Examples with SpeciesContext cbit.vcell.model.SpeciesContext used on opensource projects

Example 56 with SpeciesContext

use of cbit.vcell.model.SpeciesContext in project vcell by virtualcell.

the class RbmSpeciesContextTreeCellRenderer method getTreeCellRendererComponent.

@Override
public Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
    super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
    setBorder(null);
    if (value instanceof BioModelNode) {
        BioModelNode node = (BioModelNode) value;
        Object userObject = node.getUserObject();
        obj = userObject;
        String text = null;
        Icon icon = null;
        String toolTip = null;
        if (userObject instanceof SpeciesContext) {
            SpeciesContext sc = (SpeciesContext) userObject;
            text = toHtml(sc);
            toolTip = toHtml(sc);
            if (sc.hasSpeciesPattern()) {
                icon = VCellIcons.rbmSpeciesBlueIcon;
            } else {
                icon = VCellIcons.rbmSpeciesGreenIcon;
            }
        } else if (userObject instanceof MolecularTypePattern) {
            MolecularTypePattern molecularTypePattern = (MolecularTypePattern) userObject;
            text = toHtml(molecularTypePattern, true);
            toolTip = toHtml(molecularTypePattern, true);
            if (owner == null) {
                icon = VCellIcons.rbmMolecularTypeSimpleIcon;
                ;
            } else {
                Graphics gc = owner.getGraphics();
                icon = new MolecularTypeSmallShape(1, 5, molecularTypePattern.getMolecularType(), null, gc, molecularTypePattern.getMolecularType(), null, issueManager);
            }
        } else if (userObject instanceof MolecularComponentPattern) {
            MolecularComponentPattern mcp = (MolecularComponentPattern) userObject;
            text = toHtml(mcp, true);
            toolTip = toHtmlWithTip(mcp, true);
            icon = VCellIcons.rbmComponentGreenIcon;
            if (mcp.getMolecularComponent().getComponentStateDefinitions().size() > 0) {
                icon = VCellIcons.rbmComponentGreenStateIcon;
            }
        } else if (userObject instanceof StateLocal) {
            // this code is still here but we don't show the states or the bonds in the tree anymore
            StateLocal sl = (StateLocal) userObject;
            text = toHtml(sl, true);
            toolTip = toHtmlWithTip(sl, true);
            icon = VCellIcons.rbmComponentStateIcon;
        } else if (userObject instanceof BondLocal) {
            BondLocal bl = (BondLocal) userObject;
            text = toHtml(bl, sel);
            toolTip = toHtmlWithTip(bl, true);
            icon = VCellIcons.rbmBondIcon;
        } else {
            if (userObject != null) {
                System.out.println(userObject.toString());
                text = userObject.toString();
            } else {
                text = "null user object";
            }
        }
        setText(text);
        setIcon(icon);
        setToolTipText(toolTip == null ? text : toolTip);
    }
    return this;
}

Example 57 with SpeciesContext

use of cbit.vcell.model.SpeciesContext in project vcell by virtualcell.

the class ReactionRulePropertiesTableModel method isCellEditable.

/**
 * Insert the method's description here.
 * Creation date: (2/24/01 12:27:46 AM)
 * @return boolean
 * @param rowIndex int
 * @param columnIndex int
 */
public boolean isCellEditable(int rowIndex, int columnIndex) {
    if (!bEditable) {
        return false;
    }
    Object o = getValueAt(rowIndex);
    if (!(o instanceof Parameter)) {
        return false;
    }
    Parameter parameter = (Parameter) o;
    if (reactionRule != null && reactionRule.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate) == parameter) {
        if (!reactionRule.isReversible()) {
            // disable Kr if rule is not reversible
            return false;
        }
    }
    switch(columnIndex) {
        case COLUMN_NAME:
            return parameter.isNameEditable();
        case COLUMN_DESCRIPTION:
            return false;
        case COLUMN_IS_GLOBAL:
            // if the parameter is reaction rate param or a ReservedSymbol in the model, it should not be editable
            if ((parameter instanceof LocalParameter) && (((LocalParameter) parameter).getRole() != RbmKineticLaw.RbmKineticLawParameterType.UserDefined)) {
                return false;
            }
            if (parameter instanceof UnresolvedParameter) {
                return false;
            }
            if (parameter instanceof LocalProxyParameter) {
                LocalProxyParameter kpp = (LocalProxyParameter) parameter;
                SymbolTableEntry ste = kpp.getTarget();
                if ((ste instanceof Model.ReservedSymbol) || (ste instanceof SpeciesContext) || (ste instanceof ModelQuantity)) {
                    return false;
                }
            }
            return true;
        case COLUMN_VALUE:
            return parameter.isExpressionEditable();
        case COLUMN_UNITS:
            return parameter.isUnitEditable();
    }
    return false;
}

