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Example 11 with ProductPattern

use of cbit.vcell.model.ProductPattern 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);
    }
}
Also used : JPanel(javax.swing.JPanel) GridBagConstraints(java.awt.GridBagConstraints) Insets(java.awt.Insets) GridBagLayout(java.awt.GridBagLayout) SpeciesPatternSmallShape(cbit.vcell.graph.SpeciesPatternSmallShape) JTextField(javax.swing.JTextField) SpeciesPattern(org.vcell.model.rbm.SpeciesPattern) RulesShapePanel(cbit.vcell.graph.gui.RulesShapePanel) DefaultTableCellRenderer(javax.swing.table.DefaultTableCellRenderer) BorderLayout(java.awt.BorderLayout) VCellSortTableModel(cbit.vcell.client.desktop.biomodel.VCellSortTableModel) List(java.util.List) ArrayList(java.util.ArrayList) AbstractComponentShape(cbit.vcell.graph.AbstractComponentShape) ReactantPattern(cbit.vcell.model.ReactantPattern) JScrollPane(javax.swing.JScrollPane) MouseEvent(java.awt.event.MouseEvent) ReactionRule(cbit.vcell.model.ReactionRule) ProductPattern(cbit.vcell.model.ProductPattern) JLabel(javax.swing.JLabel) Dimension(java.awt.Dimension) Point(java.awt.Point) Point(java.awt.Point) Graphics(java.awt.Graphics) MouseMotionAdapter(java.awt.event.MouseMotionAdapter) JTable(javax.swing.JTable) BioModel(cbit.vcell.biomodel.BioModel) DefaultScrollTableCellRenderer(org.vcell.util.gui.DefaultScrollTableCellRenderer) EditorScrollTable(org.vcell.util.gui.EditorScrollTable) Border(javax.swing.border.Border) EtchedBorder(javax.swing.border.EtchedBorder)

Example 12 with ProductPattern

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

the class RulebasedMathMapping method addStrictMassActionParticleJumpProcess.

