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Example 11 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class SBMLExporter method addRateRules.

/**
 * Export rate rules
 */
protected void addRateRules() {
    RateRule[] vcRateRules = getSelectedSimContext().getRateRules();
    if (vcRateRules != null) {
        for (RateRule vcRateRule : vcRateRules) {
            // set name
            org.sbml.jsbml.RateRule sbmlRateRule = sbmlModel.createRateRule();
            sbmlRateRule.setId(vcRateRule.getName());
            // set rate rule variable
            sbmlRateRule.setVariable(vcRateRule.getRateRuleVar().getName());
            // set rate rule math/expression
            Expression rateRuleExpr = vcRateRule.getRateRuleExpression();
            ASTNode math = getFormulaFromExpression(rateRuleExpr);
            sbmlRateRule.setMath(math);
        // set unit?? Same as rate rule var (symbolTableEntry) unit?
        }
    }
}
Also used : Expression(cbit.vcell.parser.Expression) ASTNode(org.sbml.jsbml.ASTNode) RateRule(cbit.vcell.mapping.RateRule)

Example 12 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class SBMLExporter method addCompartments.

/**
 * addCompartments comment.
 * @throws XMLStreamException
 * @throws SbmlException
 */
protected void addCompartments() throws XMLStreamException, SbmlException {
    Model vcModel = vcBioModel.getModel();
    cbit.vcell.model.Structure[] vcStructures = vcModel.getStructures();
    for (int i = 0; i < vcStructures.length; i++) {
        Compartment sbmlCompartment = sbmlModel.createCompartment();
        sbmlCompartment.setId(TokenMangler.mangleToSName(vcStructures[i].getName()));
        sbmlCompartment.setName(vcStructures[i].getName());
        VCUnitDefinition sbmlSizeUnit = null;
        StructureTopology structTopology = getSelectedSimContext().getModel().getStructureTopology();
        Structure parentStructure = structTopology.getParentStructure(vcStructures[i]);
        if (vcStructures[i] instanceof Feature) {
            sbmlCompartment.setSpatialDimensions(3);
            String outside = null;
            if (parentStructure != null) {
                outside = TokenMangler.mangleToSName(parentStructure.getName());
            }
            if (outside != null) {
                if (outside.length() > 0) {
                    sbmlCompartment.setOutside(outside);
                }
            }
            sbmlSizeUnit = sbmlExportSpec.getVolumeUnits();
            UnitDefinition unitDefn = getOrCreateSBMLUnit(sbmlSizeUnit);
            sbmlCompartment.setUnits(unitDefn);
        } else if (vcStructures[i] instanceof Membrane) {
            Membrane vcMembrane = (Membrane) vcStructures[i];
            sbmlCompartment.setSpatialDimensions(2);
            Feature outsideFeature = structTopology.getOutsideFeature(vcMembrane);
            if (outsideFeature != null) {
                sbmlCompartment.setOutside(TokenMangler.mangleToSName(outsideFeature.getName()));
                sbmlSizeUnit = sbmlExportSpec.getAreaUnits();
                UnitDefinition unitDefn = getOrCreateSBMLUnit(sbmlSizeUnit);
                sbmlCompartment.setUnits(unitDefn);
            } else if (lg.isEnabledFor(Level.WARN)) {
                lg.warn(this.sbmlModel.getName() + " membrame " + vcMembrane.getName() + " has not outside feature");
            }
        }
        sbmlCompartment.setConstant(true);
        StructureMapping vcStructMapping = getSelectedSimContext().getGeometryContext().getStructureMapping(vcStructures[i]);
        try {
            if (vcStructMapping.getSizeParameter().getExpression() != null) {
                sbmlCompartment.setSize(vcStructMapping.getSizeParameter().getExpression().evaluateConstant());
            } else {
            // really no need to set sizes of compartments in spatial ..... ????
            // throw new RuntimeException("Compartment size not set for compartment \"" + vcStructures[i].getName() + "\" ; Please set size and try exporting again.");
            }
        } catch (cbit.vcell.parser.ExpressionException e) {
            // If it is in the catch block, it means that the compartment size was probably not a double, but an assignment.
            // Check if the expression for the compartment size is not null and add it as an assignment rule.
