Examples with SpeciesContextSpec cbit.vcell.mapping.SpeciesContextSpec used on opensource projects

Example 51 with SpeciesContextSpec

use of cbit.vcell.mapping.SpeciesContextSpec 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 52 with SpeciesContextSpec

use of cbit.vcell.mapping.SpeciesContextSpec in project vcell by virtualcell.

the class SBMLExporter method addSpecies.

/**
 * addSpecies comment.
 * @throws XMLStreamException
 * @throws SbmlException
 */
protected void addSpecies() throws XMLStreamException, SbmlException {
    Model vcModel = vcBioModel.getModel();
    SpeciesContext[] vcSpeciesContexts = vcModel.getSpeciesContexts();
    for (int i = 0; i < vcSpeciesContexts.length; i++) {
        org.sbml.jsbml.Species sbmlSpecies = sbmlModel.createSpecies();
        sbmlSpecies.setId(vcSpeciesContexts[i].getName());
        // Assuming that at this point, the compartment(s) for the model are already filled in.
        Compartment compartment = sbmlModel.getCompartment(TokenMangler.mangleToSName(vcSpeciesContexts[i].getStructure().getName()));
        if (compartment != null) {
            sbmlSpecies.setCompartment(compartment.getId());
        }
        // 'hasSubstanceOnly' field will be 'false', since VC deals only with initial concentrations and not initial amounts.
        sbmlSpecies.setHasOnlySubstanceUnits(false);
        // Get (and set) the initial concentration value
        if (getSelectedSimContext() == null) {
            throw new RuntimeException("No simcontext (application) specified; Cannot proceed.");
        }
        // Get the speciesContextSpec in the simContext corresponding to the 'speciesContext'; and extract its initial concentration value.
        SpeciesContextSpec vcSpeciesContextsSpec = getSelectedSimContext().getReactionContext().getSpeciesContextSpec(vcSpeciesContexts[i]);
        // we need to convert concentration from uM -> molecules/um3; this can be achieved by dividing by KMOLE.
        try {
            sbmlSpecies.setInitialConcentration(vcSpeciesContextsSpec.getInitialConditionParameter().getExpression().evaluateConstant());
        } catch (cbit.vcell.parser.ExpressionException e) {
            // If exporting to L2V3, if species concentration is not an expr with x, y, z or other species, add as InitialAssignment, else complain.
            if (vcSpeciesContextsSpec.getInitialConditionParameter().getExpression() != null) {
                Expression initConcExpr = vcSpeciesContextsSpec.getInitialConditionParameter().getExpression();
                if ((sbmlLevel == 2 && sbmlVersion >= 3) || (sbmlLevel > 2)) {
                    // L2V3 and above - add expression as init assignment
                    ASTNode initAssgnMathNode = getFormulaFromExpression(initConcExpr);
                    InitialAssignment initAssignment = sbmlModel.createInitialAssignment();
                    initAssignment.setSymbol(vcSpeciesContexts[i].getName());
                    initAssignment.setMath(initAssgnMathNode);
                } else {
                    // L2V1 (or L1V2 also??)
                    // L2V1 (and L1V2?) and species is 'fixed' (constant), and not fn of x,y,z, other sp, add expr as assgn rule
                    ASTNode assgnRuleMathNode = getFormulaFromExpression(initConcExpr);
                    AssignmentRule assgnRule = sbmlModel.createAssignmentRule();
                    assgnRule.setVariable(vcSpeciesContexts[i].getName());
                    assgnRule.setMath(assgnRuleMathNode);
                }
            }
        }
        // Get (and set) the boundary condition value
        boolean bBoundaryCondition = getBoundaryCondition(vcSpeciesContexts[i]);
        sbmlSpecies.setBoundaryCondition(bBoundaryCondition);
        // mandatory for L3, optional for L2
        sbmlSpecies.setConstant(false);
        // set species substance units as 'molecules' - same as defined in the model; irrespective of it is in surface or volume.
        UnitDefinition unitDefn = getOrCreateSBMLUnit(sbmlExportSpec.getSubstanceUnits());
        sbmlSpecies.setSubstanceUnits(unitDefn);
        // need to do the following if exporting to SBML spatial
