Examples with SymbolTableEntry cbit.vcell.parser.SymbolTableEntry used on opensource projects

Example 26 with SymbolTableEntry

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

the class PdeTimePlotMultipleVariablesPanel method showTimePlot.

public void showTimePlot() {
    if ((plotChangeTimer = ClientTaskDispatcher.getBlockingTimer(this, multiTimePlotHelper.getPdeDatacontext(), null, plotChangeTimer, new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e2) {
            showTimePlot();
        }
    }, "PdeTimePlotMultipleVariablesPanel update...")) != null) {
        return;
    }
    VariableType varType = multiTimePlotHelper.getVariableType();
    Object[] selectedValues = variableJList.getSelectedValues();
    DataIdentifier[] selectedDataIdentifiers = new DataIdentifier[selectedValues.length];
    System.arraycopy(selectedValues, 0, selectedDataIdentifiers, 0, selectedValues.length);
    if (selectedDataIdentifiers.length > 1) {
        for (DataIdentifier selectedDataIdentifier : selectedDataIdentifiers) {
            if (!selectedDataIdentifier.getVariableType().getVariableDomain().equals(varType.getVariableDomain())) {
                PopupGenerator.showErrorDialog(this, "Please choose VOLUME variables or MEMBRANE variables only");
                variableJList.clearSelection();
                variableJList.setSelectedValue(multiTimePlotHelper.getPdeDatacontext().getVariableName(), true);
                return;
            }
        }
    }
    try {
        final int numSelectedVariables = selectedDataIdentifiers.length;
        final int numSelectedSpatialPoints = pointVector.size();
        int[][] indices = new int[numSelectedVariables][numSelectedSpatialPoints];
        // 
        for (int i = 0; i < numSelectedSpatialPoints; i++) {
            for (int v = 0; v < numSelectedVariables; v++) {
                if (selectedDataIdentifiers[v].getVariableType().equals(varType)) {
                    if (varType.equals(VariableType.VOLUME) || varType.equals(VariableType.VOLUME_REGION) || varType.equals(VariableType.POSTPROCESSING)) {
                        SpatialSelectionVolume ssv = (SpatialSelectionVolume) pointVector.get(i);
                        indices[v][i] = ssv.getIndex(0);
                    } else if (varType.equals(VariableType.MEMBRANE) || varType.equals(VariableType.MEMBRANE_REGION)) {
                        SpatialSelectionMembrane ssm = (SpatialSelectionMembrane) pointVector.get(i);
                        indices[v][i] = ssm.getIndex(0);
                    }
                } else {
                    if (varType.equals(VariableType.VOLUME) || varType.equals(VariableType.VOLUME_REGION) || varType.equals(VariableType.POSTPROCESSING)) {
                        SpatialSelectionVolume ssv = (SpatialSelectionVolume) pointVector2.get(i);
                        indices[v][i] = ssv.getIndex(0);
                    } else if (varType.equals(VariableType.MEMBRANE) || varType.equals(VariableType.MEMBRANE_REGION)) {
