Examples with MolecularTypeLargeShape cbit.vcell.graph.MolecularTypeLargeShape used on opensource projects

Example 1 with MolecularTypeLargeShape

use of cbit.vcell.graph.MolecularTypeLargeShape in project vcell by virtualcell.

the class SpeciesPropertiesPanel method initialize.

/**
 * Initialize the class.
 */
private void initialize() {
    try {
        Border border = BorderFactory.createLineBorder(Color.gray);
        shapePanel = new // glyph (shape) panel
        LargeShapePanel() {

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

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

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

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

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

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

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

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

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

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

            @Override
            public boolean isViewSingleRow() {
                return true;
            }
        };
        shapePanel.setBorder(border);
        shapePanel.setBackground(Color.white);
        shapePanel.setZoomFactor(-1);
        shapePanel.setEditable(true);
        shapePanel.setShowMoleculeColor(true);
        shapePanel.setShowNonTrivialOnly(true);
        // Dimension ms = new Dimension(350, 80);
        // shapePanel.setMinimumSize(ms);
        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();
                spls.turnHighlightOffRecursive(g);
                if (spls.contains(locationContext)) {
                    // check if mouse is inside shape
                    System.out.println("left click inside shape " + locationContext.getDeepestShape().toString());
                }
                locationContext.highlightDeepestShape();
                locationContext.paintDeepestShape(g);
            }
        });
        shapePanel.addMouseMotionListener(new MouseMotionAdapter() {

            public void mouseMoved(MouseEvent e) {
                Point overWhat = e.getPoint();
                PointLocationInShapeContext locationContext = new PointLocationInShapeContext(overWhat);
                spls.contains(locationContext);
                HighlightableShapeInterface hsi = locationContext.getDeepestShape();
                if (hsi == null) {
                    shapePanel.setToolTipText(null);
                } else {
                    shapePanel.setToolTipText("Right click for " + hsi.getDisplayType() + " menus");
                }
                for (MolecularTypeLargeShape mtls : spls.getMolecularTypeLargeShapes()) {
                    Rectangle r = mtls.getAnchorHotspot();
                    if (r != null && r.contains(overWhat)) {
                        mtls.getMolecularType();
                        shapePanel.setToolTipText(mtls.getAnchorsHTML());
                        break;
                    }
                }
            }
        });
        // ----------------------------------------------------------------------------------
        leftPanel = new JPanel();
        GridBagLayout mgr = new GridBagLayout();
        mgr.rowHeights = new int[] { 100, 100 };
        leftPanel.setLayout(mgr);
        leftPanel.setBackground(Color.white);
        speciesPropertiesTree = new BioModelNodeEditableTree();
        speciesPropertiesTreeModel = new SpeciesPropertiesTreeModel(speciesPropertiesTree);
        speciesPropertiesTree.setModel(speciesPropertiesTreeModel);
        JPanel generalPanel = new JPanel();
        generalPanel.setLayout(new GridBagLayout());
        Dimension size = new Dimension(100, 150);
        generalPanel.setMinimumSize(size);
        nameTextField = new JTextField();
        nameTextField.setEditable(false);
        int gridy = 0;
        GridBagConstraints gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.insets = new Insets(2, 4, 2, 4);
        gbc.anchor = GridBagConstraints.LINE_END;
