Example 1 with UniformTimeCourse
use of org.jlibsedml.UniformTimeCourse in project vcell by virtualcell.
the class SEDMLExporter method translateBioModelToSedML.
private void translateBioModelToSedML(String savePath) {
sbmlFilePathStrAbsoluteList.clear();
// models
try {
SimulationContext[] simContexts = vcBioModel.getSimulationContexts();
cbit.vcell.model.Model vcModel = vcBioModel.getModel();
// "urn:sedml:language:sbml";
String sbmlLanguageURN = SUPPORTED_LANGUAGE.SBML_GENERIC.getURN();
String bioModelName = TokenMangler.mangleToSName(vcBioModel.getName());
// String usrHomeDirPath = ResourceUtil.getUserHomeDir().getAbsolutePath();
// to get Xpath string for variables.
SBMLSupport sbmlSupport = new SBMLSupport();
// for model count, task subcount
int simContextCnt = 0;
// for dtaGenerator count.
int varCount = 0;
boolean bSpeciesAddedAsDataGens = false;
String sedmlNotesStr = "";
for (SimulationContext simContext : simContexts) {
String simContextName = simContext.getName();
// export all applications that are not spatial stochastic
if (!(simContext.getGeometry().getDimension() > 0 && simContext.isStoch())) {
// to compute and set the sizes of the remaining structures.
if (!simContext.getGeometryContext().isAllSizeSpecifiedPositive()) {
Structure structure = simContext.getModel().getStructure(0);
double structureSize = 1.0;
StructureMapping structMapping = simContext.getGeometryContext().getStructureMapping(structure);
StructureSizeSolver.updateAbsoluteStructureSizes(simContext, structure, structureSize, structMapping.getSizeParameter().getUnitDefinition());
}
// Export the application itself to SBML, with default overrides
String sbmlString = null;
int level = 2;
int version = 4;
boolean isSpatial = simContext.getGeometry().getDimension() > 0 ? true : false;
SimulationJob simJob = null;
// if (simContext.getGeometry().getDimension() > 0) {
// sbmlString = XmlHelper.exportSBML(vcBioModel, 2, 4, 0, true, simContext, null);
// } else {
// sbmlString = XmlHelper.exportSBML(vcBioModel, 2, 4, 0, false, simContext, null);
// }
//
// TODO: we need to salvage from the SBMLExporter info about the fate of local parameters
// some of them may stay as locals, some others may become globals
// Any of these, if used in a repeated task or change or whatever, needs to be used in a consistent way,
// that is, if a param becomes a global in SBML, we need to refer at it in SEDML as the same global
//
// We'll use:
// Map<Pair <String reaction, String param>, String global> - if local converted to global
// Set<Pair <String reaction, String param>> (if needed?) - if local stays local
//
// local to global translation map
Map<Pair<String, String>, String> l2gMap = null;
if (vcBioModel instanceof BioModel) {
try {
// check if model to be exported to SBML has units compatible with SBML default units (default units in SBML can be assumed only until SBML Level2)
ModelUnitSystem forcedModelUnitSystem = simContext.getModel().getUnitSystem();
if (level < 3 && !ModelUnitSystem.isCompatibleWithDefaultSBMLLevel2Units(forcedModelUnitSystem)) {
forcedModelUnitSystem = ModelUnitSystem.createDefaultSBMLLevel2Units();
}
// create new Biomodel with new (SBML compatible) unit system
BioModel modifiedBiomodel = ModelUnitConverter.createBioModelWithNewUnitSystem(simContext.getBioModel(), forcedModelUnitSystem);
// extract the simContext from new Biomodel. Apply overrides to *this* modified simContext
SimulationContext simContextFromModifiedBioModel = modifiedBiomodel.getSimulationContext(simContext.getName());
SBMLExporter sbmlExporter = new SBMLExporter(modifiedBiomodel, level, version, isSpatial);
sbmlExporter.setSelectedSimContext(simContextFromModifiedBioModel);
// no sim job
sbmlExporter.setSelectedSimulationJob(null);
sbmlString = sbmlExporter.getSBMLFile();
l2gMap = sbmlExporter.getLocalToGlobalTranslationMap();
} catch (ExpressionException | SbmlException e) {
e.printStackTrace(System.out);
throw new XmlParseException(e);
}
} else {
throw new RuntimeException("unsupported Document Type " + vcBioModel.getClass().getName() + " for SBML export");
}
String sbmlFilePathStrAbsolute = savePath + FileUtils.WINDOWS_SEPARATOR + bioModelName + "_" + simContextName + ".xml";
String sbmlFilePathStrRelative = bioModelName + "_" + simContextName + ".xml";
XmlUtil.writeXMLStringToFile(sbmlString, sbmlFilePathStrAbsolute, true);
sbmlFilePathStrAbsoluteList.add(sbmlFilePathStrRelative);
String simContextId = TokenMangler.mangleToSName(simContextName);
sedmlModel.addModel(new Model(simContextId, simContextName, sbmlLanguageURN, sbmlFilePathStrRelative));
// required for mathOverrides, if any
MathMapping mathMapping = simContext.createNewMathMapping();
MathSymbolMapping mathSymbolMapping = mathMapping.getMathSymbolMapping();
// create sedml simulation objects and tasks (mapping each sim with current simContext)
int simCount = 0;
String taskRef = null;
int overrideCount = 0;
for (Simulation vcSimulation : simContext.getSimulations()) {
List<DataGenerator> dataGeneratorsOfSim = new ArrayList<DataGenerator>();
// if simContext is non-spatial stochastic, check if sim is histogram
SolverTaskDescription simTaskDesc = vcSimulation.getSolverTaskDescription();
if (simContext.getGeometry().getDimension() == 0 && simContext.isStoch()) {
long numOfTrials = simTaskDesc.getStochOpt().getNumOfTrials();
if (numOfTrials > 1) {
String msg = "\n\t" + simContextName + " ( " + vcSimulation.getName() + " ) : export of non-spatial stochastic simulation with histogram option to SEDML not supported at this time.";
