/// <summary>
/// Creates a "standard" MoBi reaction by a given one compartment reaction.
/// </summary>
private void CreateStandardReaction(Reaction sbmlReaction, Model model)
{
var reactionBuilder = ObjectBaseFactory.Create <IReactionBuilder>()
.WithName(sbmlReaction.getId())
.WithDescription(sbmlReaction.getNotesString());
CreateModifiers(sbmlReaction, reactionBuilder, String.Empty, model);
var parameters = CreateLocalParameters(sbmlReaction);
if (parameters != null)
{
parameters.ForEach(reactionBuilder.AddParameter);
}
if (sbmlReaction.isSetKineticLaw())
{
CreateKineticLaw(sbmlReaction.getKineticLaw(), reactionBuilder, false);
}
CreateProducts(sbmlReaction, reactionBuilder, model);
CreateEducts(sbmlReaction, reactionBuilder, model);
if (reactionBuilder != null)
{
ReactionBuilderList.Add(reactionBuilder);
}
}
public void setUp()
{
string filename = "../../sbml/annotation/test/test-data/annotationL3.xml";
d = libsbml.readSBML(filename);
m = d.getModel();
c = m.getCompartment(0);
}
/// <summary>
/// A passive Transport is created when two Species with the same name are reacting with
/// each other.
/// </summary>
private bool IsPassiveTransport(Reaction sbmlReaction, Model model)
{
var educt = sbmlReaction.getReactant(0).getSpecies();
var product = sbmlReaction.getProduct(0).getSpecies();
var eductSpecies = GetSpeciesById(educt, model);
var productSpecies = GetSpeciesById(product, model);
if (eductSpecies.getName() != productSpecies.getName())
{
return(false);
}
var molinfoEduct = _sbmlInformation.MoleculeInformation.FirstOrDefault(info => info.SpeciesIds.Any(s => s == educt));
var molinfoProduct = _sbmlInformation.MoleculeInformation.FirstOrDefault(info => info.SpeciesIds.Any(s => s == product));
if (molinfoEduct == null)
{
return(false);
}
if (molinfoProduct == null)
{
return(false);
}
var reactantMolecule = molinfoEduct.GetMoleculeBuilder();
var productMolecule = molinfoProduct.GetMoleculeBuilder();
return(reactantMolecule == productMolecule);
}
/// <summary>
/// Creates a Ghostreaction to import a SBML multicompartment reaction.
/// </summary>
private void CreateGhostReaction(Reaction sbmlReaction, Model model)
{
var eductCompartmentMoleculeDictionary = ComputeEducts(sbmlReaction, model);
var productCompartmentMoleculeDictionary = ComputeProducts(sbmlReaction, model);
CreateGhostReactions(sbmlReaction, eductCompartmentMoleculeDictionary, productCompartmentMoleculeDictionary, model);
}
protected override void Because()
{
var model = new Model(3, 1);
model.setName("TestModel");
model.setNotes("TestNotes");
model.setMetaId("TestMetaId");
sut.CreateEventsTopContainer();
sut.CreateTopContainer(model);
var compartment = new Compartment(3, 1);
compartment.setName("Compartment");
compartment.setId("c1");
compartment.setSpatialDimensions(1);
compartment.setSize(5);
var compartment2 = new Compartment(3, 1);
compartment2.setName("Compartment");
compartment2.setId("c2");
compartment2.setSpatialDimensions(2);
compartment2.setSize(5);
var compartment3 = new Compartment(3, 1);
compartment3.setName("Compartment");
compartment3.setId("c3");
compartment3.setSpatialDimensions(3);
compartment3.setSize(5);
_container = sut.CreateContainerFromCompartment(compartment);
_container2 = sut.CreateContainerFromCompartment(compartment2);
_container3 = sut.CreateContainerFromCompartment(compartment3);
sut.CreateSpatialStructureFromModel(sut._topContainer, model);
}
public void setUp()
{
M = new Model(3,1);
if (M == null);
{
}
}
/// <summary>
/// Sets all the autogenerated Molecule Start Values to the right values and updates their
/// "IsPresent" property.
