Examples with SpatialProcess cbit.vcell.mapping.spatial.processes.SpatialProcess used on opensource projects

Example 1 with SpatialProcess

use of cbit.vcell.mapping.spatial.processes.SpatialProcess in project vcell by virtualcell.

the class DefaultScrollTableCellRenderer method isMatchWithSelectedObject.

private boolean isMatchWithSelectedObject(JTable table, int row) {
    SpatialProcessTableModel tm = (SpatialProcessTableModel) table.getModel();
    SelectionManager selectionManager = tm.getSelectionManager();
    boolean found = false;
    if (selectionManager != null) {
        for (Object ob : selectionManager.getSelectedObjects()) {
            if (ob instanceof SpatialObject) {
                // a SpatialObject selected
                List<SpatialProcess> spList = ((SpatialObject) ob).getRelatedSpatialProcesses();
                for (SpatialProcess theirs : spList) {
                    SpatialProcess ours = tm.getValueAt(row);
                    if (ours == theirs) {
                        found = true;
                        break;
                    }
                }
            }
            if (found == true) {
                break;
            }
        }
    }
    return found;
}

Example 2 with SpatialProcess

use of cbit.vcell.mapping.spatial.processes.SpatialProcess in project vcell by virtualcell.

the class DefaultScrollTableCellRenderer method isMatchWithSelectedProcess.

private boolean isMatchWithSelectedProcess(JTable table, int row) {
    SpatialObjectTableModel tm = (SpatialObjectTableModel) table.getModel();
    SelectionManager selectionManager = tm.getSelectionManager();
    boolean found = false;
    if (selectionManager != null) {
        for (Object ob : selectionManager.getSelectedObjects()) {
            if (ob instanceof SpatialProcess) {
                // a SpatialProcess selected
                List<SpatialObject> soList = ((SpatialProcess) ob).getSpatialObjects();
                for (SpatialObject theirs : soList) {
                    SpatialObject ours = tm.getValueAt(row);
                    if (ours == theirs) {
                        found = true;
                        break;
                    }
                }
            }
            if (found == true) {
                break;
            }
        }
    }
    return found;
}

Example 3 with SpatialProcess

use of cbit.vcell.mapping.spatial.processes.SpatialProcess 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 (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 4 with SpatialProcess

use of cbit.vcell.mapping.spatial.processes.SpatialProcess in project vcell by virtualcell.

the class XmlReader method getSimulationContext.

