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

Example 61 with SpeciesContext

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

the class BioModelEditor method setRightBottomPanelOnSelection.

@Override
protected void setRightBottomPanelOnSelection(Object[] selections) {
    if (selections == null) {
        return;
    }
    JComponent bottomComponent = rightBottomEmptyPanel;
    int destComponentIndex = DocumentEditorTabID.object_properties.ordinal();
    boolean bShowInDatabaseProperties = false;
    boolean bShowPathway = false;
    if (selections.length == 1) {
        Object singleSelection = selections[0];
        if (singleSelection instanceof ReactionStep) {
            bottomComponent = getReactionPropertiesPanel();
        } else if (singleSelection instanceof ReactionRule) {
            bottomComponent = getReactionRulePropertiesPanel();
        } else if (singleSelection instanceof SpeciesContext) {
            bottomComponent = getSpeciesPropertiesPanel();
        } else if (singleSelection instanceof MolecularType) {
            bottomComponent = getMolecularTypePropertiesPanel();
        } else if (singleSelection instanceof RbmObservable) {
            bottomComponent = getObservablePropertiesPanel();
        } else if (singleSelection instanceof Structure) {
            bottomComponent = getStructurePropertiesPanel();
            getStructurePropertiesPanel().setModel(bioModel.getModel());
        } else if (singleSelection instanceof Parameter) {
            bottomComponent = getParameterPropertiesPanel();
        } else if (singleSelection instanceof SimulationContext) {
            bottomComponent = getApplicationPropertiesPanel();
        } else if (singleSelection instanceof ParameterEstimationTask) {
            bottomComponent = parameterEstimationTaskPropertiesPanel;
        } else if (singleSelection instanceof Product || singleSelection instanceof Reactant) {
            bottomComponent = getReactionParticipantPropertiesPanel();
        } else if (singleSelection instanceof BioModelInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = bioModelMetaDataPanel;
        } else if (singleSelection instanceof MathModelInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = mathModelMetaDataPanel;
        } else if (singleSelection instanceof GeometryInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = geometryMetaDataPanel;
        } else if (singleSelection instanceof SpeciesContextSpec) {
            bottomComponent = getSpeciesContextSpecPanel();
        } else if (singleSelection instanceof ReactionSpec) {
            bottomComponent = getKineticsTypeTemplatePanel();
        } else if (singleSelection instanceof ReactionRuleSpec) {
            // 
            bottomComponent = getReactionRuleSpecPropertiesPanel();
        } else if (singleSelection instanceof BioModelsNetModelInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = getBioModelsNetPropertiesPanel();
        } else if (singleSelection instanceof Simulation) {
            bottomComponent = getSimulationSummaryPanel();
        } else if (singleSelection instanceof DataSymbol) {
            bottomComponent = getDataSymbolsSpecPanel();
        } else if (singleSelection instanceof BioEvent) {
            bottomComponent = getEventPanel();
        } else if (singleSelection instanceof SpatialObject) {
            bottomComponent = getSpatialObjectPropertyPanel();
        } else if (singleSelection instanceof SpatialProcess) {
            bottomComponent = getSpatialProcessPropertyPanel();
        } else if (singleSelection instanceof BioPaxObject) {
            bottomComponent = bioPaxObjectPropertiesPanel;
        } else if (singleSelection instanceof BioModel || singleSelection instanceof VCMetaData) {
