use of cbit.vcell.model.Product in project vcell by virtualcell.
the class ReactionCartoonTool method getLineTypeFromAttachment.
private LineType getLineTypeFromAttachment(SpeciesContext speciesContext, Point worldPoint) throws Exception {
Shape mouseOverShape = getReactionCartoon().pickWorld(worldPoint);
if (mouseOverShape instanceof ReactionStepShape) {
// check if the ReactionStep already has a ReactionParticipant for
// this SpeciesContext
ReactionStep reactionStep = (ReactionStep) mouseOverShape.getModelObject();
ReactionParticipant[] rps = reactionStep.getReactionParticipants();
if (mouseOverShape instanceof SimpleReactionShape) {
switch(mouseOverShape.getAttachmentFromAbs(worldPoint)) {
case Shape.ATTACH_LEFT:
{
for (int i = 0; i < rps.length; i++) {
if (rps[i] instanceof Reactant && rps[i].getSpeciesContext() == speciesContext) {
return LineType.NULL;
}
}
return LineType.REACTANT;
}
case Shape.ATTACH_CENTER:
{
for (int i = 0; i < rps.length; i++) {
if (rps[i] instanceof Catalyst && rps[i].getSpeciesContext() == speciesContext) {
return LineType.NULL;
}
}
return LineType.CATALYST;
}
case Shape.ATTACH_RIGHT:
{
for (int i = 0; i < rps.length; i++) {
if (rps[i] instanceof Product && rps[i].getSpeciesContext() == speciesContext) {
return LineType.NULL;
}
}
return LineType.PRODUCT;
}
}
} else if (mouseOverShape instanceof FluxReactionShape) {
switch(mouseOverShape.getAttachmentFromAbs(worldPoint)) {
case Shape.ATTACH_LEFT:
{
// return LineType.FLUX;
for (int i = 0; i < rps.length; i++) {
if (rps[i] instanceof Reactant && rps[i].getSpeciesContext() == speciesContext) {
return LineType.NULL;
}
}
return LineType.REACTANT;
}
case Shape.ATTACH_CENTER:
{
for (int i = 0; i < rps.length; i++) {
if (rps[i] instanceof Catalyst && rps[i].getSpeciesContext() == speciesContext) {
return LineType.NULL;
}
}
return LineType.CATALYST;
}
case Shape.ATTACH_RIGHT:
{
for (int i = 0; i < rps.length; i++) {
// return LineType.FLUX;
if (rps[i] instanceof Product && rps[i].getSpeciesContext() == speciesContext) {
return LineType.NULL;
}
}
return LineType.PRODUCT;
}
}
}
}
return LineType.NULL;
}
use of cbit.vcell.model.Product 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.Product in project vcell by virtualcell.
the class DBReactionWizardPanel method parameterNameSelectionChanged.
/**
* Comment
*/
private void parameterNameSelectionChanged() {
try {
javax.swing.DefaultListModel dlm = (javax.swing.DefaultListModel) getParameterValuesJList().getModel();
dlm.removeAllElements();
//
if (getParameterNamesJList().getSelectedValue() != null) {
// final cbit.vcell.clientdb.DocumentManager docManager = getDocumentManager();
// final javax.swing.JList jlist = getReactionsJList();
final MapStringToObject parameNameMSO = (MapStringToObject) getParameterNamesJList().getSelectedValue();
final KeyValue reactionStepKey = ((ReactionStepInfo) parameNameMSO.getToObject()).getReactionKey();
//
final String RXSTEP_HASH_VALUE_KEY = "rxStep";
AsynchClientTask searchReactions = new AsynchClientTask("Getting Full Reaction", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
public void run(Hashtable<String, Object> hash) throws Exception {
Model reactionModel = getDocumentManager().getReactionStepAsModel(reactionStepKey);
ReactionStep rStep = reactionModel.getReactionStep(((ReactionStepInfo) parameNameMSO.getToObject()).getReactionName());
if (rStep != null) {
rStep.rebindAllToModel(reactionModel);
hash.put(RXSTEP_HASH_VALUE_KEY, rStep);
}
}
};
//
