc.getCompartmentSubDomain(outsideName);
    if (outsideRef == null) {
        throw new XmlParseException("The reference to the CompartmentSubDomain " + outsideName + ", could not be resolved!");
    }
    // *** create new filamentSubDomain object ***
    FilamentSubDomain filDomain = new FilamentSubDomain(name, outsideRef);
    // add OdeEquations
    Iterator<Element> iterator = param.getChildren(XMLTags.OdeEquationTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempElement = (Element) iterator.next();
        try {
            filDomain.addEquation(getOdeEquation(tempElement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("A MathException was fired when adding an OdeEquation to the FilamentSubDomain " + name, e);
        }
    }
    // Add the FastSytem
    filDomain.setFastSystem(getFastSystem(param.getChild(XMLTags.FastSystemTag, vcNamespace), mathDesc));
    return filDomain;
}