Examples with RbmObservable cbit.vcell.model.RbmObservable used on opensource projects

Example 31 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class MolecularTypeLargeShape method adjustForSize.

private String adjustForSize() {
    if (shapePanel.getZoomFactor() < LargeShapeCanvas.SmallestZoomFactorWithText) {
        // when we zoom to very small shapes we must stop writing the text
        return "  ";
    }
    // we truncate to 12 characters any name longer than 12 characters
    // we keep the first 7 letters, then 2 points, then the last 3 letters
    String s = null;
    if (mt == null) {
        if (owner instanceof SpeciesContext) {
            s = owner.getDisplayName();
        } else if (owner instanceof RbmObservable) {
            s = owner.getDisplayName();
        } else {
            s = "?";
        }
    } else {
        s = mt.getDisplayName();
    }
    int len = s.length();
    if (len > 12) {
        return (s.substring(0, 7) + ".." + s.substring(len - 3, len));
    } else {
        return (s);
    }
}

Example 32 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class BioModelEditorModelPanel method newButtonPressed.

private void newButtonPressed() throws ModelException, PropertyVetoException {
    newObject = null;
    computeCurrentSelectedTable();
    if (currentSelectedTable == speciesTable) {
        if (bioModel.getModel().getNumStructures() == 1) {
            newObject = bioModel.getModel().createSpeciesContext(bioModel.getModel().getStructures()[0]);
        } else if (bioModel.getModel().getNumStructures() > 1) {
            final JPopupMenu menu = new JPopupMenu("Choose compartment");
            for (int i = 0; i < bioModel.getModel().getNumStructures(); i++) {
                Structure s = bioModel.getModel().getStructure(i);
                String sName = s.getName();
                JMenuItem menuItem = new JMenuItem("In " + s.getTypeName() + " " + sName);
                menuItem.setIcon(new StructureToolShapeIcon(17));
                menu.add(menuItem);
                menuItem.addActionListener(new ActionListener() {

                    public void actionPerformed(ActionEvent e) {
                        newObject = bioModel.getModel().createSpeciesContext(s);
                    }
                });
            }
            menu.show(newButton, 0, newButton.getHeight());
        }
    } else if (currentSelectedTable == molecularTypeTable) {
        if (bioModel.getModel().getRbmModelContainer() != null) {
            MolecularType mt = bioModel.getModel().getRbmModelContainer().createMolecularType();
            bioModel.getModel().getRbmModelContainer().addMolecularType(mt, true);
            newObject = mt;
        }
    } else if (currentSelectedTable == observablesTable) {
        if (bioModel.getModel().getRbmModelContainer() != null) {
            if (bioModel.getModel().getRbmModelContainer().getMolecularTypeList().isEmpty()) {
                PopupGenerator.showInfoDialog(this, VCellErrorMessages.MustBeRuleBased);
                return;
            }
            if (bioModel.getModel().getNumStructures() == 1) {
                RbmObservable o = bioModel.getModel().getRbmModelContainer().createObservable(RbmObservable.ObservableType.Molecules);
                bioModel.getModel().getRbmModelContainer().addObservable(o);
                SpeciesPattern sp = new SpeciesPattern();
                o.addSpeciesPattern(sp);
                newObject = o;
            } else if (bioModel.getModel().getNumStructures() > 1) {
                final JPopupMenu menu = new JPopupMenu("Choose compartment");
                for (int i = 0; i < bioModel.getModel().getNumStructures(); i++) {
                    Structure s = bioModel.getModel().getStructure(i);
                    String sName = s.getName();
                    JMenuItem menuItem = new JMenuItem("In " + s.getTypeName() + " " + sName);
                    menuItem.setIcon(new StructureToolShapeIcon(17));
                    menu.add(menuItem);
                    menuItem.addActionListener(new ActionListener() {

                        public void actionPerformed(ActionEvent e) {
                            RbmObservable o = bioModel.getModel().getRbmModelContainer().createObservable(RbmObservable.ObservableType.Molecules, null, s);
                            o.setStructure(s);
                            try {
                                bioModel.getModel().getRbmModelContainer().addObservable(o);
                            } catch (ModelException | PropertyVetoException e1) {
                                e1.printStackTrace();
                                throw new RuntimeException(e1.getMessage(), e1);
                            }
                            SpeciesPattern sp = new SpeciesPattern();
                            o.addSpeciesPattern(sp);
                            newObject = o;
                            if (newObject != null) {
                                for (int i = 0; i < currentSelectedTableModel.getRowCount(); i++) {
                                    if (currentSelectedTableModel.getValueAt(i) == newObject) {
                                        currentSelectedTable.setRowSelectionInterval(i, i);
                                        break;
                                    }
                                }
                            }
                        }
                    });
                }
                menu.show(newButton, 0, newButton.getHeight());
            }
        }
    } else if (currentSelectedTable == structuresTable) {
        try {
            Feature feature = bioModel.getModel().createFeature();
            newObject = feature;
        } catch (Exception e) {
            e.printStackTrace();
            DialogUtils.showErrorDialog(this, e.getMessage(), e);
        }
    } else if (currentSelectedTable == reactionsTable) {
        if (bioModel.getModel().getNumStructures() == 1) {
            SimpleReaction reactionStep = bioModel.getModel().createSimpleReaction(bioModel.getModel().getStructures()[0]);
            newObject = reactionStep;
        } else {
            addNewReaction();
        }
    }
    if (newObject != null) {
        for (int i = 0; i < currentSelectedTableModel.getRowCount(); i++) {
            if (currentSelectedTableModel.getValueAt(i) == newObject) {
                currentSelectedTable.setRowSelectionInterval(i, i);
                break;
            }
        }
    }
}

