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

Example 1 with MathSymbolMapping

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

the class ParameterMappingPanel method jMenuItemPaste_ActionPerformed.

/**
 * Comment
 */
private void jMenuItemPaste_ActionPerformed(java.awt.event.ActionEvent actionEvent) {
    java.util.Vector<String> pasteDescriptionsV = new java.util.Vector<String>();
    java.util.Vector<Expression> newExpressionsV = new java.util.Vector<Expression>();
    java.util.Vector<ParameterMappingSpec> changedParametersV = new java.util.Vector<ParameterMappingSpec>();
    try {
        if (actionEvent.getSource() == getJMenuItemPaste() || actionEvent.getSource() == getJMenuItemPasteAll()) {
            Object pasteThis = VCellTransferable.getFromClipboard(VCellTransferable.OBJECT_FLAVOR);
            SimulationContext sc = getParameterEstimationTask().getModelOptimizationSpec().getSimulationContext();
            MathSymbolMapping msm = null;
            Exception mathMappingException = null;
            try {
                MathMapping mm = sc.createNewMathMapping();
                msm = mm.getMathSymbolMapping();
            } catch (Exception e) {
                mathMappingException = e;
                e.printStackTrace(System.out);
            }
            // if(msm == null){
            // try{
            // getParameterEstimationTask().refreshMappings();
            // msm = getParameterEstimationTask().getMathSymbolMapping();
            // }catch(Exception e){
            // e.printStackTrace();
            // }
            // }
            int[] rows = null;
            if (actionEvent.getSource() == getJMenuItemPasteAll()) {
                rows = new int[getScrollPaneTable().getRowCount()];
                for (int i = 0; i < rows.length; i += 1) {
                    rows[i] = i;
                }
            } else {
                rows = getScrollPaneTable().getSelectedRows();
            }
            // 
            // Check paste
            // 
            StringBuffer errors = null;
            for (int i = 0; i < rows.length; i += 1) {
                ParameterMappingSpec pms = parameterMappingTableModel.getValueAt(rows[i]);
                try {
                    if (pasteThis instanceof VCellTransferable.ResolvedValuesSelection) {
                        VCellTransferable.ResolvedValuesSelection rvs = (VCellTransferable.ResolvedValuesSelection) pasteThis;
                        for (int j = 0; j < rvs.getPrimarySymbolTableEntries().length; j += 1) {
                            ParameterMappingSpec pasteDestination = null;
                            Parameter clipboardBiologicalParameter = null;
                            if (rvs.getPrimarySymbolTableEntries()[j] instanceof Parameter) {
                                clipboardBiologicalParameter = (Parameter) rvs.getPrimarySymbolTableEntries()[j];
                            } else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof Parameter) {
                                clipboardBiologicalParameter = (Parameter) rvs.getAlternateSymbolTableEntries()[j];
                            }
                            if (clipboardBiologicalParameter == null) {
                                Variable pastedMathVariable = null;
                                if (rvs.getPrimarySymbolTableEntries()[j] instanceof Variable) {
                                    pastedMathVariable = (Variable) rvs.getPrimarySymbolTableEntries()[j];
                                } else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof Variable) {
                                    pastedMathVariable = (Variable) rvs.getAlternateSymbolTableEntries()[j];
                                }
                                if (pastedMathVariable != null) {
                                    if (msm == null) {
                                        throw mathMappingException;
                                    }
                                    Variable localMathVariable = msm.findVariableByName(pastedMathVariable.getName());
                                    if (localMathVariable != null) {
                                        SymbolTableEntry[] localBiologicalSymbolArr = msm.getBiologicalSymbol(localMathVariable);
                                        for (int k = 0; k < localBiologicalSymbolArr.length; k += 1) {
                                            if (localBiologicalSymbolArr[k] == pms.getModelParameter()) {
                                                pasteDestination = pms;
                                                break;
                                            }
                                        }
                                    }
                                }
                            } else {
                                if (pms.getModelParameter().getName().equals(clipboardBiologicalParameter.getName()) && pms.getModelParameter().getClass().equals(clipboardBiologicalParameter.getClass()) && pms.getModelParameter().getNameScope().getName().equals(clipboardBiologicalParameter.getNameScope().getName())) {
                                    pasteDestination = pms;
                                }
                            }
                            if (pasteDestination != null) {
                                changedParametersV.add(pasteDestination);
                                newExpressionsV.add(rvs.getExpressionValues()[j]);
                                pasteDescriptionsV.add(VCellCopyPasteHelper.formatPasteList(pms.getModelParameter().getNameScope().getName(), pms.getModelParameter().getName(), pasteDestination.getCurrent() + "", rvs.getExpressionValues()[j].infix()));
                            }
                        }
                    }
                } catch (Throwable e) {
                    if (errors == null) {
                        errors = new StringBuffer();
                    }
                    errors.append(pms.getModelParameter().getName() + " (" + e.getClass().getName() + ") " + e.getMessage() + "\n");
                }
            }
            if (errors != null) {
                throw new Exception(errors.toString());
            }
        }
    } catch (Throwable e) {
        PopupGenerator.showErrorDialog(this, "Paste failed during pre-check (no changes made).\n" + e.getMessage(), e);
        return;
    }
    // Do paste
    try {
        if (pasteDescriptionsV.size() > 0) {
            String[] pasteDescriptionArr = new String[pasteDescriptionsV.size()];
            pasteDescriptionsV.copyInto(pasteDescriptionArr);
            ParameterMappingSpec[] changedParametersArr = new ParameterMappingSpec[changedParametersV.size()];
            changedParametersV.copyInto(changedParametersArr);
            Expression[] newExpressionsArr = new Expression[newExpressionsV.size()];
            newExpressionsV.copyInto(newExpressionsArr);
            VCellCopyPasteHelper.chooseApplyPaste(this, pasteDescriptionArr, changedParametersArr, newExpressionsArr);
        } else {
            PopupGenerator.showInfoDialog(this, "No paste items match the destination (no changes made).");
        }
    } catch (Throwable e) {
        PopupGenerator.showErrorDialog(this, "Paste Error\n" + e.getMessage(), e);
    }
}

Example 2 with MathSymbolMapping

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

the class SEDMLExporter method translateBioModelToSedML.