        if (bSpatial) {
            // Required for setting BoundaryConditions : structureMapping for vcSpeciesContext[i] & sbmlGeometry.coordinateComponents
            StructureMapping sm = getSelectedSimContext().getGeometryContext().getStructureMapping(vcSpeciesContexts[i].getStructure());
            SpatialModelPlugin mplugin = (SpatialModelPlugin) sbmlModel.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
            org.sbml.jsbml.ext.spatial.Geometry sbmlGeometry = mplugin.getGeometry();
            CoordinateComponent ccX = sbmlGeometry.getListOfCoordinateComponents().get(vcModel.getX().getName());
            CoordinateComponent ccY = sbmlGeometry.getListOfCoordinateComponents().get(vcModel.getY().getName());
            CoordinateComponent ccZ = sbmlGeometry.getListOfCoordinateComponents().get(vcModel.getZ().getName());
            // add diffusion, advection, boundary condition parameters for species, if they exist
            Parameter[] scsParams = vcSpeciesContextsSpec.getParameters();
            if (scsParams != null) {
                for (int j = 0; j < scsParams.length; j++) {
                    if (scsParams[j] != null) {
                        SpeciesContextSpecParameter scsParam = (SpeciesContextSpecParameter) scsParams[j];
                        // no need to add parameters in SBML for init conc or init count
                        int role = scsParam.getRole();
                        switch(role) {
                            case SpeciesContextSpec.ROLE_BoundaryValueXm:
                                {
                                    break;
                                }
                            case SpeciesContextSpec.ROLE_BoundaryValueXp:
                                {
                                    break;
                                }
                            case SpeciesContextSpec.ROLE_BoundaryValueYm:
                                {
                                    break;
                                }
                            case SpeciesContextSpec.ROLE_BoundaryValueYp:
                                {
                                    break;
                                }
                            case SpeciesContextSpec.ROLE_BoundaryValueZm:
                                {
                                    break;
                                }
                            case SpeciesContextSpec.ROLE_BoundaryValueZp:
                                {
                                    break;
                                }
                            case SpeciesContextSpec.ROLE_DiffusionRate:
                                {
                                    break;
                                }
                            case SpeciesContextSpec.ROLE_InitialConcentration:
                                {
                                    // done elsewhere??
                                    continue;
                                // break;
                                }
                            case SpeciesContextSpec.ROLE_InitialCount:
                                {
                                    // done elsewhere??
                                    continue;
                                // break;
                                }
                            case SpeciesContextSpec.ROLE_VelocityX:
                                {
                                    break;
                                }
                            case SpeciesContextSpec.ROLE_VelocityY:
                                {
                                    break;
                                }
                            case SpeciesContextSpec.ROLE_VelocityZ:
                                {
                                    break;
                                }
                            default:
                                {
                                    throw new RuntimeException("SpeciesContext Specification parameter with role " + SpeciesContextSpec.RoleNames[role] + " not yet supported for SBML export");
                                }
                        }