Example 33 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class BioModelEditorModelPanel method initialize.

private void initialize() {
    newButton = new JButton("New");
    newButton2 = new JButton("New Rule");
    newMemButton = new JButton("New Membrane");
    deleteButton = new JButton("Delete");
    duplicateButton = new JButton("Duplicate");
    pathwayButton = new JButton("Pathway Links", new DownArrowIcon());
    pathwayButton.setHorizontalTextPosition(SwingConstants.LEFT);
    textFieldSearch = new JTextField();
    textFieldSearch.putClientProperty("JTextField.variant", "search");
    structuresTable = new EditorScrollTable();
    reactionsTable = new EditorScrollTable();
    speciesTable = new EditorScrollTable();
    molecularTypeTable = new EditorScrollTable();
    observablesTable = new EditorScrollTable();
    structureTableModel = new BioModelEditorStructureTableModel(structuresTable);
    reactionTableModel = new BioModelEditorReactionTableModel(reactionsTable);
    speciesTableModel = new BioModelEditorSpeciesTableModel(speciesTable);
    molecularTypeTableModel = new MolecularTypeTableModel(molecularTypeTable);
    observableTableModel = new ObservableTableModel(observablesTable);
    structuresTable.setModel(structureTableModel);
    reactionsTable.setModel(reactionTableModel);
    speciesTable.setModel(speciesTableModel);
    molecularTypeTable.setModel(molecularTypeTableModel);
    observablesTable.setModel(observableTableModel);
    reactionCartoonEditorPanel = new ReactionCartoonEditorPanel();
    reactionCartoonEditorPanel.addPropertyChangeListener(eventHandler);
    reactionCartoonEditorPanel.getReactionCartoonFull().addPropertyChangeListener(eventHandler);
    reactionCartoonEditorPanel.getReactionCartoonMolecule().addPropertyChangeListener(eventHandler);
    reactionCartoonEditorPanel.getReactionCartoonRule().addPropertyChangeListener(eventHandler);
    // cartoonEditorPanel  = new CartoonEditorPanelFixed();
    // cartoonEditorPanel.getStructureCartoon().addPropertyChangeListener(eventHandler);
    /* button panel */
    buttonPanel = new JPanel();
    buttonPanel.setLayout(new GridBagLayout());
    GridBagConstraints gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 0;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.anchor = GridBagConstraints.LINE_END;
    buttonPanel.add(newButton, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 1;
    gbc.gridy = 0;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.anchor = GridBagConstraints.LINE_END;
    buttonPanel.add(newButton2, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 2;
    gbc.gridy = 0;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.anchor = GridBagConstraints.LINE_END;
    buttonPanel.add(newMemButton, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 3;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.gridy = 0;
    gbc.anchor = GridBagConstraints.LINE_END;
    buttonPanel.add(duplicateButton, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 4;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.gridy = 0;
    gbc.anchor = GridBagConstraints.LINE_END;
    buttonPanel.add(deleteButton, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 5;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.gridy = 0;
    gbc.anchor = GridBagConstraints.LINE_END;
    buttonPanel.add(pathwayButton, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 6;
    gbc.gridy = 0;
    gbc.weightx = 0.5;
    gbc.fill = GridBagConstraints.HORIZONTAL;
    gbc.insets = new Insets(4, 4, 4, 4);
    buttonPanel.add(Box.createRigidArea(new Dimension(5, 5)), gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 7;
    gbc.gridy = 0;
    gbc.anchor = GridBagConstraints.LINE_END;
    gbc.insets = new Insets(4, 4, 4, 4);
    buttonPanel.add(new JLabel("Search "), gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 8;
    gbc.gridy = 0;
    gbc.weightx = 1.5;
    gbc.anchor = GridBagConstraints.LINE_START;
    gbc.fill = GridBagConstraints.HORIZONTAL;
    gbc.insets = new Insets(4, 4, 4, 4);
    buttonPanel.add(textFieldSearch, gbc);
    /* button panel */
    tabbedPane = new JTabbedPaneEnhanced();
    tabbedPane.setTabLayoutPolicy(JTabbedPane.SCROLL_TAB_LAYOUT);
    modelPanelTabs[ModelPanelTabID.reaction_diagram.ordinal()] = new ModelPanelTab(ModelPanelTabID.reaction_diagram, reactionCartoonEditorPanel, VCellIcons.diagramIcon);
    // modelPanelTabs[ModelPanelTabID.structure_diagram.ordinal()] = new ModelPanelTab(ModelPanelTabID.structure_diagram, cartoonEditorPanel, VCellIcons.structureIcon);
    modelPanelTabs[ModelPanelTabID.reaction_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.reaction_table, reactionsTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
    modelPanelTabs[ModelPanelTabID.structure_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.structure_table, structuresTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
    modelPanelTabs[ModelPanelTabID.species_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.species_table, speciesTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
    modelPanelTabs[ModelPanelTabID.species_definitions_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.species_definitions_table, molecularTypeTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
    modelPanelTabs[ModelPanelTabID.observables_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.observables_table, observablesTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
    tabbedPane.addChangeListener(eventHandler);
    tabbedPane.addMouseListener(eventHandler);
    for (ModelPanelTab tab : modelPanelTabs) {
        tab.getComponent().setBorder(GuiConstants.TAB_PANEL_BORDER);
        tabbedPane.addTab(tab.getName(), tab.getIcon(), tab.getComponent());
    }
    // tabbedPane.addChangeListener(changeListener);
    setLayout(new BorderLayout());
    add(tabbedPane, BorderLayout.CENTER);
    add(buttonPanel, BorderLayout.SOUTH);
    newButton.addActionListener(eventHandler);
    newButton2.addActionListener(eventHandler);
    newMemButton.addActionListener(eventHandler);
    duplicateButton.addActionListener(eventHandler);
    duplicateButton.setEnabled(false);
    deleteButton.addActionListener(eventHandler);
    deleteButton.setEnabled(false);
    pathwayButton.addActionListener(eventHandler);
    pathwayButton.setEnabled(false);
    textFieldSearch.addActionListener(eventHandler);
    textFieldSearch.getDocument().addDocumentListener(eventHandler);
    structuresTable.getSelectionModel().addListSelectionListener(eventHandler);
    reactionsTable.getSelectionModel().addListSelectionListener(eventHandler);
    speciesTable.getSelectionModel().addListSelectionListener(eventHandler);
    molecularTypeTable.getSelectionModel().addListSelectionListener(eventHandler);
