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

Example 16 with MathException

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

the class SimulationData method getSimDataBlock.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.simdata.DataBlock
 * @param user cbit.vcell.server.User
 * @param simID java.lang.String
 */
public synchronized SimDataBlock getSimDataBlock(OutputContext outputContext, String varName, double time) throws DataAccessException, IOException {
    refreshLogFile();
    try {
        getFunctionDataIdentifiers(outputContext);
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
    }
    try {
        if (isPostProcessing(outputContext, varName)) {
            PDEDataInfo pdeDataInfo = new PDEDataInfo(vcDataId.getOwner(), vcDataId.getID(), varName, time, lastDataProcessingOutputInfoTime);
            DataProcessingOutputDataValuesOP dataProcessingOutputDataValuesOP = new DataProcessingOutputDataValuesOP(vcDataId, varName, TimePointHelper.createSingleTimeTimePointHelper(extractClosestPostProcessTime(time)), DataIndexHelper.createAllDataIndexesDataIndexHelper(), outputContext, null);
            DataProcessingOutputDataValues dataProcessingOutputDataValues = (DataProcessingOutputDataValues) DataSetControllerImpl.getDataProcessingOutput(dataProcessingOutputDataValuesOP, getDataProcessingOutputSourceFileHDF5());
            return new SimDataBlock(pdeDataInfo, dataProcessingOutputDataValues.getDataValues()[0], /*1 time only*/
            VariableType.POSTPROCESSING);
        }
    } catch (Exception e) {
        // ignore
        e.printStackTrace();
    }
    File pdeFile = getPDEDataFile(time);
    if (pdeFile == null) {
        return null;
    }
    DataSet dataSet = getPDEDataSet(pdeFile, time);
    File zipFile = null;
    try {
        zipFile = getPDEDataZipFile(time);
    } catch (DataAccessException ex) {
        zipFile = null;
    }
    long lastModified = getLastModified(pdeFile, zipFile);
    DataSetIdentifier dsi = getDataSetIdentifier(varName);
    if (dsi == null) {
        throw new DataAccessException("data not found for variable " + varName);
    }
    final String varNameInDataSet = dsi.getQualifiedName();
    double[] data = dataSet.getData(varNameInDataSet, zipFile, time, amplistorHelper.solverDataType);
    int varTypeInt = dataSet.getVariableTypeInteger(varNameInDataSet);
    VariableType variableType = null;
    try {
        variableType = VariableType.getVariableTypeFromInteger(varTypeInt);
    } catch (IllegalArgumentException e) {
        e.printStackTrace(System.out);
        System.out.println("invalid varTypeInt = " + varTypeInt + " for variable " + varName + " at time " + time);
        try {
            variableType = SimulationData.getVariableTypeFromLength(getMesh(), data.length);
        } catch (MathException ex) {
            ex.printStackTrace(System.out);
            throw new DataAccessException(ex.getMessage());
        }
    }
    PDEDataInfo pdeDataInfo = new PDEDataInfo(vcDataId.getOwner(), vcDataId.getID(), varName, time, lastModified);
    if (data != null) {
        return new SimDataBlock(pdeDataInfo, data, variableType);
    } else {
        return null;
    }
}

Example 17 with MathException

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

the class SimulationData method refreshMeshFile.

/**
 * This method was created in VisualAge.
 */
private synchronized void refreshMeshFile() throws DataAccessException, MathException {
    // 
    // (re)read the log file if necessary
    // 
    VCMongoMessage.sendTrace("SimulationData.refreshMeshFile() <<BEGIN>>");
    try {
        readMesh(getMeshFile(), getMembraneMeshMetricsFile());
        VCMongoMessage.sendTrace("SimulationData.refreshMeshFile() <<EXIT normally>>");
    } catch (FileNotFoundException e) {
        VCMongoMessage.sendTrace("SimulationData.refreshMeshFile() <<EXIT-file not found>>");
    } catch (Exception e) {
        e.printStackTrace(System.out);
        VCMongoMessage.sendTrace("SimulationData.refreshMeshFile() <<EXIT-IOException>>");
        throw new DataAccessException(e.getMessage());
    }
}

Example 18 with MathException

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

the class SimulationData method getVarAndFunctionDataIdentifiers.