private void translateBioModelToSedML(String savePath) {
    sbmlFilePathStrAbsoluteList.clear();
    // models
    try {
        SimulationContext[] simContexts = vcBioModel.getSimulationContexts();
        cbit.vcell.model.Model vcModel = vcBioModel.getModel();
        // "urn:sedml:language:sbml";
        String sbmlLanguageURN = SUPPORTED_LANGUAGE.SBML_GENERIC.getURN();
        String bioModelName = TokenMangler.mangleToSName(vcBioModel.getName());
        // String usrHomeDirPath = ResourceUtil.getUserHomeDir().getAbsolutePath();
        // to get Xpath string for variables.
        SBMLSupport sbmlSupport = new SBMLSupport();
        // for model count, task subcount
        int simContextCnt = 0;
        // for dtaGenerator count.
        int varCount = 0;
        boolean bSpeciesAddedAsDataGens = false;
        String sedmlNotesStr = "";
        for (SimulationContext simContext : simContexts) {
            String simContextName = simContext.getName();
            // export all applications that are not spatial stochastic
            if (!(simContext.getGeometry().getDimension() > 0 && simContext.isStoch())) {
                // to compute and set the sizes of the remaining structures.
                if (!simContext.getGeometryContext().isAllSizeSpecifiedPositive()) {
                    Structure structure = simContext.getModel().getStructure(0);
                    double structureSize = 1.0;
                    StructureMapping structMapping = simContext.getGeometryContext().getStructureMapping(structure);
                    StructureSizeSolver.updateAbsoluteStructureSizes(simContext, structure, structureSize, structMapping.getSizeParameter().getUnitDefinition());
                }
                // Export the application itself to SBML, with default overrides
                String sbmlString = null;
                int level = 2;
                int version = 4;
                boolean isSpatial = simContext.getGeometry().getDimension() > 0 ? true : false;
                SimulationJob simJob = null;
                // if (simContext.getGeometry().getDimension() > 0) {
                // sbmlString = XmlHelper.exportSBML(vcBioModel, 2, 4, 0, true, simContext, null);
                // } else {
                // sbmlString = XmlHelper.exportSBML(vcBioModel, 2, 4, 0, false, simContext, null);
                // }
                // 
                // TODO: we need to salvage from the SBMLExporter info about the fate of local parameters
                // some of them may stay as locals, some others may become globals
                // Any of these, if used in a repeated task or change or whatever, needs to be used in a consistent way,
                // that is, if a param becomes a global in SBML, we need to refer at it in SEDML as the same global
                // 
                // We'll use:
                // Map<Pair <String reaction, String param>, String global>		- if local converted to global
                // Set<Pair <String reaction, String param>>	(if needed?)	- if local stays local
                // 
                // local to global translation map
                Map<Pair<String, String>, String> l2gMap = null;
                if (vcBioModel instanceof BioModel) {
                    try {
                        // check if model to be exported to SBML has units compatible with SBML default units (default units in SBML can be assumed only until SBML Level2)
                        ModelUnitSystem forcedModelUnitSystem = simContext.getModel().getUnitSystem();
                        if (level < 3 && !ModelUnitSystem.isCompatibleWithDefaultSBMLLevel2Units(forcedModelUnitSystem)) {
                            forcedModelUnitSystem = ModelUnitSystem.createDefaultSBMLLevel2Units();
                        }
                        // create new Biomodel with new (SBML compatible)  unit system
                        BioModel modifiedBiomodel = ModelUnitConverter.createBioModelWithNewUnitSystem(simContext.getBioModel(), forcedModelUnitSystem);
                        // extract the simContext from new Biomodel. Apply overrides to *this* modified simContext
                        SimulationContext simContextFromModifiedBioModel = modifiedBiomodel.getSimulationContext(simContext.getName());
                        SBMLExporter sbmlExporter = new SBMLExporter(modifiedBiomodel, level, version, isSpatial);
                        sbmlExporter.setSelectedSimContext(simContextFromModifiedBioModel);
                        // no sim job
                        sbmlExporter.setSelectedSimulationJob(null);
                        sbmlString = sbmlExporter.getSBMLFile();
                        l2gMap = sbmlExporter.getLocalToGlobalTranslationMap();
                    } catch (ExpressionException | SbmlException e) {
                        e.printStackTrace(System.out);
                        throw new XmlParseException(e);
                    }
                } else {
                    throw new RuntimeException("unsupported Document Type " + vcBioModel.getClass().getName() + " for SBML export");
                }
                String sbmlFilePathStrAbsolute = savePath + FileUtils.WINDOWS_SEPARATOR + bioModelName + "_" + simContextName + ".xml";
                String sbmlFilePathStrRelative = bioModelName + "_" + simContextName + ".xml";
                XmlUtil.writeXMLStringToFile(sbmlString, sbmlFilePathStrAbsolute, true);
                sbmlFilePathStrAbsoluteList.add(sbmlFilePathStrRelative);
                String simContextId = TokenMangler.mangleToSName(simContextName);
                sedmlModel.addModel(new Model(simContextId, simContextName, sbmlLanguageURN, sbmlFilePathStrRelative));
                // required for mathOverrides, if any
                MathMapping mathMapping = simContext.createNewMathMapping();
                MathSymbolMapping mathSymbolMapping = mathMapping.getMathSymbolMapping();
                // create sedml simulation objects and tasks (mapping each sim with current simContext)
                int simCount = 0;
                String taskRef = null;
                int overrideCount = 0;
                for (Simulation vcSimulation : simContext.getSimulations()) {
                    List<DataGenerator> dataGeneratorsOfSim = new ArrayList<DataGenerator>();
                    // if simContext is non-spatial stochastic, check if sim is histogram
                    SolverTaskDescription simTaskDesc = vcSimulation.getSolverTaskDescription();
                    if (simContext.getGeometry().getDimension() == 0 && simContext.isStoch()) {
                        long numOfTrials = simTaskDesc.getStochOpt().getNumOfTrials();
                        if (numOfTrials > 1) {
                            String msg = "\n\t" + simContextName + " ( " + vcSimulation.getName() + " ) : export of non-spatial stochastic simulation with histogram option to SEDML not supported at this time.";
                            sedmlNotesStr += msg;
                            continue;
                        }
                    }
                    // create Algorithm and sedmlSimulation (UniformtimeCourse)
                    SolverDescription vcSolverDesc = simTaskDesc.getSolverDescription();
                    // String kiSAOIdStr = getKiSAOIdFromSimulation(vcSolverDesc);	// old way of doing it, going directly to the web site
                    String kiSAOIdStr = vcSolverDesc.getKisao();
                    Algorithm sedmlAlgorithm = new Algorithm(kiSAOIdStr);
                    TimeBounds vcSimTimeBounds = simTaskDesc.getTimeBounds();
                    double startingTime = vcSimTimeBounds.getStartingTime();
                    String simName = vcSimulation.getName();
                    UniformTimeCourse utcSim = new UniformTimeCourse(TokenMangler.mangleToSName(simName), simName, startingTime, startingTime, vcSimTimeBounds.getEndingTime(), (int) simTaskDesc.getExpectedNumTimePoints(), sedmlAlgorithm);
                    // if solver is not CVODE, add a note to utcSim to indicate actual solver name
                    if (!vcSolverDesc.equals(SolverDescription.CVODE)) {
                        String simNotesStr = "Actual Solver Name : '" + vcSolverDesc.getDisplayLabel() + "'.";
                        utcSim.addNote(createNotesElement(simNotesStr));
                    }
                    sedmlModel.addSimulation(utcSim);
                    // add SEDML tasks (map simulation to model:simContext)
                    // repeated tasks
                    MathOverrides mathOverrides = vcSimulation.getMathOverrides();
                    if (mathOverrides != null && mathOverrides.hasOverrides()) {
                        String[] overridenConstantNames = mathOverrides.getOverridenConstantNames();
                        String[] scannedConstantsNames = mathOverrides.getScannedConstantNames();
                        HashMap<String, String> scannedParamHash = new HashMap<String, String>();
                        HashMap<String, String> unscannedParamHash = new HashMap<String, String>();
                        for (String name : scannedConstantsNames) {
                            scannedParamHash.put(name, name);
                        }
                        for (String name : overridenConstantNames) {
                            if (!scannedParamHash.containsKey(name)) {
                                unscannedParamHash.put(name, name);
                            }
                        }
                        if (!unscannedParamHash.isEmpty() && scannedParamHash.isEmpty()) {
                            // only parameters with simple overrides (numeric/expression) no scans
