Examples with MolecularTypePattern org.vcell.model.rbm.MolecularTypePattern used on opensource projects

Example 41 with MolecularTypePattern

use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.

the class RbmTableRenderer method toHtml.

public static String toHtml(SpeciesPattern speciesPattern, boolean bSelected) {
    StringBuilder buffer = new StringBuilder("");
    List<MolecularTypePattern> molecularTypePatterns = speciesPattern.getMolecularTypePatterns();
    for (int i = 0; i < molecularTypePatterns.size(); ++i) {
        if (i > 0) {
            buffer.append(".");
        }
        MolecularTypePattern molecularTypePattern = molecularTypePatterns.get(i);
        buffer.append(molecularTypePattern.getMolecularType().getName());
        buffer.append("(");
        List<MolecularComponentPattern> componentPatterns = molecularTypePattern.getComponentPatternList();
        boolean bAddComma = false;
        for (MolecularComponentPattern mcp : componentPatterns) {
            if (mcp.isImplied()) {
                continue;
            }
            if (bAddComma) {
                buffer.append(",");
            }
            boolean bShowColor = false;
            if (mcp.getBondType() == BondType.Specified && !bSelected) {
                bShowColor = true;
                Color color = GraphConstants.bondHtmlColors[mcp.getBondId()];
                buffer.append("<font color=\"rgb(" + color.getRed() + "," + color.getGreen() + "," + color.getBlue() + ")\">");
            }
            buffer.append(mcp.getMolecularComponent().getName());
            if (mcp.getComponentStatePattern() != null) {
                buffer.append(RbmUtils.toBnglString(mcp.getComponentStatePattern().getComponentStateDefinition()));
            }
            switch(mcp.getBondType()) {
                case Exists:
                    buffer.append("!+");
                    break;
                case None:
                    break;
                case Possible:
                    buffer.append("!?");
                    break;
                case Specified:
                    buffer.append("!" + mcp.getBondId());
                    break;
            }
            if (bShowColor) {
                buffer.append("</font>");
            }
            bAddComma = true;
        }
        buffer.append(")");
    }
    return buffer.toString();
}

Example 42 with MolecularTypePattern

use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.

the class RbmTreeCellEditor method getTreeCellEditorComponent.

@Override
public Component getTreeCellEditorComponent(JTree tree, Object value, boolean isSelected, boolean expanded, boolean leaf, int row) {
    Component component = null;
    realEditor = defaultCellEditor;
    if (value instanceof BioModelNode) {
        BioModelNode node = (BioModelNode) value;
        Object userObject = node.getUserObject();
        String text = null;
        Icon icon = null;
        if (userObject instanceof MolecularType) {
            text = ((MolecularType) userObject).getName();
            icon = VCellIcons.rbmMolecularTypeIcon;
        } else if (userObject instanceof MolecularTypePattern) {
            text = ((MolecularTypePattern) userObject).getMolecularType().getName();
            icon = VCellIcons.rbmMolecularTypeIcon;
        } else if (userObject instanceof MolecularComponent) {
            BioModelNode parentNode = (BioModelNode) node.getParent();
            Object parentObject = parentNode == null ? null : parentNode.getUserObject();
            // TODO: look for the proper icon
            icon = VCellIcons.rbmComponentErrorIcon;
            if (parentObject instanceof MolecularType) {
                text = ((MolecularComponent) userObject).getName();
            } else if (parentObject instanceof MolecularTypePattern) {
                realEditor = getMolecularComponentPatternCellEditor();
                getMolecularComponentPatternCellEditor().molecularTypePattern = ((MolecularTypePattern) parentObject);
                // find SpeciesPattern
                while (true) {
                    parentNode = (BioModelNode) parentNode.getParent();
                    if (parentNode == null) {
                        break;
                    }
                    if (parentNode.getUserObject() instanceof RbmObservable) {
                        ((MolecularComponentPatternCellEditor) realEditor).owner = MolecularComponentPatternCellEditor.observable;
                        getMolecularComponentPatternCellEditor().speciesPattern = ((RbmObservable) parentNode.getUserObject()).getSpeciesPattern(0);
                        break;
                    }
                    if (parentNode.getUserObject() instanceof ReactionRule) {
                        ((MolecularComponentPatternCellEditor) realEditor).owner = MolecularComponentPatternCellEditor.reaction;
                        ReactionRulePropertiesTreeModel tm = (ReactionRulePropertiesTreeModel) tree.getModel();
                        switch(tm.getParticipantType()) {
                            case Reactant:
                                getMolecularComponentPatternCellEditor().speciesPattern = ((ReactionRule) parentNode.getUserObject()).getReactantPattern(0).getSpeciesPattern();
                                break;
                            case Product:
                                getMolecularComponentPatternCellEditor().speciesPattern = ((ReactionRule) parentNode.getUserObject()).getProductPattern(0).getSpeciesPattern();
                                break;
                        }
                    }
                    if (parentNode.getUserObject() instanceof SpeciesContext) {
                        ((MolecularComponentPatternCellEditor) realEditor).owner = MolecularComponentPatternCellEditor.species;
                        getMolecularComponentPatternCellEditor().speciesPattern = ((SpeciesContext) parentNode.getUserObject()).getSpeciesPattern();
                        break;
                    }
                }
            }
        } else if (userObject instanceof ComponentStateDefinition) {
            text = ((ComponentStateDefinition) userObject).getName();
            icon = VCellIcons.rbmComponentStateIcon;
        } else if (userObject instanceof RbmObservable) {
            text = ((RbmObservable) userObject).getName();
            icon = VCellIcons.rbmObservableIcon;
        }
        renderer.setOpenIcon(icon);
        renderer.setClosedIcon(icon);
        renderer.setLeafIcon(icon);
        component = super.getTreeCellEditorComponent(tree, value, isSelected, expanded, leaf, row);
        if (editingComponent instanceof JTextField) {
            JTextField textField = (JTextField) editingComponent;
            textField.setText(text);
        }
    }
    return component;
}