Example 58 with SpeciesContext

use of cbit.vcell.model.SpeciesContext in project vcell by virtualcell.

the class ReactionRulePropertiesTableModel method setValueAt.

public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
    Object o = getValueAt(rowIndex);
    if (!(o instanceof Parameter)) {
        return;
    }
    Parameter parameter = (Parameter) o;
    // try {
    switch(columnIndex) {
        case COLUMN_NAME:
            {
                try {
                    if (aValue instanceof String) {
                        String newName = (String) aValue;
                        if (!parameter.getName().equals(newName)) {
                            if (parameter instanceof LocalParameter) {
                                reactionRule.getKineticLaw().renameParameter(parameter.getName(), newName);
                            } else if (parameter instanceof LocalProxyParameter) {
                                parameter.setName(newName);
                            }
                            fireTableRowsUpdated(rowIndex, rowIndex);
                        }
                    }
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Error changing parameter name:\n" + e.getMessage());
                } catch (PropertyVetoException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Error changing parameter name:\n" + e.getMessage());
                }
                break;
            }
        case COLUMN_IS_GLOBAL:
            {
                if (aValue.equals(Boolean.FALSE)) {
                    // check box has been <unset> (<true> to <false>) : change param from global to local
                    if ((parameter instanceof LocalProxyParameter) && ((((LocalProxyParameter) parameter).getTarget() instanceof Model.ReservedSymbol) || (((LocalProxyParameter) parameter).getTarget() instanceof SpeciesContext) || (((LocalProxyParameter) parameter).getTarget() instanceof ModelQuantity))) {
                        PopupGenerator.showErrorDialog(ownerTable, "Parameter : \'" + parameter.getName() + "\' is a " + ((LocalProxyParameter) parameter).getTarget().getClass() + " in the model; cannot convert it to a local kinetic parameter.");
                    } else {
                        try {
                            reactionRule.getKineticLaw().convertParameterType(parameter, false);
                        } catch (PropertyVetoException pve) {
                            pve.printStackTrace(System.out);
                            PopupGenerator.showErrorDialog(ownerTable, "Unable to convert parameter : \'" + parameter.getName() + "\' to local kinetics parameter : " + pve.getMessage());
                        } catch (ExpressionBindingException e) {
                            e.printStackTrace(System.out);
                            PopupGenerator.showErrorDialog(ownerTable, "Unable to convert parameter : \'" + parameter.getName() + "\' to local kinetics parameter : " + e.getMessage());
                        }
                    }
                } else {
                    // check box has been <set> (<false> to <true>) : change param from local to global
                    if ((parameter instanceof LocalParameter) && (((LocalParameter) parameter).getRole() != RbmKineticLaw.RbmKineticLawParameterType.UserDefined)) {
                        PopupGenerator.showErrorDialog(ownerTable, "Parameter : \'" + parameter.getName() + "\' is a pre-defined kinetics parameter (not user-defined); cannot convert it to a model level (global) parameter.");
                    } else {
                        ModelParameter mp = reactionRule.getModel().getModelParameter(parameter.getName());
                        // model already had the model parameter 'param', but check if 'param' value is different from
                        // model parameter with same name. If it is, the local value will be overridden by global (model) param
                        // value, and user should be warned.
                        String choice = "Ok";
                        if (mp != null && !(mp.getExpression().compareEqual(parameter.getExpression()))) {
                            String msgStr = "Model already has a global parameter named : \'" + parameter.getName() + "\'; with value = \'" + mp.getExpression().infix() + "\'; This local parameter \'" + parameter.getName() + "\' with value = \'" + parameter.getExpression().infix() + "\' will be overridden by the global value. \nPress \'Ok' to override " + "local value with global value of \'" + parameter.getName() + "\'. \nPress \'Cancel\' to retain new local value.";
                            choice = PopupGenerator.showWarningDialog(ownerTable, msgStr, new String[] { "Ok", "Cancel" }, "Ok");
                        }