/// </summary>
private void SetMoleculeStartValues(Model model)
{
foreach (var molInfo in _sbmlInformation.MoleculeInformation)
{
foreach (var msv in _moleculeStartValuesBuildingBlock)
{
if (msv.Name != molInfo.GetMoleculeBuilderName())
{
continue;
}
if (molInfo.GetContainer().Any(x => x.Name == msv.ContainerPath.LastOrDefault()))
{
msv.IsPresent = true;
var sbmlSpecies = molInfo.GetSpeciesIfOne();
if (sbmlSpecies == null)
{
return;
}
var amountDimension = GetDimension(sbmlSpecies, model);
//unit is set by the Unit of SubstanceUnit
if (sbmlSpecies.isSetInitialAmount())
{
msv.StartValue = sbmlSpecies.getInitialAmount();
if (amountDimension != null)
{
msv.Dimension = amountDimension;
molInfo.SetDimension(amountDimension);
}
}
if (!sbmlSpecies.isSetInitialConcentration())
{
continue;
}
//unit is {unit of amount}/{unit of size}
msv.StartValue = sbmlSpecies.getInitialConcentration();
var sizeDimension = GetSizeDimensionFromCompartment(sbmlSpecies, model);
if (amountDimension == null)
{
continue;
}
if (sizeDimension == null)
{
continue;
}
var newDim = CreateNewDimension(amountDimension, sizeDimension);
msv.Dimension = newDim;
molInfo.SetDimension(newDim);
}
else
{
msv.IsPresent = false;
msv.StartValue = 0;
}
}
}
}
private void ImportInitialAssignment(InitialAssignment initialAssignment, Model model)
{
var symbol = initialAssignment.getSymbol();
if (IsParameter(symbol))
{
var parameter = GetParameter(symbol);
SetPSV(initialAssignment.getMath(), parameter, String.Empty);
return;
}
if (IsContainerSizeParameter(symbol))
{
var sizeParameter = GetContainerSizeParameter(symbol);
SetPSV(initialAssignment.getMath(), sizeParameter, symbol);
return;
}
if (IsSpeciesAssignment(symbol))
{
DoSpeciesAssignment(symbol, initialAssignment.getMath(), isInitialAssignment: true);
}
CheckSpeciesReferences(initialAssignment.getId(), symbol, model);
}
protected override void Because()
{
var sbmlModel = new Model(3, 1);
//Event
var sbmlEvent = sbmlModel.createEvent();
sbmlEvent.setId("e1");
sbmlEvent.setName("e1_name");
sbmlEvent.setNotes("eventNotes");
//Trigger
var trigger = sbmlModel.createTrigger();
trigger.setMath(libsbml.parseFormula("1 > 0 "));
sbmlEvent.setTrigger(trigger);
//Event Assignment
var assign = new EventAssignment(3, 1);
assign.setId("ea1");
assign.setName("ea1_name");
assign.setVariable("x1");
assign.setMath(libsbml.parseFormula("1+2"));
sbmlEvent.addEventAssignment(assign);
sbmlModel.addEvent(sbmlEvent);
sut.DoImport(sbmlModel, new MoBiProject(), A.Fake <SBMLInformation>(), new MoBiMacroCommand());
}
/// <summary>
/// Sets all the autogenerated Molecule Start Values to the right values and updates their
/// "IsPresent" property.
/// </summary>
private void SetMoleculeStartValues(Model model)
{
foreach (var molInfo in _sbmlInformation.MoleculeInformation)
{
foreach (var msv in _moleculeStartValuesBuildingBlock)
{
if (msv.Name != molInfo.GetMoleculeBuilderName())
{
continue;
}
if (molInfo.GetContainer().Any(x => x.Name == msv.ContainerPath.LastOrDefault()))
{
msv.IsPresent = true;
msv.NegativeValuesAllowed = true;
var sbmlSpecies = molInfo.GetSpeciesIfOne();
if (sbmlSpecies == null)
{
return;
}
var sbmlUnit = GetUnit(sbmlSpecies, model);
var amountDimension = _unitDefinitionImporter.DimensionFor(sbmlUnit);
//unit is set by the Unit of SubstanceUnit
if (sbmlSpecies.isSetInitialAmount())
{
msv.StartValue = sbmlSpecies.getInitialAmount();
if (amountDimension != null)
{
msv.Dimension = amountDimension;
molInfo.SetDimension(amountDimension);
}
}
if (!sbmlSpecies.isSetInitialConcentration())
{
continue;
}
//unit is {unit of amount}/{unit of size}
var baseValue = _unitDefinitionImporter.ToMobiBaseUnit(sbmlUnit, sbmlSpecies.getInitialConcentration());
msv.StartValue = baseValue.value;
msv.Formula = _context.Create <ExplicitFormula>($"{msv.Name}_0").WithName($"{msv.Name}_0").WithDimension(amountDimension).WithFormulaString($"{baseValue.value} * {Constants.VOLUME_ALIAS}");
msv.Formula.AddObjectPath(
ObjectPathFactory.CreateFormulaUsablePathFrom(ObjectPath.PARENT_CONTAINER, Constants.Parameters.VOLUME)
.WithAlias(Constants.VOLUME_ALIAS)
.WithDimension(_moBiDimensionFactory.Dimension(Constants.Dimension.VOLUME))
);
_moleculeStartValuesBuildingBlock.AddFormula(msv.Formula);
msv.Dimension = amountDimension;
molInfo.SetDimension(amountDimension);
UseConcentrations = true;
}
else
{
msv.IsPresent = false;
msv.StartValue = 0;
}
}
}
}
/// <summary>
/// Imports all Reactions of the SBML Model.
