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Example 1 with RuleParticipantLongSignature

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

the class ReactionCartoonFull method applyDefaults.

public void applyDefaults(Diagram diagram) {
    List<NodeReference> nodeList = diagram.getNodeFullList();
    List<NodeReference> orphansList = new ArrayList<NodeReference>();
    for (int i = 0; i < nodeList.size(); i++) {
        NodeReference node = nodeList.get(i);
        Object obj = null;
        Structure struct = diagram.getStructure();
        boolean found = false;
        switch(node.nodeType) {
            case NodeReference.SIMPLE_REACTION_NODE:
                obj = getModel().getReactionStep(node.name);
                if (!(obj instanceof SimpleReaction)) {
                    System.out.println("ReactionCartoon.applyDefaults(), diagram reaction " + node.name + " type mismatch in model, using location anyway");
                }
                break;
            case NodeReference.FLUX_REACTION_NODE:
                obj = getModel().getReactionStep(node.name);
                if (!(obj instanceof FluxReaction)) {
                    System.out.println("ReactionCartoon.applyDefaults(), diagram flux " + node.name + " type mismatch in model, using location anyway");
                }
                break;
            case NodeReference.SPECIES_CONTEXT_NODE:
                obj = getModel().getSpeciesContext(node.name);
                break;
            case NodeReference.REACTION_RULE_NODE:
                obj = getModel().getRbmModelContainer().getReactionRule(node.name);
                break;
            case // obj is a RuleParticipantSignature
            NodeReference.RULE_PARTICIPANT_SIGNATURE_FULL_NODE:
                for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                    if (signature instanceof RuleParticipantLongSignature && signature.getStructure() == struct && signature.compareByCriteria(node.getName(), GroupingCriteria.full)) {
                        obj = signature;
                        found = true;
                        break;
                    }
                }
                if (!found) {
                    orphansList.add(node);
                }
                break;
            case NodeReference.RULE_PARTICIPANT_SIGNATURE_SHORT_NODE:
                System.out.println("ReactionCartoonFull, RULE_PARTICIPANT_SIGNATURE_SHORT_NODE detected");
                for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                    if (signature instanceof RuleParticipantShortSignature && signature.getStructure() == struct && signature.compareByCriteria(node.getName(), GroupingCriteria.full)) {
                        obj = signature;
                        found = true;
                        break;
                    }
                }
                if (!found) {
                    orphansList.add(node);
                }
                break;
        }
        // -- switch
        Shape shape = getShapeFromModelObject(obj);
        if (shape != null) {
            Point relPosOld = shape.getRelPos();
            Point relPosNew = node.location;
            // In old models, the same node can appear in multiple diagrams.
            // Now, we have only one diagram, so if a node has multiple positions,
            // some would overwrite others.
            // This attempts to prevent overwriting a position with a worse one.
            // if(relPosOld.x + relPosOld.y < relPosNew.x + relPosNew.y) {
            shape.setRelPos(relPosNew);
        // }
        }
    }
    if (!orphansList.isEmpty()) {
        diagram.removeNodeReferences(NodeReference.Mode.full, orphansList);
    }
}
Also used : RuleParticipantSignature(cbit.vcell.model.RuleParticipantSignature) RuleParticipantLongSignature(cbit.vcell.model.RuleParticipantLongSignature) SimpleReaction(cbit.vcell.model.SimpleReaction) Shape(cbit.gui.graph.Shape) NodeReference(cbit.vcell.model.NodeReference) ArrayList(java.util.ArrayList) FluxReaction(cbit.vcell.model.FluxReaction) Point(java.awt.Point) Point(java.awt.Point) RuleParticipantShortSignature(cbit.vcell.model.RuleParticipantShortSignature) Structure(cbit.vcell.model.Structure)

Example 2 with RuleParticipantLongSignature

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

the class ReactionCartoonFull method refreshAll.