            Expression sizeExpr = vcStructMapping.getSizeParameter().getExpression();
            if (sizeExpr != null) {
                ASTNode ruleFormulaNode = getFormulaFromExpression(sizeExpr);
                AssignmentRule assignRule = sbmlModel.createAssignmentRule();
                assignRule.setVariable(vcStructures[i].getName());
                assignRule.setMath(ruleFormulaNode);
                // If compartmentSize is specified by an assignment rule, the 'constant' field should be set to 'false' (default - true).
                sbmlCompartment.setConstant(false);
                sbmlModel.addRule(assignRule);
            }
        }
        // Add the outside compartment of given compartment as annotation to the compartment.
        // This is required later while trying to read in compartments ...
        Element sbmlImportRelatedElement = null;
        // if (parentStructure != null) {
        // sbmlImportRelatedElement = new Element(XMLTags.VCellRelatedInfoTag, sbml_vcml_ns);
        // Element compartmentElement = new Element(XMLTags.OutsideCompartmentTag, sbml_vcml_ns);
        // compartmentElement.setAttribute(XMLTags.NameAttrTag, TokenMangler.mangleToSName(parentStructure.getName()));
        // sbmlImportRelatedElement.addContent(compartmentElement);
        // }
        // Get annotation (RDF and non-RDF) for reactionStep from SBMLAnnotationUtils
        sbmlAnnotationUtil.writeAnnotation(vcStructures[i], sbmlCompartment, sbmlImportRelatedElement);
        // Now set notes,
        sbmlAnnotationUtil.writeNotes(vcStructures[i], sbmlCompartment);
    }
}
Also used : StructureTopology(cbit.vcell.model.Model.StructureTopology) Compartment(org.sbml.jsbml.Compartment) AssignmentRule(org.sbml.jsbml.AssignmentRule) Element(org.jdom.Element) ExpressionException(cbit.vcell.parser.ExpressionException) Feature(cbit.vcell.model.Feature) StructureMapping(cbit.vcell.mapping.StructureMapping) InteriorPoint(org.sbml.jsbml.ext.spatial.InteriorPoint) VCUnitDefinition(cbit.vcell.units.VCUnitDefinition) Expression(cbit.vcell.parser.Expression) Model(cbit.vcell.model.Model) BioModel(cbit.vcell.biomodel.BioModel) ASTNode(org.sbml.jsbml.ASTNode) Membrane(cbit.vcell.model.Membrane) Structure(cbit.vcell.model.Structure) VCUnitDefinition(cbit.vcell.units.VCUnitDefinition) UnitDefinition(org.sbml.jsbml.UnitDefinition)

Example 13 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class SBMLExporter method addReactions.

/**
 * addReactions comment.
 * @throws SbmlException
 * @throws XMLStreamException
 */
protected void addReactions() throws SbmlException, XMLStreamException {
    // Check if any reaction has electrical mapping
    boolean bCalculatePotential = false;
    StructureMapping[] structureMappings = getSelectedSimContext().getGeometryContext().getStructureMappings();
    for (int i = 0; i < structureMappings.length; i++) {
        if (structureMappings[i] instanceof MembraneMapping) {
            if (((MembraneMapping) structureMappings[i]).getCalculateVoltage()) {
                bCalculatePotential = true;
            }
        }
    }
    // If it does, VCell doesn't export it to SBML (no representation).
    if (bCalculatePotential) {
        throw new RuntimeException("This VCell model has Electrical mapping; cannot be exported to SBML at this time");
    }
    l2gMap.clear();
    ReactionSpec[] vcReactionSpecs = getSelectedSimContext().getReactionContext().getReactionSpecs();
    for (int i = 0; i < vcReactionSpecs.length; i++) {
        if (vcReactionSpecs[i].isExcluded()) {
            continue;
        }
        ReactionStep vcReactionStep = vcReactionSpecs[i].getReactionStep();
        // Create sbml reaction
        String rxnName = vcReactionStep.getName();
        org.sbml.jsbml.Reaction sbmlReaction = sbmlModel.createReaction();
        sbmlReaction.setId(org.vcell.util.TokenMangler.mangleToSName(rxnName));
        sbmlReaction.setName(rxnName);
        // If the reactionStep is a flux reaction, add the details to the annotation (structure, carrier valence, flux carrier, fluxOption, etc.)
        // If reactionStep is a simple reaction, add annotation to indicate the structure of reaction.
        // Useful when roundtripping ...
