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Example 36 with Feature

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

the class BioCartoonTool method pasteReactionSteps0.

/**
 * pasteReactionSteps0 : does the actual pasting. First called with a cloned model, to track issues. If user still wants to proceed, the paste
 * is performed on the original model.
 *
 * Insert the method's description here.
 * Creation date: (5/10/2003 3:55:25 PM)
 * @param pasteToModel cbit.vcell.model.Model
 * @param pasteToStructure cbit.vcell.model.Structure
 * @param bNew boolean
 */
private static final PasteHelper pasteReactionSteps0(HashMap<String, HashMap<ReactionParticipant, Structure>> rxPartMapStructure, Component parent, IssueContext issueContext, ReactionStep[] copyFromRxSteps, Model pasteToModel, Structure pasteToStructure, boolean bNew, /*boolean bUseDBSpecies,*/
UserResolvedRxElements userResolvedRxElements) throws Exception {
    HashMap<BioModelEntityObject, BioModelEntityObject> reactionsAndSpeciesContexts = new HashMap<>();
    if (copyFromRxSteps == null || copyFromRxSteps.length == 0 || pasteToModel == null || pasteToStructure == null) {
        throw new IllegalArgumentException("CartoonTool.pasteReactionSteps Error " + (copyFromRxSteps == null || copyFromRxSteps.length == 0 ? "reactionStepsArr empty " : "") + (pasteToModel == null ? "model is null " : "") + (pasteToStructure == null ? "struct is null " : ""));
    }
    if (!pasteToModel.contains(pasteToStructure)) {
        throw new IllegalArgumentException("CartoonTool.pasteReactionSteps model " + pasteToModel.getName() + " does not contain structure " + pasteToStructure.getName());
    }
    // Check PasteToModel has preferred targets if set
    if (userResolvedRxElements != null) {
        for (int i = 0; i < userResolvedRxElements.toSpeciesArr.length; i++) {
            if (userResolvedRxElements.toSpeciesArr[i] != null) {
                if (!pasteToModel.contains(userResolvedRxElements.toSpeciesArr[i])) {
                    throw new RuntimeException("PasteToModel does not contain preferred Species " + userResolvedRxElements.toSpeciesArr[i]);
                }
            }
            if (userResolvedRxElements.toStructureArr[i] != null) {
                if (!pasteToModel.contains(userResolvedRxElements.toStructureArr[i])) {
                    throw new RuntimeException("PasteToModel does not contain preferred Structure " + userResolvedRxElements.toStructureArr[i]);
                }
            }
        }
    }
    int counter = 0;
    Structure currentStruct = pasteToStructure;
    String copiedStructName = copyFromRxSteps[counter].getStructure().getName();
    StructureTopology structTopology = (copyFromRxSteps[counter].getModel() == null ? pasteToModel.getStructureTopology() : copyFromRxSteps[counter].getModel().getStructureTopology());
    IdentityHashMap<Species, Species> speciesHash = new IdentityHashMap<Species, Species>();
    IdentityHashMap<SpeciesContext, SpeciesContext> speciesContextHash = new IdentityHashMap<SpeciesContext, SpeciesContext>();
    Vector<Issue> issueVector = new Vector<Issue>();
    do {
        // create a new reaction, instead of cloning the old one; set struc
        ReactionStep copyFromReactionStep = copyFromRxSteps[counter];
        String newName = copyFromReactionStep.getName();
        while (pasteToModel.getReactionStep(newName) != null) {
            newName = org.vcell.util.TokenMangler.getNextEnumeratedToken(newName);
        }
        ReactionStep newReactionStep = null;
        if (copyFromReactionStep instanceof SimpleReaction) {
            newReactionStep = new SimpleReaction(pasteToModel, currentStruct, newName, copyFromReactionStep.isReversible());
        } else if (copyFromReactionStep instanceof FluxReaction && currentStruct instanceof Membrane) {
            newReactionStep = new FluxReaction(pasteToModel, (Membrane) currentStruct, null, newName, copyFromReactionStep.isReversible());
        }
        pasteToModel.addReactionStep(newReactionStep);
        reactionsAndSpeciesContexts.put(newReactionStep, copyFromReactionStep);
        Structure toRxnStruct = newReactionStep.getStructure();
        Structure fromRxnStruct = copyFromReactionStep.getStructure();
        if (!fromRxnStruct.getClass().equals(pasteToStructure.getClass())) {
            throw new Exception("Cannot copy reaction from " + fromRxnStruct.getTypeName() + " to " + pasteToStructure.getTypeName() + ".");
        }
        // add appropriate reactionParticipants to newReactionStep.
        StructureTopology toStructureTopology = pasteToModel.getStructureTopology();
        ReactionParticipant[] copyFromRxParticipantArr = copyFromReactionStep.getReactionParticipants();
