Example 6 with ExpressionBindingException
use of cbit.vcell.parser.ExpressionBindingException in project vcell by virtualcell.
the class Kinetics method cleanupParameters.
/**
* This method was created in VisualAge.
*/
private final void cleanupParameters() throws ModelException, ExpressionException, PropertyVetoException {
if (bReading) {
return;
}
//
if (fieldKineticsParameters != null) {
for (int i = 0; i < fieldKineticsParameters.length; i++) {
if (fieldKineticsParameters[i].getRole() == ROLE_UserDefined && !isReferenced(fieldKineticsParameters[i], 0)) {
removeKineticsParameter(fieldKineticsParameters[i]);
i--;
}
}
}
if (fieldUnresolvedParameters != null) {
for (int i = 0; i < fieldUnresolvedParameters.length; i++) {
if (!isReferenced(fieldUnresolvedParameters[i], 0)) {
removeUnresolvedParameter(fieldUnresolvedParameters[i]);
i--;
}
}
}
if (fieldProxyParameters != null) {
for (int i = 0; i < fieldProxyParameters.length; i++) {
if (!isReferenced(fieldProxyParameters[i], 0)) {
removeProxyParameter(fieldProxyParameters[i]);
i--;
}
}
}
if (fieldKineticsParameters != null) {
for (int i = 0; i < fieldKineticsParameters.length; i++) {
Expression exp = fieldKineticsParameters[i].getExpression();
if (exp != null) {
try {
exp.bindExpression(reactionStep);
} catch (ExpressionBindingException e) {
System.out.println("error binding expression '" + exp.infix() + "': " + e.getMessage());
}
}
}
}
// resolveUndefinedUnits();
}
Also used :
Expression(cbit.vcell.parser.Expression)
ExpressionBindingException(cbit.vcell.parser.ExpressionBindingException)
Example 7 with ExpressionBindingException
use of cbit.vcell.parser.ExpressionBindingException in project vcell by virtualcell.
the class Model method refreshDependencies.
/**
* Insert the method's description here.
* Creation date: (5/22/00 10:50:08 PM)
*/
public void refreshDependencies() {
removePropertyChangeListener(this);
removeVetoableChangeListener(this);
addVetoableChangeListener(this);
addPropertyChangeListener(this);
for (int i = 0; i < fieldStructures.length; i++) {
fieldStructures[i].removePropertyChangeListener(this);
fieldStructures[i].removeVetoableChangeListener(this);
fieldStructures[i].addPropertyChangeListener(this);
fieldStructures[i].addVetoableChangeListener(this);
fieldStructures[i].getStructureSize().removePropertyChangeListener(this);
fieldStructures[i].getStructureSize().removeVetoableChangeListener(this);
fieldStructures[i].getStructureSize().addPropertyChangeListener(this);
fieldStructures[i].getStructureSize().addVetoableChangeListener(this);
if (fieldStructures[i] instanceof Membrane) {
((Membrane) fieldStructures[i]).getMembraneVoltage().removePropertyChangeListener(this);
((Membrane) fieldStructures[i]).getMembraneVoltage().removeVetoableChangeListener(this);
((Membrane) fieldStructures[i]).getMembraneVoltage().addPropertyChangeListener(this);
((Membrane) fieldStructures[i]).getMembraneVoltage().addVetoableChangeListener(this);
}
fieldStructures[i].setModel(this);
}
for (int i = 0; i < fieldSpecies.length; i++) {
fieldSpecies[i].removeVetoableChangeListener(this);
fieldSpecies[i].addVetoableChangeListener(this);
fieldSpecies[i].refreshDependencies();
}
for (int i = 0; i < fieldSpeciesContexts.length; i++) {
fieldSpeciesContexts[i].removePropertyChangeListener(this);
fieldSpeciesContexts[i].removeVetoableChangeListener(this);
fieldSpeciesContexts[i].addPropertyChangeListener(this);
fieldSpeciesContexts[i].addVetoableChangeListener(this);
fieldSpeciesContexts[i].setModel(this);
fieldSpeciesContexts[i].refreshDependencies();
}
for (int i = 0; i < fieldReactionSteps.length; i++) {
fieldReactionSteps[i].removePropertyChangeListener(this);
fieldReactionSteps[i].removeVetoableChangeListener(this);
fieldReactionSteps[i].getKinetics().removePropertyChangeListener(this);
fieldReactionSteps[i].getKinetics().removeVetoableChangeListener(this);
fieldReactionSteps[i].getKinetics().addPropertyChangeListener(this);
fieldReactionSteps[i].getKinetics().addVetoableChangeListener(this);
fieldReactionSteps[i].addPropertyChangeListener(this);
fieldReactionSteps[i].addVetoableChangeListener(this);
fieldReactionSteps[i].setModel(this);
try {
fieldReactionSteps[i].rebindAllToModel(this);
} catch (Exception e) {
e.printStackTrace(System.out);
}
fieldReactionSteps[i].refreshDependencies();
}
for (int i = 0; i < fieldModelParameters.length; i++) {
fieldModelParameters[i].removeVetoableChangeListener(this);
fieldModelParameters[i].removePropertyChangeListener(this);
fieldModelParameters[i].addVetoableChangeListener(Parameter.PROPERTYNAME_NAME, this);
fieldModelParameters[i].addPropertyChangeListener(this);
try {
fieldModelParameters[i].getExpression().bindExpression(this);
} catch (ExpressionBindingException e) {
e.printStackTrace(System.out);
throw new RuntimeException("Error binding global parameter '" + fieldModelParameters[i].getName() + "' to model." + e.getMessage());
}
}
for (int i = 0; i < getRbmModelContainer().getReactionRuleList().size(); i++) {
ReactionRule reactionRule = getRbmModelContainer().getReactionRule(i);
reactionRule.removePropertyChangeListener(this);
reactionRule.removeVetoableChangeListener(this);
reactionRule.getKineticLaw().removePropertyChangeListener(this);
