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

Example 1 with SpeciesContext

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

the class ViewObservablesMapPanel method initialize.

private void initialize() {
    try {
        // --------------------------------------- the split panels
        setName("ViewGeneratedSpeciesPanel");
        setLayout(new BorderLayout());
        JPanel topPanel = new JPanel();
        topPanel.setLayout(new GridBagLayout());
        JPanel bottomPanel = new JPanel();
        bottomPanel.setLayout(new GridBagLayout());
        JSplitPane splitPaneHorizontal = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
        splitPaneHorizontal.setDividerSize(10);
        splitPaneHorizontal.setOneTouchExpandable(true);
        splitPaneHorizontal.setDividerLocation(260);
        splitPaneHorizontal.setResizeWeight(0.5);
        splitPaneHorizontal.setTopComponent(topPanel);
        splitPaneHorizontal.setBottomComponent(bottomPanel);
        add(splitPaneHorizontal, BorderLayout.CENTER);
        // ---------------------------------------- species shape panel
        shapePanelSpecies = new LargeShapePanel() {

            @Override
            public void paintComponent(Graphics g) {
                super.paintComponent(g);
                if (spls != null) {
                    spls.paintSelf(g);
                }
            }

            @Override
            public DisplayMode getDisplayMode() {
                return DisplayMode.other;
            }

            @Override
            public RuleAnalysisChanged hasStateChanged(String reactionRuleName, MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasStateChanged(MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasBondChanged(String reactionRuleName, MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasBondChanged(MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasNoMatch(String reactionRuleName, MolecularTypePattern mtp) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasNoMatch(MolecularTypePattern molecularTypePattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleParticipantSignature getSignature() {
                return null;
            }

            @Override
            public GroupingCriteria getCriteria() {
                return null;
            }

            @Override
            public boolean isViewSingleRow() {
                return true;
            }
        };
        shapePanelSpecies.setLayout(new GridBagLayout());
        shapePanelSpecies.setBackground(Color.white);
        // not really editable but we don't want the brown contours here
        shapePanelSpecies.setEditable(true);
        shapePanelSpecies.setShowMoleculeColor(true);
        shapePanelSpecies.setShowNonTrivialOnly(true);
        Border loweredBevelBorder = BorderFactory.createLoweredBevelBorder();
        JScrollPane scrollPaneSpecies = new JScrollPane(shapePanelSpecies);
        scrollPaneSpecies.setBorder(loweredBevelBorder);
        scrollPaneSpecies.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
        scrollPaneSpecies.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_NEVER);
        JPanel optionsPanelSpecies = new JPanel();
        optionsPanelSpecies.setLayout(new GridBagLayout());
        getZoomSmallerButtonSpecies().setEnabled(true);
        getZoomLargerButtonSpecies().setEnabled(true);
        shapePanelSpecies.zoomSmaller();
        shapePanelSpecies.zoomSmaller();
        GridBagConstraints gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 0;
        gbc.insets = new Insets(0, 0, 0, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanelSpecies.add(getZoomLargerButtonSpecies(), gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 1;
        gbc.insets = new Insets(2, 0, 4, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanelSpecies.add(getZoomSmallerButtonSpecies(), gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 2;
        gbc.weightx = 1;
        // fake cell used for filling all the vertical empty space
        gbc.weighty = 1;
        gbc.anchor = GridBagConstraints.WEST;
        gbc.insets = new Insets(4, 4, 4, 10);
        optionsPanelSpecies.add(new JLabel(""), gbc);
        JPanel containerOfScrollPanelSpecies = new JPanel();
        containerOfScrollPanelSpecies.setLayout(new BorderLayout());
        containerOfScrollPanelSpecies.add(optionsPanelSpecies, BorderLayout.WEST);
        containerOfScrollPanelSpecies.add(scrollPaneSpecies, BorderLayout.CENTER);
        Dimension dimS = new Dimension(500, 125);
        // dimension of shape panel
        containerOfScrollPanelSpecies.setPreferredSize(dimS);
        containerOfScrollPanelSpecies.setMinimumSize(dimS);
        containerOfScrollPanelSpecies.setMaximumSize(dimS);
        shapePanelObservable = new LargeShapePanel() {