sedmlNotesStr += msg;
continue;
}
}
// create Algorithm and sedmlSimulation (UniformtimeCourse)
SolverDescription vcSolverDesc = simTaskDesc.getSolverDescription();
// String kiSAOIdStr = getKiSAOIdFromSimulation(vcSolverDesc); // old way of doing it, going directly to the web site
String kiSAOIdStr = vcSolverDesc.getKisao();
Algorithm sedmlAlgorithm = new Algorithm(kiSAOIdStr);
TimeBounds vcSimTimeBounds = simTaskDesc.getTimeBounds();
double startingTime = vcSimTimeBounds.getStartingTime();
String simName = vcSimulation.getName();
UniformTimeCourse utcSim = new UniformTimeCourse(TokenMangler.mangleToSName(simName), simName, startingTime, startingTime, vcSimTimeBounds.getEndingTime(), (int) simTaskDesc.getExpectedNumTimePoints(), sedmlAlgorithm);
// if solver is not CVODE, add a note to utcSim to indicate actual solver name
if (!vcSolverDesc.equals(SolverDescription.CVODE)) {
String simNotesStr = "Actual Solver Name : '" + vcSolverDesc.getDisplayLabel() + "'.";
utcSim.addNote(createNotesElement(simNotesStr));
}
sedmlModel.addSimulation(utcSim);
// add SEDML tasks (map simulation to model:simContext)
// repeated tasks
MathOverrides mathOverrides = vcSimulation.getMathOverrides();
if (mathOverrides != null && mathOverrides.hasOverrides()) {
String[] overridenConstantNames = mathOverrides.getOverridenConstantNames();
String[] scannedConstantsNames = mathOverrides.getScannedConstantNames();
HashMap<String, String> scannedParamHash = new HashMap<String, String>();
HashMap<String, String> unscannedParamHash = new HashMap<String, String>();
for (String name : scannedConstantsNames) {
scannedParamHash.put(name, name);
}
for (String name : overridenConstantNames) {
if (!scannedParamHash.containsKey(name)) {
unscannedParamHash.put(name, name);
}
}
if (!unscannedParamHash.isEmpty() && scannedParamHash.isEmpty()) {
// only parameters with simple overrides (numeric/expression) no scans
// create new model with change for each parameter that has override; add simple task
String overriddenSimContextId = simContextId + "_" + overrideCount;
String overriddenSimContextName = simContextName + " modified";
Model sedModel = new Model(overriddenSimContextId, overriddenSimContextName, sbmlLanguageURN, simContextId);
overrideCount++;
for (String unscannedParamName : unscannedParamHash.values()) {
SymbolTableEntry ste = getSymbolTableEntryForModelEntity(mathSymbolMapping, unscannedParamName);
Expression unscannedParamExpr = mathOverrides.getActualExpression(unscannedParamName, 0);
if (unscannedParamExpr.isNumeric()) {
// if expression is numeric, add ChangeAttribute to model created above
XPathTarget targetXpath = getTargetAttributeXPath(ste, l2gMap);
ChangeAttribute changeAttribute = new ChangeAttribute(targetXpath, unscannedParamExpr.infix());
sedModel.addChange(changeAttribute);
} else {
// non-numeric expression : add 'computeChange' to modified model
ASTNode math = Libsedml.parseFormulaString(unscannedParamExpr.infix());
XPathTarget targetXpath = getTargetXPath(ste, l2gMap);
ComputeChange computeChange = new ComputeChange(targetXpath, math);
String[] exprSymbols = unscannedParamExpr.getSymbols();
for (String symbol : exprSymbols) {
String symbolName = TokenMangler.mangleToSName(symbol);
SymbolTableEntry ste1 = vcModel.getEntry(symbol);
if (ste != null) {
if (ste1 instanceof SpeciesContext || ste1 instanceof Structure || ste1 instanceof ModelParameter) {
XPathTarget ste1_XPath = getTargetXPath(ste1, l2gMap);
org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(symbolName, symbolName, taskRef, ste1_XPath.getTargetAsString());
computeChange.addVariable(sedmlVar);
} else {
double doubleValue = 0.0;
if (ste1 instanceof ReservedSymbol) {
doubleValue = getReservedSymbolValue(ste1);
}
Parameter sedmlParameter = new Parameter(symbolName, symbolName, doubleValue);
computeChange.addParameter(sedmlParameter);
}
} else {
throw new RuntimeException("Symbol '" + symbol + "' used in expression for '" + unscannedParamName + "' not found in model.");
}
}
sedModel.addChange(computeChange);
}
}
sedmlModel.addModel(sedModel);
String taskId = "tsk_" + simContextCnt + "_" + simCount;
Task sedmlTask = new Task(taskId, taskId, sedModel.getId(), utcSim.getId());
sedmlModel.addTask(sedmlTask);
// to be used later to add dataGenerators : one set of DGs per model (simContext).
taskRef = taskId;
} else if (!scannedParamHash.isEmpty() && unscannedParamHash.isEmpty()) {
// only parameters with scans : only add 1 Task and 1 RepeatedTask
String taskId = "tsk_" + simContextCnt + "_" + simCount;
Task sedmlTask = new Task(taskId, taskId, simContextId, utcSim.getId());
sedmlModel.addTask(sedmlTask);
String repeatedTaskId = "repTsk_" + simContextCnt + "_" + simCount;
// TODO: temporary solution - we use as range here the first range
String scn = scannedConstantsNames[0];
String rId = "range_" + simContextCnt + "_" + simCount + "_" + scn;
RepeatedTask rt = new RepeatedTask(repeatedTaskId, repeatedTaskId, true, rId);
// to be used later to add dataGenerators - in our case it has to be the repeated task
taskRef = repeatedTaskId;
SubTask subTask = new SubTask("0", taskId);
rt.addSubtask(subTask);
for (String scannedConstName : scannedConstantsNames) {
ConstantArraySpec constantArraySpec = mathOverrides.getConstantArraySpec(scannedConstName);
String rangeId = "range_" + simContextCnt + "_" + simCount + "_" + scannedConstName;
// list of Ranges, if sim is parameter scan.