/**
 * This method returns a SimulationContext from a XML representation.
 * Creation date: (4/2/2001 3:19:01 PM)
 * @return cbit.vcell.mapping.SimulationContext
 * @param param org.jdom.Element
 */
private SimulationContext getSimulationContext(Element param, BioModel biomodel) throws XmlParseException {
    // get the attributes
    // name
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    boolean bStoch = false;
    boolean bRuleBased = false;
    boolean bUseConcentration = true;
    boolean bRandomizeInitCondition = false;
    boolean bInsufficientIterations = false;
    boolean bInsufficientMaxMolecules = false;
    NetworkConstraints nc = null;
    Element ncElement = param.getChild(XMLTags.RbmNetworkConstraintsTag, vcNamespace);
    if (ncElement != null) {
        // one network constraint element
        nc = getAppNetworkConstraints(ncElement, biomodel.getModel());
    } else {
        if (legacyNetworkConstraints != null) {
            nc = legacyNetworkConstraints;
        }
    }
    if ((param.getAttributeValue(XMLTags.StochAttrTag) != null) && (param.getAttributeValue(XMLTags.StochAttrTag).equals("true"))) {
        bStoch = true;
    }
    if (bStoch) {
        // stochastic and using concentration vs amount
        if ((param.getAttributeValue(XMLTags.ConcentrationAttrTag) != null) && (param.getAttributeValue(XMLTags.ConcentrationAttrTag).equals("false"))) {
            bUseConcentration = false;
        }
        // stochastic and randomizing initial conditions or not (for non-spatial)
        if ((param.getAttributeValue(XMLTags.RandomizeInitConditionTag) != null) && (param.getAttributeValue(XMLTags.RandomizeInitConditionTag).equals("true"))) {
            bRandomizeInitCondition = true;
        }
    }
    if ((param.getAttributeValue(XMLTags.InsufficientIterationsTag) != null) && (param.getAttributeValue(XMLTags.InsufficientIterationsTag).equals("true"))) {
        bInsufficientIterations = true;
    }
    if ((param.getAttributeValue(XMLTags.InsufficientMaxMoleculesTag) != null) && (param.getAttributeValue(XMLTags.InsufficientMaxMoleculesTag).equals("true"))) {
        bInsufficientMaxMolecules = true;
    }
    if ((param.getAttributeValue(XMLTags.RuleBasedAttrTag) != null) && (param.getAttributeValue(XMLTags.RuleBasedAttrTag).equals("true"))) {
        bRuleBased = true;
        if ((param.getAttributeValue(XMLTags.ConcentrationAttrTag) != null) && (param.getAttributeValue(XMLTags.ConcentrationAttrTag).equals("false"))) {
            bUseConcentration = false;
        }
        if ((param.getAttributeValue(XMLTags.RandomizeInitConditionTag) != null) && (param.getAttributeValue(XMLTags.RandomizeInitConditionTag).equals("true"))) {
            // we propagate the flag but we don't use it for now
            bRandomizeInitCondition = true;
        }
    }
    // Retrieve Geometry
    Geometry newgeometry = null;
    try {
        newgeometry = getGeometry(param.getChild(XMLTags.GeometryTag, vcNamespace));
    } catch (Throwable e) {
        e.printStackTrace();
        String stackTrace = null;
        try {
            java.io.ByteArrayOutputStream bos = new java.io.ByteArrayOutputStream();
            java.io.PrintStream ps = new java.io.PrintStream(bos);
            e.printStackTrace(ps);
            ps.flush();
            bos.flush();
            stackTrace = new String(bos.toByteArray());
            ps.close();
            bos.close();
        } catch (Exception e2) {
        // do Nothing
        }
        throw new XmlParseException("A Problem occurred while retrieving the geometry for the simulationContext " + name, e);
    }
    // Retrieve MathDescription(if there is no MathDescription skip it)
    MathDescription newmathdesc = null;
    Element xmlMathDescription = param.getChild(XMLTags.MathDescriptionTag, vcNamespace);
    if (xmlMathDescription != null) {
        newmathdesc = getMathDescription(xmlMathDescription, newgeometry);
    }
    // Retrieve Version (Metada)
    Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    // ------ Create SimContext ------
    SimulationContext newsimcontext = null;
    try {
        newsimcontext = new SimulationContext(biomodel.getModel(), newgeometry, newmathdesc, version, bStoch, bRuleBased);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("A propertyveto exception was generated when creating the new SimulationContext " + name, e);
    }
    // set attributes
    try {
        newsimcontext.setName(name);
        // Add annotation
        String annotation = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotation != null && annotation.length() > 0) {
            newsimcontext.setDescription(unMangle(annotation));
        }
        // set if using concentration
        newsimcontext.setUsingConcentration(bUseConcentration);
        // set if randomizing init condition or not (for stochastic applications
        if (bStoch) {
            newsimcontext.setRandomizeInitConditions(bRandomizeInitCondition);
        }
        if (bInsufficientIterations) {
            newsimcontext.setInsufficientIterations(bInsufficientIterations);
        }
        if (bInsufficientMaxMolecules) {
            newsimcontext.setInsufficientMaxMolecules(bInsufficientMaxMolecules);
        }
        if (nc != null) {
            newsimcontext.setNetworkConstraints(nc);