/// </summary>
protected override void Import(Model model)
{
for (long i = 0; i < model.getNumReactions(); i++)
{
CreateReaction(model.getReaction(i), model);
}
AddToProject();
}
protected override void Import(Model model)
{
for (long i = 0; i < model.getNumInitialAssignments(); i++)
{
ImportInitialAssignment(model.getInitialAssignment(i), model);
}
AddToProject();
}
private void CreateMoleculeStartValueBuildingBlock(Model model)
{
_moleculeStartValuesBuildingBlock = _moleculeStartValuesCreator.CreateFrom(GetMainSpatialStructure(model),
MoleculeBuildingBlock)
.WithId(SBMLConstants.SBML_MOLECULESTARTVALUES_BB)
.WithName(SBMLConstants.SBML_MOLECULESTARTVALUES_BB)
.WithDescription(SBMLConstants.SBML_MOLECULESTARTVALUES_DESCRIPTION);
}
protected override void Import(Model model)
{
for (long i = 0; i < model.getNumFunctionDefinitions(); i++)
{
_functionDefinitions.Add(model.getFunctionDefinition(i));
}
_astHandler.FunctionDefinitions = _functionDefinitions;
}
/// <summary>
/// Creates the TopContainer of the Spatial Structure.
/// </summary>
internal void CreateTopContainer(Model model)
{
_topContainer = _objectBaseFactory.Create <IContainer>()
.WithId(SBMLConstants.SBML_TOP_CONTAINER)
.WithName("TOPCONTAINER" + SBMLConstants.SBML + model.getName())
.WithMode(ContainerMode.Logical)
.WithContainerType(ContainerType.Compartment);
}
/// <summary>
/// The creation of Algrebraic Rules is not supported.
/// </summary>
private void CreateAlgebraicRule(Model model)
{
var msg = new NotificationMessage(GetMainSpatialStructure(model), MessageOrigin.All, null, NotificationType.Warning)
{
Message = SBMLConstants.SBML_FEATURE_NOT_SUPPORTED + ": SBML Algebraic Rule was not imported."
};
_sbmlInformation.NotificationMessages.Add(msg);
}
public void test_CompartmentType_parent_create()
{
Model m = new Model(2,4);
CompartmentType ct = m.createCompartmentType();
ListOf lo = m.getListOfCompartmentTypes();
assertTrue( lo == m.getCompartmentType(0).getParentSBMLObject() );
assertTrue( lo == ct.getParentSBMLObject() );
assertTrue( m == lo.getParentSBMLObject() );
}
public void test_AssignmentRule_parent_create()
{
Model m = new Model(2,4);
AssignmentRule r = m.createAssignmentRule();
ListOf lo = m.getListOfRules();
assertTrue( lo == m.getRule(0).getParentSBMLObject() );
assertTrue( lo == r.getParentSBMLObject() );
assertTrue( m == lo.getParentSBMLObject() );
}
protected override void Import(Model model)
{
if (model == null) return;
if (_sbmlProject == null) return;
for (long i = 0; i < model.getNumUnitDefinitions(); i++)
{
ConvertUnit(model.getUnitDefinition(i));
}
}
/// <summary>
/// Creates the Spatial Structure of the SBML Model with the TopContainer.