                        if (choice.equals("Ok")) {
                            try {
                                // Now 'parameter' is a local kinetic parameter. If it is not numeric, and if its expression
                                // contains other local kinetic parameters, warn user that 'parameter' cannot be promoted because
                                // of its expression containing other local parameters.
                                boolean bPromoteable = true;
                                if (!parameter.getExpression().isNumeric()) {
                                    String[] symbols = parameter.getExpression().getSymbols();
                                    for (int i = 0; i < symbols.length; i++) {
                                        if (reactionRule.getKineticLaw().getLocalParameter(symbols[i]) != null) {
                                            PopupGenerator.showErrorDialog(ownerTable, "Parameter \'" + parameter.getName() + "\' contains other local kinetic parameters; Cannot convert it to global until the referenced parameters are global.");
                                            bPromoteable = false;
                                        }
                                    }
                                }
                                if (bPromoteable) {
                                    reactionRule.getKineticLaw().convertParameterType(parameter, true);
                                }
                            } catch (PropertyVetoException pve) {
                                pve.printStackTrace(System.out);
                                PopupGenerator.showErrorDialog(ownerTable, "Cannot convert parameter \'" + parameter.getName() + "\' to global parameter : " + pve.getMessage());
                            } catch (ExpressionBindingException e) {
                                e.printStackTrace(System.out);
                                PopupGenerator.showErrorDialog(ownerTable, "Cannot convert parameter \'" + parameter.getName() + "\' to global parameter : " + e.getMessage());
                            }
                        }
                    }
                }
                fireTableRowsUpdated(rowIndex, rowIndex);
                break;
            }
        case COLUMN_VALUE:
            {
                try {
                    if (aValue instanceof ScopedExpression) {
                        // }
                        throw new RuntimeException("unexpected value type ScopedExpression");
                    } else if (aValue instanceof String) {
                        String newExpressionString = (String) aValue;
                        if (parameter instanceof LocalParameter) {
                            LocalParameter localParameter = (LocalParameter) parameter;
                            reactionRule.getKineticLaw().setParameterValue(localParameter, new Expression(newExpressionString), true);
                        } else if (parameter instanceof LocalProxyParameter) {
                            parameter.setExpression(new Expression(newExpressionString));
                        }
                    }
                    reactionRule.getKineticLaw().resolveUndefinedUnits();
                    fireTableRowsUpdated(rowIndex, rowIndex);
                } catch (java.beans.PropertyVetoException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Error:\n" + e.getMessage());
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Expression error:\n" + e.getMessage());
                }
                break;
            }
        case COLUMN_UNITS:
            {
                try {
                    if (aValue instanceof String && parameter instanceof LocalParameter && ((LocalParameter) parameter).getRole() == RbmKineticLaw.RbmKineticLawParameterType.UserDefined) {
                        String newUnitString = (String) aValue;
                        LocalParameter kineticsParm = (LocalParameter) parameter;
                        ModelUnitSystem modelUnitSystem = reactionRule.getModel().getUnitSystem();
                        if (!kineticsParm.getUnitDefinition().getSymbol().equals(newUnitString)) {
                            kineticsParm.setUnitDefinition(modelUnitSystem.getInstance(newUnitString));
                            reactionRule.getKineticLaw().resolveUndefinedUnits();
                            fireTableRowsUpdated(rowIndex, rowIndex);
                        }
                    }
                } catch (VCUnitException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Error changing parameter unit:\n" + e.getMessage());
                }
                break;
            }
    }
// }catch (java.beans.PropertyVetoException e){
// e.printStackTrace(System.out);
// }
}

