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

Example 1 with ReactionRuleParticipant

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

the class RulebasedTransformer method parseBngOutput.

private void parseBngOutput(SimulationContext simContext, Set<ReactionRule> fromReactions, BNGOutput bngOutput) {
    Model model = simContext.getModel();
    Document bngNFSimXMLDocument = bngOutput.getNFSimXMLDocument();
    bngRootElement = bngNFSimXMLDocument.getRootElement();
    Element modelElement = bngRootElement.getChild("model", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
    Element listOfReactionRulesElement = modelElement.getChild("ListOfReactionRules", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
    List<Element> reactionRuleChildren = new ArrayList<Element>();
    reactionRuleChildren = listOfReactionRulesElement.getChildren("ReactionRule", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
    for (Element reactionRuleElement : reactionRuleChildren) {
        ReactionRuleAnalysisReport rar = new ReactionRuleAnalysisReport();
        boolean bForward = true;
        String rule_id_str = reactionRuleElement.getAttributeValue("id");
        ruleElementMap.put(rule_id_str, reactionRuleElement);
        String rule_name_str = reactionRuleElement.getAttributeValue("name");
        String symmetry_factor_str = reactionRuleElement.getAttributeValue("symmetry_factor");
        Double symmetry_factor_double = Double.parseDouble(symmetry_factor_str);
        ReactionRule rr = null;
        if (rule_name_str.startsWith("_reverse_")) {
            bForward = false;
            rule_name_str = rule_name_str.substring("_reverse_".length());
            rr = model.getRbmModelContainer().getReactionRule(rule_name_str);
            RbmKineticLaw rkl = rr.getKineticLaw();
            try {
                if (symmetry_factor_double != 1.0 && fromReactions.contains(rr)) {
                    Expression expression = rkl.getLocalParameterValue(RbmKineticLawParameterType.MassActionReverseRate);
                    expression = Expression.div(expression, new Expression(symmetry_factor_double));
                    rkl.setLocalParameterValue(RbmKineticLawParameterType.MassActionReverseRate, expression);
                }
            } catch (ExpressionException | PropertyVetoException exc) {
                exc.printStackTrace();
                throw new RuntimeException("Unexpected transform exception: " + exc.getMessage());
            }
            rulesReverseMap.put(rr, rar);
        } else {
            rr = model.getRbmModelContainer().getReactionRule(rule_name_str);
            RbmKineticLaw rkl = rr.getKineticLaw();
            try {
                if (symmetry_factor_double != 1.0 && fromReactions.contains(rr)) {
                    Expression expression = rkl.getLocalParameterValue(RbmKineticLawParameterType.MassActionForwardRate);
                    expression = Expression.div(expression, new Expression(symmetry_factor_double));
                    rkl.setLocalParameterValue(RbmKineticLawParameterType.MassActionForwardRate, expression);
                }
            } catch (ExpressionException | PropertyVetoException exc) {
                exc.printStackTrace();
                throw new RuntimeException("Unexpected transform exception: " + exc.getMessage());
            }
            rulesForwardMap.put(rr, rar);
        }
        rar.symmetryFactor = symmetry_factor_double;
        System.out.println("rule id=" + rule_id_str + ", name=" + rule_name_str + ", symmetry factor=" + symmetry_factor_str);
        keyMap.put(rule_id_str, rr);
        Element listOfReactantPatternsElement = reactionRuleElement.getChild("ListOfReactantPatterns", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        List<Element> reactantPatternChildren = new ArrayList<Element>();
        reactantPatternChildren = listOfReactantPatternsElement.getChildren("ReactantPattern", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (int i = 0; i < reactantPatternChildren.size(); i++) {
            Element reactantPatternElement = reactantPatternChildren.get(i);
            String pattern_id_str = reactantPatternElement.getAttributeValue("id");
            ReactionRuleParticipant p = bForward ? rr.getReactantPattern(i) : rr.getProductPattern(i);
            SpeciesPattern sp = p.getSpeciesPattern();
            System.out.println("  reactant id=" + pattern_id_str + ", name=" + sp.toString());
            keyMap.put(pattern_id_str, sp);
            // list of molecules
            extractMolecules(sp, model, reactantPatternElement);
            // list of bonds (not implemented)
            extractBonds(reactantPatternElement);
        }
        Element listOfProductPatternsElement = reactionRuleElement.getChild("ListOfProductPatterns", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        List<Element> productPatternChildren = new ArrayList<Element>();
        productPatternChildren = listOfProductPatternsElement.getChildren("ProductPattern", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (int i = 0; i < productPatternChildren.size(); i++) {
            Element productPatternElement = productPatternChildren.get(i);
            String pattern_id_str = productPatternElement.getAttributeValue("id");
            ReactionRuleParticipant p = bForward ? rr.getProductPattern(i) : rr.getReactantPattern(i);
            SpeciesPattern sp = p.getSpeciesPattern();
            System.out.println("  product  id=" + pattern_id_str + ", name=" + sp.toString());
            keyMap.put(pattern_id_str, sp);
            extractMolecules(sp, model, productPatternElement);
            extractBonds(productPatternElement);
        }
        // extract the Map for this rule
        Element listOfMapElement = reactionRuleElement.getChild("Map", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        List<Element> mapChildren = new ArrayList<Element>();
        mapChildren = listOfMapElement.getChildren("MapItem", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (Element mapElement : mapChildren) {
            String target_id_str = mapElement.getAttributeValue("targetID");
            String source_id_str = mapElement.getAttributeValue("sourceID");
            System.out.println("Map: target=" + target_id_str + " source=" + source_id_str);
            RbmObject target_object = keyMap.get(target_id_str);
            RbmObject source_object = keyMap.get(source_id_str);
            if (target_object == null)
                System.out.println("!!! Missing map target  " + target_id_str);
