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

Example 16 with ProductPattern

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

the class BioModelEditorModelPanel method makeReactionRule.

private Object makeReactionRule(Structure structure) {
    ReactionRule rr = bioModel.getModel().getRbmModelContainer().createReactionRule(structure);
    if (rr != null) {
        try {
            rr.setReversible(false);
            bioModel.getModel().getRbmModelContainer().addReactionRule(rr);
            SpeciesPattern sp = new SpeciesPattern();
            ReactantPattern rp = new ReactantPattern(sp, rr.getStructure());
            rr.addReactant(rp);
            sp = new SpeciesPattern();
            ProductPattern pp = new ProductPattern(sp, rr.getStructure());
            rr.addProduct(pp);
            return rr;
        } catch (Exception e) {
            e.printStackTrace();
            DialogUtils.showErrorDialog(this, e.getMessage(), e);
        }
    } else {
        throw new RuntimeException("Reaction Rule is null");
    }
    return null;
}

Example 17 with ProductPattern

use of cbit.vcell.model.ProductPattern 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 18 with ProductPattern

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

the class XmlReader method getRbmProductPatternsList.

private void getRbmProductPatternsList(Element e, ReactionRule r, Model newModel) {
    if (e != null) {
        List<Element> ppChildren = e.getChildren(XMLTags.RbmProductPatternTag, vcNamespace);
        for (Element ppElement : ppChildren) {
            Structure structure = null;
            String structureName = ppElement.getAttributeValue(XMLTags.StructureAttrTag);
            if (structureName == null || structureName.isEmpty()) {
                // the tag is missing
                throw new RuntimeException("XMLReader: structure missing for reaction rule pattern.");
            } else {
                structure = newModel.getStructure(structureName);
            }
            Element spe = ppElement.getChild(XMLTags.RbmSpeciesPatternTag, vcNamespace);
            SpeciesPattern s = getSpeciesPattern(spe, newModel);
            if (s != null) {
                r.addProduct(new ProductPattern(s, structure), false);
            }
        }
        // older models have the species pattern saved directly and using the structure or the rule
        List<Element> spChildren = GenericUtils.convert(e.getChildren(XMLTags.RbmSpeciesPatternTag, vcNamespace), Element.class);
        for (Element element : spChildren) {
            SpeciesPattern s = getSpeciesPattern(element, newModel);
            if (s != null) {
                r.addProduct(new ProductPattern(s, r.getStructure()), false);
            }
        }
    }
}

Example 19 with ProductPattern

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

the class RbmUtils method parseReactionRule.

public static ReactionRule parseReactionRule(String inputString, String name, Structure structure, BioModel bioModel) throws ParseException {
    try {
        String label = name;
        // int labelIndex = inputString.indexOf(':');		// TODO: the way we edit reaction rules now, we have no labels here
        // String label = "";
        // if(labelIndex>=0) {
        // label = inputString.substring(0, labelIndex);
        // inputString = inputString.substring(labelIndex+1);
        // }
        // if(label.isEmpty() || (reactionRuleNames.indexOf(label) != -1)) {
        // do {	// no label or label in use, we generate new label
        // label = generateReactionRuleName();
        // } while(reactionRuleNames.indexOf(label) != -1);
        // reactionRuleNames.add(label);
        // } else {
        // reactionRuleNames.add(label);
        // }
        int arrowIndex = inputString.indexOf("<->");
        boolean bReversible = true;
        if (arrowIndex < 0) {
            arrowIndex = inputString.indexOf("->");
            bReversible = false;
        }
        String left = inputString.substring(0, arrowIndex).trim();
        String right = inputString.substring(arrowIndex + (bReversible ? 3 : 2)).trim();
        if (left.length() == 0 && right.length() == 0) {
            return null;
        }
        // note that the constructor will try to honor the label from the editor but will generate a new one if already in use
        ReactionRule reactionRule = bioModel.getModel().getRbmModelContainer().createReactionRule(label, structure, bReversible);
        String regex = "[^!]\\+";
        String[] patterns = left.split(regex);
        for (String sp : patterns) {
            SpeciesPattern speciesPattern = parseSpeciesPattern(sp, bioModel.getModel());
            reactionRule.addReactant(new ReactantPattern(speciesPattern, reactionRule.getStructure()));
        }
        patterns = right.split(regex);
        for (String sp : patterns) {
            SpeciesPattern speciesPattern = parseSpeciesPattern(sp, bioModel.getModel());
            reactionRule.addProduct(new ProductPattern(speciesPattern, reactionRule.getStructure()));
        }
        return reactionRule;
    } catch (Throwable ex) {
        ex.printStackTrace();
        throw new ParseException(ex.getMessage());
    }
}