                            // create new model with change for each parameter that has override; add simple task
                            String overriddenSimContextId = simContextId + "_" + overrideCount;
                            String overriddenSimContextName = simContextName + " modified";
                            Model sedModel = new Model(overriddenSimContextId, overriddenSimContextName, sbmlLanguageURN, simContextId);
                            overrideCount++;
                            for (String unscannedParamName : unscannedParamHash.values()) {
                                SymbolTableEntry ste = getSymbolTableEntryForModelEntity(mathSymbolMapping, unscannedParamName);
                                Expression unscannedParamExpr = mathOverrides.getActualExpression(unscannedParamName, 0);
                                if (unscannedParamExpr.isNumeric()) {
                                    // if expression is numeric, add ChangeAttribute to model created above
                                    XPathTarget targetXpath = getTargetAttributeXPath(ste, l2gMap);
                                    ChangeAttribute changeAttribute = new ChangeAttribute(targetXpath, unscannedParamExpr.infix());
                                    sedModel.addChange(changeAttribute);
                                } else {
                                    // non-numeric expression : add 'computeChange' to modified model
                                    ASTNode math = Libsedml.parseFormulaString(unscannedParamExpr.infix());
                                    XPathTarget targetXpath = getTargetXPath(ste, l2gMap);
                                    ComputeChange computeChange = new ComputeChange(targetXpath, math);
                                    String[] exprSymbols = unscannedParamExpr.getSymbols();
                                    for (String symbol : exprSymbols) {
                                        String symbolName = TokenMangler.mangleToSName(symbol);
                                        SymbolTableEntry ste1 = vcModel.getEntry(symbol);
                                        if (ste != null) {
                                            if (ste1 instanceof SpeciesContext || ste1 instanceof Structure || ste1 instanceof ModelParameter) {
                                                XPathTarget ste1_XPath = getTargetXPath(ste1, l2gMap);
                                                org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(symbolName, symbolName, taskRef, ste1_XPath.getTargetAsString());
                                                computeChange.addVariable(sedmlVar);
                                            } else {
                                                double doubleValue = 0.0;
                                                if (ste1 instanceof ReservedSymbol) {
                                                    doubleValue = getReservedSymbolValue(ste1);
                                                }
                                                Parameter sedmlParameter = new Parameter(symbolName, symbolName, doubleValue);
                                                computeChange.addParameter(sedmlParameter);
                                            }
                                        } else {
                                            throw new RuntimeException("Symbol '" + symbol + "' used in expression for '" + unscannedParamName + "' not found in model.");
                                        }
                                    }
                                    sedModel.addChange(computeChange);
                                }
                            }
                            sedmlModel.addModel(sedModel);
                            String taskId = "tsk_" + simContextCnt + "_" + simCount;
                            Task sedmlTask = new Task(taskId, taskId, sedModel.getId(), utcSim.getId());
                            sedmlModel.addTask(sedmlTask);
                            // to be used later to add dataGenerators : one set of DGs per model (simContext).
                            taskRef = taskId;
                        } else if (!scannedParamHash.isEmpty() && unscannedParamHash.isEmpty()) {
                            // only parameters with scans : only add 1 Task and 1 RepeatedTask
                            String taskId = "tsk_" + simContextCnt + "_" + simCount;
                            Task sedmlTask = new Task(taskId, taskId, simContextId, utcSim.getId());
                            sedmlModel.addTask(sedmlTask);
                            String repeatedTaskId = "repTsk_" + simContextCnt + "_" + simCount;
                            // TODO: temporary solution - we use as range here the first range
                            String scn = scannedConstantsNames[0];
                            String rId = "range_" + simContextCnt + "_" + simCount + "_" + scn;
                            RepeatedTask rt = new RepeatedTask(repeatedTaskId, repeatedTaskId, true, rId);
                            // to be used later to add dataGenerators - in our case it has to be the repeated task
                            taskRef = repeatedTaskId;
                            SubTask subTask = new SubTask("0", taskId);
                            rt.addSubtask(subTask);
                            for (String scannedConstName : scannedConstantsNames) {
                                ConstantArraySpec constantArraySpec = mathOverrides.getConstantArraySpec(scannedConstName);
                                String rangeId = "range_" + simContextCnt + "_" + simCount + "_" + scannedConstName;
                                // list of Ranges, if sim is parameter scan.
                                if (constantArraySpec != null) {
                                    Range r = null;
                                    System.out.println("     " + constantArraySpec.toString());
                                    if (constantArraySpec.getType() == ConstantArraySpec.TYPE_INTERVAL) {
                                        // ------ Uniform Range
                                        r = new UniformRange(rangeId, constantArraySpec.getMinValue(), constantArraySpec.getMaxValue(), constantArraySpec.getNumValues());
                                        rt.addRange(r);
                                    } else {
                                        // ----- Vector Range
                                        cbit.vcell.math.Constant[] cs = constantArraySpec.getConstants();
                                        ArrayList<Double> values = new ArrayList<Double>();
                                        for (int i = 0; i < cs.length; i++) {
                                            String value = cs[i].getExpression().infix();
                                            values.add(Double.parseDouble(value));
                                        }
                                        r = new VectorRange(rangeId, values);
                                        rt.addRange(r);
                                    }
                                    // list of Changes
                                    SymbolTableEntry ste = getSymbolTableEntryForModelEntity(mathSymbolMapping, scannedConstName);
                                    XPathTarget target = getTargetXPath(ste, l2gMap);
                                    // ASTNode math1 = new ASTCi(r.getId());		// was scannedConstName
                                    ASTNode math1 = Libsedml.parseFormulaString(r.getId());
                                    SetValue setValue = new SetValue(target, r.getId(), simContextId);
                                    setValue.setMath(math1);
                                    rt.addChange(setValue);
                                } else {
                                    throw new RuntimeException("No scan ranges found for scanned parameter : '" + scannedConstName + "'.");
                                }
                            }
                            sedmlModel.addTask(rt);
                        } else {
                            // both scanned and simple parameters : create new model with change for each simple override; add RepeatedTask
                            // create new model with change for each unscanned parameter that has override
                            String overriddenSimContextId = simContextId + "_" + overrideCount;
                            String overriddenSimContextName = simContextName + " modified";
                            Model sedModel = new Model(overriddenSimContextId, overriddenSimContextName, sbmlLanguageURN, simContextId);
                            overrideCount++;
                            String taskId = "tsk_" + simContextCnt + "_" + simCount;
                            Task sedmlTask = new Task(taskId, taskId, overriddenSimContextId, utcSim.getId());
                            sedmlModel.addTask(sedmlTask);
                            // scanned parameters
                            String repeatedTaskId = "repTsk_" + simContextCnt + "_" + simCount;
                            // TODO: temporary solution - we use as range here the first range
                            String scn = scannedConstantsNames[0];
                            String rId = "range_" + simContextCnt + "_" + simCount + "_" + scn;
                            RepeatedTask rt = new RepeatedTask(repeatedTaskId, repeatedTaskId, true, rId);
                            // to be used later to add dataGenerators - in our case it has to be the repeated task
                            taskRef = repeatedTaskId;
                            SubTask subTask = new SubTask("0", taskId);