                        SpatialSelectionMembrane ssm = (SpatialSelectionMembrane) pointVector2.get(i);
                        indices[v][i] = ssm.getIndex(0);
                    }
                }
            }
        }
        final String[] selectedVarNames = new String[numSelectedVariables];
        for (int i = 0; i < selectedVarNames.length; i++) {
            selectedVarNames[i] = selectedDataIdentifiers[i].getName();
        }
        final double[] timePoints = multiTimePlotHelper.getPdeDatacontext().getTimePoints();
        TimeSeriesJobSpec tsjs = new TimeSeriesJobSpec(selectedVarNames, indices, null, timePoints[0], 1, timePoints[timePoints.length - 1], VCDataJobID.createVCDataJobID(multiTimePlotHelper.getUser(), true));
        if (!tsjs.getVcDataJobID().isBackgroundTask()) {
            throw new RuntimeException("Use getTimeSeries(...) if not a background job");
        }
        Hashtable<String, Object> hash = new Hashtable<String, Object>();
        hash.put(PDEDataViewer.StringKey_timeSeriesJobSpec, tsjs);
        AsynchClientTask task1 = new PDEDataViewer.TimeSeriesDataRetrievalTask("Retrieving Data", multiTimePlotHelper, multiTimePlotHelper.getPdeDatacontext());
        AsynchClientTask task2 = new AsynchClientTask("showing time plot", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                TSJobResultsNoStats tsJobResultsNoStats = (TSJobResultsNoStats) hashTable.get(PDEDataViewer.StringKey_timeSeriesJobResults);
                int plotCount = numSelectedVariables * numSelectedSpatialPoints;
                SymbolTableEntry[] symbolTableEntries = new SymbolTableEntry[plotCount];
                String[] plotNames = new String[plotCount];
                double[][] plotDatas = new double[1 + plotCount][];
                plotDatas[0] = timePoints;
                int plotIndex = 0;
                for (int v = 0; v < numSelectedVariables; v++) {
                    String varName = selectedVarNames[v];
                    double[][] data = tsJobResultsNoStats.getTimesAndValuesForVariable(varName);
                    for (int i = 1; i < data.length; i++) {
                        symbolTableEntries[plotIndex] = multiTimePlotHelper.getsimulation().getMathDescription().getEntry(varName);
                        plotNames[plotIndex] = varName + " at P[" + (i - 1) + "]";
                        plotDatas[plotIndex + 1] = data[i];
                        plotIndex++;
                    }
                }
                Plot2D plot2D = new SingleXPlot2D(symbolTableEntries, multiTimePlotHelper.getDataSymbolMetadataResolver(), ReservedVariable.TIME.getName(), plotNames, plotDatas, new String[] { "Time Plot", ReservedVariable.TIME.getName(), "" });
                plotPane.setPlot2D(plot2D);
            }
        };
        ClientTaskDispatcher.dispatch(this, hash, new AsynchClientTask[] { task1, task2 }, false, true, true, null, false);
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}