if (constantArraySpec != null) {
Range r = null;
System.out.println(" " + constantArraySpec.toString());
if (constantArraySpec.getType() == ConstantArraySpec.TYPE_INTERVAL) {
// ------ Uniform Range
r = new UniformRange(rangeId, constantArraySpec.getMinValue(), constantArraySpec.getMaxValue(), constantArraySpec.getNumValues());
rt.addRange(r);
} else {
// ----- Vector Range
cbit.vcell.math.Constant[] cs = constantArraySpec.getConstants();
ArrayList<Double> values = new ArrayList<Double>();
for (int i = 0; i < cs.length; i++) {
String value = cs[i].getExpression().infix();
values.add(Double.parseDouble(value));
}
r = new VectorRange(rangeId, values);
rt.addRange(r);
}
// list of Changes
SymbolTableEntry ste = getSymbolTableEntryForModelEntity(mathSymbolMapping, scannedConstName);
XPathTarget target = getTargetXPath(ste, l2gMap);
// ASTNode math1 = new ASTCi(r.getId()); // was scannedConstName
ASTNode math1 = Libsedml.parseFormulaString(r.getId());
SetValue setValue = new SetValue(target, r.getId(), simContextId);
setValue.setMath(math1);
rt.addChange(setValue);
} else {
throw new RuntimeException("No scan ranges found for scanned parameter : '" + scannedConstName + "'.");
}
}
sedmlModel.addTask(rt);
} else {
// both scanned and simple parameters : create new model with change for each simple override; add RepeatedTask
// create new model with change for each unscanned parameter that has override
String overriddenSimContextId = simContextId + "_" + overrideCount;
String overriddenSimContextName = simContextName + " modified";
Model sedModel = new Model(overriddenSimContextId, overriddenSimContextName, sbmlLanguageURN, simContextId);
overrideCount++;
String taskId = "tsk_" + simContextCnt + "_" + simCount;
Task sedmlTask = new Task(taskId, taskId, overriddenSimContextId, utcSim.getId());
sedmlModel.addTask(sedmlTask);
// scanned parameters
String repeatedTaskId = "repTsk_" + simContextCnt + "_" + simCount;
// TODO: temporary solution - we use as range here the first range
String scn = scannedConstantsNames[0];
String rId = "range_" + simContextCnt + "_" + simCount + "_" + scn;
RepeatedTask rt = new RepeatedTask(repeatedTaskId, repeatedTaskId, true, rId);
// to be used later to add dataGenerators - in our case it has to be the repeated task
taskRef = repeatedTaskId;
SubTask subTask = new SubTask("0", taskId);
rt.addSubtask(subTask);
for (String scannedConstName : scannedConstantsNames) {
ConstantArraySpec constantArraySpec = mathOverrides.getConstantArraySpec(scannedConstName);
String rangeId = "range_" + simContextCnt + "_" + simCount + "_" + scannedConstName;
// list of Ranges, if sim is parameter scan.
if (constantArraySpec != null) {
Range r = null;
System.out.println(" " + constantArraySpec.toString());
if (constantArraySpec.getType() == ConstantArraySpec.TYPE_INTERVAL) {
// ------ Uniform Range
r = new UniformRange(rangeId, constantArraySpec.getMinValue(), constantArraySpec.getMaxValue(), constantArraySpec.getNumValues());
rt.addRange(r);
} else {
// ----- Vector Range
cbit.vcell.math.Constant[] cs = constantArraySpec.getConstants();
ArrayList<Double> values = new ArrayList<Double>();
for (int i = 0; i < cs.length; i++) {
String value = cs[i].getExpression().infix() + ", ";
values.add(Double.parseDouble(value));
}
r = new VectorRange(rangeId, values);
rt.addRange(r);
}
// use scannedParamHash to store rangeId for that param, since it might be needed if unscanned param has a scanned param in expr.
if (scannedParamHash.get(scannedConstName).equals(scannedConstName)) {
// the hash was originally populated as <scannedParamName, scannedParamName>. Replace 'value' with rangeId for scannedParam
scannedParamHash.put(scannedConstName, r.getId());
}
// create setValue for scannedConstName
SymbolTableEntry ste2 = getSymbolTableEntryForModelEntity(mathSymbolMapping, scannedConstName);
XPathTarget target1 = getTargetXPath(ste2, l2gMap);
ASTNode math1 = new ASTCi(scannedConstName);
SetValue setValue1 = new SetValue(target1, r.getId(), sedModel.getId());
setValue1.setMath(math1);
rt.addChange(setValue1);
} else {
throw new RuntimeException("No scan ranges found for scanned parameter : '" + scannedConstName + "'.");
}
}
// for unscanned parameter overrides
for (String unscannedParamName : unscannedParamHash.values()) {
SymbolTableEntry ste = getSymbolTableEntryForModelEntity(mathSymbolMapping, unscannedParamName);
Expression unscannedParamExpr = mathOverrides.getActualExpression(unscannedParamName, 0);
if (unscannedParamExpr.isNumeric()) {
// if expression is numeric, add ChangeAttribute to model created above
XPathTarget targetXpath = getTargetAttributeXPath(ste, l2gMap);
ChangeAttribute changeAttribute = new ChangeAttribute(targetXpath, unscannedParamExpr.infix());
sedModel.addChange(changeAttribute);
} else {
// check for any scanned parameter in unscanned parameter expression
ASTNode math = Libsedml.parseFormulaString(unscannedParamExpr.infix());
String[] exprSymbols = unscannedParamExpr.getSymbols();
boolean bHasScannedParameter = false;
String scannedParamNameInUnscannedParamExp = null;
for (String symbol : exprSymbols) {
if (scannedParamHash.get(symbol) != null) {
bHasScannedParameter = true;
scannedParamNameInUnscannedParamExp = new String(symbol);
// @TODO check for multiple scannedParameters in expression.
break;
}
}
// (scanned parameter in expr) ? (add setValue for unscanned param in repeatedTask) : (add computeChange to modifiedModel)
if (bHasScannedParameter && scannedParamNameInUnscannedParamExp != null) {
// create setValue for unscannedParamName (which contains a scanned param in its expression)
SymbolTableEntry entry = getSymbolTableEntryForModelEntity(mathSymbolMapping, unscannedParamName);
XPathTarget target = getTargetXPath(entry, l2gMap);
String rangeId = scannedParamHash.get(scannedParamNameInUnscannedParamExp);
// @TODO: we have no range??
SetValue setValue = new SetValue(target, rangeId, sedModel.getId());
setValue.setMath(math);
rt.addChange(setValue);
} else {
// non-numeric expression : add 'computeChange' to modified model
XPathTarget targetXpath = getTargetXPath(ste, l2gMap);
ComputeChange computeChange = new ComputeChange(targetXpath, math);
for (String symbol : exprSymbols) {
String symbolName = TokenMangler.mangleToSName(symbol);
SymbolTableEntry ste1 = vcModel.getEntry(symbol);
// ste1 could be a math parameter, hence the above could return null
if (ste1 == null) {
ste1 = simContext.getMathDescription().getEntry(symbol);
}
if (ste1 != null) {
if (ste1 instanceof SpeciesContext || ste1 instanceof Structure || ste1 instanceof ModelParameter) {
XPathTarget ste1_XPath = getTargetXPath(ste1, l2gMap);
org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(symbolName, symbolName, taskRef, ste1_XPath.getTargetAsString());
computeChange.addVariable(sedmlVar);
} else {
double doubleValue = 0.0;
if (ste1 instanceof ReservedSymbol) {
doubleValue = getReservedSymbolValue(ste1);
} else if (ste instanceof Function) {
try {
doubleValue = ste.getExpression().evaluateConstant();
} catch (Exception e) {
e.printStackTrace(System.out);
throw new RuntimeException("Unable to evaluate function '" + ste.getName() + "' used in '" + unscannedParamName + "' expression : ", e);
}
} else {
doubleValue = ste.getConstantValue();
}
// TODO: shouldn't be s1_init_uM which is a math symbol, should be s0 (so use the ste-something from above)
// TODO: revert to Variable, not Parameter
Parameter sedmlParameter = new Parameter(symbolName, symbolName, doubleValue);
computeChange.addParameter(sedmlParameter);
}
} else {
throw new RuntimeException("Symbol '" + symbol + "' used in expression for '" + unscannedParamName + "' not found in model.");
}
}
sedModel.addChange(computeChange);
}
}
}
sedmlModel.addModel(sedModel);
sedmlModel.addTask(rt);
}
} else {
// no math overrides, add basic task.
