Examples with LocalParameter cbit.vcell.mapping.ParameterContext.LocalParameter used on opensource projects

Example 26 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class ElectricalStimulus method parameterVCMLSet.

/**
 * This method was created by a SmartGuide.
 * @param tokens java.util.StringTokenizer
 * @exception java.lang.Exception The exception description.
 */
public final void parameterVCMLSet(CommentStringTokenizer tokens) throws ExpressionException, PropertyVetoException {
    if (tokens == null) {
        return;
    }
    Vector<LocalParameter> esParametersV = new Vector<LocalParameter>();
    if (!tokens.nextToken().equalsIgnoreCase(VCMODL.ElectricalStimulus) || !tokens.nextToken().equalsIgnoreCase(GENERAL_PROTOCOL) || !tokens.nextToken().equalsIgnoreCase(VCMODL.BeginBlock)) {
        throw new RuntimeException(ElectricalStimulus.class.getName() + ".parameterVCMLRead, unexpected token ");
    }
    String token = null;
    ModelUnitSystem modelUnitSystem = simulationContext.getModel().getUnitSystem();
    while (tokens.hasMoreTokens()) {
        token = tokens.nextToken();
        if (token.equalsIgnoreCase(VCMODL.EndBlock)) {
            break;
        }
        if (token.equalsIgnoreCase(VCMODL.Parameter)) {
            String roleName = tokens.nextToken();
            ElectricalStimulusParameterType parameterType = null;
            for (ElectricalStimulusParameterType role : ElectricalStimulusParameterType.values()) {
                if (roleName.equals(role.databaseRoleTag)) {
                    parameterType = role;
                    break;
                }
            }
            if (parameterType == null) {
                throw new RuntimeException(ElectricalStimulus.class.getName() + ".parameterVCMLRead, unexpected token for roleName " + roleName);
            }
            String parameterName = tokens.nextToken();
            Expression exp = MathFunctionDefinitions.fixFunctionSyntax(tokens);
            String unitsString = tokens.nextToken();
            VCUnitDefinition unitDef = modelUnitSystem.getInstance_TBD();
            if (unitsString.startsWith("[")) {
                while (!unitsString.endsWith("]")) {
                    String tempToken = tokens.nextToken();
                    unitsString = unitsString + " " + tempToken;
                }
                // 
                // now string starts with '[' and ends with ']'
                // 
                unitDef = modelUnitSystem.getInstance(unitsString.substring(1, unitsString.length() - 1));
            } else {
                tokens.pushToken(unitsString);
            }
            LocalParameter esp = parameterContext.new LocalParameter(parameterName, exp, parameterType, unitDef, parameterType.databaseRoleTag);
            esParametersV.add(esp);
        } else {
            throw new RuntimeException(ElectricalStimulus.class.getName() + ".parameterVCMLRead, unexpected token for paramter tag " + token);
        }
    }
    if (esParametersV.size() > 0) {
        LocalParameter[] espArr = new LocalParameter[esParametersV.size()];
        esParametersV.copyInto(espArr);
        parameterContext.setLocalParameters(espArr);
    } else {
        parameterContext.setLocalParameters(null);
    }
}

Example 27 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class NetworkTransformer method applyKineticsExpressions.

