Examples with TitledBorder javax.swing.border.TitledBorder used on opensource projects

Example 61 with TitledBorder

use of javax.swing.border.TitledBorder in project vcell by virtualcell.

the class ResultDisplayPanel method getTablePanel.

private JPanel getTablePanel() {
    if (tablePanel == null) {
        final GridBagLayout gridBagLayout = new GridBagLayout();
        gridBagLayout.rowHeights = new int[] { 0, 0, 0, 7, 7 };
        tablePanel = new JPanel(gridBagLayout);
        // new Color(153, 186,243)
        tablePanel.setBorder(new TitledBorder(new LineBorder(new Color(153, 186, 243), 1), "Best Parameters"));
        JScrollPane tableScroll = new JScrollPane(ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED, ScrollPaneConstants.HORIZONTAL_SCROLLBAR_AS_NEEDED);
        tableScroll.setName("");
        tableScroll.setViewportView(getRestultTable());
        GridBagConstraints gridBagConstraints1 = new GridBagConstraints();
        gridBagConstraints1.ipady = 235;
        gridBagConstraints1.ipadx = 300;
        gridBagConstraints1.gridheight = 3;
        gridBagConstraints1.insets = new Insets(0, 5, 0, 5);
        gridBagConstraints1.gridx = 0;
        gridBagConstraints1.gridy = 0;
        // gridBagConstraints1.ipady = 0;
        // gridBagConstraints1.ipadx = 0;
        gridBagConstraints1.anchor = GridBagConstraints.WEST;
        tablePanel.add(tableScroll, gridBagConstraints1);
    }
    return tablePanel;
}

Example 62 with TitledBorder

use of javax.swing.border.TitledBorder in project vcell by virtualcell.

the class DefineROI_SummaryPanel method getInfoPanel.

