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

Example 6 with NodeReference

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

the class ReactionCartoonMolecule method setPositionsFromReactionCartoon.

public void setPositionsFromReactionCartoon(Diagram diagram) {
    List<NodeReference> nodeList = new ArrayList<NodeReference>();
    NodeReference.Mode mode = NodeReference.Mode.molecule;
    for (Shape shape : getShapes()) {
        if (shape instanceof FluxReactionShape) {
            nodeList.add(new NodeReference(mode, NodeReference.FLUX_REACTION_NODE, ((FluxReaction) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof SimpleReactionShape) {
            nodeList.add(new NodeReference(mode, NodeReference.SIMPLE_REACTION_NODE, ((ReactionStep) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof ReactionRuleDiagramShape) {
            nodeList.add(new NodeReference(mode, NodeReference.REACTION_RULE_NODE, ((ReactionRule) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof SpeciesContextShape) {
            nodeList.add(new NodeReference(mode, NodeReference.SPECIES_CONTEXT_NODE, ((SpeciesContext) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof RuleParticipantSignatureFullDiagramShape) {
            System.out.println("ReactionCartoonMolecule, Invalid shape type 'RuleParticipantSignatureFullDiagramShape'");
            RuleParticipantSignature ruleParticipantSignature = (RuleParticipantSignature) shape.getModelObject();
            if (ruleParticipantSignature.getStructure() == diagram.getStructure()) {
                String spAsString = ruleParticipantSignature.getFirstSpeciesPatternAsString();
                NodeReference nr = new NodeReference(mode, NodeReference.RULE_PARTICIPANT_SIGNATURE_FULL_NODE, spAsString, shape.getSpaceManager().getRelPos());
                nr.speciesPattern = ruleParticipantSignature.getSpeciesPattern();
                nodeList.add(nr);
            }
        } else if (shape instanceof RuleParticipantSignatureShortDiagramShape) {
            RuleParticipantSignature ruleParticipantSignature = (RuleParticipantSignature) shape.getModelObject();
            if (ruleParticipantSignature.getStructure() == diagram.getStructure()) {
                String spAsString = ruleParticipantSignature.getFirstSpeciesPatternAsString();
                NodeReference nr = new NodeReference(mode, NodeReference.RULE_PARTICIPANT_SIGNATURE_SHORT_NODE, spAsString, shape.getSpaceManager().getRelPos());
                nr.speciesPattern = ruleParticipantSignature.getSpeciesPattern();
                nodeList.add(nr);
            }
        }
    }
    diagram.setNodeReferences(mode, nodeList);
}

Example 7 with NodeReference

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

the class ReactionCartoonMolecule method rebindAll.

// for the RULE_PARTICIPANT_SIGNATURE_NODE nodes we initialize the node's speciesPattern field
// from the matching signature
public void rebindAll(Diagram diagram) {
    String nodeStructure = diagram.getStructure().getName();
    List<NodeReference> nodeList = diagram.getNodeMoleculeList();
    for (int i = 0; i < nodeList.size(); i++) {
        NodeReference node = nodeList.get(i);
        if (node.nodeType == NodeReference.RULE_PARTICIPANT_SIGNATURE_SHORT_NODE) {
            if (node.speciesPattern != null) {
                continue;
            }
            for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                if (!signature.getStructure().getName().equals(nodeStructure)) {
                    continue;
                }
                String speciesPatternName = signature.getFirstSpeciesPatternAsString();
                if (speciesPatternName.equals(node.name)) {
                    node.speciesPattern = signature.getSpeciesPattern();
                    break;
                }
            }
        } else if (node.nodeType == NodeReference.RULE_PARTICIPANT_SIGNATURE_FULL_NODE) {
            System.out.println("ReactionCartoonMolecule, rebindAll(), wrong NodeReference type RULE_PARTICIPANT_SIGNATURE_FULL_NODE");
        }
    }
}

Example 8 with NodeReference

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

the class ReactionCartoonFull method rebindAll.

// for the RULE_PARTICIPANT_SIGNATURE_NODE nodes we initialize the node's speciesPattern field
// from the matching signature
public void rebindAll(Diagram diagram) {
    String nodeStructure = diagram.getStructure().getName();
    List<NodeReference> nodeList = diagram.getNodeFullList();
    for (int i = 0; i < nodeList.size(); i++) {
        NodeReference node = nodeList.get(i);
        if (node.nodeType == NodeReference.RULE_PARTICIPANT_SIGNATURE_FULL_NODE) {
            if (node.speciesPattern != null) {
                continue;
            }
            for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                if (!signature.getStructure().getName().equals(nodeStructure)) {
                    continue;
                }
                String speciesPatternName = signature.getFirstSpeciesPatternAsString();
                if (speciesPatternName.equals(node.name)) {
                    node.speciesPattern = signature.getSpeciesPattern();
                    break;
                }
            }
        } else if (node.nodeType == NodeReference.RULE_PARTICIPANT_SIGNATURE_SHORT_NODE) {
            System.out.println("ReactionCartoonFull, rebindAll(), wrong NodeReference type RULE_PARTICIPANT_SIGNATURE_SHORT_NODE");
        }
    }
}

Example 9 with NodeReference

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

Example 10 with NodeReference

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