use of org.vcell.util.Issue in project vcell by virtualcell.
the class ModelOptimizationSpec method removeUncoupledParameters.
public void removeUncoupledParameters() {
try {
localIssueList.clear();
MathMapping mathMapping = getSimulationContext().createNewMathMapping();
MathDescription mathDesc = mathMapping.getMathDescription();
MathSystemHash mathSystemHash = fromMath(mathDesc);
Graph graph = mathSystemHash.getDependencyGraph(mathSystemHash.getSymbols());
Tree[] spanningTrees = graph.getSpanningForest();
//
for (int i = 0; i < spanningTrees.length; i++) {
Node[] treeNodes = spanningTrees[i].getNodes();
boolean bHasStateVariables = false;
for (int j = 0; j < treeNodes.length; j++) {
Node node = treeNodes[j];
Variable var = mathDesc.getVariable(node.getName());
if (var instanceof VolVariable || var instanceof MemVariable || var instanceof FilamentVariable || var instanceof VolumeRegionVariable || var instanceof MembraneRegionVariable || var instanceof FilamentRegionVariable) {
bHasStateVariables = true;
break;
}
}
if (!bHasStateVariables) {
spanningTrees = (Tree[]) BeanUtils.removeElement(spanningTrees, spanningTrees[i]);
i--;
}
}
//
// remove parameters not mapped to a surviving tree (not coupled to any state variables
//
ArrayList<ParameterMappingSpec> paramMappingSpecsList = new ArrayList<ParameterMappingSpec>();
paramMappingSpecsList.addAll(Arrays.asList(fieldParameterMappingSpecs));
for (int i = 0; i < paramMappingSpecsList.size(); i++) {
Parameter parameter = paramMappingSpecsList.get(i).getModelParameter();
String mathName = mathMapping.getMathSymbolMapping().getVariable(parameter).getName();
boolean bFoundInTree = false;
for (int j = 0; j < spanningTrees.length; j++) {
Node node = spanningTrees[j].getNode(mathName);
if (node != null) {
bFoundInTree = true;
}
}
if (!bFoundInTree) {
paramMappingSpecsList.remove(i);
i--;
}
}
ParameterMappingSpec[] parameterMappingSpecs = new ParameterMappingSpec[paramMappingSpecsList.size()];
paramMappingSpecsList.toArray(parameterMappingSpecs);
setParameterMappingSpecs(parameterMappingSpecs);
} catch (Exception e) {
e.printStackTrace(System.out);
localIssueList.add(new Issue(this, localIssueContext, IssueCategory.ParameterEstimationGeneralWarning, e.getMessage(), Issue.SEVERITY_WARNING));
// throw new RuntimeException(e.getMessage());
}
}
use of org.vcell.util.Issue in project vcell by virtualcell.
the class SBMLImporter method createSBMLUnitSystemForVCModel.
private ModelUnitSystem createSBMLUnitSystemForVCModel() throws Exception {
if (sbmlModel == null) {
throw new SBMLImportException("SBML model is NULL");
}
ListOf listofUnitDefns = sbmlModel.getListOfUnitDefinitions();
if (listofUnitDefns == null) {
System.out.println("No Unit Definitions");
// @TODO: deal with SBML level < 3.