// reactionRule.getKineticLaw().removeVetoableChangeListener(this);
reactionRule.getKineticLaw().addPropertyChangeListener(this);
// reactionRule.getKineticLaw().addVetoableChangeListener(this);
reactionRule.addPropertyChangeListener(this);
reactionRule.addVetoableChangeListener(this);
reactionRule.setModel(this);
try {
reactionRule.rebindAllToModel(this);
} catch (Exception e) {
e.printStackTrace(System.out);
}
reactionRule.refreshDependencies();
}
for (RbmObservable observable : getRbmModelContainer().getObservableList()) {
observable.removePropertyChangeListener(this);
observable.removeVetoableChangeListener(this);
observable.addPropertyChangeListener(this);
observable.addVetoableChangeListener(this);
observable.setModel(this);
}
for (MolecularType molType : getRbmModelContainer().getMolecularTypeList()) {
molType.removePropertyChangeListener(this);
molType.removeVetoableChangeListener(this);
molType.addPropertyChangeListener(this);
molType.addVetoableChangeListener(this);
molType.setModel(this);
}
}
Also used :
MolecularType(org.vcell.model.rbm.MolecularType)
ExpressionBindingException(cbit.vcell.parser.ExpressionBindingException)
VCUnitException(cbit.vcell.units.VCUnitException)
PropertyVetoException(java.beans.PropertyVetoException)
ExpressionBindingException(cbit.vcell.parser.ExpressionBindingException)
ExpressionException(cbit.vcell.parser.ExpressionException)
Example 8 with ExpressionBindingException
use of cbit.vcell.parser.ExpressionBindingException in project vcell by virtualcell.
the class MathDescription method gatherIssues.
/**
* This method was created in VisualAge.
* @return boolean
*/
public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
issueContext = issueContext.newChildContext(ContextType.MathDescription, this);
setWarning(null);
if (geometry == null) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_NoGeometry, VCellErrorMessages.MATH_DESCRIPTION_GEOMETRY_1, Issue.SEVERITY_ERROR);
issueList.add(issue);
}
if (isSpatialStoch() && geometry.getDimension() != 3) {
Issue issue = new Issue(geometry, issueContext, IssueCategory.Smoldyn_Geometry_3DWarning, "VCell spatial stochastic models only support 3D geometry.", Issue.SEVERITY_ERROR);
issueList.add(issue);
}
// check Constant are really constants
for (int i = 0; i < variableList.size(); i++) {
Variable var = variableList.get(i);
if (var instanceof Constant) {
try {
((Constant) var).getExpression().evaluateConstant();
} catch (Exception ex) {
ex.printStackTrace(System.out);
Issue issue = new Issue(var, issueContext, IssueCategory.MathDescription_Constant_NotANumber, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_CONSTANT, var.getExpression().infix()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
}
}
//
// count number of variables of each type
//
int volVarCount = 0;
int memVarCount = 0;
int filVarCount = 0;
int volRegionVarCount = 0;
int memRegionVarCount = 0;
int filRegionVarCount = 0;
int stochVarCount = 0;
int pointVarCount = 0;
for (int i = 0; i < variableList.size(); i++) {
Variable var = variableList.get(i);
if (var instanceof VolVariable) {
volVarCount++;
} else if (var instanceof MemVariable) {
memVarCount++;
} else if (var instanceof FilamentVariable) {
filVarCount++;
} else if (var instanceof VolumeRegionVariable) {
volRegionVarCount++;
} else if (var instanceof MembraneRegionVariable) {
memRegionVarCount++;
} else if (var instanceof FilamentRegionVariable) {
filRegionVarCount++;
} else if (var instanceof StochVolVariable) {
stochVarCount++;
} else if (var instanceof PointVariable) {
pointVarCount++;
}
}
//
for (int i = 0; i < subDomainList.size(); i++) {
try {
SubDomain subDomain = subDomainList.get(i);
Enumeration<Equation> equEnum = subDomain.getEquations();
while (equEnum.hasMoreElements()) {
Equation equ = equEnum.nextElement();
equ.checkValid(this, subDomain);
equ.bind(this);
}
FastSystem fastSystem = subDomain.getFastSystem();
if (fastSystem != null) {
Enumeration<FastRate> frEnum = fastSystem.getFastRates();
while (frEnum.hasMoreElements()) {
FastRate fr = frEnum.nextElement();
fr.bind(this);
}
Enumeration<FastInvariant> fiEnum = fastSystem.getFastInvariants();
while (fiEnum.hasMoreElements()) {
FastInvariant fi = fiEnum.nextElement();
fi.bind(this);
}
}
for (ParticleProperties pp : subDomain.getParticleProperties()) {
pp.bind(this);
}
for (ParticleJumpProcess pjp : subDomain.getParticleJumpProcesses()) {
pjp.bind(this);
Expression rateDefinition = null;
JumpProcessRateDefinition jprd = pjp.getParticleRateDefinition();
if (jprd instanceof MacroscopicRateConstant) {
rateDefinition = MathUtilities.substituteFunctions(((MacroscopicRateConstant) jprd).getExpression(), this);
} else if (jprd instanceof InteractionRadius) {
rateDefinition = MathUtilities.substituteFunctions(((InteractionRadius) jprd).getExpression(), this);
} else {
new RuntimeException("The jump process rate definition is not supported");
}
String[] symbols = rateDefinition.getSymbols();
if (symbols != null) {
for (String symbol : symbols) {
// throw exception for particle variables, particle variable cannot be referenced
Variable var = getVariable(symbol);
if (var instanceof ParticleVariable) {
throw new MathException("Stochastic variables can not be referenced in functions and equations.");