// private Expression substituteFakeParameters(Expression paramExpression) throws ExpressionException {
// Expression newExp = new Expression(paramExpression);
// String[] fakeSymbols = paramExpression.getSymbols();
// for (String fakeSymbol : fakeSymbols){
// FakeReactionRuleRateParameter fakeParameter = FakeReactionRuleRateParameter.fromString(fakeSymbol);
// if (fakeParameter == null){
// throw new RuntimeException("unexpected identifier "+fakeSymbol+" in kinetic law during network generation");
// }
// LocalParameter localParameter = this.kineticsParameterMap.get(fakeParameter);
// Expression ruleExpression = localParameter.getExpression();
// newExp.substituteInPlace(new Expression(fakeSymbol), new Expression(ruleExpression));
// }
// return newExp;
// }
private Expression applyKineticsExpressions(BNGReaction bngReaction, KineticsParameter rateParameter, MassActionKinetics targetKinetics) throws ExpressionException {
    ReactionRule reactionRule = null;
    Expression paramExpression = bngReaction.getParamExpression();
    Expression newExp = new Expression(paramExpression);
    String[] fakeSymbols = paramExpression.getSymbols();
    for (String fakeSymbol : fakeSymbols) {
        FakeReactionRuleRateParameter fakeParameter = FakeReactionRuleRateParameter.fromString(fakeSymbol);
        if (fakeParameter == null) {
            throw new RuntimeException("unexpected identifier " + fakeSymbol + " in kinetic law during network generation");
        }
        LocalParameter localParameter = this.kineticsParameterMap.get(fakeParameter);
        System.out.println(localParameter.getNameScope());
        if (localParameter.getNameScope() instanceof ReactionRule.ReactionRuleNameScope) {
            reactionRule = ((ReactionRule.ReactionRuleNameScope) localParameter.getNameScope()).getReactionRule();
        }
        Expression ruleExpression = localParameter.getExpression();
        newExp.substituteInPlace(new Expression(fakeSymbol), new Expression(ruleExpression));
    }
    // 
    try {
        targetKinetics.setParameterValue(rateParameter, newExp);
    } catch (PropertyVetoException e) {
        e.printStackTrace();
        throw new RuntimeException("failed to set kinetics expression for reaction " + targetKinetics.getReactionStep().getName() + ": " + e.getMessage(), e);
    }
    // 
    if (reactionRule != null) {
        // try to set values from user-defined parameters into the target kinetics
        for (LocalParameter localParameter : reactionRule.getKineticLaw().getLocalParameters()) {
            if (localParameter.getRole() == RbmKineticLawParameterType.UserDefined) {
                KineticsParameter userDefinedParam = targetKinetics.getKineticsParameter(localParameter.getName());
                if (userDefinedParam != null) {
                    try {
                        targetKinetics.setParameterValue(userDefinedParam, localParameter.getExpression());
                    } catch (PropertyVetoException e) {
                        e.printStackTrace();
                        throw new RuntimeException("failed to set kinetics expression for reaction " + targetKinetics.getReactionStep().getName() + ": " + e.getMessage(), e);
                    }
                }
            }
        }
    }
    return newExp;
}

Example 28 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class AbstractMathMapping method getMathSymbol0.