        JLabel label = new JLabel("Species Name");
        generalPanel.add(label, gbc);
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 1;
        gbc.gridy = gridy;
        // significantly longer than the sbmlName text field
        gbc.weightx = 0.7;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(2, 4, 2, 4);
        gbc.anchor = GridBagConstraints.LINE_START;
        generalPanel.add(nameTextField, gbc);
        sbmlNameTextField = new JTextField();
        sbmlNameTextField.setEditable(false);
        sbmlNameTextField.setEnabled(false);
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 2;
        gbc.gridy = gridy;
        gbc.insets = new Insets(2, 8, 2, 2);
        gbc.anchor = GridBagConstraints.LINE_END;
        generalPanel.add(new JLabel("Sbml Name"), gbc);
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 3;
        gbc.gridy = gridy;
        gbc.weightx = 0.3;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(2, 4, 2, 4);
        gbc.anchor = GridBagConstraints.LINE_START;
        generalPanel.add(sbmlNameTextField, gbc);
        gridy++;
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.insets = new Insets(2, 4, 2, 4);
        gbc.anchor = GridBagConstraints.FIRST_LINE_END;
        generalPanel.add(new JLabel("Linked Pathway Object(s)"), gbc);
        linkedPOScrollPane = new JScrollPane();
        gbc = new java.awt.GridBagConstraints();
        gbc.weightx = 1.0;
        gbc.weighty = 0.1;
        gbc.gridx = 1;
        gbc.gridy = gridy;
        gbc.gridwidth = 3;
        gbc.anchor = GridBagConstraints.LINE_START;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(2, 4, 2, 4);
        generalPanel.add(linkedPOScrollPane, gbc);
        GridBagConstraints gbc1 = new GridBagConstraints();
        gbc1.gridx = 0;
        gbc1.gridy = 0;
        gbc1.gridwidth = 1;
        gbc1.weightx = 1;
        gbc1.weighty = 1;
        gbc1.fill = GridBagConstraints.BOTH;
        leftPanel.add(generalPanel, gbc1);
        scrollPane = new JScrollPane(shapePanel);
        scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
        scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
        // -----------------------------------------------------------
        JPanel optionsPanel = new JPanel();
        optionsPanel.setLayout(new GridBagLayout());
        getZoomSmallerButton().setEnabled(true);
        getZoomLargerButton().setEnabled(true);
        GridBagConstraints gbc2 = new GridBagConstraints();
        gbc2.gridx = 0;
        gbc2.gridy = 0;
        gbc2.insets = new Insets(4, 4, 0, 10);
        gbc2.anchor = GridBagConstraints.WEST;
        optionsPanel.add(getZoomLargerButton(), gbc2);
        gbc2 = new GridBagConstraints();
        gbc2.gridx = 0;
        gbc2.gridy = 1;
        gbc2.insets = new Insets(4, 4, 4, 10);
        gbc2.anchor = GridBagConstraints.WEST;
        optionsPanel.add(getZoomSmallerButton(), gbc2);
        gbc2 = new GridBagConstraints();
        gbc2.gridx = 0;
        gbc2.gridy = 2;
        gbc2.weightx = 1;
        // fake cell used for filling all the vertical empty space
        gbc2.weighty = 1;
        gbc2.anchor = GridBagConstraints.WEST;
        gbc2.insets = new Insets(4, 4, 4, 10);
        optionsPanel.add(new JLabel(""), gbc2);
        JPanel containerOfScrollPanel = new JPanel();
        containerOfScrollPanel.setLayout(new BorderLayout());
        containerOfScrollPanel.add(optionsPanel, BorderLayout.WEST);
        containerOfScrollPanel.add(scrollPane, BorderLayout.CENTER);
        // gbc1 = new GridBagConstraints();
        gbc1.gridx = 0;
        gbc1.gridy = 1;
        gbc1.weightx = 1;
        gbc1.weighty = 0.1;
        gbc1.fill = GridBagConstraints.BOTH;
        leftPanel.add(containerOfScrollPanel, gbc1);
        setName("SpeciesEditorPanel");
        setLayout(new BorderLayout());
        setBackground(Color.white);
        add(leftPanel, BorderLayout.CENTER);
        initConnections();
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 2 with MolecularTypeLargeShape