String taskId = "tsk_" + simContextCnt + "_" + simCount;
Task sedmlTask = new Task(taskId, taskId, simContextId, utcSim.getId());
sedmlModel.addTask(sedmlTask);
// to be used later to add dataGenerators : one set of DGs per model (simContext).
taskRef = taskId;
}
// add one dataGenerator for 'time' for entire SEDML model.
// (using the id of the first task in model for 'taskRef' field of var since
String timeDataGenPrefix = DATAGENERATOR_TIME_NAME + "_" + taskRef;
DataGenerator timeDataGen = sedmlModel.getDataGeneratorWithId(timeDataGenPrefix);
if (timeDataGen == null) {
// org.jlibsedml.Variable timeVar = new org.jlibsedml.Variable(DATAGENERATOR_TIME_SYMBOL, DATAGENERATOR_TIME_SYMBOL, sedmlModel.getTasks().get(0).getId(), VariableSymbol.TIME);
org.jlibsedml.Variable timeVar = new org.jlibsedml.Variable(DATAGENERATOR_TIME_SYMBOL, DATAGENERATOR_TIME_SYMBOL, taskRef, VariableSymbol.TIME);
ASTNode math = Libsedml.parseFormulaString(DATAGENERATOR_TIME_SYMBOL);
timeDataGen = new DataGenerator(timeDataGenPrefix, timeDataGenPrefix, math);
timeDataGen.addVariable(timeVar);
sedmlModel.addDataGenerator(timeDataGen);
dataGeneratorsOfSim.add(timeDataGen);
}
// add dataGenerators for species
// get species list from SBML model.
String dataGenIdPrefix = "dataGen_" + taskRef;
String[] varNamesList = SimSpec.fromSBML(sbmlString).getVarsList();
for (String varName : varNamesList) {
org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(varName, varName, taskRef, sbmlSupport.getXPathForSpecies(varName));
ASTNode varMath = Libsedml.parseFormulaString(varName);
// "dataGen_" + varCount; - old code
String dataGenId = dataGenIdPrefix + "_" + TokenMangler.mangleToSName(varName);
DataGenerator dataGen = new DataGenerator(dataGenId, dataGenId, varMath);
dataGen.addVariable(sedmlVar);
sedmlModel.addDataGenerator(dataGen);
dataGeneratorsOfSim.add(dataGen);
varCount++;
}
// add DataGenerators for output functions here
ArrayList<AnnotatedFunction> outputFunctions = simContext.getOutputFunctionContext().getOutputFunctionsList();
for (AnnotatedFunction annotatedFunction : outputFunctions) {
Expression functionExpr = annotatedFunction.getExpression();
ASTNode funcMath = Libsedml.parseFormulaString(functionExpr.infix());
// "dataGen_" + varCount; - old code
String dataGenId = dataGenIdPrefix + "_" + TokenMangler.mangleToSName(annotatedFunction.getName());
DataGenerator dataGen = new DataGenerator(dataGenId, dataGenId, funcMath);
String[] functionSymbols = functionExpr.getSymbols();
for (String symbol : functionSymbols) {
String symbolName = TokenMangler.mangleToSName(symbol);
// try to get symbol from model, if null, try simContext.mathDesc
SymbolTableEntry ste = vcModel.getEntry(symbol);
if (ste == null) {
ste = simContext.getMathDescription().getEntry(symbol);
}
if (ste instanceof SpeciesContext || ste instanceof Structure || ste instanceof ModelParameter) {
XPathTarget targetXPath = getTargetXPath(ste, l2gMap);
org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(symbolName, symbolName, taskRef, targetXPath.getTargetAsString());
dataGen.addVariable(sedmlVar);
} else {
double value = 0.0;
if (ste instanceof Function) {
try {
value = ste.getExpression().evaluateConstant();
} catch (Exception e) {
e.printStackTrace(System.out);
throw new RuntimeException("Unable to evaluate function '" + ste.getName() + "' for output function '" + annotatedFunction.getName() + "'.", e);
}
} else {
value = ste.getConstantValue();
}
Parameter sedmlParameter = new Parameter(symbolName, symbolName, value);
dataGen.addParameter(sedmlParameter);
}
}
sedmlModel.addDataGenerator(dataGen);
dataGeneratorsOfSim.add(dataGen);
varCount++;
}
simCount++;
// ignoring output for spatial deterministic (spatial stochastic is not exported to SEDML) and non-spatial stochastic applications with histogram
if (!(simContext.getGeometry().getDimension() > 0)) {
// ignore Output (Plot2d) for non-spatial stochastic simulation with histogram.
boolean bSimHasHistogram = false;
if (simContext.isStoch()) {
long numOfTrials = simTaskDesc.getStochOpt().getNumOfTrials();
if (numOfTrials > 1) {
// not histogram {
bSimHasHistogram = true;
}
}
if (!bSimHasHistogram) {
String plot2dId = "plot2d_" + TokenMangler.mangleToSName(vcSimulation.getName());
Plot2D sedmlPlot2d = new Plot2D(plot2dId, simContext.getName() + "plots");
sedmlPlot2d.addNote(createNotesElement("Plot of all variables and output functions from application '" + simContext.getName() + "' ; simulation '" + vcSimulation.getName() + "' in VCell model"));
List<DataGenerator> dataGenerators = sedmlModel.getDataGenerators();
String xDataRef = sedmlModel.getDataGeneratorWithId(DATAGENERATOR_TIME_NAME + "_" + taskRef).getId();
// add a curve for each dataGenerator in SEDML model
int curveCnt = 0;
for (DataGenerator dataGenerator : dataGeneratorsOfSim) {
// no curve for time, since time is xDateReference
if (dataGenerator.getId().equals(xDataRef)) {
continue;
}
String curveId = "curve_" + curveCnt++;
Curve curve = new Curve(curveId, curveId, false, false, xDataRef, dataGenerator.getId());
sedmlPlot2d.addCurve(curve);
}
sedmlModel.addOutput(sedmlPlot2d);
}
}
}
// end - for 'sims'
} else {
// end if (!(simContext.getGeometry().getDimension() > 0 && simContext.isStoch()))
String msg = "\n\t" + simContextName + " : export of spatial stochastic (Smoldyn solver) applications to SEDML not supported at this time.";
sedmlNotesStr += msg;
}
// end : if-else simContext is not spatial stochastic
simContextCnt++;
}
// if sedmlNotesStr is not null, there were some applications that could not be exported to SEDML (eg., spatial stochastic). Create a notes element and add it to sedml Model.