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

Example 3 with RuleParticipantLongSignature

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

the class ReactionCartoonMolecule method applyDefaults.

public void applyDefaults(Diagram diagram) {
    List<NodeReference> nodeList = diagram.getNodeMoleculeList();
    List<NodeReference> orphansList = new ArrayList<NodeReference>();
    for (int i = 0; i < nodeList.size(); i++) {
        NodeReference node = nodeList.get(i);
        Object obj = null;
        Structure struct = diagram.getStructure();
        boolean found = false;
        switch(node.nodeType) {
            case NodeReference.SIMPLE_REACTION_NODE:
                obj = getModel().getReactionStep(node.name);
                if (!(obj instanceof SimpleReaction)) {
                    System.out.println("ReactionCartoon.applyDefaults(), diagram reaction " + node.name + " type mismatch in model, using location anyway");
                }
                break;
            case NodeReference.FLUX_REACTION_NODE:
                obj = getModel().getReactionStep(node.name);
                if (!(obj instanceof FluxReaction)) {
                    System.out.println("ReactionCartoon.applyDefaults(), diagram flux " + node.name + " type mismatch in model, using location anyway");
                }
                break;
            case NodeReference.SPECIES_CONTEXT_NODE:
                obj = getModel().getSpeciesContext(node.name);
                break;
            case NodeReference.REACTION_RULE_NODE:
                obj = getModel().getRbmModelContainer().getReactionRule(node.name);
                break;
            case // obj is a RuleParticipantSignature
            NodeReference.RULE_PARTICIPANT_SIGNATURE_FULL_NODE:
                System.out.println("ReactionCartoonMolecule, RULE_PARTICIPANT_SIGNATURE_FULL_NODE detected");
                for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                    if (signature instanceof RuleParticipantLongSignature && signature.getStructure() == struct && signature.compareByCriteria(node.getName(), GroupingCriteria.full)) {
                        obj = signature;
                        found = true;
                        break;
                    }
                }
                if (!found) {
                    orphansList.add(node);
                }
                break;
            case NodeReference.RULE_PARTICIPANT_SIGNATURE_SHORT_NODE:
                for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                    if (signature instanceof RuleParticipantShortSignature && signature.getStructure() == struct && signature.compareByCriteria(node.getName(), GroupingCriteria.full)) {
                        obj = signature;
                        found = true;
                        break;
                    }
                }
                if (!found) {
                    orphansList.add(node);
                }
                break;
        }
        // -- switch
        Shape shape = getShapeFromModelObject(obj);
        if (shape != null) {
            Point relPosOld = shape.getRelPos();
            Point relPosNew = node.location;
            // In old models, the same node can appear in multiple diagrams.
            // Now, we have only one diagram, so if a node has multiple positions,
            // some would overwrite others.
            // This attempts to prevent overwriting a position with a worse one.
            // if(relPosOld.x + relPosOld.y < relPosNew.x + relPosNew.y) {
            shape.setRelPos(relPosNew);
        // }
        }
    }
    if (!orphansList.isEmpty()) {
        diagram.removeNodeReferences(NodeReference.Mode.molecule, orphansList);
    }
}
Also used : RuleParticipantSignature(cbit.vcell.model.RuleParticipantSignature) RuleParticipantLongSignature(cbit.vcell.model.RuleParticipantLongSignature) SimpleReaction(cbit.vcell.model.SimpleReaction) Shape(cbit.gui.graph.Shape) NodeReference(cbit.vcell.model.NodeReference) ArrayList(java.util.ArrayList) FluxReaction(cbit.vcell.model.FluxReaction) Point(java.awt.Point) Point(java.awt.Point) RuleParticipantShortSignature(cbit.vcell.model.RuleParticipantShortSignature) Structure(cbit.vcell.model.Structure)

Example 4 with RuleParticipantLongSignature

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

the class ReactionCartoonMolecule method refreshAll.

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

Example 5 with RuleParticipantLongSignature

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

the class ReactionCartoonRule method applyDefaults.