use of cbit.vcell.graph.MolecularTypeLargeShape in project vcell by virtualcell.

the class SpeciesPropertiesPanel method showPopupMenu.

private void showPopupMenu(MouseEvent e, PointLocationInShapeContext locationContext) {
    if (popupFromShapeMenu == null) {
        popupFromShapeMenu = new JPopupMenu();
    }
    if (popupFromShapeMenu.isShowing()) {
        return;
    }
    final Object deepestShape = locationContext.getDeepestShape();
    final RbmElementAbstract selectedObject;
    if (deepestShape == null) {
        selectedObject = null;
        // when cursor is outside any species pattern we offer to add a new one
        System.out.println("outside");
    // popupFromShapeMenu.add(getAddSpeciesPatternFromShapeMenuItem());
    } else if (deepestShape instanceof ComponentStateLargeShape) {
        System.out.println("inside state");
        if (((ComponentStateLargeShape) deepestShape).isHighlighted()) {
            selectedObject = ((ComponentStateLargeShape) deepestShape).getComponentStatePattern();
        } else {
            return;
        }
    } else if (deepestShape instanceof MolecularComponentLargeShape) {
        System.out.println("inside component");
        if (((MolecularComponentLargeShape) deepestShape).isHighlighted()) {
            selectedObject = ((MolecularComponentLargeShape) deepestShape).getMolecularComponentPattern();
        } else {
            return;
        }
    } else if (deepestShape instanceof MolecularTypeLargeShape) {
        System.out.println("inside molecule");
        if (((MolecularTypeLargeShape) deepestShape).isHighlighted()) {
            selectedObject = ((MolecularTypeLargeShape) deepestShape).getMolecularTypePattern();
        } else {
            return;
        }
    } else if (deepestShape instanceof SpeciesPatternLargeShape) {
        System.out.println("inside species pattern");
        if (((SpeciesPatternLargeShape) deepestShape).isHighlighted()) {
            selectedObject = ((SpeciesPatternLargeShape) deepestShape).getSpeciesPattern();
        } else {
            if (!fieldSpeciesContext.hasSpeciesPattern()) {
                selectedObject = new SpeciesPattern();
            } else {
                return;
            }
        }
    } else {
        selectedObject = null;
        System.out.println("inside something else?");
        return;
    }
    System.out.println(selectedObject);
    popupFromShapeMenu.removeAll();
    Point mousePoint = e.getPoint();
    if (selectedObject instanceof SpeciesPattern) {
        final SpeciesPattern sp = (SpeciesPattern) selectedObject;
        JMenu addMenuItem = new JMenu(VCellErrorMessages.SpecifyMolecularTypes);
        popupFromShapeMenu.add(addMenuItem);
        addMenuItem.removeAll();
        for (final MolecularType mt : bioModel.getModel().getRbmModelContainer().getMolecularTypeList()) {
            JMenuItem menuItem = new JMenuItem(mt.getName());
            Graphics gc = shapePanel.getGraphics();
            Icon icon = new MolecularTypeSmallShape(1, 4, mt, null, gc, mt, null, issueManager);
            menuItem.setIcon(icon);
            addMenuItem.add(menuItem);
            menuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    MolecularTypePattern molecularTypePattern = new MolecularTypePattern(mt);
                    for (MolecularComponentPattern mcp : molecularTypePattern.getComponentPatternList()) {
                        mcp.setBondType(BondType.None);
                    }
                    if (!fieldSpeciesContext.hasSpeciesPattern()) {
                        fieldSpeciesContext.setSpeciesPattern(sp);
                    }
                    fieldSpeciesContext.getSpeciesPattern().addMolecularTypePattern(molecularTypePattern);
                }
            });
        }
    // JMenu compartmentMenuItem = new JMenu("Specify structure");
    // popupFromShapeMenu.add(compartmentMenuItem);
    // compartmentMenuItem.removeAll();
    // for (final Structure struct : bioModel.getModel().getStructures()) {
    // JMenuItem menuItem = new JMenuItem(struct.getName());
    // compartmentMenuItem.add(menuItem);
    // menuItem.addActionListener(new ActionListener() {
    // public void actionPerformed(ActionEvent e) {
    // String nameStruct = e.getActionCommand();
    // Structure struct = bioModel.getModel().getStructure(nameStruct);
    // fieldSpeciesContext.setStructure(struct);
    // }
    // });
    // }
    } else if (selectedObject instanceof MolecularTypePattern) {
        MolecularTypePattern mtp = (MolecularTypePattern) selectedObject;
        String moveRightMenuText = "Move <b>" + "right" + "</b>";
        moveRightMenuText = "<html>" + moveRightMenuText + "</html>";
        JMenuItem moveRightMenuItem = new JMenuItem(moveRightMenuText);
        Icon icon = VCellIcons.moveRightIcon;
        moveRightMenuItem.setIcon(icon);
        moveRightMenuItem.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                MolecularTypePattern from = (MolecularTypePattern) selectedObject;
                SpeciesPattern sp = locationContext.sps.getSpeciesPattern();
                sp.shiftRight(from);
                speciesPropertiesTreeModel.populateTree();
            }
        });
        popupFromShapeMenu.add(moveRightMenuItem);
        String moveLeftMenuText = "Move <b>" + "left" + "</b>";
        moveLeftMenuText = "<html>" + moveLeftMenuText + "</html>";
        JMenuItem moveLeftMenuItem = new JMenuItem(moveLeftMenuText);
        icon = VCellIcons.moveLeftIcon;
        moveLeftMenuItem.setIcon(icon);
        moveLeftMenuItem.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                MolecularTypePattern from = (MolecularTypePattern) selectedObject;
                SpeciesPattern sp = locationContext.sps.getSpeciesPattern();
                sp.shiftLeft(from);
                speciesPropertiesTreeModel.populateTree();
            }
        });
        popupFromShapeMenu.add(moveLeftMenuItem);
        popupFromShapeMenu.add(new JSeparator());
        String deleteMenuText = "Delete <b>" + mtp.getMolecularType().getName() + "</b>";
        deleteMenuText = "<html>" + deleteMenuText + "</html>";
        JMenuItem deleteMenuItem = new JMenuItem(deleteMenuText);
        deleteMenuItem.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                MolecularTypePattern mtp = (MolecularTypePattern) selectedObject;
                SpeciesPattern sp = locationContext.sps.getSpeciesPattern();
                sp.removeMolecularTypePattern(mtp);
                if (sp.getMolecularTypePatterns().isEmpty()) {
                    fieldSpeciesContext.setSpeciesPattern(null);
                }
            }
        });
        popupFromShapeMenu.add(deleteMenuItem);
    } else if (selectedObject instanceof MolecularComponentPattern) {
        manageComponentPatternFromShape(selectedObject, locationContext, ShowWhat.ShowBond);
    } else if (selectedObject instanceof ComponentStatePattern) {
        MolecularComponentPattern mcp = ((ComponentStateLargeShape) deepestShape).getMolecularComponentPattern();
        manageComponentPatternFromShape(mcp, locationContext, ShowWhat.ShowState);
    } else {
        System.out.println("Where am I ???");
    }
    popupFromShapeMenu.show(e.getComponent(), mousePoint.x, mousePoint.y);
}

