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

Example 1 with SpeciesPatternSmallShape

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

the class ViewObservablesMapPanel method initialize.

private void initialize() {
    try {
        // --------------------------------------- the split panels
        setName("ViewGeneratedSpeciesPanel");
        setLayout(new BorderLayout());
        JPanel topPanel = new JPanel();
        topPanel.setLayout(new GridBagLayout());
        JPanel bottomPanel = new JPanel();
        bottomPanel.setLayout(new GridBagLayout());
        JSplitPane splitPaneHorizontal = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
        splitPaneHorizontal.setDividerSize(10);
        splitPaneHorizontal.setOneTouchExpandable(true);
        splitPaneHorizontal.setDividerLocation(260);
        splitPaneHorizontal.setResizeWeight(0.5);
        splitPaneHorizontal.setTopComponent(topPanel);
        splitPaneHorizontal.setBottomComponent(bottomPanel);
        add(splitPaneHorizontal, BorderLayout.CENTER);
        // ---------------------------------------- species shape panel
        shapePanelSpecies = new 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;
            }
        };
        shapePanelSpecies.setLayout(new GridBagLayout());
        shapePanelSpecies.setBackground(Color.white);
        // not really editable but we don't want the brown contours here
        shapePanelSpecies.setEditable(true);
        shapePanelSpecies.setShowMoleculeColor(true);
        shapePanelSpecies.setShowNonTrivialOnly(true);
        Border loweredBevelBorder = BorderFactory.createLoweredBevelBorder();
        JScrollPane scrollPaneSpecies = new JScrollPane(shapePanelSpecies);
        scrollPaneSpecies.setBorder(loweredBevelBorder);
        scrollPaneSpecies.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
        scrollPaneSpecies.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_NEVER);
        JPanel optionsPanelSpecies = new JPanel();
        optionsPanelSpecies.setLayout(new GridBagLayout());
        getZoomSmallerButtonSpecies().setEnabled(true);
        getZoomLargerButtonSpecies().setEnabled(true);
        shapePanelSpecies.zoomSmaller();
        shapePanelSpecies.zoomSmaller();
        GridBagConstraints gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 0;
        gbc.insets = new Insets(0, 0, 0, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanelSpecies.add(getZoomLargerButtonSpecies(), gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 1;
        gbc.insets = new Insets(2, 0, 4, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanelSpecies.add(getZoomSmallerButtonSpecies(), 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);
        optionsPanelSpecies.add(new JLabel(""), gbc);
        JPanel containerOfScrollPanelSpecies = new JPanel();
        containerOfScrollPanelSpecies.setLayout(new BorderLayout());
        containerOfScrollPanelSpecies.add(optionsPanelSpecies, BorderLayout.WEST);
        containerOfScrollPanelSpecies.add(scrollPaneSpecies, BorderLayout.CENTER);
        Dimension dimS = new Dimension(500, 125);
        // dimension of shape panel
        containerOfScrollPanelSpecies.setPreferredSize(dimS);
        containerOfScrollPanelSpecies.setMinimumSize(dimS);
        containerOfScrollPanelSpecies.setMaximumSize(dimS);
        shapePanelObservable = 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;
            }
        };
        // 
        DefaultScrollTableCellRenderer rbmSpeciesPatternCellRenderer = new DefaultScrollTableCellRenderer() {

            @Override
            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
                if (table.getModel() instanceof GeneratedSpeciesTableModel2) {
                    Object selectedObject = null;
                    if (table.getModel() == speciesTableModel) {
                        selectedObject = speciesTableModel.getValueAt(row);
                    }
                    if (selectedObject != null) {
                        if (selectedObject instanceof GeneratedSpeciesTableRow && value instanceof String) {
                            SpeciesPattern sp = ((GeneratedSpeciesTableRow) selectedObject).getSpecies().getSpeciesPattern();
                            String text = "<html>";
                            text += RbmTableRenderer.toHtml(sp, isSelected);
                            text += "</html>";
                            setText(text);
                        }
                    }
                }
                return this;
            }
        };
        // shapePanelObservable.setLayout(null);
        shapePanelObservable.setLayout(new GridBagLayout());
        shapePanelObservable.setBackground(Color.white);
        shapePanelObservable.setEditable(true);
        shapePanelObservable.setShowMoleculeColor(true);
        shapePanelObservable.setShowNonTrivialOnly(true);
        JScrollPane scrollPaneObservable = new JScrollPane(shapePanelObservable);
        scrollPaneObservable.setBorder(loweredBevelBorder);
        scrollPaneObservable.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
        scrollPaneObservable.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_NEVER);
        JPanel optionsPanelObservable = new JPanel();
        optionsPanelObservable.setLayout(new GridBagLayout());
        getZoomSmallerButtonObservable().setEnabled(true);
        getZoomLargerButtonObservable().setEnabled(true);
        shapePanelObservable.zoomSmaller();
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 0;
        gbc.insets = new Insets(0, 0, 0, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanelObservable.add(getZoomLargerButtonObservable(), gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 1;
        gbc.insets = new Insets(2, 0, 4, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanelObservable.add(getZoomSmallerButtonObservable(), 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);
        optionsPanelObservable.add(new JLabel(""), gbc);
        JPanel containerOfScrollPanelObservable = new JPanel();
        containerOfScrollPanelObservable.setLayout(new BorderLayout());
        containerOfScrollPanelObservable.add(optionsPanelObservable, BorderLayout.WEST);
        containerOfScrollPanelObservable.add(scrollPaneObservable, BorderLayout.CENTER);
        Dimension dimO = new Dimension(500, 100);
        // dimension of shape panel
        containerOfScrollPanelObservable.setPreferredSize(dimO);
        containerOfScrollPanelObservable.setMinimumSize(dimO);
        containerOfScrollPanelObservable.setMaximumSize(dimO);
        // -------------- connection between tables, table models, selection models, renderers, event handlers
        speciesTable = new EditorScrollTable();
        speciesTableModel = new GeneratedSpeciesTableModel2(speciesTable, owner);
        speciesTable.setModel(speciesTableModel);
        speciesTable.getSelectionModel().addListSelectionListener(eventHandlerS);
        speciesTable.getModel().addTableModelListener(eventHandlerS);
        observablesTable = new EditorScrollTable();
        observablesTableModel = new ObservablesGroupTableModel(observablesTable, owner, speciesTableModel);
        observablesTable.setModel(observablesTableModel);
        observablesTable.getSelectionModel().addListSelectionListener(eventHandlerO);
        observablesTable.getModel().addTableModelListener(eventHandlerO);
        speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColDefinition).setCellRenderer(rbmSpeciesPatternCellRenderer);
        DefaultTableCellRenderer rightRenderer = new DefaultTableCellRenderer();
        rightRenderer.setHorizontalAlignment(JLabel.RIGHT);
        // speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColMultiplier).setCellRenderer(rightRenderer);	// right align
        // left column wide enough for title
        speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColMultiplier).setMaxWidth(70);
        speciesTable.addMouseMotionListener(new // add toolTipText for each table cell
        MouseMotionAdapter() {