                            rt.addSubtask(subTask);
                            for (String scannedConstName : scannedConstantsNames) {
                                ConstantArraySpec constantArraySpec = mathOverrides.getConstantArraySpec(scannedConstName);
                                String rangeId = "range_" + simContextCnt + "_" + simCount + "_" + scannedConstName;
                                // list of Ranges, if sim is parameter scan.
                                if (constantArraySpec != null) {
                                    Range r = null;
                                    System.out.println("     " + constantArraySpec.toString());
                                    if (constantArraySpec.getType() == ConstantArraySpec.TYPE_INTERVAL) {
                                        // ------ Uniform Range
                                        r = new UniformRange(rangeId, constantArraySpec.getMinValue(), constantArraySpec.getMaxValue(), constantArraySpec.getNumValues());
                                        rt.addRange(r);
                                    } else {
                                        // ----- Vector Range
                                        cbit.vcell.math.Constant[] cs = constantArraySpec.getConstants();
                                        ArrayList<Double> values = new ArrayList<Double>();
                                        for (int i = 0; i < cs.length; i++) {
                                            String value = cs[i].getExpression().infix() + ", ";
                                            values.add(Double.parseDouble(value));
                                        }
                                        r = new VectorRange(rangeId, values);
                                        rt.addRange(r);
                                    }
                                    // use scannedParamHash to store rangeId for that param, since it might be needed if unscanned param has a scanned param in expr.
                                    if (scannedParamHash.get(scannedConstName).equals(scannedConstName)) {
                                        // the hash was originally populated as <scannedParamName, scannedParamName>. Replace 'value' with rangeId for scannedParam
                                        scannedParamHash.put(scannedConstName, r.getId());
                                    }
                                    // create setValue for scannedConstName
                                    SymbolTableEntry ste2 = getSymbolTableEntryForModelEntity(mathSymbolMapping, scannedConstName);
                                    XPathTarget target1 = getTargetXPath(ste2, l2gMap);
                                    ASTNode math1 = new ASTCi(scannedConstName);
                                    SetValue setValue1 = new SetValue(target1, r.getId(), sedModel.getId());
                                    setValue1.setMath(math1);
                                    rt.addChange(setValue1);
                                } else {
                                    throw new RuntimeException("No scan ranges found for scanned parameter : '" + scannedConstName + "'.");
                                }
                            }
                            // for unscanned parameter overrides
                            for (String unscannedParamName : unscannedParamHash.values()) {
                                SymbolTableEntry ste = getSymbolTableEntryForModelEntity(mathSymbolMapping, unscannedParamName);
                                Expression unscannedParamExpr = mathOverrides.getActualExpression(unscannedParamName, 0);
                                if (unscannedParamExpr.isNumeric()) {
                                    // if expression is numeric, add ChangeAttribute to model created above
                                    XPathTarget targetXpath = getTargetAttributeXPath(ste, l2gMap);
                                    ChangeAttribute changeAttribute = new ChangeAttribute(targetXpath, unscannedParamExpr.infix());
                                    sedModel.addChange(changeAttribute);
                                } else {
                                    // check for any scanned parameter in unscanned parameter expression
                                    ASTNode math = Libsedml.parseFormulaString(unscannedParamExpr.infix());
                                    String[] exprSymbols = unscannedParamExpr.getSymbols();
                                    boolean bHasScannedParameter = false;
                                    String scannedParamNameInUnscannedParamExp = null;
                                    for (String symbol : exprSymbols) {
                                        if (scannedParamHash.get(symbol) != null) {
                                            bHasScannedParameter = true;
                                            scannedParamNameInUnscannedParamExp = new String(symbol);
                                            // @TODO check for multiple scannedParameters in expression.
                                            break;
                                        }
                                    }
                                    // (scanned parameter in expr) ? (add setValue for unscanned param in repeatedTask) : (add computeChange to modifiedModel)
                                    if (bHasScannedParameter && scannedParamNameInUnscannedParamExp != null) {
                                        // create setValue for unscannedParamName (which contains a scanned param in its expression)
                                        SymbolTableEntry entry = getSymbolTableEntryForModelEntity(mathSymbolMapping, unscannedParamName);
                                        XPathTarget target = getTargetXPath(entry, l2gMap);
                                        String rangeId = scannedParamHash.get(scannedParamNameInUnscannedParamExp);
                                        // @TODO: we have no range??
                                        SetValue setValue = new SetValue(target, rangeId, sedModel.getId());
                                        setValue.setMath(math);
                                        rt.addChange(setValue);
                                    } else {
                                        // non-numeric expression : add 'computeChange' to modified model
                                        XPathTarget targetXpath = getTargetXPath(ste, l2gMap);
                                        ComputeChange computeChange = new ComputeChange(targetXpath, math);
                                        for (String symbol : exprSymbols) {
                                            String symbolName = TokenMangler.mangleToSName(symbol);
                                            SymbolTableEntry ste1 = vcModel.getEntry(symbol);
                                            // ste1 could be a math parameter, hence the above could return null
                                            if (ste1 == null) {
                                                ste1 = simContext.getMathDescription().getEntry(symbol);
                                            }
                                            if (ste1 != null) {
                                                if (ste1 instanceof SpeciesContext || ste1 instanceof Structure || ste1 instanceof ModelParameter) {
                                                    XPathTarget ste1_XPath = getTargetXPath(ste1, l2gMap);
                                                    org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(symbolName, symbolName, taskRef, ste1_XPath.getTargetAsString());
                                                    computeChange.addVariable(sedmlVar);
                                                } else {
                                                    double doubleValue = 0.0;
                                                    if (ste1 instanceof ReservedSymbol) {
                                                        doubleValue = getReservedSymbolValue(ste1);
                                                    } else if (ste instanceof Function) {
                                                        try {
                                                            doubleValue = ste.getExpression().evaluateConstant();
                                                        } catch (Exception e) {
                                                            e.printStackTrace(System.out);
                                                            throw new RuntimeException("Unable to evaluate function '" + ste.getName() + "' used in '" + unscannedParamName + "' expression : ", e);
                                                        }
                                                    } else {
                                                        doubleValue = ste.getConstantValue();
                                                    }
                                                    // TODO: shouldn't be s1_init_uM which is a math symbol, should be s0 (so use the ste-something from above)
                                                    // TODO: revert to Variable, not Parameter
                                                    Parameter sedmlParameter = new Parameter(symbolName, symbolName, doubleValue);
                                                    computeChange.addParameter(sedmlParameter);
                                                }
                                            } else {
                                                throw new RuntimeException("Symbol '" + symbol + "' used in expression for '" + unscannedParamName + "' not found in model.");