        Element sbmlImportRelatedElement = null;
        // try {
        // sbmlImportRelatedElement = getAnnotationElement(vcReactionStep);
        // } catch (XmlParseException e1) {
        // e1.printStackTrace(System.out);
        // //			throw new RuntimeException("Error ");
        // }
        // Get annotation (RDF and non-RDF) for reactionStep from SBMLAnnotationUtils
        sbmlAnnotationUtil.writeAnnotation(vcReactionStep, sbmlReaction, sbmlImportRelatedElement);
        // Now set notes,
        sbmlAnnotationUtil.writeNotes(vcReactionStep, sbmlReaction);
        // Get reaction kineticLaw
        Kinetics vcRxnKinetics = vcReactionStep.getKinetics();
        org.sbml.jsbml.KineticLaw sbmlKLaw = sbmlReaction.createKineticLaw();
        try {
            // Convert expression from kinetics rate parameter into MathML and use libSBMl utilities to convert it to formula
            // (instead of directly using rate parameter's expression infix) to maintain integrity of formula :
            // for example logical and inequalities are not handled gracefully by libSBMl if expression.infix is used.
            final Expression localRateExpr;
            final Expression lumpedRateExpr;
            if (vcRxnKinetics instanceof DistributedKinetics) {
                localRateExpr = ((DistributedKinetics) vcRxnKinetics).getReactionRateParameter().getExpression();
                lumpedRateExpr = null;
            } else if (vcRxnKinetics instanceof LumpedKinetics) {
                localRateExpr = null;
                lumpedRateExpr = ((LumpedKinetics) vcRxnKinetics).getLumpedReactionRateParameter().getExpression();
            } else {
                throw new RuntimeException("unexpected Rate Law '" + vcRxnKinetics.getClass().getSimpleName() + "', not distributed or lumped type");
            }
            // if (vcRxnKinetics instanceof DistributedKinetics)
            // Expression correctedRateExpr = kineticsAdapter.getExpression();
            // Add parameters, if any, to the kineticLaw
            Kinetics.KineticsParameter[] vcKineticsParams = vcRxnKinetics.getKineticsParameters();
            // In the first pass thro' the kinetic params, store the non-numeric param names and expressions in arrays
            String[] kinParamNames = new String[vcKineticsParams.length];
            Expression[] kinParamExprs = new Expression[vcKineticsParams.length];
            for (int j = 0; j < vcKineticsParams.length; j++) {
                if (true) {
                    // Since local reaction parameters cannot be defined by a rule, such parameters (with rules) are exported as global parameters.
                    if ((vcKineticsParams[j].getRole() == Kinetics.ROLE_CurrentDensity && (!vcKineticsParams[j].getExpression().isZero())) || (vcKineticsParams[j].getRole() == Kinetics.ROLE_LumpedCurrent && (!vcKineticsParams[j].getExpression().isZero()))) {
                        throw new RuntimeException("Electric current not handled by SBML export; failed to export reaction \"" + vcReactionStep.getName() + "\" at this time");
                    }
                    if (!vcKineticsParams[j].getExpression().isNumeric()) {
                        // NON_NUMERIC KINETIC PARAM
                        // Create new name for kinetic parameter and store it in kinParamNames, store corresponding exprs in kinParamExprs
                        // Will be used later to add this param as global.
