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

Example 41 with ReactionParticipant

use of cbit.vcell.model.ReactionParticipant 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 42 with ReactionParticipant

use of cbit.vcell.model.ReactionParticipant 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 43 with ReactionParticipant

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

the class BioModelEditorModelPanel method addNewReaction.

private void addNewReaction() {
    if (reactionEditorPanel == null) {
        reactionEditorPanel = new ReactionEditorPanel();
    }
    Model model = getModel();
    reactionEditorPanel.setModel(model);
    while (true) {
        int confirm = DialogUtils.showComponentOKCancelDialog(this, reactionEditorPanel, "New Reaction");
        if (confirm == javax.swing.JOptionPane.OK_OPTION) {
            Structure reactionStructure = reactionEditorPanel.getStructure();
            String reactionName = reactionEditorPanel.getReactionName();
            String equationString = reactionEditorPanel.getEquationString();
            try {
                if (reactionName == null || reactionName.trim().length() == 0 || equationString == null || equationString.trim().length() == 0) {
                    throw new RuntimeException("Reaction name or equation cannot be empty.");
                }
                if (getModel().getReactionStep(reactionName) != null) {
                    throw new RuntimeException("Reaction '" + reactionName + "' already exists.");
                }
                ReactionStep simpleReaction = new SimpleReaction(model, reactionStructure, "dummy", true);
                ReactionParticipant[] rpArray = ModelProcessEquation.parseReaction(simpleReaction, getModel(), equationString);
                // StructureTopology structTopology = getModel().getStructureTopology();
                // for (ReactionParticipant reactionParticipant : rpArray) {
                // if (reactionParticipant.getStructure() == reactionStructure) {
                // continue;
                // }
                // if (reactionStructure instanceof Feature) {
                // throw new RuntimeException("Species '" + reactionParticipant.getSpeciesContext().getName() + "' must be in the same volume compartment as reaction.");
                // } else if (reactionStructure instanceof Membrane) {
                // if (structTopology.getInsideFeature((Membrane)reactionStructure) != reactionParticipant.getStructure()
                // && (structTopology.getOutsideFeature((Membrane)reactionStructure)) != reactionParticipant.getStructure()) {
                // throw new RuntimeException("Species '" + reactionParticipant.getSpeciesContext().getName() + "' must be adjacent to " +
                // "or within reaction's structure '" + reactionStructure.getName() + "'.");
                // }
                // }
                // }
                simpleReaction = getModel().createSimpleReaction(reactionStructure);
                for (ReactionParticipant rp : rpArray) {
                    SpeciesContext speciesContext = rp.getSpeciesContext();
                    if (bioModel.getModel().getSpeciesContext(speciesContext.getName()) == null) {
                        bioModel.getModel().addSpecies(speciesContext.getSpecies());
                        bioModel.getModel().addSpeciesContext(speciesContext);
                    }
                }
                simpleReaction.setReactionParticipants(rpArray);
                simpleReaction.setName(reactionName);
                setSelectedObjects(new Object[] { simpleReaction });
                break;
            } catch (Exception e) {
                e.printStackTrace();
                DialogUtils.showErrorDialog(this, e.getMessage());
            }
        } else {
            break;
        }
    }
}

Example 44 with ReactionParticipant

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

the class BNGOutputPanel method getCollapsedReactionSteps.