Example 20 with ProductPattern

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

the class ReactionRuleEditorPropertiesPanel method showPopupMenu.

private void showPopupMenu(MouseEvent e, PointLocationInShapeContext locationContext) {
    if (popupFromShapeMenu == null) {
        popupFromShapeMenu = new JPopupMenu();
    }
    if (popupFromShapeMenu.isShowing()) {
        return;
    }
    popupFromShapeMenu.removeAll();
    Point mousePoint = e.getPoint();
    final Object deepestShape = locationContext.getDeepestShape();
    final RbmObject selectedObject;
    if (deepestShape == null) {
        selectedObject = null;
        // when cursor is outside any species pattern we offer to add a new one
        System.out.println("outside");
    // popupFromShapeMenu.add(getAddSpeciesPatternFromShapeMenuItem());
    } else if (deepestShape instanceof ComponentStateLargeShape) {
        System.out.println("inside state");
        if (((ComponentStateLargeShape) deepestShape).isHighlighted()) {
            selectedObject = ((ComponentStateLargeShape) deepestShape).getComponentStatePattern();
        } else {
            return;
        }
    } else if (deepestShape instanceof MolecularComponentLargeShape) {
        System.out.println("inside component");
        if (((MolecularComponentLargeShape) deepestShape).isHighlighted()) {
            selectedObject = ((MolecularComponentLargeShape) deepestShape).getMolecularComponentPattern();
        } else {
            return;
        }
    } else if (deepestShape instanceof MolecularTypeLargeShape) {
        System.out.println("inside molecule");
        if (((MolecularTypeLargeShape) deepestShape).isHighlighted()) {
            selectedObject = ((MolecularTypeLargeShape) deepestShape).getMolecularTypePattern();
        } else {
            return;
        }
    } else if (deepestShape instanceof SpeciesPatternLargeShape) {
        System.out.println("inside species pattern");
        if (((SpeciesPatternLargeShape) deepestShape).isHighlighted()) {
            selectedObject = ((SpeciesPatternLargeShape) deepestShape).getSpeciesPattern();
        } else {
            return;
        }
    } else if (deepestShape instanceof ReactionRulePatternLargeShape) {
        System.out.println("inside reactant line or products line");
        if (((ReactionRulePatternLargeShape) deepestShape).isHighlighted()) {
            selectedObject = ((ReactionRulePatternLargeShape) deepestShape).getReactionRule();
        } else {
            return;
        }
    } else {
        selectedObject = null;
        System.out.println("inside something else?");
        return;
    }
    boolean bReactantsZone = false;
    int xExtent = SpeciesPatternLargeShape.calculateXExtent(shapePanel);
    Rectangle2D reactantRectangle = new Rectangle2D.Double(xOffsetInitial - xExtent, yOffsetReactantInitial - 3, 3000, 80 - 2 + GraphConstants.ReactionRuleDisplay_ReservedSpaceForNameOnYAxis);
    Rectangle2D productRectangle = new Rectangle2D.Double(xOffsetInitial - xExtent, yOffsetProductInitial - 3, 3000, 80 - 2 + GraphConstants.ReactionRuleDisplay_ReservedSpaceForNameOnYAxis);
    if (locationContext.isInside(reactantRectangle)) {
        // clicked inside the reactant rectangle (above yOffsetProductInitial)
        bReactantsZone = true;
    } else if (locationContext.isInside(productRectangle)) {
        // clicked inside the product rectangle (below yOffsetProductInitial)
        bReactantsZone = false;
    } else {
        return;
    }
    // -------------------------------- reactant zone --------------------------------------------------------
    if (bReactantsZone) {
        if (selectedObject == null) {
            return;
        } else if (selectedObject instanceof ReactionRule) {
            // add reactant pattern
            JMenuItem addMenuItem = new JMenuItem("Add Reactant");
            addMenuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    reactionRule.addReactant(new ReactantPattern(new SpeciesPattern(), reactionRule.getStructure()));
                    shapePanel.repaint();
                }
            });
            popupFromShapeMenu.add(addMenuItem);
        } else if (selectedObject instanceof SpeciesPattern) {
            // delete (pattern) / specify molecule
            final SpeciesPattern sp = (SpeciesPattern) selectedObject;
            JMenuItem deleteMenuItem = new JMenuItem("Delete");
            deleteMenuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    for (ReactantPattern rp : reactionRule.getReactantPatterns()) {
                        if (rp.getSpeciesPattern() == sp) {
                            reactionRule.removeReactant(rp);
                            Structure st = rp.getStructure();
                            if (reactionRule.getReactantPatterns().isEmpty()) {
                                reactionRule.addReactant(new ReactantPattern(new SpeciesPattern(), st));
                                shapePanel.repaint();
                            }
                        }
                    }
                }
            });
            popupFromShapeMenu.add(deleteMenuItem);
            JMenu addMenuItem = new JMenu(VCellErrorMessages.SpecifyMolecularTypes);
            popupFromShapeMenu.add(addMenuItem);
            addMenuItem.removeAll();
            for (final MolecularType mt : bioModel.getModel().getRbmModelContainer().getMolecularTypeList()) {
                JMenuItem menuItem = new JMenuItem(mt.getName());
                Graphics gc = shapePanel.getGraphics();
                Icon icon = new MolecularTypeSmallShape(1, 4, mt, null, gc, mt, null, issueManager);
                menuItem.setIcon(icon);
                addMenuItem.add(menuItem);
                menuItem.addActionListener(new ActionListener() {