}
if (subDomain instanceof CompartmentSubDomain) {
if ((var instanceof MembraneRegionVariable || var instanceof MemVariable)) {
throw new MathException("Volume reaction: " + pjp.getName() + " cannot reference membrane variable: " + var.getName() + ".");
}
}
}
}
}
} catch (ExpressionBindingException e) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_ExpressionBindingException, e.getMessage(), Issue.SEVERITY_ERROR);
issueList.add(issue);
} catch (ExpressionException e) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_ExpressionException, e.getMessage(), Issue.SEVERITY_ERROR);
issueList.add(issue);
} catch (MathException e) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_MathException, e.getMessage(), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
}
//
if (geometry.getDimension() == 0) {
//
if (subDomainList.size() != 1) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_1, Issue.SEVERITY_ERROR);
issueList.add(issue);
} else if (subDomainList.size() == 1) {
if (!(subDomainList.get(0) instanceof CompartmentSubDomain)) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_2, Issue.SEVERITY_ERROR);
issueList.add(issue);
}
CompartmentSubDomain subDomain = (CompartmentSubDomain) subDomainList.get(0);
// distinguish ODE model and stochastic model
if (isNonSpatialStoch()) {
if (stochVarCount == 0) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_StochasticModel, VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_STOCHASTIC_MODEL_1, Issue.SEVERITY_ERROR);
issueList.add(issue);
}
if (subDomain.getJumpProcesses().size() == 0) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_StochasticModel, VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_STOCHASTIC_MODEL_2, Issue.SEVERITY_ERROR);
issueList.add(issue);
}
// check variable initial condition
for (VarIniCondition varIniCondition : subDomain.getVarIniConditions()) {
Expression iniExp = varIniCondition.getIniVal();
try {
iniExp.bindExpression(this);
} catch (Exception ex) {
ex.printStackTrace(System.out);
setWarning(ex.getMessage());
}
}
// check probability rate
for (JumpProcess jumpProcess : subDomain.getJumpProcesses()) {
Expression probExp = jumpProcess.getProbabilityRate();
try {
probExp.bindExpression(this);
} catch (Exception ex) {
ex.printStackTrace(System.out);
setWarning(ex.getMessage());
}
}
} else if (isRuleBased()) {
} else {
// ODE model
//
// Check that all equations are ODEs
//
int odeCount = 0;
Enumeration<Equation> enum_equ = subDomain.getEquations();
while (enum_equ.hasMoreElements()) {
Equation equ = enum_equ.nextElement();
if (equ instanceof OdeEquation) {
odeCount++;
} else {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_3, Issue.SEVERITY_ERROR);
issueList.add(issue);
}
}
if (odeCount == 0) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_4, Issue.SEVERITY_ERROR);
issueList.add(issue);
}
if (volVarCount != odeCount) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_5, Issue.SEVERITY_ERROR);
issueList.add(issue);
}
if (memVarCount > 0) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_6, VCML.MembraneVariable), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
if (filVarCount > 0) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_6, VCML.FilamentVariable), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
if (volRegionVarCount > 0) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_6, VCML.VolumeRegionVariable), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
if (memRegionVarCount > 0) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_6, VCML.MembraneRegionVariable), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
if (filRegionVarCount > 0) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_CompartmentalModel, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_COMPARTMENT_MODEL_6, VCML.FilamentRegionVariable), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
}
}
//
// spatial (PDE and ODE)
//
} else {
//
// Check that the number of CompartmentSubdomains equals the number of VolumeSubVolumes in the Geometry
// Check that the number of FilamentSubdomains equals the number of Filaments in the Geometry
//
int compartmentCount = 0;
int membraneCount = 0;
int filamentCount = 0;
int pointCount = 0;
for (int i = 0; i < subDomainList.size(); i++) {
SubDomain subDomain = (SubDomain) subDomainList.get(i);
if (subDomain instanceof CompartmentSubDomain) {
if (geometry.getGeometrySpec().getSubVolume(subDomain.getName()) == null) {
Issue issue = new Issue(subDomain, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_1, subDomain.getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
compartmentCount++;
} else if (subDomain instanceof MembraneSubDomain) {
membraneCount++;
} else if (subDomain instanceof FilamentSubDomain) {
filamentCount++;
} else if (subDomain instanceof PointSubDomain) {
pointCount++;
} else {
Issue issue = new Issue(subDomain, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_2, subDomain.getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
}
if (geometry.getGeometrySpec().getNumSubVolumes() != compartmentCount) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_SpatialModel, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_3, geometry.getGeometrySpec().getNumSubVolumes(), compartmentCount), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