Example 27 with SymbolTableEntry

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

the class ODESolverPlotSpecificationPanel method regeneratePlot2D.

/**
 * Comment
 */
private void regeneratePlot2D() throws ExpressionException, ObjectNotFoundException {
    if (getMyDataInterface() == null) {
        return;
    }
    if (!getMyDataInterface().isMultiTrialData()) {
        if (getXAxisComboBox_frm().getSelectedIndex() < 0) {
            return;
        } else {
            // double[] xData = getOdeSolverResultSet().extractColumn(getPlottableColumnIndices()[getXIndex()]);
            // getUnfilteredSortedXAxisNames
            double[] xData = getMyDataInterface().extractColumn((String) getXAxisComboBox_frm().getSelectedItem());
            double[][] allData = new double[((DefaultListModel) getYAxisChoice().getModel()).size() + 1][xData.length];
            String[] yNames = new String[((DefaultListModel) getYAxisChoice().getModel()).size()];
            allData[0] = xData;
            double[] yData = new double[xData.length];
            double currParamValue = 0.0;
            double deltaParamValue = 0.0;
            // Extrapolation calculations!
            if (getSensitivityParameter() != null) {
                int val = getSensitivityParameterSlider().getValue();
                double nominalParamValue = getSensitivityParameter().getConstantValue();
                double pMax = nominalParamValue * 1.1;
                double pMin = nominalParamValue * 0.9;
                int iMax = getSensitivityParameterSlider().getMaximum();
                int iMin = getSensitivityParameterSlider().getMinimum();
                double slope = (pMax - pMin) / (iMax - iMin);
                currParamValue = slope * val + pMin;
                deltaParamValue = currParamValue - nominalParamValue;
                getMaxLabel().setText(Double.toString(pMax));
                getMinLabel().setText(Double.toString(pMin));
                getCurLabel().setText(Double.toString(currParamValue));
            }
            if (!getLogSensCheckbox().getModel().isSelected()) {
                // When log sensitivity check box is not selected.
                for (int i = 0; i < allData.length - 1; i++) {
                    // If sensitivity analysis is enabled, extrapolate values for State vars and non-sensitivity functions
                    if (getSensitivityParameter() != null) {
                        ColumnDescription cd = getMyDataInterface().getColumnDescription((String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i));
                        double[] sens = getSensValues(cd);
                        yData = getMyDataInterface().extractColumn(cd.getName());
                        // sens array != null for non-sensitivity state vars and functions, so extrapolate
                        if (sens != null) {
                            for (int j = 0; j < sens.length; j++) {
                                if (Math.abs(yData[j]) > 1e-6) {
                                    // away from zero, exponential extrapolation
                                    allData[i + 1][j] = yData[j] * Math.exp(deltaParamValue * sens[j] / yData[j]);
                                } else {
                                    // around zero - linear extrapolation
                                    allData[i + 1][j] = yData[j] + sens[j] * deltaParamValue;
                                }
                            }
                        // sens array == null for sensitivity state vars and functions, so don't change their original values
                        } else {
                            allData[i + 1] = getMyDataInterface().extractColumn((String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i));
                        }
                    } else {
                        // No sensitivity analysis case, so do not alter the original values for any variable or function
                        allData[i + 1] = getMyDataInterface().extractColumn((String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i));
                    }
                    yNames[i] = (String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i);
                }
            } else {
                // When log sensitivity checkbox is selected.
                // Get sensitivity parameter and its value to compute log sensitivity
                Constant sensParam = getSensitivityParameter();
                double sensParamValue = sensParam.getConstantValue();
                getJLabelSensitivityParameter().setText("Sensitivity wrt Parameter " + sensParam.getName());
                // 
                for (int i = 0; i < allData.length - 1; i++) {
                    // Finding sensitivity var column for each column in result set.
                    ColumnDescription cd = getMyDataInterface().getColumnDescription((String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i));
                    String sensVarName = null;
                    ColumnDescription[] allColumnDescriptions = getMyDataInterface().getAllColumnDescriptions();
                    for (int j = 0; j < allColumnDescriptions.length; j++) {
                        String obj = "sens_" + cd.getName() + "_wrt_" + sensParam.getName();
                        if (allColumnDescriptions[j].getName().equals(obj)) {
                            sensVarName = obj;
                            break;
                        }
                    }
                    int sensIndex = -1;
                    if (sensVarName != null) {
                        for (int j = 0; j < ((DefaultListModel) getYAxisChoice().getModel()).getSize(); j++) {