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("Exception", e);
    }
    String tempchar = param.getAttributeValue(XMLTags.CharacteristicSizeTag);
    if (tempchar != null) {
        try {
            newsimcontext.setCharacteristicSize(Double.valueOf(tempchar));
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("A PropertyVetoException was fired when setting the CharacteristicSize " + tempchar, e);
        }
    }
    // Retrieve DataContext
    Element dataContextElement = param.getChild(XMLTags.DataContextTag, vcNamespace);
    if (dataContextElement != null) {
        DataContext dataContext = newsimcontext.getDataContext();
        ArrayList<DataSymbol> dataSymbols = getDataSymbols(dataContextElement, dataContext, newsimcontext.getModel().getUnitSystem());
        for (int i = 0; i < dataSymbols.size(); i++) {
            dataContext.addDataSymbol(dataSymbols.get(i));
        }
    }
    // Retrieve spatialObjects and add to simContext
    Element spatialObjectsElement = param.getChild(XMLTags.SpatialObjectsTag, vcNamespace);
    if (spatialObjectsElement != null) {
        SpatialObject[] spatialObjects = getSpatialObjects(newsimcontext, spatialObjectsElement);
        try {
            newsimcontext.setSpatialObjects(spatialObjects);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding spatialObjects to simulationContext", e);
        }
    }
    // Retrieve application parameters and add to simContext
    Element appParamsElement = param.getChild(XMLTags.ApplicationParametersTag, vcNamespace);
    if (appParamsElement != null) {
        SimulationContextParameter[] appParameters = getSimulationContextParams(appParamsElement, newsimcontext);
        try {
            newsimcontext.setSimulationContextParameters(appParameters);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding application parameters to simulationContext", e);
        }
    }
    // 
    // -Process the GeometryContext-
    // 
    Element tempelement = param.getChild(XMLTags.GeometryContextTag, vcNamespace);
    LinkedList<StructureMapping> maplist = new LinkedList<StructureMapping>();
    // Retrieve FeatureMappings
    Iterator<Element> iterator = tempelement.getChildren(XMLTags.FeatureMappingTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        maplist.add(getFeatureMapping((Element) (iterator.next()), newsimcontext));
    }
    // Retrieve MembraneMappings
    iterator = tempelement.getChildren(XMLTags.MembraneMappingTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        maplist.add(getMembraneMapping((Element) (iterator.next()), newsimcontext));
    }
    // Add these mappings to the internal geometryContext of this simcontext
    StructureMapping[] structarray = new StructureMapping[maplist.size()];
    maplist.toArray(structarray);
    try {
        newsimcontext.getGeometryContext().setStructureMappings(structarray);
        newsimcontext.getGeometryContext().refreshStructureMappings();
        newsimcontext.refreshSpatialObjects();
    } catch (MappingException e) {
        e.printStackTrace();
        throw new XmlParseException("A MappingException was fired when trying to set the StructureMappings array to the Geometrycontext of the SimContext " + name, e);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("A PopertyVetoException was fired when trying to set the StructureMappings array to the Geometrycontext of the SimContext " + name, e);
    }
    // 
    // -Process the ReactionContext-
    // 
    tempelement = param.getChild(XMLTags.ReactionContextTag, vcNamespace);
    // Retrieve ReactionSpecs
    List<Element> children = tempelement.getChildren(XMLTags.ReactionSpecTag, vcNamespace);
    if (children.size() != 0) {
        if (children.size() != biomodel.getModel().getReactionSteps().length) {
            throw new XmlParseException("The number of reactions is not consistent.\n" + "Model reactions=" + biomodel.getModel().getReactionSteps().length + ", Reaction specs=" + children.size());
        }
        // *NOTE: Importing a model from other languages does not generates reaction specs.
        // A more robust code will read the reactions in the source file and replace the ones created by the default by the VirtualCell framework.
        ReactionSpec[] reactionSpecs = new ReactionSpec[children.size()];
        int rSpecCounter = 0;
        for (Element rsElement : children) {
            reactionSpecs[rSpecCounter] = getReactionSpec(rsElement, newsimcontext);
            rSpecCounter++;
        }
        try {
            newsimcontext.getReactionContext().setReactionSpecs(reactionSpecs);
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("A PropertyVetoException occurred while setting the ReactionSpecs to the SimContext " + name, e);
        }
    }
    // Retrieve ReactionRuleSpecs
    Element reactionRuleSpecsElement = tempelement.getChild(XMLTags.ReactionRuleSpecsTag, vcNamespace);
    if (reactionRuleSpecsElement != null) {
        ReactionRuleSpec[] reactionRuleSpecs = getReactionRuleSpecs(newsimcontext, reactionRuleSpecsElement);
        try {
            newsimcontext.getReactionContext().setReactionRuleSpecs(reactionRuleSpecs);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("A PropertyVetoException occurred while setting the ReactionRuleSpecs to the SimContext " + name, e);
        }
    }