        if (rxPartMapStructure == null) {
            // null during 'issues' trial
            rxPartMapStructure = new HashMap<String, HashMap<ReactionParticipant, Structure>>();
        }
        if (rxPartMapStructure.get(copyFromReactionStep.getName()) == null) {
            // Ask user to assign species to compartments for each reaction to be pasted
            rxPartMapStructure.put(copyFromReactionStep.getName(), askUserResolveMembraneConnections(parent, pasteToModel.getStructures(), currentStruct, fromRxnStruct, toRxnStruct, copyFromRxParticipantArr, toStructureTopology, structTopology));
        }
        for (int i = 0; i < copyFromRxParticipantArr.length; i += 1) {
            Structure pasteToStruct = currentStruct;
            // if(toRxnStruct instanceof Membrane){
            pasteToStruct = rxPartMapStructure.get(copyFromReactionStep.getName()).get(copyFromRxParticipantArr[i]);
            // if(pasteToStruct == null){
            // for(ReactionParticipant myRXPart:rxPartMapStructure.get(copyFromReactionStep.getName()).keySet()){
            // if(myRXPart.getSpeciesContext().getName().equals(copyFromRxParticipantArr[i].getSpeciesContext().getName())){
            // pasteToStruct = rxPartMapStructure.get(copyFromReactionStep.getName()).get(myRXPart);
            // break;
            // }
            // }
            // }
            // }
            // this adds the speciesContexts and species (if any) to the model)
            String rootSC = ReactionCartoonTool.speciesContextRootFinder(copyFromRxParticipantArr[i].getSpeciesContext());
            SpeciesContext newSc = null;
            SpeciesContext[] matchSC = pasteToModel.getSpeciesContexts();
            for (int j = 0; matchSC != null && j < matchSC.length; j++) {
                String matchRoot = ReactionCartoonTool.speciesContextRootFinder(matchSC[j]);
                if (matchRoot != null && matchRoot.equals(rootSC) && matchSC[j].getStructure().getName().equals(pasteToStruct.getName())) {
                    newSc = matchSC[j];
                    reactionsAndSpeciesContexts.put(newSc, matchSC[j]);
                    break;
                }
            }
            if (newSc == null) {
                newSc = pasteSpecies(parent, copyFromRxParticipantArr[i].getSpecies(), rootSC, pasteToModel, pasteToStruct, bNew, /*bUseDBSpecies,*/
                speciesHash, UserResolvedRxElements.getPreferredReactionElement(userResolvedRxElements, copyFromRxParticipantArr[i]));
                reactionsAndSpeciesContexts.put(newSc, copyFromRxParticipantArr[i].getSpeciesContext());
            }
            // record the old-new speciesContexts (reactionparticipants) in the IdHashMap, this is useful, esp for 'Paste new', while replacing proxyparams.
            SpeciesContext oldSc = copyFromRxParticipantArr[i].getSpeciesContext();
            if (speciesContextHash.get(oldSc) == null) {
                speciesContextHash.put(oldSc, newSc);
            }
            if (copyFromRxParticipantArr[i] instanceof Reactant) {
                newReactionStep.addReactionParticipant(new Reactant(null, newReactionStep, newSc, copyFromRxParticipantArr[i].getStoichiometry()));
            } else if (copyFromRxParticipantArr[i] instanceof Product) {
                newReactionStep.addReactionParticipant(new Product(null, newReactionStep, newSc, copyFromRxParticipantArr[i].getStoichiometry()));
            } else if (copyFromRxParticipantArr[i] instanceof Catalyst) {
                newReactionStep.addCatalyst(newSc);
            }
        }
        // // If 'newReactionStep' is a fluxRxn, set its fluxCarrier
        // if (newReactionStep instanceof FluxReaction) {
        // if (fluxCarrierSp != null) {
        // ((FluxReaction)newReactionStep).setFluxCarrier(fluxCarrierSp, pasteToModel);
        // } else {
        // throw new RuntimeException("Could not set FluxCarrier species for the flux reaction to be pasted");
        // }
        // }
        // For each kinetic parameter expression for new kinetics, replace the proxyParams from old kinetics with proxyParams in new kinetics
        // i.e., if the proxyParams are speciesContexts, replace with corresponding speciesContext in newReactionStep;
        // if the proxyParams are structureSizes or MembraneVoltages, replace with corresponding structure quantity in newReactionStep
        Kinetics oldKinetics = copyFromReactionStep.getKinetics();
        KineticsParameter[] oldKps = oldKinetics.getKineticsParameters();
        KineticsProxyParameter[] oldKprps = oldKinetics.getProxyParameters();
        Hashtable<String, Expression> paramExprHash = new Hashtable<String, Expression>();
        for (int i = 0; oldKps != null && i < oldKps.length; i++) {