                        String newParamName = TokenMangler.mangleToSName(vcKineticsParams[j].getName() + "_" + vcReactionStep.getName());
                        kinParamNames[j] = newParamName;
                        kinParamExprs[j] = new Expression(vcKineticsParams[j].getExpression());
                    }
                }
            }
            // If so, these need to be added as global param (else the SBML doc will not be valid)
            for (int j = 0; j < vcKineticsParams.length; j++) {
                final KineticsParameter vcKParam = vcKineticsParams[j];
                if ((vcKParam.getRole() != Kinetics.ROLE_ReactionRate) && (vcKParam.getRole() != Kinetics.ROLE_LumpedReactionRate)) {
                    // if expression of kinetic param evaluates to a double, the parameter value is set
                    if ((vcKParam.getRole() == Kinetics.ROLE_CurrentDensity && (!vcKParam.getExpression().isZero())) || (vcKParam.getRole() == Kinetics.ROLE_LumpedCurrent && (!vcKParam.getExpression().isZero()))) {
                        throw new RuntimeException("Electric current not handled by SBML export; failed to export reaction \"" + vcReactionStep.getName() + "\" at this time");
                    }
                    if (vcKParam.getExpression().isNumeric()) {
                        // NUMERIC KINETIC PARAM
                        // check if it is used in other parameters that have expressions,
                        boolean bAddedParam = false;
                        String origParamName = vcKParam.getName();
                        String newParamName = TokenMangler.mangleToSName(origParamName + "_" + vcReactionStep.getName());
                        VCUnitDefinition vcUnit = vcKParam.getUnitDefinition();
                        for (int k = 0; k < vcKineticsParams.length; k++) {
                            if (kinParamExprs[k] != null) {
                                // The param could be in the expression for any other param
                                if (kinParamExprs[k].hasSymbol(origParamName)) {
                                    // mangle its name to avoid conflict with other globals
                                    if (globalParamNamesHash.get(newParamName) == null) {
                                        globalParamNamesHash.put(newParamName, newParamName);
                                        org.sbml.jsbml.Parameter sbmlKinParam = sbmlModel.createParameter();
                                        sbmlKinParam.setId(newParamName);
                                        sbmlKinParam.setValue(vcKParam.getConstantValue());
                                        final boolean constValue = vcKParam.isConstant();
                                        sbmlKinParam.setConstant(true);
                                        // Set SBML units for sbmlParam using VC units from vcParam
                                        if (!vcUnit.isTBD()) {
                                            UnitDefinition unitDefn = getOrCreateSBMLUnit(vcUnit);
                                            sbmlKinParam.setUnits(unitDefn);
                                        }
                                        Pair<String, String> origParam = new Pair<String, String>(rxnName, origParamName);
                                        l2gMap.put(origParam, newParamName);
                                        bAddedParam = true;
                                    } else {
                                    // need to get another name for param and need to change all its refereces in the other kinParam euqations.
                                    }
                                    // update the expression to contain new name, since the globalparam has new name
                                    kinParamExprs[k].substituteInPlace(new Expression(origParamName), new Expression(newParamName));
                                }
                            }
                        }
                        // If the param hasn't been added yet, it is definitely a local param. add it to kineticLaw now.
                        if (!bAddedParam) {
                            org.sbml.jsbml.LocalParameter sbmlKinParam = sbmlKLaw.createLocalParameter();
                            sbmlKinParam.setId(origParamName);
                            sbmlKinParam.setValue(vcKParam.getConstantValue());
                            System.out.println("tis constant " + sbmlKinParam.isExplicitlySetConstant());
                            // Set SBML units for sbmlParam using VC units from vcParam
                            if (!vcUnit.isTBD()) {
                                UnitDefinition unitDefn = getOrCreateSBMLUnit(vcUnit);
                                sbmlKinParam.setUnits(unitDefn);
                            }
                        } else {
                            // hence change its occurance in rate expression if it contains that param name
                            if (localRateExpr != null && localRateExpr.hasSymbol(origParamName)) {
                                localRateExpr.substituteInPlace(new Expression(origParamName), new Expression(newParamName));
                            }
                            if (lumpedRateExpr != null && lumpedRateExpr.hasSymbol(origParamName)) {
                                lumpedRateExpr.substituteInPlace(new Expression(origParamName), new Expression(newParamName));
                            }
                        }
                    }
                }
            }
            // (using the kinParamNames and kinParamExprs above) to ensure uniqueness in the global parameter names.