AsynchClientTask updateRXParams = new AsynchClientTask("updateRXParams", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
public void run(Hashtable<String, Object> hash) throws DataAccessException {
ReactionStep rStep = (ReactionStep) hash.get(RXSTEP_HASH_VALUE_KEY);
if (rStep != null) {
Kinetics.KineticsParameter[] kpArr = rStep.getKinetics().getKineticsParameters();
ReactionParticipant[] rpArr = rStep.getReactionParticipants();
//
javax.swing.DefaultListModel pvdlm = (javax.swing.DefaultListModel) getParameterValuesJList().getModel();
pvdlm.removeAllElements();
for (int i = 0; i < kpArr.length; i += 1) {
pvdlm.addElement("Parameter - " + kpArr[i].getName().toString() + " = " + kpArr[i].getExpression().infix());
}
pvdlm.addElement("PhysicsOption=" + rStep.getPhysicsOptions());
for (int i = 0; i < rpArr.length; i += 1) {
String role = "Unknown";
if (rpArr[i] instanceof Reactant) {
role = "Reactant";
} else if (rpArr[i] instanceof Product) {
role = "Product";
} else if (rpArr[i] instanceof Catalyst) {
role = "Catalyst";
}
String fluxFlag = "";
// if(rStep instanceof FluxReaction){
// Membrane rStepStruct = (Membrane)rStep.getStructure();
// if(rpArr[i] instanceof Flux){
// if(rpArr[i].getStructure().equals(getModel().getStructureTopology().getOutsideFeature(rStepStruct))){
// fluxFlag = "Outside";
// }else{
// fluxFlag = "Inside";
// }
// }
// }
pvdlm.addElement("RXParticipant(" + role + ") " + fluxFlag + " " + (rpArr[i].getSpecies().getDBSpecies() != null ? "*" : "-") + " " + rpArr[i].getSpeciesContext().getName());
}
}
setReactionStep(rStep);
configureBFN();
}
};
//
Hashtable<String, Object> hashTemp = new Hashtable<String, Object>();
ClientTaskDispatcher.dispatch(this, hashTemp, new AsynchClientTask[] { searchReactions, updateRXParams }, true);
} else {
setReactionStep(null);
}
} catch (Exception e) {
PopupGenerator.showErrorDialog(this, e.getMessage(), e);
}
//
configureBFN();
}
use of cbit.vcell.model.Product in project vcell by virtualcell.
the class SimulationContext method checkValidity.
public void checkValidity() throws MappingException {
// spatial
if (getGeometry().getDimension() > 0) {
//
// fail if any enabled Reactions have LumpedKinetics.
//
// StringBuffer buffer = new StringBuffer();
// ReactionSpec[] reactionSpecs = getReactionContext().getReactionSpecs();
// for (int i = 0; i < reactionSpecs.length; i++) {
// if (!reactionSpecs[i].isExcluded() && reactionSpecs[i].getReactionStep().getKinetics() instanceof LumpedKinetics){
// buffer.append("reaction \""+reactionSpecs[i].getReactionStep().getName()+"\" in compartment \""+reactionSpecs[i].getReactionStep().getStructure().getName()+"\"\n");
// }
// }
// if (buffer.length()>0){
// throw new MappingException("Spatial application \""+getName()+"\" cannot process reactions with spatially lumped kinetics, see kinetics for :\n"+buffer.toString());
//
// }
} else {
// old-style ODE models should still work
if (applicationType == Application.NETWORK_DETERMINISTIC && getGeometryContext().isAllVolFracAndSurfVolSpecified() && getGeometryContext().isAllSizeSpecifiedNull()) {
// old style ODE models
return;
}
// otherwise, all sizes should be present and positive.
if (!getGeometryContext().isAllSizeSpecifiedPositive()) {
throw new MappingException("Application " + getName() + ":\nAll structure sizes must be assigned positive values.\nPlease go to StructureMapping tab to check the sizes.");
}
// if rate rules are present, if any species has a rate rules, it should not be a reaction participant in any reaction.