Example 43 with MolecularTypePattern

use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.

the class ReactionRuleEditorPropertiesPanel method manageComponentPatternFromShape.

public void manageComponentPatternFromShape(final Object selectedObject, PointLocationInShapeContext locationContext, final ReactionRulePropertiesTreeModel treeModel, ShowWhat showWhat, boolean bIsReactant) {
    popupFromShapeMenu.removeAll();
    final MolecularComponentPattern mcp = (MolecularComponentPattern) selectedObject;
    final MolecularComponent mc = mcp.getMolecularComponent();
    boolean anyStateProhibited = false;
    boolean explicitStateProhibited = false;
    boolean existBondProhibited = false;
    boolean noneBondProhibited = false;
    boolean possibleBondProhibited = false;
    boolean specifiedBondProhibited = false;
    if (!bIsReactant) {
        // product has restrictions for states and bonds, depending on reactant
        BondType reactantComponentBondType = reactionRule.getReactantComponentBondType(mcp);
        if (reactantComponentBondType != null && reactantComponentBondType == BondType.Exists) {
            // has external		+
            // existBondProhibited = true;
            noneBondProhibited = true;
            possibleBondProhibited = true;
            specifiedBondProhibited = true;
        } else if (reactantComponentBondType != null && reactantComponentBondType == BondType.None) {
            // is unbound		-
            existBondProhibited = true;
            // noneBondProhibited = true;
            possibleBondProhibited = true;
        // specifiedBondProhibited = true;
        } else if (reactantComponentBondType != null && reactantComponentBondType == BondType.Possible) {
            // may be bound		?
            existBondProhibited = true;
            noneBondProhibited = true;
            // possibleBondProhibited = true;
            specifiedBondProhibited = true;
        } else if (reactantComponentBondType != null && reactantComponentBondType == BondType.Specified) {
            existBondProhibited = true;
            // noneBondProhibited = true;
            possibleBondProhibited = true;
        // specifiedBondProhibited = true;
        }
        // if it's null nothing is prohibited
        ComponentStatePattern reactantComponentStatePattern = reactionRule.getReactantComponentState(mcp);
        if (reactantComponentStatePattern != null && reactantComponentStatePattern.isAny()) {
            explicitStateProhibited = true;
        } else if (reactantComponentStatePattern != null && !reactantComponentStatePattern.isAny()) {
            anyStateProhibited = true;
        }
    // if reactantComponentStatePattern is null nothing is prohibited, we may not have a matching reactant for this product
    }
    // ------------------------------------------------------------------- State
    if (showWhat == ShowWhat.ShowState && mc.getComponentStateDefinitions().size() != 0) {
        String prefix = "State:  ";
        String csdCurrentName = "";
        final Map<String, String> itemMap = new LinkedHashMap<String, String>();
        if (mcp.getComponentStatePattern() == null || mcp.getComponentStatePattern().isAny()) {
            csdCurrentName = "<html>" + prefix + "<b>" + ComponentStatePattern.strAny + "</b></html>";
        } else {
            csdCurrentName = "<html>" + prefix + ComponentStatePattern.strAny + "</html>";
        }
        itemMap.put(csdCurrentName, ComponentStatePattern.strAny);
        for (final ComponentStateDefinition csd : mc.getComponentStateDefinitions()) {
            csdCurrentName = "";
            if (mcp.getComponentStatePattern() != null && !mcp.getComponentStatePattern().isAny()) {
                ComponentStateDefinition csdCurrent = mcp.getComponentStatePattern().getComponentStateDefinition();
                csdCurrentName = csdCurrent.getName();
            }
            String name = csd.getName();
            if (name.equals(csdCurrentName)) {
                // currently selected menu item is shown in bold
                name = "<html>" + prefix + "<b>" + name + "</b></html>";
            } else {
                name = "<html>" + prefix + name + "</html>";
            }
            itemMap.put(name, csd.getName());
        }
        for (String key : itemMap.keySet()) {
            JMenuItem menuItem = new JMenuItem(key);
            if (!bIsReactant) {
                String name = itemMap.get(key);
                if (name.equals(ComponentStatePattern.strAny) && anyStateProhibited) {
                    menuItem.setEnabled(false);
                } else if (!name.equals(ComponentStatePattern.strAny) && explicitStateProhibited) {
                    menuItem.setEnabled(false);
                }
            }
            popupFromShapeMenu.add(menuItem);
            menuItem.setIcon(VCellIcons.rbmComponentStateIcon);
            menuItem.addActionListener(new ActionListener() {