            Expression newExpression = new Expression(oldKps[i].getExpression());
            for (int j = 0; oldKprps != null && j < oldKprps.length; j++) {
                // check if kinetic proxy parameter is in kinetic parameter expression
                if (newExpression.hasSymbol(oldKprps[j].getName())) {
                    SymbolTableEntry ste = oldKprps[j].getTarget();
                    Model pasteFromModel = copyFromReactionStep.getModel();
                    if (ste instanceof SpeciesContext) {
                        // if newRxnStruct is a feature/membrane, get matching spContexts from old reaction and replace them in new rate expr.
                        SpeciesContext oldSC = (SpeciesContext) ste;
                        SpeciesContext newSC = speciesContextHash.get(oldSC);
                        if (newSC == null) {
                            // check if oldSc is present in paste-model; if not, add it.
                            if (!pasteToModel.equals(pasteFromModel)) {
                                if (pasteToModel.getSpeciesContext(oldSC.getName()) == null) {
                                    // if paste-model has oldSc struct, paste it there,
                                    Structure newSCStruct = pasteToModel.getStructure(oldSC.getStructure().getName());
                                    if (newSCStruct != null) {
                                        newSC = pasteSpecies(parent, oldSC.getSpecies(), null, pasteToModel, newSCStruct, bNew, /*bUseDBSpecies,*/
                                        speciesHash, UserResolvedRxElements.getPreferredReactionElement(userResolvedRxElements, oldSC));
                                        speciesContextHash.put(oldSC, newSC);
                                    } else {
                                        // oldStruct wasn't found in paste-model, paste it in newRxnStruct and add warning to issues list
                                        newSC = pasteSpecies(parent, oldSC.getSpecies(), null, pasteToModel, toRxnStruct, bNew, /*bUseDBSpecies,*/
                                        speciesHash, UserResolvedRxElements.getPreferredReactionElement(userResolvedRxElements, oldSC));
                                        speciesContextHash.put(oldSC, newSC);
                                        Issue issue = new Issue(oldSC, issueContext, IssueCategory.CopyPaste, "SpeciesContext '" + oldSC.getSpecies().getCommonName() + "' was not found in compartment '" + oldSC.getStructure().getName() + "' in the model; the species was added to the compartment '" + toRxnStruct.getName() + "' where the reaction was pasted.", Issue.SEVERITY_WARNING);
                                        issueVector.add(issue);
                                    }
                                }
                            }
                        // if models are the same and newSc is null, then oldSc is not a rxnParticipant. Leave it as is in the expr.
                        }
                        if (newSC != null) {
                            reactionsAndSpeciesContexts.put(newSC, oldSC);
                            newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(newSC.getName()));
                        }
                    // SpeciesContext sc = null;
                    // Species newSp = model.getSpecies(oldSc.getSpecies().getCommonName());
                    // if  (oldSc.getStructure() == (oldRxnStruct)) {
                    // sc = model.getSpeciesContext(newSp, newRxnStruct);
                    // } else {
                    // if (newRxnStruct instanceof Membrane) {
                    // // for a membrane, we need to make sure that inside-outside spContexts used are appropriately replaced.
                    // if (oldSc.getStructure() == ((Membrane)oldRxnStruct).getOutsideFeature()) {
                    // // old speciesContext is outside (old) membrane, new spContext should be outside new membrane
                    // sc = model.getSpeciesContext(newSp, ((Membrane)newRxnStruct).getOutsideFeature());
                    // } else if (oldSc.getStructure() == ((Membrane)oldRxnStruct).getInsideFeature()) {
                    // // old speciesContext is inside (old) membrane, new spContext should be inside new membrane
                    // sc = model.getSpeciesContext(newSp, ((Membrane)newRxnStruct).getInsideFeature());
                    // }
                    // }
                    // }
                    // if (sc != null) {
                    // newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(sc.getName()));
                    // }
                    } else if (ste instanceof StructureSize) {
