Examples with DocumentEditorTreeFolderClass cbit.vcell.client.desktop.biomodel.DocumentEditorTreeModel.DocumentEditorTreeFolderClass used on opensource projects

Example 6 with DocumentEditorTreeFolderClass

use of cbit.vcell.client.desktop.biomodel.DocumentEditorTreeModel.DocumentEditorTreeFolderClass in project vcell by virtualcell.

the class MathModelEditor method setRightTopPanel.

private void setRightTopPanel(Object selectedObject) {
    JComponent newTopPanel = emptyPanel;
    int dividerLocation = rightSplitPane.getDividerLocation();
    if (selectedObject == mathModel) {
        newTopPanel = mathModelPropertiesPanel;
        mathModelPropertiesPanel.setMathModel(mathModel);
    } else if (selectedObject instanceof DocumentEditorTreeFolderNode) {
        DocumentEditorTreeFolderNode folderNode = (DocumentEditorTreeFolderNode) selectedObject;
        DocumentEditorTreeFolderClass folderClass = folderNode.getFolderClass();
        if (folderClass == DocumentEditorTreeFolderClass.MATH_ANNOTATION_NODE) {
            newTopPanel = mathModelPropertiesPanel;
        } else if (folderClass == DocumentEditorTreeFolderClass.MATH_VCML_NODE) {
            newTopPanel = vcmlEditorPanel;
        } else if (folderClass == DocumentEditorTreeFolderClass.MATH_GEOMETRY_NODE) {
            newTopPanel = geometryViewer;
        } else if (folderClass == DocumentEditorTreeFolderClass.MATH_SIMULATIONS_NODE) {
            newTopPanel = simulationListPanel;
        } else if (folderClass == DocumentEditorTreeFolderClass.MATH_OUTPUT_FUNCTIONS_NODE) {
            newTopPanel = outputFunctionsPanel;
            outputFunctionsPanel.setSimulationWorkspace(mathModelWindowManager.getSimulationWorkspace());
        }
    }
    Component rightTopComponent = rightSplitPane.getTopComponent();
    if (rightTopComponent != newTopPanel) {
        newTopPanel.setBorder(GuiConstants.TAB_PANEL_BORDER);
        rightSplitPane.setTopComponent(newTopPanel);
    }
    rightSplitPane.setDividerLocation(dividerLocation);
}

Example 7 with DocumentEditorTreeFolderClass

use of cbit.vcell.client.desktop.biomodel.DocumentEditorTreeModel.DocumentEditorTreeFolderClass in project vcell by virtualcell.

the class MathModelEditorTreeCellRenderer method getTreeCellRendererComponent.

// public void setMathModel(MathModel mm) {
// mathModel = mm;
// }
public Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
    super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
    if (regularFont == null) {
        regularFont = getFont();
        boldFont = regularFont.deriveFont(Font.BOLD);
    }
    Font font = regularFont;
    Icon icon = null;
    String labelText = null;
    String toolTipPrefix = "";
    String toolTipSuffix = "";
    if (value instanceof BioModelNode) {
        BioModelNode node = (BioModelNode) value;
        if (node.getChildCount() > 0) {
            icon = getIcon();
        }
        Object userObj = node.getUserObject();
        if (userObj instanceof MathModel) {
            font = boldFont;
            icon = VCellIcons.documentIcon;
            labelText = ((MathModel) userObj).getName();
            toolTipPrefix = "MathModel: ";
        } else if (userObj instanceof DocumentEditorTreeFolderNode) {
            // --- 1st level folders
            DocumentEditorTreeFolderNode folder = (DocumentEditorTreeFolderNode) userObj;
            labelText = folder.getName();
            if (folder.isBold()) {
                font = boldFont;
            }
            DocumentEditorTreeFolderClass folderClass = folder.getFolderClass();
            switch(folderClass) {
                case MATH_VCML_NODE:
                    icon = VCellIcons.textNotesIcon;
                    break;
                case MATH_GEOMETRY_NODE:
                    icon = VCellIcons.geometryIcon;
                    break;
                case MATH_SIMULATIONS_NODE:
                    icon = VCellIcons.simulationIcon;
                    break;
                case MATH_OUTPUT_FUNCTIONS_NODE:
                    icon = VCellIcons.getOutputFunctionIcon();
                    break;
            }
        }
    }
    setIcon(icon);
    setFont(font);
    setText(labelText);
    if (toolTipSuffix.length() == 0) {
        toolTipSuffix = labelText;
    }
    setToolTipText(toolTipPrefix + toolTipSuffix);
    return this;
}