/**
 * This method was created in VisualAge.
 * @return java.lang.String[]
 */
public synchronized DataIdentifier[] getVarAndFunctionDataIdentifiers(OutputContext outputContext) throws IOException, DataAccessException {
    // Is this zip format?
    boolean bIsChombo = false;
    try {
        bIsChombo = isChombo();
    } catch (FileNotFoundException e) {
        e.printStackTrace(System.out);
    }
    File zipFile1 = getZipFile(bIsChombo, null);
    File zipFile2 = getZipFile(bIsChombo, 0);
    bZipFormat1 = false;
    bZipFormat2 = false;
    if (zipFile1.exists()) {
        bZipFormat1 = true;
    } else if (zipFile2.exists()) {
        bZipFormat2 = true;
    }
    refreshLogFile();
    boolean bIsComsol = false;
    try {
        bIsComsol = isComsol();
    } catch (FileNotFoundException e) {
        e.printStackTrace(System.out);
    }
    if (!bIsComsol) {
        try {
            refreshMeshFile();
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage());
        }
    }
    if (!isRulesData && !getIsODEData() && !bIsComsol && dataFilenames != null) {
        // read variables only when I have never read the file since variables don't change
        if (dataSetIdentifierList.size() == 0) {
            File file = getPDEDataFile(0.0);
            DataSet dataSet = getPDEDataSet(file, 0.0);
            String[] varNames = dataSet.getDataNames();
            int[] varTypeInts = dataSet.getVariableTypeIntegers();
            if (varNames == null) {
                return null;
            }
            dataSetIdentifierList.clear();
            for (int i = 0; i < varNames.length; i++) {
                VariableType varType = null;
                try {
                    varType = VariableType.getVariableTypeFromInteger(varTypeInts[i]);
                } catch (IllegalArgumentException e) {
                    if (LG.isWarnEnabled()) {
                        LG.warn("Exception typing " + varNames[i] + " has unsupported type " + varTypeInts[i] + ": " + e.getMessage());
                    }
                    varType = SimulationData.getVariableTypeFromLength(mesh, dataSet.getDataLength(varNames[i]));
                }
                Domain domain = Variable.getDomainFromCombinedIdentifier(varNames[i]);
                String varName = Variable.getNameFromCombinedIdentifier(varNames[i]);
                dataSetIdentifierList.addElement(new DataSetIdentifier(varName, varType, domain));
            }
            refreshDataProcessingOutputInfo(outputContext);
            if (dataProcessingOutputInfo != null) {
                for (int i = 0; i < dataProcessingOutputInfo.getVariableNames().length; i++) {
                    if (dataProcessingOutputInfo.getPostProcessDataType(dataProcessingOutputInfo.getVariableNames()[i]).equals(DataProcessingOutputInfo.PostProcessDataType.image)) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(dataProcessingOutputInfo.getVariableNames()[i], VariableType.POSTPROCESSING, null));
                    }
                }
            }
        }
        // always read functions file since functions might change
        getFunctionDataIdentifiers(outputContext);
    }
    if ((isRulesData || getIsODEData()) && dataSetIdentifierList.size() == 0) {
        ODEDataBlock odeDataBlock = getODEDataBlock();
        if (odeDataBlock == null) {
            throw new DataAccessException("Results are not availabe yet. Please try again later.");
        }
        ODESimData odeSimData = odeDataBlock.getODESimData();
        int colCount = odeSimData.getColumnDescriptionsCount();
        // assume index=0 is time "t"
        int DATA_OFFSET = 1;
        dataSetIdentifierList.clear();
        for (int i = 0; i < (colCount - DATA_OFFSET); i++) {
            String varName = odeSimData.getColumnDescriptions(i + DATA_OFFSET).getDisplayName();
            // TODO domain
            Domain domain = null;
            dataSetIdentifierList.addElement(new DataSetIdentifier(varName, VariableType.NONSPATIAL, domain));
        }
    }
    if (bIsComsol && dataSetIdentifierList.size() == 0) {
        ComsolSimFiles comsolSimFiles = getComsolSimFiles();
        if (comsolSimFiles.simTaskXMLFile != null) {
            try {
                String xmlString = FileUtils.readFileToString(comsolSimFiles.simTaskXMLFile);
                SimulationTask simTask = XmlHelper.XMLToSimTask(xmlString);
                Enumeration<Variable> variablesEnum = simTask.getSimulation().getMathDescription().getVariables();
                while (variablesEnum.hasMoreElements()) {
                    Variable var = variablesEnum.nextElement();
                    if (var instanceof VolVariable) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.VOLUME, var.getDomain()));
                    } else if (var instanceof MemVariable) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.MEMBRANE, var.getDomain()));
                    } else if (var instanceof Function) {
                        VariableType varType = VariableType.UNKNOWN;
                        if (var.getDomain() != null && var.getDomain().getName() != null) {
                            SubDomain subDomain = simTask.getSimulation().getMathDescription().getSubDomain(var.getDomain().getName());
                            if (subDomain instanceof CompartmentSubDomain) {
                                varType = VariableType.VOLUME;
                            } else if (subDomain instanceof MembraneSubDomain) {
                                varType = VariableType.MEMBRANE;
                            } else if (subDomain instanceof FilamentSubDomain) {
                                throw new RuntimeException("filament subdomains not supported");
                            } else if (subDomain instanceof PointSubDomain) {
                                varType = VariableType.POINT_VARIABLE;
                            }
                        }
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), varType, var.getDomain()));
                    } else if (var instanceof Constant) {
                        System.out.println("ignoring Constant " + var.getName());
                    } else if (var instanceof InsideVariable) {
                        System.out.println("ignoring InsideVariable " + var.getName());
                    } else if (var instanceof OutsideVariable) {
                        System.out.println("ignoring OutsideVariable " + var.getName());
                    } else {
                        throw new RuntimeException("unexpected variable " + var.getName() + " of type " + var.getClass().getName());
                    }
                }
            } catch (XmlParseException | ExpressionException e) {
                e.printStackTrace();
                throw new RuntimeException("failed to read sim task file, msg: " + e.getMessage(), e);
            }
        }
    }
    DataIdentifier[] dis = new DataIdentifier[dataSetIdentifierList.size()];
    for (int i = 0; i < dataSetIdentifierList.size(); i++) {
        DataSetIdentifier dsi = (DataSetIdentifier) dataSetIdentifierList.elementAt(i);
        String displayName = dsi.getName();
        if (dsi.isFunction()) {
            AnnotatedFunction f = null;
            for (int j = 0; j < annotatedFunctionList.size(); j++) {
                AnnotatedFunction function = (AnnotatedFunction) annotatedFunctionList.elementAt(j);
                if (function.getName().equals(dsi.getName())) {
                    f = function;
                    break;
                }
            }
            if (f != null) {
                displayName = f.getDisplayName();
            }
        }
        dis[i] = new DataIdentifier(dsi.getName(), dsi.getVariableType(), dsi.getDomain(), dsi.isFunction(), displayName);
    }
    return dis;
}

Example 19 with MathException

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

the class DataSetControllerImpl method getSimDataBlock.