            @Override
            public void paintComponent(Graphics g) {
                super.paintComponent(g);
                for (SpeciesPatternLargeShape sps : spsList) {
                    if (sps == null) {
                        continue;
                    }
                    sps.paintSelf(g);
                }
            }

            @Override
            public DisplayMode getDisplayMode() {
                return DisplayMode.other;
            }

            @Override
            public RuleAnalysisChanged hasStateChanged(String reactionRuleName, MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasStateChanged(MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasBondChanged(String reactionRuleName, MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasBondChanged(MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasNoMatch(String reactionRuleName, MolecularTypePattern mtp) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasNoMatch(MolecularTypePattern molecularTypePattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleParticipantSignature getSignature() {
                return null;
            }

            @Override
            public GroupingCriteria getCriteria() {
                return null;
            }

            @Override
            public boolean isViewSingleRow() {
                return true;
            }
        };
        // 
        DefaultScrollTableCellRenderer rbmSpeciesPatternCellRenderer = new DefaultScrollTableCellRenderer() {

            @Override
            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
                if (table.getModel() instanceof GeneratedSpeciesTableModel2) {
                    Object selectedObject = null;
                    if (table.getModel() == speciesTableModel) {
                        selectedObject = speciesTableModel.getValueAt(row);
                    }
                    if (selectedObject != null) {
                        if (selectedObject instanceof GeneratedSpeciesTableRow && value instanceof String) {
                            SpeciesPattern sp = ((GeneratedSpeciesTableRow) selectedObject).getSpecies().getSpeciesPattern();
                            String text = "<html>";
                            text += RbmTableRenderer.toHtml(sp, isSelected);
                            text += "</html>";
                            setText(text);
                        }
                    }
                }
                return this;
            }
        };
        // shapePanelObservable.setLayout(null);
        shapePanelObservable.setLayout(new GridBagLayout());
        shapePanelObservable.setBackground(Color.white);
        shapePanelObservable.setEditable(true);
        shapePanelObservable.setShowMoleculeColor(true);
        shapePanelObservable.setShowNonTrivialOnly(true);
        JScrollPane scrollPaneObservable = new JScrollPane(shapePanelObservable);
        scrollPaneObservable.setBorder(loweredBevelBorder);
        scrollPaneObservable.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
        scrollPaneObservable.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_NEVER);
        JPanel optionsPanelObservable = new JPanel();
        optionsPanelObservable.setLayout(new GridBagLayout());
        getZoomSmallerButtonObservable().setEnabled(true);
        getZoomLargerButtonObservable().setEnabled(true);
        shapePanelObservable.zoomSmaller();
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 0;
        gbc.insets = new Insets(0, 0, 0, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanelObservable.add(getZoomLargerButtonObservable(), gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 1;
        gbc.insets = new Insets(2, 0, 4, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanelObservable.add(getZoomSmallerButtonObservable(), gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 2;
        gbc.weightx = 1;
        // fake cell used for filling all the vertical empty space
        gbc.weighty = 1;
        gbc.anchor = GridBagConstraints.WEST;
        gbc.insets = new Insets(4, 4, 4, 10);
        optionsPanelObservable.add(new JLabel(""), gbc);
        JPanel containerOfScrollPanelObservable = new JPanel();
        containerOfScrollPanelObservable.setLayout(new BorderLayout());
        containerOfScrollPanelObservable.add(optionsPanelObservable, BorderLayout.WEST);
        containerOfScrollPanelObservable.add(scrollPaneObservable, BorderLayout.CENTER);
        Dimension dimO = new Dimension(500, 100);
        // dimension of shape panel
        containerOfScrollPanelObservable.setPreferredSize(dimO);
        containerOfScrollPanelObservable.setMinimumSize(dimO);
        containerOfScrollPanelObservable.setMaximumSize(dimO);
        // -------------- connection between tables, table models, selection models, renderers, event handlers
        speciesTable = new EditorScrollTable();
        speciesTableModel = new GeneratedSpeciesTableModel2(speciesTable, owner);
        speciesTable.setModel(speciesTableModel);
        speciesTable.getSelectionModel().addListSelectionListener(eventHandlerS);
        speciesTable.getModel().addTableModelListener(eventHandlerS);
        observablesTable = new EditorScrollTable();
        observablesTableModel = new ObservablesGroupTableModel(observablesTable, owner, speciesTableModel);
        observablesTable.setModel(observablesTableModel);
        observablesTable.getSelectionModel().addListSelectionListener(eventHandlerO);
        observablesTable.getModel().addTableModelListener(eventHandlerO);
        speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColDefinition).setCellRenderer(rbmSpeciesPatternCellRenderer);
        DefaultTableCellRenderer rightRenderer = new DefaultTableCellRenderer();
        rightRenderer.setHorizontalAlignment(JLabel.RIGHT);
        // speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColMultiplier).setCellRenderer(rightRenderer);	// right align
        // left column wide enough for title
        speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColMultiplier).setMaxWidth(70);
        speciesTable.addMouseMotionListener(new // add toolTipText for each table cell
        MouseMotionAdapter() {