if (geometry.getGeometrySpec().getFilamentGroup().getFilamentCount() != filamentCount) {
// setWarning("Spatial model, there are "+geometry.getGeometrySpec().getFilamentGroup().getFilamentCount()+" filaments in geometry, but "+filamentCount+" "+VCML.FilamentSubDomain+"'s, must be equal");
// return false;
}
if (filamentCount == 0 && (filVarCount > 0 || filRegionVarCount > 0)) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_SpatialModel, VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_4, Issue.SEVERITY_ERROR);
issueList.add(issue);
}
if (membraneCount == 0 && (memVarCount > 0 || memRegionVarCount > 0)) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_SpatialModel, VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_5, Issue.SEVERITY_ERROR);
issueList.add(issue);
}
//
for (int i = 0; i < subDomainList.size(); i++) {
SubDomain subDomain1 = (SubDomain) subDomainList.get(i);
for (int j = 0; j < subDomainList.size(); j++) {
if (i != j) {
SubDomain subDomain2 = (SubDomain) subDomainList.get(j);
if (subDomain1.getName().equals(subDomain2.getName())) {
Issue issue = new Issue(subDomain1, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_6, subDomain1.getName(), subDomain2.getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
if (subDomain1 instanceof MembraneSubDomain && subDomain2 instanceof MembraneSubDomain) {
MembraneSubDomain memSubDomain1 = (MembraneSubDomain) subDomain1;
MembraneSubDomain memSubDomain2 = (MembraneSubDomain) subDomain2;
if ((memSubDomain1.getInsideCompartment() == memSubDomain2.getInsideCompartment() && memSubDomain1.getOutsideCompartment() == memSubDomain2.getOutsideCompartment()) || (memSubDomain1.getInsideCompartment() == memSubDomain2.getOutsideCompartment() && memSubDomain1.getOutsideCompartment() == memSubDomain2.getInsideCompartment())) {
Issue issue = new Issue(subDomain1, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_7, memSubDomain1.getInsideCompartment().getName(), memSubDomain1.getOutsideCompartment().getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
}
}
}
}
// check periodic boundary conditons
for (int i = 0; i < subDomainList.size(); i++) {
SubDomain subDomain = (SubDomain) subDomainList.get(i);
if (subDomain instanceof CompartmentSubDomain) {
CompartmentSubDomain compartmentSubDomain = (CompartmentSubDomain) subDomain;
BoundaryConditionType bctM = compartmentSubDomain.getBoundaryConditionXm();
BoundaryConditionType bctP = compartmentSubDomain.getBoundaryConditionXp();
if (bctM.isPERIODIC() && !bctP.isPERIODIC() || !bctM.isPERIODIC() && bctP.isPERIODIC()) {
Issue issue = new Issue(subDomain, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_9, "Xm", "Xp", subDomain.getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
bctM = compartmentSubDomain.getBoundaryConditionYm();
bctP = compartmentSubDomain.getBoundaryConditionYp();
if (bctM.isPERIODIC() && !bctP.isPERIODIC() || !bctM.isPERIODIC() && bctP.isPERIODIC()) {
Issue issue = new Issue(subDomain, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_9, "Ym", "Yp", subDomain.getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
bctM = compartmentSubDomain.getBoundaryConditionZm();
bctP = compartmentSubDomain.getBoundaryConditionZp();
if (bctM.isPERIODIC() && !bctP.isPERIODIC() || !bctM.isPERIODIC() && bctP.isPERIODIC()) {
Issue issue = new Issue(subDomain, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_9, "Zm", "Zp", subDomain.getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
} else if (subDomain instanceof MembraneSubDomain) {
MembraneSubDomain membraneSubDomain = (MembraneSubDomain) subDomain;
BoundaryConditionType bctM = membraneSubDomain.getBoundaryConditionXm();
BoundaryConditionType bctP = membraneSubDomain.getBoundaryConditionXp();
if (bctM.isPERIODIC() && !bctP.isPERIODIC() || !bctM.isPERIODIC() && bctP.isPERIODIC()) {
Issue issue = new Issue(subDomain, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_9, "Xm", "Xp", subDomain.getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
bctM = membraneSubDomain.getBoundaryConditionYm();
bctP = membraneSubDomain.getBoundaryConditionYp();
if (bctM.isPERIODIC() && !bctP.isPERIODIC() || !bctM.isPERIODIC() && bctP.isPERIODIC()) {
Issue issue = new Issue(subDomain, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_9, "Ym", "Yp", subDomain.getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
bctM = membraneSubDomain.getBoundaryConditionZm();
bctP = membraneSubDomain.getBoundaryConditionZp();
if (bctM.isPERIODIC() && !bctP.isPERIODIC() || !bctM.isPERIODIC() && bctP.isPERIODIC()) {
Issue issue = new Issue(subDomain, issueContext, IssueCategory.MathDescription_SpatialModel_Subdomain, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_9, "Zm", "Zp", subDomain.getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
}
}
try {
if (geometry.getGeometrySpec().getDimension() > 0) {
//
// Check that there is a MembraneSubdomain for each unique subVolume-subVolume interface in Geometry
// each ResolvedSurfaceLocation is an instance of a subVolume-subVolume interface (one-to-one with region boundaries).