                        Structure str = ((StructureSize) ste).getStructure();
                        // if the structure size used is same as the structure in which the reaction is present, change the structSize to appropriate new struct
                        if (str.compareEqual(fromRxnStruct)) {
                            newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(toRxnStruct.getStructureSize().getName()));
                        } else {
                            if (fromRxnStruct instanceof Membrane) {
                                if (str.equals(structTopology.getOutsideFeature((Membrane) fromRxnStruct))) {
                                    newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(structTopology.getOutsideFeature((Membrane) toRxnStruct).getStructureSize().getName()));
                                } else if (str.equals(structTopology.getInsideFeature((Membrane) fromRxnStruct))) {
                                    newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(structTopology.getInsideFeature((Membrane) toRxnStruct).getStructureSize().getName()));
                                }
                            }
                        }
                    } else if (ste instanceof MembraneVoltage) {
                        Membrane membr = ((MembraneVoltage) ste).getMembrane();
                        // if the MembraneVoltage used is same as that of the membrane in which the reaction is present, change the MemVoltage
                        if ((fromRxnStruct instanceof Membrane) && (membr.compareEqual(fromRxnStruct))) {
                            newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(((Membrane) toRxnStruct).getMembraneVoltage().getName()));
                        }
                    } else if (ste instanceof ModelParameter) {
                        // see if model has this global parameter (if rxn is being pasted into another model, it won't)
                        if (!pasteToModel.equals(pasteFromModel)) {
                            ModelParameter oldMp = (ModelParameter) ste;
                            ModelParameter mp = pasteToModel.getModelParameter(oldMp.getName());
                            boolean bNonNumeric = false;
                            String newMpName = oldMp.getName();
                            if (mp != null) {
                                // new model has a model parameter with same name - are they the same param?
                                if (!mp.getExpression().equals(oldMp.getExpression())) {
                                    // no, they are not the same param, so mangle the 'ste' name and add as global in the other model
                                    while (pasteToModel.getModelParameter(newMpName) != null) {
                                        newMpName = TokenMangler.getNextEnumeratedToken(newMpName);
                                    }
                                    // if expression if numeric, add it as such. If not, set it to 0.0 and add it as global
                                    Expression exp = oldMp.getExpression();
                                    if (!exp.flatten().isNumeric()) {
                                        exp = new Expression(0.0);
                                        bNonNumeric = true;
                                    }
                                    ModelParameter newMp = pasteToModel.new ModelParameter(newMpName, exp, Model.ROLE_UserDefined, oldMp.getUnitDefinition());
                                    String annotation = "Copied from model : " + pasteFromModel.getNameScope();
                                    newMp.setModelParameterAnnotation(annotation);
                                    pasteToModel.addModelParameter(newMp);
                                    // if global param name had to be changed, make sure newExpr is updated as well.
                                    if (!newMpName.equals(oldMp.getName())) {
                                        newExpression.substituteInPlace(new Expression(oldMp.getName()), new Expression(newMpName));
                                    }
                                }
                            } else {
                                // no global param with same name was found in other model, so add it to other model.
                                // if expression if numeric, add it as such. If not, set it to 0.0 and add it as global
                                Expression exp = oldMp.getExpression();
                                if (!exp.flatten().isNumeric()) {
                                    exp = new Expression(0.0);
                                    bNonNumeric = true;
                                }