    observablesTable.getSelectionModel().addListSelectionListener(eventHandler);
    DefaultScrollTableCellRenderer tableRenderer = 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 (value instanceof Structure) {
                setText(((Structure) value).getName());
            } else if (value instanceof Kinetics) {
                setText(((Kinetics) value).getKineticsDescription().getDescription());
            } else if (value instanceof RbmKineticLaw) {
                setText(((RbmKineticLaw) value).getRateLawType().name());
            }
            return this;
        }
    };
    RbmTableRenderer rbmTableRenderer = new RbmTableRenderer();
    structuresTable.setDefaultRenderer(Structure.class, tableRenderer);
    speciesTable.setDefaultRenderer(Structure.class, tableRenderer);
    reactionsTable.setDefaultRenderer(Structure.class, tableRenderer);
    reactionsTable.setDefaultRenderer(Kinetics.class, tableRenderer);
    reactionsTable.setDefaultRenderer(RbmKineticLaw.class, tableRenderer);
    reactionsTable.setDefaultRenderer(ModelProcessDynamics.class, tableRenderer);
    DefaultScrollTableCellRenderer tableCellRenderer = 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);
            BioModelEntityObject bioModelEntityObject = null;
            if (table.getModel() instanceof VCellSortTableModel<?>) {
                if (table.getModel() == reactionTableModel && reactionTableModel.getValueAt(row) instanceof BioModelEntityObject) {
                    bioModelEntityObject = (BioModelEntityObject) reactionTableModel.getValueAt(row);
                } else if (table.getModel() == speciesTableModel) {
                    bioModelEntityObject = speciesTableModel.getValueAt(row);
                } else if (table.getModel() == molecularTypeTableModel) {
                    bioModelEntityObject = molecularTypeTableModel.getValueAt(row);
                }
                if (bioModelEntityObject != null) {
                    Set<RelationshipObject> relationshipSet = bioModel.getRelationshipModel().getRelationshipObjects(bioModelEntityObject);
                    if (relationshipSet.size() > 0) {
                        StringBuilder tooltip = new StringBuilder("<html>Links to Pathway objects:<br>");
                        for (RelationshipObject ro : relationshipSet) {
                            tooltip.append("<li>" + ro.getBioPaxObject() + "</li>");
                        }
                        if (!isSelected) {
                            setForeground(Color.blue);
                        }
                        String finalName = null;
                        BioPaxObject bioPaxObject = relationshipSet.iterator().next().getBioPaxObject();
                        if (bioPaxObject instanceof EntityImpl && ((EntityImpl) bioPaxObject).getName() != null && ((EntityImpl) bioPaxObject).getName().size() > 0) {
                            finalName = ((EntityImpl) bioPaxObject).getName().get(0);
                        } else if (bioPaxObject instanceof Conversion) {
                            Conversion mp = (Conversion) bioPaxObject;
                            finalName = "[" + bioPaxObject.getIDShort() + "]";
                        } else {
                            finalName = bioModelEntityObject.getName();
                        }
                        final int LIMIT = 40;
                        final String DOTS = "...";
                        if (finalName != null && finalName.length() > LIMIT) {
                            finalName = finalName.substring(0, LIMIT - DOTS.length() - 1) + DOTS;
                        }
                        setText("<html><u>" + finalName + "</u></html>");
                        setToolTipText(tooltip.toString());
                    }
                }
            }
            return this;
        }
    };
    DefaultScrollTableCellRenderer rbmReactionExpressionCellRenderer = 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 VCellSortTableModel<?>) {
                Object selectedObject = null;
                if (table.getModel() == reactionTableModel) {
                    selectedObject = reactionTableModel.getValueAt(row);
                }
                if (selectedObject != null) {
                    if (selectedObject instanceof ReactionRule && value instanceof ModelProcessEquation) {
                        String text = "<html>";
                        text += "Reaction Rule";
                        text += "</html>";
                        setText(text);
                    } else {
                        // plain reaction, check if reactants have species pattern
                        ReactionStep rs = (ReactionStep) selectedObject;
                        String text = "<html>";
                        for (int i = 0; i < rs.getNumReactants(); i++) {
                            Reactant p = rs.getReactant(i);
                            if (p.getSpeciesContext().hasSpeciesPattern()) {
                                text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
                                // text += "<b>" + p.getName() + "</b>";
                                text += p.getName();
                            } else {
                                text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
                                text += p.getName();
                            }
                            if (i < rs.getNumReactants() - 1) {
                                text += " + ";
                            }
                        }
                        text += " -&gt; ";
                        for (int i = 0; i < rs.getNumProducts(); i++) {
                            Product p = rs.getProduct(i);
                            if (p.getSpeciesContext().hasSpeciesPattern()) {
                                text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
                                // text += "<b>" + p.getName() + "</b>";
                                text += p.getName();
                            } else {
                                text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
                                text += p.getName();
                            }
                            if (i < rs.getNumProducts() - 1) {
                                text += " + ";
                            }
                        }
                        text += "</html>";
                        setText(text);
                    }
                }
            }
            return this;
        }
    };
    DefaultScrollTableCellRenderer rbmReactionDefinitionCellRenderer = 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 VCellSortTableModel<?>) {
                Object selectedObject = null;