                            if (((String) ((DefaultListModel) getYAxisChoice().getModel()).get(j)).equals(sensVarName)) {
                                sensIndex = j;
                                break;
                            }
                        }
                    }
                    yData = getMyDataInterface().extractColumn(cd.getName());
                    // If sensitivity var exists, compute log sensitivity
                    if (sensVarName != null) {
                        double[] sens = getMyDataInterface().extractColumn(sensVarName);
                        for (int k = 0; k < yData.length; k++) {
                            // Extrapolated statevars and functions
                            if (Math.abs(yData[k]) > 1e-6) {
                                // away from zero, exponential extrapolation
                                allData[i + 1][k] = yData[k] * Math.exp(deltaParamValue * sens[k] / yData[k]);
                            } else {
                                // around zero - linear extrapolation
                                allData[i + 1][k] = yData[k] + sens[k] * deltaParamValue;
                            }
                            // Log sensitivity for the state variables and functions
                            // default if floating point problems
                            double logSens = 0.0;
                            if (Math.abs(yData[k]) > 0) {
                                double tempLogSens = sens[k] * sensParamValue / yData[k];
                                if (tempLogSens != Double.NEGATIVE_INFINITY && tempLogSens != Double.POSITIVE_INFINITY && tempLogSens != Double.NaN) {
                                    logSens = tempLogSens;
                                }
                            }
                            if (sensIndex > -1) {
                                allData[sensIndex + 1][k] = logSens;
                            }
                        }
                    // If sensitivity var does not exist, retain  original value of column (var or function).
                    } else {
                        if (!cd.getName().startsWith("sens_")) {
                            allData[i + 1] = yData;
                        }
                    }
                    yNames[i] = (String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i);
                }
            }
            String title = "";
            String xLabel = (String) getXAxisComboBox_frm().getSelectedItem();
            String yLabel = "";
            if (yNames.length == 1) {
                yLabel = yNames[0];
            }
            // Update Sensitivity parameter label depending on whether Log sensitivity check box is checked or not.
            if (!getLogSensCheckbox().getModel().isSelected()) {
                getJLabelSensitivityParameter().setText("");
            }
            SymbolTableEntry[] symbolTableEntries = null;
            if (getSymbolTable() != null && yNames != null && yNames.length > 0) {
                symbolTableEntries = new SymbolTableEntry[yNames.length];
                for (int i = 0; i < yNames.length; i += 1) {
                    SymbolTableEntry ste = getSymbolTable().getEntry(yNames[i]);
                    symbolTableEntries[i] = ste;
                }
            }
            SingleXPlot2D plot2D = new SingleXPlot2D(symbolTableEntries, getMyDataInterface().getDataSymbolMetadataResolver(), xLabel, yNames, allData, new String[] { title, xLabel, yLabel });
            refreshVisiblePlots(plot2D);
            // here fire "singleXPlot2D" event, ODEDataViewer's event handler listens to it.
            setPlot2D(plot2D);
        }
    } else // end of none MultitrialData
    // multitrial data
    {
        // a column of data get from ODESolverRestultSet, which is actually the results for a specific variable during multiple trials
        double[] rowData = new double[getMyDataInterface().getRowCount()];
        PlotData[] plotData = new PlotData[((DefaultListModel) getYAxisChoice().getModel()).size()];
        for (int i = 0; i < plotData.length; i++) {
            ColumnDescription cd = getMyDataInterface().getColumnDescription((String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i));
            rowData = getMyDataInterface().extractColumn(cd.getName());
            Point2D[] histogram = generateHistogram(rowData);
            double[] x = new double[histogram.length];
            double[] y = new double[histogram.length];
            for (int j = 0; j < histogram.length; j++) {
                x[j] = histogram[j].getX();
                y[j] = histogram[j].getY();
            }
            plotData[i] = new PlotData(x, y);
        }
        SymbolTableEntry[] symbolTableEntries = null;
        if (getSymbolTable() != null && ((DefaultListModel) getYAxisChoice().getModel()).size() > 0) {
            symbolTableEntries = new SymbolTableEntry[((DefaultListModel) getYAxisChoice().getModel()).size()];
            for (int i = 0; i < symbolTableEntries.length; i += 1) {
                symbolTableEntries[i] = getSymbolTable().getEntry((String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i));
            }
        }
        String title = "Probability Distribution of Species";
        String xLabel = "Number of Particles";
        String yLabel = "";
        String[] yNames = new String[((DefaultListModel) getYAxisChoice().getModel()).size()];
        ((DefaultListModel) getYAxisChoice().getModel()).copyInto(yNames);
        Plot2D plot2D = new Plot2D(symbolTableEntries, getMyDataInterface().getDataSymbolMetadataResolver(), yNames, plotData, new String[] { title, xLabel, yLabel });
        refreshVisiblePlots(plot2D);
        setPlot2D(plot2D);
    }
}