                        // if diffusion is 0 && vel terms are not specified, boundary condition not present
                        if (vcSpeciesContextsSpec.isAdvecting() || vcSpeciesContextsSpec.isDiffusing()) {
                            Expression diffExpr = vcSpeciesContextsSpec.getDiffusionParameter().getExpression();
                            boolean bDiffExprNull = (diffExpr == null);
                            boolean bDiffExprIsZero = false;
                            if (!bDiffExprNull && diffExpr.isNumeric()) {
                                try {
                                    bDiffExprIsZero = (diffExpr.evaluateConstant() == 0.0);
                                } catch (Exception e) {
                                    e.printStackTrace(System.out);
                                    throw new RuntimeException("Unable to evalute numeric value of diffusion parameter for speciesContext '" + vcSpeciesContexts[i] + "'.");
                                }
                            }
                            boolean bDiffusionZero = (bDiffExprNull || bDiffExprIsZero);
                            Expression velX_Expr = vcSpeciesContextsSpec.getVelocityXParameter().getExpression();
                            SpatialQuantity[] velX_Quantities = vcSpeciesContextsSpec.getVelocityQuantities(QuantityComponent.X);
                            boolean bVelX_ExprIsNull = (velX_Expr == null && velX_Quantities.length == 0);
                            Expression velY_Expr = vcSpeciesContextsSpec.getVelocityYParameter().getExpression();
                            SpatialQuantity[] velY_Quantities = vcSpeciesContextsSpec.getVelocityQuantities(QuantityComponent.Y);
                            boolean bVelY_ExprIsNull = (velY_Expr == null && velY_Quantities.length == 0);
                            Expression velZ_Expr = vcSpeciesContextsSpec.getVelocityZParameter().getExpression();
                            SpatialQuantity[] velZ_Quantities = vcSpeciesContextsSpec.getVelocityQuantities(QuantityComponent.Z);
                            boolean bVelZ_ExprIsNull = (velZ_Expr == null && velZ_Quantities.length == 0);
                            boolean bAdvectionNull = (bVelX_ExprIsNull && bVelY_ExprIsNull && bVelZ_ExprIsNull);
                            if (bDiffusionZero && bAdvectionNull) {
                                continue;
                            }
                        }
                        // for example, if scsParam is BC_Zm and if coordinateComponent 'ccZ' is null, no SBML parameter should be created for BC_Zm
                        if ((((role == SpeciesContextSpec.ROLE_BoundaryValueXm) || (role == SpeciesContextSpec.ROLE_BoundaryValueXp)) && (ccX == null)) || (((role == SpeciesContextSpec.ROLE_BoundaryValueYm) || (role == SpeciesContextSpec.ROLE_BoundaryValueYp)) && (ccY == null)) || (((role == SpeciesContextSpec.ROLE_BoundaryValueZm) || (role == SpeciesContextSpec.ROLE_BoundaryValueZp)) && (ccZ == null))) {
                            continue;
                        }
                        org.sbml.jsbml.Parameter sbmlParam = createSBMLParamFromSpeciesParam(vcSpeciesContexts[i], (SpeciesContextSpecParameter) scsParams[j]);
                        if (sbmlParam != null) {
                            BoundaryConditionType vcBCType_Xm = vcSelectedSimContext.getGeometryContext().getStructureMapping(vcSpeciesContexts[i].getStructure()).getBoundaryConditionTypeXm();
                            BoundaryConditionType vcBCType_Xp = vcSelectedSimContext.getGeometryContext().getStructureMapping(vcSpeciesContexts[i].getStructure()).getBoundaryConditionTypeXp();
                            BoundaryConditionType vcBCType_Ym = vcSelectedSimContext.getGeometryContext().getStructureMapping(vcSpeciesContexts[i].getStructure()).getBoundaryConditionTypeYm();
                            BoundaryConditionType vcBCType_Yp = vcSelectedSimContext.getGeometryContext().getStructureMapping(vcSpeciesContexts[i].getStructure()).getBoundaryConditionTypeYp();
                            BoundaryConditionType vcBCType_Zm = vcSelectedSimContext.getGeometryContext().getStructureMapping(vcSpeciesContexts[i].getStructure()).getBoundaryConditionTypeZm();
