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

Example 51 with MathException

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

the class XmlReader method getKinetics.

/**
 * This method returns a Kinetics object from a XML Element based on the value of the kinetics type attribute.
 * Creation date: (3/19/2001 4:42:04 PM)
 * @return cbit.vcell.model.Kinetics
 * @param param org.jdom.Element
 */
private Kinetics getKinetics(Element param, ReactionStep reaction, Model model) throws XmlParseException {
    VariableHash varHash = new VariableHash();
    addResevedSymbols(varHash, model);
    String type = param.getAttributeValue(XMLTags.KineticsTypeAttrTag);
    Kinetics newKinetics = null;
    try {
        if (type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralKinetics)) {
            // create a general kinetics
            newKinetics = new GeneralKinetics(reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralCurrentKinetics)) {
            // Create GeneralCurrentKinetics
            newKinetics = new GeneralCurrentKinetics(reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeMassAction) && reaction instanceof SimpleReaction) {
            // create a Mass Action kinetics
            newKinetics = new MassActionKinetics((SimpleReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeNernst) && reaction instanceof FluxReaction) {
            // create NernstKinetics
            newKinetics = new NernstKinetics((FluxReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeGHK) && reaction instanceof FluxReaction) {
            // create GHKKinetics
            newKinetics = new GHKKinetics((FluxReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeHMM_Irr) && reaction instanceof SimpleReaction) {
            // create HMM_IrrKinetics
            newKinetics = new HMM_IRRKinetics((SimpleReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeHMM_Rev) && reaction instanceof SimpleReaction) {
            // create HMM_RevKinetics
            newKinetics = new HMM_REVKinetics((SimpleReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralTotal_oldname)) {
            // create GeneralTotalKinetics
            newKinetics = new GeneralLumpedKinetics(reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralLumped)) {
            // create GeneralLumpedKinetics
            newKinetics = new GeneralLumpedKinetics(reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralCurrentLumped)) {
            // create GeneralCurrentLumpedKinetics
            newKinetics = new GeneralCurrentLumpedKinetics(reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralPermeability) && reaction instanceof FluxReaction) {
            // create GeneralPermeabilityKinetics
            newKinetics = new GeneralPermeabilityKinetics((FluxReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeMacroscopic_Irr) && reaction instanceof SimpleReaction) {
            // create Macroscopic_IRRKinetics
            newKinetics = new Macroscopic_IRRKinetics((SimpleReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeMicroscopic_Irr) && reaction instanceof SimpleReaction) {
            // create Microscopic_IRRKinetics
            newKinetics = new Microscopic_IRRKinetics((SimpleReaction) reaction);
        } else {
            throw new XmlParseException("Unknown kinetics type: " + type);
        }
    } catch (ExpressionException e) {
        e.printStackTrace();
        throw new XmlParseException("Error creating the kinetics for reaction: " + reaction.getName(), e);
    }
    try {
        // transaction begin flag ... yeah, this is a hack
        newKinetics.reading(true);
        // Read all of the parameters
        List<Element> list = param.getChildren(XMLTags.ParameterTag, vcNamespace);
        // add constants that may be used in kinetics.
        // VariableHash varHash = getVariablesHash();
        ArrayList<String> reserved = new ArrayList<String>();
        ReservedSymbol[] reservedSymbols = reaction.getModel().getReservedSymbols();
        for (ReservedSymbol rs : reservedSymbols) {
            reserved.add(rs.getName());
        }
        try {
            if (reaction.getStructure() instanceof Membrane) {
                Membrane membrane = (Membrane) reaction.getStructure();
                varHash.addVariable(new Constant(membrane.getMembraneVoltage().getName(), new Expression(0.0)));
                reserved.add(membrane.getMembraneVoltage().getName());
            }
            // 
            // add Reactants, Products, and Catalysts (ReactionParticipants)
            // 
            ReactionParticipant[] rp = reaction.getReactionParticipants();
            for (int i = 0; i < rp.length; i++) {
                varHash.addVariable(new Constant(rp[i].getName(), new Expression(0.0)));
            }
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("error reordering parameters according to dependencies: ", e);
        }
        // 
        for (Element xmlParam : list) {
            String paramName = unMangle(xmlParam.getAttributeValue(XMLTags.NameAttrTag));
            String role = xmlParam.getAttributeValue(XMLTags.ParamRoleAttrTag);
            String paramExpStr = xmlParam.getText();
            Expression paramExp = unMangleExpression(paramExpStr);
            try {
                if (varHash.getVariable(paramName) == null) {
                    varHash.addVariable(new Function(paramName, paramExp, null));
                } else {
                    if (reserved.contains(paramName)) {
                        varHash.removeVariable(paramName);
                        varHash.addVariable(new Function(paramName, paramExp, null));
                    }
                }
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException("error reordering parameters according to dependencies: ", e);
            }
            Kinetics.KineticsParameter tempParam = null;
            if (!role.equals(XMLTags.ParamRoleUserDefinedTag)) {
                tempParam = newKinetics.getKineticsParameterFromRole(Kinetics.getParamRoleFromDefaultDesc(role));
            } else {
                continue;
            }
            // hack for bringing in General Total kinetics without breaking.
            if (tempParam == null && newKinetics instanceof GeneralLumpedKinetics) {
                if (role.equals(Kinetics.GTK_AssumedCompartmentSize_oldname) || role.equals(Kinetics.GTK_ReactionRate_oldname) || role.equals(Kinetics.GTK_CurrentDensity_oldname)) {
                    continue;
                } else if (role.equals(VCMODL.TotalRate_oldname)) {
                    tempParam = newKinetics.getKineticsParameterFromRole(Kinetics.ROLE_LumpedReactionRate);
                }
            }
            // hack from bringing in chargeValence parameters without breaking
            if (tempParam == null && Kinetics.getParamRoleFromDefaultDesc(role) == Kinetics.ROLE_ChargeValence) {
                tempParam = newKinetics.getChargeValenceParameter();
            }
            if (tempParam == null) {
                throw new XmlParseException("parameter with role '" + role + "' not found in kinetics type '" + type + "'");
            }
            // 
            if (!tempParam.getName().equals(paramName)) {
                Kinetics.KineticsParameter multNameParam = newKinetics.getKineticsParameter(paramName);
                int n = 0;
                while (multNameParam != null) {
                    String tempName = paramName + "_" + n++;
                    newKinetics.renameParameter(paramName, tempName);
                    multNameParam = newKinetics.getKineticsParameter(tempName);
                }
                newKinetics.renameParameter(tempParam.getName(), paramName);
            }
        }
        // 
        // create unresolved parameters for all unresolved symbols
        // 
        String unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
        while (unresolvedSymbol != null) {
            try {
                // will turn into an UnresolvedParameter.
                varHash.addVariable(new Function(unresolvedSymbol, new Expression(0.0), null));
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e);
            }
            newKinetics.addUnresolvedParameter(unresolvedSymbol);
            unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
        }
        Variable[] sortedVariables = varHash.getTopologicallyReorderedVariables();
        ModelUnitSystem modelUnitSystem = reaction.getModel().getUnitSystem();
        for (int i = sortedVariables.length - 1; i >= 0; i--) {
            if (sortedVariables[i] instanceof Function) {
                Function paramFunction = (Function) sortedVariables[i];
                Element xmlParam = null;
                for (int j = 0; j < list.size(); j++) {
                    Element tempParam = (Element) list.get(j);
                    if (paramFunction.getName().equals(unMangle(tempParam.getAttributeValue(XMLTags.NameAttrTag)))) {
                        xmlParam = tempParam;
                        break;
                    }
                }
                if (xmlParam == null) {
                    // must have been an unresolved parameter
                    continue;
                }
                String symbol = xmlParam.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
                VCUnitDefinition unit = null;
                if (symbol != null) {
                    unit = modelUnitSystem.getInstance(symbol);
                }
                Kinetics.KineticsParameter tempParam = newKinetics.getKineticsParameter(paramFunction.getName());
                if (tempParam == null) {
                    newKinetics.addUserDefinedKineticsParameter(paramFunction.getName(), paramFunction.getExpression(), unit);
                } else {
                    newKinetics.setParameterValue(tempParam, paramFunction.getExpression());
                    tempParam.setUnitDefinition(unit);
                }
            }
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("Exception while setting parameters for Reaction : " + reaction.getName(), e);
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("Exception while settings parameters for Reaction : " + reaction.getName(), e);
    } finally {
        newKinetics.reading(false);
    }
    return newKinetics;
}