    children = tempelement.getChildren(XMLTags.SpeciesContextSpecTag, vcNamespace);
    getSpeciesContextSpecs(children, newsimcontext.getReactionContext(), biomodel.getModel());
    // Retrieve output functions
    Element outputFunctionsElement = param.getChild(XMLTags.OutputFunctionsTag, vcNamespace);
    if (outputFunctionsElement != null) {
        ArrayList<AnnotatedFunction> outputFunctions = getOutputFunctions(outputFunctionsElement);
        try {
            // construct OutputFnContext from mathDesc in newSimContext and add output functions that were read in from XML.
            OutputFunctionContext outputFnContext = newsimcontext.getOutputFunctionContext();
            for (AnnotatedFunction outputFunction : outputFunctions) {
                outputFnContext.addOutputFunction(outputFunction);
            }
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException(e);
        }
    }
    // Retrieve Electrical context
    org.jdom.Element electElem = param.getChild(XMLTags.ElectricalContextTag, vcNamespace);
    // this information is optional!
    if (electElem != null) {
        if (electElem.getChild(XMLTags.ClampTag, vcNamespace) != null) {
            // read clamp
            ElectricalStimulus[] electArray = new ElectricalStimulus[1];
            electArray[0] = getElectricalStimulus(electElem.getChild(XMLTags.ClampTag, vcNamespace), newsimcontext);
            try {
                newsimcontext.setElectricalStimuli(electArray);
            } catch (java.beans.PropertyVetoException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e);
            }
        }
        // read ground electrode
        if (electElem.getChild(XMLTags.ElectrodeTag, vcNamespace) != null) {
            Electrode groundElectrode = getElectrode(electElem.getChild(XMLTags.ElectrodeTag, vcNamespace), newsimcontext);
            try {
                newsimcontext.setGroundElectrode(groundElectrode);
            } catch (java.beans.PropertyVetoException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e);
            }
        }
    }
    // Retrieve (bio)events and add to simContext
    tempelement = param.getChild(XMLTags.BioEventsTag, vcNamespace);
    if (tempelement != null) {
        BioEvent[] bioEvents = getBioEvents(newsimcontext, tempelement);
        try {
            newsimcontext.setBioEvents(bioEvents);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding events to simulationContext", e);
        }
    }
    // Retrieve spatialProcesses and add to simContext
    tempelement = param.getChild(XMLTags.SpatialProcessesTag, vcNamespace);
    if (tempelement != null) {
        SpatialProcess[] spatialProcesses = getSpatialProcesses(newsimcontext, tempelement);
        try {
            newsimcontext.setSpatialProcesses(spatialProcesses);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding spatialProcesses to simulationContext", e);
        }
    }
    // Retrieve rate rules and add to simContext
    tempelement = param.getChild(XMLTags.RateRulesTag, vcNamespace);
    if (tempelement != null) {
        RateRule[] rateRules = getRateRules(newsimcontext, tempelement);
        try {
            newsimcontext.setRateRules(rateRules);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding rate rules to simulationContext", e);
        }
    }
    org.jdom.Element analysisTaskListElement = param.getChild(XMLTags.AnalysisTaskListTag, vcNamespace);
    if (analysisTaskListElement != null) {
        children = analysisTaskListElement.getChildren(XMLTags.ParameterEstimationTaskTag, vcNamespace);
        if (children.size() != 0) {
            Vector<ParameterEstimationTask> analysisTaskList = new Vector<ParameterEstimationTask>();
            for (Element parameterEstimationTaskElement : children) {
                try {
                    ParameterEstimationTask parameterEstimationTask = ParameterEstimationTaskXMLPersistence.getParameterEstimationTask(parameterEstimationTaskElement, newsimcontext);
                    analysisTaskList.add(parameterEstimationTask);
                } catch (Exception e) {
                    e.printStackTrace(System.out);
                    throw new XmlParseException("An Exception occurred when parsing AnalysisTasks of SimContext " + name, e);
                }
            }
            try {
                AnalysisTask[] analysisTasks = (AnalysisTask[]) BeanUtils.getArray(analysisTaskList, AnalysisTask.class);
                newsimcontext.setAnalysisTasks(analysisTasks);
            } catch (java.beans.PropertyVetoException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException("A PropertyVetoException occurred when setting the AnalysisTasks of the SimContext " + name, e);
            }
        }
    }
    // Microscope Measurement
    org.jdom.Element element = param.getChild(XMLTags.MicroscopeMeasurement, vcNamespace);
    if (element != null) {
        getMicroscopeMeasurement(element, newsimcontext);
    }
    for (GeometryClass gc : newsimcontext.getGeometry().getGeometryClasses()) {
        try {
            StructureSizeSolver.updateUnitStructureSizes(newsimcontext, gc);
        } catch (Exception e) {
            e.printStackTrace();
        }
    }
    newsimcontext.getGeometryContext().enforceHierarchicalBoundaryConditions(newsimcontext.getModel().getStructureTopology());
    return newsimcontext;
}