return ModelUnitSystem.createDefaultVCModelUnitSystem();
}
@SuppressWarnings("serial") VCUnitSystem tempVCUnitSystem = new VCUnitSystem() {
};
sbmlUnitIdentifierHash = new HashMap<String, VCUnitDefinition>();
// add base SI unit identifiers (as defined in SBML spec) to hash
sbmlUnitIdentifierHash.put("ampere", tempVCUnitSystem.getInstance("A"));
sbmlUnitIdentifierHash.put("avogadro", tempVCUnitSystem.getInstance("6.02e23"));
// sbmlUnitIdentifierHash.put("becquerel",
// tempVCUnitSystem.getInstance("becquerel"));
// sbmlUnitIdentifierHash.put("candela",
// tempVCUnitSystem.getInstance("candela"));
sbmlUnitIdentifierHash.put("coulomb", tempVCUnitSystem.getInstance("C"));
sbmlUnitIdentifierHash.put("dimensionless", tempVCUnitSystem.getInstance("1"));
sbmlUnitIdentifierHash.put("farad", tempVCUnitSystem.getInstance("F"));
sbmlUnitIdentifierHash.put("gram", tempVCUnitSystem.getInstance("g"));
// sbmlUnitIdentifierHash.put("gray",
// tempVCUnitSystem.getInstance("gray"));
sbmlUnitIdentifierHash.put("henry", tempVCUnitSystem.getInstance("H"));
sbmlUnitIdentifierHash.put("hertz", tempVCUnitSystem.getInstance("Hz"));
sbmlUnitIdentifierHash.put("item", tempVCUnitSystem.getInstance("molecules"));
sbmlUnitIdentifierHash.put("joule", tempVCUnitSystem.getInstance("J"));
// sbmlUnitIdentifierHash.put("katal",
// tempVCUnitSystem.getInstance("katal"));
sbmlUnitIdentifierHash.put("kelvin", tempVCUnitSystem.getInstance("K"));
sbmlUnitIdentifierHash.put("kilogram", tempVCUnitSystem.getInstance("kg"));
sbmlUnitIdentifierHash.put("litre", tempVCUnitSystem.getInstance("litre"));
// sbmlUnitIdentifierHash.put("lumen",
// tempVCUnitSystem.getInstance("lumen"));
// sbmlUnitIdentifierHash.put("lux",
// tempVCUnitSystem.getInstance("lux"));
sbmlUnitIdentifierHash.put("metre", tempVCUnitSystem.getInstance("m"));
sbmlUnitIdentifierHash.put("mole", tempVCUnitSystem.getInstance("mol"));
sbmlUnitIdentifierHash.put("newton", tempVCUnitSystem.getInstance("N"));
// sbmlUnitIdentifierHash.put("ohm",
// tempVCUnitSystem.getInstance("ohm"));
// sbmlUnitIdentifierHash.put("pascal",
// tempVCUnitSystem.getInstance("pascal"));
// sbmlUnitIdentifierHash.put("radian",
// tempVCUnitSystem.getInstance("radian"));
sbmlUnitIdentifierHash.put("second", tempVCUnitSystem.getInstance("s"));
sbmlUnitIdentifierHash.put("siemens", tempVCUnitSystem.getInstance("S"));
// sbmlUnitIdentifierHash.put("sievert",
// tempVCUnitSystem.getInstance("sievert"));
// sbmlUnitIdentifierHash.put("steradian",
// tempVCUnitSystem.getInstance("steradian"));
// sbmlUnitIdentifierHash.put("tesla",
// tempVCUnitSystem.getInstance("tesla"));
sbmlUnitIdentifierHash.put("volt", tempVCUnitSystem.getInstance("V"));
sbmlUnitIdentifierHash.put("watt", tempVCUnitSystem.getInstance("W"));
sbmlUnitIdentifierHash.put("weber", tempVCUnitSystem.getInstance("Wb"));
long sbmlLevel = sbmlModel.getLevel();
if (sbmlLevel < 3) {
// SBML predefined unit identifiers
sbmlUnitIdentifierHash.put(UnitDefinition.SUBSTANCE, tempVCUnitSystem.getInstance("mole"));
sbmlUnitIdentifierHash.put(UnitDefinition.VOLUME, tempVCUnitSystem.getInstance("litre"));
sbmlUnitIdentifierHash.put(UnitDefinition.AREA, tempVCUnitSystem.getInstance("m2"));
sbmlUnitIdentifierHash.put(UnitDefinition.LENGTH, tempVCUnitSystem.getInstance("m"));
sbmlUnitIdentifierHash.put(UnitDefinition.TIME, tempVCUnitSystem.getInstance("s"));
}
if (sbmlModel.isSetSubstanceUnits()) {
UnitDefinition ud = sbmlModel.getSubstanceUnitsInstance();
VCUnitDefinition vcUnitDef = SBMLUnitTranslator.getVCUnitDefinition(ud, tempVCUnitSystem);
sbmlUnitIdentifierHash.put(UnitDefinition.SUBSTANCE, vcUnitDef);