public JPanel getInfoPanel() {
    if (infoPanel == null) {
        final GridBagLayout gridBagLayout = new GridBagLayout();
        gridBagLayout.rowHeights = new int[] { 0, 7, 7, 7 };
        gridBagLayout.columnWidths = new int[] { 7, 7, 7, 0, 0, 7, 7, 7, 0, 0, 7 };
        infoPanel = new JPanel(gridBagLayout);
        GridBagConstraints gridBagConstraints1 = new GridBagConstraints();
        gridBagConstraints1.anchor = GridBagConstraints.WEST;
        gridBagConstraints1.gridy = 0;
        gridBagConstraints1.gridx = 1;
        infoPanel.add(new JLabel("Image size after cropping: "), gridBagConstraints1);
        final JLabel eTimeLabel = new JLabel();
        eTimeLabel.setText("Image size X");
        GridBagConstraints gridBagConstraints3 = new GridBagConstraints();
        gridBagConstraints3.anchor = GridBagConstraints.EAST;
        gridBagConstraints3.gridy = 0;
        gridBagConstraints3.gridx = 5;
        infoPanel.add(eTimeLabel, gridBagConstraints3);
        imgXTextField = new JTextField(12);
        final GridBagConstraints gridBagConstraints = new GridBagConstraints();
        gridBagConstraints.gridy = 0;
        gridBagConstraints.gridx = 7;
        infoPanel.add(imgXTextField, gridBagConstraints);
        final JLabel sLabel2 = new JLabel();
        sLabel2.setText("um");
        final GridBagConstraints gridBagConstraints_8 = new GridBagConstraints();
        gridBagConstraints_8.gridy = 0;
        gridBagConstraints_8.gridx = 9;
        infoPanel.add(sLabel2, gridBagConstraints_8);
        final JLabel eTimeLabel_1 = new JLabel();
        eTimeLabel_1.setText("Image size Y");
        final GridBagConstraints gridBagConstraints_2 = new GridBagConstraints();
        gridBagConstraints_2.gridy = 1;
        gridBagConstraints_2.gridx = 5;
        infoPanel.add(eTimeLabel_1, gridBagConstraints_2);
        imgYTextField = new JTextField();
        imgYTextField.setColumns(12);
        final GridBagConstraints gridBagConstraints_4 = new GridBagConstraints();
        gridBagConstraints_4.gridy = 1;
        gridBagConstraints_4.gridx = 7;
        infoPanel.add(imgYTextField, gridBagConstraints_4);
        final JLabel sLabel2_1 = new JLabel();
        sLabel2_1.setText("um");
        final GridBagConstraints gridBagConstraints_3 = new GridBagConstraints();
        gridBagConstraints_3.gridy = 1;
        gridBagConstraints_3.gridx = 9;
        infoPanel.add(sLabel2_1, gridBagConstraints_3);
        final JLabel cellAreaRoiLabel = new JLabel();
        cellAreaRoiLabel.setText("Cell area ROI: ");
        final GridBagConstraints gridBagConstraints_5 = new GridBagConstraints();
        gridBagConstraints_5.anchor = GridBagConstraints.EAST;
        gridBagConstraints_5.gridy = 3;
        gridBagConstraints_5.gridx = 1;
        infoPanel.add(cellAreaRoiLabel, gridBagConstraints_5);
        cellROIDefined = new JCheckBox();
        cellROIDefined.setText("Defined");
        final GridBagConstraints gridBagConstraints_6 = new GridBagConstraints();
        gridBagConstraints_6.anchor = GridBagConstraints.WEST;
        gridBagConstraints_6.gridy = 3;
        gridBagConstraints_6.gridx = 5;
        infoPanel.add(cellROIDefined, gridBagConstraints_6);
        cellROIUndefined = new JCheckBox();
        cellROIUndefined.setText("Not Defined");
        final GridBagConstraints gridBagConstraints_7 = new GridBagConstraints();
        gridBagConstraints_7.anchor = GridBagConstraints.WEST;
        gridBagConstraints_7.gridy = 3;
        gridBagConstraints_7.gridx = 7;
        infoPanel.add(cellROIUndefined, gridBagConstraints_7);
        final JLabel bleachedRoiLabel = new JLabel();
        bleachedRoiLabel.setText("Bleached ROI: ");
        final GridBagConstraints gridBagConstraints_9 = new GridBagConstraints();
        gridBagConstraints_9.anchor = GridBagConstraints.EAST;
        gridBagConstraints_9.gridy = 4;
        gridBagConstraints_9.gridx = 1;
        infoPanel.add(bleachedRoiLabel, gridBagConstraints_9);
        bleachROIDefined = new JCheckBox();
        bleachROIDefined.setText("Defined");
        final GridBagConstraints gridBagConstraints_10 = new GridBagConstraints();
        gridBagConstraints_10.anchor = GridBagConstraints.WEST;
        gridBagConstraints_10.gridy = 4;
        gridBagConstraints_10.gridx = 5;
        infoPanel.add(bleachROIDefined, gridBagConstraints_10);
        bleachROIUndefined = new JCheckBox();
        bleachROIUndefined.setText("Not Defined");
        final GridBagConstraints gridBagConstraints_11 = new GridBagConstraints();
        gridBagConstraints_11.anchor = GridBagConstraints.WEST;
        gridBagConstraints_11.gridy = 4;
        gridBagConstraints_11.gridx = 7;
        infoPanel.add(bleachROIUndefined, gridBagConstraints_11);
        final JLabel backgroundRoiLabel = new JLabel();
        backgroundRoiLabel.setText("Background ROI: ");
        final GridBagConstraints gridBagConstraints_12 = new GridBagConstraints();
        gridBagConstraints_12.anchor = GridBagConstraints.EAST;
        gridBagConstraints_12.gridy = 5;
        gridBagConstraints_12.gridx = 1;
        infoPanel.add(backgroundRoiLabel, gridBagConstraints_12);
        bgROIDefined = new JCheckBox();
        bgROIDefined.setText("Defined");
        final GridBagConstraints gridBagConstraints_13 = new GridBagConstraints();
        gridBagConstraints_13.anchor = GridBagConstraints.WEST;
        gridBagConstraints_13.gridy = 5;
        gridBagConstraints_13.gridx = 5;
        infoPanel.add(bgROIDefined, gridBagConstraints_13);
        bgROIUndefined = new JCheckBox();
        bgROIUndefined.setText("Not Defined");
        final GridBagConstraints gridBagConstraints_14 = new GridBagConstraints();
        gridBagConstraints_14.anchor = GridBagConstraints.WEST;
        gridBagConstraints_14.gridy = 5;
        gridBagConstraints_14.gridx = 7;
        infoPanel.add(bgROIUndefined, gridBagConstraints_14);
        infoPanel.setBorder(new TitledBorder(new LineBorder(new Color(153, 186, 243), 1), "Image & ROI Info"));
    }
    return infoPanel;
}