                    public void actionPerformed(ActionEvent e) {
                        MolecularTypePattern molecularTypePattern = new MolecularTypePattern(mt);
                        for (MolecularComponentPattern mcp : molecularTypePattern.getComponentPatternList()) {
                            mcp.setBondType(BondType.Possible);
                        }
                        sp.addMolecularTypePattern(molecularTypePattern);
                        shapePanel.repaint();
                    }
                });
            }
            JMenu compartmentMenuItem = new JMenu("Specify structure");
            popupFromShapeMenu.add(compartmentMenuItem);
            if (sp.getMolecularTypePatterns().isEmpty()) {
                compartmentMenuItem.setEnabled(false);
            }
            compartmentMenuItem.removeAll();
            for (final Structure struct : bioModel.getModel().getStructures()) {
                JMenuItem menuItem = new JMenuItem(struct.getName());
                compartmentMenuItem.add(menuItem);
                for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
                    MolecularType mt = mtp.getMolecularType();
                    if (mt.isAnchorAll()) {
                        // no restrictions (no anchor exclusion) for this molecular type
                        continue;
                    }
                    if (!mt.getAnchors().contains(struct)) {
                        // sp can't be in this struct if any of its molecules is excluded (not anchored)
                        menuItem.setEnabled(false);
                        break;
                    }
                }
                menuItem.addActionListener(new ActionListener() {

                    public void actionPerformed(ActionEvent e) {
                        String nameStruct = e.getActionCommand();
                        Structure struct = bioModel.getModel().getStructure(nameStruct);
                        ReactantPattern rp = reactionRule.getReactantPattern(sp);
                        rp.setStructure(struct);
                        productTreeModel.populateTree();
                        shapePanel.repaint();
                    }
                });
            }
        } else if (selectedObject instanceof MolecularTypePattern) {
            // move left / right / delete molecule / reassign match
            MolecularTypePattern mtp = (MolecularTypePattern) selectedObject;
            int numMtp = locationContext.sps.getSpeciesPattern().getMolecularTypePatterns().size();
            String moveRightMenuText = "Move <b>" + "right" + "</b>";
            moveRightMenuText = "<html>" + moveRightMenuText + "</html>";
            JMenuItem moveRightMenuItem = new JMenuItem(moveRightMenuText);
            Icon icon = VCellIcons.moveRightIcon;
            moveRightMenuItem.setIcon(icon);
            moveRightMenuItem.setEnabled(numMtp < 2 ? false : true);
            moveRightMenuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    MolecularTypePattern from = (MolecularTypePattern) selectedObject;
                    SpeciesPattern sp = locationContext.sps.getSpeciesPattern();
                    sp.shiftRight(from);
                    reactantTreeModel.populateTree();
                    productTreeModel.populateTree();
                    shapePanel.repaint();
                }
            });
            popupFromShapeMenu.add(moveRightMenuItem);
            String moveLeftMenuText = "Move <b>" + "left" + "</b>";
            moveLeftMenuText = "<html>" + moveLeftMenuText + "</html>";
            JMenuItem moveLeftMenuItem = new JMenuItem(moveLeftMenuText);
            icon = VCellIcons.moveLeftIcon;
            moveLeftMenuItem.setIcon(icon);
            moveLeftMenuItem.setEnabled(numMtp < 2 ? false : true);
            moveLeftMenuItem.addActionListener(new ActionListener() {