private void addStrictMassActionParticleJumpProcess(VariableHash varHash, GeometryClass geometryClass, SubDomain subDomain, ReactionRule reactionRule, String jpName, ArrayList<ParticleVariable> reactantParticles, ArrayList<ParticleVariable> productParticles, ArrayList<Action> forwardActions, ArrayList<Action> reverseActions) throws ExpressionException, ExpressionBindingException, PropertyVetoException, MathException, MappingException {
    String reactionRuleName = reactionRule.getName();
    RbmKineticLaw kinetics = reactionRule.getKineticLaw();
    RulebasedTransformation ruleBasedTransformation = ((RulebasedTransformation) getTransformation());
    if (kinetics.getRateLawType() != RbmKineticLaw.RateLawType.MassAction) {
        throw new RuntimeException("expecting mass action kinetics for reaction rule " + reactionRuleName);
    }
    // 
    // construct stochastic forward or reverse rate expression (separately).  Transform from
    // original expression of "concentrationRate" in terms of rateParameter and reactants/products in concentrations
    // to
    // new stochastic expression of "molecularRate" in terms of forwardRateParameter, reactants/products in molecules, structure sizes, and unit conversions.
    // 
    // (1)  concentrationRate = K * [s0] * [s1]    [uM.s-1]  or   [molecules.um-3.s-1]   or   [molecules.um-2.s-1]  (or other)
    // (2)  molecularRate = P * <s0> * <s1>        [molecules.s-1]
    // 
    // in this math description, we are using <s_i> [molecules], but original kinetics were in [s_i] [uM or molecules.um-2].
    // so through a change in variable to get things in terms of <s_i>.  <<<< Here P is the desired stochastic rate coefficient. >>>
    // 
    // (3)  let [s_i] = <s_i>/structsize(s_i)*unitConversionFactor(substanceunit([s_i])/substanceunit(<s_i>))
    // 
    // in addition to the change in variables, we need to transform the entire expression from concentration/time to molecules/time
    // 
    // (4)  let molecularRate = concentrationRate * structSize(reaction) * unitConversionFactor(substanceunit(molecularRate)/substanceunit(concentrationRate))
    // 
    // (5)  in general, concentationRate = K * PRODUCT([s_i])
    // 
    // change of variables into stochastic variables used in MathDescription, substituting (3) into (5)
    // 
    // (6)  concentrationRate = K * PRODUCT(<s_i>/structsize(s_i)*unitConversionFactor(substanceunit([s_i])/substanceunit(<s_i>)))
    // 
    // reordering to separate the sizes, the unit conversions and the <s_i>
    // 
    // (7)  concentrationRate = K * PRODUCT(<s_i>) * PRODUCT(1/structsize(s_i)) * unitConversionFactor(PRODUCT(substanceunit([s_i])/substanceunit(<s_i>)))
    // 
    // combining (4) and (7)
    // 
    // (8) molecularRate = K * PRODUCT(<s_i>) * PRODUCT(1/structsize(s_i)) * unitConversionFactor(PRODUCT(substanceunit([s_i])/substanceunit(<s_i>))) * structSize(reaction) * unitConversionFactor(substanceunit(molecularRate)/substanceunit(concentrationRate))
    // 
    // collecting terms of sizes and unit conversions
    // 
    // (9)  molecularRate = K * PRODUCT(<s_i>) * structSize(reaction) / PRODUCT(structsize(s_i)) * unitConversionFactor(substanceunit(molecularRate)/substanceunit(concentrationRate) * PRODUCT(substanceunit([s_i])/substanceunit(<s_i>)))
    // 
    // (10) molecularRate = K * PRODUCT(<s_i>) * sizeFactor * unitConversionFactor(substanceConversionUnit)
    // 
    // where
    // 
    // (11) sizeFactor = structSize(reaction) / PRODUCT(structsize(s_i))
    // (12) substanceConversionUnit = substanceunit(molecularRate)/substanceunit(concentrationRate) * PRODUCT(substanceunit([s_i])/substanceunit(<s_i>))
    // 
    // The ParticleJumpCondition wants a single new rate stochastic, P from equation (2).  Note that PRODUCT(<s_i>) will be captured separately the the reactantPatterns.
    // comparing (2) and (10) we have found P.
    // 
    // (13) P = K * sizeFactor * unitConversionFactor(substanceConversionUnit)
    // 
    // the framework also needs the proper unit for P
    // 
    // (14) Unit(P) = Unit(K) * Unit(sizeFactor) * substanceConversionUnit
    // 
    // 
    ModelUnitSystem modelUnitSystem = getSimulationContext().getModel().getUnitSystem();
    VCUnitDefinition stochasticSubstanceUnit = modelUnitSystem.getStochasticSubstanceUnit();
    VCUnitDefinition reactionRuleSubstanceUnit = modelUnitSystem.getSubstanceUnit(reactionRule.getStructure());
    int forwardRuleIndex = 0;
    // 
    // get forward rate parameter and make sure it is constant valued.
    // 
    Parameter forward_rateParameter = kinetics.getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate);
    Expression substitutedForwardRate = MathUtilities.substituteModelParameters(forward_rateParameter.getExpression(), reactionRule.getNameScope().getScopedSymbolTable());
    if (!substitutedForwardRate.flatten().isNumeric()) {
        throw new MappingException("forward rate constant for reaction rule " + reactionRule.getName() + " is not constant");
    }
    // 
    // create forward sizeExp and forward unitFactor
    // 
    VCUnitDefinition forward_substanceConversionUnit = stochasticSubstanceUnit.divideBy(reactionRuleSubstanceUnit);
    VCUnitDefinition forward_sizeFactorUnit = reactionRule.getStructure().getStructureSize().getUnitDefinition();
    Expression forward_sizeFactor = new Expression(reactionRule.getStructure().getStructureSize(), getNameScope());
    for (ReactantPattern reactantPattern : reactionRule.getReactantPatterns()) {
        Expression reactantSizeExp = new Expression(reactantPattern.getStructure().getStructureSize(), getNameScope());
        VCUnitDefinition reactantSizeUnit = reactantPattern.getStructure().getStructureSize().getUnitDefinition();
        VCUnitDefinition reactantSubstanceUnit = modelUnitSystem.getSubstanceUnit(reactantPattern.getStructure());
        forward_sizeFactor = Expression.div(forward_sizeFactor, reactantSizeExp);
        forward_sizeFactorUnit = forward_sizeFactorUnit.divideBy(reactantSizeUnit);
        forward_substanceConversionUnit = forward_substanceConversionUnit.multiplyBy(reactantSubstanceUnit).divideBy(stochasticSubstanceUnit);
    }
    // simplify sizeFactor (often has size/size/size)
    try {
        forward_sizeFactor = RationalExpUtils.getRationalExp(forward_sizeFactor).simplifyAsExpression();
        forward_sizeFactor.bindExpression(getSimulationContext().getModel());
    } catch (ParseException e) {
        e.printStackTrace();
    }
    Expression forward_rateExp = Expression.mult(new Expression(forward_rateParameter, getNameScope()), forward_sizeFactor, getUnitFactor(forward_substanceConversionUnit)).flatten();
    VCUnitDefinition forward_rateUnit = forward_rateParameter.getUnitDefinition().multiplyBy(forward_sizeFactorUnit).multiplyBy(forward_substanceConversionUnit);
    ProbabilityParameter forward_probParm = addProbabilityParameter(PARAMETER_PROBABILITYRATE_PREFIX + jpName, forward_rateExp, PARAMETER_ROLE_P, forward_rateUnit, reactionRule);
