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);
}
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);
}
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;
}
}
}
}
}
}
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();
}
}
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);
}
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