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

                public void actionPerformed(ActionEvent e) {
                    MolecularTypePattern mtp = (MolecularTypePattern) selectedObject;
                    SpeciesPattern sp = locationContext.sps.getSpeciesPattern();
                    sp.removeMolecularTypePattern(mtp);
                    shapePanel.repaint();
                }
            });
            popupFromShapeMenu.add(deleteMenuItem);
            if (mtp.hasExplicitParticipantMatch()) {
                String newKey = mtp.getParticipantMatchLabel();
                List<String> keyCandidates = new ArrayList<String>();
                List<MolecularTypePattern> mtpReactantList = reactionRule.populateMaps(mtp.getMolecularType(), ReactionRuleParticipantType.Reactant);
                List<MolecularTypePattern> mtpProductList = reactionRule.populateMaps(mtp.getMolecularType(), ReactionRuleParticipantType.Product);
                for (MolecularTypePattern mtpCandidate : mtpReactantList) {
                    // we can look for indexes in any list, we should find the same
                    if (mtpCandidate.hasExplicitParticipantMatch() && !mtpCandidate.getParticipantMatchLabel().equals(newKey)) {
                        keyCandidates.add(mtpCandidate.getParticipantMatchLabel());
                    }
                }
                if (!keyCandidates.isEmpty()) {
                    JMenu reassignMatchMenuItem = new JMenu();
                    reassignMatchMenuItem.setText("Reassign match to");
                    for (int i = 0; i < keyCandidates.size(); i++) {
                        JMenuItem menuItem = new JMenuItem(keyCandidates.get(i));
                        reassignMatchMenuItem.add(menuItem);
                        menuItem.addActionListener(new ActionListener() {

                            public void actionPerformed(ActionEvent e) {
                                String oldKey = e.getActionCommand();
                                MolecularTypePattern orphanReactant = reactionRule.findMatch(oldKey, mtpReactantList);
                                mtp.setParticipantMatchLabel(oldKey);
                                orphanReactant.setParticipantMatchLabel(newKey);
                                // TODO: replace the populate tree with reactantPatternShapeList.update() and productPatternShapeList.update()
                                // when the tree will be gone
                                reactantTreeModel.populateTree();
                                productTreeModel.populateTree();
                                shapePanel.repaint();
                                SwingUtilities.invokeLater(new Runnable() {