/**
 * This method was created by a SmartGuide.
 * @return double[]
 * @param varName java.lang.String
 * @param time double
 */
public SimDataBlock getSimDataBlock(OutputContext outputContext, VCDataIdentifier vcdID, String varName, double time) throws DataAccessException {
    VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ")  <<ENTER>>");
    try {
        // 
        // check if already cached for non-function variables
        // 
        VCData simData = getVCData(vcdID);
        VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ") got VCData");
        long dataBlockTimeStamp = simData.getDataBlockTimeStamp(PDE_DATA, time);
        VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ") got dataBlockTimeStamp");
        PDEDataInfo pdeDataInfo = new PDEDataInfo(vcdID.getOwner(), vcdID.getID(), varName, time, dataBlockTimeStamp);
        SimDataBlock simDataBlock = null;
        AnnotatedFunction function = getFunction(outputContext, vcdID, varName);
        VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ") got function");
        if (function == null) {
            simDataBlock = (cacheTable0 != null ? cacheTable0.get(pdeDataInfo) : null);
            if (simDataBlock == null) {
                simDataBlock = simData.getSimDataBlock(outputContext, varName, time);
                if (simDataBlock != null && dataCachingEnabled) {
                    // cacheTable.put(pdeDataInfo,simDataBlock);
                    if (cacheTable0 != null) {
                        try {
                            cacheTable0.put(pdeDataInfo, simDataBlock);
                        } catch (CacheException e) {
                            // if can't cache the data, it is ok
                            e.printStackTrace();
                        }
                    }
                }
            }
        } else {
            if (simData instanceof SimulationData) {
                function = ((SimulationData) simData).simplifyFunction(function);
            }
            VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ") evaluating function");
            simDataBlock = evaluateFunction(outputContext, vcdID, simData, function, time);
        }
        CartesianMesh mesh = getMesh(vcdID);
        if (mesh != null && mesh.isChomboMesh()) {
            for (int i = 0; i < simDataBlock.getData().length; i++) {
                if (simDataBlock.getData()[i] == 1.23456789e300) {
                    simDataBlock.getData()[i] = Double.NaN;
                }
            }
        }
        if (simDataBlock != null) {
            VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ")  <<EXIT-simDataBlock not null>>");
            return simDataBlock;
        } else {
            String msg = "failure reading " + varName + " at t=" + time + " for " + vcdID.getOwner().getName() + "'s " + vcdID.getID();
            if (lg.isWarnEnabled())
                lg.warn("DataSetControllerImpl.getDataBlockValues(): " + msg);
            VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ")  <<EXIT-Exception>>");
            throw new DataAccessException(msg);
        }
    } catch (MathException e) {
        lg.error(e.getMessage(), e);
        VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ")  <<EXIT-Exception>>");
        throw new DataAccessException(e.getMessage());
    } catch (IOException e) {
        lg.error(e.getMessage(), e);
        VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ")  <<EXIT-Exception>>");
        throw new DataAccessException(e.getMessage());
    } catch (ExpressionException e) {
        lg.error(e.getMessage(), e);
        VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ")  <<EXIT-Exception>>");
        throw new DataAccessException(e.getMessage());
    }
}

Example 20 with MathException

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

the class NFsimXMLWriter method writeNFsimXML.