Example 52 with MathException

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

the class XmlReader method getJumpProcess.

/**
 * The method returns a JumpProcess object from a XML element.
 * Creation date: (7/24/2006 6:28:42 PM)
 * @return cbit.vcell.math.JumpProcess
 * @param param org.jdom.Element
 * @param md cbit.vcell.math.MathDescription
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private JumpProcess getJumpProcess(Element param, MathDescription md) throws XmlParseException {
    // name
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    // probability rate
    Element pb = param.getChild(XMLTags.ProbabilityRateTag, vcNamespace);
    Expression exp = unMangleExpression(pb.getText());
    JumpProcess jump = new JumpProcess(name, exp);
    // add actions
    Iterator<Element> iterator = param.getChildren(XMLTags.ActionTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            jump.addAction(getAction(tempelement, md));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding a new Action to the JumpProcess " + name, e);
        } catch (ExpressionException e) {
            e.printStackTrace();
        }
    }
    return jump;
}

Example 53 with MathException

use of cbit.vcell.math.MathException 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 54 with MathException

use of cbit.vcell.math.MathException 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;
}

Example 55 with MathException

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

the class XmlReader method getPostProcessingBlock.

private void getPostProcessingBlock(MathDescription mathDesc, Element element) throws XmlParseException {
    Iterator<Element> iterator = element.getChildren(XMLTags.ExplicitDataGenerator, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        ExplicitDataGenerator explicitDataGenerator = getExplicitDataGenerator(tempelement);
        try {
            mathDesc.getPostProcessingBlock().addDataGenerator(explicitDataGenerator);
        } catch (MathException e) {
            throw new XmlParseException(e);
        }
    }
    iterator = element.getChildren(XMLTags.ProjectionDataGenerator, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        ProjectionDataGenerator projectionDataGenerator = getProjectionDataGenerator(tempelement);
        try {
            mathDesc.getPostProcessingBlock().addDataGenerator(projectionDataGenerator);
        } catch (MathException e) {
            throw new XmlParseException(e);
        }
    }
    iterator = element.getChildren(XMLTags.ConvolutionDataGenerator, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        ConvolutionDataGenerator convolutionDataGenerator = getConvolutionDataGenerator(tempelement);
        try {
            mathDesc.getPostProcessingBlock().addDataGenerator(convolutionDataGenerator);
        } catch (MathException e) {
            throw new XmlParseException(e);
        }
    }
}