            public void mouseMoved(MouseEvent e) {
                Point p = e.getPoint();
                int row = speciesTable.rowAtPoint(p);
                int column = speciesTable.columnAtPoint(p);
                speciesTable.setToolTipText(String.valueOf(speciesTable.getValueAt(row, column)));
            }
        });
        // ---------------------------------------------- top panel
        int gridy = 0;
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.weightx = 1.0;
        gbc.weighty = 1.0;
        gbc.gridwidth = 8;
        gbc.fill = GridBagConstraints.BOTH;
        gbc.insets = new Insets(4, 4, 4, 4);
        observablesTable.setPreferredScrollableViewportSize(new Dimension(400, 200));
        topPanel.add(observablesTable.getEnclosingScrollPane(), gbc);
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.anchor = GridBagConstraints.LINE_END;
        gbc.insets = new Insets(4, 4, 4, 4);
        topPanel.add(new JLabel("Search "), gbc);
        textFieldSearchObservables = new JTextField(70);
        textFieldSearchObservables.addActionListener(eventHandlerO);
        textFieldSearchObservables.getDocument().addDocumentListener(eventHandlerO);
        textFieldSearchObservables.putClientProperty("JTextField.variant", "search");
        gbc = new java.awt.GridBagConstraints();
        gbc.weightx = 1.0;
        gbc.gridx = 1;
        gbc.gridy = gridy;
        gbc.gridwidth = 3;
        gbc.anchor = GridBagConstraints.LINE_START;
        gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
        gbc.insets = new Insets(4, 0, 4, 4);
        topPanel.add(textFieldSearchObservables, gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 4;
        gbc.gridy = gridy;
        gbc.fill = GridBagConstraints.HORIZONTAL;
        gbc.insets = new Insets(4, 4, 4, 10);
        topPanel.add(totalObservablesLabel, gbc);
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        // gbc.weightx = 1.0;
        gbc.gridwidth = 8;
        gbc.anchor = GridBagConstraints.LINE_END;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(4, 4, 4, 4);
        topPanel.add(containerOfScrollPanelObservable, gbc);
        // -------------------------------------------- bottom panel
        gridy = 0;
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.weightx = 1.0;
        gbc.weighty = 1.0;
        gbc.gridwidth = 8;
        gbc.fill = GridBagConstraints.BOTH;
        gbc.insets = new Insets(4, 4, 4, 4);
        speciesTable.setPreferredScrollableViewportSize(new Dimension(400, 200));
        bottomPanel.add(speciesTable.getEnclosingScrollPane(), gbc);
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.anchor = GridBagConstraints.LINE_END;
        gbc.insets = new Insets(4, 4, 4, 4);
        bottomPanel.add(new JLabel("Search "), gbc);
        textFieldSearchSpecies = new JTextField(70);
        textFieldSearchSpecies.addActionListener(eventHandlerS);
        textFieldSearchSpecies.getDocument().addDocumentListener(eventHandlerS);
        textFieldSearchSpecies.putClientProperty("JTextField.variant", "search");
        gbc = new java.awt.GridBagConstraints();
        gbc.weightx = 1.0;
        gbc.gridx = 1;
        gbc.gridy = gridy;
        gbc.gridwidth = 3;
        gbc.anchor = GridBagConstraints.LINE_START;
        gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
        gbc.insets = new Insets(4, 0, 4, 4);
        bottomPanel.add(textFieldSearchSpecies, gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 4;
        gbc.gridy = gridy;
        gbc.fill = GridBagConstraints.HORIZONTAL;
        gbc.insets = new Insets(4, 4, 4, 10);
        bottomPanel.add(totalSpeciesLabel, gbc);
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        // gbc.weightx = 1.0;
        gbc.gridwidth = 8;
        gbc.anchor = GridBagConstraints.LINE_END;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(4, 4, 4, 4);
        bottomPanel.add(containerOfScrollPanelSpecies, gbc);
        // rendering the small shapes of the flattened species in the Depiction column of this viewer table)
        // TODO: this renderer is almost identical with the one in BioModelEditorModelPanel (which paints the small shapes
        // of a species context in the Depiction column of the species table)
        DefaultScrollTableCellRenderer rbmSpeciesShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {

            SpeciesPatternSmallShape spss = null;

            @Override
            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
                if (table.getModel() instanceof VCellSortTableModel<?>) {
                    Object selectedObject = null;
                    if (table.getModel() == speciesTableModel) {
                        selectedObject = speciesTableModel.getValueAt(row);
                    }
                    if (selectedObject != null) {
                        if (selectedObject instanceof GeneratedSpeciesTableRow) {
                            SpeciesContext sc = ((GeneratedSpeciesTableRow) selectedObject).getSpecies();
                            // sp cannot be null
                            SpeciesPattern sp = sc.getSpeciesPattern();
                            Graphics panelContext = table.getGraphics();
                            spss = new SpeciesPatternSmallShape(4, 2, sp, panelContext, sc, isSelected, issueManager);
                        }
                    } else {
                        spss = null;
                    }
                }
                setText("");
                return this;
            }

            @Override
            public void paintComponent(Graphics g) {
                super.paintComponent(g);
                if (spss != null) {
                    spss.paintSelf(g);
                }
            }
        };
        speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColDepiction).setCellRenderer(rbmSpeciesShapeDepictionCellRenderer);
        speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColDepiction).setPreferredWidth(400);
        speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColDepiction).setMinWidth(400);
        speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColDefinition).setPreferredWidth(30);
        speciesTable.setAutoResizeMode(JTable.AUTO_RESIZE_LAST_COLUMN);
        DefaultScrollTableCellRenderer rbmObservableShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {

            List<SpeciesPatternSmallShape> spssList = new ArrayList<SpeciesPatternSmallShape>();

            SpeciesPatternSmallShape spss = null;

            @Override
            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
                if (table.getModel() instanceof VCellSortTableModel<?>) {
                    Object selectedObject = null;
                    if (table.getModel() == observablesTableModel) {
                        selectedObject = observablesTableModel.getValueAt(row);
                    }
                    if (selectedObject != null && selectedObject instanceof ObservablesGroupTableRow) {
                        ObservablesGroupTableRow ogtr = ((ObservablesGroupTableRow) selectedObject);
                        String obsName = ogtr.getObservableGroupObject().getObservableGroupName();
                        RbmObservable observable = ogtr.getObservable(obsName);
                        Graphics panelContext = table.getGraphics();
                        int xPos = 4;
                        spssList.clear();
                        for (int i = 0; i < observable.getSpeciesPatternList().size(); i++) {
                            SpeciesPattern sp = observable.getSpeciesPatternList().get(i);
                            spss = new SpeciesPatternSmallShape(xPos, 2, sp, panelContext, observable, isSelected, issueManager);
                            xPos += spss.getWidth() + 6;
                            spssList.add(spss);
                        }
                    } else {
                        spssList.clear();
                    }
                }
                setText("");
                return this;
            }

            @Override
            public void paintComponent(Graphics g) {
                super.paintComponent(g);
                for (SpeciesPatternSmallShape spss : spssList) {
                    if (spss == null) {
                        continue;
                    }
                    spss.paintSelf(g);
                }
            }
        };
        observablesTable.getColumnModel().getColumn(ObservablesGroupTableModel.iColDepiction).setCellRenderer(rbmObservableShapeDepictionCellRenderer);
        observablesTable.getColumnModel().getColumn(ObservablesGroupTableModel.iColDepiction).setPreferredWidth(150);
        observablesTable.getColumnModel().getColumn(ObservablesGroupTableModel.iColDepiction).setMinWidth(150);
        observablesTable.getColumnModel().getColumn(ObservablesGroupTableModel.iColDefinition).setPreferredWidth(80);
        observablesTable.getColumnModel().getColumn(ObservablesGroupTableModel.iColExpression).setPreferredWidth(100);
        observablesTable.setAutoResizeMode(JTable.AUTO_RESIZE_LAST_COLUMN);
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 2 with SpeciesPatternSmallShape

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

the class OutputSpeciesResultsPanel method initialize.