            bottomComponent = bioModelEditorAnnotationPanel;
        } else if (singleSelection instanceof PathwayData) {
            bShowPathway = true;
            bottomComponent = getBioModelEditorPathwayPanel();
        } else if (singleSelection instanceof Model) {
        } else if (singleSelection instanceof RuleParticipantSignature) {
            bottomComponent = getReactionRuleParticipantSignaturePropertiesPanel();
        } else if (singleSelection instanceof CSGObject) {
            bottomComponent = csgObjectPropertiesPanel;
            csgObjectPropertiesPanel.setSimulationContext(getSelectedSimulationContext());
        } else if (singleSelection instanceof DocumentEditorTreeFolderNode) {
            DocumentEditorTreeFolderClass folderClass = ((DocumentEditorTreeFolderNode) singleSelection).getFolderClass();
            if ((folderClass == DocumentEditorTreeFolderClass.REACTIONS_NODE) && !(singleSelection instanceof ReactionRule)) {
                bottomComponent = getReactionPropertiesPanel();
            } else if ((folderClass == DocumentEditorTreeFolderClass.REACTIONS_NODE) && (singleSelection instanceof ReactionRule)) {
                bottomComponent = getReactionRulePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.STRUCTURES_NODE) {
                bottomComponent = getStructurePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.SPECIES_NODE) {
                bottomComponent = getSpeciesPropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.MOLECULAR_TYPES_NODE) {
                bottomComponent = getMolecularTypePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.OBSERVABLES_NODE) {
                bottomComponent = getObservablePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.APPLICATIONS_NODE) {
                bottomComponent = getApplicationsPropertiesPanel();
                getApplicationsPropertiesPanel().setBioModel(bioModel);
            } else if (folderClass == DocumentEditorTreeFolderClass.PARAMETER_ESTIMATION_NODE) {
                bottomComponent = parameterEstimationTaskPropertiesPanel;
            }
        }
    }
    if (bShowPathway) {
        for (destComponentIndex = 0; destComponentIndex < rightBottomTabbedPane.getTabCount(); destComponentIndex++) {
            if (rightBottomTabbedPane.getComponentAt(destComponentIndex) == bottomComponent) {
                break;
            }
        }
        String tabTitle = "Pathway Preview";
        if (rightBottomTabbedPane.getTabCount() == destComponentIndex) {
            rightBottomTabbedPane.addTab(tabTitle, new TabCloseIcon(), bottomComponent);
        }
    } else if (bShowInDatabaseProperties) {
        for (destComponentIndex = 0; destComponentIndex < rightBottomTabbedPane.getTabCount(); destComponentIndex++) {
            Component c = rightBottomTabbedPane.getComponentAt(destComponentIndex);
            if (c == bioModelMetaDataPanel || c == mathModelMetaDataPanel || c == geometryMetaDataPanel || c == getBioModelsNetPropertiesPanel()) {
                break;
            }
        }
        if (rightBottomTabbedPane.getTabCount() == destComponentIndex) {
            rightBottomTabbedPane.addTab(DATABASE_PROPERTIES_TAB_TITLE, new TabCloseIcon(), bottomComponent);
        }
    }
    if (rightBottomTabbedPane.getComponentAt(destComponentIndex) != bottomComponent) {
        bottomComponent.setBorder(GuiConstants.TAB_PANEL_BORDER);
        rightBottomTabbedPane.setComponentAt(destComponentIndex, bottomComponent);
        rightSplitPane.repaint();
    }
    if (rightBottomTabbedPane.getSelectedComponent() != bottomComponent) {
        rightBottomTabbedPane.setSelectedComponent(bottomComponent);
    }
}