/**
 * Substitutes appropriate variables for speciesContext bindings
 *
 * @return cbit.vcell.parser.Expression
 * @param origExp cbit.vcell.parser.Expression
 * @param structureMapping cbit.vcell.mapping.StructureMapping
 */
protected final String getMathSymbol0(SymbolTableEntry ste, GeometryClass geometryClass) throws MappingException {
    String steName = ste.getName();
    if (ste instanceof Kinetics.KineticsParameter) {
        Integer count = localNameCountHash.get(steName);
        if (count == null) {
            throw new MappingException("KineticsParameter " + steName + " not found in local name count");
        }
        if (count > 1 || steName.equals("J")) {
            return steName + "_" + ste.getNameScope().getName();
        // return getNameScope().getSymbolName(ste);
        } else {
            return steName;
        }
    }
    if (ste instanceof LocalParameter && ((LocalParameter) ste).getNameScope() instanceof ReactionRule.ReactionRuleNameScope) {
        Integer count = localNameCountHash.get(steName);
        if (count == null) {
            throw new MappingException("Reaction Rule Parameter " + steName + " not found in local name count");
        }
        if (count > 1 || steName.equals("J")) {
            return steName + "_" + ste.getNameScope().getName();
        // return getNameScope().getSymbolName(ste);
        } else {
            return steName;
        }
    }
    if (ste instanceof ProbabilityParameter) {
        // be careful here, to see if we need mangle the reaction name
        ProbabilityParameter probParm = (ProbabilityParameter) ste;
        return probParm.getName() + PARAMETER_PROBABLIITY_RATE_SUFFIX;
    }
    if (ste instanceof SpeciesConcentrationParameter) {
        SpeciesConcentrationParameter concParm = (SpeciesConcentrationParameter) ste;
        return concParm.getSpeciesContext().getName() + MATH_FUNC_SUFFIX_SPECIES_CONCENTRATION;
    }
    if (ste instanceof SpeciesCountParameter) {
        SpeciesCountParameter countParm = (SpeciesCountParameter) ste;
        return countParm.getSpeciesContext().getName() + MATH_VAR_SUFFIX_SPECIES_COUNT;
    }
    if (ste instanceof ObservableConcentrationParameter) {
        ObservableConcentrationParameter concParm = (ObservableConcentrationParameter) ste;
        return concParm.getObservable().getName() + MATH_FUNC_SUFFIX_SPECIES_CONCENTRATION;
    }
    if (ste instanceof ObservableCountParameter) {
        ObservableCountParameter countParm = (ObservableCountParameter) ste;
        return countParm.getObservable().getName() + MATH_VAR_SUFFIX_SPECIES_COUNT;
    }
    if (ste instanceof RbmObservable) {
        RbmObservable observable = (RbmObservable) ste;
        return observable.getName() + MATH_FUNC_SUFFIX_SPECIES_CONCENTRATION;
    }
    if (ste instanceof EventAssignmentOrRateRuleInitParameter) {
        EventAssignmentOrRateRuleInitParameter eventInitParm = (EventAssignmentOrRateRuleInitParameter) ste;
        // + MATH_FUNC_SUFFIX_EVENTASSIGN_OR_RATE_INIT;
        return eventInitParm.getName();
    }
    if (ste instanceof RateRuleRateParameter) {
        RateRuleRateParameter rateRuleRateParm = (RateRuleRateParameter) ste;
        // + MATH_FUNC_SUFFIX_RATERULE_RATE;
        return rateRuleRateParm.getName();
    }
    if (ste instanceof Model.ReservedSymbol) {
        return steName;
    }
    if (ste instanceof Membrane.MembraneVoltage) {
        return steName;
    }
    if (ste instanceof Structure.StructureSize) {
        Structure structure = ((Structure.StructureSize) ste).getStructure();
        StructureMapping.StructureMappingParameter sizeParameter = simContext.getGeometryContext().getStructureMapping(structure).getSizeParameter();
        return getMathSymbol(sizeParameter, geometryClass);
    }
    if (ste instanceof ProxyParameter) {
        ProxyParameter pp = (ProxyParameter) ste;
        return getMathSymbol0(pp.getTarget(), geometryClass);
    }
    // 
    if (ste instanceof ModelParameter) {
        ModelParameter mp = (ModelParameter) ste;
        return mp.getName();
    }
    if (ste instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
        SpeciesContextSpec.SpeciesContextSpecParameter scsParm = (SpeciesContextSpec.SpeciesContextSpecParameter) ste;
        SpeciesContext speciesContext = ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext();
        SpeciesContextMapping scm = getSpeciesContextMapping(speciesContext);
        String speciesContextVarName = null;
        if (scm.getVariable() != null) {
            speciesContextVarName = scm.getVariable().getName();
        } else {
            speciesContextVarName = speciesContext.getName();
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_InitialConcentration) {
            return speciesContextVarName + MATH_FUNC_SUFFIX_SPECIES_INIT_CONC_UNIT_PREFIX + TokenMangler.fixTokenStrict(scsParm.getUnitDefinition().getSymbol());
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_InitialCount) {
            return speciesContextVarName + MATH_FUNC_SUFFIX_SPECIES_INIT_COUNT;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_DiffusionRate) {
            return speciesContextVarName + PARAMETER_DIFFUSION_RATE_SUFFIX;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueXm) {
            return speciesContextVarName + PARAMETER_BOUNDARY_XM_SUFFIX;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueXp) {
            return speciesContextVarName + PARAMETER_BOUNDARY_XP_SUFFIX;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueYm) {
            return speciesContextVarName + PARAMETER_BOUNDARY_YM_SUFFIX;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueYp) {
            return speciesContextVarName + PARAMETER_BOUNDARY_YP_SUFFIX;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueZm) {
            return speciesContextVarName + PARAMETER_BOUNDARY_ZM_SUFFIX;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueZp) {
            return speciesContextVarName + PARAMETER_BOUNDARY_ZP_SUFFIX;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_VelocityX) {
            return speciesContextVarName + PARAMETER_VELOCITY_X_SUFFIX;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_VelocityY) {
            return speciesContextVarName + PARAMETER_VELOCITY_Y_SUFFIX;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_VelocityZ) {
            return speciesContextVarName + PARAMETER_VELOCITY_Z_SUFFIX;
        }
    }
    if (ste instanceof ElectricalDevice.ElectricalDeviceParameter) {
        ElectricalDevice.ElectricalDeviceParameter edParm = (ElectricalDevice.ElectricalDeviceParameter) ste;
        ElectricalDevice electricalDevice = (ElectricalDevice) edParm.getNameScope().getScopedSymbolTable();
