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

Example 16 with SimulationContext

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

the class ViewGeneratedReactionsPanel method updateShape.

public void updateShape(int selectedRow) {
    GeneratedReactionTableRow reactionTableRow = tableModel.getValueAt(selectedRow);
    String inputString = reactionTableRow.getExpression();
    System.out.println(selectedRow + ": " + inputString);
    // ReactionRule newReactionRule = (ReactionRule)RbmUtils.parseReactionRule(inputString, bioModel);
    Model tempModel = null;
    try {
        tempModel = new Model("MyTempModel");
        tempModel.addFeature("c0");
    } catch (ModelException | PropertyVetoException e1) {
        e1.printStackTrace();
    }
    if (owner != null && owner.getSimulationContext() != null) {
        List<MolecularType> mtList = owner.getSimulationContext().getModel().getRbmModelContainer().getMolecularTypeList();
        try {
            tempModel.getRbmModelContainer().setMolecularTypeList(mtList);
        } catch (PropertyVetoException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Unexpected exception setting " + MolecularType.typeName + " list: " + e1.getMessage(), e1);
        }
    } else {
        // This should not be possible
        throw new RuntimeException("Owner or SimulationContext are null.");
    }
    int arrowIndex = inputString.indexOf("<->");
    boolean bReversible = true;
    if (arrowIndex < 0) {
        arrowIndex = inputString.indexOf("->");
        bReversible = false;
    }
    String left = inputString.substring(0, arrowIndex).trim();
    String right = inputString.substring(arrowIndex + (bReversible ? 3 : 2)).trim();
    if (left.length() == 0 && right.length() == 0) {
        return;
    }
    // we recover the original rule that generated the flattened reaction we now try to transform back into a fake rule
    BNGReaction reactionObject = reactionTableRow.getReactionObject();
    String name = reactionObject.getRuleName();
    if (name.contains(GeneratedReactionTableModel.reverse)) {
        name = name.substring(GeneratedReactionTableModel.reverse.length());
    }
    if (name.endsWith(ReactionRule.DirectHalf)) {
        name = name.substring(0, name.indexOf(ReactionRule.DirectHalf));
    }
    if (name.endsWith(ReactionRule.InverseHalf)) {
        name = name.substring(0, name.indexOf(ReactionRule.InverseHalf));
    }
    // get the name of the original structure from the original rule and make here another structure with the same name
    String strStructure = null;
    Structure ruleStructure;
    SimulationContext sc = owner.getSimulationContext();
    ReactionRule rr = sc.getModel().getRbmModelContainer().getReactionRule(name);
    if (rr != null && rr.getStructure() != null) {
        strStructure = rr.getStructure().getName();
    }
    if (strStructure != null) {
        if (tempModel.getStructure(strStructure) == null) {
            try {
                if (rr.getStructure().getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                    tempModel.addMembrane(strStructure);
                } else {
                    tempModel.addFeature(strStructure);
                }
            } catch (ModelException | PropertyVetoException e) {
                e.printStackTrace();
            }
        }
        ruleStructure = tempModel.getStructure(strStructure);
    } else {
        throw new RuntimeException("Failed to recover a Structure name from the Reaction Rule: " + name);
    }
    // making the fake rules just for display purpose, actually they are the flattened reactions resulted from bngl
    // the name is probably not unique, it's likely that many flattened reactions are derived from the same rule
    ReactionRule reactionRule = tempModel.getRbmModelContainer().createReactionRule(name, ruleStructure, bReversible);
    String regex = "[^!]\\+";
    String[] patterns = left.split(regex);
    for (String spString : patterns) {
        try {
            spString = spString.trim();
            // if compartments are present, we're cheating big time making some fake compartments just for compartment name display purposes
            SpeciesPattern speciesPattern = (SpeciesPattern) RbmUtils.parseSpeciesPattern(spString, tempModel);
            strStructure = RbmUtils.parseCompartment(spString, tempModel);
            speciesPattern.resolveBonds();
            Structure structure;
            if (strStructure != null) {
                if (tempModel.getStructure(strStructure) == null) {
                    if (sc.getModel().getStructure(strStructure).getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                        tempModel.addMembrane(strStructure);
                    } else {
                        tempModel.addFeature(strStructure);
                    }
                }
                structure = tempModel.getStructure(strStructure);
            } else {
                // if nothing explicit for a participant, we use by default the structure of the rule