Example 62 with SpeciesContext

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

the class BioModelEditorModelPanel method deleteButtonPressed.

private void deleteButtonPressed() {
    try {
        ArrayList<Object> deleteList = new ArrayList<Object>();
        int selectedIndex = tabbedPane.getSelectedIndex();
        if (selectedIndex == ModelPanelTabID.reaction_diagram.ordinal()) {
            deleteList.addAll(Arrays.asList(reactionCartoonEditorPanel.getReactionCartoon().getSelectedObjects()));
        // } else if (selectedIndex == ModelPanelTabID.structure_diagram.ordinal()) {
        // deleteList.addAll(Arrays.asList(cartoonEditorPanel.getStructureCartoon().getSelectedObjects()));
        } else {
            computeCurrentSelectedTable();
            int[] rows = currentSelectedTable.getSelectedRows();
            if (rows == null || rows.length == 0) {
                return;
            }
            if (currentSelectedTable == speciesTable) {
                for (int r : rows) {
                    if (r < speciesTableModel.getRowCount()) {
                        SpeciesContext speciesContext = speciesTableModel.getValueAt(r);
                        if (speciesContext != null) {
                            deleteList.add(speciesContext);
                        }
                    }
                }
            } else if (currentSelectedTable == molecularTypeTable) {
                // TODO: delete stuff
                for (int r : rows) {
                    if (r < molecularTypeTableModel.getRowCount()) {
                        MolecularType mt = molecularTypeTableModel.getValueAt(r);
                        if (mt != null) {
                            deleteList.add(mt);
                        }
                    }
                }
            } else if (currentSelectedTable == observablesTable) {
                for (int r : rows) {
                    if (r < observableTableModel.getRowCount()) {
                        RbmObservable o = observableTableModel.getValueAt(r);
                        if (o != null) {
                            deleteList.add(o);
                        }
                    }
                }
            } else if (currentSelectedTable == structuresTable) {
                for (int r : rows) {
                    if (r < structureTableModel.getRowCount()) {
                        Structure rowValue = structureTableModel.getValueAt(r);
                        if (rowValue instanceof Feature || rowValue instanceof Membrane) {
                            deleteList.add(rowValue);
                        }
                    }
                }
            } else if (currentSelectedTable == reactionsTable) {
                for (int r : rows) {
                    if (r < reactionTableModel.getRowCount()) {
                        ModelProcess reaction = reactionTableModel.getValueAt(r);
                        if (reaction != null) {
                            deleteList.add(reaction);
                        }
                    }
                }
            }
        }
        if (deleteList.size() == 0) {
            return;
        }
        StringBuilder deleteListText = new StringBuilder();
        for (Object object : deleteList) {
            if (object instanceof SpeciesContext) {
                deleteListText.append("Species\t'" + ((SpeciesContext) object).getName() + "'\n");
            } else if (object instanceof MolecularType) {
                deleteListText.append(((MolecularType) object).getDisplayType() + "\t'" + ((MolecularType) object).getDisplayName() + "'\n");
            } else if (object instanceof RbmObservable) {
                deleteListText.append("Observable\t'" + ((RbmObservable) object).getName() + "'\n");
            } else if (object instanceof ReactionStep) {
                deleteListText.append("Reaction\t'" + ((ReactionStep) object).getName() + "'\n");
            } else if (object instanceof ReactionRule) {
                deleteListText.append("Reaction rule\t'" + ((ReactionRule) object).getName() + "'\n");