Example 59 with SpeciesContext

use of cbit.vcell.model.SpeciesContext in project vcell by virtualcell.

the class Generate2DExpModelOpAbstract method generateModel.

public final GeneratedModelResults generateModel(double deltaX, double bleachRadius, double cellRadius, double bleachDuration, double bleachRate, double postbleachDelay, double postbleachDuration, double psfSigma, double outputTimeStep, double primaryDiffusionRate, double primaryFraction, double bleachMonitorRate, double secondaryDiffusionRate, double secondaryFraction, String extracellularName, String cytosolName, Context context) throws PropertyVetoException, ExpressionException, GeometryException, ImageException, ModelException, MappingException, MathException, MatrixException {
    double domainSize = 2.2 * cellRadius;
    Extent extent = new Extent(domainSize, domainSize, 1.0);
    Origin origin = new Origin(-extent.getX() / 2.0, -extent.getY() / 2.0, -extent.getZ() / 2.0);
    String EXTRACELLULAR_NAME = extracellularName;
    String CYTOSOL_NAME = cytosolName;
    AnalyticSubVolume cytosolSubVolume = new AnalyticSubVolume(CYTOSOL_NAME, new Expression("pow(x,2)+pow(y,2)<pow(" + cellRadius + ",2)"));
    AnalyticSubVolume extracellularSubVolume = new AnalyticSubVolume(EXTRACELLULAR_NAME, new Expression(1.0));
    Geometry geometry = new Geometry("geometry", 2);
    geometry.getGeometrySpec().setExtent(extent);
    geometry.getGeometrySpec().setOrigin(origin);
    geometry.getGeometrySpec().addSubVolume(extracellularSubVolume);
    geometry.getGeometrySpec().addSubVolume(cytosolSubVolume, true);
    geometry.getGeometrySurfaceDescription().updateAll();
    BioModel bioModel = new BioModel(null);
    bioModel.setName("unnamed");
    Model model = new Model("model");
    bioModel.setModel(model);
    model.addFeature(EXTRACELLULAR_NAME);
    Feature extracellular = (Feature) model.getStructure(EXTRACELLULAR_NAME);
    model.addFeature(CYTOSOL_NAME);
    Feature cytosol = (Feature) model.getStructure(CYTOSOL_NAME);
    SpeciesContext immobileSC = model.createSpeciesContext(cytosol);
    SpeciesContext primarySC = model.createSpeciesContext(cytosol);
    SpeciesContext secondarySC = model.createSpeciesContext(cytosol);
    // 
    // common bleaching rate for all species
    // 
    double bleachStart = 10 * outputTimeStep - bleachDuration - postbleachDelay;
    double bleachEnd = bleachStart + bleachDuration;
    Expression bleachRateExp = createBleachExpression(bleachRadius, bleachRate, bleachMonitorRate, bleachStart, bleachEnd);
    {
        SimpleReaction immobileBWM = model.createSimpleReaction(cytosol);
        GeneralKinetics immobileBWMKinetics = new GeneralKinetics(immobileBWM);
        immobileBWM.setKinetics(immobileBWMKinetics);
        immobileBWM.addReactant(immobileSC, 1);
        immobileBWMKinetics.getReactionRateParameter().setExpression(Expression.mult(bleachRateExp, new Expression(immobileSC.getName())));
    }
    {
        SimpleReaction primaryBWM = model.createSimpleReaction(cytosol);
        GeneralKinetics primaryBWMKinetics = new GeneralKinetics(primaryBWM);
        primaryBWM.setKinetics(primaryBWMKinetics);
        primaryBWM.addReactant(primarySC, 1);
        primaryBWMKinetics.getReactionRateParameter().setExpression(Expression.mult(bleachRateExp, new Expression(primarySC.getName())));
    }
    {
        SimpleReaction secondaryBWM = model.createSimpleReaction(cytosol);
        GeneralKinetics secondaryBWMKinetics = new GeneralKinetics(secondaryBWM);
        secondaryBWM.setKinetics(secondaryBWMKinetics);
        secondaryBWM.addReactant(secondarySC, 1);
        secondaryBWMKinetics.getReactionRateParameter().setExpression(Expression.mult(bleachRateExp, new Expression(secondarySC.getName())));
    }
    // create simulation context
    SimulationContext simContext = bioModel.addNewSimulationContext("simContext", SimulationContext.Application.NETWORK_DETERMINISTIC);
    simContext.setGeometry(geometry);
    FeatureMapping cytosolFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(cytosol);
    FeatureMapping extracellularFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(extracellular);
    SubVolume cytSubVolume = geometry.getGeometrySpec().getSubVolume(CYTOSOL_NAME);
    SubVolume exSubVolume = geometry.getGeometrySpec().getSubVolume(EXTRACELLULAR_NAME);
    // unused? SurfaceClass pmSurfaceClass = geometry.getGeometrySurfaceDescription().getSurfaceClass(exSubVolume, cytSubVolume);
    cytosolFeatureMapping.setGeometryClass(cytSubVolume);
    extracellularFeatureMapping.setGeometryClass(exSubVolume);
    cytosolFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    extracellularFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    double fixedFraction = 1.0 - primaryFraction - secondaryFraction;