                                ModelParameter newMp = pasteToModel.new ModelParameter(newMpName, exp, Model.ROLE_UserDefined, oldMp.getUnitDefinition());
                                String annotation = "Copied from model : " + pasteFromModel.getNameScope();
                                newMp.setModelParameterAnnotation(annotation);
                                pasteToModel.addModelParameter(newMp);
                            }
                            // if a non-numeric parameter was encountered in the old model, it was added as a numeric (0.0), warn user of change.
                            if (bNonNumeric) {
                                Issue issue = new Issue(oldMp, issueContext, IssueCategory.CopyPaste, "Global parameter '" + oldMp.getName() + "' was non-numeric; it has been added " + "as global parameter '" + newMpName + "' in the new model with value = 0.0. " + "Please update its value, if required, before using it.", Issue.SEVERITY_WARNING);
                                issueVector.add(issue);
                            }
                        }
                    }
                }
            // end - if newExpr.hasSymbol(ProxyParam)
            }
            // now if store <param names, new expression> in hashTable
            if (paramExprHash.get(oldKps[i].getName()) == null) {
                paramExprHash.put(oldKps[i].getName(), newExpression);
            }
        }
        // end for - oldKps (old kinetic parameters)
        // use this new expression to generate 'vcml' for the (new) kinetics (easier way to transfer all kinetic parameters)
        String newKineticsStr = oldKinetics.writeTokensWithReplacingProxyParams(paramExprHash);
        // convert the kinetics 'vcml' to tokens.
        CommentStringTokenizer kineticsTokens = new CommentStringTokenizer(newKineticsStr);
        // skip the first token;
        kineticsTokens.nextToken();
        // second token is the kinetic type; use this to create a dummy kinetics
        String kineticType = kineticsTokens.nextToken();
        Kinetics newkinetics = KineticsDescription.fromVCMLKineticsName(kineticType).createKinetics(newReactionStep);
        // use the remaining tokens to construct the new kinetics
        newkinetics.fromTokens(newKineticsStr);
        // bind newkinetics to newReactionStep and add it to newReactionStep
        newkinetics.bind(newReactionStep);
        newReactionStep.setKinetics(newkinetics);
        counter += 1;
        if (counter == copyFromRxSteps.length) {
            break;
        }
        if (!copiedStructName.equals(fromRxnStruct.getName())) {
            if (currentStruct instanceof Feature) {
                currentStruct = structTopology.getMembrane((Feature) currentStruct);
            } else if (currentStruct instanceof Membrane) {
                currentStruct = structTopology.getInsideFeature((Membrane) currentStruct);
            }
        }
        copiedStructName = fromRxnStruct.getName();
    } while (true);
    return new PasteHelper(issueVector, rxPartMapStructure, reactionsAndSpeciesContexts);
}
Also used : Issue(org.vcell.util.Issue) IdentityHashMap(java.util.IdentityHashMap) HashMap(java.util.HashMap) LinkedHashMap(java.util.LinkedHashMap) IdentityHashMap(java.util.IdentityHashMap) Product(cbit.vcell.model.Product) FluxReaction(cbit.vcell.model.FluxReaction) SpeciesContext(cbit.vcell.model.SpeciesContext) Reactant(cbit.vcell.model.Reactant) Feature(cbit.vcell.model.Feature) SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry) KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter) Membrane(cbit.vcell.model.Membrane) Structure(cbit.vcell.model.Structure) Species(cbit.vcell.model.Species) Vector(java.util.Vector) SimpleReaction(cbit.vcell.model.SimpleReaction) KineticsProxyParameter(cbit.vcell.model.Kinetics.KineticsProxyParameter) StructureTopology(cbit.vcell.model.Model.StructureTopology) Hashtable(java.util.Hashtable) BioModelEntityObject(cbit.vcell.model.BioModelEntityObject) StructureSize(cbit.vcell.model.Structure.StructureSize) PropertyVetoException(java.beans.PropertyVetoException) ExpressionBindingException(cbit.vcell.parser.ExpressionBindingException) ModelException(cbit.vcell.model.ModelException) UserCancelException(org.vcell.util.UserCancelException) ModelParameter(cbit.vcell.model.Model.ModelParameter) Expression(cbit.vcell.parser.Expression) MembraneVoltage(cbit.vcell.model.Membrane.MembraneVoltage) ReactionStep(cbit.vcell.model.ReactionStep) Model(cbit.vcell.model.Model) CommentStringTokenizer(org.vcell.util.CommentStringTokenizer) Kinetics(cbit.vcell.model.Kinetics) ReactionParticipant(cbit.vcell.model.ReactionParticipant) Catalyst(cbit.vcell.model.Catalyst)