private ReactionStep[] getCollapsedReactionSteps(ReactionStep[] reactionSteps) {
    Vector<ReactionStep> collapsedRxnStepsVector = new Vector<ReactionStep>();
    Vector<ReactionStep> rxnStepsVector = new Vector<ReactionStep>();
    for (int i = 0; i < reactionSteps.length; i++) {
        rxnStepsVector.addElement(reactionSteps[i]);
    }
    for (int i = 0; i < rxnStepsVector.size(); i++) {
        ReactionStep fwdRStep = rxnStepsVector.elementAt(i);
        // Get the reactionParticipants and the corresponding reactants and products in an array
        ReactionParticipant[] rps = fwdRStep.getReactionParticipants();
        Vector<SpeciesContext> fwdReactantsVector = new Vector<SpeciesContext>();
        Vector<SpeciesContext> fwdProductsVector = new Vector<SpeciesContext>();
        for (int j = 0; j < rps.length; j++) {
            if (rps[j] instanceof Reactant) {
                fwdReactantsVector.addElement(rps[j].getSpeciesContext());
            } else if (rps[j] instanceof Product) {
                fwdProductsVector.addElement(rps[j].getSpeciesContext());
            }
        }
        SpeciesContext[] fwdReactants = (SpeciesContext[]) BeanUtils.getArray(fwdReactantsVector, SpeciesContext.class);
        SpeciesContext[] fwdProducts = (SpeciesContext[]) BeanUtils.getArray(fwdProductsVector, SpeciesContext.class);
        boolean bReverseReactionFound = false;
        // Loop through all the reactions to find the corresponding reverse reaction
        for (int ii = 0; ii < reactionSteps.length; ii++) {
            ReactionStep revRStep = reactionSteps[ii];
            // Get the reactionParticipants and the corresponding reactants and products in an array
            ReactionParticipant[] revRps = revRStep.getReactionParticipants();
            Vector<SpeciesContext> revReactantsVector = new Vector<SpeciesContext>();
            Vector<SpeciesContext> revProductsVector = new Vector<SpeciesContext>();
            for (int j = 0; j < revRps.length; j++) {
                if (revRps[j] instanceof Reactant) {
                    revReactantsVector.addElement(revRps[j].getSpeciesContext());
                } else if (revRps[j] instanceof Product) {
                    revProductsVector.addElement(revRps[j].getSpeciesContext());
                }
            }
            SpeciesContext[] revReactants = (SpeciesContext[]) BeanUtils.getArray(revReactantsVector, SpeciesContext.class);
            SpeciesContext[] revProducts = (SpeciesContext[]) BeanUtils.getArray(revProductsVector, SpeciesContext.class);
            // Check if reactants of reaction in outer 'for' loop match products in inner 'for' loop and vice versa.
            if (BeanUtils.arrayEquals(fwdReactants, revProducts) && BeanUtils.arrayEquals(fwdProducts, revReactants)) {
                // Set the reverse kinetic rate expression for the reaction in outer loop with the forward rate from reactionStep in inner loop
                // inner 'for' loop
                MassActionKinetics revMAKinetics = (MassActionKinetics) revRStep.getKinetics();
                // outer 'for' loop
                MassActionKinetics fwdMAKinetics = (MassActionKinetics) fwdRStep.getKinetics();
                try {
                    fwdMAKinetics.setParameterValue(fwdMAKinetics.getReverseRateParameter(), revMAKinetics.getForwardRateParameter().getExpression());
                    Kinetics.KineticsParameter param = revMAKinetics.getKineticsParameter(revMAKinetics.getForwardRateParameter().getExpression().infix());
                    fwdMAKinetics.setParameterValue(param, param.getExpression());
                } catch (Exception e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException(e.getMessage());
                }
                // Add this to the collapsedRxnStepsVector
                collapsedRxnStepsVector.addElement(fwdRStep);
                rxnStepsVector.removeElement(revRStep);
                bReverseReactionFound = true;
                break;
            }
        }
        // Add it as is to the 'collapsedRxnStepsVector'
        if (!bReverseReactionFound) {
            collapsedRxnStepsVector.addElement(fwdRStep);
        }
    }
    // Convert the vector into an array of reactionSteps and return
    ReactionStep[] collapsedRxnSteps = (ReactionStep[]) BeanUtils.getArray(collapsedRxnStepsVector, ReactionStep.class);
    return collapsedRxnSteps;
}

Example 45 with ReactionParticipant

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

the class XmlReader method getKinetics.