                if (table.getModel() == reactionTableModel) {
                    selectedObject = reactionTableModel.getValueAt(row);
                }
                if (selectedObject != null) {
                    if (selectedObject instanceof ReactionRule && value instanceof ModelProcessEquation) {
                        ReactionRule rr = (ReactionRule) selectedObject;
                        String text = "<html>";
                        for (int i = 0; i < rr.getReactantPatterns().size(); i++) {
                            ReactantPattern rp = rr.getReactantPattern(i);
                            if (rp.getStructure() != null && !rp.getSpeciesPattern().getMolecularTypePatterns().isEmpty()) {
                                text += "@" + rp.getStructure().getName() + ":";
                            }
                            text += RbmUtils.toBnglString(rp.getSpeciesPattern(), null, CompartmentMode.hide, 0);
                            // text += RbmTableRenderer.toHtml(rp.getSpeciesPattern(), isSelected);
                            if (i < rr.getReactantPatterns().size() - 1) {
                                text += "+";
                            }
                        }
                        if (rr.isReversible()) {
                            // &lt;-&gt;  <->
                            text += " &lt;-&gt; ";
                        } else {
                            text += " -&gt; ";
                        }
                        for (int i = 0; i < rr.getProductPatterns().size(); i++) {
                            ProductPattern pp = rr.getProductPattern(i);
                            if (pp.getStructure() != null && !pp.getSpeciesPattern().getMolecularTypePatterns().isEmpty()) {
                                text += "@" + pp.getStructure().getName() + ":";
                            }
                            text += RbmUtils.toBnglString(pp.getSpeciesPattern(), null, CompartmentMode.hide, 0);
                            if (i < rr.getProductPatterns().size() - 1) {
                                text += "+";
                            }
                        }
                        text += "</html>";
                        setText(text);
                    } else {
                        // plain reaction, check if reactants have species pattern
                        ReactionStep rs = (ReactionStep) selectedObject;
                        String text = "<html>";
                        for (int i = 0; i < rs.getNumReactants(); i++) {
                            Reactant p = rs.getReactant(i);
                            if (p.getSpeciesContext().hasSpeciesPattern()) {
                                text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
                                text += p.getName();
                            } else {
                                text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
                                text += p.getName();
                            }
                            if (i < rs.getNumReactants() - 1) {
                                text += " + ";
                            }
                        }
                        if (rs.isReversible()) {
                            // &lt;-&gt;  <->
                            text += " &lt;-&gt; ";
                        } else {
                            text += " -&gt; ";
                        }
                        for (int i = 0; i < rs.getNumProducts(); i++) {
                            Product p = rs.getProduct(i);
                            if (p.getSpeciesContext().hasSpeciesPattern()) {
                                text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
                                text += p.getName();
                            } else {
                                text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
                                text += p.getName();
                            }
                            if (i < rs.getNumProducts() - 1) {
                                text += " + ";
                            }
                        }
                        text += "</html>";
                        setText(text);
                    }
                }
            }
            return this;
        }
    };
    DefaultScrollTableCellRenderer rbmObservablePatternCellRenderer = 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 VCellSortTableModel<?>) {
                Object selectedObject = null;
                if (table.getModel() == observableTableModel) {
                    selectedObject = observableTableModel.getValueAt(row);
                }
                if (selectedObject != null) {
                    if (selectedObject instanceof RbmObservable && value instanceof String) {
                        RbmObservable o = (RbmObservable) selectedObject;
                        String text = "<html>";
                        for (int i = 0; i < o.getSpeciesPatternList().size(); i++) {
                            SpeciesPattern sp = o.getSpeciesPattern(i);
                            text += RbmTableRenderer.toHtml(sp, isSelected);
                            if (i < o.getSpeciesPatternList().size() - 1) {
                                text += " ";
                            }
                        }
                        text = RbmUtils.appendSequence(text, o);
                        text += "</html>";
                        setText(text);
                    }
                }
            }
            return this;
        }
    };
    DefaultScrollTableCellRenderer rbmSpeciesNameCellRenderer = 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 VCellSortTableModel<?>) {
                Object selectedObject = null;
                if (table.getModel() == speciesTableModel) {
                    selectedObject = speciesTableModel.getValueAt(row);
                }
                if (selectedObject != null) {
                    if (selectedObject instanceof SpeciesContext) {
                        SpeciesContext sc = (SpeciesContext) selectedObject;
                        String text = "<html>";
                        if (sc.hasSpeciesPattern()) {
                            text += "<b>" + sc.getName() + "</b>";
                        } else {
                            text += sc.getName();
                        }
                        text += "</html>";
                        setText(text);
                    }
                }
            }
            return this;
        }
    };
    // 
    // this renderer only paints the molecular type small shape in the MolecularType Table
    // 
    DefaultScrollTableCellRenderer rbmMolecularTypeShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {

        MolecularTypeSmallShape stls = 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() == molecularTypeTableModel) {
                    selectedObject = molecularTypeTableModel.getValueAt(row);
                }
                if (selectedObject != null) {
                    if (selectedObject instanceof MolecularType) {
                        MolecularType mt = (MolecularType) selectedObject;
                        Graphics cellContext = table.getGraphics();
                        if (mt != null) {
                            stls = new MolecularTypeSmallShape(4, 3, mt, null, cellContext, mt, null, issueManager);
                        }
                    }
                } else {
                    stls = null;
                }
            }
            return this;
        }

        @Override
        public void paintComponent(Graphics g) {
            super.paintComponent(g);
            if (stls != null) {
                stls.paintSelf(g);
            }
        }
    };
    // painting of species patterns small shapes inside the species context 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 SpeciesContext) {
                        SpeciesContext sc = (SpeciesContext) selectedObject;
                        // sp may be null for "plain" species contexts
                        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);
            }
        }
    };
    // ---------------------------------------------------------------------------------------------------------------------------------
    DefaultScrollTableCellRenderer rbmReactionShapeDepictionCellRenderer = 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() == reactionTableModel) {
                    selectedObject = reactionTableModel.getValueAt(row);
                }
                if (selectedObject != null) {
                    if (selectedObject instanceof ReactionRule) {
                        ReactionRule rr = (ReactionRule) selectedObject;
                        Graphics panelContext = table.getGraphics();
                        spssList.clear();
                        List<ReactantPattern> rpList = rr.getReactantPatterns();
                        int xPos = 4;
                        for (int i = 0; i < rpList.size(); i++) {
                            SpeciesPattern sp = rr.getReactantPattern(i).getSpeciesPattern();
                            spss = new SpeciesPatternSmallShape(xPos, 2, sp, null, panelContext, rr, isSelected, issueManager);
                            if (i < rpList.size() - 1) {
                                spss.addEndText("+");
                            } else {
                                if (rr.isReversible()) {
                                    spss.addEndText("<->");
                                    xPos += 7;
                                } else {
                                    spss.addEndText("->");
                                }
                            }
                            xPos += spss.getWidth() + 15;
                            spssList.add(spss);
                        }
                        List<ProductPattern> ppList = rr.getProductPatterns();
                        xPos += 7;
                        for (int i = 0; i < ppList.size(); i++) {
                            SpeciesPattern sp = rr.getProductPattern(i).getSpeciesPattern();
                            spss = new SpeciesPatternSmallShape(xPos, 2, sp, null, panelContext, rr, isSelected, issueManager);
                            if (i < ppList.size() - 1) {
                                spss.addEndText("+");
                            }
                            xPos += spss.getWidth() + 15;
                            spssList.add(spss);
                        }
                    } else {
                        ReactionStep rs = (ReactionStep) selectedObject;
                        Graphics panelContext = table.getGraphics();
                        spssList.clear();
                        int xPos = 4;
                        int extraSpace = 0;
                        for (int i = 0; i < rs.getNumReactants(); i++) {
                            SpeciesPattern sp = rs.getReactant(i).getSpeciesContext().getSpeciesPattern();
                            spss = new SpeciesPatternSmallShape(xPos, 2, sp, panelContext, rs, isSelected, issueManager);
                            if (i < rs.getNumReactants() - 1) {
                                spss.addEndText("+");
                            } else {
                                if (rs.isReversible()) {
                                    spss.addEndText("<->");
                                    extraSpace += 7;