            } else if (object instanceof Structure) {
                deleteListText.append("Structure\t'" + ((Structure) object).getName() + "'\n");
            }
        }
        // TODO: once we display reaction rules in the carton editor panel we'll have to change the way we delete reaction rules
        if (deleteList.get(0) instanceof SpeciesContext || deleteList.get(0) instanceof ReactionStep) {
            try {
                ArrayList<SpeciesContext> speciesContextArrList = new ArrayList<SpeciesContext>();
                ArrayList<ReactionStep> reactionStepArrList = new ArrayList<ReactionStep>();
                for (Object obj : deleteList) {
                    if (obj instanceof SpeciesContext) {
                        speciesContextArrList.add((SpeciesContext) obj);
                    } else if (obj instanceof ReactionStep) {
                        reactionStepArrList.add((ReactionStep) obj);
                    } else {
                        throw new Exception("Unexpected delete object " + obj.getClass().getName());
                    }
                }
                ReactionCartoonTool.deleteReactionsAndSpecies(reactionCartoonEditorPanel, reactionStepArrList.toArray(new ReactionStep[0]), speciesContextArrList.toArray(new SpeciesContext[0]));
            } catch (UserCancelException uce) {
                return;
            }
            return;
        } else {
            String confirm = DialogUtils.showOKCancelWarningDialog(this, "Deleting", "You are going to delete the following:\n\n" + deleteListText + "\n Continue?");
            if (confirm.equals(UserMessage.OPTION_CANCEL)) {
                return;
            }
            for (Object object : deleteList) {
                if (object instanceof ReactionRule) {
                    ReactionRule rr = (ReactionRule) object;
                    bioModel.getModel().getRbmModelContainer().removeReactionRule(rr);
                } else if (object instanceof MolecularType) {
                    Map<String, Pair<Displayable, SpeciesPattern>> usedHere = new LinkedHashMap<String, Pair<Displayable, SpeciesPattern>>();
                    MolecularType mt = (MolecularType) object;
                    if (!bioModel.getModel().getRbmModelContainer().isDeleteAllowed(mt, usedHere)) {
                        String errMsg = mt.getDisplayType() + " <b>'" + mt + "'</b> cannot be deleted because it's already being used by:<br>";
                        final int MaxListSize = 7;
                        int count = 0;
                        for (String key : usedHere.keySet()) {
                            System.out.println(key);
                            if (count >= MaxListSize) {
                                errMsg += "<br> ... and more.";
                                break;
                            }
                            Pair<Displayable, SpeciesPattern> o = usedHere.get(key);
                            Displayable e = o.one;
                            SpeciesPattern sp = o.two;
                            errMsg += "<br> - " + e.getDisplayType().toLowerCase() + " <b>" + e.getDisplayName() + "</b>";
                            errMsg += ", " + sp.getDisplayType().toLowerCase() + " " + " <b>" + sp.getDisplayName() + "</b>";
                            count++;
                        }
                        errMsg = "<html>" + errMsg + "</html>";
                        throw new RuntimeException(errMsg);
                    }
                    bioModel.getModel().getRbmModelContainer().removeMolecularType(mt);
                } else if (object instanceof RbmObservable) {
                    RbmObservable o = (RbmObservable) object;
                    bioModel.getModel().getRbmModelContainer().removeObservable(o);
                } else {
                    bioModel.getModel().removeObject(object);
                }
            }
        }
    } catch (Exception ex) {
        ex.printStackTrace();
        DialogUtils.showErrorDialog(this, ex.getMessage());
    }
}