}
if (sbmlModel.isSetVolumeUnits()) {
UnitDefinition ud = sbmlModel.getVolumeUnitsInstance();
VCUnitDefinition vcUnitDef = SBMLUnitTranslator.getVCUnitDefinition(ud, tempVCUnitSystem);
sbmlUnitIdentifierHash.put(UnitDefinition.VOLUME, vcUnitDef);
}
if (sbmlModel.isSetAreaUnits()) {
UnitDefinition ud = sbmlModel.getAreaUnitsInstance();
VCUnitDefinition vcUnitDef = SBMLUnitTranslator.getVCUnitDefinition(ud, tempVCUnitSystem);
sbmlUnitIdentifierHash.put(UnitDefinition.AREA, vcUnitDef);
}
if (sbmlModel.isSetLengthUnits()) {
UnitDefinition ud = sbmlModel.getLengthUnitsInstance();
VCUnitDefinition vcUnitDef = SBMLUnitTranslator.getVCUnitDefinition(ud, tempVCUnitSystem);
sbmlUnitIdentifierHash.put(UnitDefinition.LENGTH, vcUnitDef);
}
if (sbmlModel.isSetTimeUnits()) {
UnitDefinition ud = sbmlModel.getTimeUnitsInstance();
VCUnitDefinition vcUnitDef = SBMLUnitTranslator.getVCUnitDefinition(ud, tempVCUnitSystem);
sbmlUnitIdentifierHash.put(UnitDefinition.TIME, vcUnitDef);
}
// read unit definition (identifiers) declared in SBML model
for (int i = 0; i < sbmlModel.getNumUnitDefinitions(); i++) {
UnitDefinition ud = (org.sbml.jsbml.UnitDefinition) listofUnitDefns.get(i);
String unitName = ud.getId();
VCUnitDefinition vcUnitDef = SBMLUnitTranslator.getVCUnitDefinition(ud, tempVCUnitSystem);
sbmlUnitIdentifierHash.put(unitName, vcUnitDef);
}
// For SBML level 2
// default units
VCUnitDefinition defaultSubstanceUnit = sbmlUnitIdentifierHash.get(UnitDefinition.SUBSTANCE);
VCUnitDefinition defaultVolumeUnit = sbmlUnitIdentifierHash.get(UnitDefinition.VOLUME);
VCUnitDefinition defaultAreaUnit = sbmlUnitIdentifierHash.get(UnitDefinition.AREA);
VCUnitDefinition defaultLengthUnit = sbmlUnitIdentifierHash.get(UnitDefinition.LENGTH);
VCUnitDefinition defaultTimeUnit = sbmlUnitIdentifierHash.get(UnitDefinition.TIME);
VCUnitDefinition modelSubstanceUnit = null;
VCUnitDefinition modelVolumeUnit = null;
VCUnitDefinition modelAreaUnit = null;
VCUnitDefinition modelLengthUnit = null;
VCUnitDefinition modelTimeUnit = null;
// units in SBML model
// compartments
ListOf<Compartment> listOfCompartments = sbmlModel.getListOfCompartments();
for (int i = 0; i < listOfCompartments.size(); i++) {
Compartment sbmlComp = listOfCompartments.get(i);
double dim = 3;
if (sbmlComp.isSetSpatialDimensions()) {
dim = sbmlComp.getSpatialDimensions();
}
String unitStr = sbmlComp.getUnits();
VCUnitDefinition sbmlUnitDefinition = null;
if (unitStr != null && unitStr.length() > 0) {
sbmlUnitDefinition = sbmlUnitIdentifierHash.get(unitStr);
} else {
// applying default unit if not defined for this compartment
if (dim == 3) {
sbmlUnitDefinition = defaultVolumeUnit;
} else if (dim == 2) {
sbmlUnitDefinition = defaultAreaUnit;
} else if (dim == 1) {
sbmlUnitDefinition = defaultLengthUnit;
}
}
if (dim == 3) {
if (sbmlUnitDefinition == null) {
sbmlUnitDefinition = defaultVolumeUnit;
}
if (modelVolumeUnit == null) {
modelVolumeUnit = sbmlUnitDefinition;
} else if (!sbmlUnitDefinition.isEquivalent(modelVolumeUnit)) {
localIssueList.add(new Issue(new SBMLIssueSource(sbmlComp), issueContext, IssueCategory.Units, "unit for compartment '" + sbmlComp.getId() + "' (" + unitStr + ") : (" + sbmlUnitDefinition.getSymbol() + ") not compatible with current vol unit (" + modelVolumeUnit.getSymbol() + ")", Issue.SEVERITY_WARNING));
// logger.sendMessage(VCLogger.Priority.MediumPriority,
// VCLogger.ErrorType.UnitError, "unit for compartment '" +
// sbmlComp.getId() + "' (" + unitStr + ") : (" +
// sbmlUnitDefinition.getSymbol() +
// ") not compatible with current vol unit (" +