                                } else {
                                    spss.addEndText("->");
                                }
                            }
                            int offset = sp == null ? 17 : 15;
                            offset += extraSpace;
                            int w = spss.getWidth();
                            xPos += w + offset;
                            spssList.add(spss);
                        }
                        xPos += 8;
                        for (int i = 0; i < rs.getNumProducts(); i++) {
                            SpeciesPattern sp = rs.getProduct(i).getSpeciesContext().getSpeciesPattern();
                            if (i == 0 && rs.getNumReactants() == 0) {
                                xPos += 14;
                            }
                            spss = new SpeciesPatternSmallShape(xPos, 2, sp, panelContext, rs, isSelected, issueManager);
                            if (i == 0 && rs.getNumReactants() == 0) {
                                spss.addStartText("->");
                            }
                            if (i < rs.getNumProducts() - 1) {
                                spss.addEndText("+");
                            }
                            int offset = sp == null ? 17 : 15;
                            int w = spss.getWidth();
                            xPos += w + offset;
                            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);
            }
        }
    };
    // -------------------------------------------------------------------------------------------------------------------------------
    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() == observableTableModel) {
                    selectedObject = observableTableModel.getValueAt(row);
                }
                if (selectedObject != null) {
                    if (selectedObject instanceof RbmObservable) {
                        RbmObservable observable = (RbmObservable) selectedObject;
                        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);
            }
        }
    };
    // TODO: here are the renderers associated with the columns
    reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_LINK).setCellRenderer(tableCellRenderer);
    reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_EQUATION).setCellRenderer(rbmReactionExpressionCellRenderer);
    reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_DEFINITION).setCellRenderer(rbmReactionDefinitionCellRenderer);
    speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_NAME).setCellRenderer(rbmSpeciesNameCellRenderer);
    speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_LINK).setCellRenderer(tableCellRenderer);
    molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.link.ordinal()).setCellRenderer(tableCellRenderer);
    observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.species_pattern.ordinal()).setCellRenderer(rbmObservablePatternCellRenderer);
    observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.structure.ordinal()).setCellRenderer(tableRenderer);
    // all "depictions" have their own renderer
    molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.depiction.ordinal()).setCellRenderer(rbmMolecularTypeShapeDepictionCellRenderer);
    molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.depiction.ordinal()).setMaxWidth(180);
    speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_DEPICTION).setCellRenderer(rbmSpeciesShapeDepictionCellRenderer);
    speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_DEFINITION).setCellRenderer(rbmTableRenderer);
    observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.depiction.ordinal()).setCellRenderer(rbmObservableShapeDepictionCellRenderer);
    reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_DEPICTION).setCellRenderer(rbmReactionShapeDepictionCellRenderer);
    reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_DEPICTION).setPreferredWidth(180);
    observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.type.ordinal()).setCellEditor(observableTableModel.getObservableTypeComboBoxEditor());
    observableTableModel.updateObservableTypeComboBox();
    reactionsTable.addMouseListener(eventHandler);
    reactionsTable.addKeyListener(eventHandler);
    speciesTable.addMouseListener(eventHandler);
    speciesTable.addKeyListener(eventHandler);
    molecularTypeTable.addMouseListener(eventHandler);
    molecularTypeTable.addKeyListener(eventHandler);
    observablesTable.addMouseListener(eventHandler);
    observablesTable.addKeyListener(eventHandler);
    structuresTable.addKeyListener(eventHandler);
}