            for (int j = 0; j < vcKineticsParams.length; j++) {
                if (((vcKineticsParams[j].getRole() != Kinetics.ROLE_ReactionRate) && (vcKineticsParams[j].getRole() != Kinetics.ROLE_LumpedReactionRate)) && !(vcKineticsParams[j].getExpression().isNumeric())) {
                    String oldName = vcKineticsParams[j].getName();
                    String newName = kinParamNames[j];
                    // change the name of this parameter in the rate expression
                    if (localRateExpr != null && localRateExpr.hasSymbol(oldName)) {
                        localRateExpr.substituteInPlace(new Expression(oldName), new Expression(newName));
                    }
                    if (lumpedRateExpr != null && lumpedRateExpr.hasSymbol(oldName)) {
                        lumpedRateExpr.substituteInPlace(new Expression(oldName), new Expression(newName));
                    }
                    // Change the occurence of this param in other param expressions
                    for (int k = 0; k < vcKineticsParams.length; k++) {
                        if (((vcKineticsParams[k].getRole() != Kinetics.ROLE_ReactionRate) && (vcKineticsParams[j].getRole() != Kinetics.ROLE_LumpedReactionRate)) && !(vcKineticsParams[k].getExpression().isNumeric())) {
                            if (k != j && vcKineticsParams[k].getExpression().hasSymbol(oldName)) {
                                // for all params except the current param represented by index j (whose name was changed)
                                kinParamExprs[k].substituteInPlace(new Expression(oldName), new Expression(newName));
                            }
                            if (k == j && vcKineticsParams[k].getExpression().hasSymbol(oldName)) {
                                throw new RuntimeException("A parameter cannot refer to itself in its expression");
                            }
                        }
                    }
                // end for - k
                }
            }
            // In the fifth pass thro' the kinetic params, the non-numeric params are added to the global params of the model
            for (int j = 0; j < vcKineticsParams.length; j++) {
                if (((vcKineticsParams[j].getRole() != Kinetics.ROLE_ReactionRate) && (vcKineticsParams[j].getRole() != Kinetics.ROLE_LumpedReactionRate)) && !(vcKineticsParams[j].getExpression().isNumeric())) {
                    // Now, add this param to the globalParamNamesHash and add a global parameter to the sbmlModel
                    String paramName = kinParamNames[j];
                    if (globalParamNamesHash.get(paramName) == null) {
                        globalParamNamesHash.put(paramName, paramName);
                    } else {
                    // need to get another name for param and need to change all its refereces in the other kinParam euqations.
                    }
                    Pair<String, String> origParam = new Pair<String, String>(rxnName, paramName);
                    // keeps its name but becomes a global (?)
                    l2gMap.put(origParam, paramName);
                    ASTNode paramFormulaNode = getFormulaFromExpression(kinParamExprs[j]);
                    AssignmentRule sbmlParamAssignmentRule = sbmlModel.createAssignmentRule();
                    sbmlParamAssignmentRule.setVariable(paramName);
                    sbmlParamAssignmentRule.setMath(paramFormulaNode);
                    org.sbml.jsbml.Parameter sbmlKinParam = sbmlModel.createParameter();
                    sbmlKinParam.setId(paramName);
                    if (!vcKineticsParams[j].getUnitDefinition().isTBD()) {
                        sbmlKinParam.setUnits(getOrCreateSBMLUnit(vcKineticsParams[j].getUnitDefinition()));
                    }
                    // Since the parameter is being specified by a Rule, its 'constant' field shoud be set to 'false' (default - true).
                    sbmlKinParam.setConstant(false);
                }
            }
            // end for (j) - fifth pass
            // After making all necessary adjustments to the rate expression, now set the sbmlKLaw.
            final ASTNode exprFormulaNode;
            if (lumpedRateExpr != null) {
                exprFormulaNode = getFormulaFromExpression(lumpedRateExpr);
            } else {
                if (bSpatial) {
                    exprFormulaNode = getFormulaFromExpression(localRateExpr);
                } else {
                    exprFormulaNode = getFormulaFromExpression(Expression.mult(localRateExpr, new Expression(vcReactionStep.getStructure().getName())));
                }
            }
            sbmlKLaw.setMath(exprFormulaNode);
        } catch (cbit.vcell.parser.ExpressionException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error getting value of parameter : " + e.getMessage());
        }
        // Add kineticLaw to sbmlReaction - not needed now, since we use sbmlRxn.createKLaw() ??
        // sbmlReaction.setKineticLaw(sbmlKLaw);
        // Add reactants, products, modifiers
        // Simple reactions have catalysts, fluxes have 'flux'
        cbit.vcell.model.ReactionParticipant[] rxnParticipants = vcReactionStep.getReactionParticipants();
        for (ReactionParticipant rxnParticpant : rxnParticipants) {
            SimpleSpeciesReference ssr = null;
            SpeciesReference sr = null;
            if (rxnParticpant instanceof cbit.vcell.model.Reactant) {
                ssr = sr = sbmlReaction.createReactant();
            } else if (rxnParticpant instanceof cbit.vcell.model.Product) {
                ssr = sr = sbmlReaction.createProduct();
            }
            if (rxnParticpant instanceof cbit.vcell.model.Catalyst) {
                ssr = sbmlReaction.createModifier();
            }
            if (ssr != null) {
                ssr.setSpecies(rxnParticpant.getSpeciesContext().getName());
            }
            if (sr != null) {
                sr.setStoichiometry(Double.parseDouble(Integer.toString(rxnParticpant.getStoichiometry())));
                String modelUniqueName = vcReactionStep.getName() + '_' + rxnParticpant.getName();
                sr.setId(TokenMangler.mangleToSName(modelUniqueName));
                // SBML-REVIEW
                sr.setConstant(true);
                // int rcode = sr.appendNotes("<
                try {
                    SBMLHelper.addNote(sr, "VCELL guess: how do we know if reaction is constant?");
                } catch (Exception e) {
                    e.printStackTrace();
                }
            }
        }
        sbmlReaction.setFast(vcReactionSpecs[i].isFast());
        // this attribute is mandatory for L3, optional for L2. So explicitly setting value.