Example 63 with TitledBorder

use of javax.swing.border.TitledBorder in project vcell by virtualcell.

the class VFrap_OverlayEditorPanelJAI method getROIAssistBasePanel.

public JPanel getROIAssistBasePanel() {
    if (roiAssistBasePanel == null) {
        roiAssistBasePanel = new JPanel(new BorderLayout());
        JPanel buttonPanel = new JPanel(new BorderLayout());
        buttonPanel.add(getRoiAssistButton(), BorderLayout.WEST);
        roiAssistBasePanel.add(buttonPanel, BorderLayout.NORTH);
        roiAssistBasePanel.add(getROIAssistPanel(), BorderLayout.CENTER);
        // set border
        TitledBorder tb = new TitledBorder(new EtchedBorder(), "");
        roiAssistBasePanel.setBorder(tb);
    }
    return roiAssistBasePanel;
}

Example 64 with TitledBorder

use of javax.swing.border.TitledBorder in project vcell by virtualcell.

the class MolecularTypePropertiesPanel method initialize.

private void initialize() {
    JPanel leftPanel = new JPanel();
    leftPanel.setLayout(new GridBagLayout());
    // leftPanel.setBackground(Color.white);
    anchorPanel = new JAnchorPanel();
    anchorScrollPanel = new JScrollPane(anchorPanel);
    molecularTypeTree = new BioModelNodeEditableTree();
    molecularTypeTreeModel = new MolecularTypeTreeModel(molecularTypeTree);
    molecularTypeTree.setModel(molecularTypeTreeModel);
    molecularTypeTree.setEditable(true);
    molecularTypeTree.setCellRenderer(new RbmMolecularTypeTreeCellRenderer(molecularTypeTree, issueManager));
    molecularTypeTree.setCellEditor(new RbmMolecularTypeTreeCellEditor(molecularTypeTree));
    int rowHeight = molecularTypeTree.getRowHeight();
    if (rowHeight < 10) {
        rowHeight = 20;
    }
    molecularTypeTree.setRowHeight(rowHeight + 2);
    molecularTypeTree.getSelectionModel().setSelectionMode(TreeSelectionModel.SINGLE_TREE_SELECTION);
    ToolTipManager.sharedInstance().registerComponent(molecularTypeTree);
    molecularTypeTree.addTreeSelectionListener(eventHandler);
    molecularTypeTree.addTreeWillExpandListener(eventHandler);
    molecularTypeTree.addMouseListener(eventHandler);
    molecularTypeTree.setLargeModel(true);
    molecularTypeTree.setRootVisible(true);
    setLayout(new GridBagLayout());
    int gridy = 0;
    GridBagConstraints gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = gridy;
    gbc.weightx = 1.0;
    gbc.insets = new Insets(4, 4, 4, 4);
    titleLabel = new JLabel("Construct Solid Geometry");
    titleLabel.setFont(titleLabel.getFont().deriveFont(Font.BOLD));
    leftPanel.add(titleLabel, gbc);
    ButtonGroup bg = new ButtonGroup();
    bg.add(getAnchorAllButton());
    bg.add(getAnchorOnlyButton());
    gridy++;
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = gridy;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.fill = GridBagConstraints.HORIZONTAL;
    leftPanel.add(getAnchorAllButton(), gbc);
    gridy++;
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = gridy;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.fill = GridBagConstraints.HORIZONTAL;
    leftPanel.add(getAnchorOnlyButton(), gbc);
    gridy++;
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = gridy;
    gbc.weightx = 1.0;
    gbc.weighty = 1.0;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.fill = GridBagConstraints.BOTH;
    leftPanel.add(anchorScrollPanel, gbc);
    // ------------------------------------------------------------------------------
    splitPaneHorizontal.setOneTouchExpandable(true);
    splitPaneHorizontal.setDividerLocation(120);
    splitPaneHorizontal.setResizeWeight(0.1);
    Border border = BorderFactory.createLineBorder(Color.gray);
    Border loweredEtchedBorder = BorderFactory.createEtchedBorder(EtchedBorder.LOWERED);
    Border loweredBevelBorder = BorderFactory.createLoweredBevelBorder();
    TitledBorder annotationBorder = BorderFactory.createTitledBorder(loweredEtchedBorder, " Annotation and Pathway Links ");
    annotationBorder.setTitleJustification(TitledBorder.LEFT);
    annotationBorder.setTitlePosition(TitledBorder.TOP);
    annotationBorder.setTitleFont(getFont().deriveFont(Font.BOLD));
    shapePanel = new LargeShapePanel() {