    // add probability to function or constant
    varHash.addVariable(newFunctionOrConstant(getMathSymbol(forward_probParm, geometryClass), getIdentifierSubstitutions(forward_rateExp, forward_rateUnit, geometryClass), geometryClass));
    // add forward ParticleJumpProcess
    String forward_name = reactionRuleName;
    Expression forward_rate = getIdentifierSubstitutions(new Expression(forward_probParm, getNameScope()), forward_probParm.getUnitDefinition(), geometryClass);
    JumpProcessRateDefinition forward_rateDefinition = new MacroscopicRateConstant(forward_rate);
    ReactionRuleAnalysisReport rrarBiomodelForward = ruleBasedTransformation.getRulesForwardMap().get(reactionRule);
    ProcessSymmetryFactor forwardSymmetryFactor = new ProcessSymmetryFactor(rrarBiomodelForward.getSymmetryFactor());
    ParticleJumpProcess forward_particleJumpProcess = new ParticleJumpProcess(forward_name, reactantParticles, forward_rateDefinition, forwardActions, forwardSymmetryFactor);
    subDomain.addParticleJumpProcess(forward_particleJumpProcess);
    // 
    for (ReactionRule rr : getSimulationContext().getModel().getRbmModelContainer().getReactionRuleList()) {
        if (rr == reactionRule) {
            break;
        }
        forwardRuleIndex++;
        if (rr.isReversible()) {
            forwardRuleIndex++;
        }
    }
    // 
    if (reactionRule.isReversible()) {
        Parameter reverse_rateParameter = kinetics.getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate);
        if (reverse_rateParameter == null || reverse_rateParameter.getExpression() == null) {
            throw new MappingException("reverse rate constant for reaction rule " + reactionRule.getName() + " is missing");
        }
        {
            Expression substitutedReverseRate = MathUtilities.substituteModelParameters(reverse_rateParameter.getExpression(), reactionRule.getNameScope().getScopedSymbolTable());
            if (!substitutedReverseRate.flatten().isNumeric()) {
                throw new MappingException("reverse rate constant for reaction rule " + reactionRule.getName() + " is not constant");
            }
        }
        // 
        // create reverse sizeExp and reverse unitFactor
        // 
        VCUnitDefinition reverse_substanceConversionUnit = stochasticSubstanceUnit.divideBy(reactionRuleSubstanceUnit);
        VCUnitDefinition reverse_sizeFactorUnit = reactionRule.getStructure().getStructureSize().getUnitDefinition();
        Expression reverse_sizeFactor = new Expression(reactionRule.getStructure().getStructureSize(), getNameScope());
        for (ProductPattern productPattern : reactionRule.getProductPatterns()) {
            Expression reactantSizeExp = new Expression(productPattern.getStructure().getStructureSize(), getNameScope());
            VCUnitDefinition reactantSizeUnit = productPattern.getStructure().getStructureSize().getUnitDefinition();
            VCUnitDefinition reactantSubstanceUnit = modelUnitSystem.getSubstanceUnit(productPattern.getStructure());
            reverse_sizeFactor = Expression.div(reverse_sizeFactor, reactantSizeExp);
            reverse_sizeFactorUnit = reverse_sizeFactorUnit.divideBy(reactantSizeUnit);
            reverse_substanceConversionUnit = reverse_substanceConversionUnit.multiplyBy(reactantSubstanceUnit).divideBy(stochasticSubstanceUnit);
        }
        // simplify sizeFactor (often has size/size/size)
        try {
            reverse_sizeFactor = RationalExpUtils.getRationalExp(reverse_sizeFactor).simplifyAsExpression();
            reverse_sizeFactor.bindExpression(getSimulationContext().getModel());
        } catch (ParseException e) {
            e.printStackTrace();
        }
        Expression reverse_rateExp = Expression.mult(new Expression(reverse_rateParameter, getNameScope()), reverse_sizeFactor, getUnitFactor(reverse_substanceConversionUnit)).flatten();
        VCUnitDefinition reverse_rateUnit = reverse_rateParameter.getUnitDefinition().multiplyBy(reverse_sizeFactorUnit).multiplyBy(reverse_substanceConversionUnit);
        // if the reaction has forward rate (Mass action,HMMs), or don't have either forward or reverse rate (some other rate laws--like general)
        // we process it as forward reaction
        // get jump process name
        ProbabilityParameter reverse_probParm = addProbabilityParameter(PARAMETER_PROBABILITYRATE_PREFIX + jpName + "_reverse", reverse_rateExp, PARAMETER_ROLE_P_reverse, reverse_rateUnit, reactionRule);
        // add probability to function or constant
        varHash.addVariable(newFunctionOrConstant(getMathSymbol(reverse_probParm, geometryClass), getIdentifierSubstitutions(reverse_rateExp, reverse_rateUnit, geometryClass), geometryClass));
        // add reverse ParticleJumpProcess
        Expression reverse_rate = getIdentifierSubstitutions(new Expression(reverse_probParm, getNameScope()), reverse_probParm.getUnitDefinition(), geometryClass);
        String reverse_name = reactionRuleName + "_reverse";
        JumpProcessRateDefinition reverse_rateDefinition = new MacroscopicRateConstant(reverse_rate);
        ReactionRuleAnalysisReport rrarBiomodelReverse = ruleBasedTransformation.getRulesReverseMap().get(reactionRule);
        ProcessSymmetryFactor reverseSymmetryFactor = new ProcessSymmetryFactor(rrarBiomodelReverse.getSymmetryFactor());
        ParticleJumpProcess reverse_particleJumpProcess = new ParticleJumpProcess(reverse_name, productParticles, reverse_rateDefinition, reverseActions, reverseSymmetryFactor);
        subDomain.addParticleJumpProcess(reverse_particleJumpProcess);
        // 
        // check reverse direction mapping and operations with RuleAnalysis.
        // 
        int reverseRuleIndex = forwardRuleIndex + 1;
        ReactionRuleAnalysisReport rrar = ruleBasedTransformation.getRulesReverseMap().get(reactionRule);
        jumpProcessMap.put(reverse_particleJumpProcess, rrar);
    }
}
Also used : ReactionRuleAnalysisReport(cbit.vcell.mapping.RulebasedTransformer.ReactionRuleAnalysisReport) JumpProcessRateDefinition(cbit.vcell.math.JumpProcessRateDefinition) ReactionRule(cbit.vcell.model.ReactionRule) ProductPattern(cbit.vcell.model.ProductPattern) ParticleJumpProcess(cbit.vcell.math.ParticleJumpProcess) RbmKineticLaw(cbit.vcell.model.RbmKineticLaw) ProcessSymmetryFactor(cbit.vcell.math.ParticleJumpProcess.ProcessSymmetryFactor) VCUnitDefinition(cbit.vcell.units.VCUnitDefinition) Expression(cbit.vcell.parser.Expression) Parameter(cbit.vcell.model.Parameter) UnresolvedParameter(cbit.vcell.mapping.ParameterContext.UnresolvedParameter) LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter) ModelParameter(cbit.vcell.model.Model.ModelParameter) MacroscopicRateConstant(cbit.vcell.math.MacroscopicRateConstant) ParseException(jscl.text.ParseException) RulebasedTransformation(cbit.vcell.mapping.RulebasedTransformer.RulebasedTransformation) ModelUnitSystem(cbit.vcell.model.ModelUnitSystem) ReactantPattern(cbit.vcell.model.ReactantPattern)