Example 8 with DocumentEditorTreeFolderClass

use of cbit.vcell.client.desktop.biomodel.DocumentEditorTreeModel.DocumentEditorTreeFolderClass in project vcell by virtualcell.

the class BioModelEditorPathwayDiagramPanel method onActiveViewChange.

@Override
protected void onActiveViewChange(ActiveView activeView) {
    super.onActiveViewChange(activeView);
    SimulationContext selectedSimContext = activeView.getSimulationContext();
    DocumentEditorTreeFolderClass folderClass = activeView.getDocumentEditorTreeFolderClass();
    if (selectedSimContext != null || folderClass == null) {
        return;
    }
    switch(folderClass) {
        case PATHWAY_DIAGRAM_NODE:
            tabbedPane.setSelectedIndex(PathwayPanelTabID.pathway_diagram.ordinal());
            break;
        case PATHWAY_OBJECTS_NODE:
            tabbedPane.setSelectedIndex(PathwayPanelTabID.pathway_objects.ordinal());
            break;
        case BIOPAX_SUMMARY_NODE:
            tabbedPane.setSelectedIndex(PathwayPanelTabID.biopax_summary.ordinal());
            break;
        case BIOPAX_TREE_NODE:
            tabbedPane.setSelectedIndex(PathwayPanelTabID.biopax_tree.ordinal());
            break;
    }
}

Example 9 with DocumentEditorTreeFolderClass

use of cbit.vcell.client.desktop.biomodel.DocumentEditorTreeModel.DocumentEditorTreeFolderClass in project vcell by virtualcell.

the class BioModelEditorTreeCellRenderer method getTreeCellRendererComponent.

public Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
    super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
    if (regularFont == null) {
        regularFont = getFont();
        boldFont = regularFont.deriveFont(Font.BOLD);
    }
    Font font = regularFont;
    Icon icon = null;
    String labelText = null;
    String toolTipPrefix = "";
    String toolTipSuffix = "";
    if (value instanceof LinkNode) {
        LinkNode ln = (LinkNode) value;
        String link = ln.getLink();
        String text = ln.getText();
        String qualifier = ln.getMiriamQualifier().getDescription();
        if (link != null) {
            String colorString = (sel) ? "white" : "blue";
            toolTipPrefix = "double-click to open link " + link;
            labelText = "<html>" + qualifier + "&nbsp;<font color=\"" + colorString + "\"><a href=" + link + ">" + text + "</a></font></html>";
        } else {
            String colorString = (sel) ? "white" : "black";
            labelText = "<html>" + qualifier + "&nbsp;<font color=\"" + colorString + "\">" + text + "</font></html>";
        }
    } else if (value instanceof BioModelNode) {
        BioModelNode node = (BioModelNode) value;
        Object userObj = node.getUserObject();
        if (userObj instanceof BioModel) {
            font = boldFont;
            icon = VCellIcons.documentIcon;
            labelText = ((BioModel) userObj).getName();
            toolTipPrefix = "BioModel: ";
        } else if (userObj instanceof SimulationContext) {
            // --- root: application name
            font = boldFont;
            // icon = VCellIcons.applicationIcon;
            SimulationContext simContext = (SimulationContext) userObj;
            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";
                }
            }
            labelText = /*"Application: " + */
            ((SimulationContext) userObj).getName();
            toolTipPrefix = "Application: ";
        } else if (userObj instanceof DocumentEditorTreeFolderNode) {
            // --- 1st level folders
            DocumentEditorTreeFolderNode folder = (DocumentEditorTreeFolderNode) userObj;
            labelText = folder.getName();
            if (folder.isBold()) {
                font = boldFont;
            }
            DocumentEditorTreeFolderClass folderClass = folder.getFolderClass();
            switch(folderClass) {
                // break;
                case REACTIONS_NODE:
                    icon = VCellIcons.tableIcon;
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        int numReactions = bioModel.getModel().getNumReactions();
                        if (bioModel.getModel().getRbmModelContainer() != null) {
                            numReactions += bioModel.getModel().getRbmModelContainer().getReactionRuleList().size();
                        }
                        labelText = folder.getName() + " (" + numReactions + ")";
                    }
                    break;
                case STRUCTURES_NODE:
                    icon = VCellIcons.tableIcon;
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        labelText = folder.getName() + " (" + bioModel.getModel().getNumStructures() + ")";
                    }
                    break;
                case SPECIES_NODE:
                    icon = VCellIcons.tableIcon;
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        labelText = folder.getName() + " (" + bioModel.getModel().getNumSpeciesContexts() + ")";
                    }
                    break;
                case MOLECULAR_TYPES_NODE:
                    icon = VCellIcons.tableIcon;
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        RbmModelContainer rbmModelContainer = bioModel.getModel().getRbmModelContainer();
                        if (rbmModelContainer == null) {
                            labelText = folder.getName() + "(00000)";
                        } else {
                            labelText = folder.getName() + " (" + rbmModelContainer.getMolecularTypeList().size() + ")";
                        }
                    }
                    break;
                case OBSERVABLES_NODE:
                    icon = VCellIcons.tableIcon;
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        RbmModelContainer rbmModelContainer = bioModel.getModel().getRbmModelContainer();
                        if (rbmModelContainer == null) {
                            labelText = folder.getName() + "(00000)";
                        } else {
                            labelText = folder.getName() + " (" + rbmModelContainer.getObservableList().size() + ")";
                        }
                    }
                    break;
                case APPLICATIONS_NODE:
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        labelText = folder.getName() + " (" + bioModel.getNumSimulationContexts() + ")";
                    }
                    break;
                case REACTION_DIAGRAM_NODE:
                    icon = VCellIcons.diagramIcon;
                    break;
                // break;
                case GEOMETRY_NODE:
                    icon = VCellIcons.geometryIcon;
                    break;
                case SPECIFICATIONS_NODE:
                    icon = VCellIcons.settingsIcon;
                    break;
                case PROTOCOLS_NODE:
                    icon = VCellIcons.protocolsIcon;
                    break;
                case SIMULATIONS_NODE:
                    icon = VCellIcons.simulationIcon;
                    break;
                case PARAMETER_ESTIMATION_NODE:
                    icon = VCellIcons.fittingIcon;
                    break;
                case PATHWAY_DIAGRAM_NODE:
                    icon = VCellIcons.diagramIcon;
                    break;
                case PATHWAY_OBJECTS_NODE:
                    icon = VCellIcons.tableIcon;
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        labelText = folder.getName() + " (" + bioModel.getPathwayModel().getBiopaxObjects().size() + ")";
                    }
                    break;
                case BIOPAX_SUMMARY_NODE:
                    icon = VCellIcons.textNotesIcon;
                    break;
                case BIOPAX_TREE_NODE:
                    icon = VCellIcons.tableIcon;
                    break;
            }
        }
    }
    setIcon(icon);
    setFont(font);
    setText(labelText);
    if (toolTipSuffix.length() == 0) {
        toolTipSuffix = labelText;
    }
    setToolTipText(toolTipPrefix + toolTipSuffix);
    return this;
}

Example 10 with DocumentEditorTreeFolderClass

use of cbit.vcell.client.desktop.biomodel.DocumentEditorTreeModel.DocumentEditorTreeFolderClass in project vcell by virtualcell.

the class DocumentEditor method construcutPopupMenu.