            public void mouseMoved(MouseEvent e) {
                Point p = e.getPoint();
                int row = speciesTable.rowAtPoint(p);
                int column = speciesTable.columnAtPoint(p);
                speciesTable.setToolTipText(String.valueOf(speciesTable.getValueAt(row, column)));
            }
        });
        // ---------------------------------------------- top panel
        int gridy = 0;
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.weightx = 1.0;
        gbc.weighty = 1.0;
        gbc.gridwidth = 8;
        gbc.fill = GridBagConstraints.BOTH;
        gbc.insets = new Insets(4, 4, 4, 4);
        observablesTable.setPreferredScrollableViewportSize(new Dimension(400, 200));
        topPanel.add(observablesTable.getEnclosingScrollPane(), gbc);
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.anchor = GridBagConstraints.LINE_END;
        gbc.insets = new Insets(4, 4, 4, 4);
        topPanel.add(new JLabel("Search "), gbc);
        textFieldSearchObservables = new JTextField(70);
        textFieldSearchObservables.addActionListener(eventHandlerO);
        textFieldSearchObservables.getDocument().addDocumentListener(eventHandlerO);
        textFieldSearchObservables.putClientProperty("JTextField.variant", "search");
        gbc = new java.awt.GridBagConstraints();
        gbc.weightx = 1.0;
        gbc.gridx = 1;
        gbc.gridy = gridy;
        gbc.gridwidth = 3;
        gbc.anchor = GridBagConstraints.LINE_START;
        gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
        gbc.insets = new Insets(4, 0, 4, 4);
        topPanel.add(textFieldSearchObservables, gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 4;
        gbc.gridy = gridy;
        gbc.fill = GridBagConstraints.HORIZONTAL;
        gbc.insets = new Insets(4, 4, 4, 10);
        topPanel.add(totalObservablesLabel, gbc);
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        // gbc.weightx = 1.0;
        gbc.gridwidth = 8;
        gbc.anchor = GridBagConstraints.LINE_END;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(4, 4, 4, 4);
        topPanel.add(containerOfScrollPanelObservable, gbc);
        // -------------------------------------------- bottom panel
        gridy = 0;
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.weightx = 1.0;
        gbc.weighty = 1.0;
        gbc.gridwidth = 8;
        gbc.fill = GridBagConstraints.BOTH;
        gbc.insets = new Insets(4, 4, 4, 4);
        speciesTable.setPreferredScrollableViewportSize(new Dimension(400, 200));
        bottomPanel.add(speciesTable.getEnclosingScrollPane(), gbc);
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.anchor = GridBagConstraints.LINE_END;
        gbc.insets = new Insets(4, 4, 4, 4);
        bottomPanel.add(new JLabel("Search "), gbc);
        textFieldSearchSpecies = new JTextField(70);
        textFieldSearchSpecies.addActionListener(eventHandlerS);
        textFieldSearchSpecies.getDocument().addDocumentListener(eventHandlerS);
        textFieldSearchSpecies.putClientProperty("JTextField.variant", "search");
        gbc = new java.awt.GridBagConstraints();
        gbc.weightx = 1.0;
        gbc.gridx = 1;
        gbc.gridy = gridy;
        gbc.gridwidth = 3;
        gbc.anchor = GridBagConstraints.LINE_START;
        gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
        gbc.insets = new Insets(4, 0, 4, 4);
        bottomPanel.add(textFieldSearchSpecies, gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 4;
        gbc.gridy = gridy;
        gbc.fill = GridBagConstraints.HORIZONTAL;
        gbc.insets = new Insets(4, 4, 4, 10);
        bottomPanel.add(totalSpeciesLabel, gbc);
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        // gbc.weightx = 1.0;
        gbc.gridwidth = 8;
        gbc.anchor = GridBagConstraints.LINE_END;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(4, 4, 4, 4);
        bottomPanel.add(containerOfScrollPanelSpecies, gbc);
        // rendering the small shapes of the flattened species in the Depiction column of this viewer table)
        // TODO: this renderer is almost identical with the one in BioModelEditorModelPanel (which paints the small shapes
        // of a species context in the Depiction column of the species table)
        DefaultScrollTableCellRenderer rbmSpeciesShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {

            SpeciesPatternSmallShape spss = null;

            @Override
            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
                if (table.getModel() instanceof VCellSortTableModel<?>) {
                    Object selectedObject = null;
                    if (table.getModel() == speciesTableModel) {
                        selectedObject = speciesTableModel.getValueAt(row);
                    }
                    if (selectedObject != null) {
                        if (selectedObject instanceof GeneratedSpeciesTableRow) {
                            SpeciesContext sc = ((GeneratedSpeciesTableRow) selectedObject).getSpecies();
                            // sp cannot be null
                            SpeciesPattern sp = sc.getSpeciesPattern();
                            Graphics panelContext = table.getGraphics();
                            spss = new SpeciesPatternSmallShape(4, 2, sp, panelContext, sc, isSelected, issueManager);
                        }
                    } else {
                        spss = null;
                    }
                }
                setText("");
                return this;
            }

            @Override
            public void paintComponent(Graphics g) {
                super.paintComponent(g);
                if (spss != null) {
                    spss.paintSelf(g);
                }
            }
        };
        speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColDepiction).setCellRenderer(rbmSpeciesShapeDepictionCellRenderer);
        speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColDepiction).setPreferredWidth(400);
        speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColDepiction).setMinWidth(400);
        speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColDefinition).setPreferredWidth(30);
        speciesTable.setAutoResizeMode(JTable.AUTO_RESIZE_LAST_COLUMN);
        DefaultScrollTableCellRenderer rbmObservableShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {

            List<SpeciesPatternSmallShape> spssList = new ArrayList<SpeciesPatternSmallShape>();

            SpeciesPatternSmallShape spss = null;

            @Override
            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
                if (table.getModel() instanceof VCellSortTableModel<?>) {
                    Object selectedObject = null;
                    if (table.getModel() == observablesTableModel) {
                        selectedObject = observablesTableModel.getValueAt(row);
                    }
                    if (selectedObject != null && selectedObject instanceof ObservablesGroupTableRow) {
                        ObservablesGroupTableRow ogtr = ((ObservablesGroupTableRow) selectedObject);
                        String obsName = ogtr.getObservableGroupObject().getObservableGroupName();
                        RbmObservable observable = ogtr.getObservable(obsName);
                        Graphics panelContext = table.getGraphics();
                        int xPos = 4;
                        spssList.clear();
                        for (int i = 0; i < observable.getSpeciesPatternList().size(); i++) {
                            SpeciesPattern sp = observable.getSpeciesPatternList().get(i);
                            spss = new SpeciesPatternSmallShape(xPos, 2, sp, panelContext, observable, isSelected, issueManager);
                            xPos += spss.getWidth() + 6;
                            spssList.add(spss);
                        }
                    } else {
                        spssList.clear();
                    }
                }
                setText("");
                return this;
            }

            @Override
            public void paintComponent(Graphics g) {
                super.paintComponent(g);
                for (SpeciesPatternSmallShape spss : spssList) {
                    if (spss == null) {
                        continue;
                    }
                    spss.paintSelf(g);
                }
            }
        };
        observablesTable.getColumnModel().getColumn(ObservablesGroupTableModel.iColDepiction).setCellRenderer(rbmObservableShapeDepictionCellRenderer);
        observablesTable.getColumnModel().getColumn(ObservablesGroupTableModel.iColDepiction).setPreferredWidth(150);
        observablesTable.getColumnModel().getColumn(ObservablesGroupTableModel.iColDepiction).setMinWidth(150);
        observablesTable.getColumnModel().getColumn(ObservablesGroupTableModel.iColDefinition).setPreferredWidth(80);
        observablesTable.getColumnModel().getColumn(ObservablesGroupTableModel.iColExpression).setPreferredWidth(100);
        observablesTable.setAutoResizeMode(JTable.AUTO_RESIZE_LAST_COLUMN);
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 2 with SpeciesContext

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

the class SEDMLExporter method translateBioModelToSedML.