Example 3 with MolecularTypeLargeShape

use of cbit.vcell.graph.MolecularTypeLargeShape 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);
    // -----------------------------------------------------------------------------------------
    // JPanel generalPanel = new JPanel();		// right bottom panel, contains just the annotation
    // 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(containerOfScrollPanel, BorderLayout.CENTER);
    setBackground(Color.white);
// annotationTextArea.addFocusListener(eventHandler);
// annotationTextArea.addMouseListener(eventHandler);
}

Example 4 with MolecularTypeLargeShape

use of cbit.vcell.graph.MolecularTypeLargeShape in project vcell by virtualcell.

the class MolecularTypePropertiesPanel method updateInterface.

public void updateInterface() {
    boolean bNonNullMolecularType = molecularType != null && bioModel != null;
    // annotationTextArea.setEditable(bNonNullMolecularType);
    if (bNonNullMolecularType) {
        VCMetaData vcMetaData = bioModel.getModel().getVcMetaData();
        String annText = vcMetaData.getFreeTextAnnotation(molecularType);
        // annotationTextArea.setText(annText);
        // annotationTextArea.setCaretPosition(0);
        // annotationTextArea.setText(molecularType.comment);
        // titleLabel.setText("Properties for " + molecularType.getDisplayType() + ": " + molecularType.getDisplayName());
        titleLabel.setText("Anchor Molecule");
        titleLabel.setToolTipText("Anchor a Molecule to a Structure to prevent it being moved to unwanted locations by a rule.");
        molecularTypeShapeList.clear();
        int maxYOffset = computeStatesVerticalOffset(molecularType);
        MolecularTypeLargeShape stls = new MolecularTypeLargeShape(xOffsetInitial, maxYOffset, molecularType, shapePanel, molecularType, issueManager);
        molecularTypeShapeList.add(stls);
        int maxXOffset = xOffsetInitial + stls.getWidth();
        Dimension preferredSize = new Dimension(maxXOffset + 100, maxYOffset + 60);
        shapePanel.setPreferredSize(preferredSize);
        shapePanel.repaint();
    // splitPane.getRightComponent().repaint();
    } else {
    // annotationTextArea.setText(null);
    }
    listLinkedPathwayObjects();
}

Example 5 with MolecularTypeLargeShape

use of cbit.vcell.graph.MolecularTypeLargeShape 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, " 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 link
    JPanel generalPanel = new JPanel();
    generalPanel.setBorder(annotationBorder);
    generalPanel.setLayout(new GridBagLayout());
    gridy = 0;
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = gridy;
    gbc.anchor = GridBagConstraints.LINE_START;
    gbc.insets = new Insets(4, 4, 4, 4);
    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 = 3;
    gbc.gridheight = 3;
    gbc.anchor = GridBagConstraints.NORTHWEST;
    gbc.fill = java.awt.GridBagConstraints.BOTH;
    gbc.insets = new Insets(4, 4, 4, 4);
    generalPanel.add(linkedPOScrollPane, gbc);
    // annotationTextArea = new JTextPane();
    // annotationTextArea.setContentType("text/html");
    // annotationTextArea.setEditable(false);
    // javax.swing.JScrollPane jsp = new javax.swing.JScrollPane(annotationTextArea);
    gridy++;
    gbc = new java.awt.GridBagConstraints();
    gbc.weightx = 1.0;
    gbc.weighty = 1.0;
    gbc.gridx = 0;
    gbc.gridy = gridy;
    gbc.gridwidth = 2;
    gbc.anchor = GridBagConstraints.LINE_START;
    gbc.fill = java.awt.GridBagConstraints.BOTH;
    gbc.insets = new Insets(4, 4, 4, 4);
    generalPanel.add(new JLabel(), 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);
    splitPaneHorizontal.setResizeWeight(1.0);
    // splitPaneHorizontal.setDividerLocation(1);
    // -----------------------------------------------------------------------------
    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);
}