        if (electricalDevice instanceof MembraneElectricalDevice) {
            String nameWithScope = ((MembraneElectricalDevice) electricalDevice).getMembraneMapping().getMembrane().getNameScope().getName();
            if (edParm.getRole() == ElectricalDevice.ROLE_TotalCurrent) {
                return PARAMETER_TOTAL_CURRENT_PREFIX + nameWithScope;
            }
            if (edParm.getRole() == ElectricalDevice.ROLE_TransmembraneCurrent) {
                return PARAMETER_TRANSMEMBRANE_CURRENT_PREFIX + nameWithScope;
            }
        // }else if (electricalDevice instanceof CurrentClampElectricalDevice) {
        // if (edParm.getRole()==ElectricalDevice.ROLE_TotalCurrentDensity){
        // return "I_"+((CurrentClampElectricalDevice)electricalDevice).getCurrentClampStimulus().getNameScope().getName();
        // }
        // if (edParm.getRole()==ElectricalDevice.ROLE_TransmembraneCurrentDensity){
        // return "F_"+((CurrentClampElectricalDevice)electricalDevice).getCurrentClampStimulus().getNameScope().getName();
        // }
        // }else if (electricalDevice instanceof VoltageClampElectricalDevice) {
        // if (edParm.getRole()==ElectricalDevice.ROLE_TotalCurrentDensity){
        // return "I_"+((VoltageClampElectricalDevice)electricalDevice).getVoltageClampStimulus().getNameScope().getName();
        // }
        // if (edParm.getRole()==ElectricalDevice.ROLE_TransmembraneCurrentDensity){
        // return "F_"+((VoltageClampElectricalDevice)electricalDevice).getVoltageClampStimulus().getNameScope().getName();
        // }
        }
    }
    if (ste instanceof LocalParameter && ((LocalParameter) ste).getNameScope() instanceof ElectricalStimulus.ElectricalStimulusNameScope) {
        LocalParameter esParm = (LocalParameter) ste;
        String nameWithScope = esParm.getNameScope().getName();
        if (esParm.getRole() == ElectricalStimulus.ElectricalStimulusParameterType.TotalCurrent) {
            return PARAMETER_TOTAL_CURRENT_PREFIX + nameWithScope;
        } else if (esParm.getRole() == ElectricalStimulus.ElectricalStimulusParameterType.Voltage) {
            return PARAMETER_VOLTAGE_PREFIX + nameWithScope;
        }
    }
    if (ste instanceof StructureMapping.StructureMappingParameter) {
        StructureMapping.StructureMappingParameter smParm = (StructureMapping.StructureMappingParameter) ste;
        Structure structure = ((StructureMapping) (smParm.getNameScope().getScopedSymbolTable())).getStructure();
        String nameWithScope = structure.getNameScope().getName();
        int role = smParm.getRole();
        if (role == StructureMapping.ROLE_InitialVoltage) {
            return smParm.getName();
        } else if (role == StructureMapping.ROLE_SpecificCapacitance) {
            return PARAMETER_SPECIFIC_CAPACITANCE_PREFIX + nameWithScope;
        } else if (role == StructureMapping.ROLE_Size) {
            if (simContext.getGeometry().getDimension() == 0) {
                // if geometry is compartmental, make sure compartment sizes are set if referenced in model.
                if (smParm.getExpression() == null || smParm.getExpression().isZero()) {
                    throw new MappingException("\nIn non-spatial application '" + getSimulationContext().getName() + "', " + "size of structure '" + structure.getName() + "' must be assigned a " + "positive value if referenced in the model.\n\nPlease go to 'Structure Mapping' tab to check the size.");
                }
            }
            return PARAMETER_SIZE_FUNCTION_PREFIX + nameWithScope;
        } else if (role == StructureMapping.ROLE_AreaPerUnitArea) {
            return "AreaPerUnitArea_" + nameWithScope;
        } else if (role == StructureMapping.ROLE_AreaPerUnitVolume) {
            return "AreaPerUnitVolume_" + nameWithScope;
        } else if (role == StructureMapping.ROLE_VolumePerUnitArea) {
            return "VolumePerUnitArea_" + nameWithScope;
        } else if (role == StructureMapping.ROLE_VolumePerUnitVolume) {
            return "VolumePerUnitVolume_" + nameWithScope;
        }
    }
    // 
    if (ste instanceof SpeciesContext) {
        SpeciesContext sc = (SpeciesContext) ste;
        SpeciesContextMapping scm = getSpeciesContextMapping(sc);
        if (scm == null) {
            throw new RuntimeException("Species '" + sc.getName() + "' is referenced in model but may have been deleted. " + "Find its references in '" + GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_BIOMODEL_PARAMETERS + "'.");
        }
        // 
        if (geometryClass instanceof SubVolume) {
            // 
            if (scm.getVariable() != null && !scm.getVariable().getName().equals(steName)) {
                return scm.getVariable().getName();
            }
        // 
        // for reactions within a surface, may need "_INSIDE" or "_OUTSIDE" for jump condition
        // 
        } else if (geometryClass instanceof SurfaceClass) {
            // 
            // if the speciesContext is also within the surface, replace SpeciesContext name with Variable name
            // 
            StructureMapping sm = simContext.getGeometryContext().getStructureMapping(sc.getStructure());
            if (sm.getGeometryClass() == geometryClass) {
                if (scm.getVariable() != null && !(scm.getVariable().getName().equals(ste.getName()))) {
                    return scm.getVariable().getName();
                }
            // 
            // if the speciesContext is "inside" or "outside" the membrane
            // 
            } else if (sm.getGeometryClass() instanceof SubVolume && ((SurfaceClass) geometryClass).isAdjacentTo((SubVolume) sm.getGeometryClass())) {
                SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
                if (!scs.isConstant()) {
                    if (!scs.isDiffusing() && !scs.isWellMixed()) {
                        throw new MappingException("Enable diffusion in Application '" + simContext.getName() + "'. This must be done for any species (e.g '" + sc.getName() + "') in flux reactions.\n\n" + "To save or run simulations, set the diffusion rate to a non-zero " + "value in Initial Conditions or disable those reactions in Specifications->Reactions.");
                    }
                }
                if (scm.getVariable() != null) {
                    return scm.getVariable().getName();
                }
            } else {
                throw new MappingException("species '" + sc.getName() + "' interacts with surface '" + geometryClass.getName() + "', but is not mapped spatially adjacent");
            }
        }
    }
    return getNameScope().getSymbolName(ste);
}