                structure = ruleStructure;
            }
            reactionRule.addReactant(new ReactantPattern(speciesPattern, structure));
        } catch (Throwable ex) {
            ex.printStackTrace();
            // error (red circle)
            SpeciesPatternLargeShape spls = new SpeciesPatternLargeShape(20, 20, -1, shapePanel, true, issueManager);
            reactantPatternShapeList.clear();
            productPatternShapeList.clear();
            reactantPatternShapeList.add(spls);
            shapePanel.repaint();
            return;
        }
    }
    patterns = right.split(regex);
    for (String spString : patterns) {
        try {
            spString = spString.trim();
            SpeciesPattern speciesPattern = (SpeciesPattern) RbmUtils.parseSpeciesPattern(spString, tempModel);
            strStructure = RbmUtils.parseCompartment(spString, tempModel);
            speciesPattern.resolveBonds();
            Structure structure;
            if (strStructure != null) {
                if (tempModel.getStructure(strStructure) == null) {
                    if (sc.getModel().getStructure(strStructure).getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                        tempModel.addMembrane(strStructure);
                    } else {
                        tempModel.addFeature(strStructure);
                    }
                }
                structure = tempModel.getStructure(strStructure);
            } else {
                structure = ruleStructure;
            }
            // BNGLParser parser = new BNGLParser(new StringReader(sp));
            // ASTSpeciesPattern astSpeciesPattern = parser.SpeciesPattern();
            // BnglObjectConstructionVisitor constructionVisitor = new BnglObjectConstructionVisitor(tempModel, null, false);
            // SpeciesPattern speciesPattern = (SpeciesPattern) astSpeciesPattern.jjtAccept(constructionVisitor, null);
            // for(MolecularTypePattern mtp : speciesPattern.getMolecularTypePatterns()) {
            // mtp.setParticipantMatchLabel("*");
            // }
            // System.out.println(speciesPattern.toString());
            reactionRule.addProduct(new ProductPattern(speciesPattern, structure));
        } catch (Throwable ex) {
            ex.printStackTrace();
            // error (red circle)
            SpeciesPatternLargeShape spls = new SpeciesPatternLargeShape(20, 20, -1, shapePanel, true, issueManager);
            reactantPatternShapeList.clear();
            productPatternShapeList.clear();
            reactantPatternShapeList.add(spls);
            shapePanel.repaint();
            return;
        }
    }
    // ----------------------------------------------------------------------------------------------------
    List<ReactantPattern> rpList = reactionRule.getReactantPatterns();
    reactantPatternShapeList.clear();
    int xOffset = 20;
    int xOffsetRound = 20;
    if (rpList != null && rpList.size() > 0) {
        for (int i = 0; i < rpList.size(); i++) {
            SpeciesPattern sp = rpList.get(i).getSpeciesPattern();
            for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
                mtp.setParticipantMatchLabel("*");
            }
            SpeciesPatternLargeShape sps = new SpeciesPatternLargeShape(xOffset, 20, -1, sp, shapePanel, reactionRule, issueManager);
            // SpeciesPatternRoundShape sps = new SpeciesPatternRoundShape(xOffsetRound, 20, -1, sp, shapePanel, reactionRule);
            if (i < rpList.size() - 1) {
                sps.addEndText("+");
            } else {
                if (reactionRule.isReversible()) {
                    sps.addEndText("<->");
                } else {
                    sps.addEndText("->");
                }
            }
            xOffset = sps.getRightEnd() + 45;
            xOffsetRound = sps.getRightEnd() + 45;
            reactantPatternShapeList.add(sps);
        }
    }
    // space for the <-> sign
    xOffset += 15;
    List<ProductPattern> ppList = reactionRule.getProductPatterns();
    productPatternShapeList.clear();
    if (ppList != null && ppList.size() > 0) {
        for (int i = 0; i < ppList.size(); i++) {
            SpeciesPattern sp = ppList.get(i).getSpeciesPattern();
            for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
                mtp.setParticipantMatchLabel("*");
            }
            SpeciesPatternLargeShape sps = new SpeciesPatternLargeShape(xOffset, 20, -1, sp, shapePanel, reactionRule, issueManager);
            // SpeciesPatternRoundShape sps = new SpeciesPatternRoundShape(xOffset, 20, -1, sp, shapePanel, reactionRule);
            if (i < ppList.size() - 1) {
                sps.addEndText("+");
            }
            xOffset = sps.getRightEnd() + 45;
            productPatternShapeList.add(sps);
        }
    }
    Dimension preferredSize = new Dimension(xOffset + 90, 50);
    shapePanel.setPreferredSize(preferredSize);
    shapePanel.repaint();
}