        @Override
        public void paintComponent(Graphics g) {
            super.paintComponent(g);
            for (LargeShape stls : molecularTypeShapeList) {
                stls.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 boolean isViewSingleRow() {
            return true;
        }

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

        @Override
        public GroupingCriteria getCriteria() {
            return null;
        }
    };
    shapePanel.setBorder(border);
    shapePanel.setLayout(null);
    shapePanel.setBackground(Color.white);
    shapePanel.setEditable(true);
    shapePanel.setShowMoleculeColor(true);
    shapePanel.setShowNonTrivialOnly(true);
    shapePanel.addMouseListener(new MouseAdapter() {

        @Override
        public void mouseClicked(MouseEvent e) {
            super.mouseClicked(e);
            stopEditing();
            if (e.getButton() == 1) {
                // left click selects the object (we highlight it)
                Point whereClicked = e.getPoint();
                PointLocationInShapeContext locationContext = new PointLocationInShapeContext(whereClicked);
                manageMouseActivity(locationContext);
            } else if (e.getButton() == 3) {
                // right click invokes popup menu (only if the object is highlighted)
                Point whereClicked = e.getPoint();
                PointLocationInShapeContext locationContext = new PointLocationInShapeContext(whereClicked);
                manageMouseActivity(locationContext);
                if (locationContext.getDeepestShape() != null && !locationContext.getDeepestShape().isHighlighted()) {
                // TODO: (maybe) add code here to highlight the shape if it's not highlighted already but don't show the menu
                // return;
                }
                showPopupMenu(e, locationContext);
            }
        }

        private void manageMouseActivity(PointLocationInShapeContext locationContext) {
            Graphics g = shapePanel.getGraphics();
            for (MolecularTypeLargeShape mtls : molecularTypeShapeList) {
                mtls.turnHighlightOffRecursive(g);
            }
            for (MolecularTypeLargeShape mtls : molecularTypeShapeList) {
                if (mtls.contains(locationContext)) {
                    // check if mouse is inside shape
                    break;
                }
            }
            locationContext.highlightDeepestShape();
            locationContext.paintDeepestShape(g);
        }
    });
    shapePanel.addMouseMotionListener(new MouseMotionAdapter() {

