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

Example 71 with ReactionRule

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

the class ParticipantSignatureShapePanel method hasBondChanged.

public RuleAnalysisChanged hasBondChanged(String key, MolecularComponentPattern molecularComponentPattern) {
    ReactionRule reactionRule = reactionRuleMap.get(key);
    if (reactionRule == null) {
        return RuleAnalysisChanged.ANALYSISFAILED;
    }
    ModelRuleEntry modelRuleEntry = modelRuleEntryMap.get(key);
    RuleAnalysisReport report = reportMap.get(key);
    if (modelRuleEntry == null || report == null) {
        System.out.println("modelRuleEntry == null || report == null,  NOT GOOD!");
    // refreshRuleAnalysis();
    }
    if (!bRuleAnalysisFailed && report != null) {
        MolecularComponentEntry molecularComponentEntry = modelRuleEntry.findMolecularComponentEntry(molecularComponentPattern);
        if (report.hasBondChanged(molecularComponentEntry)) {
            return RuleAnalysisChanged.CHANGED;
        } else {
            return RuleAnalysisChanged.UNCHANGED;
        }
    } else {
        return RuleAnalysisChanged.ANALYSISFAILED;
    }
}

Example 72 with ReactionRule

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

the class ParticipantSignatureShapePanel method hasNoMatch.

public RuleAnalysisChanged hasNoMatch(String key, MolecularTypePattern molecularTypePattern) {
    ReactionRule reactionRule = reactionRuleMap.get(key);
    if (reactionRule == null) {
        return RuleAnalysisChanged.ANALYSISFAILED;
    }
    ModelRuleEntry modelRuleEntry = modelRuleEntryMap.get(key);
    RuleAnalysisReport report = reportMap.get(key);
    if (modelRuleEntry == null || report == null) {
        System.out.println("modelRuleEntry == null || report == null,  NOT GOOD!");
    // refreshRuleAnalysis();
    }
    if (!bRuleAnalysisFailed && report != null) {
        MolecularTypeEntry molecularTypeEntry = modelRuleEntry.findMolecularTypeEntry(molecularTypePattern);
        if (report.hasNoMatch(molecularTypeEntry)) {
            return RuleAnalysisChanged.CHANGED;
        } else {
            return RuleAnalysisChanged.UNCHANGED;
        }
    } else {
        return RuleAnalysisChanged.ANALYSISFAILED;
    }
}

Example 73 with ReactionRule

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

the class BioCartoonTool method pasteRules.

private static List<ReactionRule> pasteRules(ReactionSpeciesCopy rsCopy, Model modelTo, Structure structTo, Vector<Issue> issueVector, IssueContext issueContext, Map<Structure, String> structuresMap) throws ExpressionBindingException {
    List<ReactionRule> rulesTo = new ArrayList<>();
    if (rsCopy.getReactionRuleArr() == null) {
        return rulesTo;
    }
    for (ReactionRule rrFrom : rsCopy.getReactionRuleArr()) {
        ReactionRule rrTo = ReactionRule.clone(modelTo, rrFrom, structTo, structuresMap, rsCopy);
        rulesTo.add(rrTo);
    }
    return rulesTo;
}

Example 74 with ReactionRule

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

the class GeneratedReactionTableRow method deriveRule.