/// </summary>
internal void CreateSpatialStructureFromModel(IContainer topContainer, Model model)
{
SpatialStructure = _spatialStructureFactory.Create().DowncastTo <IMoBiSpatialStructure>()
.WithName(SBMLConstants.SBML_MODEL + model.getName())
.WithTopContainer(topContainer)
.WithDescription(SBMLConstants.SBML_NOTES + model.getNotesString() + SBMLConstants.SPACE +
SBMLConstants.SBML_METAID + model.getMetaId());
SpatialStructure.AddTopContainer(_eventsTopContainer);
}
public void test_Model_addCompartment2()
{
Model m = new Model(2,2);
Compartment c = new Compartment(2,1);
c.setId( "c");
int i = m.addCompartment(c);
assertTrue( i == libsbml.LIBSBML_VERSION_MISMATCH );
assertTrue( m.getNumCompartments() == 0 );
c = null;
m = null;
}
/// <summary>
/// Creates a MoBi reaction by a given SBML Reaction.
/// </summary>
internal void CreateReaction(Reaction sbmlReaction, Model model)
{
if (IsMultiCompartmentReaction(sbmlReaction, model))
{
CreateMulticompartmentReaction(sbmlReaction, model);
}
else
{
CreateStandardReaction(sbmlReaction, model);
}
}
public void test_SBMLDocument_setLevelAndVersion()
{
SBMLDocument d = new SBMLDocument(2,2);
Model m1 = new Model(2,2);
d.setModel(m1);
assertTrue( d.setLevelAndVersion(2,3,false) == true );
assertTrue( d.setLevelAndVersion(2,1,false) == true );
assertTrue( d.setLevelAndVersion(1,2,false) == true );
assertTrue( d.setLevelAndVersion(1,1,false) == false );
d = null;
}
/// <summary>
/// Gets a SBML species by it's Id.
/// </summary>
private Species GetSpeciesById(string speciesId, Model model)
{
for (long i = 0; i < model.getNumSpecies(); i++)
{
if (model.getSpecies(i).getId() == speciesId)
{
return(model.getSpecies(i));
}
}
return(null);
}
public void test_CompartmentType_parent_add()
{
CompartmentType ct = new CompartmentType(2,4);
Model m = new Model(2,4);
ct.setId("ct");
m.addCompartmentType(ct);
ct = null;
ListOf lo = m.getListOfCompartmentTypes();
assertTrue( lo == m.getCompartmentType(0).getParentSBMLObject() );
assertTrue( m == lo.getParentSBMLObject() );
}
/// <summary>
/// Imports all Reactions of the SBML Model.
/// </summary>
protected override void Import(Model model)
{
_astHandler.FunctionDefinitions = _functionDefinitionImporter.FunctionDefinitions;
_astHandler.SetUnitDefinitionImporter(_unitDefinitionImporter);
_astHandler.UseConcentrations = _speciesImporter.UseConcentrations;
for (long i = 0; i < model.getNumReactions(); i++)
{
CreateReaction(model.getReaction(i), model);
}
AddToProject();
}
/// <summary>
/// Creates a multicompartment reaction.
/// </summary>
private void CreateMulticompartmentReaction(Reaction sbmlReaction, Model model)
{
if ((sbmlReaction.getNumReactants() + sbmlReaction.getNumProducts() == 2) && (IsPassiveTransport(sbmlReaction, model)))
{
CreatePassiveTransport(sbmlReaction, model);
}
else
{
CreateGhostReaction(sbmlReaction, model);
}
}
private void reportConstraints(IMoBiProject project, Model model)
{
if (model.getNumConstraints() != 0)
{
var msg = new NotificationMessage(project, MessageOrigin.All, null, NotificationType.Warning)
{
Message = ("SBML Constraints are not supported.")
};
SBMLInformation.NotificationMessages.Add(msg);
}
}
/// <summary>
/// Imports all Events of the SBML Model.