Example 37 with Feature

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

the class ReactionCartoonTool method lineAction.

private void lineAction(Structure startStructure, SpeciesContext speciesContextEnd) throws PropertyVetoException, Exception {
    Structure endStructure = speciesContextEnd.getStructure();
    Model model = getModel();
    ReactionStep reaction = null;
    Point startPos = edgeShape.getStart();
    Point endPos = edgeShape.getEnd();
    Structure reactionStructure = null;
    if (startStructure != endStructure) {
        if (startStructure instanceof Feature && endStructure instanceof Feature) {
            // Feature ==> Feature-speciesContext
            Feature startFeature = (Feature) startStructure;
            Feature endFeature = (Feature) endStructure;
            // Feature ==> feature-speciesContext with no membrane between : create a 0th-order simpleReaction in startFeature with GeneralLumpedKinetics
            reactionStructure = startStructure;
            reaction = model.createSimpleReaction(reactionStructure);
            reaction.setKinetics(new GeneralLumpedKinetics(reaction));
        } else if (startStructure instanceof Feature && endStructure instanceof Membrane) {
            // Feature ==> membrane-species : Create volume species ; create membrane reaction ; add volume species as reactant and membrane species(End) as product.
            reactionStructure = endStructure;
            reaction = model.createSimpleReaction(reactionStructure);
            SpeciesContext startingSpeciesContext = model.createSpeciesContext(startStructure);
            reaction.addReactant(startingSpeciesContext, 1);
            positionShapeForObject(startStructure, startingSpeciesContext, startPos);
        } else if (startStructure instanceof Membrane && endStructure instanceof Feature) {
            // Membrane ==> Feature-species : 0th-order reaction in membrane
            reactionStructure = startStructure;
            reaction = model.createSimpleReaction(reactionStructure);
        } else if (startStructure instanceof Membrane && endStructure instanceof Membrane) {
            // Membrane ==> membrane-species : the 2 membranes are different : create a 0th-order lumped simpleReaction in startMembrane
            reactionStructure = startStructure;
            reaction = model.createSimpleReaction(reactionStructure);
            reaction.setKinetics(new GeneralLumpedKinetics(reaction));
        }
    } else {
        // startStructure == endStructure : 0th-order simplereaction in structure
        reactionStructure = startStructure;
        reaction = model.createSimpleReaction(reactionStructure);
    }
    // speciesContextEnd should be added as a product to reaction (if not flux).
    if (!(reaction instanceof FluxReaction)) {
        reaction.addProduct(speciesContextEnd, 1);
    }
    positionShapeForObject(reactionStructure, reaction, new Point((2 * startPos.x + 8 * endPos.x) / 10, (2 * startPos.y + 8 * endPos.y) / 10));
    getReactionCartoon().notifyChangeEvent();
    getGraphModel().clearSelection();
    getGraphModel().select(reaction);
}
Also used : ReactionStep(cbit.vcell.model.ReactionStep) Model(cbit.vcell.model.Model) BioModel(cbit.vcell.biomodel.BioModel) GraphModel(cbit.gui.graph.GraphModel) Membrane(cbit.vcell.model.Membrane) FluxReaction(cbit.vcell.model.FluxReaction) Point(java.awt.Point) GeneralLumpedKinetics(cbit.vcell.model.GeneralLumpedKinetics) SpeciesContext(cbit.vcell.model.SpeciesContext) Structure(cbit.vcell.model.Structure) Feature(cbit.vcell.model.Feature)

Example 38 with Feature

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

the class ReactStepDbDriver method populateStructureAndElectricalTopology.