                                            }
                                        }
                                        sedModel.addChange(computeChange);
                                    }
                                }
                            }
                            sedmlModel.addModel(sedModel);
                            sedmlModel.addTask(rt);
                        }
                    } else {
                        // no math overrides, add basic task.
                        String taskId = "tsk_" + simContextCnt + "_" + simCount;
                        Task sedmlTask = new Task(taskId, taskId, simContextId, utcSim.getId());
                        sedmlModel.addTask(sedmlTask);
                        // to be used later to add dataGenerators : one set of DGs per model (simContext).
                        taskRef = taskId;
                    }
                    // add one dataGenerator for 'time' for entire SEDML model.
                    // (using the id of the first task in model for 'taskRef' field of var since
                    String timeDataGenPrefix = DATAGENERATOR_TIME_NAME + "_" + taskRef;
                    DataGenerator timeDataGen = sedmlModel.getDataGeneratorWithId(timeDataGenPrefix);
                    if (timeDataGen == null) {
                        // org.jlibsedml.Variable timeVar = new org.jlibsedml.Variable(DATAGENERATOR_TIME_SYMBOL, DATAGENERATOR_TIME_SYMBOL, sedmlModel.getTasks().get(0).getId(), VariableSymbol.TIME);
                        org.jlibsedml.Variable timeVar = new org.jlibsedml.Variable(DATAGENERATOR_TIME_SYMBOL, DATAGENERATOR_TIME_SYMBOL, taskRef, VariableSymbol.TIME);
                        ASTNode math = Libsedml.parseFormulaString(DATAGENERATOR_TIME_SYMBOL);
                        timeDataGen = new DataGenerator(timeDataGenPrefix, timeDataGenPrefix, math);
                        timeDataGen.addVariable(timeVar);
                        sedmlModel.addDataGenerator(timeDataGen);
                        dataGeneratorsOfSim.add(timeDataGen);
                    }
                    // add dataGenerators for species
                    // get species list from SBML model.
                    String dataGenIdPrefix = "dataGen_" + taskRef;
                    String[] varNamesList = SimSpec.fromSBML(sbmlString).getVarsList();
                    for (String varName : varNamesList) {
                        org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(varName, varName, taskRef, sbmlSupport.getXPathForSpecies(varName));
                        ASTNode varMath = Libsedml.parseFormulaString(varName);
                        // "dataGen_" + varCount; - old code
                        String dataGenId = dataGenIdPrefix + "_" + TokenMangler.mangleToSName(varName);
                        DataGenerator dataGen = new DataGenerator(dataGenId, dataGenId, varMath);
                        dataGen.addVariable(sedmlVar);
                        sedmlModel.addDataGenerator(dataGen);
                        dataGeneratorsOfSim.add(dataGen);
                        varCount++;
                    }
                    // add DataGenerators for output functions here
                    ArrayList<AnnotatedFunction> outputFunctions = simContext.getOutputFunctionContext().getOutputFunctionsList();
                    for (AnnotatedFunction annotatedFunction : outputFunctions) {
                        Expression functionExpr = annotatedFunction.getExpression();
                        ASTNode funcMath = Libsedml.parseFormulaString(functionExpr.infix());
                        // "dataGen_" + varCount; - old code
                        String dataGenId = dataGenIdPrefix + "_" + TokenMangler.mangleToSName(annotatedFunction.getName());
                        DataGenerator dataGen = new DataGenerator(dataGenId, dataGenId, funcMath);
                        String[] functionSymbols = functionExpr.getSymbols();
                        for (String symbol : functionSymbols) {
                            String symbolName = TokenMangler.mangleToSName(symbol);
                            // try to get symbol from model, if null, try simContext.mathDesc
                            SymbolTableEntry ste = vcModel.getEntry(symbol);
                            if (ste == null) {
                                ste = simContext.getMathDescription().getEntry(symbol);
                            }
                            if (ste instanceof SpeciesContext || ste instanceof Structure || ste instanceof ModelParameter) {
                                XPathTarget targetXPath = getTargetXPath(ste, l2gMap);
                                org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(symbolName, symbolName, taskRef, targetXPath.getTargetAsString());
                                dataGen.addVariable(sedmlVar);
                            } else {
                                double value = 0.0;
                                if (ste instanceof Function) {
                                    try {
                                        value = ste.getExpression().evaluateConstant();
                                    } catch (Exception e) {
                                        e.printStackTrace(System.out);
                                        throw new RuntimeException("Unable to evaluate function '" + ste.getName() + "' for output function '" + annotatedFunction.getName() + "'.", e);
                                    }
                                } else {
                                    value = ste.getConstantValue();
                                }
                                Parameter sedmlParameter = new Parameter(symbolName, symbolName, value);
                                dataGen.addParameter(sedmlParameter);
                            }
                        }
                        sedmlModel.addDataGenerator(dataGen);
                        dataGeneratorsOfSim.add(dataGen);
                        varCount++;
                    }
                    simCount++;
                    // ignoring output for spatial deterministic (spatial stochastic is not exported to SEDML) and non-spatial stochastic applications with histogram
                    if (!(simContext.getGeometry().getDimension() > 0)) {
                        // ignore Output (Plot2d)  for non-spatial stochastic simulation with histogram.
                        boolean bSimHasHistogram = false;
                        if (simContext.isStoch()) {
                            long numOfTrials = simTaskDesc.getStochOpt().getNumOfTrials();
                            if (numOfTrials > 1) {
                                // not histogram {
                                bSimHasHistogram = true;
                            }
                        }
                        if (!bSimHasHistogram) {
                            String plot2dId = "plot2d_" + TokenMangler.mangleToSName(vcSimulation.getName());
                            Plot2D sedmlPlot2d = new Plot2D(plot2dId, simContext.getName() + "plots");
                            sedmlPlot2d.addNote(createNotesElement("Plot of all variables and output functions from application '" + simContext.getName() + "' ; simulation '" + vcSimulation.getName() + "' in VCell model"));
                            List<DataGenerator> dataGenerators = sedmlModel.getDataGenerators();
                            String xDataRef = sedmlModel.getDataGeneratorWithId(DATAGENERATOR_TIME_NAME + "_" + taskRef).getId();
                            // add a curve for each dataGenerator in SEDML model
                            int curveCnt = 0;
                            for (DataGenerator dataGenerator : dataGeneratorsOfSim) {
                                // no curve for time, since time is xDateReference
                                if (dataGenerator.getId().equals(xDataRef)) {
                                    continue;
                                }
                                String curveId = "curve_" + curveCnt++;
                                Curve curve = new Curve(curveId, curveId, false, false, xDataRef, dataGenerator.getId());
                                sedmlPlot2d.addCurve(curve);
                            }
                            sedmlModel.addOutput(sedmlPlot2d);
                        }
                    }
                }
            // end - for 'sims'
            } else {
                // end if (!(simContext.getGeometry().getDimension() > 0 && simContext.isStoch()))
                String msg = "\n\t" + simContextName + " : export of spatial stochastic (Smoldyn solver) applications to SEDML not supported at this time.";
                sedmlNotesStr += msg;
            }
            // end : if-else simContext is not spatial stochastic
            simContextCnt++;
        }
        // if sedmlNotesStr is not null, there were some applications that could not be exported to SEDML (eg., spatial stochastic). Create a notes element and add it to sedml Model.
        if (sedmlNotesStr.length() > 0) {
            sedmlNotesStr = "\n\tThe following applications in the VCell model were not exported to VCell : " + sedmlNotesStr;
            sedmlModel.addNote(createNotesElement(sedmlNotesStr));
        }
        // error check : if there are no non-spatial deterministic applications (=> no models in SEDML document), complain.
        if (sedmlModel.getModels().isEmpty()) {
            throw new RuntimeException("No applications in biomodel to export to Sedml.");
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new RuntimeException("Error adding model to SEDML document : " + e.getMessage());
    }
}