/**
 * This method returns a Kinetics object from a XML Element based on the value of the kinetics type attribute.
 * Creation date: (3/19/2001 4:42:04 PM)
 * @return cbit.vcell.model.Kinetics
 * @param param org.jdom.Element
 */
private Kinetics getKinetics(Element param, ReactionStep reaction, Model model) throws XmlParseException {
    VariableHash varHash = new VariableHash();
    addResevedSymbols(varHash, model);
    String type = param.getAttributeValue(XMLTags.KineticsTypeAttrTag);
    Kinetics newKinetics = null;
    try {
        if (type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralKinetics)) {
            // create a general kinetics
            newKinetics = new GeneralKinetics(reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralCurrentKinetics)) {
            // Create GeneralCurrentKinetics
            newKinetics = new GeneralCurrentKinetics(reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeMassAction) && reaction instanceof SimpleReaction) {
            // create a Mass Action kinetics
            newKinetics = new MassActionKinetics((SimpleReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeNernst) && reaction instanceof FluxReaction) {
            // create NernstKinetics
            newKinetics = new NernstKinetics((FluxReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeGHK) && reaction instanceof FluxReaction) {
            // create GHKKinetics
            newKinetics = new GHKKinetics((FluxReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeHMM_Irr) && reaction instanceof SimpleReaction) {
            // create HMM_IrrKinetics
            newKinetics = new HMM_IRRKinetics((SimpleReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeHMM_Rev) && reaction instanceof SimpleReaction) {
            // create HMM_RevKinetics
            newKinetics = new HMM_REVKinetics((SimpleReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralTotal_oldname)) {
            // create GeneralTotalKinetics
            newKinetics = new GeneralLumpedKinetics(reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralLumped)) {
            // create GeneralLumpedKinetics
            newKinetics = new GeneralLumpedKinetics(reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralCurrentLumped)) {
            // create GeneralCurrentLumpedKinetics
            newKinetics = new GeneralCurrentLumpedKinetics(reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralPermeability) && reaction instanceof FluxReaction) {
            // create GeneralPermeabilityKinetics
            newKinetics = new GeneralPermeabilityKinetics((FluxReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeMacroscopic_Irr) && reaction instanceof SimpleReaction) {
            // create Macroscopic_IRRKinetics
            newKinetics = new Macroscopic_IRRKinetics((SimpleReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeMicroscopic_Irr) && reaction instanceof SimpleReaction) {
            // create Microscopic_IRRKinetics
            newKinetics = new Microscopic_IRRKinetics((SimpleReaction) reaction);
        } else {
            throw new XmlParseException("Unknown kinetics type: " + type);
        }
    } catch (ExpressionException e) {
        e.printStackTrace();
        throw new XmlParseException("Error creating the kinetics for reaction: " + reaction.getName(), e);
    }
    try {
        // transaction begin flag ... yeah, this is a hack
        newKinetics.reading(true);
        // Read all of the parameters
        List<Element> list = param.getChildren(XMLTags.ParameterTag, vcNamespace);
        // add constants that may be used in kinetics.
        // VariableHash varHash = getVariablesHash();
        ArrayList<String> reserved = new ArrayList<String>();
        ReservedSymbol[] reservedSymbols = reaction.getModel().getReservedSymbols();
        for (ReservedSymbol rs : reservedSymbols) {
            reserved.add(rs.getName());
        }
        try {
            if (reaction.getStructure() instanceof Membrane) {
                Membrane membrane = (Membrane) reaction.getStructure();
                varHash.addVariable(new Constant(membrane.getMembraneVoltage().getName(), new Expression(0.0)));
                reserved.add(membrane.getMembraneVoltage().getName());
            }
            // 
            // add Reactants, Products, and Catalysts (ReactionParticipants)
            // 
            ReactionParticipant[] rp = reaction.getReactionParticipants();
            for (int i = 0; i < rp.length; i++) {
                varHash.addVariable(new Constant(rp[i].getName(), new Expression(0.0)));
            }
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("error reordering parameters according to dependencies: ", e);
        }
        // 
        for (Element xmlParam : list) {
            String paramName = unMangle(xmlParam.getAttributeValue(XMLTags.NameAttrTag));
            String role = xmlParam.getAttributeValue(XMLTags.ParamRoleAttrTag);
            String paramExpStr = xmlParam.getText();
            Expression paramExp = unMangleExpression(paramExpStr);