private void initialize() {
    try {
        setName("ViewGeneratedSpeciesPanel");
        setLayout(new GridBagLayout());
        shapePanel = new 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;
            }
        };
        Border loweredBevelBorder = BorderFactory.createLoweredBevelBorder();
        shapePanel.setLayout(new GridBagLayout());
        shapePanel.setBackground(Color.white);
        // not really editable but we don't want the brown contours here
        shapePanel.setEditable(true);
        shapePanel.setShowMoleculeColor(true);
        shapePanel.setShowNonTrivialOnly(true);
        JScrollPane scrollPane = new JScrollPane(shapePanel);
        scrollPane.setBorder(loweredBevelBorder);
        scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
        scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_NEVER);
        JPanel optionsPanel = new JPanel();
        optionsPanel.setLayout(new GridBagLayout());
        getZoomSmallerButton().setEnabled(true);
        getZoomLargerButton().setEnabled(false);
        GridBagConstraints gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 0;
        gbc.insets = new Insets(0, 0, 0, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanel.add(getZoomLargerButton(), gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 1;
        gbc.insets = new Insets(2, 0, 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);
        Dimension dim = new Dimension(500, 135);
        // dimension of shape panel
        containerOfScrollPanel.setPreferredSize(dim);
        containerOfScrollPanel.setMinimumSize(dim);
        containerOfScrollPanel.setMaximumSize(dim);
        // ------------------------------------------------------------------------
        table = new EditorScrollTable();
        tableModel = new OutputSpeciesResultsTableModel();
        table.setModel(tableModel);
        table.getSelectionModel().addListSelectionListener(eventHandler);
        table.getModel().addTableModelListener(eventHandler);
        DefaultTableCellRenderer rightRenderer = new DefaultTableCellRenderer();
        rightRenderer.setHorizontalAlignment(JLabel.RIGHT);
        int gridy = 0;
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.weightx = 1.0;
        gbc.weighty = 1.0;
        gbc.gridwidth = 8;
        gbc.fill = GridBagConstraints.BOTH;
        gbc.insets = new Insets(4, 4, 4, 4);
        table.setPreferredScrollableViewportSize(new Dimension(400, 200));
        add(table.getEnclosingScrollPane(), gbc);
        // add toolTipText for each table cell
        table.addMouseMotionListener(new MouseMotionAdapter() {

            public void mouseMoved(MouseEvent e) {
                Point p = e.getPoint();
                int row = table.rowAtPoint(p);
                int column = table.columnAtPoint(p);
                table.setToolTipText(String.valueOf(table.getValueAt(row, column)));
            }
        });
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.anchor = GridBagConstraints.LINE_END;
        gbc.insets = new Insets(4, 4, 4, 4);
        add(new JLabel("Search "), gbc);
        textFieldSearch = new JTextField(70);
        textFieldSearch.addActionListener(eventHandler);
        textFieldSearch.getDocument().addDocumentListener(eventHandler);
        textFieldSearch.putClientProperty("JTextField.variant", "search");
        gbc = new java.awt.GridBagConstraints();
        gbc.weightx = 1.0;
        gbc.gridx = 1;
        gbc.gridy = gridy;
        gbc.gridwidth = 3;
        gbc.anchor = GridBagConstraints.LINE_START;
        gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
        gbc.insets = new Insets(4, 0, 4, 4);
        add(textFieldSearch, gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 4;
        gbc.gridy = gridy;
        gbc.fill = GridBagConstraints.HORIZONTAL;
        gbc.insets = new Insets(4, 4, 4, 10);
        add(totalSpeciesLabel, gbc);
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        // gbc.weightx = 1.0;
        gbc.gridwidth = 8;
        gbc.anchor = GridBagConstraints.LINE_END;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(4, 4, 4, 4);
        add(containerOfScrollPanel, gbc);
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.weightx = 1.0;
        gbc.gridwidth = 2;
        gbc.anchor = GridBagConstraints.WEST;
        gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
        gbc.insets = new Insets(4, 4, 4, 4);
        add(getSpeciesFileLocationPanel(), gbc);
        // // button to copy to clipboard the content of the JTextField.
        // // TODO: do not delete! this is how it's done
        // JButton buttonCopy = new JButton("Copy");
        // buttonCopy.setToolTipText("Copy to clipboard the species file path");
        // buttonCopy.addActionListener(new ActionListener() {
        // public void actionPerformed(ActionEvent le) {
        // if(speciesFileLocationTextField.getSelectionStart() == speciesFileLocationTextField.getSelectionEnd()) {
        // speciesFileLocationTextField.setSelectionStart(0);
        // speciesFileLocationTextField.setSelectionEnd(speciesFileLocationTextField.getText().length());
        // }
        // speciesFileLocationTextField.copy();
        // speciesFileLocationTextField.setSelectionStart(0);
        // speciesFileLocationTextField.setSelectionEnd(0);
        // }
        // });
        // gbc = new GridBagConstraints();
        // gbc.gridx = 4;
        // gbc.gridy = gridy;
        // gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
        // gbc.insets = new Insets(4,4,4,4);
        // add(buttonCopy, gbc);
        // rendering the small shapes of the flattened species in the Depiction column of this viewer table)
        DefaultScrollTableCellRenderer rbmSpeciesShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {

            SpeciesPatternSmallShape spss = null;

            @Override
            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
                if (table.getModel() instanceof VCellSortTableModel<?>) {
                    Object selectedObject = null;
                    if (table.getModel() == tableModel) {
                        selectedObject = tableModel.getValueAt(row);
                    }
                    if (selectedObject != null) {
                        if (selectedObject instanceof GeneratedSpeciesTableRow) {
                            SpeciesContext sc = ((GeneratedSpeciesTableRow) selectedObject).species;
                            if (sc == null || sc.getSpeciesPattern() == null) {
                                spss = null;
                            } else {
                                SpeciesPattern sp = sc.getSpeciesPattern();
                                Graphics panelContext = table.getGraphics();
                                spss = new SpeciesPatternSmallShape(4, 2, sp, panelContext, sc, isSelected, issueManager);
                            }
                        }
                    } else {
                        spss = null;
                    }
                }
                setText("");
                return this;
            }