private void deriveRule(String inputString, Model tempModel) {
    if (owner != null && owner.getSimulationContext() != null) {
        List<MolecularType> mtList = owner.getSimulationContext().getModel().getRbmModelContainer().getMolecularTypeList();
        try {
            tempModel.getRbmModelContainer().setMolecularTypeList(mtList);
        } catch (PropertyVetoException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Unexpected exception setting " + MolecularType.typeName + " list: " + e1.getMessage(), e1);
        }
    } else {
        // This should not be possible
        throw new RuntimeException("Owner or SimulationContext are null.");
    }
    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;
    }
    String name = reactionObject.getRuleName();
    if (name.contains(GeneratedReactionTableModel.reverse)) {
        name = name.substring(GeneratedReactionTableModel.reverse.length());
    }
    if (name.endsWith(ReactionRule.DirectHalf)) {
        name = name.substring(0, name.indexOf(ReactionRule.DirectHalf));
    }
    if (name.endsWith(ReactionRule.InverseHalf)) {
        name = name.substring(0, name.indexOf(ReactionRule.InverseHalf));
    }
    // try to get the name of the original structure from the original rule and make here another structure with the same name
    String strStructure = null;
    Structure ruleStructure;
    SimulationContext sc = owner.getSimulationContext();
    ReactionRule rr = sc.getModel().getRbmModelContainer().getReactionRule(name);
    if (rr != null && rr.getStructure() != null) {
        strStructure = rr.getStructure().getName();
    }
    if (strStructure != null) {
        if (tempModel.getStructure(strStructure) == null) {
            try {
                tempModel.addFeature(strStructure);
            } catch (ModelException | PropertyVetoException e) {
                e.printStackTrace();
            }
        }
        ruleStructure = tempModel.getStructure(strStructure);
    } else {
        throw new RuntimeException("Failed to recover a Structure name from the Reaction Rule: " + name);
    }
    // making the fake rules just for display purpose, actually they are the flattened reactions resulted from bngl
    // the name is probably not unique, it's likely that many flattened reactions are derived from the same rule
    reactionRule = tempModel.getRbmModelContainer().createReactionRule(name, ruleStructure, bReversible);
    String regex = "[^!]\\+";
    String[] patterns = left.split(regex);
    for (String spString : patterns) {
        try {
            spString = spString.trim();
            // if compartments are present, we're making some fake compartments in the tempModel just for compartment name display purposes
            SpeciesPattern speciesPattern = (SpeciesPattern) RbmUtils.parseSpeciesPattern(spString, tempModel);
            strStructure = RbmUtils.parseCompartment(spString, tempModel);
            speciesPattern.resolveBonds();
            Structure structure;
            if (strStructure != null) {
                if (tempModel.getStructure(strStructure) == null) {
                    tempModel.addFeature(strStructure);
                }
                structure = tempModel.getStructure(strStructure);
            } else {
                // if nothing explicit for a participant, we use by default the structure of the rule
                structure = ruleStructure;
            }
            reactionRule.addReactant(new ReactantPattern(speciesPattern, structure));
        } catch (Throwable ex) {
            ex.printStackTrace();
            return;
        }
    }
    patterns = right.split(regex);
    for (String spString : patterns) {
        try {
            spString = spString.trim();
            SpeciesPattern speciesPattern = (SpeciesPattern) RbmUtils.parseSpeciesPattern(spString, tempModel);
            strStructure = RbmUtils.parseCompartment(spString, tempModel);
            speciesPattern.resolveBonds();
            Structure structure;
            if (strStructure != null) {
                if (tempModel.getStructure(strStructure) == null) {
                    tempModel.addFeature(strStructure);
                }
                structure = tempModel.getStructure(strStructure);
            } else {
                structure = ruleStructure;
            }
            reactionRule.addProduct(new ProductPattern(speciesPattern, structure));
        } catch (Throwable ex) {
            ex.printStackTrace();
            return;
        }
    }
}

Example 75 with ReactionRule

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

the class ViewGeneratedReactionsPanel method initialize.

private void initialize() {
    try {
        setName("ViewGeneratedReactionsPanel");
        setLayout(new GridBagLayout());
        shapePanel = new RulesShapePanel() {

            @Override
            public void paintComponent(Graphics g) {
                super.paintComponent(g);
                for (AbstractComponentShape stls : reactantPatternShapeList) {
                    stls.paintSelf(g);
                }
                for (AbstractComponentShape stls : productPatternShapeList) {
                    stls.paintSelf(g);
                }
            }
        };
        Border loweredEtchedBorder = BorderFactory.createEtchedBorder(EtchedBorder.LOWERED);
        Border loweredBevelBorder = BorderFactory.createLoweredBevelBorder();
        shapePanel.setLayout(new GridBagLayout());
        shapePanel.setBackground(Color.white);
        // don't show the brown contour even though it's not editable
        shapePanel.setEditable(true);
        shapePanel.setShowMoleculeColor(true);
        shapePanel.setShowNonTrivialOnly(true);
        JScrollPane scrollPane = new JScrollPane(shapePanel);
        scrollPane.setBorder(loweredBevelBorder);
        scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
        scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_NEVER);
        JPanel optionsPanel = new JPanel();
        optionsPanel.setLayout(new GridBagLayout());
        getZoomSmallerButton().setEnabled(true);
        getZoomLargerButton().setEnabled(false);
        GridBagConstraints gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 0;
        gbc.insets = new Insets(0, 0, 0, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanel.add(getZoomLargerButton(), gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 1;
        gbc.insets = new Insets(2, 0, 4, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanel.add(getZoomSmallerButton(), gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 2;
        gbc.weightx = 1;
        // fake cell used for filling all the vertical empty space
        gbc.weighty = 1;
        gbc.anchor = GridBagConstraints.WEST;
        gbc.insets = new Insets(4, 4, 4, 10);
        optionsPanel.add(new JLabel(""), gbc);
        JPanel containerOfScrollPanel = new JPanel();
        containerOfScrollPanel.setLayout(new BorderLayout());
        containerOfScrollPanel.add(optionsPanel, BorderLayout.WEST);
        containerOfScrollPanel.add(scrollPane, BorderLayout.CENTER);
        Dimension dim = new Dimension(500, 140);
        // dimension of shape panel
        containerOfScrollPanel.setPreferredSize(dim);
        containerOfScrollPanel.setMinimumSize(dim);
        containerOfScrollPanel.setMaximumSize(dim);
        // -----------------------------------------------------------------------------
        table = new EditorScrollTable();
        tableModel = new GeneratedReactionTableModel(table, owner);
        table.setModel(tableModel);
        table.getSelectionModel().addListSelectionListener(eventHandler);
        table.getModel().addTableModelListener(eventHandler);
        DefaultTableCellRenderer rightRenderer = new DefaultTableCellRenderer();
        rightRenderer.setHorizontalAlignment(JLabel.RIGHT);
        // table.getColumnModel().getColumn(GeneratedReactionTableModel.iColIndex).setCellRenderer(rightRenderer);	// right align first table column
        // table.getColumnModel().getColumn(GeneratedReactionTableModel.iColIndex).setMaxWidth(60);				// left column wide enough for 6-7 digits
        int gridy = 0;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.weightx = 1.0;
        gbc.weighty = 1.0;
        gbc.gridwidth = 8;
        gbc.fill = GridBagConstraints.BOTH;
        gbc.insets = new Insets(4, 4, 4, 4);
        // table.setPreferredScrollableViewportSize(new Dimension(400,200));
        add(table.getEnclosingScrollPane(), gbc);
        // add toolTipText for each table cell
        table.addMouseMotionListener(new MouseMotionAdapter() {