private void construcutPopupMenu() {
    popupMenu.removeAll();
    TreePath[] selectedPaths = documentEditorTree.getSelectionPaths();
    boolean bRename = false;
    boolean bExpand = true;
    boolean bAddNew = false;
    boolean bAddNewApp = false;
    boolean bCopyApp = false;
    boolean bDelete = false;
    boolean bNewBiomodel = false;
    boolean bRemoveApps = false;
    DocumentEditorTreeFolderClass folderClass = null;
    for (TreePath tp : selectedPaths) {
        Object obj = tp.getLastPathComponent();
        if (obj == null || !(obj instanceof BioModelNode)) {
            continue;
        }
        if (documentEditorTree.getModel().isLeaf(obj)) {
            bExpand = false;
        }
        BioModelNode selectedNode = (BioModelNode) obj;
        Object userObject = selectedNode.getUserObject();
        if (userObject instanceof DocumentEditorTreeFolderNode) {
            folderClass = ((DocumentEditorTreeFolderNode) userObject).getFolderClass();
            if (folderClass == DocumentEditorTreeFolderClass.APPLICATIONS_NODE) {
                bAddNewApp = true;
                if (selectedNode.getChildCount() > 0) {
                    bRemoveApps = true;
                }
            } else if (folderClass == DocumentEditorTreeFolderClass.REACTIONS_NODE || folderClass == DocumentEditorTreeFolderClass.STRUCTURES_NODE || folderClass == DocumentEditorTreeFolderClass.SPECIES_NODE || folderClass == DocumentEditorTreeFolderClass.MOLECULAR_TYPES_NODE || folderClass == DocumentEditorTreeFolderClass.OBSERVABLES_NODE || folderClass == DocumentEditorTreeFolderClass.MATH_SIMULATIONS_NODE) {
                bAddNew = (selectedPaths.length == 1);
                bRename = false;
            }
        } else if (userObject instanceof SimulationContext) {
            bRename = true;
            bCopyApp = true;
            bDelete = true;
            bNewBiomodel = true;
        }
    }
    if (selectedPaths.length != 1) {
        bRename = false;
    }
    if (bAddNewApp) {
        if (addNewAppMenu == null) {
            addNewAppMenu = new JMenu("New Application");
            addNewAppDeterministicMenuItem = new JMenuItem(GuiConstants.MENU_TEXT_DETERMINISTIC_APPLICATION);
            addNewAppDeterministicMenuItem.addActionListener(eventHandler);
            addNewAppStochasticMenuItem = new JMenuItem(GuiConstants.MENU_TEXT_STOCHASTIC_APPLICATION);
            addNewAppStochasticMenuItem.addActionListener(eventHandler);
            addNewAppRulebasedMenuItem = new JMenuItem(GuiConstants.MENU_TEXT_RULEBASED_APPLICATION);
            addNewAppRulebasedMenuItem.addActionListener(eventHandler);
            addNewAppMenu.add(addNewAppDeterministicMenuItem);
            addNewAppMenu.add(addNewAppStochasticMenuItem);
            addNewAppMenu.add(addNewAppRulebasedMenuItem);
        }
        popupMenu.add(addNewAppMenu);
    }
    if (bRemoveApps) {
        if (removeAppsMenu == null) {
            removeAppsMenu = new JMenuItem("Remove Apps...");
            removeAppsMenu.addActionListener(eventHandler);
        }
        popupMenu.add(removeAppsMenu);
    }
    if (bAddNew) {
        String addText = "New";
        if (folderClass == DocumentEditorTreeFolderClass.REACTIONS_NODE) {
            addText += " Reaction";
        } else if (folderClass == DocumentEditorTreeFolderClass.STRUCTURES_NODE) {
            addText += " Compartment";
        } else if (folderClass == DocumentEditorTreeFolderClass.SPECIES_NODE) {
            addText += " Species";
        } else if (folderClass == DocumentEditorTreeFolderClass.MOLECULAR_TYPES_NODE) {
            addText += " Molecule";