public static Element writeNFsimXML(SimulationTask origSimTask, long randomSeed, NFsimSimulationOptions nfsimSimulationOptions, boolean bUseLocationMarks) throws SolverException {
    try {
        System.out.println("VCML ORIGINAL .... START\n" + origSimTask.getSimulation().getMathDescription().getVCML_database() + "\nVCML ORIGINAL .... END\n====================\n");
    } catch (MathException e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    }
    SimulationTask clonedSimTask = null;
    try {
        clonedSimTask = (SimulationTask) BeanUtils.cloneSerializable(origSimTask);
    } catch (Exception eee) {
        throw new SolverException("failed to clone mathDescription while preparing NFSim input: " + eee.getMessage(), eee);
    }
    MathDescription clonedMathDesc = clonedSimTask.getSimulation().getMathDescription();
    if (bUseLocationMarks) {
        try {
            // 
            // get list of Compartment Names (stored in locations).
            // 
            ArrayList<String> locations = new ArrayList<String>();
            Enumeration<Variable> varEnum = clonedMathDesc.getVariables();
            ArrayList<VolumeParticleSpeciesPattern> volumeParticleSpeciesPatterns = new ArrayList<VolumeParticleSpeciesPattern>();
            while (varEnum.hasMoreElements()) {
                Variable var = varEnum.nextElement();
                if (var instanceof VolumeParticleSpeciesPattern) {
                    VolumeParticleSpeciesPattern speciesPattern = (VolumeParticleSpeciesPattern) var;
                    if (!locations.contains(speciesPattern.getLocationName())) {
                        locations.add(speciesPattern.getLocationName());
                    }
                    volumeParticleSpeciesPatterns.add(speciesPattern);
                }
            }
            // 
            for (ParticleMolecularType particleMolecularType : clonedMathDesc.getParticleMolecularTypes()) {
                String pmcLocationName = RbmUtils.SiteStruct;
                String pmcLocationId = particleMolecularType.getName() + "_" + RbmUtils.SiteStruct;
                ParticleMolecularComponent locationComponent = new ParticleMolecularComponent(pmcLocationId, pmcLocationName);
                for (String location : locations) {
                    locationComponent.addComponentStateDefinition(new ParticleComponentStateDefinition(location));
                }
                particleMolecularType.insertMolecularComponent(0, locationComponent);
                String pmcMarkName = RbmUtils.SiteProduct;
                String pmcMarkId = particleMolecularType.getName() + "_" + RbmUtils.SiteProduct;
                ParticleMolecularComponent markComponent = new ParticleMolecularComponent(pmcMarkId, pmcMarkName);
                markComponent.addComponentStateDefinition(new ParticleComponentStateDefinition("0"));
                markComponent.addComponentStateDefinition(new ParticleComponentStateDefinition("1"));
                particleMolecularType.insertMolecularComponent(1, markComponent);
            }
            // 
            for (VolumeParticleSpeciesPattern speciesPattern : volumeParticleSpeciesPatterns) {
                for (ParticleMolecularTypePattern molTypePattern : speciesPattern.getParticleMolecularTypePatterns()) {
                    // 
                    // add location component to pattern ... state=<location>
                    // 
                    {
                        final ParticleMolecularComponent locationComponentDefinition = molTypePattern.getMolecularType().getComponentList().get(0);
                        ParticleMolecularComponentPattern locationPattern = new ParticleMolecularComponentPattern(locationComponentDefinition);
                        ParticleComponentStateDefinition locationStateDefinition = null;
                        for (ParticleComponentStateDefinition stateDef : locationComponentDefinition.getComponentStateDefinitions()) {
                            if (stateDef.getName().equals(speciesPattern.getLocationName())) {
                                locationStateDefinition = stateDef;
                            }
                        }
                        ParticleComponentStatePattern locationStatePattern = new ParticleComponentStatePattern(locationStateDefinition);
                        locationPattern.setComponentStatePattern(locationStatePattern);
                        locationPattern.setBondType(ParticleBondType.None);
                        locationPattern.setBondId(-1);
                        molTypePattern.insertMolecularComponentPattern(0, locationPattern);
                    }
                    // 
                    // add mark component to pattern ... state="0" (for observables and reactants ... later we will clone and use "1" for products).
                    {
                        final ParticleMolecularComponent markComponentDefinition = molTypePattern.getMolecularType().getComponentList().get(1);
                        ParticleMolecularComponentPattern markPattern = new ParticleMolecularComponentPattern(markComponentDefinition);
                        final int clearStateIndex = 0;
                        final int setStateIndex = 1;
                        ParticleComponentStateDefinition markStateClearedDefinition = markComponentDefinition.getComponentStateDefinitions().get(clearStateIndex);
                        ParticleComponentStatePattern markStatePattern = new ParticleComponentStatePattern(markStateClearedDefinition);
                        markPattern.setComponentStatePattern(markStatePattern);
                        markPattern.setBondType(ParticleBondType.None);
                        markPattern.setBondId(-1);
                        molTypePattern.insertMolecularComponentPattern(1, markPattern);
                    }
                }
            }
            // 
            // when processing ParticleJumpProcesses, we add a new "product" species pattern (by cloning the original speciesPattern)
            // and setting the mark site to "1", change name to name+"_PRODUCT", and add to math model if it doesn't already exist.
            // 
            // cloned the "standard" reactant/observable speciesPattern, set the mark for all molecules, and add to mathDesc.
            // 
            CompartmentSubDomain subDomain = (CompartmentSubDomain) clonedMathDesc.getSubDomains().nextElement();
            for (ParticleJumpProcess particleJumpProcess : subDomain.getParticleJumpProcesses()) {
                for (Action action : particleJumpProcess.getActions()) {
                    if (action.getOperation().equals(Action.ACTION_CREATE)) {