// modelVolumeUnit.getSymbol() + ")");
}
} else if (dim == 2) {
if (modelAreaUnit == null) {
modelAreaUnit = sbmlUnitDefinition;
} else if (!sbmlUnitDefinition.isEquivalent(modelAreaUnit)) {
localIssueList.add(new Issue(new SBMLIssueSource(sbmlComp), issueContext, IssueCategory.Units, "unit for compartment '" + sbmlComp.getId() + "' (" + unitStr + ") : (" + sbmlUnitDefinition.getSymbol() + ") not compatible with current area unit (" + modelAreaUnit.getSymbol() + ")", Issue.SEVERITY_WARNING));
// logger.sendMessage(VCLogger.Priority.MediumPriority,
// VCLogger.ErrorType.UnitError, "unit for compartment '" +
// sbmlComp.getId() + "' (" + unitStr + ") : (" +
// sbmlUnitDefinition.getSymbol() +
// ") not compatible with current area unit (" +
// modelAreaUnit.getSymbol() + ")");
}
}
}
// species
ListOf<org.sbml.jsbml.Species> listOfSpecies = sbmlModel.getListOfSpecies();
for (int i = 0; i < listOfSpecies.size(); i++) {
org.sbml.jsbml.Species sbmlSpecies = listOfSpecies.get(i);
String unitStr = sbmlSpecies.getSubstanceUnits();
VCUnitDefinition sbmlUnitDefinition = null;
if (unitStr != null && unitStr.length() > 0) {
sbmlUnitDefinition = sbmlUnitIdentifierHash.get(unitStr);
} else {
// apply default substance unit
sbmlUnitDefinition = defaultSubstanceUnit;
}
if (modelSubstanceUnit == null) {
modelSubstanceUnit = sbmlUnitDefinition;
} else if (!sbmlUnitDefinition.isEquivalent(modelSubstanceUnit)) {
localIssueList.add(new Issue(new SBMLIssueSource(sbmlSpecies), issueContext, IssueCategory.Units, "unit for species '" + sbmlSpecies.getId() + "' (" + unitStr + ") : (" + sbmlUnitDefinition.getSymbol() + ") not compatible with current substance unit (" + modelSubstanceUnit.getSymbol() + ")", Issue.SEVERITY_WARNING));
// logger.sendMessage(VCLogger.Priority.MediumPriority,
// VCLogger.ErrorType.UnitError, "unit for species '" +
// sbmlSpecies.getId() + "' (" + unitStr + ") : (" +
// sbmlUnitDefinition.getSymbol() +
// ") not compatible with current substance unit (" +
// modelSubstanceUnit.getSymbol() + ")");
}
}
// reactions for SBML level 2 version < 3
long sbmlVersion = sbmlModel.getVersion();
if (sbmlVersion < 3) {
ListOf<Reaction> listOfReactions = sbmlModel.getListOfReactions();
for (int i = 0; i < listOfReactions.size(); i++) {
Reaction sbmlReaction = listOfReactions.get(i);
KineticLaw kineticLaw = sbmlReaction.getKineticLaw();
if (kineticLaw != null) {
// first check substance unit
String unitStr = kineticLaw.getSubstanceUnits();
VCUnitDefinition sbmlUnitDefinition = null;
if (unitStr != null && unitStr.length() > 0) {
sbmlUnitDefinition = sbmlUnitIdentifierHash.get(unitStr);
} else {
// apply default substance unit
sbmlUnitDefinition = defaultSubstanceUnit;
}
if (modelSubstanceUnit == null) {
modelSubstanceUnit = sbmlUnitDefinition;
} else if (!sbmlUnitDefinition.isEquivalent(modelSubstanceUnit)) {
localIssueList.add(new Issue(new SBMLIssueSource(sbmlReaction), issueContext, IssueCategory.Units, "substance unit for reaction '" + sbmlReaction.getId() + "' (" + unitStr + ") : (" + sbmlUnitDefinition.getSymbol() + ") not compatible with current substance unit (" + modelSubstanceUnit.getSymbol() + ")", Issue.SEVERITY_WARNING));
// logger.sendMessage(VCLogger.Priority.MediumPriority,
// VCLogger.ErrorType.UnitError,
// "substance unit for reaction '" +
// sbmlReaction.getId() + "' (" + unitStr + ") : (" +
// sbmlUnitDefinition.getSymbol() +
// ") not compatible with current substance unit (" +
// modelSubstanceUnit.getSymbol() + ")");
}
// check time unit
unitStr = kineticLaw.getTimeUnits();
if (unitStr != null && unitStr.length() > 0) {