                            BoundaryConditionType vcBCType_Zp = vcSelectedSimContext.getGeometryContext().getStructureMapping(vcSpeciesContexts[i].getStructure()).getBoundaryConditionTypeZp();
                            SpatialParameterPlugin spplugin = (SpatialParameterPlugin) sbmlParam.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
                            if (role == SpeciesContextSpec.ROLE_DiffusionRate) {
                                // set diffusionCoefficient element in SpatialParameterPlugin for param
                                DiffusionCoefficient sbmlDiffCoeff = new DiffusionCoefficient();
                                sbmlDiffCoeff.setVariable(vcSpeciesContexts[i].getName());
                                sbmlDiffCoeff.setDiffusionKind(DiffusionKind.isotropic);
                                sbmlDiffCoeff.setSpeciesRef(vcSpeciesContexts[i].getName());
                                spplugin.setParamType(sbmlDiffCoeff);
                            }
                            if ((role == SpeciesContextSpec.ROLE_BoundaryValueXm) && (ccX != null)) {
                                // set BoundaryCondn Xm element in SpatialParameterPlugin for param
                                BoundaryCondition sbmlBCXm = new BoundaryCondition();
                                spplugin.setParamType(sbmlBCXm);
                                sbmlBCXm.setType(getBoundaryConditionKind(vcBCType_Xm));
                                sbmlBCXm.setVariable(vcSpeciesContexts[i].getName());
                                sbmlBCXm.setCoordinateBoundary(ccX.getBoundaryMinimum().getId());
                            }
                            if ((role == SpeciesContextSpec.ROLE_BoundaryValueXp) && (ccX != null)) {
                                // set BoundaryCondn Xp element in SpatialParameterPlugin for param
                                BoundaryCondition sbmlBCXp = new BoundaryCondition();
                                spplugin.setParamType(sbmlBCXp);
                                sbmlBCXp.setType(getBoundaryConditionKind(vcBCType_Xp));
                                sbmlBCXp.setVariable(vcSpeciesContexts[i].getName());
                                sbmlBCXp.setType(sm.getBoundaryConditionTypeXp().boundaryTypeStringValue());
                                sbmlBCXp.setCoordinateBoundary(ccX.getBoundaryMaximum().getId());
                            }
                            if ((role == SpeciesContextSpec.ROLE_BoundaryValueYm) && (ccY != null)) {
                                // set BoundaryCondn Ym element in SpatialParameterPlugin for param
                                BoundaryCondition sbmlBCYm = new BoundaryCondition();
                                spplugin.setParamType(sbmlBCYm);
                                sbmlBCYm.setType(getBoundaryConditionKind(vcBCType_Yp));
                                sbmlBCYm.setVariable(vcSpeciesContexts[i].getName());
                                sbmlBCYm.setType(sm.getBoundaryConditionTypeYm().boundaryTypeStringValue());
                                sbmlBCYm.setCoordinateBoundary(ccY.getBoundaryMinimum().getId());
                            }
                            if ((role == SpeciesContextSpec.ROLE_BoundaryValueYp) && (ccY != null)) {
                                // set BoundaryCondn Yp element in SpatialParameterPlugin for param
                                BoundaryCondition sbmlBCYp = new BoundaryCondition();
                                spplugin.setParamType(sbmlBCYp);
                                sbmlBCYp.setType(getBoundaryConditionKind(vcBCType_Yp));
                                sbmlBCYp.setVariable(vcSpeciesContexts[i].getName());
                                sbmlBCYp.setType(sm.getBoundaryConditionTypeYp().boundaryTypeStringValue());
                                sbmlBCYp.setCoordinateBoundary(ccY.getBoundaryMaximum().getId());
                            }
                            if ((role == SpeciesContextSpec.ROLE_BoundaryValueZm) && (ccZ != null)) {
                                // set BoundaryCondn Zm element in SpatialParameterPlugin for param