Example 34 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class BioModelEditorModelPanel method duplicateButtonPressed.

private void duplicateButtonPressed() {
    computeCurrentSelectedTable();
    int row = currentSelectedTable.getSelectedRow();
    System.out.println("Duplicate Button Pressed for row " + row);
    if (currentSelectedTable == reactionsTable) {
        ModelProcess mp = reactionTableModel.getValueAt(row);
        if (!(mp instanceof ReactionRule)) {
            return;
        }
        ReactionRule oldRule = (ReactionRule) mp;
        if (bioModel.getModel().getNumStructures() == 1) {
            duplicateReactionRule(oldRule, oldRule.getStructure());
        } else if (bioModel.getModel().getNumStructures() > 1) {
            final JPopupMenu menu = new JPopupMenu("Choose compartment");
            for (int i = 0; i < bioModel.getModel().getNumStructures(); i++) {
                String ourType = oldRule.getStructure().getTypeName();
                Structure s = bioModel.getModel().getStructure(i);
                String theirType = s.getTypeName();
                if (!ourType.equals(theirType)) {
                    // offer to duplicate only within structures of the same type as the original,
                    continue;
                // otherwise units will be meaningless (surface vs volume)
                }
                String sName = s.getName();
                JMenuItem menuItem = new JMenuItem("In " + s.getTypeName() + " " + sName);
                menuItem.setIcon(new StructureToolShapeIcon(17));
                menu.add(menuItem);
                menuItem.addActionListener(new ActionListener() {

                    @Override
                    public void actionPerformed(ActionEvent e) {
                        newObject = duplicateReactionRule(oldRule, s);
                    // moves selection on the newly created object
                    // if (newObject != null) {
                    // for (int i = 0; i < currentSelectedTableModel.getRowCount(); i ++) {
                    // if (currentSelectedTableModel.getValueAt(i) == newObject) {
                    // currentSelectedTable.setRowSelectionInterval(i, i);
                    // break;
                    // }
                    // }
                    // }
                    }
                });
            }
            menu.show(duplicateButton, 0, duplicateButton.getHeight());
        }
    } else if (currentSelectedTable == speciesTable) {
        SpeciesContext sc = speciesTableModel.getValueAt(row);
        if (!sc.hasSpeciesPattern()) {
            return;
        }
        if (bioModel.getModel().getNumStructures() == 1) {
            duplicateSpecies(sc, sc.getStructure(), bioModel.getModel());
        } else if (bioModel.getModel().getNumStructures() > 1) {
            final JPopupMenu menu = new JPopupMenu("Choose compartment");
            for (int i = 0; i < bioModel.getModel().getNumStructures(); i++) {
                String ourType = sc.getStructure().getTypeName();
                Structure s = bioModel.getModel().getStructure(i);
                String theirType = s.getTypeName();
                if (!ourType.equals(theirType)) {
                    continue;
                }
                String sName = s.getName();
                JMenuItem menuItem = new JMenuItem("In " + s.getTypeName() + " " + sName);
                menuItem.setIcon(new StructureToolShapeIcon(17));
                menu.add(menuItem);
                menuItem.addActionListener(new ActionListener() {

                    @Override
                    public void actionPerformed(ActionEvent e) {
                        newObject = duplicateSpecies(sc, s, bioModel.getModel());
                    }
                });
            }
            menu.show(duplicateButton, 0, duplicateButton.getHeight());
        }
    } else if (currentSelectedTable == observablesTable) {
        RbmObservable o = observableTableModel.getValueAt(row);
        if (o.getSpeciesPatternList().isEmpty()) {
            return;
        }
        if (bioModel.getModel().getNumStructures() == 1) {
            duplicateObservable(o, o.getStructure(), bioModel.getModel());
        } else if (bioModel.getModel().getNumStructures() > 1) {
            final JPopupMenu menu = new JPopupMenu("Choose compartment");
            for (int i = 0; i < bioModel.getModel().getNumStructures(); i++) {
                Structure s = bioModel.getModel().getStructure(i);
                String sName = s.getName();
                JMenuItem menuItem = new JMenuItem("In " + s.getTypeName() + " " + sName);
                menuItem.setIcon(new StructureToolShapeIcon(17));
                menu.add(menuItem);
                menuItem.addActionListener(new ActionListener() {

                    @Override
                    public void actionPerformed(ActionEvent e) {
                        newObject = duplicateObservable(o, s, bioModel.getModel());
                    }
                });
            }
            menu.show(duplicateButton, 0, duplicateButton.getHeight());
        }
    }
}

Example 35 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class BioModelEditorModelPanel method refreshButtons.