                        VolumeParticleSpeciesPattern volumeParticleSpeciesPattern = (VolumeParticleSpeciesPattern) action.getVar();
                        String newSpeciesPatternName = volumeParticleSpeciesPattern.getName() + "_" + particleJumpProcess.getName();
                        VolumeParticleSpeciesPattern productPattern = new VolumeParticleSpeciesPattern(volumeParticleSpeciesPattern, newSpeciesPatternName);
                        // VolumeParticleSpeciesPattern productPattern = (VolumeParticleSpeciesPattern) BeanUtils.cloneSerializable(volumeParticleSpeciesPattern);
                        for (ParticleMolecularTypePattern productMolTypePattern : productPattern.getParticleMolecularTypePatterns()) {
                            ParticleComponentStateDefinition markSet = productMolTypePattern.getMolecularType().getComponentList().get(1).getComponentStateDefinitions().get(1);
                            productMolTypePattern.getMolecularComponentPatternList().get(1).setComponentStatePattern(new ParticleComponentStatePattern(markSet));
                        }
                        System.out.println(productPattern.getName());
                        if (clonedMathDesc.getVariable(productPattern.getName()) == null) {
                            clonedMathDesc.addVariable(productPattern);
                        }
                        action.setVar(productPattern);
                    }
                }
            }
            try {
                System.out.println("===============================\n ----------- VCML HACKED .... START\n" + clonedMathDesc.getVCML_database() + "\nVCML HACKED .... END\n====================\n");
            } catch (MathException e1) {
                // TODO Auto-generated catch block
                e1.printStackTrace();
            }
        } catch (Exception e) {
            throw new SolverException("failed to apply location mark transformation: " + e.getMessage(), e);
        }
    }
    Element sbmlElement = new Element("sbml");
    Element modelElement = new Element("model");
    modelElement.setAttribute("id", "nameless");
    SimulationSymbolTable simulationSymbolTable = new SimulationSymbolTable(clonedSimTask.getSimulation(), clonedSimTask.getSimulationJob().getJobIndex());
    Element listOfParametersElement = getListOfParameters(clonedMathDesc, simulationSymbolTable);
    Element listOfMoleculeTypesElement = getListOfMoleculeTypes(clonedMathDesc);
    Element listOfSpeciesElement = getListOfSpecies(clonedMathDesc, simulationSymbolTable);
    CompartmentSubDomain compartmentSubDomain = (CompartmentSubDomain) clonedMathDesc.getSubDomains().nextElement();
    Element listOfReactionRules = new Element("ListOfReactionRules");
    for (int reactionRuleIndex = 0; reactionRuleIndex < compartmentSubDomain.getParticleJumpProcesses().size(); reactionRuleIndex++) {
        ParticleJumpProcess particleJumpProcess = compartmentSubDomain.getParticleJumpProcesses().get(reactionRuleIndex);
        MathRuleFactory mathRuleFactory = new MathRuleFactory();
        MathRuleEntry rule = mathRuleFactory.createRuleEntry(particleJumpProcess, reactionRuleIndex);
        RuleAnalysisReport report = RuleAnalysis.analyze(rule, true);
        // remember, we have to add RateLaw
        Element reactionRuleElement = RuleAnalysis.getNFSimXML(rule, report);
        // ArrayList<MolecularTypeOfReactionParticipant> currentReactantElementsOfReaction = new ArrayList<MolecularTypeOfReactionParticipant>();
        // ArrayList<ComponentOfMolecularTypeOfReactionParticipant> currentComponentOfReactantElementsOfReaction = new ArrayList<ComponentOfMolecularTypeOfReactionParticipant>();
        // ArrayList<MolecularTypeOfReactionParticipant> currentProductElementsOfReaction = new ArrayList<MolecularTypeOfReactionParticipant>();
        // ArrayList<ComponentOfMolecularTypeOfReactionParticipant> currentComponentOfProductElementsOfReaction = new ArrayList<ComponentOfMolecularTypeOfReactionParticipant>();
        // currentMappingOfReactionParticipants.clear();
        // reactionProductBondSites.clear();
        // reactionReactantBondSites.clear();
        // 
        // Element reactionRuleElement = new Element("ReactionRule");
        // String reactionRuleID = "RR" + (reactionRuleIndex + 1);
        // reactionRuleElement.setAttribute("id",reactionRuleID);
        // reactionRuleElement.setAttribute("name",particleJumpProcess.getName());
        // reactionRuleElement.setAttribute("symmetry_factor","1");
        // reactionRule.resolveBonds();
        // 
        // ArrayList<VolumeParticleSpeciesPattern> selectedPatterns = new ArrayList<VolumeParticleSpeciesPattern>();
        // for (ParticleVariable particleVariable : particleJumpProcess.getParticleVariables()){
        // if (!(particleVariable instanceof VolumeParticleSpeciesPattern)){
        // throw new SolverException("expecting only "+VolumeParticleSpeciesPattern.class.getSimpleName()+"s for "+ParticleJumpProcess.class.getSimpleName()+" "+particleJumpProcess.getName());
        // }
        // selectedPatterns.add((VolumeParticleSpeciesPattern) particleVariable);
        // }
        // ArrayList<VolumeParticleSpeciesPattern> createdPatterns = new ArrayList<VolumeParticleSpeciesPattern>();
        // HashSet<VolumeParticleSpeciesPattern> destroyedPatterns = new HashSet<VolumeParticleSpeciesPattern>();
        // for (Action action : particleJumpProcess.getActions()){
        // if (!(action.getVar() instanceof VolumeParticleSpeciesPattern)){
        // throw new SolverException("expecting only "+VolumeParticleSpeciesPattern.class.getSimpleName()+"s for "+ParticleJumpProcess.class.getSimpleName()+" "+particleJumpProcess.getName());
        // }
        // if (action.getOperation().equals(Action.ACTION_CREATE)){
        // createdPatterns.add((VolumeParticleSpeciesPattern) action.getVar());
        // }else if (action.getOperation().equals(Action.ACTION_DESTROY)){
        // destroyedPatterns.add((VolumeParticleSpeciesPattern) action.getVar());
        // }else{
        // throw new RuntimeException("unexpected action operation "+action.getOperation()+" for jump process "+particleJumpProcess.getName());
        // }
        // }
        // 
        // Element listOfReactantPatternsElement = new Element("ListOfReactantPatterns");
        // for(int reactantPatternIndex=0; reactantPatternIndex < selectedPatterns.size(); reactantPatternIndex++) {
        // VolumeParticleSpeciesPattern reactantSpeciesPattern = selectedPatterns.get(reactantPatternIndex);
        // String reactantPatternID = "RP" + (reactantPatternIndex + 1);