public void applyDefaults(Diagram diagram) {
    List<NodeReference> nodeList = diagram.getNodeRuleList();
    List<NodeReference> orphansList = new ArrayList<NodeReference>();
    for (int i = 0; i < nodeList.size(); i++) {
        NodeReference node = nodeList.get(i);
        Object obj = null;
        Structure struct = diagram.getStructure();
        boolean found = false;
        switch(node.nodeType) {
            case NodeReference.SIMPLE_REACTION_NODE:
                obj = getModel().getReactionStep(node.name);
                if (!(obj instanceof SimpleReaction)) {
                    System.out.println("ReactionCartoon.applyDefaults(), diagram reaction " + node.name + " type mismatch in model, using location anyway");
                }
                break;
            case NodeReference.FLUX_REACTION_NODE:
                obj = getModel().getReactionStep(node.name);
                if (!(obj instanceof FluxReaction)) {
                    System.out.println("ReactionCartoon.applyDefaults(), diagram flux " + node.name + " type mismatch in model, using location anyway");
                }
                break;
            case NodeReference.SPECIES_CONTEXT_NODE:
                obj = getModel().getSpeciesContext(node.name);
                break;
            case // TODO: aici
            NodeReference.REACTION_RULE_NODE:
                obj = getModel().getRbmModelContainer().getReactionRule(node.name);
                break;
            case // obj is a RuleParticipantSignature
            NodeReference.RULE_PARTICIPANT_SIGNATURE_FULL_NODE:
                System.out.println("ReactionCartoonRule, RULE_PARTICIPANT_SIGNATURE_FULL_NODE detected");
                for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                    if (signature instanceof RuleParticipantLongSignature && signature.getStructure() == struct && signature.compareByCriteria(node.getName(), GroupingCriteria.full)) {
                        obj = signature;
                        found = true;
                        break;
                    }
                }
                if (!found) {
                    orphansList.add(node);
                }
                break;
            case NodeReference.RULE_PARTICIPANT_SIGNATURE_SHORT_NODE:
                for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                    if (signature instanceof RuleParticipantShortSignature && signature.getStructure() == struct && signature.compareByCriteria(node.getName(), GroupingCriteria.full)) {
                        obj = signature;
                        found = true;
                        break;
                    }
                }
                if (!found) {
                    orphansList.add(node);
                }
                break;
        }
        // -- switch
        Shape shape = getShapeFromModelObject(obj);
        if (shape != null) {
            Point relPosOld = shape.getRelPos();
            Point relPosNew = node.location;
            // In old models, the same node can appear in multiple diagrams.
            // Now, we have only one diagram, so if a node has multiple positions,
            // some would overwrite others.
            // This attempts to prevent overwriting a position with a worse one.
            // if(relPosOld.x + relPosOld.y < relPosNew.x + relPosNew.y) {
            shape.setRelPos(relPosNew);
        // }
        }
    }
    if (!orphansList.isEmpty()) {
        diagram.removeNodeReferences(NodeReference.Mode.rule, orphansList);
    }
}
Also used : RuleParticipantSignature(cbit.vcell.model.RuleParticipantSignature) RuleParticipantLongSignature(cbit.vcell.model.RuleParticipantLongSignature) SimpleReaction(cbit.vcell.model.SimpleReaction) Shape(cbit.gui.graph.Shape) NodeReference(cbit.vcell.model.NodeReference) ArrayList(java.util.ArrayList) FluxReaction(cbit.vcell.model.FluxReaction) Point(java.awt.Point) Point(java.awt.Point) RuleParticipantShortSignature(cbit.vcell.model.RuleParticipantShortSignature) Structure(cbit.vcell.model.Structure)

Aggregations

Shape (cbit.gui.graph.Shape)5 FluxReaction (cbit.vcell.model.FluxReaction)5 RuleParticipantLongSignature (cbit.vcell.model.RuleParticipantLongSignature)5 RuleParticipantShortSignature (cbit.vcell.model.RuleParticipantShortSignature)5 RuleParticipantSignature (cbit.vcell.model.RuleParticipantSignature)5 SimpleReaction (cbit.vcell.model.SimpleReaction)5 Structure (cbit.vcell.model.Structure)5 Point (java.awt.Point)5 ArrayList (java.util.ArrayList)5 NodeReference (cbit.vcell.model.NodeReference)3 GraphEvent (cbit.gui.graph.GraphEvent)2 Catalyst (cbit.vcell.model.Catalyst)2 Diagram (cbit.vcell.model.Diagram)2 Feature (cbit.vcell.model.Feature)2 Membrane (cbit.vcell.model.Membrane)2 Product (cbit.vcell.model.Product)2 ProductPattern (cbit.vcell.model.ProductPattern)2 Reactant (cbit.vcell.model.Reactant)2 ReactantPattern (cbit.vcell.model.ReactantPattern)2 ReactionParticipant (cbit.vcell.model.ReactionParticipant)2