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

            public void actionPerformed(ActionEvent e) {
                String name = e.getActionCommand();
                BondType btBefore = mcp.getBondType();
                if (name.equals(noneString)) {
                    if (btBefore == BondType.Specified) {
                        // specified -> not specified
                        // change the partner to possible
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.None);
                    mcp.setBond(null);
                } else if (name.equals(existsString)) {
                    if (btBefore == BondType.Specified) {
                        // specified -> exists
                        // change the partner to possible
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.Exists);
                    mcp.setBond(null);
                } else if (name.equals(possibleString)) {
                    if (btBefore == BondType.Specified) {
                        // specified -> possible
                        // change the partner to possible
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.Possible);
                    mcp.setBond(null);
                } else {
                    if (btBefore != BondType.Specified) {
                        // if we go from a non-specified to a specified we need to find the next available
                        // bond id, so that we can choose the color for displaying the bond
                        // a bad bond id, like -1, will crash badly when trying to choose the color
                        int bondId = sp.nextBondId();
                        mcp.setBondId(bondId);
                    } else {
                        // specified -> specified
                        // change the old partner to possible, continue using the bond id
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.Specified);
                    Bond b = itemMap.get(name);
                    mcp.setBond(b);
                    mcp.getBond().molecularComponentPattern.setBondId(mcp.getBondId());
                    sp.resolveBonds();
                }
                // when the tree will be gone
                if (bIsReactant) {
                    reflectBondToProduct(mcp);
                    productTreeModel.populateTree();
                }
                treeModel.populateTree();
                shapePanel.repaint();
            }
        });
        index++;
    }
    popupFromShapeMenu.add(editBondMenu);
}

Example 44 with MolecularTypePattern

use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.

the class ReactionRuleEditorPropertiesPanel method delete.

public void delete() {
    Object obj = rightClickSourceTree.getLastSelectedPathComponent();
    if (obj == null || !(obj instanceof BioModelNode)) {
        return;
    }
    BioModelNode selectedNode = (BioModelNode) obj;
    TreeNode parent = selectedNode.getParent();
    if (!(parent instanceof BioModelNode)) {
        return;
    }
    BioModelNode parentNode = (BioModelNode) parent;
    Object selectedUserObject = selectedNode.getUserObject();
    if (selectedUserObject instanceof ReactionRuleParticipantLocal) {
        ReactionRuleParticipantLocal reactionRuleParticipant = (ReactionRuleParticipantLocal) selectedUserObject;
        switch(reactionRuleParticipant.type) {
            case Reactant:
                reactionRule.removeReactant((ReactantPattern) (reactionRuleParticipant.speciesPattern));
                break;
            case Product:
                reactionRule.removeProduct((ProductPattern) (reactionRuleParticipant.speciesPattern));
                break;
        }
    } else if (selectedUserObject instanceof MolecularTypePattern) {
        MolecularTypePattern mtp = (MolecularTypePattern) selectedUserObject;
        Object parentObject = parentNode.getUserObject();
        if (parentObject instanceof ReactionRuleParticipantLocal) {
            ReactionRuleParticipantLocal rrp = (ReactionRuleParticipantLocal) parentObject;
            rrp.speciesPattern.getSpeciesPattern().removeMolecularTypePattern(mtp);
            if (rrp.type == ReactionRuleParticipantType.Reactant) {
                // we reset the "opposite" tree because it too might have changed
                productTreeModel.populateTree();
            } else if (rrp.type == ReactionRuleParticipantType.Product) {
                reactantTreeModel.populateTree();
            }
        }
    }
}

Example 45 with MolecularTypePattern

use of org.vcell.model.rbm.MolecularTypePattern 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);
}