private void refreshButtons() {
    int selectedIndex = tabbedPane.getSelectedIndex();
    newMemButton.setVisible(false);
    newButton2.setVisible(false);
    duplicateButton.setVisible(false);
    if (selectedIndex == ModelPanelTabID.reaction_diagram.ordinal() || // || selectedIndex == ModelPanelTabID.structure_diagram.ordinal()
    selectedIndex == ModelPanelTabID.species_table.ordinal() && (bioModel == null || bioModel.getModel().getNumStructures() < 1)) {
        newButton.setVisible(false);
    } else {
        Icon downArrow = null;
        if (bioModel.getModel().getNumStructures() > 1) {
            downArrow = new DownArrowIcon();
        }
        newButton.setVisible(true);
        if (selectedIndex == ModelPanelTabID.structure_table.ordinal()) {
            newButton.setText("New Compartment");
            newButton.setIcon(null);
            newMemButton.setVisible(true);
            newMemButton.setIcon(null);
        } else if (selectedIndex == ModelPanelTabID.reaction_table.ordinal()) {
            newButton.setText("New Reaction");
            if (bioModel.getModel().getRbmModelContainer().getMolecularTypeList().isEmpty()) {
                // show rule-related buttons only if rules are possible
                newButton2.setVisible(false);
                duplicateButton.setVisible(false);
            } else {
                newButton2.setVisible(true);
                duplicateButton.setVisible(true);
            }
            newButton2.setText("New Rule");
            newButton2.setIcon(downArrow);
            newButton2.setHorizontalTextPosition(SwingConstants.LEFT);
            duplicateButton.setIcon(downArrow);
            duplicateButton.setHorizontalTextPosition(SwingConstants.LEFT);
        } else if (selectedIndex == ModelPanelTabID.species_table.ordinal()) {
            newButton.setVisible(true);
            newButton.setIcon(downArrow);
            newButton.setHorizontalTextPosition(SwingConstants.LEFT);
            if (bioModel.getModel().getRbmModelContainer().getMolecularTypeList().isEmpty()) {
                duplicateButton.setVisible(false);
            } else {
                duplicateButton.setVisible(true);
            }
            duplicateButton.setIcon(downArrow);
            duplicateButton.setHorizontalTextPosition(SwingConstants.LEFT);
            newButton.setText("New Species");
        } else if (selectedIndex == ModelPanelTabID.observables_table.ordinal()) {
            newButton.setVisible(true);
            newButton.setIcon(downArrow);
            newButton.setText("New Observable");
            if (bioModel.getModel().getRbmModelContainer().getMolecularTypeList().isEmpty()) {
                duplicateButton.setVisible(false);
            } else {
                duplicateButton.setVisible(true);
            }
            duplicateButton.setIcon(downArrow);
            duplicateButton.setHorizontalTextPosition(SwingConstants.LEFT);
        } else if (selectedIndex == ModelPanelTabID.species_definitions_table.ordinal()) {
            newButton.setText("New Molecule");
        }
    }
    deleteButton.setEnabled(false);
    pathwayButton.setEnabled(false);
    duplicateButton.setEnabled(false);
    getShowPathwayMenuItem().setEnabled(false);
    Object[] selectedObjects = null;
    if (selectedIndex == ModelPanelTabID.reaction_diagram.ordinal()) {
        selectedObjects = reactionCartoonEditorPanel.getReactionCartoon().getSelectedObjects();
    // } else if (selectedIndex == ModelPanelTabID.structure_diagram.ordinal()) {
    // selectedObjects = cartoonEditorPanel.getStructureCartoon().getSelectedObjects();
    } else {
        computeCurrentSelectedTable();
        if (currentSelectedTableModel != null) {
            int[] rows = currentSelectedTable.getSelectedRows();
            ArrayList<Object> objectList = new ArrayList<Object>();
            for (int r = 0; r < rows.length; r++) {
                Object object = currentSelectedTableModel.getValueAt(rows[r]);
                if (object != null) {
                    objectList.add(object);
                }
            }
            selectedObjects = objectList.toArray(new Object[0]);
        }
    }
    if (selectedObjects != null) {
        deleteButton.setEnabled(selectedObjects.length > 0);
        if (selectedObjects.length == 1 && (selectedObjects[0] instanceof ReactionRule || selectedObjects[0] instanceof RbmObservable)) {
            duplicateButton.setEnabled(true);
        } else if (selectedObjects.length == 1 && selectedObjects[0] instanceof SpeciesContext) {
            SpeciesContext sp = (SpeciesContext) selectedObjects[0];
            if (sp.hasSpeciesPattern()) {
                duplicateButton.setEnabled(true);
            } else {
                duplicateButton.setEnabled(false);
            }
        }
        if (selectedObjects.length == 1 && selectedObjects[0] instanceof BioModelEntityObject) {
            pathwayButton.setEnabled(true);
            if (bioModel.getRelationshipModel().getRelationshipObjects((BioModelEntityObject) selectedObjects[0]).size() > 0) {
                getShowPathwayMenuItem().setEnabled(true);
            }
        }
    }
}