if (sedmlNotesStr.length() > 0) {
sedmlNotesStr = "\n\tThe following applications in the VCell model were not exported to VCell : " + sedmlNotesStr;
sedmlModel.addNote(createNotesElement(sedmlNotesStr));
}
// error check : if there are no non-spatial deterministic applications (=> no models in SEDML document), complain.
if (sedmlModel.getModels().isEmpty()) {
throw new RuntimeException("No applications in biomodel to export to Sedml.");
}
} catch (Exception e) {
e.printStackTrace(System.out);
throw new RuntimeException("Error adding model to SEDML document : " + e.getMessage());
}
}
Also used :
Task(org.jlibsedml.Task)
SubTask(org.jlibsedml.SubTask)
RepeatedTask(org.jlibsedml.RepeatedTask)
HashMap(java.util.HashMap)
ArrayList(java.util.ArrayList)
SpeciesContext(cbit.vcell.model.SpeciesContext)
ConstantArraySpec(cbit.vcell.solver.ConstantArraySpec)
ExpressionException(cbit.vcell.parser.ExpressionException)
ChangeAttribute(org.jlibsedml.ChangeAttribute)
ComputeChange(org.jlibsedml.ComputeChange)
SolverTaskDescription(cbit.vcell.solver.SolverTaskDescription)
SubTask(org.jlibsedml.SubTask)
AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction)
Curve(org.jlibsedml.Curve)
SBMLExporter(org.vcell.sbml.vcell.SBMLExporter)
XmlParseException(cbit.vcell.xml.XmlParseException)
VectorRange(org.jlibsedml.VectorRange)
UniformRange(org.jlibsedml.UniformRange)
Range(org.jlibsedml.Range)
Algorithm(org.jlibsedml.Algorithm)
MathOverrides(cbit.vcell.solver.MathOverrides)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
DataGenerator(org.jlibsedml.DataGenerator)
MathMapping(cbit.vcell.mapping.MathMapping)
UniformTimeCourse(org.jlibsedml.UniformTimeCourse)
Plot2D(org.jlibsedml.Plot2D)
SbmlException(org.vcell.sbml.SbmlException)
VectorRange(org.jlibsedml.VectorRange)
SolverDescription(cbit.vcell.solver.SolverDescription)
ReservedSymbol(cbit.vcell.model.Model.ReservedSymbol)
StructureMapping(cbit.vcell.mapping.StructureMapping)
TimeBounds(cbit.vcell.solver.TimeBounds)
AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction)
Function(cbit.vcell.math.Function)
SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry)
ASTCi(org.jmathml.ASTCi)
RepeatedTask(org.jlibsedml.RepeatedTask)
ASTNode(org.jmathml.ASTNode)
Structure(cbit.vcell.model.Structure)
SimulationJob(cbit.vcell.solver.SimulationJob)
Pair(org.vcell.util.Pair)
ModelUnitSystem(cbit.vcell.model.ModelUnitSystem)
SimulationContext(cbit.vcell.mapping.SimulationContext)
MathSymbolMapping(cbit.vcell.mapping.MathSymbolMapping)
SbmlException(org.vcell.sbml.SbmlException)
TransformerException(javax.xml.transform.TransformerException)
XmlParseException(cbit.vcell.xml.XmlParseException)
IOException(java.io.IOException)
ExpressionException(cbit.vcell.parser.ExpressionException)
ParserConfigurationException(javax.xml.parsers.ParserConfigurationException)
SBMLSupport(org.jlibsedml.modelsupport.SBMLSupport)
Simulation(cbit.vcell.solver.Simulation)
Expression(cbit.vcell.parser.Expression)
BioModel(cbit.vcell.biomodel.BioModel)
UniformRange(org.jlibsedml.UniformRange)
BioModel(cbit.vcell.biomodel.BioModel)
Model(org.jlibsedml.Model)
StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
ProxyParameter(cbit.vcell.model.ProxyParameter)
Parameter(org.jlibsedml.Parameter)
XPathTarget(org.jlibsedml.XPathTarget)
SetValue(org.jlibsedml.SetValue)
Example 2 with UniformTimeCourse
use of org.jlibsedml.UniformTimeCourse in project vcell by virtualcell.
the class StandaloneSEDMLTest method doit.
public static void doit(File archiveFile) throws Exception {
ArchiveComponents ac = null;
ac = Libsedml.readSEDMLArchive(new FileInputStream(archiveFile));
SEDMLDocument sedmlDoc = ac.getSedmlDocument();
SedML sedml = sedmlDoc.getSedMLModel();
if (sedml == null || sedml.getModels().isEmpty()) {
throw new RuntimeException("sedml null or empty");
}
ModelResolver resolver = new ModelResolver(sedml);
// resolver.add(new FileModelResolver());
resolver.add(new ArchiveModelResolver(ac));
resolver.add(new BioModelsModelsRetriever());
resolver.add(new URLResourceRetriever());
// resolver.add(new RelativeFileModelResolver(FileUtils.getFullPath(archiveFile.getAbsolutePath())));
//
// iterate through all the elements and show them at the console
//
List<org.jlibsedml.Model> mmm = sedml.getModels();
for (Model mm : mmm) {
System.out.println(mm.toString());
}
List<org.jlibsedml.Simulation> sss = sedml.getSimulations();
for (org.jlibsedml.Simulation ss : sss) {
System.out.println(ss.toString());
}
List<AbstractTask> ttt = sedml.getTasks();
for (AbstractTask tt : ttt) {
System.out.println(tt.toString());
}
List<DataGenerator> ddd = sedml.getDataGenerators();
for (DataGenerator dd : ddd) {
System.out.println(dd.toString());
}
List<Output> ooo = sedml.getOutputs();
for (Output oo : ooo) {
System.out.println(oo.toString());
}
//
// extract models referenced in tasks.