Example 3 with MathSymbolMapping

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

the class XmlHelper method applyOverridesForSBML.

/**
 * applyOverrides: private method to apply overrides from the simulation in 'simJob' to simContext, if any.
 * 				Start off by cloning biomodel, since all the references are required in cloned simContext and is
 * 				best retained by cloning biomodel.
 * @param bm - biomodel to be cloned
 * @param sc - simulationContext to be cloned and overridden using math overrides in simulation
 * @param simJob - simulationJob from where simulation with overrides is obtained.
 * @return
 */
public static SimulationContext applyOverridesForSBML(BioModel bm, SimulationContext sc, SimulationJob simJob) {
    SimulationContext overriddenSimContext = sc;
    if (simJob != null) {
        Simulation sim = simJob.getSimulation();
        // need to clone Biomodel, simContext, etc. only if simulation has override(s)
        try {
            if (sim != null && sim.getMathOverrides().hasOverrides()) {
                // BioModel clonedBM = (BioModel)BeanUtils.cloneSerializable(bm);
                BioModel clonedBM = XMLToBioModel(new XMLSource(bioModelToXML(bm)));
                clonedBM.refreshDependencies();
                // get the simContext in cloned Biomodel that corresponds to 'sc'
                SimulationContext[] simContexts = clonedBM.getSimulationContexts();
                for (int i = 0; i < simContexts.length; i++) {
                    if (simContexts[i].getName().equals(sc.getName())) {
                        overriddenSimContext = simContexts[i];
                        break;
                    }
                }
                // 
                overriddenSimContext.getModel().refreshDependencies();
                overriddenSimContext.refreshDependencies();
                MathMapping mathMapping = overriddenSimContext.createNewMathMapping();
                MathSymbolMapping msm = mathMapping.getMathSymbolMapping();
                MathOverrides mathOverrides = sim.getMathOverrides();
                String[] moConstNames = mathOverrides.getOverridenConstantNames();
                for (int i = 0; i < moConstNames.length; i++) {
                    cbit.vcell.math.Constant overriddenConstant = mathOverrides.getConstant(moConstNames[i]);
                    // Expression overriddenExpr = mathOverrides.getActualExpression(moConstNames[i], 0);
                    Expression overriddenExpr = mathOverrides.getActualExpression(moConstNames[i], simJob.getJobIndex());
                    // The above constant (from mathoverride) is not the same instance as the one in the MathSymbolMapping hash.
                    // Hence retreive the correct instance from mathSymbolMapping (mathMapping -> mathDescription) and use it to
                    // retrieve its value (symbolTableEntry) from hash.
                    cbit.vcell.math.Variable overriddenVar = msm.findVariableByName(overriddenConstant.getName());
                    cbit.vcell.parser.SymbolTableEntry[] stes = msm.getBiologicalSymbol(overriddenVar);
                    if (stes == null) {
                        throw new NullPointerException("No matching biological symbol for : " + overriddenConstant.getName());
                    }
                    if (stes.length > 1) {
                        throw new RuntimeException("Cannot have more than one mapping entry for constant : " + overriddenConstant.getName());
                    }
                    if (stes[0] instanceof Parameter) {
                        Parameter param = (Parameter) stes[0];
                        if (param.isExpressionEditable()) {
                            if (param instanceof Kinetics.KineticsParameter) {
                                // Kinetics param has to be set separately for the integrity of the kinetics object
                                Kinetics.KineticsParameter kinParam = (Kinetics.KineticsParameter) param;
                                ReactionStep[] rs = overriddenSimContext.getModel().getReactionSteps();
                                for (int j = 0; j < rs.length; j++) {
                                    if (rs[j].getNameScope().getName().equals(kinParam.getNameScope().getName())) {
                                        rs[j].getKinetics().setParameterValue(kinParam, overriddenExpr);
                                    }
                                }
                            } else if (param instanceof cbit.vcell.model.ExpressionContainer) {
                                // If it is any other editable param, set its expression with the
                                ((cbit.vcell.model.ExpressionContainer) param).setExpression(overriddenExpr);
                            }
                        }
                    }
                // end - if (stes[0] is Parameter)
                }
            // end  - for moConstNames
            }
        // end if (sim has MathOverrides)
        } catch (Exception e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Could not apply overrides from simulation to application parameters : " + e.getMessage());
        }
    }
    // end if (simJob != null)
    return overriddenSimContext;
}