                                    public void run() {
                                        reactantShape.flash(oldKey);
                                        productShape.flash(oldKey);
                                    }
                                });
                            }
                        });
                    }
                    popupFromShapeMenu.add(reassignMatchMenuItem);
                }
            }
        } else if (selectedObject instanceof MolecularComponentPattern) {
            // edit bond / edit state
            manageComponentPatternFromShape(selectedObject, locationContext, reactantTreeModel, ShowWhat.ShowBond, bReactantsZone);
        } else if (selectedObject instanceof ComponentStatePattern) {
            // edit state
            MolecularComponentPattern mcp = ((ComponentStateLargeShape) deepestShape).getMolecularComponentPattern();
            manageComponentPatternFromShape(mcp, locationContext, reactantTreeModel, ShowWhat.ShowState, bReactantsZone);
        }
    // ---------------------------------------- product zone ---------------------------------------------
    } else if (!bReactantsZone) {
        if (selectedObject == null) {
            return;
        } else if (selectedObject instanceof ReactionRule) {
            // add product pattern
            JMenuItem addMenuItem = new JMenuItem("Add Product");
            addMenuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    reactionRule.addProduct(new ProductPattern(new SpeciesPattern(), reactionRule.getStructure()));
                    shapePanel.repaint();
                }
            });
            popupFromShapeMenu.add(addMenuItem);
        } else if (selectedObject instanceof SpeciesPattern) {
            // delete (pattern) / specify molecule
            final SpeciesPattern sp = (SpeciesPattern) selectedObject;
            JMenuItem deleteMenuItem = new JMenuItem("Delete");
            deleteMenuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    for (ProductPattern pp : reactionRule.getProductPatterns()) {
                        if (pp.getSpeciesPattern() == sp) {
                            reactionRule.removeProduct(pp);
                            Structure st = pp.getStructure();
                            if (reactionRule.getProductPatterns().isEmpty()) {
                                reactionRule.addProduct(new ProductPattern(new SpeciesPattern(), st));
                                shapePanel.repaint();
                            }
                        }
                    }
                }
            });
            popupFromShapeMenu.add(deleteMenuItem);
            JMenu addMenuItem = new JMenu(VCellErrorMessages.SpecifyMolecularTypes);
            popupFromShapeMenu.add(addMenuItem);
            addMenuItem.removeAll();
            for (final MolecularType mt : bioModel.getModel().getRbmModelContainer().getMolecularTypeList()) {
                JMenuItem menuItem = new JMenuItem(mt.getName());
                Graphics gc = shapePanel.getGraphics();
                Icon icon = new MolecularTypeSmallShape(1, 4, mt, null, gc, mt, null, issueManager);
                menuItem.setIcon(icon);
                addMenuItem.add(menuItem);
                menuItem.addActionListener(new ActionListener() {

                    public void actionPerformed(ActionEvent e) {
                        MolecularTypePattern molecularTypePattern = new MolecularTypePattern(mt);
                        for (MolecularComponentPattern mcp : molecularTypePattern.getComponentPatternList()) {
                            mcp.setBondType(BondType.Possible);
                        }
                        sp.addMolecularTypePattern(molecularTypePattern);
                        shapePanel.repaint();
                    }
                });
            }
            // specify structure
            JMenu compartmentMenuItem = new JMenu("Specify structure");
            popupFromShapeMenu.add(compartmentMenuItem);
            compartmentMenuItem.removeAll();
            if (sp.getMolecularTypePatterns().isEmpty()) {
                compartmentMenuItem.setEnabled(false);
            }
            for (final Structure struct : bioModel.getModel().getStructures()) {
                JMenuItem menuItem = new JMenuItem(struct.getName());
                compartmentMenuItem.add(menuItem);
                for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
                    MolecularType mt = mtp.getMolecularType();
                    if (mt.isAnchorAll()) {
                        // no restrictions for this molecular type
                        continue;
                    }
                    if (!mt.getAnchors().contains(struct)) {
                        // sp can't be in this struct if any of its molecules is excluded (not anchored)
                        menuItem.setEnabled(false);
                        break;
                    }
                }
                menuItem.addActionListener(new ActionListener() {

                    public void actionPerformed(ActionEvent e) {
                        String nameStruct = e.getActionCommand();
                        Structure struct = bioModel.getModel().getStructure(nameStruct);
                        ProductPattern pp = reactionRule.getProductPattern(sp);
                        pp.setStructure(struct);
                        productTreeModel.populateTree();
                        shapePanel.repaint();
                    }
                });
            }
        } else if (selectedObject instanceof MolecularTypePattern) {
            // move left / right / delete molecule / reassign match
            MolecularTypePattern mtp = (MolecularTypePattern) selectedObject;
            int numMtp = locationContext.sps.getSpeciesPattern().getMolecularTypePatterns().size();
            String moveRightMenuText = "Move <b>" + "right" + "</b>";
            moveRightMenuText = "<html>" + moveRightMenuText + "</html>";
            JMenuItem moveRightMenuItem = new JMenuItem(moveRightMenuText);
            Icon icon = VCellIcons.moveRightIcon;
            moveRightMenuItem.setIcon(icon);
            moveRightMenuItem.setEnabled(numMtp < 2 ? false : true);
            moveRightMenuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    MolecularTypePattern from = (MolecularTypePattern) selectedObject;
                    SpeciesPattern sp = locationContext.sps.getSpeciesPattern();
                    sp.shiftRight(from);
                    reactantTreeModel.populateTree();
                    productTreeModel.populateTree();
                    shapePanel.repaint();
                }
            });
            popupFromShapeMenu.add(moveRightMenuItem);
            String moveLeftMenuText = "Move <b>" + "left" + "</b>";
            moveLeftMenuText = "<html>" + moveLeftMenuText + "</html>";
            JMenuItem moveLeftMenuItem = new JMenuItem(moveLeftMenuText);
            icon = VCellIcons.moveLeftIcon;
            moveLeftMenuItem.setIcon(icon);
            moveLeftMenuItem.setEnabled(numMtp < 2 ? false : true);
            moveLeftMenuItem.addActionListener(new ActionListener() {