Example 17 with SimulationContext

use of cbit.vcell.mapping.SimulationContext 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 18 with SimulationContext

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

the class ObservablesGroupTableModel method getValueAt.

public Object getValueAt(int iRow, int iCol) {
    ObservablesGroupTableRow observablesTableRow = getValueAt(iRow);
    String obsName = observablesTableRow.getObservableGroupObject().getObservableGroupName();
    RbmObservable obs = observablesTableRow.getObservable(obsName);
    String obsDefinition = ObservablesGroupTableRow.toBnglString(obs);
    switch(iCol) {
        case iColOriginalName:
            return obsName;
        case iColStructure:
            {
                if (obsDefinition.startsWith("@") && obsDefinition.contains(":")) {
                    String structName = obsDefinition.substring(1, obsDefinition.indexOf(":"));
                    return structName;
                } else {
                    SimulationContext sc = owner.getSimulationContext();
                    if (sc.getModel().getStructures().length > 1) {
                        // if we have more than 1 compartments
                        return "?";
                    } else {
                        Structure struct = sc.getModel().getStructure(0);
                        return struct.getName();
                    }
                }
            }
        case iColDepiction:
            return obsDefinition;
        case iColDefinition:
            switch(obs.getSequence()) {
                case Multimolecular:
                    return obsDefinition;
                case PolymerLengthEqual:
                    return obsDefinition + "=" + obs.getSequenceLength();
                case PolymerLengthGreater:
                    return obsDefinition + ">" + obs.getSequenceLength();
                default:
                    return obsDefinition;
            }
        case iColExpression:
            String exp;
            BNGSpecies[] speciesList = observablesTableRow.getObservableGroupObject().getListofSpecies();
            if (speciesList == null || speciesList.length == 0) {
                exp = "<html><font color=\"red\">No generated species</html>";
            } else {
                exp = getExpressionAsString(observablesTableRow.getObservableGroupObject());
            }
            return exp;
        case iColCount:
            return obs.getType().name();
        default:
            return null;
    }
}

Example 19 with SimulationContext

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

the class DefaultScrollTableCellRenderer method getTableCellRendererComponent.

/**
 * Insert the method's description here.
 * Creation date: (3/27/2001 1:07:02 PM)
 * @return java.awt.Component
 * @param table javax.swing.JTable
 * @param value java.lang.Object
 * @param isSelected boolean
 * @param hasFocus boolean
 * @param row int
 * @param column int
 */
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
    defaultToolTipText = null;
    super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
    defaultToolTipText = getToolTipText();
    setBorder(DEFAULT_GAP);
    if (isSelected) {
        setBackground(table.getSelectionBackground());
        setForeground(table.getSelectionForeground());
    } else {
        if (table instanceof ScrollTable && ((ScrollTable) table).getHoverRow() == row) {
            setBackground(hoverColor);
        } else {
            setBackground(row % 2 == 0 ? table.getBackground() : everyOtherRowColor);
        }
        if (table.getModel() instanceof SpatialProcessTableModel) /* && column == SpatialProcessTableModel.COLUMN_SpatialProcess_SPATIALOBJECTS */
        {
            boolean found = isMatchWithSelectedObject(table, row);
            if (found == true) {
                setBackground(Color.yellow);
            }
        } else if (table.getModel() instanceof SpatialObjectTableModel) /* && column == SpatialObjectTableModel.COLUMN_SpatialObject_NAME */
        {
            boolean found = isMatchWithSelectedProcess(table, row);
            if (found == true) {
                setBackground(Color.yellow);
            }
        }
        setForeground(table.getForeground());
    }
    TableModel tableModel = table.getModel();
    if (bEnableUneditableForeground && (!table.isEnabled() || !tableModel.isCellEditable(row, column))) {
        if (!isSelected) {
            setForeground(uneditableForeground);
            if (tableModel instanceof NetworkConstraintsTableModel && column == NetworkConstraintsTableModel.iColValue) {
                NetworkConstraintsTableModel tm = (NetworkConstraintsTableModel) tableModel;
                String def = (String) tm.getValueAt(row, NetworkConstraintsTableModel.iColDefault);
                String val = (String) value;
                if (!val.equals(def)) {
                    value = "<html><b>" + value + "</b></html>";
                    setForeground(Color.red);
                }
            }
        }
    }
    if (value instanceof Double) {
        Double doubleValue = (Double) value;
        setText(nicelyFormattedDouble(doubleValue));
    } else if (value instanceof JComponent) {
        JComponent jc = (JComponent) value;
        if (hasFocus) {
            jc.setBorder(focusHighlightBorder);
        } else {
            jc.setBorder(noFocusBorder);
        }
        return jc;
    }
    if (BioModelEditorRightSideTableModel.ADD_NEW_HERE_TEXT.equals(value)) {
        setText(BioModelEditorRightSideTableModel.ADD_NEW_HERE_HTML);
    } else if (value instanceof ModelProcessEquation && BioModelEditorRightSideTableModel.ADD_NEW_HERE_REACTION_TEXT.equals(((ModelProcessEquation) value).toString())) {
        setText(BioModelEditorRightSideTableModel.ADD_NEW_REACTION_OR_RULE_HTML);
    }
    if (tableModel instanceof BioModelEditorApplicationsTableModel) {
        // for the applications table we show the icons with the app type
        Icon icon = null;
        String toolTipSuffix = "";
        BioModelEditorApplicationsTableModel bmeatm = (BioModelEditorApplicationsTableModel) tableModel;
        SimulationContext simContext = (SimulationContext) (bmeatm.getValueAt(row));
        if (simContext.isRuleBased()) {
            if (simContext.getGeometry().getDimension() == 0) {
                icon = VCellIcons.appRbmNonspIcon;
                toolTipSuffix = "Rule Based / Non spatial";
            }
        } else if (simContext.isStoch()) {
            if (simContext.getGeometry().getDimension() == 0) {
                icon = VCellIcons.appStoNonspIcon;
                toolTipSuffix = "Stochastic / Non spatial";
            } else {
                icon = VCellIcons.appStoSpatialIcon;
                toolTipSuffix = "Stochastic / Spatial";
            }
        } else {
            // deterministic
            if (simContext.getGeometry().getDimension() == 0) {
                icon = VCellIcons.appDetNonspIcon;
                toolTipSuffix = "Deterministic / Non spatial";
            } else {
                icon = VCellIcons.appDetSpatialIcon;
                toolTipSuffix = "Deterministic / Spatial";
            }
        }
        String toolTipPrefix = "Application: ";
        setToolTipText(toolTipPrefix + toolTipSuffix);
        if (column == 0) {
            setIcon(icon);
        } else {
            setIcon(null);
        }
    } else if (column == 2 && tableModel instanceof SpatialProcessTableModel) {
        Icon icon = null;
        SpatialProcess spatialProcess = (SpatialProcess) (((SpatialProcessTableModel) tableModel).getValueAt(row));
        if (spatialProcess instanceof PointLocation) {
            icon = VCellIcons.spatialPointIcon;
        } else if (spatialProcess instanceof PointKinematics) {
            icon = VCellIcons.spatialPointIcon;
        } else if (spatialProcess instanceof SurfaceKinematics) {
            icon = VCellIcons.spatialMembraneIcon;
        } else {
            icon = VCellIcons.spatialVolumeIcon;
        }
        setIcon(icon);
    } else if (tableModel instanceof SortTableModel) {
        // for most other tables we reserve the icon spot to display issues
        DefaultScrollTableCellRenderer.issueRenderer(this, defaultToolTipText, table, row, column, (SortTableModel) tableModel);
    }
    return this;
}