//
KisaoOntology kisaoInstance = KisaoOntology.getInstance();
// HashMap<String,Model> flattenedModels = new HashMap<String, Model>();
List<AbstractTask> taskList = sedml.getTasks();
for (AbstractTask task : taskList) {
String modelReference = task.getModelReference();
org.jlibsedml.Model sedmlOriginalModel = sedml.getModelWithId(modelReference);
String sbmlModelString = resolver.getModelString(sedmlOriginalModel);
// sbmlSource with all the changes applied
XMLSource sbmlSource = new XMLSource(sbmlModelString);
org.jlibsedml.Simulation sedmlSimulation = sedml.getSimulation(task.getSimulationReference());
Algorithm algorithm = sedmlSimulation.getAlgorithm();
KisaoTerm sedmlKisao = kisaoInstance.getTermById(algorithm.getKisaoID());
//
// try to find a VCell solverDescription to match the Kisao term
//
// UniformTimeCourse [initialTime=0.0, numberOfPoints=1000, outputEndTime=1.0, outputStartTime=0.0,
// Algorithm [kisaoID=KISAO:0000019], getId()=SimSlow]
// identify the vCell solvers that would match best the sedml solver kisao id
List<SolverDescription> solverDescriptions = new ArrayList<>();
for (SolverDescription sd : SolverDescription.values()) {
KisaoTerm solverKisaoTerm = kisaoInstance.getTermById(sd.getKisao());
if (solverKisaoTerm == null) {
break;
}
boolean isExactlySame = solverKisaoTerm.equals(sedmlKisao);
if (isExactlySame && !solverKisaoTerm.isObsolete()) {
// we make a list with all the solvers that match the kisao
solverDescriptions.add(sd);
}
}
if (solverDescriptions.isEmpty()) {
throw new RuntimeException("cannot find the solverDescription with exact match for Kisao term '" + sedmlKisao + "'");
}
// choose first one
SolverDescription solverDescription = solverDescriptions.get(0);
// find out everything else we need about the application we're going to use,
// some of the info will be needed when we parse the sbml file
boolean bSpatial = false;
Application appType = Application.NETWORK_DETERMINISTIC;
Set<SolverDescription.SolverFeature> sfList = solverDescription.getSupportedFeatures();
for (SolverDescription.SolverFeature sf : sfList) {
switch(sf) {
case Feature_Rulebased:
appType = Application.RULE_BASED_STOCHASTIC;
break;
case Feature_Stochastic:
appType = Application.NETWORK_STOCHASTIC;
break;
case Feature_Deterministic:
appType = Application.NETWORK_DETERMINISTIC;
break;
case Feature_Spatial:
bSpatial = true;
break;
default:
break;
}
}
BioModel bioModel = (BioModel) XmlHelper.importSBML(transLogger, sbmlSource, bSpatial);
//
// we already have an application loaded from the sbml file, with initial conditions and stuff
// which may be not be suitable because the sedml kisao may need a different app type
// so we do a "copy as" to the right type and then delete the original we loaded from the sbml file
//
// the new application we're making from the old one
SimulationContext newSimulationContext = null;
if (bioModel.getSimulationContexts().length == 1) {
SimulationContext oldSimulationContext = bioModel.getSimulationContext(0);
String newSCName = bioModel.getFreeSimulationContextName();
newSimulationContext = SimulationContext.copySimulationContext(oldSimulationContext, newSCName, bSpatial, appType);
bioModel.addSimulationContext(newSimulationContext);
bioModel.removeSimulationContext(oldSimulationContext);
} else {
newSimulationContext = bioModel.addNewSimulationContext("App1", appType);
}
//
// making the new vCell simulation based on the sedml simulation
//
newSimulationContext.refreshDependencies();
MathMappingCallback callback = new MathMappingCallbackTaskAdapter(progressListener);
newSimulationContext.refreshMathDescription(callback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
Simulation newSimulation = new Simulation(newSimulationContext.getMathDescription());
newSimulation.setName(sedmlSimulation.getName());
bioModel.addSimulation(newSimulation);
// and set the vCell simulation parameters accordingly
if (sedmlSimulation instanceof UniformTimeCourse) {
} else if (sedmlSimulation instanceof OneStep) {
} else if (sedmlSimulation instanceof SteadyState) {
} else {
}
System.out.println(XmlHelper.bioModelToXML(bioModel));
}
}
Also used :
AbstractTask(org.jlibsedml.AbstractTask)
SolverDescription(cbit.vcell.solver.SolverDescription)
ArrayList(java.util.ArrayList)
OneStep(org.jlibsedml.OneStep)
ModelResolver(org.jlibsedml.execution.ModelResolver)
ArchiveModelResolver(org.jlibsedml.execution.ArchiveModelResolver)
SteadyState(org.jlibsedml.SteadyState)
SedML(org.jlibsedml.SedML)
ArchiveComponents(org.jlibsedml.ArchiveComponents)
Output(org.jlibsedml.Output)
MathMappingCallbackTaskAdapter(cbit.vcell.mapping.MathMappingCallbackTaskAdapter)
MathMappingCallback(cbit.vcell.mapping.SimulationContext.MathMappingCallback)
BioModelsModelsRetriever(org.jlibsedml.modelsupport.BioModelsModelsRetriever)
SimulationContext(cbit.vcell.mapping.SimulationContext)
Algorithm(org.jlibsedml.Algorithm)
FileInputStream(java.io.FileInputStream)
KisaoTerm(org.jlibsedml.modelsupport.KisaoTerm)
Simulation(cbit.vcell.solver.Simulation)
URLResourceRetriever(org.jlibsedml.modelsupport.URLResourceRetriever)
KisaoOntology(org.jlibsedml.modelsupport.KisaoOntology)
ArchiveModelResolver(org.jlibsedml.execution.ArchiveModelResolver)
Model(org.jlibsedml.Model)
SEDMLDocument(org.jlibsedml.SEDMLDocument)
DataGenerator(org.jlibsedml.DataGenerator)
BioModel(cbit.vcell.biomodel.BioModel)
BioModel(cbit.vcell.biomodel.BioModel)
Model(org.jlibsedml.Model)
UniformTimeCourse(org.jlibsedml.UniformTimeCourse)
XMLSource(cbit.vcell.xml.XMLSource)
Application(cbit.vcell.mapping.SimulationContext.Application)
Example 3 with UniformTimeCourse
use of org.jlibsedml.UniformTimeCourse in project vcell by virtualcell.
the class XmlHelper method sedmlToBioModel.