            public void mouseMoved(MouseEvent e) {
                Point p = e.getPoint();
                int row = table.rowAtPoint(p);
                int column = table.columnAtPoint(p);
                table.setToolTipText(String.valueOf(table.getValueAt(row, column)));
            }
        });
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.anchor = GridBagConstraints.LINE_END;
        gbc.insets = new Insets(4, 4, 4, 4);
        add(new JLabel("Search "), gbc);
        textFieldSearch = new JTextField(70);
        textFieldSearch.addActionListener(eventHandler);
        textFieldSearch.getDocument().addDocumentListener(eventHandler);
        textFieldSearch.putClientProperty("JTextField.variant", "search");
        gbc = new GridBagConstraints();
        gbc.weightx = 1.0;
        gbc.gridx = 1;
        gbc.gridy = gridy;
        gbc.gridwidth = 3;
        gbc.anchor = GridBagConstraints.LINE_START;
        gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
        gbc.insets = new Insets(4, 0, 4, 4);
        add(textFieldSearch, gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 4;
        gbc.gridy = gridy;
        gbc.fill = GridBagConstraints.HORIZONTAL;
        gbc.insets = new Insets(4, 4, 4, 10);
        add(totalReactionsLabel, gbc);
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        // gbc.weightx = 1.0;
        // gbc.weighty = 1.0;
        gbc.gridwidth = 8;
        gbc.anchor = GridBagConstraints.LINE_END;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(4, 4, 4, 4);
        add(containerOfScrollPanel, gbc);
        // rendering the small shapes of a fake rule in the Depiction column of this viewer table)
        // TODO: this renderer is almost identical with the one in BioModelEditorModelPanel (which paints the small shapes
        // of a rule in the Depiction column of the reaction table)
        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() == tableModel) {
                        selectedObject = tableModel.getValueAt(row);
                    }
                    if (selectedObject != null) {
                        if (selectedObject instanceof GeneratedReactionTableRow) {
                            ReactionRule rr = ((GeneratedReactionTableRow) selectedObject).getReactionRule();
                            Graphics panelContext = table.getGraphics();
                            BioModel bioModel = owner.getSimulationContext().getBioModel();
                            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() + 14;
                                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() + 14;
                                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);
                }
            }
        };
        table.getColumnModel().getColumn(GeneratedReactionTableModel.iColDepiction).setCellRenderer(rbmReactionShapeDepictionCellRenderer);
        table.getColumnModel().getColumn(GeneratedReactionTableModel.iColDepiction).setPreferredWidth(400);
        table.getColumnModel().getColumn(GeneratedReactionTableModel.iColDepiction).setMinWidth(400);
        table.getColumnModel().getColumn(GeneratedReactionTableModel.iColDefinition).setPreferredWidth(30);
        table.setAutoResizeMode(JTable.AUTO_RESIZE_LAST_COLUMN);
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}