        public void mouseMoved(MouseEvent e) {
            Point overWhat = e.getPoint();
            PointLocationInShapeContext locationContext = new PointLocationInShapeContext(overWhat);
            for (MolecularTypeLargeShape mtls : molecularTypeShapeList) {
                if (mtls.contains(locationContext)) {
                    break;
                }
            }
            HighlightableShapeInterface hsi = locationContext.getDeepestShape();
            if (hsi == null) {
                shapePanel.setToolTipText(null);
            } else {
                shapePanel.setToolTipText("Right click for " + hsi.getDisplayType() + " menus");
            }
            for (MolecularTypeLargeShape mtls : molecularTypeShapeList) {
                Rectangle r = mtls.getAnchorHotspot();
                if (r != null && r.contains(overWhat)) {
                    mtls.getMolecularType();
                    shapePanel.setToolTipText(mtls.getAnchorsHTML());
                    break;
                }
            }
        }
    });
    // -------------------------------------------------------------------------------------------
    // right bottom panel, contains just the annotation
    JPanel generalPanel = new JPanel();
    generalPanel.setBorder(annotationBorder);
    generalPanel.setLayout(new GridBagLayout());
    gridy = 0;
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 0;
    gbc.anchor = GridBagConstraints.LINE_START;
    JLabel pathwayLink = new JLabel("Linked Pathway Object(s): ");
    generalPanel.add(pathwayLink, gbc);
    linkedPOScrollPane = new JScrollPane();
    gbc = new java.awt.GridBagConstraints();
    gbc.gridx = 1;
    gbc.gridy = gridy;
    gbc.weightx = 1.0;
    gbc.gridwidth = GridBagConstraints.REMAINDER;
    gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
    gbc.insets = new Insets(4, 4, 4, 4);
    generalPanel.add(linkedPOScrollPane, gbc);
    gridy++;
    // annotationTextArea = new javax.swing.JTextArea("", 1, 30);
    // annotationTextArea.setLineWrap(true);
    // annotationTextArea.setWrapStyleWord(true);
    // annotationTextArea.setFont(new Font("monospaced", Font.PLAIN, 11));
    annotationTextArea = new JTextPane();
    annotationTextArea.setContentType("text/html");
    annotationTextArea.setEditable(false);
    javax.swing.JScrollPane jsp = new javax.swing.JScrollPane(annotationTextArea);
    gbc = new java.awt.GridBagConstraints();
    gbc.weightx = 1.0;
    gbc.weighty = 1.0;
    gbc.gridx = 0;
    gbc.gridy = gridy;
    gbc.gridwidth = 2;
    gbc.weightx = 1.0;
    gbc.weighty = 1.0;
    gbc.anchor = GridBagConstraints.LINE_START;
    gbc.fill = java.awt.GridBagConstraints.BOTH;
    gbc.insets = new Insets(4, 4, 4, 4);
    generalPanel.add(jsp, gbc);
    scrollPane = new JScrollPane(shapePanel);
    scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
    scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
    splitPaneHorizontal.setTopComponent(scrollPane);
    splitPaneHorizontal.setBottomComponent(generalPanel);
    // -----------------------------------------------------------------------------
    splitPane.setOneTouchExpandable(true);
    splitPane.setLeftComponent(leftPanel);
    splitPane.setRightComponent(splitPaneHorizontal);
    splitPane.setResizeWeight(0.0);
    splitPane.getLeftComponent().setMaximumSize(new Dimension(120, 200));
    splitPane.getLeftComponent().setPreferredSize(new Dimension(120, 200));
    // splitPane.setDividerLocation(0.0d);		// completely hides the left component
    // attempt to use the preferred size
    splitPane.setDividerLocation(-1);
    setName("MolecularTypePropertiesPanel");
    setLayout(new BorderLayout());
    add(splitPane, BorderLayout.CENTER);
    setBackground(Color.white);
    annotationTextArea.addFocusListener(eventHandler);
    annotationTextArea.addMouseListener(eventHandler);
}

Example 65 with TitledBorder

use of javax.swing.border.TitledBorder in project vcell by virtualcell.

the class ObservablePropertiesPanel method initialize.

private void initialize() {
    observableTree = new BioModelNodeEditableTree();
    observableTreeModel = new ObservableTreeModel(observableTree);
    observableTree.setModel(observableTreeModel);
    setLayout(new GridBagLayout());
    // --------------------------------------------------------------------------------------------------------
    splitPaneHorizontal.setOneTouchExpandable(true);
    splitPaneHorizontal.setDividerLocation(120);
    splitPaneHorizontal.setResizeWeight(0.1);
    Border border = BorderFactory.createLineBorder(Color.gray);
    Border loweredEtchedBorder = BorderFactory.createEtchedBorder(EtchedBorder.LOWERED);
    Border loweredBevelBorder = BorderFactory.createLoweredBevelBorder();
    TitledBorder annotationBorder = BorderFactory.createTitledBorder(loweredEtchedBorder, " Annotation ");
    annotationBorder.setTitleJustification(TitledBorder.LEFT);
    annotationBorder.setTitlePosition(TitledBorder.TOP);
    annotationBorder.setTitleFont(getFont().deriveFont(Font.BOLD));
    shapePanel = 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;
        }
    };
    shapePanel.setBorder(border);
    shapePanel.setBackground(Color.white);
    shapePanel.setLayout(null);
    shapePanel.setZoomFactor(-1);
    shapePanel.setEditable(true);
    shapePanel.setShowMoleculeColor(true);
    shapePanel.setShowNonTrivialOnly(true);
    shapePanel.addMouseListener(new MouseAdapter() {