    SpeciesContextSpec immobileSCS = simContext.getReactionContext().getSpeciesContextSpec(immobileSC);
    immobileSCS.getInitialConditionParameter().setExpression(new Expression(fixedFraction));
    immobileSCS.getDiffusionParameter().setExpression(new Expression(0.0));
    SpeciesContextSpec primarySCS = simContext.getReactionContext().getSpeciesContextSpec(primarySC);
    primarySCS.getInitialConditionParameter().setExpression(new Expression(primaryFraction));
    primarySCS.getDiffusionParameter().setExpression(new Expression(primaryDiffusionRate));
    SpeciesContextSpec secondarySCS = simContext.getReactionContext().getSpeciesContextSpec(secondarySC);
    secondarySCS.getInitialConditionParameter().setExpression(new Expression(secondaryFraction));
    secondarySCS.getDiffusionParameter().setExpression(new Expression(secondaryDiffusionRate));
    simContext.getMicroscopeMeasurement().addFluorescentSpecies(immobileSC);
    simContext.getMicroscopeMeasurement().addFluorescentSpecies(primarySC);
    simContext.getMicroscopeMeasurement().addFluorescentSpecies(secondarySC);
    simContext.getMicroscopeMeasurement().setConvolutionKernel(new GaussianConvolutionKernel(new Expression(psfSigma), new Expression(psfSigma)));
    MathMapping mathMapping = simContext.createNewMathMapping();
    MathDescription mathDesc = mathMapping.getMathDescription();
    simContext.setMathDescription(mathDesc);
    User owner = context.getDefaultOwner();
    int meshSize = (int) (domainSize / deltaX);
    if (meshSize % 2 == 0) {
        // want an odd-sized mesh in x and y ... so centered at the origin.
        meshSize = meshSize + 1;
    }
    TimeBounds timeBounds = new TimeBounds(0.0, postbleachDuration);
    // 
    // simulation to use for data generation (output time steps as recorded by the microscope)
    // 
    double bleachBlackoutBegin = bleachStart - postbleachDelay;
    double bleachBlackoutEnd = bleachEnd + postbleachDelay;
    // ArrayList<Double> times = new ArrayList<Double>();
    // double time = 0;
    // while (time<=timeBounds.getEndingTime()){
    // if (time<=bleachBlackoutBegin || time>bleachBlackoutEnd){
    // // postbleachDelay is the time it takes to switch the filters.
    // times.add(time);
    // }
    // time += outputTimeStep.getData();
    // }
    // double[] timeArray = new double[times.size()];
    // for (int i=0;i<timeArray.length;i++){
    // timeArray[i] = times.get(i);
    // }
    // OutputTimeSpec fakeDataSimOutputTimeSpec = new ExplicitOutputTimeSpec(timeArray);
    OutputTimeSpec fakeDataSimOutputTimeSpec = new UniformOutputTimeSpec(outputTimeStep);
    KeyValue fakeDataSimKey = context.createNewKeyValue();
    SimulationVersion fakeDataSimVersion = new SimulationVersion(fakeDataSimKey, "fakeDataSim", owner, new GroupAccessNone(), new KeyValue("0"), new BigDecimal(0), new Date(), VersionFlag.Current, "", null);
    Simulation fakeDataSim = new Simulation(fakeDataSimVersion, mathDesc);
    simContext.addSimulation(fakeDataSim);
    fakeDataSim.getSolverTaskDescription().setTimeBounds(timeBounds);
    fakeDataSim.getMeshSpecification().setSamplingSize(new ISize(meshSize, meshSize, 1));
    fakeDataSim.getSolverTaskDescription().setSolverDescription(SolverDescription.SundialsPDE);
    fakeDataSim.getSolverTaskDescription().setOutputTimeSpec(fakeDataSimOutputTimeSpec);
    // 
    // simulation to use for viewing the protocol (output time steps to understand the physics)
    // 
    KeyValue fullExperimentSimKey = context.createNewKeyValue();
    SimulationVersion fullExperimentSimVersion = new SimulationVersion(fullExperimentSimKey, "fullExperiment", owner, new GroupAccessNone(), new KeyValue("0"), new BigDecimal(0), new Date(), VersionFlag.Current, "", null);
    Simulation fullExperimentSim = new Simulation(fullExperimentSimVersion, mathDesc);
    simContext.addSimulation(fullExperimentSim);
    OutputTimeSpec fullExperimentOutputTimeSpec = new UniformOutputTimeSpec(outputTimeStep / 10.0);
    fullExperimentSim.getSolverTaskDescription().setTimeBounds(timeBounds);
    fullExperimentSim.getMeshSpecification().setSamplingSize(new ISize(meshSize, meshSize, 1));
    fullExperimentSim.getSolverTaskDescription().setSolverDescription(SolverDescription.SundialsPDE);
    fullExperimentSim.getSolverTaskDescription().setOutputTimeSpec(fullExperimentOutputTimeSpec);
    GeneratedModelResults results = new GeneratedModelResults();
    results.bioModel_2D = bioModel;
    results.simulation_2D = fakeDataSim;
    results.bleachBlackoutBeginTime = bleachBlackoutBegin;
    results.bleachBlackoutEndTime = bleachBlackoutEnd;
    return results;
}