sbmlUnitDefinition = sbmlUnitIdentifierHash.get(unitStr);
} else {
// apply default time unit
sbmlUnitDefinition = defaultTimeUnit;
}
if (modelTimeUnit == null) {
modelTimeUnit = sbmlUnitDefinition;
} else if (!sbmlUnitDefinition.isEquivalent(modelTimeUnit)) {
localIssueList.add(new Issue(new SBMLIssueSource(sbmlReaction), issueContext, IssueCategory.Units, "time unit for reaction '" + sbmlReaction.getId() + "' (" + unitStr + ") : (" + sbmlUnitDefinition.getSymbol() + ") not compatible with current time unit (" + modelTimeUnit.getSymbol() + ")", Issue.SEVERITY_WARNING));
// logger.sendMessage(VCLogger.Priority.MediumPriority,
// VCLogger.ErrorType.UnitError,
// "time unit for reaction '" + sbmlReaction.getId() +
// "' (" + unitStr + ") : (" +
// sbmlUnitDefinition.getSymbol() +
// ") not compatible with current time unit (" +
// modelTimeUnit.getSymbol() + ")");
}
}
}
}
if (modelSubstanceUnit == null) {
modelSubstanceUnit = defaultSubstanceUnit;
}
if (modelVolumeUnit == null) {
modelVolumeUnit = defaultVolumeUnit;
}
if (modelAreaUnit == null) {
modelAreaUnit = defaultAreaUnit;
}
if (modelLengthUnit == null) {
modelLengthUnit = defaultLengthUnit;
}
if (modelTimeUnit == null) {
modelTimeUnit = defaultTimeUnit;
}
if (modelSubstanceUnit == null && modelVolumeUnit == null && modelAreaUnit == null && modelLengthUnit == null && modelTimeUnit == null) {
// default (VC)modelUnitSystem
return ModelUnitSystem.createDefaultVCModelUnitSystem();
} else {
return ModelUnitSystem.createSBMLUnitSystem(modelSubstanceUnit, modelVolumeUnit, modelAreaUnit, modelLengthUnit, modelTimeUnit);
}
}
use of org.vcell.util.Issue in project vcell by virtualcell.
the class SBMLImporter method checkIdentifiersNameLength.
private void checkIdentifiersNameLength() throws Exception {
// Check compartment name lengths
ListOf listofIds = sbmlModel.getListOfCompartments();
boolean bLongCompartmentName = false;
SBase issueSource = null;
for (int i = 0; i < sbmlModel.getNumCompartments(); i++) {
Compartment compartment = (Compartment) listofIds.get(i);
String compartmentName = compartment.getId();
if (compartmentName.length() > 64) {
bLongCompartmentName = true;
issueSource = compartment;
}
}
// Check species name lengths
listofIds = sbmlModel.getListOfSpecies();
boolean bLongSpeciesName = false;
for (int i = 0; i < sbmlModel.getNumSpecies(); i++) {
org.sbml.jsbml.Species species = (org.sbml.jsbml.Species) listofIds.get(i);
String speciesName = species.getId();
if (speciesName.length() > 64) {
bLongSpeciesName = true;
issueSource = species;
}
}
// Check parameter name lengths
listofIds = sbmlModel.getListOfParameters();
boolean bLongParameterName = false;
for (int i = 0; i < sbmlModel.getNumParameters(); i++) {
Parameter param = (Parameter) listofIds.get(i);
String paramName = param.getId();
if (paramName.length() > 64) {
bLongParameterName = true;
issueSource = param;
}
}
// Check reaction name lengths
listofIds = sbmlModel.getListOfReactions();
boolean bLongReactionName = false;
for (int i = 0; i < sbmlModel.getNumReactions(); i++) {
Reaction rxn = (Reaction) listofIds.get(i);
String rxnName = rxn.getId();
if (rxnName.length() > 64) {
bLongReactionName = true;
issueSource = rxn;
}
}
if (bLongCompartmentName || bLongSpeciesName || bLongParameterName || bLongReactionName) {
String warningMsg = "WARNING: The imported model has one or more ";
if (bLongCompartmentName) {
warningMsg = warningMsg + "compartments, ";
}
if (bLongSpeciesName) {
warningMsg = warningMsg + "species, ";
}
if (bLongParameterName) {
warningMsg = warningMsg + "global parameters, ";
