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

Example 1 with PointLocationInShapeContext

use of cbit.vcell.graph.PointLocationInShapeContext 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 PointLocationInShapeContext

use of cbit.vcell.graph.PointLocationInShapeContext 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 3 with PointLocationInShapeContext

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

the class ReactionRuleSpecPropertiesPanel method initialize.

private void initialize() {
    try {
        shapePanel = new // glyph (shape) panel
        RulesShapePanel() {

            @Override
            public void paintComponent(Graphics g) {
                super.paintComponent(g);
                reactantShape.paintSelf(g);
                productShape.paintSelf(g);
            }
        };
        shapePanel.addMouseMotionListener(new MouseMotionAdapter() {

            public void mouseMoved(MouseEvent e) {
                Point overWhat = e.getPoint();
                PointLocationInShapeContext locationContext = new PointLocationInShapeContext(overWhat);
                reactantShape.contains(locationContext);
                productShape.contains(locationContext);
                shapePanel.setToolTipText("View-Only panel.");
            }
        });
        shapePanel.setBackground(new Color(0xe0e0e0));
        shapePanel.setZoomFactor(-2);
        // colored with a shade of brown, close to DefaultScrollTableCellRenderer.uneditableForeground
        shapePanel.setEditable(false);
        shapePanel.setViewSingleRow(true);
        shapePanel.setShowMoleculeColor(false);
        shapePanel.setShowNonTrivialOnly(false);
        // shapePanel.setShowDifferencesOnly(true);
        // ----------------------------------------------------------------------------------
        JPanel upperPanel = new JPanel();
        upperPanel.setName("ReactionRuleSpecKineticsPanel");
        upperPanel.setLayout(new GridBagLayout());
        upperPanel.setBackground(Color.white);
        int gridy = 0;
        GridBagConstraints gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.gridwidth = 3;
        gbc.insets = new java.awt.Insets(0, 4, 0, 4);
        gbc.fill = GridBagConstraints.HORIZONTAL;
        JLabel label = new JLabel("<html><u>View only. Edit properties in Physiology</u></html>");
        label.setHorizontalAlignment(SwingConstants.CENTER);
        label.setFont(label.getFont().deriveFont(Font.BOLD));
        upperPanel.add(label, gbc);
        isReversibleCheckBox = new JCheckBox("Reversible");
        isReversibleCheckBox.setHorizontalTextPosition(SwingConstants.LEFT);
        isReversibleCheckBox.setEnabled(false);
        isReversibleCheckBox.setBackground(upperPanel.getBackground());
        gridy++;
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.insets = new java.awt.Insets(0, 8, 4, 4);
        upperPanel.add(isReversibleCheckBox, gbc);
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 1;
        gbc.gridy = gridy;
        gbc.anchor = GridBagConstraints.LINE_END;
        gbc.insets = new java.awt.Insets(0, 8, 4, 4);
        upperPanel.add(new JLabel("Kinetic Type"), gbc);
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 2;
        gbc.gridy = gridy;
        gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
        gbc.weightx = 1.0;
        gbc.insets = new java.awt.Insets(0, 4, 4, 4);
        upperPanel.add(getKineticsTypeComboBox(), gbc);
        getKineticsTypeComboBox().setEnabled(false);
        gridy++;
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.fill = GridBagConstraints.BOTH;
        gbc.weightx = 1.0;
        gbc.weighty = 1.0;
        gbc.gridwidth = 3;
        upperPanel.add(getScrollPaneTable().getEnclosingScrollPane(), gbc);
        getScrollPaneTable().setModel(getReactionRulePropertiesTableModel());
        scrollPane = new JScrollPane(shapePanel);
        scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
        scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
        JPanel optionsPanel = new JPanel();
        optionsPanel.setLayout(new GridBagLayout());
        getZoomSmallerButton().setEnabled(true);
        getZoomLargerButton().setEnabled(true);
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 0;
        gbc.insets = new Insets(4, 4, 0, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanel.add(getZoomLargerButton(), gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 1;
        gbc.insets = new Insets(4, 4, 4, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanel.add(getZoomSmallerButton(), gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 2;
        gbc.weightx = 1;
        // fake cell used for filling all the vertical empty space
        gbc.weighty = 1;
        gbc.anchor = GridBagConstraints.WEST;
        gbc.insets = new Insets(4, 4, 4, 10);
        optionsPanel.add(new JLabel(""), gbc);
        JPanel containerOfScrollPanel = new JPanel();
        containerOfScrollPanel.setLayout(new BorderLayout());
        containerOfScrollPanel.add(optionsPanel, BorderLayout.WEST);
        containerOfScrollPanel.add(scrollPane, BorderLayout.CENTER);
        // -------------------------------------------------------------------------------
        splitPaneHorizontal.setTopComponent(upperPanel);
        splitPaneHorizontal.setBottomComponent(containerOfScrollPanel);
        splitPaneHorizontal.setOneTouchExpandable(true);
        splitPaneHorizontal.setDividerLocation(125);
        splitPaneHorizontal.setResizeWeight(1);
        setLayout(new BorderLayout());
        add(splitPaneHorizontal, BorderLayout.CENTER);
        setBackground(Color.white);
        setName("ReactionRuleSpecPropertiesPanel");
        initConnections();
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 4 with PointLocationInShapeContext