Example 63 with SpeciesContext

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

the class InitialConditionsPanel method initialize.

/**
 * Initialize the class.
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void initialize() {
    try {
        // user code begin {1}
        // user code end
        setName("InitialConditionsPanel");
        setLayout(new BorderLayout());
        add(getRadioButtonAndCheckboxPanel(), BorderLayout.NORTH);
        add(getScrollPaneTable().getEnclosingScrollPane(), BorderLayout.CENTER);
        getScrollPaneTable().getSelectionModel().addListSelectionListener(ivjEventHandler);
        getJMenuItemPaste().addActionListener(ivjEventHandler);
        getJMenuItemCopy().addActionListener(ivjEventHandler);
        getJMenuItemCopyAll().addActionListener(ivjEventHandler);
        getJMenuItemPasteAll().addActionListener(ivjEventHandler);
        getAmountRadioButton().addActionListener(ivjEventHandler);
        getConcentrationRadioButton().addActionListener(ivjEventHandler);
        getRandomizeInitCondnCheckbox().addActionListener(ivjEventHandler);
        DefaultTableCellRenderer renderer = new DefaultScrollTableCellRenderer() {

            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
                setIcon(null);
                defaultToolTipText = null;
                if (value instanceof Species) {
                    setText(((Species) value).getCommonName());
                    defaultToolTipText = getText();
                    setToolTipText(defaultToolTipText);
                } else if (value instanceof SpeciesContext) {
                    setText(((SpeciesContext) value).getName());
                    defaultToolTipText = getText();
                    setToolTipText(defaultToolTipText);
                } else if (value instanceof Structure) {
                    setText(((Structure) value).getName());
                    defaultToolTipText = getText();
                    setToolTipText(defaultToolTipText);
                } else if (value instanceof ScopedExpression) {
                    SpeciesContextSpec scSpec = tableModel.getValueAt(row);
                    VCUnitDefinition unit = null;
                    if (table.getColumnName(column).equals(SpeciesContextSpecsTableModel.ColumnType.COLUMN_INITIAL.label)) {
                        SpeciesContextSpecParameter initialConditionParameter = scSpec.getInitialConditionParameter();
                        unit = initialConditionParameter.getUnitDefinition();
                    } else if (table.getColumnName(column).equals(SpeciesContextSpecsTableModel.ColumnType.COLUMN_DIFFUSION.label)) {
                        SpeciesContextSpecParameter diffusionParameter = scSpec.getDiffusionParameter();
                        unit = diffusionParameter.getUnitDefinition();
                    }
                    if (unit != null) {
                        setHorizontalTextPosition(JLabel.LEFT);
                        setIcon(new TextIcon("[" + unit.getSymbolUnicode() + "]", DefaultScrollTableCellRenderer.uneditableForeground));
                    }
                    int rgb = 0x00ffffff & DefaultScrollTableCellRenderer.uneditableForeground.getRGB();
                    defaultToolTipText = "<html>" + StringEscapeUtils.escapeHtml4(getText()) + " <font color=#" + Integer.toHexString(rgb) + "> [" + unit.getSymbolUnicode() + "] </font></html>";
                    setToolTipText(defaultToolTipText);
                    if (unit != null) {
                        setText(defaultToolTipText);
                    }
                }
                TableModel tableModel = table.getModel();
                if (tableModel instanceof SortTableModel) {
                    DefaultScrollTableCellRenderer.issueRenderer(this, defaultToolTipText, table, row, column, (SortTableModel) tableModel);
                    setHorizontalTextPosition(JLabel.TRAILING);
                }
                return this;
            }
        };
        DefaultTableCellRenderer 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() == tableModel) {
                        selectedObject = tableModel.getValueAt(row);
                    }
                    if (selectedObject != null) {
                        if (selectedObject instanceof SpeciesContextSpec) {
                            SpeciesContextSpec scs = (SpeciesContextSpec) selectedObject;
                            SpeciesContext sc = scs.getSpeciesContext();
                            // sp may be null for "plain" species contexts
                            SpeciesPattern sp = sc.getSpeciesPattern();
                            Graphics panelContext = table.getGraphics();
                            spss = new SpeciesPatternSmallShape(4, 2, sp, shapeManager, 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);
                }
            }
        };
        getScrollPaneTable().setDefaultRenderer(SpeciesContext.class, renderer);
        getScrollPaneTable().setDefaultRenderer(Structure.class, renderer);
        getScrollPaneTable().setDefaultRenderer(SpeciesPattern.class, rbmSpeciesShapeDepictionCellRenderer);
        getScrollPaneTable().setDefaultRenderer(Species.class, renderer);
        getScrollPaneTable().setDefaultRenderer(ScopedExpression.class, renderer);
        getScrollPaneTable().setDefaultRenderer(Boolean.class, new ScrollTableBooleanCellRenderer());
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 64 with SpeciesContext

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

the class ReactionCartoonTool method lineAction.

private void lineAction(ReactionStep reactionStart, Structure endStructure) throws Exception {
    Structure startStructure = reactionStart.getStructure();
    if (StructureUtil.reactionHereCanHaveParticipantThere(startStructure, endStructure)) {
        // if reactionStart is a SimpleRxn OR FluxRxn without a product, add speciesContext as pdt
        if ((reactionStart instanceof SimpleReaction) || ((reactionStart instanceof FluxReaction) && !reactionStart.hasProduct())) {
            SpeciesContext speciesContext = getModel().createSpeciesContext(endStructure);
            reactionStart.addProduct(speciesContext, 1);
            positionShapeForObject(endStructure, speciesContext, edgeShape.getEnd());
        }
        if (((startStructure instanceof Feature && endStructure instanceof Feature) || (startStructure instanceof Membrane && endStructure instanceof Membrane)) && startStructure != endStructure) {
        // ============ change kinetics to lumped or warn user ?????????
        // reactionStart.setKinetics(new GeneralLumpedKinetics(reactionStart));
        }
        getReactionCartoon().notifyChangeEvent();
    }
}

Example 65 with SpeciesContext

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

the class ReactionCartoonTool method menuAction.

