Examples with GraphPane cbit.gui.graph.gui.GraphPane used on opensource projects

Example 1 with GraphPane

use of cbit.gui.graph.gui.GraphPane in project vcell by virtualcell.

the class ReactionCartoonEditorPanel method getGraphPane.

private GraphPane getGraphPane() {
    if (graphPane == null) {
        try {
            graphPane = new GraphPane();
            graphPane.setName("GraphPane");
            graphPane.setBounds(0, 0, 372, 364);
        } catch (Throwable throwable) {
            handleException(throwable);
        }
    }
    return graphPane;
}

Example 2 with GraphPane

use of cbit.gui.graph.gui.GraphPane in project vcell by virtualcell.

the class ReactionCartoonTool method deleteReactionsAndSpecies.

public static void deleteReactionsAndSpecies(Component requester, ReactionStep[] reactionStepArr, SpeciesContext[] speciesContextArr) throws Exception, UserCancelException {
    if ((speciesContextArr == null && reactionStepArr == null) || (reactionStepArr == null && speciesContextArr != null && speciesContextArr.length == 0) || (speciesContextArr == null && reactionStepArr != null && reactionStepArr.length == 0) || (speciesContextArr != null && speciesContextArr.length == 0 && reactionStepArr != null && reactionStepArr.length == 0)) {
        return;
    }
    int rxCount = (reactionStepArr != null ? reactionStepArr.length : 0);
    int speciesCount = (speciesContextArr != null ? speciesContextArr.length : 0);
    boolean bHasBoth = speciesCount > 0 && rxCount > 0;
    ReactionCartoon rxCartoon = null;
    if (requester instanceof GraphPane && ((GraphPane) requester).getGraphModel() instanceof ReactionCartoon) {
        rxCartoon = (ReactionCartoon) (((GraphPane) requester).getGraphModel());
    } else if (requester instanceof ReactionCartoonEditorPanel) {
        rxCartoon = ((ReactionCartoonEditorPanel) requester).getReactionCartoon();
    } else {
        throw new IllegalArgumentException("ReactionCartoonTool.deleteSpeciesContext not implemented for type '" + requester.getClass().getName() + "'");
    }
    DeleteSpeciesInfo deleteSpeciesInfo = null;
    final String DETAILS = "Details...";
    while (true) {
        String response = DialogUtils.showWarningDialog(requester, RXSPECIES_DELETE + " " + (bHasBoth ? "Reactions and Species." : (rxCount > 0 ? "Reactions." : (speciesCount > 0 ? "Species." : ""))), RXSPECIES_DELETE + " " + (bHasBoth ? rxCount + " Reactions and " + speciesCount + " Species." : (rxCount > 0 ? rxCount + " Reactions." : (speciesCount > 0 ? speciesCount + " Species." : ""))), new String[] { RXSPECIES_DELETE, DETAILS, RXSPECIES_CANCEL }, RXSPECIES_DELETE);
        if (response == null || response.equals(RXSPECIES_CANCEL)) {
            throw UserCancelException.CANCEL_GENERIC;
        }
        deleteSpeciesInfo = (deleteSpeciesInfo == null ? detailsDeleteSpecies(requester, speciesContextArr, reactionStepArr, rxCartoon) : deleteSpeciesInfo);