Example 28 with SymbolTableEntry

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

the class ParameterTableModel 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;
    }
    Parameter parameter = getValueAt(rowIndex);
    if (reactionStep != null && parameter instanceof KineticsParameter) {
        KineticsParameter kp = (KineticsParameter) parameter;
        if (kp.getRole() == Kinetics.ROLE_KReverse) {
            if (!reactionStep.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 KineticsParameter) && (((KineticsParameter) parameter).getRole() != Kinetics.ROLE_UserDefined)) {
                return false;
            }
            if (parameter instanceof UnresolvedParameter) {
                return false;
            }
            if (parameter instanceof KineticsProxyParameter) {
                KineticsProxyParameter kpp = (KineticsProxyParameter) 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 29 with SymbolTableEntry

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

the class IssueTableModel method getSourceObjectPathDescription.

private String getSourceObjectPathDescription(VCDocument vcDocument, Issue issue) {
    VCAssert.assertValid(issue);
    Object source = issue.getSource();
    {
        IssueOrigin io = BeanUtils.downcast(IssueOrigin.class, source);
        if (io != null) {
            return io.getDescription();
        }
    }
    if (vcDocument instanceof BioModel) {
        BioModel bioModel = (BioModel) vcDocument;
        String description = "";
        if (source instanceof SymbolTableEntry) {
            if (source instanceof SpeciesContext) {
                description = "Model / Species";
            } else if (source instanceof RbmObservable) {
                description = "Model / Observables";
            } else {
                description = ((SymbolTableEntry) source).getNameScope().getPathDescription();
            }
        } else if (source instanceof MolecularType) {
            description = "Model / Molecules";
        } else if (source instanceof ReactionStep) {
            ReactionStep reactionStep = (ReactionStep) source;
            description = ((ReactionNameScope) reactionStep.getNameScope()).getPathDescription();
        } else if (source instanceof ReactionRule) {
            ReactionRule reactionRule = (ReactionRule) source;
            description = ((ReactionRuleNameScope) reactionRule.getNameScope()).getPathDescription();
        } else if (source instanceof SpeciesPattern) {
            // if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
            // description = "Model / Species";
            // }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
            // ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
            // description = ((ReactionRuleNameScope)thing.getNameScope()).getPathDescription();
            // }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
            // description = "Model / Observables";
            // } else {
            System.err.println("Bad issue context for " + ((SpeciesPattern) source).toString());
            description = ((SpeciesPattern) source).toString();
        // }
        } else if (source instanceof Structure) {
            Structure structure = (Structure) source;
            description = "Model / " + structure.getTypeName() + "(" + structure.getName() + ")";
        } else if (source instanceof StructureMapping) {
            StructureMapping structureMapping = (StructureMapping) source;
            description = ((StructureMappingNameScope) structureMapping.getNameScope()).getPathDescription();
        } else if (source instanceof OutputFunctionIssueSource) {
            SimulationContext simulationContext = (SimulationContext) ((OutputFunctionIssueSource) source).getOutputFunctionContext().getSimulationOwner();
            description = "App(" + simulationContext.getName() + ") / " + "Simulations" + " / " + "Output Functions";
        } else if (source instanceof Simulation) {
            Simulation simulation = (Simulation) source;
            try {
                SimulationContext simulationContext = bioModel.getSimulationContext(simulation);
                description = "App(" + simulationContext.getName() + ") / Simulations";
