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

Example 51 with ReactionRule

use of cbit.vcell.model.ReactionRule 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);
}

Example 52 with ReactionRule

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

the class ReactionRuleKineticsPropertiesPanel method setReactionRule.

public void setReactionRule(ReactionRule newValue) {
    if (reactionRule == newValue) {
        return;
    }
    ReactionRule oldValue = reactionRule;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(eventHandler);
    }
    reactionRule = newValue;
    if (newValue != null) {
        newValue.addPropertyChangeListener(eventHandler);
    }
    getReactionRulePropertiesTableModel().setReactionRule(reactionRule);
    updateInterface();
}

Example 53 with ReactionRule

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

the class ReactionRuleParticipantSignaturePropertiesPanel method findRulesForSignature.

private void findRulesForSignature() {
    reactionRuleMap.clear();
    if (signature == null) {
        return;
    }
    // ReactionCartoon rc = (ReactionCartoon) signature.getModelCartoon();
    // RuleParticipantSignature.Criteria crit = rc.getRuleParticipantGroupingCriteria();
    // shapePanel.setCriteria(crit);
    GroupingCriteria crit = signature.getGroupingCriteria();
    shapePanel.setCriteria(crit);
    for (ReactionRule rr : bioModel.getModel().getRbmModelContainer().getReactionRuleList()) {
        boolean found = false;
        for (ReactionRuleParticipant participant : rr.getReactionRuleParticipants()) {
            if (signature.getStructure() == participant.getStructure() && signature.compareByCriteria(participant.getSpeciesPattern(), crit)) {
                found = true;
                break;
            }
        }
        if (!found) {
            // this rule has no participant with this signature, go to next
            continue;
        }
        reactionRuleMap.put(rr.getName(), rr);
    }
}

Example 54 with ReactionRule

use of cbit.vcell.model.ReactionRule 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 55 with ReactionRule

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

the class ReactionRulePropertiesTableModel method propertyChange.

/**
 * This method gets called when a bound property is changed.
 * @param evt A PropertyChangeEvent object describing the event source
 *   and the property that has changed.
 */
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    if (evt.getSource() == this && evt.getPropertyName().equals("reactionRule")) {
        ReactionRule oldValue = (ReactionRule) evt.getOldValue();
        if (oldValue != null) {
            oldValue.removePropertyChangeListener(this);
            oldValue.getKineticLaw().removePropertyChangeListener(this);
            for (int i = 0; i < oldValue.getKineticLaw().getLocalParameters().length; i++) {
                oldValue.getKineticLaw().getLocalParameters()[i].removePropertyChangeListener(this);
            }
            for (int i = 0; i < oldValue.getKineticLaw().getProxyParameters().length; i++) {
                oldValue.getKineticLaw().getProxyParameters()[i].removePropertyChangeListener(this);
            }
        }
        ReactionRule newValue = (ReactionRule) evt.getNewValue();
        if (newValue != null) {
            newValue.addPropertyChangeListener(this);
            newValue.getKineticLaw().addPropertyChangeListener(this);
            for (int i = 0; i < newValue.getKineticLaw().getLocalParameters().length; i++) {
                newValue.getKineticLaw().getLocalParameters()[i].addPropertyChangeListener(this);
            }
            for (int i = 0; i < newValue.getKineticLaw().getProxyParameters().length; i++) {
                newValue.getKineticLaw().getProxyParameters()[i].addPropertyChangeListener(this);
            }
            autoCompleteSymbolFilter = reactionRule.getAutoCompleteSymbolFilter();
        }
        refreshData();
    }
    if (evt.getSource() == reactionRule && evt.getPropertyName().equals(ReactionRule.PROPERTY_NAME_KINETICLAW)) {
        RbmKineticLaw oldValue = (RbmKineticLaw) evt.getOldValue();
        if (oldValue != null) {
            oldValue.removePropertyChangeListener(this);
            for (int i = 0; i < oldValue.getLocalParameters().length; i++) {
                oldValue.getLocalParameters()[i].removePropertyChangeListener(this);
            }
            for (int i = 0; i < oldValue.getProxyParameters().length; i++) {
                oldValue.getProxyParameters()[i].removePropertyChangeListener(this);
            }
        }
        RbmKineticLaw newValue = (RbmKineticLaw) evt.getNewValue();
        if (newValue != null) {
            newValue.addPropertyChangeListener(this);
            for (int i = 0; i < newValue.getLocalParameters().length; i++) {
                newValue.getLocalParameters()[i].addPropertyChangeListener(this);
            }
            for (int i = 0; i < newValue.getProxyParameters().length; i++) {
                newValue.getProxyParameters()[i].addPropertyChangeListener(this);
            }
        }
        refreshData();
    }
    if (evt.getSource() instanceof RbmKineticLaw && (evt.getPropertyName().equals("localParameters") || evt.getPropertyName().equals("proxyParameters"))) {
        Parameter[] oldParams = (Parameter[]) evt.getOldValue();
        Parameter[] newParams = (Parameter[]) evt.getNewValue();
        for (int i = 0; oldParams != null && i < oldParams.length; i++) {
            oldParams[i].removePropertyChangeListener(this);
        }
        for (int i = 0; newParams != null && i < newParams.length; i++) {
            newParams[i].addPropertyChangeListener(this);
        }
        refreshData();
    }
    if (evt.getSource() instanceof LocalParameter || evt.getSource() instanceof LocalProxyParameter) {
        refreshData();
    }
    if (evt.getSource() instanceof Parameter) {
        fireTableRowsUpdated(0, getRowCount() - 1);
    }
}