Example 4 with MathSymbolMapping

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

the class InitialConditionsPanel method jMenuItemCopy_ActionPerformed.

/**
 * Comment
 */
private void jMenuItemCopy_ActionPerformed(java.awt.event.ActionEvent actionEvent) {
    if (actionEvent.getSource() == getJMenuItemCopy() || actionEvent.getSource() == getJMenuItemCopyAll()) {
        try {
            // 
            // Copy Symbols and Values Init Conditions
            // 
            int[] rows = null;
            if (actionEvent.getSource() == getJMenuItemCopyAll()) {
                rows = new int[getScrollPaneTable().getRowCount()];
                for (int i = 0; i < rows.length; i += 1) {
                    rows[i] = i;
                }
            } else {
                rows = getScrollPaneTable().getSelectedRows();
            }
            MathSymbolMapping msm = null;
            try {
                msm = getSimulationContext().createNewMathMapping().getMathSymbolMapping();
            } catch (Exception e) {
                e.printStackTrace(System.out);
                DialogUtils.showWarningDialog(this, "current math not valid, some paste operations will be limited\n\nreason: " + e.getMessage());
            }
            StringBuffer sb = new StringBuffer();
            sb.append("initial Conditions Parameters for (BioModel)" + getSimulationContext().getBioModel().getName() + " (App)" + getSimulationContext().getName() + "\n");
            java.util.Vector<SymbolTableEntry> primarySymbolTableEntriesV = new java.util.Vector<SymbolTableEntry>();
            java.util.Vector<SymbolTableEntry> alternateSymbolTableEntriesV = new java.util.Vector<SymbolTableEntry>();
            java.util.Vector<Expression> resolvedValuesV = new java.util.Vector<Expression>();
            for (int i = 0; i < rows.length; i += 1) {
                SpeciesContextSpec scs = tableModel.getValueAt(rows[i]);
                if (scs.isConstant()) {
                    // need to change
                    primarySymbolTableEntriesV.add(scs.getInitialConditionParameter());
                    if (msm != null) {
                        alternateSymbolTableEntriesV.add(msm.getVariable(scs.getSpeciesContext()));
                    } else {
                        alternateSymbolTableEntriesV.add(null);
                    }
                    resolvedValuesV.add(new Expression(scs.getInitialConditionParameter().getExpression()));
                    sb.append(scs.getSpeciesContext().getName() + "\t" + scs.getInitialConditionParameter().getName() + "\t" + scs.getInitialConditionParameter().getExpression().infix() + "\n");
                } else {
                    for (int j = 0; j < scs.getParameters().length; j += 1) {
                        SpeciesContextSpec.SpeciesContextSpecParameter scsp = (SpeciesContextSpec.SpeciesContextSpecParameter) scs.getParameters()[j];
                        if (VCellCopyPasteHelper.isSCSRoleForDimension(scsp.getRole(), getSimulationContext().getGeometry().getDimension())) {
                            Expression scspExpression = scsp.getExpression();
                            sb.append(scs.getSpeciesContext().getName() + "\t" + scsp.getName() + "\t" + (scspExpression != null ? scspExpression.infix() : "") + "\n");
                            if (scspExpression != null) {
                                // "Default" boundary conditions can't be copied
                                primarySymbolTableEntriesV.add(scsp);
                                if (msm != null) {
                                    alternateSymbolTableEntriesV.add(msm.getVariable(scsp));
                                } else {
                                    alternateSymbolTableEntriesV.add(null);
                                }
                                resolvedValuesV.add(new Expression(scspExpression));
                            }
                        }
                    }
                }
            }
            // 
            // Send to clipboard
            // 
            VCellTransferable.ResolvedValuesSelection rvs = new VCellTransferable.ResolvedValuesSelection((SymbolTableEntry[]) BeanUtils.getArray(primarySymbolTableEntriesV, SymbolTableEntry.class), (SymbolTableEntry[]) BeanUtils.getArray(alternateSymbolTableEntriesV, SymbolTableEntry.class), (Expression[]) BeanUtils.getArray(resolvedValuesV, Expression.class), sb.toString());
            VCellTransferable.sendToClipboard(rvs);
        } catch (Throwable e) {
            PopupGenerator.showErrorDialog(InitialConditionsPanel.this, "InitialConditionsPanel Copy failed.  " + e.getMessage(), e);
        }
    }
}

Example 5 with MathSymbolMapping

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

the class InitialConditionsPanel method jMenuItemPaste_ActionPerformed.