                                BoundaryCondition sbmlBCZm = new BoundaryCondition();
                                spplugin.setParamType(sbmlBCZm);
                                sbmlBCZm.setType(getBoundaryConditionKind(vcBCType_Zm));
                                sbmlBCZm.setVariable(vcSpeciesContexts[i].getName());
                                sbmlBCZm.setType(sm.getBoundaryConditionTypeZm().boundaryTypeStringValue());
                                sbmlBCZm.setCoordinateBoundary(ccZ.getBoundaryMinimum().getId());
                            }
                            if ((role == SpeciesContextSpec.ROLE_BoundaryValueZp) && (ccZ != null)) {
                                // set BoundaryCondn Zp element in SpatialParameterPlugin for param
                                BoundaryCondition sbmlBCZp = new BoundaryCondition();
                                spplugin.setParamType(sbmlBCZp);
                                sbmlBCZp.setType(getBoundaryConditionKind(vcBCType_Zp));
                                sbmlBCZp.setVariable(vcSpeciesContexts[i].getName());
                                sbmlBCZp.setType(sm.getBoundaryConditionTypeZp().boundaryTypeStringValue());
                                sbmlBCZp.setCoordinateBoundary(ccZ.getBoundaryMaximum().getId());
                            }
                            if (role == SpeciesContextSpec.ROLE_VelocityX) {
                                // set advectionCoeff X element in SpatialParameterPlugin for param
                                AdvectionCoefficient sbmlAdvCoeffX = new AdvectionCoefficient();
                                spplugin.setParamType(sbmlAdvCoeffX);
                                sbmlAdvCoeffX.setVariable(vcSpeciesContexts[i].getName());
                                sbmlAdvCoeffX.setCoordinate(CoordinateKind.cartesianX);
                            }
                            if (role == SpeciesContextSpec.ROLE_VelocityY) {
                                // set advectionCoeff Y element in SpatialParameterPlugin for param
                                AdvectionCoefficient sbmlAdvCoeffY = new AdvectionCoefficient();
                                spplugin.setParamType(sbmlAdvCoeffY);
                                sbmlAdvCoeffY.setVariable(vcSpeciesContexts[i].getName());
                                sbmlAdvCoeffY.setCoordinate(CoordinateKind.cartesianY);
                            }
                            if (role == SpeciesContextSpec.ROLE_VelocityZ) {
                                // set advectionCoeff Z element in SpatialParameterPlugin for param
                                AdvectionCoefficient sbmlAdvCoeffZ = new AdvectionCoefficient();
                                spplugin.setParamType(sbmlAdvCoeffZ);
                                sbmlAdvCoeffZ.setVariable(vcSpeciesContexts[i].getName());
                                sbmlAdvCoeffZ.setCoordinate(CoordinateKind.cartesianZ);
                            }
                        }
                    // if sbmlParam != null
                    }
                // if scsParams[j] != null
                }
            // end for scsParams
            }
        // end scsParams != null
        }
        // end if (bSpatial)
        // Add the common name of species to annotation, and add an annotation element to the species.
        // This is required later while trying to read in fluxes ...
        // new Element(XMLTags.VCellRelatedInfoTag, sbml_vcml_ns);
        Element sbmlImportRelatedElement = null;
        // Element speciesElement = new Element(XMLTags.SpeciesTag, sbml_vcml_ns);
        // speciesElement.setAttribute(XMLTags.NameAttrTag, TokenMangler.mangleToSName(vcSpeciesContexts[i].getSpecies().getCommonName()));
        // sbmlImportRelatedElement.addContent(speciesElement);
        // Get RDF annotation for species from SBMLAnnotationUtils
        sbmlAnnotationUtil.writeAnnotation(vcSpeciesContexts[i].getSpecies(), sbmlSpecies, sbmlImportRelatedElement);
        // Now set notes,
        sbmlAnnotationUtil.writeNotes(vcSpeciesContexts[i].getSpecies(), sbmlSpecies);
    }
}