Example 13 with ProductPattern

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

the class SpeciesPatternLargeShape method getStructure.

public Structure getStructure() {
    Structure structure = null;
    if (owner instanceof ReactionRule) {
        ReactionRule rr = (ReactionRule) owner;
        ReactantPattern rp = rr.getReactantPattern(sp);
        ProductPattern pp = rr.getProductPattern(sp);
        if (rp != null) {
            structure = rp.getStructure();
        } else if (pp != null) {
            structure = pp.getStructure();
        } else {
            structure = ((ReactionRule) owner).getStructure();
        }
    } else if (owner instanceof SpeciesContext && ((SpeciesContext) owner).hasSpeciesPattern()) {
        structure = ((SpeciesContext) owner).getStructure();
    } else if (owner instanceof RbmObservable) {
        structure = ((RbmObservable) owner).getStructure();
    }
    return structure;
}
Also used : ReactionRule(cbit.vcell.model.ReactionRule) ProductPattern(cbit.vcell.model.ProductPattern) RbmObservable(cbit.vcell.model.RbmObservable) SpeciesContext(cbit.vcell.model.SpeciesContext) Structure(cbit.vcell.model.Structure) ReactantPattern(cbit.vcell.model.ReactantPattern)

Example 14 with ProductPattern

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

the class ReactionCartoonFull method refreshAll.

