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

Example 1 with NodeReference

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

the class XmlReader method getNodeReference.

/**
 * This method returns a nodeReference onject from a XML representation.
 * Creation date: (4/24/2001 5:35:56 PM)
 * @return cbit.vcell.model.NodeReference
 * @param param org.jdom.Element
 */
private NodeReference getNodeReference(Element param) throws XmlParseException {
    String tempname = param.getName();
    NodeReference newNodeRef = null;
    int type = NodeReference.UNKNOWN_NODE;
    String name = null;
    // determine the type of nodereference to create
    if (tempname.equalsIgnoreCase(XMLTags.SpeciesContextShapeTag)) {
        type = NodeReference.SPECIES_CONTEXT_NODE;
        name = unMangle(param.getAttributeValue(XMLTags.SpeciesContextRefAttrTag));
    } else if (tempname.equalsIgnoreCase(XMLTags.SimpleReactionShapeTag)) {
        type = NodeReference.SIMPLE_REACTION_NODE;
        name = unMangle(param.getAttributeValue(XMLTags.SimpleReactionRefAttrTag));
    } else if (tempname.equalsIgnoreCase(XMLTags.FluxReactionShapeTag)) {
        type = NodeReference.FLUX_REACTION_NODE;
        name = unMangle(param.getAttributeValue(XMLTags.FluxReactionRefAttrTag));
    } else if (tempname.equalsIgnoreCase(XMLTags.ReactionRuleShapeTag)) {
        type = NodeReference.REACTION_RULE_NODE;
        name = unMangle(param.getAttributeValue(XMLTags.ReactionRuleRef2AttrTag));
    } else if (tempname.equalsIgnoreCase(XMLTags.RuleParticipantFullShapeTag) || tempname.equalsIgnoreCase(XMLTags.RuleParticipantShapeTag)) {
        type = NodeReference.RULE_PARTICIPANT_SIGNATURE_FULL_NODE;
        name = unMangle(param.getAttributeValue(XMLTags.RuleParticipantRefAttrTag));
    } else if (tempname.equalsIgnoreCase(XMLTags.RuleParticipantShortShapeTag)) {
        type = NodeReference.RULE_PARTICIPANT_SIGNATURE_SHORT_NODE;
        name = unMangle(param.getAttributeValue(XMLTags.RuleParticipantRefAttrTag));
    } else {
        throw new XmlParseException("An unknown type was found " + tempname + ",when processing noderefence!");
    }
    String modeString = unMangle(param.getAttributeValue(XMLTags.NodeReferenceModeAttrTag));
    NodeReference.Mode mode = NodeReference.Mode.none;
    if (modeString != null) {
        mode = Mode.fromValue(modeString);
    }
    java.awt.Point location = new java.awt.Point(Integer.parseInt(param.getAttributeValue(XMLTags.LocationXAttrTag)), Integer.parseInt(param.getAttributeValue(XMLTags.LocationYAttrTag)));
    newNodeRef = new NodeReference(mode, type, name, location);
    return newNodeRef;
}

Example 2 with NodeReference

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

the class XmlReader method getDiagram.

/**
 * This method returns a Diagram object from a XML element.
 * Creation date: (4/4/2001 4:20:52 PM)
 * @return cbit.vcell.model.Diagram
 * @param param org.jdom.Element
 */
private Diagram getDiagram(Element param, Model model) throws XmlParseException {
    // get Attibutes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String structureName = unMangle(param.getAttributeValue(XMLTags.StructureAttrTag));
    Structure structureref = model.getStructure(structureName);
    if (structureref == null) {
        throw new XmlParseException("The structure " + structureName + "could not be resolved!");
    }
    // try to create the new Diagram
    Diagram newdiagram = new Diagram(structureref, name);
    // Add Nodereferences (Shapes)
    List<Element> children = param.getChildren();
    if (children.size() > 0) {
        List<NodeReference> nodeRefList = new ArrayList<>();
        for (int i = 0; i < children.size(); i++) {
            nodeRefList.add(getNodeReference(children.get(i)));
        }
        newdiagram.setNodeReferences(nodeRefList);
    }
    return newdiagram;
}

Example 3 with NodeReference

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

the class ReactionCartoonRule method setPositionsFromReactionCartoon.

public void setPositionsFromReactionCartoon(Diagram diagram) {
    List<NodeReference> nodeList = new ArrayList<NodeReference>();
    NodeReference.Mode mode = NodeReference.Mode.rule;
    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 ReactionRuleShortDiagramShape) {
            // can only be short
            ReactionRuleShortSignature signature = (ReactionRuleShortSignature) shape.getModelObject();
            // the display name is the number of rules in the signature's list of rules
            String name = signature.getDisplayName();
            NodeReference nr = new NodeReference(mode, NodeReference.REACTION_RULE_NODE, name, shape.getSpaceManager().getRelPos());
            nodeList.add(nr);
        } 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("ReactionCartoonRule, 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);
            }
        }
    }
    // add all to nodeRuleList
    diagram.setNodeReferences(mode, nodeList);
}

Example 4 with NodeReference

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

the class ReactionCartoonFull method setPositionsFromReactionCartoon.

public void setPositionsFromReactionCartoon(Diagram diagram) {
    List<NodeReference> nodeList = new ArrayList<NodeReference>();
    NodeReference.Mode mode = NodeReference.Mode.full;
    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) {
            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) {
            System.out.println("ReactionCartoonFull, Invalid shape type '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 5 with NodeReference

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