        // patternReactantBondSites.clear();
        // Element reactantPatternElement = getReactionParticipantPattern1(reactionRuleID, reactantPatternID, reactantSpeciesPattern,
        // currentReactantElementsOfReaction, currentComponentOfReactantElementsOfReaction, "ReactantPattern");
        // listOfReactantPatternsElement.addContent(reactantPatternElement);
        // reactionReactantBondSites.addAll(patternReactantBondSites);
        // }
        // reactionRuleElement.addContent(listOfReactantPatternsElement);
        // 
        // Element listOfProductPatternsElement = new Element("ListOfProductPatterns");
        // ArrayList<VolumeParticleSpeciesPattern> productSpeciesPatterns = new ArrayList<VolumeParticleSpeciesPattern>(selectedPatterns);
        // productSpeciesPatterns.removeAll(destroyedPatterns);
        // productSpeciesPatterns.addAll(createdPatterns);
        // // for products, add all "created" species from Actions and all "particles" that are selected but not destroyed
        // for(int productPatternIndex=0; productPatternIndex < productSpeciesPatterns.size(); productPatternIndex++) {
        // VolumeParticleSpeciesPattern productSpeciesPattern = productSpeciesPatterns.get(productPatternIndex);
        // String productPatternID = "PP" + (productPatternIndex + 1);
        // patternProductBondSites.clear();
        // Element productPatternElement = getReactionParticipantPattern1(reactionRuleID, productPatternID, productSpeciesPattern,
        // currentProductElementsOfReaction, currentComponentOfProductElementsOfReaction, "ProductPattern");
        // listOfProductPatternsElement.addContent(productPatternElement);
        // reactionProductBondSites.addAll(patternProductBondSites);
        // }
        // reactionRuleElement.addContent(listOfProductPatternsElement);
        // <RateLaw id="RR1_RateLaw" type="Ele" totalrate="0">
        // <ListOfRateConstants>
        // <RateConstant value="kon"/>
        // </ListOfRateConstants>
        // </RateLaw>
        Element rateLawElement = new Element("RateLaw");
        rateLawElement.setAttribute("id", RuleAnalysis.getID(rule));
        String rateConstantValue = null;
        JumpProcessRateDefinition particleProbabilityRate = particleJumpProcess.getParticleRateDefinition();
        if (particleProbabilityRate.getExpressions().length > 0) {
            JumpProcessRateDefinition particleRateDefinition = particleJumpProcess.getParticleRateDefinition();
            Expression expression = null;
            if (particleRateDefinition instanceof MacroscopicRateConstant) {
                expression = ((MacroscopicRateConstant) particleProbabilityRate).getExpression();
            } else {
                throw new SolverException("ParticleRateDefinition type " + particleRateDefinition.getClass().getSimpleName() + " not supported");
            }
            rateConstantValue = expression.infixBng();
            // all rates constants are being flattened and given reserved names
            Expression substitutedValExpr = null;
            try {
                substitutedValExpr = simulationSymbolTable.substituteFunctions(expression);
            } catch (MathException | ExpressionException e) {
                e.printStackTrace(System.out);
                throw new SolverException("ParticleJumpProcess " + particleJumpProcess.getName() + " substitution failed : exp = \"" + expression.infix() + "\": " + e.getMessage());
            }
            Double value = null;
            try {
                value = substitutedValExpr.evaluateConstant();
                Element parameterElement = new Element("Parameter");
                String id = "K_reserved_" + reactionRuleIndex;
                parameterElement.setAttribute("id", id);
                if (value != null) {
                    parameterElement.setAttribute("type", "Constant");
                    parameterElement.setAttribute("value", value.toString());
                    parameterElement.addContent(new Comment(rateConstantValue));
                    rateConstantValue = id;
                    listOfParametersElement.addContent(parameterElement);
                }
            } catch (ExpressionException e) {
                System.out.println("ParticleJumpProcess " + particleJumpProcess.getName() + " = " + substitutedValExpr.infix() + " does not have a constant value");
            }
        }
        if (isFunction(rateConstantValue, clonedMathDesc, simulationSymbolTable)) {
            rateLawElement.setAttribute("type", "Function");
            rateLawElement.setAttribute("totalrate", "0");
            rateLawElement.setAttribute("name", rateConstantValue);
        } else {
            rateLawElement.setAttribute("type", "Ele");
            rateLawElement.setAttribute("totalrate", "0");
            Element listOfRateConstantsElement = new Element("ListOfRateConstants");
            Element rateConstantElement = new Element("RateConstant");
            // System.out.println(" --- " + particleJumpProcess.getParticleRateDefinition().getExpressions());
            if (particleProbabilityRate.getExpressions().length > 0) {
                rateConstantElement.setAttribute("value", rateConstantValue);
            }
            listOfRateConstantsElement.addContent(rateConstantElement);
            rateLawElement.addContent(listOfRateConstantsElement);
        }
        reactionRuleElement.addContent(rateLawElement);
        // //  <Map>
        // //    <MapItem sourceID="RR1_RP1_M1" targetID="RR1_PP1_M1"/>
        // //    <MapItem sourceID="RR1_RP1_M1_C1" targetID="RR1_PP1_M1_C1"/>
        // //    <MapItem sourceID="RR1_RP1_M1_C2" targetID="RR1_PP1_M1_C2"/>
        // //    <MapItem sourceID="RR1_RP2_M1" targetID="RR1_PP1_M2"/>
        // //    <MapItem sourceID="RR1_RP2_M1_C1" targetID="RR1_PP1_M2_C1"/>
        // //  </Map>
        // Element mapElement = new Element("Map");
        // System.out.println("----------------------------------------------------------------------");
        // for(MolecularTypeOfReactionParticipant p : currentReactantElementsOfReaction) {
        // System.out.println(p.moleculeName + ", " + p.elementID);
        // }
        // for(ComponentOfMolecularTypeOfReactionParticipant c : currentComponentOfReactantElementsOfReaction) {
        // System.out.println(c.moleculeName + ", " + c.componentName + ", " + c.elementID);
        // }
        // System.out.println("----------------------------------------------------------------------");
        // for(MolecularTypeOfReactionParticipant p : currentProductElementsOfReaction) {