@Override
protected void refreshAll(boolean reallocateShapes) {
    try {
        if (getModel() == null || getStructureSuite() == null) {
            return;
        }
        System.out.println("ReactionCartoonFull, RefreshAll()");
        for (Structure structure : structureSuite.getStructures()) {
            Diagram diagram = getModel().getDiagram(structure);
            if (diagram != null) {
                // Maintain consistency between rule participant nodes, signatures and
                // species pattern when a molecule is being modified.
                rebindAll(diagram);
            }
        }
        // calculate species context weight (number of reactions for which it's a participant)
        Map<SpeciesContext, Integer> scWeightMap = new HashMap<>();
        // all the species contexts that are catalysts
        Set<SpeciesContext> scCatalystSet = new HashSet<>();
        // calculate species context length (number of species patterns it contains, 1 if has no species patterns)
        for (ReactionStep rs : getModel().getReactionSteps()) {
            ReactionParticipant[] rpList = rs.getReactionParticipants();
            for (int i = 0; i < rpList.length; i++) {
                ReactionParticipant rp = rpList[i];
                SpeciesContext sc = rp.getSpeciesContext();
                // int increment = rp.getStoichiometry();
                int increment = 1;
                if (rp instanceof Catalyst) {
                    scCatalystSet.add(sc);
                }
                if (scWeightMap.containsKey(sc)) {
                    int weight = scWeightMap.get(sc);
                    weight += increment;
                    scWeightMap.put(sc, weight);
                } else {
                    scWeightMap.put(sc, increment);
                }
            }
        }
        Set<Shape> unwantedShapes = new HashSet<Shape>();
        Set<RuleParticipantSignature> unwantedSignatures = new HashSet<RuleParticipantSignature>();
        unwantedShapes.addAll(getShapes());
        unwantedSignatures.addAll(ruleParticipantSignatures);
        ContainerContainerShape containerShape = (ContainerContainerShape) getShapeFromModelObject(getModel());
        List<ReactionContainerShape> reactionContainerShapeList = new ArrayList<ReactionContainerShape>();
        List<Structure> structureList = new ArrayList<Structure>(getStructureSuite().getStructures());
        // create all ReactionContainerShapes (one for each Structure)
        for (Structure structure : structureList) {
            if (structure instanceof Membrane) {
                Membrane membrane = (Membrane) structure;
                ReactionContainerShape membraneShape = (ReactionContainerShape) getShapeFromModelObject(membrane);
                if (membraneShape == null) {
                    membraneShape = new ReactionContainerShape(membrane, structureSuite, this);
                    addShape(membraneShape);
                    membrane.getMembraneVoltage().removePropertyChangeListener(this);
                    membrane.getMembraneVoltage().addPropertyChangeListener(this);
                } else {
                    membraneShape.setStructureSuite(structureSuite);
                }
                membrane.removePropertyChangeListener(this);
                membrane.addPropertyChangeListener(this);
                membraneShape.refreshLabel();
                unwantedShapes.remove(membraneShape);
                reactionContainerShapeList.add(membraneShape);
            } else if (structure instanceof Feature) {
                Feature feature = (Feature) structure;
                ReactionContainerShape featureShape = (ReactionContainerShape) getShapeFromModelObject(feature);
                if (featureShape == null) {
                    featureShape = new ReactionContainerShape(feature, structureSuite, this);
                    addShape(featureShape);
                } else {
                    featureShape.setStructureSuite(structureSuite);
                }
                feature.removePropertyChangeListener(this);
                feature.addPropertyChangeListener(this);
                featureShape.refreshLabel();
                unwantedShapes.remove(featureShape);
                reactionContainerShapeList.add(featureShape);
            }
        }
        if (containerShape == null) {
            containerShape = new ContainerContainerShape(this, getModel(), reactionContainerShapeList);
            addShape(containerShape);
        } else {
            containerShape.setReactionContainerShapeList(reactionContainerShapeList);
        }
        containerShape.refreshLabel();
        unwantedShapes.remove(containerShape);
        // add all species context shapes within the structures
        for (Structure structure : getStructureSuite().getStructures()) {
            ReactionContainerShape reactionContainerShape = (ReactionContainerShape) getShapeFromModelObject(structure);
            structure.removePropertyChangeListener(this);
            structure.addPropertyChangeListener(this);
            for (SpeciesContext structSpeciesContext : getModel().getSpeciesContexts(structure)) {
                SpeciesContextShape ss = (SpeciesContextShape) getShapeFromModelObject(structSpeciesContext);
                if (ss == null) {
                    ss = new SpeciesContextShape(structSpeciesContext, this);
                    ss.truncateLabelName(false);
                    structSpeciesContext.getSpecies().removePropertyChangeListener(this);
                    structSpeciesContext.getSpecies().addPropertyChangeListener(this);
                    reactionContainerShape.addChildShape(ss);
                    addShape(ss);
                    ss.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                }
                if (speciesSizeOption == SpeciesSizeOptions.weight) {
                    // this number sets the diameter of the shape
                    Integer weight = scWeightMap.get(structSpeciesContext);
                    if (weight != null) {
                        // we cap the diameter of the shape to something reasonable
                        weight = Math.min(weight, 16);
                    }
                    ss.setFilters(highlightCatalystOption ? scCatalystSet.contains(structSpeciesContext) : false, weight);
                } else if (speciesSizeOption == SpeciesSizeOptions.length) {
                    Integer length = null;
                    if (structSpeciesContext.getSpeciesPattern() != null && !structSpeciesContext.getSpeciesPattern().getMolecularTypePatterns().isEmpty()) {
                        length = structSpeciesContext.getSpeciesPattern().getMolecularTypePatterns().size() * 2;
                        length = Math.min(length, 16);
                    }
                    ss.setFilters(highlightCatalystOption ? scCatalystSet.contains(structSpeciesContext) : false, length);
                } else {
                    ss.setFilters(highlightCatalystOption ? scCatalystSet.contains(structSpeciesContext) : false, null);
                }
                structSpeciesContext.removePropertyChangeListener(this);
                structSpeciesContext.addPropertyChangeListener(this);
                ss.refreshLabel();
                unwantedShapes.remove(ss);
            }
        }
        // add all reactionSteps that are in this structure (ReactionContainerShape), and draw the lines
        getModel().removePropertyChangeListener(this);
        getModel().addPropertyChangeListener(this);
        // 
        for (ReactionRule rr : getModel().getRbmModelContainer().getReactionRuleList()) {
            rr.removePropertyChangeListener(this);
            rr.addPropertyChangeListener(this);
            Structure structure = rr.getStructure();
            if (getStructureSuite().areReactionsShownFor(structure)) {
                ReactionContainerShape reactionContainerShape = (ReactionContainerShape) getShapeFromModelObject(structure);
                ReactionRuleFullDiagramShape rrShape = (ReactionRuleFullDiagramShape) getShapeFromModelObject(rr);
                if (rrShape == null) {
                    rrShape = new ReactionRuleFullDiagramShape(rr, this);
                    addShape(rrShape);
                    rrShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                    reactionContainerShape.addChildShape(rrShape);
                    rrShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                }
                rrShape.refreshLabel();
                unwantedShapes.remove(rrShape);
                // 
                // add reaction participants as edges and SignatureShapes as needed
                // 
                List<ReactionRuleParticipant> participants = rr.getReactionRuleParticipants();
                List<RuleParticipantEdgeDiagramShape> ruleEdges = new ArrayList<>();
                for (ReactionRuleParticipant participant : participants) {
                    participant.getSpeciesPattern().removePropertyChangeListener(this);
                    participant.getSpeciesPattern().addPropertyChangeListener(this);
                    Structure speciesStructure = participant.getStructure();
                    Structure reactionStructure = rr.getStructure();
                    if (getStructureSuite().getStructures().contains(speciesStructure) && getStructureSuite().areReactionsShownFor(reactionStructure)) {
                        // 
                        // find existing RuleParticipantSignatureShape in cartoon
                        // 
                        RuleParticipantLongSignature ruleParticipantLongSignature = null;
                        for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                            if (signature instanceof RuleParticipantLongSignature && signature.getStructure() == participant.getStructure() && signature.compareByCriteria(participant.getSpeciesPattern(), GroupingCriteria.full)) {
                                ruleParticipantLongSignature = (RuleParticipantLongSignature) signature;
                                break;
                            }
                        }
                        for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                            if (signature instanceof RuleParticipantShortSignature && signature.getStructure() == participant.getStructure()) {
                                System.out.println("ReactionCartoonFull, refreshAll(), RuleParticipantShortSignature");
                            }
                        }
                        // 
                        // if didn't find signature in cartoons list of signatures, then create one (and create a shape for it).
                        // 