Example 29 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class AbstractMathMapping method refreshLocalNameCount.

protected void refreshLocalNameCount() {
    localNameCountHash.clear();
    ReactionStep[] reactionSteps = simContext.getModel().getReactionSteps();
    for (int j = 0; j < reactionSteps.length; j++) {
        KineticsParameter[] params = reactionSteps[j].getKinetics().getKineticsParameters();
        for (KineticsParameter kp : params) {
            String name = kp.getName();
            if (localNameCountHash.containsKey(name)) {
                localNameCountHash.put(name, localNameCountHash.get(name) + 1);
            } else {
                localNameCountHash.put(name, 1);
            }
        }
    }
    List<ReactionRule> reactionRules = simContext.getModel().getRbmModelContainer().getReactionRuleList();
    for (ReactionRule reactionRule : reactionRules) {
        LocalParameter[] params = reactionRule.getKineticLaw().getLocalParameters();
        for (LocalParameter kp : params) {
            String name = kp.getName();
            if (localNameCountHash.containsKey(name)) {
                localNameCountHash.put(name, localNameCountHash.get(name) + 1);
            } else {
                localNameCountHash.put(name, 1);
            }
        }
    }
    SpeciesContext[] scs = simContext.getModel().getSpeciesContexts();
    for (SpeciesContext sc : scs) {
        String name = sc.getName();
        if (localNameCountHash.containsKey(name)) {
            localNameCountHash.put(name, localNameCountHash.get(name) + 1);
        } else {
            localNameCountHash.put(name, 1);
        }
    }
    ModelParameter[] mps = simContext.getModel().getModelParameters();
    for (ModelParameter mp : mps) {
        String name = mp.getName();
        if (localNameCountHash.containsKey(name)) {
            localNameCountHash.put(name, localNameCountHash.get(name) + 1);
        } else {
            localNameCountHash.put(name, 1);
        }
    }
}

Example 30 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class BioEvent method setTimeList.

public void setTimeList(Expression[] listExps) throws ExpressionBindingException, PropertyVetoException {
    if (triggerType != TriggerType.ListOfTimes) {
        throw new RuntimeException("list of times only available for " + TriggerType.ListOfTimes.name() + " trigger type");
    }
    // 
    // remove any existing TimeListItem parameters
    // 
    ArrayList<LocalParameter> parameters = new ArrayList<LocalParameter>();
    for (LocalParameter p : getEventParameters()) {
        if (p.getRole() != BioEventParameterType.TimeListItem) {
            parameters.add(p);
        }
    }
    // 
    // generate new TimeListItem parameters from function arguments
    // 
    VCUnitDefinition timeUnit = getSimulationContext().getModel().getUnitSystem().getTimeUnit();
    String name = "t0";
    for (Expression exp : listExps) {
        String description = BioEventParameterType.TimeListItem.description;
        parameters.add(parameterContext.new LocalParameter(name, exp, BioEventParameterType.TimeListItem, timeUnit, description));
        name = TokenMangler.getNextEnumeratedToken(name);
    }
    setParameters(parameters.toArray(new LocalParameter[0]));
}