Example 5 with SpatialProcess

use of cbit.vcell.mapping.spatial.processes.SpatialProcess in project vcell by virtualcell.

the class Xmlproducer method getXML.

/**
 * This method returns a XML representation of a SimulationContext object.
 * Creation date: (2/22/2001 2:15:14 PM)
 * @return Element
 * @param param cbit.vcell.mapping.SimulationContext
 */
public Element getXML(SimulationContext param, BioModel bioModel) throws XmlParseException {
    SimulationContext.Application applicationType = param.getApplicationType();
    Element simulationcontext = new Element(XMLTags.SimulationSpecTag);
    // add attributes
    String name = mangle(param.getName());
    simulationcontext.setAttribute(XMLTags.NameAttrTag, name);
    // set isStoch, isUsingConcentration attributes
    if (applicationType == Application.NETWORK_STOCHASTIC) {
        simulationcontext.setAttribute(XMLTags.StochAttrTag, "true");
        setBooleanAttribute(simulationcontext, XMLTags.ConcentrationAttrTag, param.isUsingConcentration());
        // write out 'randomizeInitConditin' flag only if non-spatial stochastic simContext
        if (param.getGeometry().getDimension() == 0) {
            setBooleanAttribute(simulationcontext, XMLTags.RandomizeInitConditionTag, param.isRandomizeInitCondition());
        }
    } else {
        simulationcontext.setAttribute(XMLTags.StochAttrTag, "false");
        simulationcontext.setAttribute(XMLTags.ConcentrationAttrTag, "true");
    }
    final boolean ruleBased = param.getApplicationType() == SimulationContext.Application.RULE_BASED_STOCHASTIC;
    setBooleanAttribute(simulationcontext, XMLTags.RuleBasedAttrTag, ruleBased);
    if (ruleBased) {
        setBooleanAttribute(simulationcontext, XMLTags.ConcentrationAttrTag, param.isUsingConcentration());
        if (param.getGeometry().getDimension() == 0) {
            // we don't use it yet but we do propagate it
            setBooleanAttribute(simulationcontext, XMLTags.RandomizeInitConditionTag, param.isRandomizeInitCondition());
        }
    }
    setBooleanAttribute(simulationcontext, XMLTags.InsufficientIterationsTag, param.isInsufficientIterations());
    setBooleanAttribute(simulationcontext, XMLTags.InsufficientMaxMoleculesTag, param.isInsufficientMaxMolecules());
    NetworkConstraints constraints = param.getNetworkConstraints();
    if (constraints != null) {
        simulationcontext.addContent(getXML(constraints));
    }
    // add annotation
    if (param.getDescription() != null && param.getDescription().length() > 0) {
        Element annotationElem = new Element(XMLTags.AnnotationTag);
        annotationElem.setText(mangle(param.getDescription()));
        simulationcontext.addContent(annotationElem);
    }
    if (param.getCharacteristicSize() != null) {
        simulationcontext.setAttribute(XMLTags.CharacteristicSizeTag, param.getCharacteristicSize().toString());
    }
    // write Geometry (or GeometryRef???)
    try {
        simulationcontext.addContent(getXML(param.getGeometryContext().getGeometry()));
    } catch (XmlParseException e) {
        e.printStackTrace();
        throw new XmlParseException("A problem occurred when trying to process the geometry for the simulationContext " + name, e);
    }
    // write GeometryContext (geometric mapping)
    simulationcontext.addContent(getXML(param.getGeometryContext()));
    // write ReactionContext (parameter/variable mapping)
    simulationcontext.addContent(getXML(param.getReactionContext()));
    // check if there is anything to write first for the electrical context
    if (param.getElectricalStimuli().length == 1 || param.getGroundElectrode() != null) {
        // create ElectricalContext
        Element electricalElement = new Element(XMLTags.ElectricalContextTag);
        // Write the electrical stimuli
        if (param.getElectricalStimuli().length == 1) {
            // write clamp
            electricalElement.addContent(getXML(param.getElectricalStimuli(0)));
        // Element clampElem = new Element(XMLTags.ClampTag);
        // clampElem.addContent(getXML(param.getElectricalStimuli(0)));
        // if (param.getElectricalStimuli()[0] instanceof VoltageClampStimulus) {
        // //this is a VOLTAGE clamp
        // clampElem.setAttribute(XMLTags.TypeAttrTag, XMLTags.VoltageClampTag);
        // clampElem.setAttribute( XMLTags.NameAttrTag, this.mangle((param.getElectricalStimuli()[0]).getName()) );
        // String tempExp = this.mangleExpression( ((VoltageClampStimulus)param.getElectricalStimuli()[0]).getVoltageParameter().getExpression() );