        sbmlReaction.setReversible(true);
        if (bSpatial) {
            // set compartment for reaction if spatial
            sbmlReaction.setCompartment(vcReactionStep.getStructure().getName());
            // CORE  HAS ALT MATH true
            // set the "isLocal" attribute = true (in 'spatial' namespace) for each species
            SpatialReactionPlugin srplugin = (SpatialReactionPlugin) sbmlReaction.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
            srplugin.setIsLocal(vcRxnKinetics instanceof DistributedKinetics);
        }
    }
}
Also used : MembraneMapping(cbit.vcell.mapping.MembraneMapping) LumpedKinetics(cbit.vcell.model.LumpedKinetics) Element(org.jdom.Element) StructureMapping(cbit.vcell.mapping.StructureMapping) SimpleSpeciesReference(org.sbml.jsbml.SimpleSpeciesReference) KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter) SpeciesReference(org.sbml.jsbml.SpeciesReference) SimpleSpeciesReference(org.sbml.jsbml.SimpleSpeciesReference) ASTNode(org.sbml.jsbml.ASTNode) VCUnitDefinition(cbit.vcell.units.VCUnitDefinition) UnitDefinition(org.sbml.jsbml.UnitDefinition) Pair(org.vcell.util.Pair) DistributedKinetics(cbit.vcell.model.DistributedKinetics) SpatialReactionPlugin(org.sbml.jsbml.ext.spatial.SpatialReactionPlugin) ReactionSpec(cbit.vcell.mapping.ReactionSpec) AssignmentRule(org.sbml.jsbml.AssignmentRule) ExpressionException(cbit.vcell.parser.ExpressionException) InteriorPoint(org.sbml.jsbml.ext.spatial.InteriorPoint) XMLStreamException(javax.xml.stream.XMLStreamException) SbmlException(org.vcell.sbml.SbmlException) ImageException(cbit.image.ImageException) SBMLException(org.sbml.jsbml.SBMLException) ExpressionException(cbit.vcell.parser.ExpressionException) VCUnitDefinition(cbit.vcell.units.VCUnitDefinition) Expression(cbit.vcell.parser.Expression) ReactionStep(cbit.vcell.model.ReactionStep) Kinetics(cbit.vcell.model.Kinetics) DistributedKinetics(cbit.vcell.model.DistributedKinetics) LumpedKinetics(cbit.vcell.model.LumpedKinetics) ReactionParticipant(cbit.vcell.model.ReactionParticipant)

Example 14 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class SBMLExporter method addEvents.