//
GeometricRegion[] regions = geometry.getGeometrySurfaceDescription().getGeometricRegions();
// }
if (regions == null) {
Issue issue = new Issue(geometry, issueContext, IssueCategory.MathDescription_SpatialModel_Geometry, VCellErrorMessages.MATH_DESCRIPTION_GEOMETRY_2, Issue.SEVERITY_ERROR);
issueList.add(issue);
} else {
for (int i = 0; i < regions.length; i++) {
if (regions[i] instanceof SurfaceGeometricRegion) {
SurfaceGeometricRegion surfaceRegion = (SurfaceGeometricRegion) regions[i];
SubVolume subVolume1 = ((VolumeGeometricRegion) surfaceRegion.getAdjacentGeometricRegions()[0]).getSubVolume();
CompartmentSubDomain compartment1 = getCompartmentSubDomain(subVolume1.getName());
if (compartment1 == null) {
Issue issue = new Issue(geometry, issueContext, IssueCategory.MathDescription_SpatialModel_Geometry, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_GEOMETRY_3, getGeometry().getName(), subVolume1.getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
SubVolume subVolume2 = ((VolumeGeometricRegion) surfaceRegion.getAdjacentGeometricRegions()[1]).getSubVolume();
CompartmentSubDomain compartment2 = getCompartmentSubDomain(subVolume2.getName());
if (compartment2 == null) {
Issue issue = new Issue(geometry, issueContext, IssueCategory.MathDescription_SpatialModel_Geometry, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_GEOMETRY_3, getGeometry().getName(), subVolume2.getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
MembraneSubDomain membraneSubDomain = getMembraneSubDomain(compartment1, compartment2);
if (compartment2 != null && compartment1 != null && membraneSubDomain == null) {
Issue issue = new Issue(geometry, issueContext, IssueCategory.MathDescription_SpatialModel_Geometry, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_GEOMETRY_4, compartment1.getName(), compartment2.getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
}
}
//
for (int i = 0; i < subDomainList.size(); i++) {
if (subDomainList.get(i) instanceof MembraneSubDomain) {
MembraneSubDomain membraneSubDomain = (MembraneSubDomain) subDomainList.get(i);
boolean bFoundSurfaceInGeometry = false;
for (int j = 0; j < regions.length; j++) {
if (regions[j] instanceof SurfaceGeometricRegion) {
SurfaceGeometricRegion surfaceRegion = (SurfaceGeometricRegion) regions[j];
VolumeGeometricRegion volumeRegion1 = (VolumeGeometricRegion) surfaceRegion.getAdjacentGeometricRegions()[0];
VolumeGeometricRegion volumeRegion2 = (VolumeGeometricRegion) surfaceRegion.getAdjacentGeometricRegions()[1];
String memInsideName = membraneSubDomain.getInsideCompartment().getName();
String memOutsideName = membraneSubDomain.getOutsideCompartment().getName();
if ((memInsideName.equals(volumeRegion1.getSubVolume().getName()) && memOutsideName.equals(volumeRegion2.getSubVolume().getName())) || (memInsideName.equals(volumeRegion2.getSubVolume().getName()) && memOutsideName.equals(volumeRegion1.getSubVolume().getName()))) {
bFoundSurfaceInGeometry = true;
break;
}
}
}
if (!bFoundSurfaceInGeometry) {
Issue issue = new Issue(geometry, issueContext, IssueCategory.MathDescription_SpatialModel_Geometry, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_GEOMETRY_5, membraneSubDomain.getInsideCompartment().getName(), membraneSubDomain.getOutsideCompartment().getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
}
}
}
}
// }catch (GeometryException e){
// e.printStackTrace(System.out);
// setWarning("error validating MathDescription: "+e.getMessage());
// return false;
// }catch (ImageException e){
// e.printStackTrace(System.out);
// setWarning("error validating MathDescription: "+e.getMessage());
// return false;
// }catch (ExpressionException e){
// e.printStackTrace(System.out);
// setWarning("error validating MathDescription: "+e.getMessage());
// return false;
} catch (Exception e) {
e.printStackTrace(System.out);
Issue issue = new Issue(geometry, issueContext, IssueCategory.MathDescription_SpatialModel_Geometry, e.getMessage(), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
//
for (int i = 0; i < variableList.size(); i++) {
Variable var = variableList.get(i);
String varName = var.getName();
if (var instanceof VolVariable) {
VolVariable volVar = (VolVariable) var;
int pdeRefCount = 0;
int odeRefCount = 0;
int steadyPdeCount = 0;
int measureCount = 0;
for (int j = 0; j < subDomainList.size(); j++) {
SubDomain subDomain = subDomainList.get(j);
Equation equ = subDomain.getEquation(volVar);
if (equ instanceof PdeEquation) {
if (((PdeEquation) equ).isSteady()) {
steadyPdeCount++;
} else {
pdeRefCount++;
}
//
for (int k = 0; k < subDomainList.size(); k++) {
SubDomain subDomain2 = subDomainList.get(k);
if (subDomain2 instanceof MembraneSubDomain) {
MembraneSubDomain membraneSubDomain = (MembraneSubDomain) subDomain2;
if (membraneSubDomain.getInsideCompartment() == subDomain || membraneSubDomain.getOutsideCompartment() == subDomain) {
JumpCondition jumpCondition = membraneSubDomain.getJumpCondition(volVar);
BoundaryConditionValue boundaryValue = ((PdeEquation) equ).getBoundaryConditionValue(membraneSubDomain.getName());
// if PDE variable does not have jump condition OR boundaryValue (neither or both are not allowed), its an error.