/**
 * Comment
 */
private void jMenuItemPaste_ActionPerformed(final java.awt.event.ActionEvent actionEvent) {
    final Vector<String> pasteDescriptionsV = new Vector<String>();
    final Vector<Expression> newExpressionsV = new Vector<Expression>();
    final Vector<SpeciesContextSpec.SpeciesContextSpecParameter> changedParametersV = new Vector<SpeciesContextSpec.SpeciesContextSpecParameter>();
    AsynchClientTask task1 = new AsynchClientTask("validating", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (actionEvent.getSource() == getJMenuItemPaste() || actionEvent.getSource() == getJMenuItemPasteAll()) {
                Object pasteThis = VCellTransferable.getFromClipboard(VCellTransferable.OBJECT_FLAVOR);
                MathSymbolMapping msm = null;
                Exception mathMappingException = null;
                try {
                    MathMapping mm = null;
                    mm = getSimulationContext().createNewMathMapping();
                    msm = mm.getMathSymbolMapping();
                } catch (Exception e) {
                    mathMappingException = e;
                    e.printStackTrace(System.out);
                }
                int[] rows = null;
                if (actionEvent.getSource() == getJMenuItemPasteAll()) {
                    rows = new int[getScrollPaneTable().getRowCount()];
                    for (int i = 0; i < rows.length; i += 1) {
                        rows[i] = i;
                    }
                } else {
                    rows = getScrollPaneTable().getSelectedRows();
                }
                // 
                // Check paste
                // 
                StringBuffer errors = null;
                for (int i = 0; i < rows.length; i += 1) {
                    SpeciesContextSpec scs = tableModel.getValueAt(rows[i]);
                    try {
                        if (pasteThis instanceof VCellTransferable.ResolvedValuesSelection) {
                            VCellTransferable.ResolvedValuesSelection rvs = (VCellTransferable.ResolvedValuesSelection) pasteThis;
                            for (int j = 0; j < rvs.getPrimarySymbolTableEntries().length; j += 1) {
                                SpeciesContextSpec.SpeciesContextSpecParameter pasteDestination = null;
                                SpeciesContextSpec.SpeciesContextSpecParameter clipboardBiologicalParameter = null;
                                if (rvs.getPrimarySymbolTableEntries()[j] instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
                                    clipboardBiologicalParameter = (SpeciesContextSpec.SpeciesContextSpecParameter) rvs.getPrimarySymbolTableEntries()[j];
                                } else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
                                    clipboardBiologicalParameter = (SpeciesContextSpec.SpeciesContextSpecParameter) rvs.getAlternateSymbolTableEntries()[j];
                                }
                                if (clipboardBiologicalParameter == null) {
                                    Variable pastedMathVariable = null;
                                    if (rvs.getPrimarySymbolTableEntries()[j] instanceof Variable) {
                                        pastedMathVariable = (Variable) rvs.getPrimarySymbolTableEntries()[j];
                                    } else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof Variable) {
                                        pastedMathVariable = (Variable) rvs.getAlternateSymbolTableEntries()[j];
                                    }
                                    if (pastedMathVariable != null) {
                                        if (msm == null) {
                                            throw mathMappingException;
                                        }
                                        Variable localMathVariable = msm.findVariableByName(pastedMathVariable.getName());
                                        if (localMathVariable == null) {
                                            // try if localMathVariable is a speciesContext init parameter
                                            String initSuffix = DiffEquMathMapping.MATH_FUNC_SUFFIX_SPECIES_INIT_CONC_UNIT_PREFIX + TokenMangler.fixTokenStrict(scs.getInitialConcentrationParameter().getUnitDefinition().getSymbol());
                                            localMathVariable = msm.findVariableByName(pastedMathVariable.getName() + initSuffix);
                                        }
                                        if (localMathVariable != null) {
                                            SymbolTableEntry[] localBiologicalSymbolArr = msm.getBiologicalSymbol(localMathVariable);
                                            for (int k = 0; k < localBiologicalSymbolArr.length; k += 1) {
                                                if (localBiologicalSymbolArr[k] instanceof SpeciesContext && scs.getSpeciesContext() == localBiologicalSymbolArr[k]) {
                                                    // need to change
                                                    pasteDestination = scs.getInitialConditionParameter();
                                                } else if (localBiologicalSymbolArr[k] instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
                                                    for (int l = 0; l < scs.getParameters().length; l += 1) {
                                                        if (scs.getParameters()[l] == localBiologicalSymbolArr[k]) {
                                                            pasteDestination = (SpeciesContextSpec.SpeciesContextSpecParameter) localBiologicalSymbolArr[k];
                                                            break;
                                                        }
                                                    }
                                                }
                                                if (pasteDestination != null) {
                                                    break;
                                                }
                                            }
                                        }
                                    }
                                } else {
                                    for (int k = 0; k < scs.getParameters().length; k += 1) {
                                        SpeciesContextSpec.SpeciesContextSpecParameter scsp = (SpeciesContextSpec.SpeciesContextSpecParameter) scs.getParameters()[k];
                                        if (scsp.getRole() == clipboardBiologicalParameter.getRole() && scs.getSpeciesContext().compareEqual(((SpeciesContextSpec) clipboardBiologicalParameter.getNameScope().getScopedSymbolTable()).getSpeciesContext())) {
                                            pasteDestination = (SpeciesContextSpec.SpeciesContextSpecParameter) scsp;
                                        }
                                    }
                                }
                                if (pasteDestination != null) {
                                    changedParametersV.add(pasteDestination);
                                    newExpressionsV.add(rvs.getExpressionValues()[j]);
                                    pasteDescriptionsV.add(VCellCopyPasteHelper.formatPasteList(scs.getSpeciesContext().getName(), pasteDestination.getName(), pasteDestination.getExpression().infix(), rvs.getExpressionValues()[j].infix()));
                                }
                            }
                        }
                    } catch (Throwable e) {
                        if (errors == null) {
                            errors = new StringBuffer();
                        }
                        errors.append(scs.getSpeciesContext().getName() + " (" + e.getClass().getName() + ") " + e.getMessage() + "\n\n");
                    }
                }
                if (errors != null) {
                    throw new Exception(errors.toString());
                }
            }
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("pasting", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // Do paste
            if (pasteDescriptionsV.size() > 0) {
                String[] pasteDescriptionArr = new String[pasteDescriptionsV.size()];
                pasteDescriptionsV.copyInto(pasteDescriptionArr);
                SpeciesContextSpec.SpeciesContextSpecParameter[] changedParametersArr = new SpeciesContextSpec.SpeciesContextSpecParameter[changedParametersV.size()];
                changedParametersV.copyInto(changedParametersArr);
                Expression[] newExpressionsArr = new Expression[newExpressionsV.size()];
                newExpressionsV.copyInto(newExpressionsArr);
                VCellCopyPasteHelper.chooseApplyPaste(InitialConditionsPanel.this, pasteDescriptionArr, changedParametersArr, newExpressionsArr);
            } else {
                PopupGenerator.showInfoDialog(InitialConditionsPanel.this, "No paste items match the destination (no changes made).");
            }
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
}