        // clampElem.setAttribute(XMLTags.ExpressionAttrTag, tempExp);
        // //add probe-electrode
        // clampElem.addContent(getXML(param.getElectricalStimuli()[0].getElectrode()));
        // } else {
        // //this is a CURRENT clamp
        // clampElem.setAttribute(XMLTags.TypeAttrTag, XMLTags.CurrentClampTag);
        // clampElem.setAttribute( XMLTags.NameAttrTag, this.mangle((param.getElectricalStimuli()[0]).getName()) );
        // String tempExp = this.mangleExpression( ((CurrentClampStimulus)param.getElectricalStimuli()[0]).getCurrentParameter().getExpression() );
        // clampElem.setAttribute(XMLTags.ExpressionAttrTag, tempExp);
        // //add probe-electrode
        // clampElem.addContent(getXML(param.getElectricalStimuli()[0].getElectrode()));
        // }
        // electricalElement.addContent(clampElem);
        // 
        } else if (param.getElectricalStimuli().length > 1) {
            // **ONLY ONE ELECTRODE IS SUPPORTED RIGHT NOW!
            throw new IllegalArgumentException("More than one electrode is not supported!");
        }
        // Process the Ground electrode
        if (param.getGroundElectrode() != null) {
            // write the ground electrode
            electricalElement.addContent(getXML(param.getGroundElectrode()));
        }
        simulationcontext.addContent(electricalElement);
    }
    // Add Mathdescription (if present)
    if (param.getMathDescription() != null) {
        simulationcontext.addContent(getXML(param.getMathDescription()));
    }
    if (param.getOutputFunctionContext() != null) {
        ArrayList<AnnotatedFunction> outputFunctions = param.getOutputFunctionContext().getOutputFunctionsList();
        if (outputFunctions != null && outputFunctions.size() > 0) {
            // get output functions
            simulationcontext.addContent(getXML(outputFunctions));
        }
    }
    // Add Simulations to the simulationSpec
    if (bioModel != null) {
        cbit.vcell.solver.Simulation[] simulations = bioModel.getSimulations(param);
        for (int i = 0; simulations != null && i < simulations.length; i++) {
            simulationcontext.addContent(getXML(simulations[i]));
        }
    }
    // Add AnalysisTasks
    if (param.getAnalysisTasks() != null && param.getAnalysisTasks().length > 0) {
        // if the task is empty (no parameters set up, no reference data), we shall not save it
        if (param.getAnalysisTasks().length == 1) {
            AnalysisTask task = param.getAnalysisTasks()[0];
            if (task instanceof ParameterEstimationTask) {
                if (!((ParameterEstimationTask) task).isEmpty()) {
                    simulationcontext.addContent(getXML(param.getAnalysisTasks()));
                }
            }
        } else // have more than one analysis task
        {
            simulationcontext.addContent(getXML(param.getAnalysisTasks()));
        }
    }
    // Add (Bio)events
    BioEvent[] bioEvents = param.getBioEvents();
    if (bioEvents != null && bioEvents.length > 0) {
        simulationcontext.addContent(getXML(bioEvents));
    }
    SimulationContextParameter[] appParams = param.getSimulationContextParameters();
    if (appParams != null && appParams.length > 0) {
        simulationcontext.addContent(getXML(appParams));
    }
    SpatialObject[] spatialObjects = param.getSpatialObjects();
    if (spatialObjects != null && spatialObjects.length > 0) {
        simulationcontext.addContent(getXML(spatialObjects));
    }
    SpatialProcess[] spatialProcesses = param.getSpatialProcesses();
    if (spatialProcesses != null && spatialProcesses.length > 0) {
        simulationcontext.addContent(getXML(spatialProcesses));
    }
    // Add rate rules
    RateRule[] rateRules = param.getRateRules();
    if (param.getRateRules() != null && rateRules.length > 0) {
        simulationcontext.addContent(getXML(rateRules));
    }
    // Add Datacontext
    if (param.getDataContext() != null && param.getDataContext().getDataSymbols().length > 0) {
        simulationcontext.addContent(getXML(param.getDataContext(), param.getModel().getUnitSystem()));
    }
    // Add Metadata (if any)
    if (param.getVersion() != null) {
        simulationcontext.addContent(getXML(param.getVersion(), param));
    }
    // Add microscope measurements
    simulationcontext.addContent(getXML(param.getMicroscopeMeasurement()));
    return simulationcontext;
}