            if (source_object == null)
                System.out.println("!!! Missing map source " + source_id_str);
            if (source_object != null) {
                // target_object may be null
                System.out.println("      target=" + target_object + " source=" + source_object);
                Pair<RbmObject, RbmObject> mapEntry = new Pair<RbmObject, RbmObject>(target_object, source_object);
                rar.objmappingList.add(mapEntry);
            }
            Pair<String, String> idmapEntry = new Pair<String, String>(target_id_str, source_id_str);
            rar.idmappingList.add(idmapEntry);
        }
        // ListOfOperations
        Element listOfOperationsElement = reactionRuleElement.getChild("ListOfOperations", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        List<Element> operationsChildren = new ArrayList<Element>();
        operationsChildren = listOfOperationsElement.getChildren("StateChange", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        System.out.println("ListOfOperations");
        for (Element operationsElement : operationsChildren) {
            String finalState_str = operationsElement.getAttributeValue("finalState");
            String site_str = operationsElement.getAttributeValue("site");
            RbmObject site_object = keyMap.get(site_str);
            if (site_object == null)
                System.out.println("!!! Missing map object " + site_str);
            if (site_object != null) {
                System.out.println("   finalState=" + finalState_str + " site=" + site_object);
                StateChangeOperation sco = new StateChangeOperation(finalState_str, site_str, site_object);
                rar.operationsList.add(sco);
            }
        }
        operationsChildren = listOfOperationsElement.getChildren("AddBond", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (Element operationsElement : operationsChildren) {
            String site1_str = operationsElement.getAttributeValue("site1");
            String site2_str = operationsElement.getAttributeValue("site2");
            RbmObject site1_object = keyMap.get(site1_str);
            RbmObject site2_object = keyMap.get(site2_str);
            if (site1_object == null)
                System.out.println("!!! Missing map object " + site1_str);
            if (site2_object == null)
                System.out.println("!!! Missing map object " + site2_str);
            if (site1_object != null && site2_object != null) {
                System.out.println("   site1=" + site1_object + " site2=" + site2_object);
                AddBondOperation abo = new AddBondOperation(site1_str, site2_str, site1_object, site2_object);
                rar.operationsList.add(abo);
            }
        }
        operationsChildren = listOfOperationsElement.getChildren("DeleteBond", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (Element operationsElement : operationsChildren) {
            String site1_str = operationsElement.getAttributeValue("site1");
            String site2_str = operationsElement.getAttributeValue("site2");
            RbmObject site1_object = keyMap.get(site1_str);
            RbmObject site2_object = keyMap.get(site2_str);
            if (site1_object == null)
                System.out.println("!!! Missing map object " + site1_str);
            if (site2_object == null)
                System.out.println("!!! Missing map object " + site2_str);
            if (site1_object != null && site2_object != null) {
                System.out.println("   site1=" + site1_object + " site2=" + site2_object);
                DeleteBondOperation dbo = new DeleteBondOperation(site1_str, site2_str, site1_object, site2_object);
                rar.operationsList.add(dbo);
            }
        }
        operationsChildren = listOfOperationsElement.getChildren("Add", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (Element operationsElement : operationsChildren) {
            String id_str = operationsElement.getAttributeValue("id");
            RbmObject id_object = keyMap.get(id_str);
            if (id_object == null)
                System.out.println("!!! Missing map object " + id_str);
            if (id_object != null) {
                System.out.println("   id=" + id_str);
                AddOperation ao = new AddOperation(id_str, id_object);
                rar.operationsList.add(ao);
            }
        }
        operationsChildren = listOfOperationsElement.getChildren("Delete", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (Element operationsElement : operationsChildren) {
            String id_str = operationsElement.getAttributeValue("id");
            String delete_molecules_str = operationsElement.getAttributeValue("DeleteMolecules");
            RbmObject id_object = keyMap.get(id_str);
            if (id_object == null)
                System.out.println("!!! Missing map object " + id_str);
            int delete_molecules_int = 0;
            if (delete_molecules_str != null) {
                delete_molecules_int = Integer.parseInt(delete_molecules_str);
            }
            if (id_object != null) {
                System.out.println("   id=" + id_str + ", DeleteMolecules=" + delete_molecules_str);
                DeleteOperation dop = new DeleteOperation(id_str, id_object, delete_molecules_int);
                rar.operationsList.add(dop);
            }
        }
    }
    System.out.println("done parsing xml file");
}

Example 2 with ReactionRuleParticipant

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

the class ReactionRulePropertiesTreeModel method findObjectPath.

public TreePath findObjectPath(BioModelNode startNode, Object object) {
    if (startNode == null) {
        startNode = rootNode;
    }
    Object userObject = startNode.getUserObject();
    if (userObject == object || userObject instanceof ReactionRuleParticipant && ((ReactionRuleParticipant) userObject).getSpeciesPattern() == object) {
        return new TreePath(startNode.getPath());
    }
    for (int i = 0; i < startNode.getChildCount(); i++) {
        BioModelNode childNode = (BioModelNode) startNode.getChildAt(i);
        TreePath path = findObjectPath(childNode, object);
        if (path != null) {
            return path;
        }
    }
    return null;
}

Example 3 with ReactionRuleParticipant

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

Example 4 with ReactionRuleParticipant

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

Example 5 with ReactionRuleParticipant

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