            } catch (ObjectNotFoundException e) {
                e.printStackTrace();
                description = "App(" + "unknown" + ") / Simulations";
            }
        } else if (source instanceof UnmappedGeometryClass) {
            UnmappedGeometryClass unmappedGC = (UnmappedGeometryClass) source;
            description = "App(" + unmappedGC.getSimulationContext().getName() + ") / Subdomain(" + unmappedGC.getGeometryClass().getName() + ")";
        } else if (source instanceof GeometryContext) {
            description = "App(" + ((GeometryContext) source).getSimulationContext().getName() + ")";
        } else if (source instanceof ModelOptimizationSpec) {
            description = "App(" + ((ModelOptimizationSpec) source).getSimulationContext().getName() + ") / Parameter Estimation";
        } else if (source instanceof MicroscopeMeasurement) {
            description = "App(" + ((MicroscopeMeasurement) source).getSimulationContext().getName() + ") / Microscope Measurements";
        } else if (source instanceof SpatialObject) {
            description = "App(" + ((SpatialObject) source).getSimulationContext().getName() + ") / Spatial Objects";
        } else if (source instanceof SpatialProcess) {
            description = "App(" + ((SpatialProcess) source).getSimulationContext().getName() + ") / Spatial Processes";
        } else if (source instanceof SpeciesContextSpec) {
            SpeciesContextSpec scs = (SpeciesContextSpec) source;
            description = "App(" + scs.getSimulationContext().getName() + ") / Specifications / Species";
        } else if (source instanceof ReactionCombo) {
            ReactionCombo rc = (ReactionCombo) source;
            description = "App(" + rc.getReactionContext().getSimulationContext().getName() + ") / Specifications / Reactions";
        } else if (source instanceof RbmModelContainer) {
            IssueCategory ic = issue.getCategory();
            switch(ic) {
                case RbmMolecularTypesTableBad:
                    description = "Model / " + MolecularType.typeName + "s";
                    break;
                case RbmReactionRulesTableBad:
                    description = "Model / Reactions";
                    break;
                case RbmObservablesTableBad:
                    description = "Model / Observables";
                    break;
                case RbmNetworkConstraintsBad:
                    description = "Network Constrains";
                    break;
                default:
                    description = "Model";
                    break;
            }
        } else if (source instanceof SimulationContext) {
            SimulationContext sc = (SimulationContext) source;
            IssueCategory ic = issue.getCategory();
            switch(ic) {
                case RbmNetworkConstraintsBad:
                    description = "Specifications / Network";
                    break;
                default:
                    description = "Application";
                    break;
            }
        } else if (source instanceof Model) {
            description = "Model";
        } else if (source instanceof BioEvent) {
            return "Protocols / Events";
        } else if (source instanceof MathDescription) {
            return "Math Description";
        } else {
            System.err.println("unknown source type in IssueTableModel.getSourceObjectPathDescription(): " + source.getClass());
        }
        return description;
    } else if (vcDocument instanceof MathModel) {
        if (source instanceof Geometry) {
            return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_GEOMETRY;
        } else if (source instanceof OutputFunctionIssueSource) {
            return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_OUTPUTFUNCTIONS;
        } else if (source instanceof Simulation) {
            return "Simulation(" + ((Simulation) source).getName() + ")";
        } else {
            return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_VCML;
        }
    } else {
        System.err.println("unknown document type in IssueTableModel.getSourceObjectPathDescription()");
        return "";
    }
}