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

the class SpeciesContextSpecPanel method initialize.

private void initialize() {
    try {
        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.addMouseMotionListener(new MouseMotionAdapter() {

            public void mouseMoved(MouseEvent e) {
                Point overWhat = e.getPoint();
                PointLocationInShapeContext locationContext = new PointLocationInShapeContext(overWhat);
                spls.contains(locationContext);
                shapePanel.setToolTipText("View-Only panel");
            }
        });
        shapePanel.setBackground(new Color(0xe0e0e0));
        shapePanel.setZoomFactor(-2);
        shapePanel.setEditable(false);
        shapePanel.setShowMoleculeColor(false);
        shapePanel.setShowNonTrivialOnly(false);
        // --------------------------------------------------------------
        JPanel upperPanel = new JPanel();
        upperPanel.setLayout(new java.awt.BorderLayout());
        upperPanel.add(getScrollPaneTable().getEnclosingScrollPane(), BorderLayout.CENTER);
        getScrollPaneTable().setModel(getSpeciesContextSpecParameterTableModel());
        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 gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 0;
        gbc.insets = new Insets(4, 4, 0, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanel.add(getZoomLargerButton(), gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 1;
        gbc.insets = new Insets(4, 4, 4, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanel.add(getZoomSmallerButton(), gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 2;
        gbc.weightx = 1;
        // fake cell used for filling all the vertical empty space
        gbc.weighty = 1;
        gbc.anchor = GridBagConstraints.WEST;
        gbc.insets = new Insets(4, 4, 4, 10);
        optionsPanel.add(new JLabel(""), gbc);
        JPanel containerOfScrollPanel = new JPanel();
        containerOfScrollPanel.setLayout(new BorderLayout());
        containerOfScrollPanel.add(optionsPanel, BorderLayout.WEST);
        containerOfScrollPanel.add(scrollPane, BorderLayout.CENTER);
        // ------------------------------------------------
        splitPaneHorizontal.setTopComponent(upperPanel);
        splitPaneHorizontal.setBottomComponent(containerOfScrollPanel);
        splitPaneHorizontal.setOneTouchExpandable(true);
        // upper panel is 165 pixel height
        splitPaneHorizontal.setDividerLocation(165);
        splitPaneHorizontal.setResizeWeight(1);
        setLayout(new BorderLayout());
        add(splitPaneHorizontal, BorderLayout.CENTER);
        setBackground(Color.white);
        setName("SpeciesContextSpecPanel");
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 5 with PointLocationInShapeContext

use of cbit.vcell.graph.PointLocationInShapeContext 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);
}