            @Override
            public void paintComponent(Graphics g) {
                super.paintComponent(g);
                if (spss != null) {
                    spss.paintSelf(g);
                }
            }
        };
        table.getColumnModel().getColumn(OutputSpeciesResultsTableModel.iColDepiction).setCellRenderer(rbmSpeciesShapeDepictionCellRenderer);
        table.getColumnModel().getColumn(OutputSpeciesResultsTableModel.iColDepiction).setPreferredWidth(400);
        table.getColumnModel().getColumn(OutputSpeciesResultsTableModel.iColDepiction).setMinWidth(400);
        table.getColumnModel().getColumn(OutputSpeciesResultsTableModel.iColDefinition).setPreferredWidth(30);
        table.setAutoResizeMode(JTable.AUTO_RESIZE_LAST_COLUMN);
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 3 with SpeciesPatternSmallShape

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

the class ObservablePropertiesPanel method manageComponentPatternFromShape.

public void manageComponentPatternFromShape(final RbmElementAbstract selectedObject, PointLocationInShapeContext locationContext, ShowWhat showWhat) {
    final MolecularComponentPattern mcp = (MolecularComponentPattern) selectedObject;
    final MolecularComponent mc = mcp.getMolecularComponent();
    popupFromShapeMenu.removeAll();
    // ------------------------------------------------------------------- State
    if (showWhat == ShowWhat.ShowState && mc.getComponentStateDefinitions().size() != 0) {
        String prefix = "State:  ";
        String csdCurrentName = "";
        final Map<String, String> itemMap = new LinkedHashMap<String, String>();
        if (mcp.getComponentStatePattern() == null || mcp.getComponentStatePattern().isAny()) {
            csdCurrentName = "<html>" + prefix + "<b>" + ComponentStatePattern.strAny + "</b></html>";
        } else {
            csdCurrentName = "<html>" + prefix + ComponentStatePattern.strAny + "</html>";
        }
        itemMap.put(csdCurrentName, ComponentStatePattern.strAny);
        for (final ComponentStateDefinition csd : mc.getComponentStateDefinitions()) {
            csdCurrentName = "";
            if (mcp.getComponentStatePattern() != null && !mcp.getComponentStatePattern().isAny()) {
                ComponentStateDefinition csdCurrent = mcp.getComponentStatePattern().getComponentStateDefinition();
                csdCurrentName = csdCurrent.getName();
            }
            String name = csd.getName();
            if (name.equals(csdCurrentName)) {
                // currently selected menu item is shown in bold
                name = "<html>" + prefix + "<b>" + name + "</b></html>";
            } else {
                name = "<html>" + prefix + name + "</html>";
            }
            itemMap.put(name, csd.getName());
        }
        for (String name : itemMap.keySet()) {
            JMenuItem menuItem = new JMenuItem(name);
            popupFromShapeMenu.add(menuItem);
            menuItem.setIcon(VCellIcons.rbmComponentStateIcon);
            menuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    String key = e.getActionCommand();
                    String name = itemMap.get(key);
                    if (name.equals(ComponentStatePattern.strAny)) {
                        ComponentStatePattern csp = new ComponentStatePattern();
                        mcp.setComponentStatePattern(csp);
                    } else {
                        ComponentStateDefinition csd = mcp.getMolecularComponent().getComponentStateDefinition(name);
                        if (csd == null) {
                            throw new RuntimeException("Missing ComponentStateDefinition " + name + " for Component " + mcp.getMolecularComponent().getName());
                        }
                        ComponentStatePattern csp = new ComponentStatePattern(csd);
                        mcp.setComponentStatePattern(csp);
                    }
                }
            });
        }
    }
    if (showWhat == ShowWhat.ShowState) {
        return;
    }
    // ------------------------------------------------------------------------------------------- Bonds
    final MolecularTypePattern mtp = locationContext.getMolecularTypePattern();
    final SpeciesPattern sp = locationContext.getSpeciesPattern();
    JMenu editBondMenu = new JMenu();
    final String specifiedString = mcp.getBondType() == BondType.Specified ? "<html><b>" + "Site bond specified" + "</b></html>" : "<html>" + "Site bond specified" + "</html>";
    editBondMenu.setText(specifiedString);
    editBondMenu.setToolTipText("Specified");
    editBondMenu.removeAll();
    final Map<String, Bond> itemMap = new LinkedHashMap<String, Bond>();
    // String noneString = "<html>Bond:&nbsp;&nbsp;<b>" + BondType.None.symbol + "</b> " + BondType.None.name() + "</html>";
    // String existsString = "<html>Bond:&nbsp;&nbsp;<b>" + BondType.Exists.symbol + "</b> " + BondType.Exists.name() + "</html>";
    // String possibleString = "<html>Bond:&nbsp;&nbsp;<b>" + BondType.Possible.symbol + "</b> " + BondType.Possible.name() + "</html>";
    String noneString = mcp.getBondType() == BondType.None ? "<html><b>" + "Site is unbound" + "</b></html>" : "<html>" + "Site is unbound" + "</html>";
    // Site is bound
    String existsString = mcp.getBondType() == BondType.Exists ? "<html><b>" + "Site has external bond" + "</b></html>" : "<html>" + "Site has external bond" + "</html>";
    String possibleString = mcp.getBondType() == BondType.Possible ? "<html><b>" + "Site may be bound" + "</b></html>" : "<html>" + "Site may be bound" + "</html>";
    itemMap.put(noneString, null);
    itemMap.put(existsString, null);
    itemMap.put(possibleString, null);
    if (mtp != null && sp != null) {
        List<Bond> bondPartnerChoices = sp.getAllBondPartnerChoices(mtp, mc);
        for (Bond b : bondPartnerChoices) {
            // if(b.equals(mcp.getBond())) {
            // continue;	// if the mcp has a bond already we don't offer it
            // }
            int index = 0;
            if (mcp.getBondType() == BondType.Specified) {
                index = mcp.getBondId();
            } else {
                index = sp.nextBondId();
            }
            // itemMap.put(b.toHtmlStringLong(mtp, mc, sp, index), b);
            itemMap.put(b.toHtmlStringLong(sp, mtp, mc, index), b);
        // itemMap.put(b.toHtmlStringLong(sp, index), b);
        }
    }
    int index = 0;
    Graphics gc = splitPaneHorizontal.getGraphics();
    for (String name : itemMap.keySet()) {
        JMenuItem menuItem = new JMenuItem(name);
        if (index == 0) {
            menuItem.setIcon(VCellIcons.rbmBondNoneIcon);
            menuItem.setToolTipText("None");
            popupFromShapeMenu.add(menuItem);
        } else if (index == 1) {
            menuItem.setIcon(VCellIcons.rbmBondExistsIcon);
            menuItem.setToolTipText("Exists");
            popupFromShapeMenu.add(menuItem);
        } else if (index == 2) {
            menuItem.setIcon(VCellIcons.rbmBondPossibleIcon);
            menuItem.setToolTipText("Possible");
            popupFromShapeMenu.add(menuItem);
        } else if (index > 2) {
            Bond b = itemMap.get(name);
            // clone of the sp, with only the bond of interest
            SpeciesPattern spBond = new SpeciesPattern(bioModel.getModel(), sp);
            spBond.resetBonds();
            spBond.resetStates();
            MolecularTypePattern mtpFrom = spBond.getMolecularTypePattern(mtp.getMolecularType().getName(), mtp.getIndex());
            MolecularComponentPattern mcpFrom = mtpFrom.getMolecularComponentPattern(mc);
            MolecularTypePattern mtpTo = spBond.getMolecularTypePattern(b.molecularTypePattern.getMolecularType().getName(), b.molecularTypePattern.getIndex());
            MolecularComponentPattern mcpTo = mtpTo.getMolecularComponentPattern(b.molecularComponentPattern.getMolecularComponent());
            spBond.setBond(mtpTo, mcpTo, mtpFrom, mcpFrom);
            Icon icon = new SpeciesPatternSmallShape(3, 4, spBond, gc, observable, false, issueManager);
            ((SpeciesPatternSmallShape) icon).setDisplayRequirements(DisplayRequirements.highlightBonds);
            menuItem.setIcon(icon);
            editBondMenu.add(menuItem);
        // } else {
        // if(index == 0) {
        // menuItem.setForeground(Color.blue);
        // }
        // popupFromShapeMenu.add(menuItem);
        }
        menuItem.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                String name = e.getActionCommand();
                BondType btBefore = mcp.getBondType();
                if (name.equals(noneString)) {
                    if (btBefore == BondType.Specified) {
                        // specified -> not specified
                        // change the partner to possible
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.None);
                    mcp.setBond(null);
                    SwingUtilities.invokeLater(new Runnable() {