Example 30 with SymbolTableEntry

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

the class IssueTableModel method getSourceObjectDescription.

private String getSourceObjectDescription(VCDocument vcDocument, Issue issue) {
    if (vcDocument instanceof BioModel) {
        Object object = issue.getSource();
        {
            DecoratedIssueSource dis = BeanUtils.downcast(DecoratedIssueSource.class, object);
            if (dis != null) {
                return dis.getSourcePath();
            }
        }
        String description = "";
        if (object instanceof SymbolTableEntry) {
            description = ((SymbolTableEntry) object).getName();
        } else if (object instanceof ReactionStep) {
            description = ((ReactionStep) object).getName();
        } else if (object instanceof ReactionRule) {
            description = ((ReactionRule) object).getName();
        } else if (object instanceof SpeciesPattern) {
            // Object parent = issue.getIssueContext().getContextObject();
            // if (parent instanceof SpeciesContext){
            // description = ((SpeciesContext)parent).getName();
            // }
            // if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
            // SpeciesContext thing = (SpeciesContext)issue.getIssueContext().getContextObject(ContextType.SpeciesContext);
            // description = thing.getName();
            // }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
            // ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
            // description = thing.getName();
            // }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
            // RbmObservable thing = (RbmObservable)issue.getIssueContext().getContextObject(ContextType.RbmObservable);
            // description = thing.getName();
            // } else {
            System.err.println("Bad issue context for " + ((SpeciesPattern) object).toString());
            description = ((SpeciesPattern) object).toString();
        // }
        } else if (object instanceof MolecularType) {
            description = ((MolecularType) object).getName();
        } else if (object instanceof MolecularComponent) {
            description = ((MolecularComponent) object).getName();
        } else if (object instanceof ComponentStateDefinition) {
            description = ((ComponentStateDefinition) object).getName();
        } else if (object instanceof Structure) {
            description = ((Structure) object).getName();
        } else if (object instanceof SubDomain) {
            description = ((SubDomain) object).getName();
        } else if (object instanceof Geometry) {
            description = ((Geometry) object).getName();
        } else if (object instanceof StructureMapping) {
            description = ((StructureMapping) object).getStructure().getName();
        } else if (object instanceof OutputFunctionIssueSource) {
            description = ((OutputFunctionIssueSource) object).getAnnotatedFunction().getName();
        } else if (object instanceof UnmappedGeometryClass) {
            description = ((UnmappedGeometryClass) object).getGeometryClass().getName();
        } else if (object instanceof MicroscopeMeasurement) {
            description = ((MicroscopeMeasurement) object).getName();
        } else if (object instanceof SpatialObject) {
            description = ((SpatialObject) object).getName();
        } else if (object instanceof SpatialProcess) {
            description = ((SpatialProcess) object).getName();
        } else if (object instanceof GeometryContext) {
            description = "Geometry";
        } else if (object instanceof ModelOptimizationSpec) {
            description = ((ModelOptimizationSpec) object).getParameterEstimationTask().getName();
        } else if (object instanceof Simulation) {
            description = ((Simulation) object).getName();
        } else if (object instanceof SpeciesContextSpec) {
            SpeciesContextSpec scs = (SpeciesContextSpec) object;
            description = scs.getSpeciesContext().getName();
        } else if (object instanceof ReactionCombo) {
            ReactionSpec rs = ((ReactionCombo) object).getReactionSpec();
            description = rs.getReactionStep().getName();
        } else if (object instanceof RbmModelContainer) {
            // RbmModelContainer mc = (RbmModelContainer)object;
            description = "Rules validator";
        } else if (object instanceof SimulationContext) {
            SimulationContext sc = (SimulationContext) object;
            description = sc.getName();
        } else if (object instanceof Model) {
            Model m = (Model) object;
            description = m.getName();
        } else if (object instanceof BioEvent) {
            return ((BioEvent) object).getName() + "";
        } else if (object instanceof MathDescription) {
            return ((MathDescription) object).getName() + "";
        } else {
            System.err.println("unknown object type in IssueTableModel.getSourceObjectDescription(): " + object.getClass());
        }
        return description;
    } else if (vcDocument instanceof MathModel) {
        Object object = issue.getSource();
        String description = "";
        if (object instanceof Variable) {
            description = ((Variable) object).getName();
        } else if (object instanceof SubDomain) {
            description = ((SubDomain) object).getName();
        } else if (object instanceof Geometry) {
            description = "Geometry";
        } else if (object instanceof OutputFunctionIssueSource) {
            description = ((OutputFunctionIssueSource) object).getAnnotatedFunction().getName();
        } else if (object instanceof MathDescription) {
            return "math";
        } else if (object instanceof Simulation) {
            return "Simulation " + ((Simulation) object).getName() + "";
        }
        return description;
    } else {
        System.err.println("unknown document type in IssueTableModel.getSourceObjectDescription()");
        return "";
    }
}