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

Example 3 with SpeciesContext

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

the class SEDMLExporter method getTargetXPath.

private XPathTarget getTargetXPath(SymbolTableEntry ste, Map<Pair<String, String>, String> l2gMap) {
    // to get Xpath string for variables.
    SBMLSupport sbmlSupport = new SBMLSupport();
    XPathTarget targetXpath = null;
    if (ste instanceof SpeciesContext || ste instanceof SpeciesContextSpecParameter) {
        String name = ste.getName();
        if (ste instanceof SpeciesContextSpecParameter) {
            name = ((SpeciesContextSpecParameter) ste).getSpeciesContext().getName();
        }
        targetXpath = new XPathTarget(sbmlSupport.getXPathForSpecies(name));
    } else if (ste instanceof ModelParameter) {
        targetXpath = new XPathTarget(sbmlSupport.getXPathForGlobalParameter(ste.getName()));
    } else if (ste instanceof Structure || ste instanceof Structure.StructureSize || (ste instanceof StructureMappingParameter && ((StructureMappingParameter) ste).getRole() == StructureMapping.ROLE_Size)) {
        String compartmentId = ste.getName();
        // can change compartment size or spatial dimension, but in vcell, we cannot change compartment dimension.
        String compartmentAttr = "";
        if (ste instanceof Structure.StructureSize) {
            compartmentId = ((StructureSize) ste).getStructure().getName();
            compartmentAttr = ((StructureSize) ste).getName();
        }
        if (ste instanceof StructureMappingParameter) {
            StructureMappingParameter smp = (StructureMappingParameter) ste;
            compartmentId = smp.getStructure().getName();
            if (smp.getRole() == StructureMapping.ROLE_Size) {
                compartmentAttr = smp.getName();
            }
        }
        if (compartmentAttr.length() < 1) {
            targetXpath = new XPathTarget(sbmlSupport.getXPathForCompartment(compartmentId));
        } else if (compartmentAttr.equalsIgnoreCase("size")) {
            targetXpath = new XPathTarget(sbmlSupport.getXPathForCompartment(compartmentId, CompartmentAttribute.size));
        } else {
            throw new RuntimeException("Unknown compartment attribute '" + compartmentAttr + "'; cannot get xpath target for compartment '" + compartmentId + "'.");
        }
    } else if (ste instanceof KineticsParameter) {
        KineticsParameter kp = (KineticsParameter) ste;
        String reactionID = kp.getKinetics().getReactionStep().getName();
        String parameterID = kp.getName();
        Pair<String, String> key = new Pair(reactionID, parameterID);
        String value = l2gMap.get(key);
        if (value == null) {
            targetXpath = new XPathTarget(sbmlSupport.getXPathForKineticLawParameter(reactionID, parameterID));
        } else {
            targetXpath = new XPathTarget(sbmlSupport.getXPathForGlobalParameter(value, ParameterAttribute.value));
        }
    } else {
        System.err.println("Entity should be SpeciesContext, Structure, ModelParameter : " + ste.getClass());
        throw new RuntimeException("Unknown entity in SBML model");
    }
    return targetXpath;
}

Example 4 with SpeciesContext

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

the class PathwayMapping method createSpeciesContextFromBioPaxObject.