        // System.out.println(p.moleculeName + ", " + p.elementID);
        // }
        // for(ComponentOfMolecularTypeOfReactionParticipant c : currentComponentOfProductElementsOfReaction) {
        // System.out.println(c.moleculeName + ", " + c.componentName + ", " + c.elementID);
        // }
        // System.out.println("----------------------------------------------------------------------");
        // 
        // List<MolecularTypeOfReactionParticipant> cloneOfReactants = new ArrayList<MolecularTypeOfReactionParticipant>(currentReactantElementsOfReaction);
        // List<MolecularTypeOfReactionParticipant> cloneOfProducts = new ArrayList<MolecularTypeOfReactionParticipant>(currentProductElementsOfReaction);
        // for(Iterator<MolecularTypeOfReactionParticipant> itReactant = cloneOfReactants.iterator(); itReactant.hasNext();) {	// participants
        // MolecularTypeOfReactionParticipant reactant = itReactant.next();
        // boolean foundProduct = false;
        // for(Iterator<MolecularTypeOfReactionParticipant> itProduct = cloneOfProducts.iterator(); itProduct.hasNext();) {
        // MolecularTypeOfReactionParticipant product = itProduct.next();
        // if(reactant.find(product)) {
        // MappingOfReactionParticipants m = new MappingOfReactionParticipants(reactant.elementID, product.elementID, "");
        // currentMappingOfReactionParticipants.add(m );
        // itProduct.remove();
        // foundProduct = true;
        // break;		// we exit inner loop if we find a match for current reactant
        // }
        // }
        // if(foundProduct == false) {
        // System.out.println("Did not found a match for reactant " + reactant.moleculeName + ", " + reactant.elementID);
        // }
        // itReactant.remove();		// found or not, we remove the reactant
        // }
        // if(!currentProductElementsOfReaction.isEmpty()) {
        // for(MolecularTypeOfReactionParticipant p : currentProductElementsOfReaction) {
        // System.out.println("Did not found a match for product " + p.moleculeName + ", " + p.elementID);
        // }
        // }
        // for(Iterator<ComponentOfMolecularTypeOfReactionParticipant> itReactant = currentComponentOfReactantElementsOfReaction.iterator(); itReactant.hasNext();) {	// components
        // ComponentOfMolecularTypeOfReactionParticipant reactant = itReactant.next();
        // boolean foundProduct = false;
        // for(Iterator<ComponentOfMolecularTypeOfReactionParticipant> itProduct = currentComponentOfProductElementsOfReaction.iterator(); itProduct.hasNext();) {
        // ComponentOfMolecularTypeOfReactionParticipant product = itProduct.next();
        // String state = "";
        // if(reactant.find(product)) {
        // if(!reactant.state.equals(product.state)) {
        // state = product.state;
        // }
        // MappingOfReactionParticipants m = new MappingOfReactionParticipants(reactant.elementID, product.elementID, state);
        // currentMappingOfReactionParticipants.add(m );
        // itProduct.remove();
        // foundProduct = true;
        // break;		// we exit inner loop if we find a match for current reactant
        // }
        // }
        // if(foundProduct == false) {
        // System.out.println("Did not found a match for reactant " + reactant.moleculeName + ", " + reactant.elementID);
        // }
        // itReactant.remove();		// found or not, we remove the reactant
        // }
        // if(!currentComponentOfProductElementsOfReaction.isEmpty()) {
        // for(ComponentOfMolecularTypeOfReactionParticipant p : currentComponentOfProductElementsOfReaction) {
        // System.out.println("Did not found a match for product " + p.moleculeName + ", " + p.elementID);
        // }
        // }
        // for(Iterator<MappingOfReactionParticipants> it = currentMappingOfReactionParticipants.iterator(); it.hasNext();) {
        // MappingOfReactionParticipants m = it.next();
        // Element mapItemElement = new Element("MapItem");
        // mapItemElement.setAttribute("sourceID", m.reactantElementID);
        // mapItemElement.setAttribute("targetID", m.productElementID);
        // mapElement.addContent(mapItemElement);
        // }
        // reactionRuleElement.addContent(mapElement);
        // 
        // //  <ListOfOperations>
        // //      <AddBond site1="RR1_RP1_M1_C1" site2="RR1_RP2_M1_C1"/>
        // //		<StateChange site="RR0_RP0_M0_C2" finalState="Y"/>
        // //  </ListOfOperations>
        // Element listOfOperationsElement = new Element("ListOfOperations");
        // 
        // // AddBond elements
        // // add any bond in the product which is not present in the reactant
        // Iterator<BondSites> it = patternProductBondSites.iterator();
        // while (it.hasNext()) {
        // BondSites bs = it.next();
        // String reactantS1 = MappingOfReactionParticipants.findMatchingReactant(bs.component1, currentMappingOfReactionParticipants);
        // String reactantS2 = MappingOfReactionParticipants.findMatchingReactant(bs.component2, currentMappingOfReactionParticipants);
        // // we check if the bonds in the product existed already in the reactant, in which case they were not "added" in this reaction
        // BondSites candidate = new BondSites(reactantS1, reactantS2);
        // boolean preExistent = false;
        // for(BondSites bsReactant : reactionReactantBondSites) {
        // if(bsReactant.equals(candidate)) {
        // preExistent = true;
        // break;
        // }
        // }
        // if(preExistent == true) {
        // continue;		// we don't add preexisting bonds
        // }
        // Element addBondElement = new Element("AddBond");
        // addBondElement.setAttribute("site1", reactantS1);
        // addBondElement.setAttribute("site2", reactantS2);
        // listOfOperationsElement.addContent(addBondElement);
        // }
        // // StateChange elements
        // for(Iterator<MappingOfReactionParticipants> it1 = currentMappingOfReactionParticipants.iterator(); it1.hasNext();) {
        // MappingOfReactionParticipants m = it1.next();
        // if(!m.componentFinalState.equals("")) {		// state has changed if it's different from ""
        // Element stateChangeElement = new Element("StateChange");
        // stateChangeElement.setAttribute("site", m.reactantElementID);
        // stateChangeElement.setAttribute("finalState", m.componentFinalState);
        // listOfOperationsElement.addContent(stateChangeElement);
        // }
        // }
        // // eliminate all the common entries (molecule types) in reactants and products