                        public void run() {
                            observableTreeModel.populateTree();
                        }
                    });
                } else if (name.equals(existsString)) {
                    if (btBefore == BondType.Specified) {
                        // specified -> exists
                        // change the partner to possible
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.Exists);
                    mcp.setBond(null);
                    SwingUtilities.invokeLater(new Runnable() {

                        public void run() {
                            observableTreeModel.populateTree();
                        }
                    });
                } else if (name.equals(possibleString)) {
                    if (btBefore == BondType.Specified) {
                        // specified -> possible
                        // change the partner to possible
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.Possible);
                    mcp.setBond(null);
                    SwingUtilities.invokeLater(new Runnable() {

                        public void run() {
                            observableTreeModel.populateTree();
                        }
                    });
                } else {
                    if (btBefore != BondType.Specified) {
                        // if we go from a non-specified to a specified we need to find the next available
                        // bond id, so that we can choose the color for displaying the bond
                        // a bad bond id, like -1, will crash badly when trying to choose the color
                        int bondId = sp.nextBondId();
                        mcp.setBondId(bondId);
                    } else {
                        // specified -> specified
                        // change the old partner to possible, continue using the bond id
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.Specified);
                    Bond b = itemMap.get(name);
                    mcp.setBond(b);
                    mcp.getBond().molecularComponentPattern.setBondId(mcp.getBondId());
                    sp.resolveBonds();
                    SwingUtilities.invokeLater(new Runnable() {

                        public void run() {
                            observableTreeModel.populateTree();
                        }
                    });
                }
            }
        });
        index++;
    }
    popupFromShapeMenu.add(editBondMenu);
}

Example 4 with SpeciesPatternSmallShape

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

the class SpeciesPropertiesPanel method manageComponentPatternFromShape.