                        RuleParticipantSignatureFullDiagramShape signatureShape = null;
                        if (ruleParticipantLongSignature == null) {
                            ruleParticipantLongSignature = RuleParticipantLongSignature.fromReactionRuleParticipant(participant, this);
                            ruleParticipantSignatures.add(ruleParticipantLongSignature);
                            signatureShape = new RuleParticipantSignatureFullDiagramShape(ruleParticipantLongSignature, this);
                            addShape(signatureShape);
                            ReactionContainerShape participantContainerShape = (ReactionContainerShape) getShapeFromModelObject(participant.getStructure());
                            signatureShape.getSpaceManager().setRelPos(participantContainerShape.getRandomPosition());
                            participantContainerShape.addChildShape(signatureShape);
                            signatureShape.getSpaceManager().setRelPos(participantContainerShape.getRandomPosition());
                        } else {
                            signatureShape = (RuleParticipantSignatureFullDiagramShape) getShapeFromModelObject(ruleParticipantLongSignature);
                        }
                        unwantedShapes.remove(signatureShape);
                        unwantedSignatures.remove(ruleParticipantLongSignature);
                        signatureShape.refreshLabel();
                        signatureShape.setVisible(true);
                        // 
                        // add edge for ReactionRuleParticipant if not already present.
                        // 
                        RuleParticipantEdgeDiagramShape ruleParticipantShape = (RuleParticipantEdgeDiagramShape) getShapeFromModelObject(participant);
                        if (ruleParticipantShape == null || ruleParticipantShape.getRuleParticipantSignatureShape() != signatureShape) {
                            if (participant instanceof ReactantPattern && signatureShape.isVisible()) {
                                ruleParticipantShape = new ReactantPatternEdgeDiagramShape((ReactantPattern) participant, rrShape, signatureShape, this);
                            } else if (participant instanceof ProductPattern && signatureShape.isVisible()) {
                                ruleParticipantShape = new ProductPatternEdgeDiagramShape((ProductPattern) participant, rrShape, signatureShape, this);
                            } else {
                                throw new RuntimeException("unsupported ReactionRuleParticipant " + participant.getClass());
                            }
                            addShape(ruleParticipantShape);
                        }
                        if (!containerShape.getChildren().contains(ruleParticipantShape)) {
                            containerShape.addChildShape(ruleParticipantShape);
                        }
                        unwantedShapes.remove(ruleParticipantShape);
                        ruleParticipantShape.refreshLabel();
                        // all the edges for this rule
                        ruleEdges.add(ruleParticipantShape);
                    }
                }
                // a product edge (a closed loop) between the rule diagram shape and the signature diagram shape
                for (RuleParticipantEdgeDiagramShape ours : ruleEdges) {
                    // reset them all
                    ours.setSibling(false);
                }
                for (RuleParticipantEdgeDiagramShape ours : ruleEdges) {
                    for (RuleParticipantEdgeDiagramShape theirs : ruleEdges) {
                        if (ours == theirs) {
                            // don't compare with self
                            continue;
                        }
                        if (ours.getRuleParticipantSignatureShape() == theirs.getRuleParticipantSignatureShape()) {
                            ours.setSibling(true);
                            theirs.setSibling(true);
                        }
                    }
                }
            }
        }
        ruleParticipantSignatures.removeAll(unwantedSignatures);
        for (ReactionStep reactionStep : getModel().getReactionSteps()) {
            reactionStep.removePropertyChangeListener(this);
            reactionStep.addPropertyChangeListener(this);
            Structure structure = reactionStep.getStructure();
            if (getStructureSuite().areReactionsShownFor(structure)) {
                ReactionContainerShape reactionContainerShape = (ReactionContainerShape) getShapeFromModelObject(structure);
                if (reactionContainerShape == null) {
                    System.out.println("Reaction container shape is null for structure " + structure + " for reaction step " + reactionStep);
                }
                ReactionStepShape reactionStepShape = (ReactionStepShape) getShapeFromModelObject(reactionStep);
                if (reactionStepShape == null) {
                    if (reactionStep instanceof SimpleReaction) {
                        reactionStepShape = new SimpleReactionShape((SimpleReaction) reactionStep, this);
                    } else if (reactionStep instanceof FluxReaction) {
                        reactionStepShape = new FluxReactionShape((FluxReaction) reactionStep, this);
                    } else {
                        throw new RuntimeException("unknown type of ReactionStep '" + reactionStep.getClass().toString());
                    }
                    addShape(reactionStepShape);
                    reactionStepShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                    reactionContainerShape.addChildShape(reactionStepShape);
                    reactionStepShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                }
                reactionStepShape.refreshLabel();
                unwantedShapes.remove(reactionStepShape);
                // add reaction participants as edges
                for (ReactionParticipant participant : reactionStep.getReactionParticipants()) {
                    participant.removePropertyChangeListener(this);
                    participant.addPropertyChangeListener(this);
                    Structure speciesStructure = participant.getStructure();
                    Structure reactionStructure = reactionStep.getStructure();
                    if (getStructureSuite().getStructures().contains(speciesStructure) && getStructureSuite().areReactionsShownFor(reactionStructure)) {
                        SpeciesContext speciesContext = getModel().getSpeciesContext(participant.getSpecies(), speciesStructure);
                        // add speciesContextShapes that are not in this structure, but are referenced from the reactionParticipants
                        // these are only when reactionParticipants are from features that are outside of the membrane being displayed
                        SpeciesContextShape speciesContextShape = (SpeciesContextShape) getShapeFromModelObject(speciesContext);
                        if (speciesContextShape == null) {
                            speciesContextShape = new SpeciesContextShape(speciesContext, this);
                            speciesContextShape.truncateLabelName(false);
                            reactionContainerShape.addChildShape(speciesContextShape);
                            addShape(speciesContextShape);
                            speciesContextShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                        }
                        speciesContextShape.refreshLabel();
                        unwantedShapes.remove(speciesContextShape);
                        ReactionParticipantShape reactionParticipantShape = (ReactionParticipantShape) getShapeFromModelObject(participant);
                        if (reactionParticipantShape == null) {
                            if (participant instanceof Reactant) {
                                reactionParticipantShape = new ReactantShape((Reactant) participant, reactionStepShape, speciesContextShape, this);
                            } else if (participant instanceof Product) {
                                reactionParticipantShape = new ProductShape((Product) participant, reactionStepShape, speciesContextShape, this);
                            } else if (participant instanceof Catalyst) {
                                reactionParticipantShape = new CatalystShape((Catalyst) participant, reactionStepShape, speciesContextShape, this);
                            } else {
                                throw new RuntimeException("unsupported ReactionParticipant " + participant.getClass());
                            }
                            addShape(reactionParticipantShape);
                        }
                        if (!containerShape.getChildren().contains(reactionParticipantShape)) {
                            containerShape.addChildShape(reactionParticipantShape);
                        }
                        unwantedShapes.remove(reactionParticipantShape);
                        reactionParticipantShape.refreshLabel();
                    }
                }
            }
        }
        for (Shape unwantedShape : unwantedShapes) {
            removeShape(unwantedShape);
        }
        // update diagrams
        for (Structure structure : structureSuite.getStructures()) {
            Diagram diagram = getModel().getDiagram(structure);
            if (diagram != null) {
                applyDefaults(diagram);
            }
        }
        fireGraphChanged(new GraphEvent(this));
    } catch (Throwable e) {
        handleException(e);
    }
}
Also used : HashMap(java.util.HashMap) ArrayList(java.util.ArrayList) Product(cbit.vcell.model.Product) FluxReaction(cbit.vcell.model.FluxReaction) SpeciesContext(cbit.vcell.model.SpeciesContext) Feature(cbit.vcell.model.Feature) Reactant(cbit.vcell.model.Reactant) HashSet(java.util.HashSet) ReactionStep(cbit.vcell.model.ReactionStep) ReactionRuleParticipant(cbit.vcell.model.ReactionRuleParticipant) ReactionParticipant(cbit.vcell.model.ReactionParticipant) Catalyst(cbit.vcell.model.Catalyst) RuleParticipantSignature(cbit.vcell.model.RuleParticipantSignature) Shape(cbit.gui.graph.Shape) GraphEvent(cbit.gui.graph.GraphEvent) RuleParticipantShortSignature(cbit.vcell.model.RuleParticipantShortSignature) Membrane(cbit.vcell.model.Membrane) Structure(cbit.vcell.model.Structure) ReactantPattern(cbit.vcell.model.ReactantPattern) RuleParticipantLongSignature(cbit.vcell.model.RuleParticipantLongSignature) SimpleReaction(cbit.vcell.model.SimpleReaction) ReactionRule(cbit.vcell.model.ReactionRule) ProductPattern(cbit.vcell.model.ProductPattern) Point(java.awt.Point) Diagram(cbit.vcell.model.Diagram)