Example 20 with SimulationContext

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

the class VCellSedMLSolver method doWork.

// everything is done here
public void doWork(ExternalDocInfo externalDocInfo, AbstractTask sedmlTask, SedML sedml) throws Exception {
    // create the VCDocument (bioModel + application + simulation), do sanity checks
    cbit.util.xml.VCLogger sedmlImportLogger = new LocalLogger();
    List<AbstractTask> tasks = new ArrayList<AbstractTask>();
    tasks.add(sedmlTask);
    List<VCDocument> docs = XmlHelper.sedmlToBioModel(sedmlImportLogger, externalDocInfo, sedml, tasks, null, false);
    VCDocument doc = docs.get(0);
    sanityCheck(doc);
    // create the work directory for this task, invoke the solver
    String docName = doc.getName();
    String outString = VCellSedMLSolver.OUT_ROOT_STRING + "/" + docName + "/" + sedmlTask.getId();
    File outDir = new File(outString);
    if (!outDir.exists()) {
        outDir.mkdirs();
    }
    BioModel bioModel = (BioModel) doc;
    SimulationContext simContext = bioModel.getSimulationContext(0);
    MathDescription mathDesc = simContext.getMathDescription();
    String vcml = mathDesc.getVCML();
    try (PrintWriter pw = new PrintWriter(outString + "/vcmlTrace.xml")) {
        pw.println(vcml);
    }
    Simulation sim = bioModel.getSimulation(0);
    SolverTaskDescription std = sim.getSolverTaskDescription();
    SolverDescription sd = std.getSolverDescription();
    String kisao = sd.getKisao();
    if (SolverDescription.CVODE.getKisao().contentEquals(kisao)) {
        ODESolverResultSet odeSolverResultSet = solveCvode(outDir, bioModel);
        System.out.println("Finished: " + docName + ": - task '" + sedmlTask.getId() + "'.");
    } else if (SolverDescription.StochGibson.getKisao().contentEquals(kisao)) {
        ODESolverResultSet odeSolverResultSet = solveGibson(outDir, bioModel);
        System.out.println("Finished: " + docName + ": - task '" + sedmlTask.getId() + "'.");
    } else if (SolverDescription.IDA.getKisao().contentEquals(kisao)) {
        ODESolverResultSet odeSolverResultSet = solveIDA(outDir, bioModel);
        System.out.println("Finished: " + docName + ": - task '" + sedmlTask.getId() + "'.");
    } else {
        System.out.println("Unsupported solver: " + kisao);
    }
    System.out.println("-------------------------------------------------------------------------");
}