public static VCDocument sedmlToBioModel(VCLogger transLogger, ExternalDocInfo externalDocInfo, SedML sedml, AbstractTask selectedTask) throws Exception {
if (sedml.getModels().isEmpty()) {
return null;
}
VCDocument doc = null;
try {
// extract the path only from the sedml file
String fullPath = FileUtils.getFullPath(externalDocInfo.getFile().getAbsolutePath());
// Namespace namespace = sedml.getNamespace();
// iterate through all the elements and show them at the console
List<org.jlibsedml.Model> mmm = sedml.getModels();
for (Model mm : mmm) {
System.out.println(mm.toString());
}
List<org.jlibsedml.Simulation> sss = sedml.getSimulations();
for (org.jlibsedml.Simulation ss : sss) {
System.out.println(ss.toString());
}
List<AbstractTask> ttt = sedml.getTasks();
for (AbstractTask tt : ttt) {
System.out.println(tt.toString());
}
List<DataGenerator> ddd = sedml.getDataGenerators();
for (DataGenerator dd : ddd) {
System.out.println(dd.toString());
}
List<Output> ooo = sedml.getOutputs();
for (Output oo : ooo) {
System.out.println(oo.toString());
}
KisaoTerm sedmlKisao = null;
// this will become the vCell simulation
org.jlibsedml.Simulation sedmlSimulation = null;
// the "original" model referred to by the task
org.jlibsedml.Model sedmlOriginalModel = null;
String sedmlOriginalModelName = null;
if (selectedTask == null) {
// no task, just pick the Model and find its sbml file
sedmlOriginalModelName = SEDMLUtil.getName(mmm.get(0));
} else {
if (selectedTask instanceof Task) {
sedmlOriginalModel = sedml.getModelWithId(selectedTask.getModelReference());
sedmlSimulation = sedml.getSimulation(selectedTask.getSimulationReference());
} else if (selectedTask instanceof RepeatedTask) {
RepeatedTask rt = (RepeatedTask) selectedTask;
assert (rt.getSubTasks().size() == 1);
// first (and only) subtask
SubTask st = rt.getSubTasks().entrySet().iterator().next().getValue();
String taskId = st.getTaskId();
AbstractTask t = sedml.getTaskWithId(taskId);
// get model and simulation from subtask
sedmlOriginalModel = sedml.getModelWithId(t.getModelReference());
sedmlSimulation = sedml.getSimulation(t.getSimulationReference());
} else {
throw new RuntimeException("Unexpected task " + selectedTask);
}
sedmlOriginalModelName = sedmlOriginalModel.getId();
sedmlKisao = KisaoOntology.getInstance().getTermById(sedmlSimulation.getAlgorithm().getKisaoID());
}
// UniformTimeCourse [initialTime=0.0, numberOfPoints=1000, outputEndTime=1.0, outputStartTime=0.0,
// Algorithm [kisaoID=KISAO:0000019], getId()=SimSlow]
// identify the vCell solvers that would match best the sedml solver kisao id
List<SolverDescription> solverDescriptions = new ArrayList<>();
for (SolverDescription sd : SolverDescription.values()) {
KisaoTerm solverKisaoTerm = KisaoOntology.getInstance().getTermById(sd.getKisao());
if (solverKisaoTerm == null) {
break;
}
boolean isExactlySame = solverKisaoTerm.equals(sedmlKisao);
if (isExactlySame && !solverKisaoTerm.isObsolete()) {
// we make a list with all the solvers that match the kisao
solverDescriptions.add(sd);
}
}
// from the list of vcell solvers that match the sedml kisao we select the ones that have a matching time step
SolverDescription solverDescription = null;
for (SolverDescription sd : solverDescriptions) {
if (true) {
solverDescription = sd;
break;
}
}
// find out everything else we need about the application we're going to use,
// some of the info will be needed when we parse the sbml file
boolean bSpatial = false;
Application appType = Application.NETWORK_DETERMINISTIC;
Set<SolverDescription.SolverFeature> sfList = solverDescription.getSupportedFeatures();
for (SolverDescription.SolverFeature sf : sfList) {
switch(sf) {
case Feature_Rulebased:
appType = Application.RULE_BASED_STOCHASTIC;
break;
case Feature_Stochastic:
appType = Application.NETWORK_STOCHASTIC;
break;
case Feature_Deterministic:
appType = Application.NETWORK_DETERMINISTIC;
break;
case Feature_Spatial:
bSpatial = true;
break;
default:
break;
}
}
// -------------------------------------------------------------------------------------------
// extract bioModel name from sedx (or sedml) file
String bioModelName = FileUtils.getBaseName(externalDocInfo.getFile().getAbsolutePath());
// if we have repeated task, we ignore them, we just use the normal resolvers for archive and changes
// once the application and simulation are built, we iterate through the repeated tasks and
// add math overrides to the simulation for each repeated task
ArchiveComponents ac = null;
if (externalDocInfo.getFile().getPath().toLowerCase().endsWith("sedx") || externalDocInfo.getFile().getPath().toLowerCase().endsWith("omex")) {
ac = Libsedml.readSEDMLArchive(new FileInputStream(externalDocInfo.getFile().getPath()));
}
ModelResolver resolver = new ModelResolver(sedml);
if (ac != null) {
resolver.add(new ArchiveModelResolver(ac));
}
resolver.add(new FileModelResolver());
resolver.add(new RelativeFileModelResolver(fullPath));
String newMdl = resolver.getModelString(sedmlOriginalModel);
// sbmlSource with all the changes applied
XMLSource sbmlSource = new XMLSource(newMdl);
doc = XmlHelper.importSBML(transLogger, sbmlSource, bSpatial);
BioModel bioModel = (BioModel) doc;
bioModel.setName(bioModelName);
// we already have an application loaded from the sbml file, with initial conditions and stuff
// which may be not be suitable because the sedml kisao may need a different app type
// so we do a "copy as" to the right type and then delete the original we loaded from the sbml file
// the new application we're making from the old one
SimulationContext newSimulationContext = null;
if (bioModel.getSimulationContexts().length == 1) {
SimulationContext oldSimulationContext = bioModel.getSimulationContext(0);
newSimulationContext = SimulationContext.copySimulationContext(oldSimulationContext, sedmlOriginalModelName, bSpatial, appType);
bioModel.removeSimulationContext(oldSimulationContext);
bioModel.addSimulationContext(newSimulationContext);
} else {
// length == 0
newSimulationContext = bioModel.addNewSimulationContext(sedmlOriginalModelName, appType);
}
// making the new vCell simulation based on the sedml simulation
newSimulationContext.refreshDependencies();
MathMappingCallback callback = new MathMappingCallbackTaskAdapter(null);
newSimulationContext.refreshMathDescription(callback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
Simulation newSimulation = new Simulation(newSimulationContext.getMathDescription());
newSimulation.setName(SEDMLUtil.getName(sedmlSimulation));
// TODO: make sure that everything has proper names
// we check the repeated tasks, if any, and add to the list of math overrides
// if(selectedTask instanceof RepeatedTask) {
// for(Change change : ((RepeatedTask) selectedTask).getChanges()) {
// if(!(change instanceof SetValue)) {
// throw new RuntimeException("Only 'SetValue' changes are supported for repeated tasks.");
// }
// SetValue setValue = (SetValue)change;
// // TODO: extract target from XPath
// // ......