        @Override
        public void mouseClicked(MouseEvent e) {
            super.mouseClicked(e);
            if (e.getButton() == 1) {
                // left click selects the object (we highlight it)
                Point whereClicked = e.getPoint();
                PointLocationInShapeContext locationContext = new PointLocationInShapeContext(whereClicked);
                manageMouseActivity(locationContext);
            } else if (e.getButton() == 3) {
                // right click invokes popup menu (only if the object is highlighted)
                Point whereClicked = e.getPoint();
                PointLocationInShapeContext locationContext = new PointLocationInShapeContext(whereClicked);
                manageMouseActivity(locationContext);
                if (locationContext.getDeepestShape() != null && !locationContext.getDeepestShape().isHighlighted()) {
                // TODO: (maybe) add code here to highlight the shape if it's not highlighted already but don't show the menu
                // return;
                }
                showPopupMenu(e, locationContext);
            }
        }

        private void manageMouseActivity(PointLocationInShapeContext locationContext) {
            Graphics g = shapePanel.getGraphics();
            for (SpeciesPatternLargeShape sps : spsList) {
                sps.turnHighlightOffRecursive(g);
            }
            for (SpeciesPatternLargeShape sps : spsList) {
                if (sps.contains(locationContext)) {
                    // check if mouse is inside shape
                    break;
                }
            }
            locationContext.highlightDeepestShape();
            locationContext.paintDeepestShape(g);
        }
    });
    // shapePanel.addMouseListener(eventHandler);		// alternately use this
    shapePanel.addMouseMotionListener(new MouseMotionAdapter() {