        if (response.equals(DETAILS)) {
            TableListResult tableListResult = showDeleteDetails(requester, deleteSpeciesInfo, reactionStepArr, false);
        // if(!tableListResult.selectedOption.equals(RXSPECIES_BACK)){
        // //if(!tableListResult.selectedOption.equals((bCut?RXSPECIES_CUT:RXSPECIES_DELETE))){
        // throw UserCancelException.CANCEL_GENERIC;
        // }
        } else {
            break;
        }
    }
    if (deleteSpeciesInfo != null) {
        for (Boolean errors : deleteSpeciesInfo.getbUnresolvableHashMap().values()) {
            if (errors) {
                while (true) {
                    String response = DialogUtils.showWarningDialog(requester, "Error warning.", "Warning: 1 or more SpeciesContexts have Model references that could cause Model corruption if " + RXSPECIES_DELETE + ".", new String[] { DETAILS, RXSPECIES_CANCEL }, DETAILS);
                    if (response == null || response.equals(RXSPECIES_CANCEL)) {
                        throw UserCancelException.CANCEL_GENERIC;
                    }
                    showDeleteDetails(requester, deleteSpeciesInfo, reactionStepArr, true);
                }
            }
        }
    }
    if (reactionStepArr != null) {
        for (int i = 0; i < reactionStepArr.length; i += 1) {
            rxCartoon.getModel().removeReactionStep(reactionStepArr[i]);
        }
    }
    if (deleteSpeciesInfo != null) {
        // remove all ReactionParticipants ("lines" between reaction and species in "Reaction Diagram") that have this speciesContext before deleting SpeciesContext
        for (SpeciesContext objSpeciesContext : deleteSpeciesInfo.getRxPartHashMap().keySet()) {
            if (deleteSpeciesInfo.getbUnresolvableHashMap().get(objSpeciesContext)) {
                continue;
            }
            Iterator<ReactionParticipant> iterRxPart = deleteSpeciesInfo.getRxPartHashMap().get(objSpeciesContext).iterator();
            while (iterRxPart.hasNext()) {
                ReactionParticipant objRxPart = iterRxPart.next();
                if (rxCartoon.getObjects().contains(objRxPart)) {
                    // Reaction delete may have already removed
                    objRxPart.getReactionStep().removeReactionParticipant(objRxPart);
                }
            }
        }
        // remove the SpeciesContext
        for (int i = 0; i < speciesContextArr.length; i++) {
            if (deleteSpeciesInfo.getbUnresolvableHashMap().get(speciesContextArr[i])) {
                continue;
            }
            if (rxCartoon.getObjects().contains(speciesContextArr[i])) {
                // Reaction delete may have already removed
                rxCartoon.getModel().removeSpeciesContext(speciesContextArr[i]);
            }
        }
    }
}