public void manageComponentPatternFromShape(final RbmElementAbstract selectedObject, PointLocationInShapeContext locationContext, ShowWhat showWhat) {
    popupFromShapeMenu.removeAll();
    final MolecularComponentPattern mcp = (MolecularComponentPattern) selectedObject;
    final MolecularComponent mc = mcp.getMolecularComponent();
    // ------------------------------------------------------------------- State
    if (showWhat == ShowWhat.ShowState && mc.getComponentStateDefinitions().size() != 0) {
        String prefix = "State:  ";
        final Map<String, String> itemMap = new LinkedHashMap<String, String>();
        // itemList.add(ComponentStatePattern.strAny);			// any is not an option for state
        String csdCurrentName;
        for (final ComponentStateDefinition csd : mc.getComponentStateDefinitions()) {
            csdCurrentName = "";
            if (mcp.getComponentStatePattern() != null && !mcp.getComponentStatePattern().isAny()) {
                ComponentStateDefinition csdCurrent = mcp.getComponentStatePattern().getComponentStateDefinition();
                csdCurrentName = csdCurrent.getName();
            }
            String name = csd.getName();
            if (name.equals(csdCurrentName)) {
                // currently selected menu item is shown in bold
                name = "<html>" + prefix + "<b>" + name + "</b></html>";
            } else {
                name = "<html>" + prefix + name + "</html>";
            }
            itemMap.put(name, csd.getName());
        }
        for (String name : itemMap.keySet()) {
            JMenuItem menuItem = new JMenuItem(name);
            popupFromShapeMenu.add(menuItem);
            menuItem.setIcon(VCellIcons.rbmComponentStateIcon);
            menuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    String key = e.getActionCommand();
                    String name = itemMap.get(key);
                    if (name.equals(ComponentStatePattern.strAny)) {
                        ComponentStatePattern csp = new ComponentStatePattern();
                        mcp.setComponentStatePattern(csp);
                    } else {
                        ComponentStateDefinition csd = mcp.getMolecularComponent().getComponentStateDefinition(name);
                        if (csd == null) {
                            throw new RuntimeException("Missing ComponentStateDefinition " + name + " for Component " + mcp.getMolecularComponent().getName());
                        }
                        ComponentStatePattern csp = new ComponentStatePattern(csd);
                        mcp.setComponentStatePattern(csp);
                    }
                }
            });
        }
    }
    if (showWhat == ShowWhat.ShowState) {
        return;
    }
    // ---------------------------------------------------------------------------- Bonds
    final MolecularTypePattern mtp = locationContext.getMolecularTypePattern();
    final SpeciesPattern sp = locationContext.getSpeciesPattern();
    JMenu editBondMenu = new JMenu();
    final String specifiedString = mcp.getBondType() == BondType.Specified ? "<html><b>" + "Site bond specified" + "</b></html>" : "<html>" + "Site bond specified" + "</html>";
    editBondMenu.setText(specifiedString);
    editBondMenu.setToolTipText("Specified");
    editBondMenu.removeAll();
    final Map<String, Bond> itemMap = new LinkedHashMap<String, Bond>();
    String noneString = mcp.getBondType() == BondType.None ? "<html><b>" + "Site is unbound" + "</b></html>" : "<html>" + "Site is unbound" + "</html>";
    itemMap.put(noneString, null);
    // itemMap.put(possibleString, null);	// not a valid option for species
    if (mtp != null && sp != null) {
        List<Bond> bondPartnerChoices = sp.getAllBondPartnerChoices(mtp, mc);
        for (Bond b : bondPartnerChoices) {
            // if(b.equals(mcp.getBond())) {
            // continue;	// if the mcp has a bond already we don't offer it
            // }
            int index = 0;
            if (mcp.getBondType() == BondType.Specified) {
                index = mcp.getBondId();
            } else {
                index = sp.nextBondId();
            }
            itemMap.put(b.toHtmlStringLong(sp, mtp, mc, index), b);
        // itemMap.put(b.toHtmlStringLong(sp, index), b);
        }
    }
    int index = 0;
    Graphics gc = shapePanel.getGraphics();
    for (String name : itemMap.keySet()) {
        JMenuItem menuItem = new JMenuItem(name);
        if (index == 0) {
            menuItem.setIcon(VCellIcons.rbmBondNoneIcon);
            menuItem.setToolTipText("None");
            popupFromShapeMenu.add(menuItem);
        } else {
            Bond b = itemMap.get(name);
            // clone of the sp, with only the bond of interest
            SpeciesPattern spBond = new SpeciesPattern(bioModel.getModel(), sp);
            spBond.resetBonds();
            spBond.resetStates();
            MolecularTypePattern mtpFrom = spBond.getMolecularTypePattern(mtp.getMolecularType().getName(), mtp.getIndex());
            MolecularComponentPattern mcpFrom = mtpFrom.getMolecularComponentPattern(mc);
            MolecularTypePattern mtpTo = spBond.getMolecularTypePattern(b.molecularTypePattern.getMolecularType().getName(), b.molecularTypePattern.getIndex());
            MolecularComponentPattern mcpTo = mtpTo.getMolecularComponentPattern(b.molecularComponentPattern.getMolecularComponent());
            spBond.setBond(mtpTo, mcpTo, mtpFrom, mcpFrom);
            Icon icon = new SpeciesPatternSmallShape(3, 4, spBond, gc, fieldSpeciesContext, false, issueManager);
            ((SpeciesPatternSmallShape) icon).setDisplayRequirements(DisplayRequirements.highlightBonds);
            menuItem.setIcon(icon);
            editBondMenu.add(menuItem);
        }
        menuItem.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                String name = e.getActionCommand();
                BondType btBefore = mcp.getBondType();
                if (name.equals(noneString)) {
                    if (btBefore == BondType.Specified) {
                        // specified -> not specified
                        // change the partner to none since this is the only option
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.None);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.None);
                    mcp.setBond(null);
                    SwingUtilities.invokeLater(new Runnable() {