/**
 * Export events
 */
protected void addEvents() {
    BioEvent[] vcBioevents = getSelectedSimContext().getBioEvents();
    if (vcBioevents != null) {
        for (BioEvent vcEvent : vcBioevents) {
            Event sbmlEvent = sbmlModel.createEvent();
            sbmlEvent.setId(vcEvent.getName());
            // create trigger
            Trigger trigger = sbmlEvent.createTrigger();
            try {
                Expression triggerExpr = vcEvent.generateTriggerExpression();
                ASTNode math = getFormulaFromExpression(triggerExpr, MathType.BOOLEAN);
                trigger.setMath(math);
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("failed to generate trigger expression for event " + vcEvent.getName() + ": " + e.getMessage());
            }
            // create delay
            LocalParameter delayParam = vcEvent.getParameter(BioEventParameterType.TriggerDelay);
            if (delayParam != null && delayParam.getExpression() != null && !delayParam.getExpression().isZero()) {
                Delay delay = sbmlEvent.createDelay();
                Expression delayExpr = delayParam.getExpression();
                ASTNode math = getFormulaFromExpression(delayExpr);
                delay.setMath(math);
                sbmlEvent.setUseValuesFromTriggerTime(vcEvent.getUseValuesFromTriggerTime());
            }
            // create eventAssignments
            ArrayList<EventAssignment> vcEventAssgns = vcEvent.getEventAssignments();
            for (int j = 0; j < vcEventAssgns.size(); j++) {
                org.sbml.jsbml.EventAssignment sbmlEA = sbmlEvent.createEventAssignment();
                SymbolTableEntry target = vcEventAssgns.get(j).getTarget();
                sbmlEA.setVariable(target.getName());
                Expression eventAssgnExpr = new Expression(vcEventAssgns.get(j).getAssignmentExpression());
                ASTNode eaMath = getFormulaFromExpression(eventAssgnExpr);
                sbmlEA.setMath(eaMath);
            }
        }
    }
}
Also used : EventAssignment(cbit.vcell.mapping.BioEvent.EventAssignment) ExpressionException(cbit.vcell.parser.ExpressionException) Delay(org.sbml.jsbml.Delay) InteriorPoint(org.sbml.jsbml.ext.spatial.InteriorPoint) LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter) SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry) Trigger(org.sbml.jsbml.Trigger) Expression(cbit.vcell.parser.Expression) ASTNode(org.sbml.jsbml.ASTNode) Event(org.sbml.jsbml.Event) BioEvent(cbit.vcell.mapping.BioEvent) BioEvent(cbit.vcell.mapping.BioEvent)

Example 15 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class SBMLImporter method getValueFromAssignmentRule.

/**
 * getSpatialDimentionBuiltInName :
 */
/*
	 * pending delete? gcw 4/2014 private String
	 * getSpatialDimensionBuiltInName(int dimension) { String name = null;
	 * switch (dimension) { case 0 : { name = SBMLUnitTranslator.DIMENSIONLESS;
	 * break; } case 1 : { name = SBMLUnitTranslator.LENGTH; break; } case 2 : {
	 * name = SBMLUnitTranslator.AREA; break; } case 3 : { name =
	 * SBMLUnitTranslator.VOLUME; break; } } return name; }
	 */
/**
 * getValueFromRuleOrFunctionDefinition : If the value of a kinetic law
 * parameter or species initial concentration/amount (or compartment volume)
 * is 0.0, check if it is given by a rule or functionDefinition, and return
 * the string (of the rule or functionDefinition expression).
 */
private Expression getValueFromAssignmentRule(String paramName) {
    Expression valueExpr = null;
    // Check if param name has an assignment rule associated with it
    int numAssgnRules = assignmentRulesHash.size();
    for (int i = 0; i < numAssgnRules; i++) {
        valueExpr = (Expression) assignmentRulesHash.get(paramName);
        if (valueExpr != null) {
            return new Expression(valueExpr);
        }
    }
    return null;
}
Also used : Expression(cbit.vcell.parser.Expression) InteriorPoint(org.sbml.jsbml.ext.spatial.InteriorPoint)

Aggregations

Expression (cbit.vcell.parser.Expression)549 ExpressionException (cbit.vcell.parser.ExpressionException)163 VCUnitDefinition (cbit.vcell.units.VCUnitDefinition)76 PropertyVetoException (java.beans.PropertyVetoException)73 Variable (cbit.vcell.math.Variable)69 ArrayList (java.util.ArrayList)58 Vector (java.util.Vector)56 MathException (cbit.vcell.math.MathException)55 VolVariable (cbit.vcell.math.VolVariable)53 SymbolTableEntry (cbit.vcell.parser.SymbolTableEntry)51 SpeciesContext (cbit.vcell.model.SpeciesContext)50 Element (org.jdom.Element)47 KineticsParameter (cbit.vcell.model.Kinetics.KineticsParameter)45 ExpressionBindingException (cbit.vcell.parser.ExpressionBindingException)45 Model (cbit.vcell.model.Model)43 Function (cbit.vcell.math.Function)42 Constant (cbit.vcell.math.Constant)41 ModelParameter (cbit.vcell.model.Model.ModelParameter)41 ModelUnitSystem (cbit.vcell.model.ModelUnitSystem)41 LocalParameter (cbit.vcell.mapping.ParameterContext.LocalParameter)38