Example 3 with GraphPane

use of cbit.gui.graph.gui.GraphPane in project vcell by virtualcell.

the class StructureMappingCartoonPanel method getStructureGraphPane.

/**
 * Return the StructureGraphPane property value.
 * @return cbit.vcell.graph.GraphPane
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private GraphPane getStructureGraphPane() {
    if (ivjStructureGraphPane == null) {
        try {
            ivjStructureGraphPane = new GraphPane();
            ivjStructureGraphPane.setName("StructureGraphPane");
            ivjStructureGraphPane.setBounds(0, 0, 290, 237);
        // user code begin {1}
        // user code end
        } catch (java.lang.Throwable ivjExc) {
            // user code begin {2}
            // user code end
            handleException(ivjExc);
        }
    }
    return ivjStructureGraphPane;
}

Example 4 with GraphPane

use of cbit.gui.graph.gui.GraphPane in project vcell by virtualcell.

the class BioModelEditorPathwayDiagramPanel method initialize.

private void initialize() {
    JToolBar layoutToolBar = createToolBar(SwingConstants.HORIZONTAL);
    sourceTextArea = new JTextArea();
    graphPane = new GraphPane();
    pathwayGraphModel = new PathwayGraphModel();
    pathwayGraphModel.addPropertyChangeListener(eventHandler);
    graphPane.setGraphModel(pathwayGraphModel);
    graphPane.addMouseListener(eventHandler);
    graphCartoonTool = new PathwayGraphTool();
    graphCartoonTool.setGraphPane(graphPane);
    graphTabPanel = new JPanel(new BorderLayout());
    graphScrollPane = new JScrollPane(graphPane);
    graphScrollPane.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_ALWAYS);
    graphScrollPane.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS);
    graphTabPanel.add(graphScrollPane, BorderLayout.CENTER);
    viewPortStabilizer = new ViewPortStabilizer(graphScrollPane);
    graphTabPanel.add(layoutToolBar, BorderLayout.NORTH);
    sourceTabPanel = new JPanel(new BorderLayout());
    sourceTabPanel.add(new JScrollPane(sourceTextArea), BorderLayout.CENTER);
    treeTabPanel.add(new JScrollPane(biopaxTree), BorderLayout.CENTER);
    pathwayModelTable = new JSortTable();
    pathwayModelTable.getSelectionModel().addListSelectionListener(eventHandler);
    pathwayModelTableModel = new PathwayModelTableModel(pathwayModelTable);
    pathwayModelTable.setModel(pathwayModelTableModel);
    searchTextField = new JTextField();
    searchTextField.putClientProperty("JTextField.variant", "search");
    searchTextField.getDocument().addDocumentListener(eventHandler);
    groupButton = new JButton("Group", new DownArrowIcon());
    groupButton.setHorizontalTextPosition(SwingConstants.LEFT);
    groupButton.addActionListener(eventHandler);
    deleteButton = new JButton("Delete");
    deleteButton.addActionListener(eventHandler);
    physiologyLinkButton = new JButton("Physiology Links", new DownArrowIcon());
    physiologyLinkButton.setHorizontalTextPosition(SwingConstants.LEFT);
    physiologyLinkButton.addActionListener(eventHandler);
    JPanel bottomPanel = new JPanel();
    bottomPanel.setLayout(new GridBagLayout());
    GridBagConstraints gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 0;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.fill = GridBagConstraints.HORIZONTAL;
    bottomPanel.add(groupButton, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 1;
    gbc.gridy = 0;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.fill = GridBagConstraints.HORIZONTAL;
    bottomPanel.add(deleteButton, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 2;
    gbc.gridy = 0;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.fill = GridBagConstraints.HORIZONTAL;
    bottomPanel.add(physiologyLinkButton, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 3;
    gbc.gridy = 0;
    gbc.insets = new Insets(4, 20, 4, 4);
    bottomPanel.add(new JLabel("Search "), gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 4;
    gbc.gridy = 0;
    gbc.weightx = 1.0;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.fill = GridBagConstraints.HORIZONTAL;
    bottomPanel.add(searchTextField, gbc);
    tabbedPane = new JTabbedPaneEnhanced();
    pathwayPanelTabs[PathwayPanelTabID.pathway_diagram.ordinal()] = new PathwayPanelTab(PathwayPanelTabID.pathway_diagram, graphTabPanel, VCellIcons.diagramIcon);
    pathwayPanelTabs[PathwayPanelTabID.pathway_objects.ordinal()] = new PathwayPanelTab(PathwayPanelTabID.pathway_objects, pathwayModelTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
    pathwayPanelTabs[PathwayPanelTabID.biopax_summary.ordinal()] = new PathwayPanelTab(PathwayPanelTabID.biopax_summary, sourceTabPanel, VCellIcons.textNotesIcon);
    pathwayPanelTabs[PathwayPanelTabID.biopax_tree.ordinal()] = new PathwayPanelTab(PathwayPanelTabID.biopax_tree, treeTabPanel, VCellIcons.tableIcon);
    tabbedPane.addChangeListener(eventHandler);
    tabbedPane.addChangeListener(eventHandler);
    for (PathwayPanelTab tab : pathwayPanelTabs) {
        tab.getComponent().setBorder(GuiConstants.TAB_PANEL_BORDER);
        tabbedPane.addTab(tab.getName(), tab.getIcon(), tab.getComponent());
    }
    setLayout(new BorderLayout());
    add(tabbedPane, BorderLayout.CENTER);
    add(bottomPanel, BorderLayout.SOUTH);
    pathwayModelTable.getColumnModel().getColumn(PathwayModelTableModel.COLUMN_ENTITY).setCellRenderer(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);
            // }
            return this;
        }
    });
}