                        public void run() {
                            speciesPropertiesTreeModel.populateTree();
                        }
                    });
                } else {
                    if (btBefore != BondType.Specified) {
                        // if we go from a non-specified to a specified we need to find the next available
                        // bond id, so that we can choose the color for displaying the bond
                        // a bad bond id, like -1, will crash badly when trying to choose the color
                        int bondId = sp.nextBondId();
                        mcp.setBondId(bondId);
                    } else {
                        // specified -> specified
                        // change the old partner to none since it's the only available option, continue using the bond id
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.None);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.Specified);
                    Bond b = itemMap.get(name);
                    mcp.setBond(b);
                    mcp.getBond().molecularComponentPattern.setBondId(mcp.getBondId());
                    sp.resolveBonds();
                    SwingUtilities.invokeLater(new Runnable() {

                        public void run() {
                            speciesPropertiesTreeModel.populateTree();
                        }
                    });
                }
            }
        });
        index++;
    }
    popupFromShapeMenu.add(editBondMenu);
}

Example 5 with SpeciesPatternSmallShape

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

the class InitialConditionsPanel method initialize.

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

            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
                setIcon(null);
                defaultToolTipText = null;
                if (value instanceof Species) {
                    setText(((Species) value).getCommonName());
                    defaultToolTipText = getText();
                    setToolTipText(defaultToolTipText);
                } else if (value instanceof SpeciesContext) {
                    setText(((SpeciesContext) value).getName());
                    defaultToolTipText = getText();
                    setToolTipText(defaultToolTipText);
                } else if (value instanceof Structure) {
                    setText(((Structure) value).getName());
                    defaultToolTipText = getText();
                    setToolTipText(defaultToolTipText);
                } else if (value instanceof ScopedExpression) {
                    SpeciesContextSpec scSpec = tableModel.getValueAt(row);
                    VCUnitDefinition unit = null;
                    if (table.getColumnName(column).equals(SpeciesContextSpecsTableModel.ColumnType.COLUMN_INITIAL.label)) {
                        SpeciesContextSpecParameter initialConditionParameter = scSpec.getInitialConditionParameter();
                        unit = initialConditionParameter.getUnitDefinition();
                    } else if (table.getColumnName(column).equals(SpeciesContextSpecsTableModel.ColumnType.COLUMN_DIFFUSION.label)) {
                        SpeciesContextSpecParameter diffusionParameter = scSpec.getDiffusionParameter();
                        unit = diffusionParameter.getUnitDefinition();
                    }
                    if (unit != null) {
                        setHorizontalTextPosition(JLabel.LEFT);
                        setIcon(new TextIcon("[" + unit.getSymbolUnicode() + "]", DefaultScrollTableCellRenderer.uneditableForeground));
                    }
                    int rgb = 0x00ffffff & DefaultScrollTableCellRenderer.uneditableForeground.getRGB();
                    defaultToolTipText = "<html>" + StringEscapeUtils.escapeHtml4(getText()) + " <font color=#" + Integer.toHexString(rgb) + "> [" + unit.getSymbolUnicode() + "] </font></html>";
                    setToolTipText(defaultToolTipText);
                    if (unit != null) {
                        setText(defaultToolTipText);
                    }
                }
                TableModel tableModel = table.getModel();
                if (tableModel instanceof SortTableModel) {
                    DefaultScrollTableCellRenderer.issueRenderer(this, defaultToolTipText, table, row, column, (SortTableModel) tableModel);
                    setHorizontalTextPosition(JLabel.TRAILING);
                }
                return this;
            }
        };
        DefaultTableCellRenderer rbmSpeciesShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {

            SpeciesPatternSmallShape spss = null;

            @Override
            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
                if (table.getModel() instanceof VCellSortTableModel<?>) {
                    Object selectedObject = null;
                    if (table.getModel() == tableModel) {
                        selectedObject = tableModel.getValueAt(row);
                    }
                    if (selectedObject != null) {
                        if (selectedObject instanceof SpeciesContextSpec) {
                            SpeciesContextSpec scs = (SpeciesContextSpec) selectedObject;
                            SpeciesContext sc = scs.getSpeciesContext();
                            // sp may be null for "plain" species contexts
                            SpeciesPattern sp = sc.getSpeciesPattern();
                            Graphics panelContext = table.getGraphics();
                            spss = new SpeciesPatternSmallShape(4, 2, sp, shapeManager, panelContext, sc, isSelected, issueManager);
                        }
                    } else {
                        spss = null;
                    }
                }
                setText("");
                return this;
            }

            @Override
            public void paintComponent(Graphics g) {
                super.paintComponent(g);
                if (spss != null) {
                    spss.paintSelf(g);
                }
            }
        };
        getScrollPaneTable().setDefaultRenderer(SpeciesContext.class, renderer);
        getScrollPaneTable().setDefaultRenderer(Structure.class, renderer);
        getScrollPaneTable().setDefaultRenderer(SpeciesPattern.class, rbmSpeciesShapeDepictionCellRenderer);
        getScrollPaneTable().setDefaultRenderer(Species.class, renderer);
        getScrollPaneTable().setDefaultRenderer(ScopedExpression.class, renderer);
        getScrollPaneTable().setDefaultRenderer(Boolean.class, new ScrollTableBooleanCellRenderer());
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}