if ((jumpCondition == null && boundaryValue == null) || (jumpCondition != null && boundaryValue != null)) {
Issue issue = new Issue(equ, issueContext, IssueCategory.MathDescription_SpatialModel_Equation, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_10, varName, subDomain.getName(), membraneSubDomain.getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
if (boundaryValue != null && (subDomain.getBoundaryConditionSpec(membraneSubDomain.getName()) == null)) {
Issue issue = new Issue(equ, issueContext, IssueCategory.MathDescription_SpatialModel_Equation, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_10A, varName, subDomain.getName(), membraneSubDomain.getName(), membraneSubDomain.getName(), subDomain.getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
}
}
}
} else if (equ instanceof OdeEquation) {
odeRefCount++;
} else if (equ instanceof MeasureEquation) {
measureCount++;
}
//
if (subDomain instanceof MembraneSubDomain) {
MembraneSubDomain memSubDomain = (MembraneSubDomain) subDomain;
JumpCondition jumpCondition = memSubDomain.getJumpCondition(volVar);
if (jumpCondition != null) {
boolean bInsidePresent = (memSubDomain.getInsideCompartment().getEquation(volVar) instanceof PdeEquation);
boolean bOutsidePresent = (memSubDomain.getOutsideCompartment().getEquation(volVar) instanceof PdeEquation);
if (!bInsidePresent && !bOutsidePresent) {
Issue issue = new Issue(equ, issueContext, IssueCategory.MathDescription_SpatialModel_Equation, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_11, varName, memSubDomain.getName(), memSubDomain.getInsideCompartment().getName(), memSubDomain.getOutsideCompartment().getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
//
if (!bInsidePresent && !jumpCondition.getInFluxExpression().isZero()) {
Issue issue = new Issue(equ, issueContext, IssueCategory.MathDescription_SpatialModel_Equation, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_12, varName, memSubDomain.getName(), memSubDomain.getInsideCompartment().getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
if (!bOutsidePresent && !jumpCondition.getOutFluxExpression().isZero()) {
Issue issue = new Issue(equ, issueContext, IssueCategory.MathDescription_SpatialModel_Equation, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_13, varName, memSubDomain.getName(), memSubDomain.getOutsideCompartment().getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
}
}
}
if (odeRefCount > 0 && pdeRefCount > 0) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_SpatialModel, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_14, varName), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
if (steadyPdeCount > 0 && pdeRefCount > 0) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_SpatialModel, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_15, varName), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
if (odeRefCount == 0 && pdeRefCount == 0 && steadyPdeCount == 0 && measureCount == 0) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_SpatialModel, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_16, varName), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
} else //
if (var instanceof MemVariable) {
int pdeRefCount = 0;
int odeRefCount = 0;
int steadyPdeCount = 0;
for (int j = 0; j < subDomainList.size(); j++) {
SubDomain subDomain = subDomainList.get(j);
Equation equ = subDomain.getEquation(var);
if (equ instanceof PdeEquation) {
if (((PdeEquation) equ).isSteady()) {
steadyPdeCount++;
} else {
pdeRefCount++;
}
} else if (equ instanceof OdeEquation) {
odeRefCount++;
}
}
if (odeRefCount > 0 && pdeRefCount > 0) {
Issue issue = new Issue(var, issueContext, IssueCategory.MathDescription_SpatialModel_Variable, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_14, varName), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
if (steadyPdeCount > 0 && pdeRefCount > 0) {
Issue issue = new Issue(var, issueContext, IssueCategory.MathDescription_SpatialModel_Variable, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_15, varName), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
if (odeRefCount == 0 && pdeRefCount == 0 && steadyPdeCount == 0) {
Issue issue = new Issue(var, issueContext, IssueCategory.MathDescription_SpatialModel_Variable, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_16, varName), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
} else //
if (var instanceof FilamentVariable) {
for (int j = 0; j < subDomainList.size(); j++) {
SubDomain subDomain = subDomainList.get(j);
if (subDomain instanceof FilamentSubDomain) {
Equation equ = subDomain.getEquation(var);