Example 53 with SpeciesContextSpec

use of cbit.vcell.mapping.SpeciesContextSpec 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 54 with SpeciesContextSpec

use of cbit.vcell.mapping.SpeciesContextSpec in project vcell by virtualcell.

the class SBMLImporter method setSpeciesInitialConditions.

/**
 * setSpeciesInitialConditions : called after speciesContexts and global
 * parameters have been set. Checks for init conditions set on species in
 * the Sbml model, and if it is set using an assignment rule, obtain the
 * corresponding expression. Obtain the sbml -> vc unit conversion factor
 * for species concentrations to adjust the species initial condition
 * units/factor.
 */
private void setSpeciesInitialConditions() {
    try {
        // fill in SpeciesContextSpec for each speciesContext
        Model vcModel = vcBioModel.getSimulationContext(0).getModel();
        SpeciesContext[] vcSpeciesContexts = vcModel.getSpeciesContexts();
        for (int i = 0; i < vcSpeciesContexts.length; i++) {
            org.sbml.jsbml.Species sbmlSpecies = (org.sbml.jsbml.Species) sbmlModel.getSpecies(vcSpeciesContexts[i].getName());
            // Sometimes, the species name can be null or a blank string; in
            // that case, use species id as the name.
            String speciesName = sbmlSpecies.getId();
            Compartment compartment = (Compartment) sbmlModel.getCompartment(sbmlSpecies.getCompartment());
            Expression initExpr = null;
            if (sbmlSpecies.isSetInitialConcentration()) {
                // If initial
                // Concentration
                // is set
                Expression initConcentration = new Expression(sbmlSpecies.getInitialConcentration());
                // check if initConc is set by a (assignment) rule. That
                // takes precedence over initConc value set on species.
                initExpr = getValueFromAssignmentRule(speciesName);
                if (initExpr == null) {
                    initExpr = new Expression(initConcentration);
                }
            } else if (sbmlSpecies.isSetInitialAmount()) {
                // If initial
                // amount is set
                double initAmount = sbmlSpecies.getInitialAmount();
                // initConcentration. Else, throw exception.
                if (compartment.isSetSize()) {
                    double compartmentSize = compartment.getSize();
                    Expression initConcentration = new Expression(0.0);
                    if (compartmentSize != 0.0) {
                        initConcentration = new Expression(initAmount / compartmentSize);
                    } else {
                        logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.UnitError, "compartment '" + compartment.getId() + "' has zero size, unable to determine initial concentration for species " + speciesName);
                    }
                    // check if initConc is set by a (assignment) rule. That
                    // takes precedence over initConc/initAmt value set on
                    // species.
                    initExpr = getValueFromAssignmentRule(speciesName);
                    if (initExpr == null) {
                        initExpr = new Expression(initConcentration);
                    }
                } else {
                    logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.SpeciesError, " Compartment '" + compartment.getId() + "' size not set or is defined by a rule; cannot calculate initConc.");
                }
            } else {
                // initConc/initAmt not set; check if species has a
                // (assignment) rule.
                initExpr = getValueFromAssignmentRule(speciesName);
                if (initExpr == null) {
                    // warning and set it to 0.0
                    if (sbmlModel.getInitialAssignment(speciesName) == null) {
                        localIssueList.add(new Issue(new SBMLIssueSource(sbmlModel.getSpecies(speciesName)), issueContext, IssueCategory.SBMLImport_MissingSpeciesInitCondition, "no initial condition for species " + speciesName + ", assuming 0.0", Issue.SEVERITY_WARNING));
                    // logger.sendMessage(VCLogger.Priority.MediumPriority,
                    // VCLogger.ErrorType.UnitError,
                    // "no initial condition for species "+speciesName+", assuming 0.0");
                    }
                    initExpr = new Expression(0.0);
                }
            }
            // similar to the conversion that is done in reactions.
            if (initExpr != null) {
                // initExpr will be changed
                initExpr = adjustExpression(initExpr, vcModel);
            }
            // If any of the symbols in the expression for speciesConc is a
            // rule, expand it.
            substituteGlobalParamRulesInPlace(initExpr, false);
            SpeciesContextSpec speciesContextSpec = vcBioModel.getSimulationContext(0).getReactionContext().getSpeciesContextSpec(vcSpeciesContexts[i]);
            speciesContextSpec.getInitialConditionParameter().setExpression(initExpr);
            speciesContextSpec.setConstant(sbmlSpecies.getBoundaryCondition() || sbmlSpecies.getConstant());
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
        throw new SBMLImportException("Error setting initial condition for species context; " + e.getMessage(), e);
    }
}

Example 55 with SpeciesContextSpec

use of cbit.vcell.mapping.SpeciesContextSpec in project vcell by virtualcell.

the class SimulationContextDbDriver method insertSpeciesContextSpecsSQL.

/**
 * This method was created in VisualAge.
 * @param con java.sql.Connection
 * @param simContextKey cbit.sql.KeyValue
 * @param simContext cbit.vcell.mapping.SimulationContext
 */
private void insertSpeciesContextSpecsSQL(Connection con, KeyValue simContextKey, SimulationContext simContext, Model updatedModel) throws SQLException {
    String sql;
    SpeciesContextSpec[] speciesContextSpecs = simContext.getReactionContext().getSpeciesContextSpecs();
    for (int i = 0; i < speciesContextSpecs.length; i++) {
        SpeciesContextSpec speciesContextSpec = speciesContextSpecs[i];
        KeyValue scKey = updatedModel.getSpeciesContext(speciesContextSpec.getSpeciesContext().getName()).getKey();
        KeyValue newSpeciesContextSpecKey = keyFactory.getNewKey(con);
        // 
        sql = "INSERT INTO " + speciesContextSpecTable.getTableName() + " " + speciesContextSpecTable.getSQLColumnList() + " VALUES " + speciesContextSpecTable.getSQLValueList(newSpeciesContextSpecKey, simContextKey, speciesContextSpec, scKey);
        // System.out.println(sql);
        updateCleanSQL(con, sql);
    }
}