// //
// String target = "s0"; // for now we just use a hardcoded thing
// ConstantArraySpec cas;
// Range range = ((RepeatedTask) selectedTask).getRange(setValue.getRangeReference());
// if(range instanceof UniformRange) {
// cas = ConstantArraySpec.createIntervalSpec(target, ((UniformRange) range).getStart(), ((UniformRange) range).getEnd(),
// range.getNumElements(), ((UniformRange) range).getType() == UniformRange.UniformType.LOG ? true : false);
// } else if(range instanceof VectorRange) {
// // List<String> constants = new ArrayList<> ();
// // for(int i=0; i<range.getNumElements(); i++) {
// // constants.add(new Constant(i+"", new Expression(range.getElementAt(i))));
// // }
// // cas = ConstantArraySpec.createListSpec(target, constants);
//
// } else {
// throw new RuntimeException("Only 'Uniform Range' and 'Vector Range' are supported at this time.");
// }
//
// }
// }
// we identify the type of sedml simulation (uniform time course, etc)
// and set the vCell simulation parameters accordingly
SolverTaskDescription simTaskDesc = newSimulation.getSolverTaskDescription();
TimeBounds timeBounds = new TimeBounds();
TimeStep timeStep = new TimeStep();
double outputTimeStep = 0.1;
if (sedmlSimulation instanceof UniformTimeCourse) {
// we translate initial time to zero, we provide output for the duration of the simulation
// because we can't select just an interval the way the SEDML simulation can
double initialTime = ((UniformTimeCourse) sedmlSimulation).getInitialTime();
double outputStartTime = ((UniformTimeCourse) sedmlSimulation).getOutputStartTime();
double outputEndTime = ((UniformTimeCourse) sedmlSimulation).getOutputEndTime();
double outputNumberOfPoints = ((UniformTimeCourse) sedmlSimulation).getNumberOfPoints();
outputTimeStep = (outputEndTime - outputStartTime) / outputNumberOfPoints;
timeBounds = new TimeBounds(0, outputEndTime - initialTime);
} else if (sedmlSimulation instanceof OneStep) {
// for anything other than UniformTimeCourse we just ignore
} else if (sedmlSimulation instanceof SteadyState) {
} else {
}
OutputTimeSpec outputTimeSpec = new UniformOutputTimeSpec(outputTimeStep);
simTaskDesc.setTimeBounds(timeBounds);
simTaskDesc.setTimeStep(timeStep);
simTaskDesc.setOutputTimeSpec(outputTimeSpec);
newSimulation.setSolverTaskDescription(simTaskDesc);
bioModel.addSimulation(newSimulation);
newSimulation.refreshDependencies();
} catch (Exception e) {
e.printStackTrace();
throw new RuntimeException("Unable to initialize bioModel for the given selection.");
}
return doc;
}
Also used :
Task(org.jlibsedml.Task)
RepeatedTask(org.jlibsedml.RepeatedTask)
SimulationTask(cbit.vcell.messaging.server.SimulationTask)
AbstractTask(org.jlibsedml.AbstractTask)
SubTask(org.jlibsedml.SubTask)
ArrayList(java.util.ArrayList)
ArchiveModelResolver(org.jlibsedml.execution.ArchiveModelResolver)
FileModelResolver(org.jlibsedml.execution.FileModelResolver)
RelativeFileModelResolver(org.vcell.sedml.RelativeFileModelResolver)
ModelResolver(org.jlibsedml.execution.ModelResolver)
SteadyState(org.jlibsedml.SteadyState)
OutputTimeSpec(cbit.vcell.solver.OutputTimeSpec)
UniformOutputTimeSpec(cbit.vcell.solver.UniformOutputTimeSpec)
SolverTaskDescription(cbit.vcell.solver.SolverTaskDescription)
SubTask(org.jlibsedml.SubTask)
VCDocument(org.vcell.util.document.VCDocument)
MathMappingCallback(cbit.vcell.mapping.SimulationContext.MathMappingCallback)
UniformOutputTimeSpec(cbit.vcell.solver.UniformOutputTimeSpec)
FileInputStream(java.io.FileInputStream)
KisaoTerm(org.jlibsedml.modelsupport.KisaoTerm)
ArchiveModelResolver(org.jlibsedml.execution.ArchiveModelResolver)
DataGenerator(org.jlibsedml.DataGenerator)
UniformTimeCourse(org.jlibsedml.UniformTimeCourse)
Application(cbit.vcell.mapping.SimulationContext.Application)
AbstractTask(org.jlibsedml.AbstractTask)
SolverDescription(cbit.vcell.solver.SolverDescription)
RelativeFileModelResolver(org.vcell.sedml.RelativeFileModelResolver)
OneStep(org.jlibsedml.OneStep)
TimeBounds(cbit.vcell.solver.TimeBounds)
TimeStep(cbit.vcell.solver.TimeStep)
ArchiveComponents(org.jlibsedml.ArchiveComponents)
RepeatedTask(org.jlibsedml.RepeatedTask)
Output(org.jlibsedml.Output)
MathMappingCallbackTaskAdapter(cbit.vcell.mapping.MathMappingCallbackTaskAdapter)
FileModelResolver(org.jlibsedml.execution.FileModelResolver)
RelativeFileModelResolver(org.vcell.sedml.RelativeFileModelResolver)
SimulationContext(cbit.vcell.mapping.SimulationContext)
XMLStreamException(javax.xml.stream.XMLStreamException)
SbmlException(org.vcell.sbml.SbmlException)
SBMLException(org.sbml.jsbml.SBMLException)
IOException(java.io.IOException)
ExpressionException(cbit.vcell.parser.ExpressionException)
Simulation(cbit.vcell.solver.Simulation)
Model(org.jlibsedml.Model)
BioModel(cbit.vcell.biomodel.BioModel)
MathModel(cbit.vcell.mathmodel.MathModel)
BioModel(cbit.vcell.biomodel.BioModel)
Model(org.jlibsedml.Model)
Aggregations
BioModel (cbit.vcell.biomodel.BioModel)3
SimulationContext (cbit.vcell.mapping.SimulationContext)3
Simulation (cbit.vcell.solver.Simulation)3
SolverDescription (cbit.vcell.solver.SolverDescription)3
ArrayList (java.util.ArrayList)3
DataGenerator (org.jlibsedml.DataGenerator)3
Model (org.jlibsedml.Model)3
UniformTimeCourse (org.jlibsedml.UniformTimeCourse)3
MathMappingCallbackTaskAdapter (cbit.vcell.mapping.MathMappingCallbackTaskAdapter)2
Application (cbit.vcell.mapping.SimulationContext.Application)2
MathMappingCallback (cbit.vcell.mapping.SimulationContext.MathMappingCallback)2
ExpressionException (cbit.vcell.parser.ExpressionException)2
SolverTaskDescription (cbit.vcell.solver.SolverTaskDescription)2
TimeBounds (cbit.vcell.solver.TimeBounds)2
FileInputStream (java.io.FileInputStream)2
IOException (java.io.IOException)2
AbstractTask (org.jlibsedml.AbstractTask)2
Algorithm (org.jlibsedml.Algorithm)2
ArchiveComponents (org.jlibsedml.ArchiveComponents)2
OneStep (org.jlibsedml.OneStep)2