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

                public void actionPerformed(ActionEvent e) {
                    MolecularTypePattern mtp = (MolecularTypePattern) selectedObject;
                    SpeciesPattern sp = locationContext.sps.getSpeciesPattern();
                    sp.removeMolecularTypePattern(mtp);
                    shapePanel.repaint();
                }
            });
            popupFromShapeMenu.add(deleteMenuItem);
            if (mtp.hasExplicitParticipantMatch()) {
                String newKey = mtp.getParticipantMatchLabel();
                List<String> keyCandidates = new ArrayList<String>();
                List<MolecularTypePattern> mtpReactantList = reactionRule.populateMaps(mtp.getMolecularType(), ReactionRuleParticipantType.Reactant);
                List<MolecularTypePattern> mtpProductList = reactionRule.populateMaps(mtp.getMolecularType(), ReactionRuleParticipantType.Product);
                for (MolecularTypePattern mtpCandidate : mtpReactantList) {
                    // we can look for indexes in any list, we should find the same
                    if (mtpCandidate.hasExplicitParticipantMatch() && !mtpCandidate.getParticipantMatchLabel().equals(newKey)) {
                        keyCandidates.add(mtpCandidate.getParticipantMatchLabel());
                    }
                }
                if (!keyCandidates.isEmpty()) {
                    JMenu reassignMatchMenuItem = new JMenu();
                    reassignMatchMenuItem.setText("Reassign match to");
                    for (int i = 0; i < keyCandidates.size(); i++) {
                        JMenuItem menuItem = new JMenuItem(keyCandidates.get(i));
                        reassignMatchMenuItem.add(menuItem);
                        menuItem.addActionListener(new ActionListener() {

                            public void actionPerformed(ActionEvent e) {
                                String oldKey = e.getActionCommand();
                                MolecularTypePattern orphanProduct = reactionRule.findMatch(oldKey, mtpProductList);
                                mtp.setParticipantMatchLabel(oldKey);
                                orphanProduct.setParticipantMatchLabel(newKey);
                                // TODO: replace the populate tree with reactantPatternShapeList.update() and productPatternShapeList.update()
                                // when the tree will be gone
                                reactantTreeModel.populateTree();
                                productTreeModel.populateTree();
                                shapePanel.repaint();
                                SwingUtilities.invokeLater(new Runnable() {

                                    public void run() {
                                        reactantShape.flash(oldKey);
                                        productShape.flash(oldKey);
                                    }
                                });
                            }
                        });
                    }
                    popupFromShapeMenu.add(reassignMatchMenuItem);
                }
            }
        } else if (selectedObject instanceof MolecularComponentPattern) {
            // edit bond / edit state
            manageComponentPatternFromShape(selectedObject, locationContext, productTreeModel, ShowWhat.ShowBond, bReactantsZone);
        } else if (selectedObject instanceof ComponentStatePattern) {
            // edit state
            MolecularComponentPattern mcp = ((ComponentStateLargeShape) deepestShape).getMolecularComponentPattern();
            manageComponentPatternFromShape(mcp, locationContext, productTreeModel, ShowWhat.ShowState, bReactantsZone);
        }
    }
    popupFromShapeMenu.show(e.getComponent(), mousePoint.x, mousePoint.y);
}