@Override
protected void menuAction(Shape shape, String menuAction) {
    if (shape == null) {
        return;
    }
    if (menuAction.equals(CartoonToolMiscActions.Properties.MENU_ACTION)) {
        if (shape instanceof FluxReactionShape) {
        // showFluxReactionPropertiesDialog((FluxReactionShape) shape);
        } else if (shape instanceof SimpleReactionShape) {
        // showSimpleReactionPropertiesDialog((SimpleReactionShape) shape);
        } else if (shape instanceof ReactantShape) {
        // Point locationOnScreen = shape.getSpaceManager().getAbsLoc();
        // Point graphPaneLocation = getGraphPane().getLocationOnScreen();
        // locationOnScreen.translate(graphPaneLocation.x,
        // graphPaneLocation.y);
        // showReactantPropertiesDialog((ReactantShape) shape,
        // locationOnScreen);
        } else if (shape instanceof ProductShape) {
        // Point locationOnScreen = shape.getSpaceManager().getAbsLoc();
        // Point graphPaneLocation = getGraphPane().getLocationOnScreen();
        // locationOnScreen.translate(graphPaneLocation.x,
        // graphPaneLocation.y);
        // showProductPropertiesDialog((ProductShape) shape,
        // locationOnScreen);
        } else if (shape instanceof SpeciesContextShape) {
        // showEditSpeciesDialog(getGraphPane(), getReactionCartoon()
        // .getModel(), ((SpeciesContextShape) shape)
        // .getSpeciesContext());
        } else if (shape instanceof ReactionContainerShape) {
        // ReactionContainerShape rcs = (ReactionContainerShape) shape;
        // if (rcs.getStructure() instanceof Feature) {
        // //
        // // showFeaturePropertyDialog is invoked in two modes:
        // //
        // // 1) parent!=null and child==null
        // // upon ok, it adds a new feature to the supplied parent.
        // //
        // // 2) parent==null and child!=null
        // // upon ok, edits the feature name
        // //
        // showFeaturePropertiesDialog(getGraphPane(),
        // (getReactionCartoon().getModel() == null ? null
        // : getReactionCartoon().getModel()), null,
        // (Feature) rcs.getStructure());
        // } else if (rcs.getStructure() instanceof Membrane) {
        // showMembranePropertiesDialog(getGraphPane(), (Membrane) rcs
        // .getStructure());
        // }
        }
    } else if (menuAction.equals(CartoonToolMiscActions.AddSpecies.MENU_ACTION)) {
        if (shape instanceof ReactionContainerShape) {
            getGraphModel().deselectShape(shape);
            // showCreateSpeciesContextDialog(getGraphPane(),
            // getReactionCartoon().getModel(),
            // ((ReactionContainerShape) shape).getStructure(), null);
            SpeciesContext speciesContext = getReactionCartoon().getModel().createSpeciesContext(((ReactionContainerShape) shape).getStructure());
            getGraphModel().select(speciesContext);
        }
    } else if (menuAction.equals(CartoonToolEditActions.Copy.MENU_ACTION)) {
        if (shape instanceof SpeciesContextShape || shape instanceof ReactionStepShape || // rule participants whose rule is not selected won't
        shape instanceof RuleParticipantSignatureDiagramShape || // be copied since standalone they are meaningless
        shape instanceof ReactionRuleDiagramShape) {
            SpeciesContext[] spArray = getSelectedSpeciesContextArray();
            ReactionStep[] rsArray = getSelectedReactionStepArray();
            ReactionRule[] rrArray = getSelectedReactionRuleArray();
            MolecularType[] mtArray = getSelectedMolecularTypeArray(rrArray, rsArray, spArray);
            Structure[] structArray = getSelectedStructuresArray(rrArray, rsArray, spArray, mtArray);
            Structure fromStruct = null;
            ReactionContainerShape rcs = null;
            Shape parentShape = shape.getParent();
            if (parentShape instanceof ReactionContainerShape) {
                rcs = (ReactionContainerShape) parentShape;
                fromStruct = rcs.getStructure();
            }