if (!(equ instanceof OdeEquation)) {
Issue issue = new Issue(var, issueContext, IssueCategory.MathDescription_SpatialModel_Variable, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_21, varName, subDomain.getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
}
}
} else //
if (var instanceof VolumeRegionVariable) {
VolumeRegionVariable volRegionVar = (VolumeRegionVariable) var;
int count = 0;
for (int j = 0; j < subDomainList.size(); j++) {
SubDomain subDomain = subDomainList.get(j);
if (subDomain instanceof CompartmentSubDomain) {
Equation equ = subDomain.getEquation(volRegionVar);
if (equ instanceof VolumeRegionEquation) {
count++;
//
for (int k = 0; k < subDomainList.size(); k++) {
SubDomain subDomain2 = subDomainList.get(k);
if (subDomain2 instanceof MembraneSubDomain) {
MembraneSubDomain membraneSubDomain = (MembraneSubDomain) subDomain2;
if (membraneSubDomain.getInsideCompartment() == subDomain || membraneSubDomain.getOutsideCompartment() == subDomain) {
if (membraneSubDomain.getJumpCondition(volRegionVar) == null) {
Issue issue = new Issue(var, issueContext, IssueCategory.MathDescription_SpatialModel_Variable, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_17, varName, subDomain.getName(), membraneSubDomain.getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
}
}
}
}
}
}
if (count == 0) {
Issue issue = new Issue(var, issueContext, IssueCategory.MathDescription_SpatialModel_Variable, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_18, varName), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
} else //
if (var instanceof MembraneRegionVariable) {
int count = 0;
for (int j = 0; j < subDomainList.size(); j++) {
SubDomain subDomain = subDomainList.get(j);
if (subDomain instanceof MembraneSubDomain) {
Equation equ = subDomain.getEquation(var);
if (equ instanceof MembraneRegionEquation) {
count++;
}
}
}
if (count == 0) {
Issue issue = new Issue(var, issueContext, IssueCategory.MathDescription_SpatialModel_Variable, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_19, varName), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
} else //
if (var instanceof FilamentRegionVariable) {
for (int j = 0; j < subDomainList.size(); j++) {
SubDomain subDomain = subDomainList.get(j);
if (subDomain instanceof FilamentSubDomain) {
Equation equ = subDomain.getEquation(var);
if (!(equ instanceof FilamentRegionEquation)) {
Issue issue = new Issue(var, issueContext, IssueCategory.MathDescription_SpatialModel_Variable, VCellErrorMessages.getErrorMessage(VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_20, varName, subDomain.getName()), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
}
}
}
}
}
if (eventList.size() > 0 && isSpatial()) {
Issue issue = new Issue(this, issueContext, IssueCategory.MathDescription_SpatialModel, VCellErrorMessages.MATH_DESCRIPTION_SPATIAL_MODEL_22, Issue.SEVERITY_ERROR);
issueList.add(issue);
}
for (Event event : eventList) {
try {
event.bind(this);
} catch (ExpressionBindingException e) {
Issue issue = new Issue(event, issueContext, IssueCategory.MathDescription_SpatialModel_Event, e.getMessage(), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
}
for (DataGenerator dataGenerator : postProcessingBlock.getDataGeneratorList()) {
try {
dataGenerator.bind(this);
} catch (ExpressionBindingException e) {
Issue issue = new Issue(dataGenerator, issueContext, IssueCategory.MathDescription_SpatialModel_PostProcessingBlock, e.getMessage(), Issue.SEVERITY_ERROR);
issueList.add(issue);
}
}
}
Also used :
Issue(org.vcell.util.Issue)
ExpressionException(cbit.vcell.parser.ExpressionException)
SubVolume(cbit.vcell.geometry.SubVolume)
VolumeGeometricRegion(cbit.vcell.geometry.surface.VolumeGeometricRegion)
VolumeGeometricRegion(cbit.vcell.geometry.surface.VolumeGeometricRegion)
SurfaceGeometricRegion(cbit.vcell.geometry.surface.SurfaceGeometricRegion)
GeometricRegion(cbit.vcell.geometry.surface.GeometricRegion)
SurfaceGeometricRegion(cbit.vcell.geometry.surface.SurfaceGeometricRegion)
ExpressionBindingException(cbit.vcell.parser.ExpressionBindingException)
ExpressionBindingException(cbit.vcell.parser.ExpressionBindingException)
NoSuchElementException(java.util.NoSuchElementException)
ExpressionException(cbit.vcell.parser.ExpressionException)
BoundaryConditionValue(cbit.vcell.math.PdeEquation.BoundaryConditionValue)
Expression(cbit.vcell.parser.Expression)
ChangeEvent(javax.swing.event.ChangeEvent)
Example 9 with ExpressionBindingException
use of cbit.vcell.parser.ExpressionBindingException in project vcell by virtualcell.
the class MathUtilities method substituteModelParameters.