        // // what's left in reactants was deleted, what's left in products was added
        // List<MolecularTypeOfReactionParticipant> commonParticipants = new ArrayList<MolecularTypeOfReactionParticipant>();
        // for(Iterator<MolecularTypeOfReactionParticipant> itReactant = currentReactantElementsOfReaction.iterator(); itReactant.hasNext();) {	// participants
        // MolecularTypeOfReactionParticipant reactant = itReactant.next();
        // for(Iterator<MolecularTypeOfReactionParticipant> itProduct = currentProductElementsOfReaction.iterator(); itProduct.hasNext();) {
        // MolecularTypeOfReactionParticipant product = itProduct.next();
        // if(reactant.find(product)) {
        // // commonParticipants contains the reactant molecules with a equivalent molecule in the product (meaning they are not in the "Deleted" category)
        // commonParticipants.add(reactant);
        // itReactant.remove();
        // itProduct.remove();
        // break;		// we exit inner loop if we find a match for current reactant
        // }
        // }
        // }
        // // DeleteBond element
        // // there is no need to mention deletion of bond if the particleSpeciesPattern
        // // or the MolecularType involved in the bond are deleted as well
        // // We only keep those "Deleted" bonds which belong to the molecules (of the reactant) present in commonParticipants
        // // Both components (sites) of the bond need to have their molecules in commonParticipants
        // boolean foundMoleculeForComponent1 = false;
        // boolean foundMoleculeForComponent2 = false;
        // HashSet<BondSites> cloneOfReactantBondSites = new HashSet<BondSites>(patternReactantBondSites);
        // Iterator<BondSites> itbs = cloneOfReactantBondSites.iterator();
        // while (itbs.hasNext()) {
        // BondSites bs = itbs.next();
        // String bondComponent1MoleculeId = BondSites.extractMoleculeId(bs.component1);
        // String bondComponent2MoleculeId = BondSites.extractMoleculeId(bs.component2);
        // for(MolecularTypeOfReactionParticipant commonReactionMoleculeule : commonParticipants) {
        // String commonReactantPatternId = commonReactionMoleculeule.elementID;
        // if(bondComponent1MoleculeId.equals(commonReactantPatternId)) {
        // foundMoleculeForComponent1 = true;
        // }
        // if(bondComponent2MoleculeId.equals(commonReactantPatternId)) {
        // foundMoleculeForComponent2 = true;
        // }
        // }
        // if(!foundMoleculeForComponent1 || !foundMoleculeForComponent2) {
        // // at least one of bond's molecule is not in common, hence we don't need to report the deletion of this bond
        // itbs.remove();
        // }
        // }
        // // the clone has now all the deleted bonds whose molecules have not been deleted
        // itbs = cloneOfReactantBondSites.iterator();
        // while (itbs.hasNext()) {
        // BondSites bs = itbs.next();
        // Element addBondElement = new Element("DeleteBond");
        // addBondElement.setAttribute("site1", bs.component1);
        // addBondElement.setAttribute("site2", bs.component2);
        // listOfOperationsElement.addContent(addBondElement);
        // }
        // // Add MolecularType element
        // for(MolecularTypeOfReactionParticipant molecule : currentProductElementsOfReaction) {
        // System.out.println("created molecule: " + molecule.elementID + "' " + molecule.moleculeName);
        // Element addMolecularTypePatternElement = new Element("Add");
        // addMolecularTypePatternElement.setAttribute("id", molecule.elementID);
        // listOfOperationsElement.addContent(addMolecularTypePatternElement);
        // }
        // // Delete MolecularType element
        // // if the reactant pattern of the molecule being deleted still exists as part of the common, then we only delete the molecule
        // // if the reactant pattern of the molecule being deleted is not as part of the common, then it's gone completely and we delete the reactant pattern
        // ArrayList<String> patternsToDelete = new ArrayList<String>();
        // for(MolecularTypeOfReactionParticipant molecule : currentReactantElementsOfReaction) {
        // String reactantPatternId = molecule.extractReactantPatternId();
        // boolean found = false;
        // for(MolecularTypeOfReactionParticipant common : commonParticipants) {
        // String commonId = common.extractReactantPatternId();
        // if(reactantPatternId.equals(commonId)) {
        // found = true;
        // break;		// some other molecule of this pattern still there, we don't delete the pattern
        // }
        // }
        // if(found == true) {		// some other molecule of this pattern still there, we don't delete the pattern
        // System.out.println("deleted molecule: " + molecule.elementID + "' " + molecule.moleculeName);
        // Element addMolecularTypePatternElement = new Element("Delete");
        // addMolecularTypePatternElement.setAttribute("id", molecule.elementID);
        // addMolecularTypePatternElement.setAttribute("DeleteMolecules", "0");
        // listOfOperationsElement.addContent(addMolecularTypePatternElement);
        // } else {				// no molecule of this pattern left, we delete the pattern
        // if(patternsToDelete.contains(reactantPatternId)) {
        // // nothing to do, we're already deleting this pattern
        // break;
        // } else {
        // patternsToDelete.add(reactantPatternId);
        // System.out.println("deleted pattern: " + reactantPatternId);
        // Element addParticleSpeciesPatternElement = new Element("Delete");
        // addParticleSpeciesPatternElement.setAttribute("id", reactantPatternId);
        // addParticleSpeciesPatternElement.setAttribute("DeleteMolecules", "0");
        // listOfOperationsElement.addContent(addParticleSpeciesPatternElement);
        // }
        // }
        // }
        // reactionRuleElement.addContent(listOfOperationsElement);
        listOfReactionRules.addContent(reactionRuleElement);
    }
    Element listOfObservablesElement = getListOfObservables(clonedMathDesc);
    Element listOfFunctionsElement = getListOfFunctions(clonedMathDesc, simulationSymbolTable);
    modelElement.addContent(listOfParametersElement);
    modelElement.addContent(listOfMoleculeTypesElement);
    modelElement.addContent(listOfSpeciesElement);
    modelElement.addContent(listOfReactionRules);
    modelElement.addContent(listOfObservablesElement);
    modelElement.addContent(listOfFunctionsElement);
    sbmlElement.addContent(modelElement);
    // //		return e1;
    return sbmlElement;
}