RateRule[] rateRules = getRateRules();
if (rateRules != null && rateRules.length > 0) {
if (getModel() != null) {
ReactionStep[] reactionSteps = getModel().getReactionSteps();
ReactionParticipant[] reactionParticipants = null;
for (ReactionStep rs : reactionSteps) {
reactionParticipants = rs.getReactionParticipants();
for (ReactionParticipant rp : reactionParticipants) {
if (rp instanceof Reactant || rp instanceof Product) {
if (getRateRule(rp.getSpeciesContext()) != null) {
throw new RuntimeException("Species '" + rp.getSpeciesContext().getName() + "' is a reactant/product in reaction '" + rs.getName() + "' ; cannot also have a rate rule.");
}
}
}
}
}
}
}
}
use of cbit.vcell.model.Product in project vcell by virtualcell.
the class SpeciesContextSpec method gatherIssues.
/**
* Insert the method's description here.
* Creation date: (11/1/2005 10:03:46 AM)
* @param issueVector java.util.Vector
*/
public void gatherIssues(IssueContext issueContext, List<Issue> issueVector) {
issueContext = issueContext.newChildContext(ContextType.SpeciesContextSpec, this);
//
for (int i = 0; i < fieldParameters.length; i++) {
RealInterval simpleBounds = parameterBounds[fieldParameters[i].getRole()];
if (simpleBounds != null) {
String parmName = fieldParameters[i].getNameScope().getName() + "." + fieldParameters[i].getName();
issueVector.add(new SimpleBoundsIssue(fieldParameters[i], issueContext, simpleBounds, "parameter " + parmName + ": must be within " + simpleBounds.toString()));
}
}
if (bForceContinuous && !bConstant && getSimulationContext().isStoch() && (getSimulationContext().getGeometry().getDimension() > 0)) {
// if it's particle or constant we're good
SpeciesContext sc = getSpeciesContext();
ReactionContext rc = getSimulationContext().getReactionContext();
ReactionSpec[] rsArray = rc.getReactionSpecs();
for (ReactionSpec rs : rsArray) {
if (!rs.isExcluded()) {
// we only care about reactions which are not excluded
// true if "this" is part of current reaction
boolean iAmParticipant = false;
// true if current reaction has at least a particle participant
boolean haveParticle = false;
ReactionStep step = rs.getReactionStep();
for (ReactionParticipant p : step.getReactionParticipants()) {
if (p instanceof Product || p instanceof Reactant) {
SpeciesContextSpec candidate = rc.getSpeciesContextSpec(p.getSpeciesContext());
if (candidate == this) {
iAmParticipant = true;
} else if (!candidate.isForceContinuous() && !candidate.isConstant()) {
haveParticle = true;
}
}
}
if (iAmParticipant && haveParticle) {
String msg = "Continuous Species won't conserve mass in particle reaction " + rs.getReactionStep().getName() + ".";
String tip = "Mass conservation for reactions of binding between discrete and continuous species is handled approximately. <br>" + "To avoid any algorithmic approximation, which may produce undesired results, the user is advised to indicate <br>" + "the continuous species in those reactions as modifiers (i.e. 'catalysts') in the physiology.";
issueVector.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, tip, Issue.SEVERITY_WARNING));
// we issue warning as soon as we found the first reaction which satisfies criteria
break;
}
}
}
}
if (!bForceContinuous && bConstant) {
if (getSimulationContext().isStoch() && (getSimulationContext().getGeometry().getDimension() > 0)) {
String msg = "Clamped Species must be continuous rather than particles.";
String tip = "If choose 'clamped', must also choose 'forceContinuous'";
issueVector.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, tip, Issue.SEVERITY_ERROR));
}
}
if (bForceContinuous && !bConstant) {
if (getSimulationContext().isStoch() && (getSimulationContext().getGeometry().getDimension() == 0)) {
String msg = "Non-constant species is forced continuous, not supported for nonspatial stochastic applications.";
issueVector.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.SEVERITY_ERROR));
}
}
}
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