        } else if (folderClass == DocumentEditorTreeFolderClass.OBSERVABLES_NODE) {
            addText += " Observable";
        } else if (folderClass == DocumentEditorTreeFolderClass.MATH_SIMULATIONS_NODE) {
            addText += " Simulation";
        }
        addNewMenuItem = new javax.swing.JMenuItem(addText);
        addNewMenuItem.addActionListener(eventHandler);
        popupMenu.add(addNewMenuItem);
    }
    if (bRename) {
        if (renameMenuItem == null) {
            renameMenuItem = new javax.swing.JMenuItem("Rename");
            renameMenuItem.addActionListener(eventHandler);
        }
        popupMenu.add(renameMenuItem);
    }
    if (bDelete) {
        if (deleteMenuItem == null) {
            deleteMenuItem = new javax.swing.JMenuItem("Delete");
            deleteMenuItem.addActionListener(eventHandler);
        }
        popupMenu.add(deleteMenuItem);
    }
    if (bCopyApp) {
        if (menuItemAppCopy == null) {
            menuItemAppCopy = new JMenuItem(GuiConstants.MENU_TEXT_APP_COPY);
            menuItemAppCopy.addActionListener(eventHandler);
            menuItemAppCopy.setActionCommand(GuiConstants.ACTIONCMD_COPY_APPLICATION);
        }
        if (menuAppCopyAs == null) {
            menuAppCopyAs = new JMenu(GuiConstants.MENU_TEXT_APP_COPYAS);
        }
        menuAppCopyAs.removeAll();
        SimulationContext selectedSimContext = getSelectedSimulationContext();
        if (selectedSimContext != null) {
            if (selectedSimContext.getGeometry().getDimension() == 0) {
                if (menuItemNonSpatialCopyDeterministic == null) {
                    menuItemNonSpatialCopyStochastic = new JMenuItem(GuiConstants.MENU_TEXT_STOCHASTIC_APPLICATION);
                    menuItemNonSpatialCopyStochastic.setActionCommand(GuiConstants.ACTIONCMD_NON_SPATIAL_COPY_TO_STOCHASTIC_APPLICATION);
                    menuItemNonSpatialCopyStochastic.addActionListener(eventHandler);
                    menuItemNonSpatialCopyDeterministic = new javax.swing.JMenuItem(GuiConstants.MENU_TEXT_DETERMINISTIC_APPLICATION);
                    menuItemNonSpatialCopyDeterministic.setActionCommand(GuiConstants.ACTIONCMD_NON_SPATIAL_COPY_TO_DETERMINISTIC_APPLICATION);
                    menuItemNonSpatialCopyDeterministic.addActionListener(eventHandler);
                    menuItemNonSpatialCopyRulebased = new javax.swing.JMenuItem(GuiConstants.MENU_TEXT_RULEBASED_APPLICATION);
                    menuItemNonSpatialCopyRulebased.setActionCommand(GuiConstants.ACTIONCMD_NON_SPATIAL_COPY_TO_RULEBASED_APPLICATION);
                    menuItemNonSpatialCopyRulebased.addActionListener(eventHandler);
                }
                menuAppCopyAs.add(menuItemNonSpatialCopyDeterministic);
                menuAppCopyAs.add(menuItemNonSpatialCopyStochastic);
                menuAppCopyAs.add(menuItemNonSpatialCopyRulebased);
            } else {
                if (menuSpatialCopyAsNonSpatial == null) {
                    menuSpatialCopyAsNonSpatial = new JMenu(GuiConstants.MENU_TEXT_NON_SPATIAL_APPLICATION);
                    menuItemSpatialCopyAsNonSpatialDeterministic = new JMenuItem(GuiConstants.MENU_TEXT_DETERMINISTIC_APPLICATION);
                    menuItemSpatialCopyAsNonSpatialDeterministic.setActionCommand(GuiConstants.ACTIONCMD_SPATIAL_COPY_TO_NON_SPATIAL_DETERMINISTIC_APPLICATION);
                    menuItemSpatialCopyAsNonSpatialDeterministic.addActionListener(eventHandler);
                    menuItemSpatialCopyAsNonSpatialStochastic = new JMenuItem(GuiConstants.MENU_TEXT_STOCHASTIC_APPLICATION);