private SpeciesContext createSpeciesContextFromBioPaxObject(BioModel bioModel, PhysicalEntity bioPaxObject, boolean addSubunits) throws Exception {
    String name;
    if (bioPaxObject.getName().size() == 0) {
        name = getSafetyName(bioPaxObject.getID());
    } else {
        name = getSafetyName(bioPaxObject.getName().get(0));
    }
    Model model = bioModel.getModel();
    SpeciesContext freeSpeciesContext = model.getSpeciesContext(name);
    if (freeSpeciesContext == null) {
        // create the new speciesContex Object, and link it to the corresponding pathway object
        if (model.getSpecies(name) == null) {
            freeSpeciesContext = model.createSpeciesContext(model.getStructures()[0]);
        } else {
            freeSpeciesContext = new SpeciesContext(model.getSpecies(name), model.getStructures()[0]);
        }
        freeSpeciesContext.setName(name);
        RelationshipObject newRelationship = new RelationshipObject(freeSpeciesContext, bioPaxObject);
        bioModel.getRelationshipModel().addRelationshipObject(newRelationship);
    } else {
        // if it is in the bioModel, then check whether it links to pathway object or not
        HashSet<RelationshipObject> linkedReObjects = bioModel.getRelationshipModel().getRelationshipObjects(freeSpeciesContext);
        if (linkedReObjects != null) {
            boolean flag = true;
            for (RelationshipObject reObject : linkedReObjects) {
                if (reObject.getBioPaxObject() == bioPaxObject) {
                    flag = false;
                    break;
                }
            }
            if (flag) {
                RelationshipObject newSpeciesContext = new RelationshipObject(freeSpeciesContext, bioPaxObject);
                bioModel.getRelationshipModel().addRelationshipObject(newSpeciesContext);
            }
        } else {
            RelationshipObject newSpeciesContext = new RelationshipObject(freeSpeciesContext, bioPaxObject);
            bioModel.getRelationshipModel().addRelationshipObject(newSpeciesContext);
        }
    }
    if (!freeSpeciesContext.hasSpeciesPattern()) {
        SpeciesPattern sp = generateSpeciesPattern(bioModel, bioPaxObject, addSubunits);
        if (sp != null && !sp.getMolecularTypePatterns().isEmpty()) {
            freeSpeciesContext.setSpeciesPattern(sp);
        }
    }
    return freeSpeciesContext;
}

Example 5 with SpeciesContext

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

the class PathwayMapping method createSpeciesContextFromTableRow.

private SpeciesContext createSpeciesContextFromTableRow(BioModel bioModel, PhysicalEntity bioPaxObject, double stoich, String id, String location, boolean addSubunits) throws Exception {
    // use user defined id as the name of the speciesContext
    String safeId = getSafetyName(id);
    String name;
    if (bioPaxObject.getName().size() == 0) {
        name = getSafetyName(bioPaxObject.getID());
    } else {
        name = getSafetyName(bioPaxObject.getName().get(0));
    }
    Model model = bioModel.getModel();
    SpeciesContext freeSpeciesContext = model.getSpeciesContext(safeId);
    if (freeSpeciesContext == null) {
        // create the new speciesContex Object, and link it to the corresponding pathway object
        if (model.getSpecies(name) == null) {
            freeSpeciesContext = model.createSpeciesContext(model.getStructure(location));
        } else {
            freeSpeciesContext = new SpeciesContext(model.getSpecies(name), model.getStructure(location));
        }
        freeSpeciesContext.setName(safeId);
        RelationshipObject newRelationship = new RelationshipObject(freeSpeciesContext, bioPaxObject);
        bioModel.getRelationshipModel().addRelationshipObject(newRelationship);
    } else {
        // if it is in the bioModel, then check whether it links to pathway object or not
        HashSet<RelationshipObject> linkedReObjects = bioModel.getRelationshipModel().getRelationshipObjects(freeSpeciesContext);
        if (linkedReObjects != null) {
            boolean flag = true;
            for (RelationshipObject reObject : linkedReObjects) {
                if (reObject.getBioPaxObject() == bioPaxObject) {
                    flag = false;
                    break;
                }
            }
            if (flag) {
                RelationshipObject newSpeciesContext = new RelationshipObject(freeSpeciesContext, bioPaxObject);
                bioModel.getRelationshipModel().addRelationshipObject(newSpeciesContext);
            }
        } else {
            RelationshipObject newSpeciesContext = new RelationshipObject(freeSpeciesContext, bioPaxObject);
            bioModel.getRelationshipModel().addRelationshipObject(newSpeciesContext);
        }
    }
    // else if it's proteine, small molecule, dna, etc the sp will consist of one molecule
    if (!freeSpeciesContext.hasSpeciesPattern()) {
        SpeciesPattern sp = generateSpeciesPattern(bioModel, bioPaxObject, addSubunits);
        if (sp != null && !sp.getMolecularTypePatterns().isEmpty()) {
            freeSpeciesContext.setSpeciesPattern(sp);
            sp.initializeBonds(MolecularComponentPattern.BondType.None);
        }
    }
    return freeSpeciesContext;
}