        public void mouseMoved(MouseEvent e) {
            Point overWhat = e.getPoint();
            PointLocationInShapeContext locationContext = new PointLocationInShapeContext(overWhat);
            for (SpeciesPatternLargeShape sps : spsList) {
                if (sps.contains(locationContext)) {
                    break;
                }
            }
            HighlightableShapeInterface hsi = locationContext.getDeepestShape();
            if (hsi == null) {
                shapePanel.setToolTipText(null);
            } else {
                shapePanel.setToolTipText("Right click for " + hsi.getDisplayType() + " menus");
            }
            for (SpeciesPatternLargeShape sps : spsList) {
                for (MolecularTypeLargeShape mtls : sps.getMolecularTypeLargeShapes()) {
                    Rectangle r = mtls.getAnchorHotspot();
                    if (r != null && r.contains(overWhat)) {
                        mtls.getMolecularType();
                        shapePanel.setToolTipText(mtls.getAnchorsHTML());
                        break;
                    }
                }
            }
        }
    });
    JPanel optionsPanel = new JPanel();
    // gray options panel
    optionsPanel.setPreferredSize(new Dimension(140, 200));
    optionsPanel.setLayout(new GridBagLayout());
    getZoomSmallerButton().setEnabled(true);
    getZoomLargerButton().setEnabled(true);
    int gridy = 0;
    GridBagConstraints gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = gridy;
    gbc.gridwidth = 3;
    // top, left bottom, right
    gbc.insets = new Insets(4, 4, 2, 4);
    gbc.fill = GridBagConstraints.HORIZONTAL;
    gbc.anchor = GridBagConstraints.NORTHWEST;
    optionsPanel.add(getAddSpeciesButton(), gbc);
    ButtonGroup bg = new ButtonGroup();
    bg.add(getSequenceMultimolecularButton());
    bg.add(getSequencePolimerEqualButton());
    bg.add(getSequencePolimerGreaterButton());
    gridy++;
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = gridy;
    gbc.gridwidth = 2;
    gbc.insets = new Insets(8, 4, 2, 4);
    gbc.fill = GridBagConstraints.HORIZONTAL;
    optionsPanel.add(getSequenceMultimolecularButton(), gbc);
    gridy++;
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = gridy;
    gbc.insets = new Insets(4, 10, 2, 4);
    gbc.fill = GridBagConstraints.HORIZONTAL;
    JLabel label = new JLabel("Polymer of");
    label.setToolTipText("Compact notation available below for single-Molecule polymers");
    optionsPanel.add(label, gbc);
    gridy++;
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = gridy;
    gbc.insets = new Insets(2, 4, 1, 2);
    gbc.fill = GridBagConstraints.HORIZONTAL;
    optionsPanel.add(getSequencePolimerEqualButton(), gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 1;
    gbc.gridy = gridy;
    gbc.gridwidth = 2;
    gbc.insets = new Insets(2, 4, 1, 4);
    gbc.fill = GridBagConstraints.HORIZONTAL;
    optionsPanel.add(getLengthEqualTextField(), gbc);
    gridy++;
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = gridy;
    gbc.insets = new Insets(1, 4, 4, 2);
    gbc.fill = GridBagConstraints.HORIZONTAL;
    optionsPanel.add(getSequencePolimerGreaterButton(), gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 1;
    gbc.gridy = gridy;
    gbc.gridwidth = 2;
    gbc.insets = new Insets(1, 4, 4, 4);
    gbc.fill = GridBagConstraints.HORIZONTAL;
    optionsPanel.add(getLengthGreaterTextField(), gbc);
    // --- zoom buttons in their own panel, for alignment ---
    JPanel buttonPanel = new JPanel();
    buttonPanel.setLayout(new GridBagLayout());
    GridBagConstraints gbc2 = new GridBagConstraints();
    gbc2.gridx = 0;
    gbc2.gridy = 0;
    gbc2.insets = new Insets(1, 1, 1, 1);
    gbc2.anchor = GridBagConstraints.WEST;
    buttonPanel.add(getZoomLargerButton(), gbc2);
    gbc2 = new GridBagConstraints();
    gbc2.gridx = 1;
    gbc2.gridy = 0;
    gbc2.insets = new Insets(1, 1, 1, 1);
    gbc2.anchor = GridBagConstraints.WEST;
    buttonPanel.add(getZoomSmallerButton(), gbc2);
    // ---------------------------------------------------
    gridy++;
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = gridy;
    gbc.anchor = GridBagConstraints.WEST;
    gbc.insets = new Insets(1, 4, 4, 2);
    gbc.fill = GridBagConstraints.HORIZONTAL;
    // zoom buttons panel
    optionsPanel.add(buttonPanel, gbc);
    gridy++;
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = gridy;
    gbc.gridwidth = 3;
    gbc.weightx = 1;
    // fake cell used for filling all the vertical empty space
    gbc.weighty = 1;
    gbc.anchor = GridBagConstraints.WEST;
    gbc.insets = new Insets(2, 1, 2, 10);
    optionsPanel.add(new JLabel(""), gbc);
    // -----------------------------------------------------------------------------------------
    // right bottom panel, contains just the annotation
    JPanel generalPanel = new JPanel();
    generalPanel.setBorder(annotationBorder);
    generalPanel.setLayout(new GridBagLayout());
    gridy = 0;
    annotationTextArea = new javax.swing.JTextArea("", 1, 30);
    annotationTextArea.setLineWrap(true);
    annotationTextArea.setWrapStyleWord(true);
    annotationTextArea.setFont(new Font("monospaced", Font.PLAIN, 11));
    annotationTextArea.setEditable(false);
    javax.swing.JScrollPane jsp = new javax.swing.JScrollPane(annotationTextArea);
    gbc = new java.awt.GridBagConstraints();
    gbc.weightx = 1.0;
    gbc.weighty = 0.1;
    gbc.gridx = 0;
    gbc.gridy = gridy;
    gbc.anchor = GridBagConstraints.LINE_START;
    gbc.fill = java.awt.GridBagConstraints.BOTH;
    gbc.insets = new Insets(4, 4, 4, 4);
    generalPanel.add(jsp, gbc);
    // where we display the shapes
    scrollPane = new JScrollPane(shapePanel);
    scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
    scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
    JPanel containerOfScrollPanel = new JPanel();
    containerOfScrollPanel.setLayout(new BorderLayout());
    containerOfScrollPanel.add(optionsPanel, BorderLayout.WEST);
    containerOfScrollPanel.add(scrollPane, BorderLayout.CENTER);
    splitPaneHorizontal.setTopComponent(containerOfScrollPanel);
    splitPaneHorizontal.setBottomComponent(generalPanel);
    splitPaneHorizontal.setResizeWeight(0.9d);
    splitPaneHorizontal.setDividerLocation(0.8d);
    setName("ObservablePropertiesPanel");
    setLayout(new BorderLayout());
    add(splitPaneHorizontal, BorderLayout.CENTER);
    setBackground(Color.white);
    annotationTextArea.addFocusListener(eventHandler);
    annotationTextArea.addMouseListener(eventHandler);
}