Example 15 with ProductPattern

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

the class ReactionCartoonMolecule method refreshAll.

@Override
protected void refreshAll(boolean reallocateShapes) {
    try {
        if (getModel() == null || getStructureSuite() == null) {
            return;
        }
        System.out.println("ReactionCartoonMolecule, RefreshAll()");
        for (Structure structure : structureSuite.getStructures()) {
            Diagram diagram = getModel().getDiagram(structure);
            if (diagram != null) {
                // Maintain consistency between rule participant nodes, signatures and
                // species pattern when a molecule is being modified.
                rebindAll(diagram);
            }
        }
        // calculate species context weight (number of reactions for which it's a participant)
        Map<SpeciesContext, Integer> scWeightMap = new HashMap<>();
        // all the species contexts that are catalysts
        Set<SpeciesContext> scCatalystSet = new HashSet<>();
        // calculate species context length (number of species patterns it contains, 1 if has no species patterns)
        for (ReactionStep rs : getModel().getReactionSteps()) {
            ReactionParticipant[] rpList = rs.getReactionParticipants();
            for (int i = 0; i < rpList.length; i++) {
                ReactionParticipant rp = rpList[i];
                SpeciesContext sc = rp.getSpeciesContext();
                int increment = 1;
                if (rp instanceof Catalyst) {
                    scCatalystSet.add(sc);
                }
                if (scWeightMap.containsKey(sc)) {
                    int weight = scWeightMap.get(sc);
                    weight += increment;
                    scWeightMap.put(sc, weight);
                } else {
                    scWeightMap.put(sc, increment);
                }
            }
        }
        Set<Shape> unwantedShapes = new HashSet<Shape>();
        Set<RuleParticipantSignature> unwantedSignatures = new HashSet<RuleParticipantSignature>();
        unwantedShapes.addAll(getShapes());
        unwantedSignatures.addAll(ruleParticipantSignatures);
        ContainerContainerShape containerShape = (ContainerContainerShape) getShapeFromModelObject(getModel());
        List<ReactionContainerShape> reactionContainerShapeList = new ArrayList<ReactionContainerShape>();
        List<Structure> structureList = new ArrayList<Structure>(getStructureSuite().getStructures());
        // create all ReactionContainerShapes (one for each Structure)
        for (Structure structure : structureList) {
            if (structure instanceof Membrane) {
                Membrane membrane = (Membrane) structure;
                ReactionContainerShape membraneShape = (ReactionContainerShape) getShapeFromModelObject(membrane);
                if (membraneShape == null) {
                    membraneShape = new ReactionContainerShape(membrane, structureSuite, this);
                    addShape(membraneShape);
                    membrane.getMembraneVoltage().removePropertyChangeListener(this);
                    membrane.getMembraneVoltage().addPropertyChangeListener(this);
                } else {
                    membraneShape.setStructureSuite(structureSuite);
                }
                membrane.removePropertyChangeListener(this);
                membrane.addPropertyChangeListener(this);
                membraneShape.refreshLabel();
                unwantedShapes.remove(membraneShape);
                reactionContainerShapeList.add(membraneShape);
            } else if (structure instanceof Feature) {
                Feature feature = (Feature) structure;
                ReactionContainerShape featureShape = (ReactionContainerShape) getShapeFromModelObject(feature);
                if (featureShape == null) {
                    featureShape = new ReactionContainerShape(feature, structureSuite, this);
                    addShape(featureShape);
                } else {
                    featureShape.setStructureSuite(structureSuite);
                }
                feature.removePropertyChangeListener(this);
                feature.addPropertyChangeListener(this);
                featureShape.refreshLabel();
                unwantedShapes.remove(featureShape);
                reactionContainerShapeList.add(featureShape);
            }
        }
        if (containerShape == null) {
            containerShape = new ContainerContainerShape(this, getModel(), reactionContainerShapeList);
            addShape(containerShape);
        } else {
            containerShape.setReactionContainerShapeList(reactionContainerShapeList);
        }
        containerShape.refreshLabel();
        unwantedShapes.remove(containerShape);
        // add all species context shapes within the structures
        for (Structure structure : getStructureSuite().getStructures()) {
            ReactionContainerShape reactionContainerShape = (ReactionContainerShape) getShapeFromModelObject(structure);
            structure.removePropertyChangeListener(this);
            structure.addPropertyChangeListener(this);
            for (SpeciesContext structSpeciesContext : getModel().getSpeciesContexts(structure)) {
                SpeciesContextShape ss = (SpeciesContextShape) getShapeFromModelObject(structSpeciesContext);
                if (ss == null) {
                    ss = new SpeciesContextShape(structSpeciesContext, this);
                    ss.truncateLabelName(false);
                    structSpeciesContext.getSpecies().removePropertyChangeListener(this);
                    structSpeciesContext.getSpecies().addPropertyChangeListener(this);
                    reactionContainerShape.addChildShape(ss);
                    addShape(ss);
                    ss.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                }
                if (speciesSizeOption == SpeciesSizeOptions.weight) {
                    // this number sets the diameter of the shape
                    Integer weight = scWeightMap.get(structSpeciesContext);
                    if (weight != null) {
                        // we cap the diameter of the shape to something reasonable
                        weight = Math.min(weight, 16);
                    }
                    ss.setFilters(highlightCatalystOption ? scCatalystSet.contains(structSpeciesContext) : false, weight);
                } else if (speciesSizeOption == SpeciesSizeOptions.length) {
                    Integer length = null;
                    if (structSpeciesContext.getSpeciesPattern() != null && !structSpeciesContext.getSpeciesPattern().getMolecularTypePatterns().isEmpty()) {
                        length = structSpeciesContext.getSpeciesPattern().getMolecularTypePatterns().size() * 2;
                        length = Math.min(length, 16);
                    }
                    ss.setFilters(highlightCatalystOption ? scCatalystSet.contains(structSpeciesContext) : false, length);
                } else {
                    ss.setFilters(highlightCatalystOption ? scCatalystSet.contains(structSpeciesContext) : false, null);
                }
                structSpeciesContext.removePropertyChangeListener(this);
                structSpeciesContext.addPropertyChangeListener(this);
                ss.refreshLabel();
                unwantedShapes.remove(ss);
            }
        }
        // add all reactionSteps that are in this structure (ReactionContainerShape), and draw the lines
        getModel().removePropertyChangeListener(this);
        getModel().addPropertyChangeListener(this);
        // 
        for (ReactionRule rr : getModel().getRbmModelContainer().getReactionRuleList()) {
            rr.removePropertyChangeListener(this);
            rr.addPropertyChangeListener(this);
            Structure structure = rr.getStructure();
            if (getStructureSuite().areReactionsShownFor(structure)) {
                ReactionContainerShape reactionContainerShape = (ReactionContainerShape) getShapeFromModelObject(structure);
                ReactionRuleFullDiagramShape rrShape = (ReactionRuleFullDiagramShape) getShapeFromModelObject(rr);
                if (rrShape == null) {
                    rrShape = new ReactionRuleFullDiagramShape(rr, this);
                    addShape(rrShape);
                    rrShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                    reactionContainerShape.addChildShape(rrShape);
                    rrShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                }
                rrShape.refreshLabel();
                unwantedShapes.remove(rrShape);
                // 
                // add reaction participants as edges and SignatureShapes as needed
                // 
                List<ReactionRuleParticipant> participants = rr.getReactionRuleParticipants();
                List<RuleParticipantEdgeDiagramShape> ruleEdges = new ArrayList<>();
                for (ReactionRuleParticipant participant : participants) {
                    participant.getSpeciesPattern().removePropertyChangeListener(this);
                    participant.getSpeciesPattern().addPropertyChangeListener(this);
                    Structure speciesStructure = participant.getStructure();
                    Structure reactionStructure = rr.getStructure();
                    if (getStructureSuite().getStructures().contains(speciesStructure) && getStructureSuite().areReactionsShownFor(reactionStructure)) {
                        // 
                        // find existing RuleParticipantSignatureShape in cartoon
                        // 
                        RuleParticipantShortSignature ruleParticipantShortSignature = null;
                        for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                            if (signature instanceof RuleParticipantLongSignature && signature.getStructure() == participant.getStructure()) {
                                System.out.println("ReactionCartoonMolecule, refreshAll(), RuleParticipantLongSignature");
                                break;
                            }
                        }
                        for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                            if (signature instanceof RuleParticipantShortSignature && signature.getStructure() == participant.getStructure() && signature.compareByCriteria(participant.getSpeciesPattern(), GroupingCriteria.molecule)) {
                                ruleParticipantShortSignature = (RuleParticipantShortSignature) signature;
                                break;
                            }
                        }
                        // 
                        // if didn't find signature in cartoons list of signatures, then create one (and create a shape for it).
                        // 
                        RuleParticipantSignatureShortDiagramShape signatureShape = null;
                        if (ruleParticipantShortSignature == null) {
                            ruleParticipantShortSignature = RuleParticipantShortSignature.fromReactionRuleParticipant(participant, this);
                            ruleParticipantSignatures.add(ruleParticipantShortSignature);