                    menuItemSpatialCopyAsNonSpatialStochastic.setActionCommand(GuiConstants.ACTIONCMD_SPATIAL_COPY_TO_NON_SPATIAL_STOCHASTIC_APPLICATION);
                    menuItemSpatialCopyAsNonSpatialStochastic.addActionListener(eventHandler);
                    menuItemSpatialCopyAsNonSpatialRulebased = new JMenuItem(GuiConstants.MENU_TEXT_RULEBASED_APPLICATION);
                    menuItemSpatialCopyAsNonSpatialRulebased.setActionCommand(GuiConstants.ACTIONCMD_SPATIAL_COPY_TO_NON_SPATIAL_RULEBASED_APPLICATION);
                    menuItemSpatialCopyAsNonSpatialRulebased.addActionListener(eventHandler);
                    menuSpatialCopyAsNonSpatial.add(menuItemSpatialCopyAsNonSpatialDeterministic);
                    menuSpatialCopyAsNonSpatial.add(menuItemSpatialCopyAsNonSpatialStochastic);
                    menuSpatialCopyAsNonSpatial.add(menuItemSpatialCopyAsNonSpatialRulebased);
                    menuSpatialCopyAsSpatial = new JMenu(GuiConstants.MENU_TEXT_SPATIAL_APPLICATION);
                    menuItemSpatialCopyAsSpatialDeterministic = new JMenuItem(GuiConstants.MENU_TEXT_DETERMINISTIC_APPLICATION);
                    menuItemSpatialCopyAsSpatialDeterministic.setActionCommand(GuiConstants.ACTIONCMD_SPATIAL_COPY_TO_SPATIAL_DETERMINISTIC_APPLICATION);
                    menuItemSpatialCopyAsSpatialDeterministic.addActionListener(eventHandler);
                    menuItemSpatialCopyAsSpatialStochastic = new JMenuItem(GuiConstants.MENU_TEXT_STOCHASTIC_APPLICATION);
                    menuItemSpatialCopyAsSpatialStochastic.setActionCommand(GuiConstants.ACTIONCMD_SPATIAL_COPY_TO_SPATIAL_STOCHASTIC_APPLICATION);
                    menuItemSpatialCopyAsSpatialStochastic.addActionListener(eventHandler);
                    menuItemSpatialCopyAsSpatialRulebased = new JMenuItem(GuiConstants.MENU_TEXT_RULEBASED_APPLICATION);
                    menuItemSpatialCopyAsSpatialRulebased.setActionCommand(GuiConstants.ACTIONCMD_SPATIAL_COPY_TO_SPATIAL_RULEBASED_APPLICATION);
                    menuItemSpatialCopyAsSpatialRulebased.addActionListener(eventHandler);
                    menuSpatialCopyAsSpatial.add(menuItemSpatialCopyAsSpatialDeterministic);
                    menuSpatialCopyAsSpatial.add(menuItemSpatialCopyAsSpatialStochastic);
                // menuSpatialCopyAsSpatial.add(menuItemSpatialCopyAsSpatialRulebased);		// not supported yet, uncomment when time comes
                }
                menuAppCopyAs.add(menuSpatialCopyAsNonSpatial);
                menuAppCopyAs.add(menuSpatialCopyAsSpatial);
            }
        }
        if (popupMenu.getComponents().length > 0) {
            popupMenu.add(new JSeparator());
        }
        popupMenu.add(menuItemAppCopy);
        popupMenu.add(menuAppCopyAs);
    }
    if (bNewBiomodel) {
        menuItemNewBiomodelFromApp = new JMenuItem(GuiConstants.MENU_TEXT_APP_NEWBIOMODEL);
        menuItemNewBiomodelFromApp.addActionListener(eventHandler);
        popupMenu.add(menuItemNewBiomodelFromApp);
    }
    if (bExpand) {
        if (expandAllMenuItem == null) {
            popupMenuSeparator = new JSeparator();
            expandAllMenuItem = new javax.swing.JMenuItem("Expand All");
            collapseAllMenuItem = new javax.swing.JMenuItem("Collapse All");
            expandAllMenuItem.addActionListener(eventHandler);
            collapseAllMenuItem.addActionListener(eventHandler);
        }
        if (popupMenu.getComponents().length > 0) {
            popupMenu.add(popupMenuSeparator);
        }
        popupMenu.add(expandAllMenuItem);
        popupMenu.add(collapseAllMenuItem);
    }
}