/**
* This method was created in VisualAge.
* @return cbit.vcell.parser.Expression
* @param exp cbit.vcell.parser.Expression
* @exception java.lang.Exception The exception description.
*/
public static Expression substituteModelParameters(Expression exp, SymbolTable symbolTable) throws ExpressionException {
Expression exp2 = new Expression(exp);
//
// do until no more functions to substitute
//
int count = 0;
boolean bSubstituted = true;
while (bSubstituted) {
bSubstituted = false;
if (count++ > 30) {
throw new ExpressionBindingException("infinite loop in eliminating function nesting");
}
String[] symbols = exp2.getSymbols();
if (symbols != null) {
for (int i = 0; i < symbols.length; i++) {
SymbolTableEntry ste = exp2.getSymbolBinding(symbols[i]);
if (ste != null && !(ste instanceof SymbolTableFunctionEntry)) {
Expression steExp = ste.getExpression();
if (steExp != null) {
exp2.substituteInPlace(new Expression(ste.getName()), steExp);
bSubstituted = true;
}
}
}
}
}
exp2.bindExpression(symbolTable);
return exp2;
}
Also used :
SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry)
Expression(cbit.vcell.parser.Expression)
ExpressionBindingException(cbit.vcell.parser.ExpressionBindingException)
SymbolTableFunctionEntry(cbit.vcell.parser.SymbolTableFunctionEntry)
Example 10 with ExpressionBindingException
use of cbit.vcell.parser.ExpressionBindingException in project vcell by virtualcell.
the class MathUtilities method getRequiredVariablesExplicit.
/**
* This method was created by a SmartGuide.
* @return java.util.Enumeration
* @param exp cbit.vcell.parser.Expression
*/
private static Enumeration<Variable> getRequiredVariablesExplicit(Expression exp, SymbolTable symbolTable) throws ExpressionException {
Vector<Variable> requiredVarList = new Vector<Variable>();
if (exp != null) {
String[] identifiers = exp.getSymbols();
if (lg.isDebugEnabled()) {
lg.debug("from expression " + exp + " parsing identifiers " + Arrays.toString(identifiers));
}
if (identifiers != null) {
for (int i = 0; i < identifiers.length; i++) {
String id = identifiers[i];
//
// look for globally bound variables
//
SymbolTableEntry entry = symbolTable.getEntry(id);
//
if (entry == null) {
entry = ReservedMathSymbolEntries.getReservedVariableEntry(id);
if (lg.isDebugEnabled()) {
lg.debug("id " + id + "not in symbol table looked for reserved symbols,found = " + (entry != null));
}
} else if (lg.isDebugEnabled()) {
lg.debug("symbolTable.getEntry( ) returned " + entry + " for " + id);
}
//
if (entry == null) {
SymbolTableEntry ste = exp.getSymbolBinding(id);
if (ste instanceof PseudoConstant) {
entry = ste;
}
if (entry == null) {
ExpressionBindingException ebe = new ExpressionBindingException("unresolved symbol " + id + " in expression " + exp);
lg.debug("found " + ste + "but it's not a PseudoConstant; throwing ", ebe);
throw ebe;
}
}
if (!(entry instanceof Variable)) {
throw new RuntimeException("MathUtilities.getRequiredVariablesExplicit() only gets required math variable. Use math side symbol table, e.g. MathDescription, SimulationSymbolTable, etc.");
}
requiredVarList.addElement((Variable) entry);
}
}
}
return requiredVarList.elements();
}
Also used :
SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry)
ExpressionBindingException(cbit.vcell.parser.ExpressionBindingException)
Vector(java.util.Vector)
Aggregations
ExpressionBindingException (cbit.vcell.parser.ExpressionBindingException)37
Expression (cbit.vcell.parser.Expression)26
ExpressionException (cbit.vcell.parser.ExpressionException)16
PropertyVetoException (java.beans.PropertyVetoException)15
Vector (java.util.Vector)8
MathException (cbit.vcell.math.MathException)7
SymbolTableEntry (cbit.vcell.parser.SymbolTableEntry)7
VCUnitDefinition (cbit.vcell.units.VCUnitDefinition)7
ArrayList (java.util.ArrayList)7
VCUnitException (cbit.vcell.units.VCUnitException)6
LocalParameter (cbit.vcell.mapping.ParameterContext.LocalParameter)5
ModelParameter (cbit.vcell.model.Model.ModelParameter)5
SpeciesContext (cbit.vcell.model.SpeciesContext)5
Issue (org.vcell.util.Issue)5
ModelException (cbit.vcell.model.ModelException)4
ModelUnitSystem (cbit.vcell.model.ModelUnitSystem)4
Structure (cbit.vcell.model.Structure)4
Element (org.jdom.Element)4
ScopedExpression (cbit.gui.ScopedExpression)3
SubVolume (cbit.vcell.geometry.SubVolume)3