                            signatureShape = new RuleParticipantSignatureShortDiagramShape(ruleParticipantShortSignature, this);
                            addShape(signatureShape);
                            ReactionContainerShape participantContainerShape = (ReactionContainerShape) getShapeFromModelObject(participant.getStructure());
                            signatureShape.getSpaceManager().setRelPos(participantContainerShape.getRandomPosition());
                            participantContainerShape.addChildShape(signatureShape);
                            signatureShape.getSpaceManager().setRelPos(participantContainerShape.getRandomPosition());
                        } else {
                            signatureShape = (RuleParticipantSignatureShortDiagramShape) getShapeFromModelObject(ruleParticipantShortSignature);
                        }
                        unwantedShapes.remove(signatureShape);
                        unwantedSignatures.remove(ruleParticipantShortSignature);
                        signatureShape.refreshLabel();
                        signatureShape.setVisible(true);
                        // 
                        // add edge for ReactionRuleParticipant if not already present.
                        // 
                        RuleParticipantEdgeDiagramShape ruleParticipantShape = (RuleParticipantEdgeDiagramShape) getShapeFromModelObject(participant);
                        if (ruleParticipantShape == null || ruleParticipantShape.getRuleParticipantSignatureShape() != signatureShape) {
                            if (participant instanceof ReactantPattern && signatureShape.isVisible()) {
                                ruleParticipantShape = new ReactantPatternEdgeDiagramShape((ReactantPattern) participant, rrShape, signatureShape, this);
                            } else if (participant instanceof ProductPattern && signatureShape.isVisible()) {
                                ruleParticipantShape = new ProductPatternEdgeDiagramShape((ProductPattern) participant, rrShape, signatureShape, this);
                            } else {
                                throw new RuntimeException("unsupported ReactionRuleParticipant " + participant.getClass());
                            }
                            addShape(ruleParticipantShape);
                        }
                        if (!containerShape.getChildren().contains(ruleParticipantShape)) {
                            containerShape.addChildShape(ruleParticipantShape);
                        }
                        unwantedShapes.remove(ruleParticipantShape);
                        ruleParticipantShape.refreshLabel();
                        // all the edges for this rule
                        ruleEdges.add(ruleParticipantShape);
                    }
                }
                // a product edge (a closed loop) between the rule diagram shape and the signature diagram shape
                for (RuleParticipantEdgeDiagramShape ours : ruleEdges) {
                    // reset them all
                    ours.setSibling(false);
                }
                for (RuleParticipantEdgeDiagramShape ours : ruleEdges) {
                    for (RuleParticipantEdgeDiagramShape theirs : ruleEdges) {
                        if (ours == theirs) {
                            // don't compare with self
                            continue;
                        }
                        if (ours.getRuleParticipantSignatureShape() == theirs.getRuleParticipantSignatureShape()) {
                            ours.setSibling(true);
                            theirs.setSibling(true);
                        }
                    }
                }
            }
        }
        ruleParticipantSignatures.removeAll(unwantedSignatures);
        for (ReactionStep reactionStep : getModel().getReactionSteps()) {
            reactionStep.removePropertyChangeListener(this);
            reactionStep.addPropertyChangeListener(this);
            Structure structure = reactionStep.getStructure();
            if (getStructureSuite().areReactionsShownFor(structure)) {
                ReactionContainerShape reactionContainerShape = (ReactionContainerShape) getShapeFromModelObject(structure);
                if (reactionContainerShape == null) {
                    System.out.println("Reaction container shape is null for structure " + structure + " for reaction step " + reactionStep);
                }
                ReactionStepShape reactionStepShape = (ReactionStepShape) getShapeFromModelObject(reactionStep);
                if (reactionStepShape == null) {
                    if (reactionStep instanceof SimpleReaction) {
                        reactionStepShape = new SimpleReactionShape((SimpleReaction) reactionStep, this);
                    } else if (reactionStep instanceof FluxReaction) {
                        reactionStepShape = new FluxReactionShape((FluxReaction) reactionStep, this);
                    } else {
                        throw new RuntimeException("unknown type of ReactionStep '" + reactionStep.getClass().toString());
                    }
                    addShape(reactionStepShape);
                    reactionStepShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                    reactionContainerShape.addChildShape(reactionStepShape);
                    reactionStepShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                }
                reactionStepShape.refreshLabel();
                unwantedShapes.remove(reactionStepShape);
                // add reaction participants as edges
                for (ReactionParticipant participant : reactionStep.getReactionParticipants()) {
                    participant.removePropertyChangeListener(this);
                    participant.addPropertyChangeListener(this);
                    Structure speciesStructure = participant.getStructure();
                    Structure reactionStructure = reactionStep.getStructure();
                    if (getStructureSuite().getStructures().contains(speciesStructure) && getStructureSuite().areReactionsShownFor(reactionStructure)) {
                        SpeciesContext speciesContext = getModel().getSpeciesContext(participant.getSpecies(), speciesStructure);
                        // add speciesContextShapes that are not in this structure, but are referenced from the reactionParticipants
                        // these are only when reactionParticipants are from features that are outside of the membrane being displayed
                        SpeciesContextShape speciesContextShape = (SpeciesContextShape) getShapeFromModelObject(speciesContext);
                        if (speciesContextShape == null) {
                            speciesContextShape = new SpeciesContextShape(speciesContext, this);
                            speciesContextShape.truncateLabelName(false);
                            reactionContainerShape.addChildShape(speciesContextShape);
                            addShape(speciesContextShape);
                            speciesContextShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                        }
                        speciesContextShape.refreshLabel();
                        unwantedShapes.remove(speciesContextShape);
                        ReactionParticipantShape reactionParticipantShape = (ReactionParticipantShape) getShapeFromModelObject(participant);
                        if (reactionParticipantShape == null) {
                            if (participant instanceof Reactant) {
                                reactionParticipantShape = new ReactantShape((Reactant) participant, reactionStepShape, speciesContextShape, this);
                            } else if (participant instanceof Product) {
                                reactionParticipantShape = new ProductShape((Product) participant, reactionStepShape, speciesContextShape, this);
                            } else if (participant instanceof Catalyst) {
                                reactionParticipantShape = new CatalystShape((Catalyst) participant, reactionStepShape, speciesContextShape, this);
                            } else {
                                throw new RuntimeException("unsupported ReactionParticipant " + participant.getClass());
                            }
                            addShape(reactionParticipantShape);
                        }
                        if (!containerShape.getChildren().contains(reactionParticipantShape)) {
                            containerShape.addChildShape(reactionParticipantShape);
                        }
                        unwantedShapes.remove(reactionParticipantShape);
                        reactionParticipantShape.refreshLabel();
                    }
                }
            }
        }
        for (Shape unwantedShape : unwantedShapes) {
            removeShape(unwantedShape);
        }
        // update diagrams
        for (Structure structure : structureSuite.getStructures()) {
            Diagram diagram = getModel().getDiagram(structure);
            if (diagram != null) {
                applyDefaults(diagram);
            }
        }
        fireGraphChanged(new GraphEvent(this));
    } catch (Throwable e) {
        handleException(e);
    }
}
Also used : HashMap(java.util.HashMap) ArrayList(java.util.ArrayList) Product(cbit.vcell.model.Product) FluxReaction(cbit.vcell.model.FluxReaction) SpeciesContext(cbit.vcell.model.SpeciesContext) Feature(cbit.vcell.model.Feature) Reactant(cbit.vcell.model.Reactant) HashSet(java.util.HashSet) ReactionStep(cbit.vcell.model.ReactionStep) ReactionRuleParticipant(cbit.vcell.model.ReactionRuleParticipant) ReactionParticipant(cbit.vcell.model.ReactionParticipant) Catalyst(cbit.vcell.model.Catalyst) RuleParticipantSignature(cbit.vcell.model.RuleParticipantSignature) Shape(cbit.gui.graph.Shape) GraphEvent(cbit.gui.graph.GraphEvent) RuleParticipantShortSignature(cbit.vcell.model.RuleParticipantShortSignature) Membrane(cbit.vcell.model.Membrane) Structure(cbit.vcell.model.Structure) ReactantPattern(cbit.vcell.model.ReactantPattern) RuleParticipantLongSignature(cbit.vcell.model.RuleParticipantLongSignature) SimpleReaction(cbit.vcell.model.SimpleReaction) ReactionRule(cbit.vcell.model.ReactionRule) ProductPattern(cbit.vcell.model.ProductPattern) Point(java.awt.Point) Diagram(cbit.vcell.model.Diagram)

Aggregations

ProductPattern (cbit.vcell.model.ProductPattern)22 ReactantPattern (cbit.vcell.model.ReactantPattern)20 ReactionRule (cbit.vcell.model.ReactionRule)17 SpeciesPattern (org.vcell.model.rbm.SpeciesPattern)12 Structure (cbit.vcell.model.Structure)10 ArrayList (java.util.ArrayList)8 SpeciesContext (cbit.vcell.model.SpeciesContext)7 MolecularType (org.vcell.model.rbm.MolecularType)6 MolecularTypePattern (org.vcell.model.rbm.MolecularTypePattern)6 RbmObservable (cbit.vcell.model.RbmObservable)5 ReactionStep (cbit.vcell.model.ReactionStep)5 ModelException (cbit.vcell.model.ModelException)4 RbmKineticLaw (cbit.vcell.model.RbmKineticLaw)4 Point (java.awt.Point)4 List (java.util.List)4 SpeciesPatternSmallShape (cbit.vcell.graph.SpeciesPatternSmallShape)3 Model (cbit.vcell.model.Model)3 Product (cbit.vcell.model.Product)3 Reactant (cbit.vcell.model.Reactant)3 Graphics (java.awt.Graphics)3