public static void populateStructureAndElectricalTopology(Model model, HashMap<KeyValue, StructureKeys> structureKeysMap) throws DataAccessException {
    // 
    for (Structure structure : model.getStructures()) {
        // get parent struct
        KeyValue parentKey = structureKeysMap.get(structure.getKey()).parentKey;
        Structure parentStructure = null;
        if (parentKey != null) {
            for (Structure struct1 : model.getStructures()) {
                if (struct1.getKey().equals(parentKey)) {
                    parentStructure = struct1;
                    break;
                }
            }
        }
        if (parentStructure != null) {
            StructureTopology structureTopology = model.getStructureTopology();
            if (structure instanceof Feature) {
                Feature feature = (Feature) structure;
                if (parentStructure instanceof Feature) {
                    // feature.setParentFeature((Feature)parent);
                    throw new DataAccessException("Feature is not permitted to be the parent of another feature");
                } else if (parentStructure instanceof Membrane) {
                    structureTopology.setInsideFeature((Membrane) parentStructure, feature);
                }
            } else if (structure instanceof Membrane) {
                Membrane membrane = (Membrane) structure;
                if (parentStructure instanceof Feature) {
                    structureTopology.setOutsideFeature(membrane, (Feature) parentStructure);
                } else {
                    throw new DataAccessException("Membrane '" + membrane.getName() + "' is not permitted to be the parent of another membrane '" + parentStructure.getName());
                }
            }
        }
        if (structure instanceof Membrane) {
            Membrane membrane = (Membrane) structure;
            KeyValue negKey = structureKeysMap.get(structure.getKey()).negKey;
            if (negKey != null) {
                for (Structure struct : model.getStructures()) {
                    if (struct instanceof Feature && struct.getKey().equals(negKey)) {
                        Feature feature = (Feature) struct;
                        model.getElectricalTopology().setNegativeFeature(membrane, feature);
                        break;
                    }
                }
            }
            KeyValue posKey = structureKeysMap.get(structure.getKey()).posKey;
            if (posKey != null) {
                for (Structure struct : model.getStructures()) {
                    if (struct instanceof Feature && struct.getKey().equals(posKey)) {
                        Feature feature = (Feature) struct;
                        model.getElectricalTopology().setPositiveFeature(membrane, feature);
                        break;
                    }
                }
            }
        }
    }
}
Also used : KeyValue(org.vcell.util.document.KeyValue) StructureTopology(cbit.vcell.model.Model.StructureTopology) Membrane(cbit.vcell.model.Membrane) Structure(cbit.vcell.model.Structure) Feature(cbit.vcell.model.Feature) DataAccessException(org.vcell.util.DataAccessException)

Example 39 with Feature

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

the class ReactionCartoonTool method lineActon.

private void lineActon(Structure startStructure, ReactionStep reactionEnd) throws Exception {
    Structure endStructure = reactionEnd.getStructure();
    if (StructureUtil.reactionHereCanHaveParticipantThere(endStructure, startStructure)) {
        // if reactionStart is a SimpleRxn OR FluxRxn without a product, add speciesContext as reactant
        if ((reactionEnd instanceof SimpleReaction) || ((reactionEnd instanceof FluxReaction) && !reactionEnd.hasReactant())) {
            SpeciesContext speciesContext = getReactionCartoon().getModel().createSpeciesContext(startStructure);
            reactionEnd.addReactant(speciesContext, 1);
            positionShapeForObject(startStructure, speciesContext, edgeShape.getStart());
        }
        if (((startStructure instanceof Feature && endStructure instanceof Feature) || (startStructure instanceof Membrane && endStructure instanceof Membrane)) && startStructure != endStructure) {
        // ============ change kinetics to lumped or warn user ?????????
        // simpleReaction.setKinetics(new GeneralLumpedKinetics(simpleReaction));
        }
        getReactionCartoon().notifyChangeEvent();
    }
}
Also used : SimpleReaction(cbit.vcell.model.SimpleReaction) Membrane(cbit.vcell.model.Membrane) FluxReaction(cbit.vcell.model.FluxReaction) SpeciesContext(cbit.vcell.model.SpeciesContext) Structure(cbit.vcell.model.Structure) Feature(cbit.vcell.model.Feature)

Example 40 with Feature

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

the class ReactionCartoonTool method lineAction.