            try {
                if (varHash.getVariable(paramName) == null) {
                    varHash.addVariable(new Function(paramName, paramExp, null));
                } else {
                    if (reserved.contains(paramName)) {
                        varHash.removeVariable(paramName);
                        varHash.addVariable(new Function(paramName, paramExp, null));
                    }
                }
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException("error reordering parameters according to dependencies: ", e);
            }
            Kinetics.KineticsParameter tempParam = null;
            if (!role.equals(XMLTags.ParamRoleUserDefinedTag)) {
                tempParam = newKinetics.getKineticsParameterFromRole(Kinetics.getParamRoleFromDefaultDesc(role));
            } else {
                continue;
            }
            // hack for bringing in General Total kinetics without breaking.
            if (tempParam == null && newKinetics instanceof GeneralLumpedKinetics) {
                if (role.equals(Kinetics.GTK_AssumedCompartmentSize_oldname) || role.equals(Kinetics.GTK_ReactionRate_oldname) || role.equals(Kinetics.GTK_CurrentDensity_oldname)) {
                    continue;
                } else if (role.equals(VCMODL.TotalRate_oldname)) {
                    tempParam = newKinetics.getKineticsParameterFromRole(Kinetics.ROLE_LumpedReactionRate);
                }
            }
            // hack from bringing in chargeValence parameters without breaking
            if (tempParam == null && Kinetics.getParamRoleFromDefaultDesc(role) == Kinetics.ROLE_ChargeValence) {
                tempParam = newKinetics.getChargeValenceParameter();
            }
            if (tempParam == null) {
                throw new XmlParseException("parameter with role '" + role + "' not found in kinetics type '" + type + "'");
            }
            // 
            if (!tempParam.getName().equals(paramName)) {
                Kinetics.KineticsParameter multNameParam = newKinetics.getKineticsParameter(paramName);
                int n = 0;
                while (multNameParam != null) {
                    String tempName = paramName + "_" + n++;
                    newKinetics.renameParameter(paramName, tempName);
                    multNameParam = newKinetics.getKineticsParameter(tempName);
                }
                newKinetics.renameParameter(tempParam.getName(), paramName);
            }
        }
        // 
        // create unresolved parameters for all unresolved symbols
        // 
        String unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
        while (unresolvedSymbol != null) {
            try {
                // will turn into an UnresolvedParameter.
                varHash.addVariable(new Function(unresolvedSymbol, new Expression(0.0), null));
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e);
            }
            newKinetics.addUnresolvedParameter(unresolvedSymbol);
            unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
        }
        Variable[] sortedVariables = varHash.getTopologicallyReorderedVariables();
        ModelUnitSystem modelUnitSystem = reaction.getModel().getUnitSystem();
        for (int i = sortedVariables.length - 1; i >= 0; i--) {
            if (sortedVariables[i] instanceof Function) {
                Function paramFunction = (Function) sortedVariables[i];
                Element xmlParam = null;
                for (int j = 0; j < list.size(); j++) {
                    Element tempParam = (Element) list.get(j);
                    if (paramFunction.getName().equals(unMangle(tempParam.getAttributeValue(XMLTags.NameAttrTag)))) {
                        xmlParam = tempParam;
                        break;
                    }
                }
                if (xmlParam == null) {
                    // must have been an unresolved parameter
                    continue;
                }
                String symbol = xmlParam.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
                VCUnitDefinition unit = null;
                if (symbol != null) {
                    unit = modelUnitSystem.getInstance(symbol);
                }
                Kinetics.KineticsParameter tempParam = newKinetics.getKineticsParameter(paramFunction.getName());
                if (tempParam == null) {
                    newKinetics.addUserDefinedKineticsParameter(paramFunction.getName(), paramFunction.getExpression(), unit);
                } else {
                    newKinetics.setParameterValue(tempParam, paramFunction.getExpression());
                    tempParam.setUnitDefinition(unit);
                }
            }
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("Exception while setting parameters for Reaction : " + reaction.getName(), e);
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("Exception while settings parameters for Reaction : " + reaction.getName(), e);
    } finally {
        newKinetics.reading(false);
    }
    return newKinetics;
}