}
if (bLongReactionName) {
warningMsg = warningMsg + "reactions ";
}
warningMsg = warningMsg + "that have ids/names that are longer than 64 characters. \n\nUser is STRONGLY recommeded to shorten " + "the names to avoid problems with the length of expressions these names might be used in.";
localIssueList.add(new Issue(new SBMLIssueSource(issueSource), issueContext, IssueCategory.SBMLImport_UnsupportedAttributeOrElement, warningMsg, Issue.SEVERITY_WARNING));
// logger.sendMessage(VCLogger.Priority.MediumPriority,
// VCLogger.ErrorType.UnsupportedConstruct, warningMsg);
}
}
use of org.vcell.util.Issue in project vcell by virtualcell.
the class SBMLImporter method addInitialAssignments.
protected void addInitialAssignments() {
if (sbmlModel == null) {
throw new SBMLImportException("SBML model is NULL");
}
ListOf listofInitialAssgns = sbmlModel.getListOfInitialAssignments();
if (listofInitialAssgns == null) {
System.out.println("No Initial Assignments specified");
return;
}
Model vcModel = vcBioModel.getSimulationContext(0).getModel();
for (int i = 0; i < sbmlModel.getNumInitialAssignments(); i++) {
try {
InitialAssignment initAssgn = (InitialAssignment) listofInitialAssgns.get(i);
String initAssgnSymbol = initAssgn.getSymbol();
Expression initAssignMathExpr = getExpressionFromFormula(initAssgn.getMath());
// support compartmentSize expressions, warn and bail out.
if (sbmlModel.getCompartment(initAssgnSymbol) != null) {
if (!initAssignMathExpr.isNumeric()) {
logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.CompartmentError, "compartment '" + initAssgnSymbol + "' size has an initial assignment, cannot handle it at this time.");
}
// if init assgn for compartment is numeric, the numeric
// value for size is set in addCompartments().
}
// or other species. Not allowed for species.
if (!bSpatial && sbmlModel.getSpecies(initAssgnSymbol) != null) {
if (initAssignMathExpr.hasSymbol(vcModel.getX().getName()) || initAssignMathExpr.hasSymbol(vcModel.getY().getName()) || initAssignMathExpr.hasSymbol(vcModel.getZ().getName())) {
logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.SpeciesError, "species '" + initAssgnSymbol + "' initial assignment expression cannot contain 'x', 'y', 'z'.");
}
}
initAssignMathExpr = adjustExpression(initAssignMathExpr, vcModel);
// set the init assgn expr on VCell species init condn or global
// parameter expression
SpeciesContextSpec scs = vcBioModel.getSimulationContext(0).getReactionContext().getSpeciesContextSpec(vcBioModel.getSimulationContext(0).getModel().getSpeciesContext(initAssgnSymbol));
ModelParameter mp = vcBioModel.getSimulationContext(0).getModel().getModelParameter(initAssgnSymbol);
if (scs != null) {
scs.getInitialConditionParameter().setExpression(initAssignMathExpr);
} else if (mp != null) {
mp.setExpression(initAssignMathExpr);
} else {
localIssueList.add(new Issue(new SBMLIssueSource(initAssgn), issueContext, IssueCategory.SBMLImport_UnsupportedAttributeOrElement, "Symbol '" + initAssgnSymbol + "' not a species or global parameter in VCell; initial assignment ignored.", Issue.SEVERITY_WARNING));
// logger.sendMessage(VCLogger.Priority.MediumPriority,
// VCLogger.ErrorType.UnsupportedConstruct,
// "Symbol '"+initAssgnSymbol+"' not a species or global parameter in VCell; initial assignment ignored..");
}
} catch (Exception e) {
e.printStackTrace(System.out);
throw new RuntimeException("Error reading InitialAssignment : " + e.getMessage());
}
}
}
use of org.vcell.util.Issue in project vcell by virtualcell.
the class SBMLImporter method setSpeciesInitialConditions.