Example 60 with SpeciesContext

use of cbit.vcell.model.SpeciesContext in project vcell by virtualcell.

the class ModelProcessEquation method parseReaction.

public static ReactionParticipant[] parseReaction(ReactionStep reactionStep, Model model, String equationString) throws ExpressionException, PropertyVetoException {
    int gotoIndex = equationString.indexOf(REACTION_GOESTO);
    if (gotoIndex < 1 && equationString.length() == 0) {
        throw new ExpressionException("Syntax error! " + REACTION_GOESTO + " not found. (e.g. a+b->c)");
    }
    if (reactionStep == null) {
        return null;
    }
    String leftHand = equationString.substring(0, gotoIndex);
    String rightHand = equationString.substring(gotoIndex + REACTION_GOESTO.length());
    StringTokenizer st = new StringTokenizer(leftHand, "+");
    ArrayList<ReactionParticipant> rplist = new ArrayList<ReactionParticipant>();
    HashMap<String, SpeciesContext> speciesContextMap = new HashMap<String, SpeciesContext>();
    Structure rxnStructure = reactionStep.getStructure();
    while (st.hasMoreElements()) {
        String nextToken = st.nextToken().trim();
        if (nextToken.length() == 0) {
            continue;
        }
        int stoichiIndex = 0;
        while (true) {
            if (Character.isDigit(nextToken.charAt(stoichiIndex))) {
                stoichiIndex++;
            } else {
                break;
            }
        }
        int stoichi = 1;
        String tmp = nextToken.substring(0, stoichiIndex);
        if (tmp.length() > 0) {
            stoichi = Integer.parseInt(tmp);
        }
        String var = nextToken.substring(stoichiIndex).trim();
        SpeciesContext sc = model.getSpeciesContext(var);
        if (sc == null) {
            sc = speciesContextMap.get(var);
            if (sc == null) {
                Species species = model.getSpecies(var);
                if (species == null) {
                    species = new Species(var, null);
                }
                sc = new SpeciesContext(species, rxnStructure);
                sc.setName(var);
                speciesContextMap.put(var, sc);
            }
        }
        // if (reactionStep instanceof SimpleReaction) {
        rplist.add(new Reactant(null, (SimpleReaction) reactionStep, sc, stoichi));
    // } else if (reactionStep instanceof FluxReaction) {
    // rplist.add(new Flux(null, (FluxReaction) reactionStep, sc));
    // }
    }
    st = new StringTokenizer(rightHand, "+");
    while (st.hasMoreElements()) {
        String nextToken = st.nextToken().trim();
        if (nextToken.length() == 0) {
            continue;
        }
        int stoichiIndex = 0;
        while (true) {
            if (Character.isDigit(nextToken.charAt(stoichiIndex))) {
                stoichiIndex++;
            } else {
                break;
            }
        }
        int stoichi = 1;
        String tmp = nextToken.substring(0, stoichiIndex);
        if (tmp.length() > 0) {
            stoichi = Integer.parseInt(tmp);
        }
        String var = nextToken.substring(stoichiIndex);
        SpeciesContext sc = model.getSpeciesContext(var);
        if (sc == null) {
            sc = speciesContextMap.get(var);
            if (sc == null) {
                Species species = model.getSpecies(var);
                if (species == null) {
                    species = new Species(var, null);
                }
                sc = new SpeciesContext(species, rxnStructure);
                sc.setName(var);
                speciesContextMap.put(var, sc);
            }
        }
        // if (reactionStep instanceof SimpleReaction) {
        rplist.add(new Product(null, (SimpleReaction) reactionStep, sc, stoichi));
    // } else if (reactionStep instanceof FluxReaction) {
    // rplist.add(new Flux(null, (FluxReaction) reactionStep, sc));
    // }
    }
    return rplist.toArray(new ReactionParticipant[0]);
}