            ReactionSpeciesCopy reactionSpeciesCopy = new ReactionSpeciesCopy(spArray, rsArray, rrArray, mtArray, fromStruct, structArray);
            VCellTransferable.sendToClipboard(reactionSpeciesCopy);
        }
    } else if (/*menuAction.equals(CartoonToolEditActions.Paste.MENU_ACTION)
				|| */
    menuAction.equals(CartoonToolEditActions.PasteNew.MENU_ACTION)) {
        if (shape instanceof ReactionContainerShape) {
            pasteReactionsAndSpecies(((ReactionContainerShape) shape).getStructure());
        }
    } else if (menuAction.equals(CartoonToolEditActions.Delete.MENU_ACTION)) {
        try {
            if (getGraphModel().getSelectedShape() instanceof ReactionContainerShape && menuAction.equals(CartoonToolEditActions.Delete.MENU_ACTION)) {
                getModel().removeStructure(((ReactionContainerShape) getGraphModel().getSelectedShape()).getStructure());
                return;
            }
            if (getSelectedReactionStepArray() != null || getSelectedSpeciesContextArray() != null) {
                deleteReactionsAndSpecies(getGraphPane(), getSelectedReactionStepArray(), getSelectedSpeciesContextArray());
            }
            if (getSelectedReactionParticipantArray() != null && menuAction.equals(CartoonToolEditActions.Delete.MENU_ACTION)) {
                ReactionParticipant[] reactionParticipantArr = getSelectedReactionParticipantArray();
                String response = DialogUtils.showWarningDialog(getGraphPane(), "Delete " + reactionParticipantArr.length + " Reaction Stoichiometries", new String[] { RXSPECIES_DELETE, RXSPECIES_CANCEL }, RXSPECIES_CANCEL);
                if (response != null && response.equals(RXSPECIES_DELETE)) {
                    for (int i = 0; i < reactionParticipantArr.length; i++) {
                        ReactionStep reactionStep = reactionParticipantArr[i].getReactionStep();
                        reactionStep.removeReactionParticipant(reactionParticipantArr[i]);
                    }
                }
            }
        } catch (UserCancelException uce) {
            return;
        } catch (PropertyVetoException e) {
            DialogUtils.showErrorDialog(getGraphPane(), e.getMessage());
        } catch (Exception e) {
            DialogUtils.showErrorDialog(getGraphPane(), e.getMessage(), e);
        }
    } else if (menuAction.equals(CartoonToolMiscActions.SearchReactions.MENU_ACTION)) {
        try {
            if (shape instanceof ReactionContainerShape) {
                showReactionBrowserDialog(((ReactionContainerShape) shape).getStructure(), null);
            }
        } catch (Exception e) {
            DialogUtils.showErrorDialog(getGraphPane(), e.getMessage(), e);
        }
    } else if (menuAction.equals(CartoonToolSaveAsImageActions.MenuAction.MENU_ACTION)) {
        try {
            String resType = null;
            if (shape instanceof ReactionContainerShape) {
                showSaveReactionImageDialog();
            }
        } catch (Exception e) {
            e.printStackTrace();
            DialogUtils.showErrorDialog(getGraphPane(), e.getMessage(), e);
        }
    } else if (menuAction.equals(CartoonToolMiscActions.Annotate.MENU_ACTION)) {
        if (shape instanceof ReactionStepShape) {
            // MIRIAMHelper.showMIRIAMAnnotationDialog(((SimpleReactionShape)shape).getReactionStep());
            // System.out.println("Menu action annotate activated...");
            ReactionStep rs = ((ReactionStepShape) shape).getReactionStep();
            VCMetaData vcMetaData = rs.getModel().getVcMetaData();
            try {
                String newAnnotation = DialogUtils.showAnnotationDialog(getGraphPane(), vcMetaData.getFreeTextAnnotation(rs));
                vcMetaData.setFreeTextAnnotation(rs, newAnnotation);
            } catch (UtilCancelException e) {
            // Do Nothing
            } catch (Throwable exc) {
                exc.printStackTrace(System.out);
                DialogUtils.showErrorDialog(getGraphPane(), "Failed to edit annotation!\n" + exc.getMessage(), exc);
            }
        }
    } else {
    // default action is to ignore
    }
}