/**
* setSpeciesInitialConditions : called after speciesContexts and global
* parameters have been set. Checks for init conditions set on species in
* the Sbml model, and if it is set using an assignment rule, obtain the
* corresponding expression. Obtain the sbml -> vc unit conversion factor
* for species concentrations to adjust the species initial condition
* units/factor.
*/
private void setSpeciesInitialConditions() {
try {
// fill in SpeciesContextSpec for each speciesContext
Model vcModel = vcBioModel.getSimulationContext(0).getModel();
SpeciesContext[] vcSpeciesContexts = vcModel.getSpeciesContexts();
for (int i = 0; i < vcSpeciesContexts.length; i++) {
org.sbml.jsbml.Species sbmlSpecies = (org.sbml.jsbml.Species) sbmlModel.getSpecies(vcSpeciesContexts[i].getName());
// Sometimes, the species name can be null or a blank string; in
// that case, use species id as the name.
String speciesName = sbmlSpecies.getId();
Compartment compartment = (Compartment) sbmlModel.getCompartment(sbmlSpecies.getCompartment());
Expression initExpr = null;
if (sbmlSpecies.isSetInitialConcentration()) {
// If initial
// Concentration
// is set
Expression initConcentration = new Expression(sbmlSpecies.getInitialConcentration());
// check if initConc is set by a (assignment) rule. That
// takes precedence over initConc value set on species.
initExpr = getValueFromAssignmentRule(speciesName);
if (initExpr == null) {
initExpr = new Expression(initConcentration);
}
} else if (sbmlSpecies.isSetInitialAmount()) {
// If initial
// amount is set
double initAmount = sbmlSpecies.getInitialAmount();
// initConcentration. Else, throw exception.
if (compartment.isSetSize()) {
double compartmentSize = compartment.getSize();
Expression initConcentration = new Expression(0.0);
if (compartmentSize != 0.0) {
initConcentration = new Expression(initAmount / compartmentSize);
} else {
logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.UnitError, "compartment '" + compartment.getId() + "' has zero size, unable to determine initial concentration for species " + speciesName);
}
// check if initConc is set by a (assignment) rule. That
// takes precedence over initConc/initAmt value set on
// species.
initExpr = getValueFromAssignmentRule(speciesName);
if (initExpr == null) {
initExpr = new Expression(initConcentration);
}
} else {
logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.SpeciesError, " Compartment '" + compartment.getId() + "' size not set or is defined by a rule; cannot calculate initConc.");
}
} else {
// initConc/initAmt not set; check if species has a
// (assignment) rule.
initExpr = getValueFromAssignmentRule(speciesName);
if (initExpr == null) {
// warning and set it to 0.0
if (sbmlModel.getInitialAssignment(speciesName) == null) {
localIssueList.add(new Issue(new SBMLIssueSource(sbmlModel.getSpecies(speciesName)), issueContext, IssueCategory.SBMLImport_MissingSpeciesInitCondition, "no initial condition for species " + speciesName + ", assuming 0.0", Issue.SEVERITY_WARNING));
// logger.sendMessage(VCLogger.Priority.MediumPriority,
// VCLogger.ErrorType.UnitError,
// "no initial condition for species "+speciesName+", assuming 0.0");
}
initExpr = new Expression(0.0);
}
}
// similar to the conversion that is done in reactions.
if (initExpr != null) {
// initExpr will be changed
initExpr = adjustExpression(initExpr, vcModel);
}
// If any of the symbols in the expression for speciesConc is a
// rule, expand it.
substituteGlobalParamRulesInPlace(initExpr, false);
SpeciesContextSpec speciesContextSpec = vcBioModel.getSimulationContext(0).getReactionContext().getSpeciesContextSpec(vcSpeciesContexts[i]);
speciesContextSpec.getInitialConditionParameter().setExpression(initExpr);
speciesContextSpec.setConstant(sbmlSpecies.getBoundaryCondition() || sbmlSpecies.getConstant());
}
} catch (Throwable e) {
e.printStackTrace(System.out);
throw new SBMLImportException("Error setting initial condition for species context; " + e.getMessage(), e);
}
}
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