private void lineAction(SpeciesContext speciesContextStart, SpeciesContext speciesContextEnd) throws Exception {
    Structure endStructure = speciesContextEnd.getStructure();
    Structure startStructure = speciesContextStart.getStructure();
    Model model = getModel();
    ReactionStep reaction = null;
    Point startPos = edgeShape.getStart();
    Point endPos = edgeShape.getEnd();
    Structure reactionStructure = null;
    boolean bLumpedKinetics = false;
    if (startStructure != endStructure) {
        if (startStructure instanceof Feature && endStructure instanceof Feature) {
            // Feature-speciesContext ==> Feature-speciesContext
            Membrane membraneBetween = model.getStructureTopology().getMembrane((Feature) startStructure, (Feature) endStructure);
            // Feature-speciesContext ==> Feature-speciesContext with membrane in between : add reaction in Membrane (scStart : reactant; scEnd : pdt)
            if (membraneBetween != null) {
                reactionStructure = membraneBetween;
            } else {
                // Feature-speciesContext ==> Feature-speciesContext with no membrane between : create a lumped reaction in startFeature
                reactionStructure = startStructure;
                bLumpedKinetics = true;
            }
        } else if (startStructure instanceof Feature && endStructure instanceof Membrane) {
            // Feature-speciesContext ==> Membrane-speciesContext : create membrane reaction ; add scStart : reactant and scEnd : pdt.
            reactionStructure = endStructure;
        } else if (startStructure instanceof Membrane && endStructure instanceof Feature) {
            // Membrane-speciesContext ==> Feature-speciesContext : create reaction in membrane; scStart : reactant, scEnd : pdt.
            reactionStructure = startStructure;
        } else if (startStructure instanceof Membrane && endStructure instanceof Membrane) {
            // Membrane-speciesContext ==> Membrane-speciesContext : the 2 membranes are different : create lumped reaction in endMembrane
            reactionStructure = endStructure;
            bLumpedKinetics = true;
        }
    } else {
        // startStructure == endStructure : create reaction in structure
        reactionStructure = startStructure;
    }
    reaction = model.createSimpleReaction(reactionStructure);
    if (bLumpedKinetics) {
        reaction.setKinetics(new GeneralLumpedKinetics(reaction));
    }
    reaction.addReactant(speciesContextStart, 1);
    reaction.addProduct(speciesContextEnd, 1);
    positionShapeForObject(reactionStructure, reaction, new Point((startPos.x + endPos.x) / 2, (startPos.y + endPos.y) / 2));
    getReactionCartoon().notifyChangeEvent();
    getGraphModel().clearSelection();
    getGraphModel().select(reaction);
}
Also used : ReactionStep(cbit.vcell.model.ReactionStep) Model(cbit.vcell.model.Model) BioModel(cbit.vcell.biomodel.BioModel) GraphModel(cbit.gui.graph.GraphModel) Membrane(cbit.vcell.model.Membrane) Point(java.awt.Point) GeneralLumpedKinetics(cbit.vcell.model.GeneralLumpedKinetics) Structure(cbit.vcell.model.Structure) Feature(cbit.vcell.model.Feature)

Aggregations

Feature (cbit.vcell.model.Feature)71 Membrane (cbit.vcell.model.Membrane)50 Structure (cbit.vcell.model.Structure)36 Expression (cbit.vcell.parser.Expression)29 SpeciesContext (cbit.vcell.model.SpeciesContext)25 PropertyVetoException (java.beans.PropertyVetoException)18 Model (cbit.vcell.model.Model)16 StructureTopology (cbit.vcell.model.Model.StructureTopology)16 SimpleReaction (cbit.vcell.model.SimpleReaction)15 SubVolume (cbit.vcell.geometry.SubVolume)14 MembraneMapping (cbit.vcell.mapping.MembraneMapping)14 SurfaceClass (cbit.vcell.geometry.SurfaceClass)13 FeatureMapping (cbit.vcell.mapping.FeatureMapping)13 ExpressionException (cbit.vcell.parser.ExpressionException)13 FluxReaction (cbit.vcell.model.FluxReaction)12 ReactionStep (cbit.vcell.model.ReactionStep)12 KeyValue (org.vcell.util.document.KeyValue)12 BioModel (cbit.vcell.biomodel.BioModel)11 StructureMapping (cbit.vcell.mapping.StructureMapping)11 ModelUnitSystem (cbit.vcell.model.ModelUnitSystem)11