/// </summary>
protected override void Import(Model model)
{
_astHandler.NeedAbsolutePath = true;
CreateEGBandEGBB();
for (long i = 0; i < model.getNumEvents(); i++)
{
CreateEvent(model.getEvent(i));
}
_astHandler.NeedAbsolutePath = false;
AddToProject();
}
protected override void Import(Model sbmlModel)
{
CreateTopContainer(sbmlModel);
CreateEventsTopContainer();
for (long i = 0; i < sbmlModel.getNumCompartments(); i++)
{
_topContainer.Add(CreateContainerFromCompartment(sbmlModel.getCompartment(i)));
}
CreateSpatialStructureFromModel(_topContainer, sbmlModel.getModel());
AddToProject();
}
protected override void Context()
{
base.Context();
_sbmlModel = new Model(3, 1);
_sbmlInformation = new SBMLInformation();
//one compartment reaction
_reaction = _sbmlModel.createReaction();
_reaction.setId("r1");
//reaction partner
var s1 = _sbmlModel.createSpecies();
s1.setId("s1");
s1.setCompartment("default");
var s2 = _sbmlModel.createSpecies();
s2.setId("s2");
s2.setCompartment("default");
var m = new MoleculeInformation(s1);
var m2 = new MoleculeInformation(s2);
_sbmlInformation.MoleculeInformation.Add(m);
_sbmlInformation.MoleculeInformation.Add(m2);
//SRef
var s1Ref = _reaction.createReactant();
s1Ref.setSpecies("s1");
s1Ref.setStoichiometry(1);
var s2Ref = _reaction.createProduct();
s2Ref.setSpecies("s2");
s2Ref.setStoichiometry(2);
_reaction.addProduct(s2Ref);
//Modifier
var mod = _reaction.createModifier();
mod.setId("mod");
mod.setName("mod");
mod.setSpecies("s1");
//Kinetic Law
var kl = _reaction.createKineticLaw();
kl.setId("kl");
kl.setMath(libsbml.parseFormula("2*3"));
}
public void test_Model_addCompartment1()
{
Model m = new Model(2,2);
Compartment c = new Compartment(2,2);
int i = m.addCompartment(c);
assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT );
c.setId( "c");
i = m.addCompartment(c);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( m.getNumCompartments() == 1 );
c = null;
m = null;
}
private string getProjectName(Model model)
{
var name = String.Empty;
if (model.isSetId())
{
name += model.getId() + SBMLConstants.SPACE;
}
if (model.isSetName())
{
name += model.getName();
}
return(name != string.Empty ? name : SBMLConstants.DEFAULT_PROJECT_NAME);
}
protected override void Import(Model model)
{
CreateMoleculeBuildingBlock();
for (long i = 0; i < model.getNumSpecies(); i++)
{
CreateMoleculeFromSpecies(model.getSpecies(i));
}
CheckMoleculeNameContainer();
CreateDummySpecies();
CreateMoleculeStartValueBuildingBlock(model);
SetMoleculeStartValues(model);
SetDummyMSVs();
AddToProject();
}
public void test_CompartmentType_ancestor_add()
{
CompartmentType ct = new CompartmentType(2,4);
Model m = new Model(2,4);
ct.setId("ct");
m.addCompartmentType(ct);
ct = null;
ListOf lo = m.getListOfCompartmentTypes();
CompartmentType obj = m.getCompartmentType(0);
assertTrue( obj.getAncestorOfType(libsbml.SBML_MODEL) == m );
assertTrue( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo );
assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
assertTrue( obj.getAncestorOfType(libsbml.SBML_EVENT) == null );
}
public void test_AssignmentRule_ancestor_create()
{
Model m = new Model(2,4);
AssignmentRule r = m.createAssignmentRule();
ListOf lo = m.getListOfRules();
assertTrue( r.getAncestorOfType(libsbml.SBML_MODEL) == m );
assertTrue( r.getAncestorOfType(libsbml.SBML_LIST_OF) == lo );
assertTrue( r.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
assertTrue( r.getAncestorOfType(libsbml.SBML_EVENT) == null );
Rule obj = m.getRule(0);
assertTrue( obj.getAncestorOfType(libsbml.SBML_MODEL) == m );
assertTrue( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo );
assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
assertTrue( obj.getAncestorOfType(libsbml.SBML_EVENT) == null );
}
public void Initialize(Model sbmlModel, SBMLDocument sbmlDoc)
{
Level = (int)sbmlDoc.getLevel();
Version = (int)sbmlDoc.getVersion();
SaveSpeciesReferences(sbmlModel);
if (sbmlModel.isSetConversionFactor())
{
ConversionFactor = sbmlModel.getConversionFactor();
}
if (sbmlModel.isSetSBOTerm())
{
SboTerm = sbmlModel.getSBOTerm();
}
}
public void test_ListOf_append()
{
Model m = new Model(2,4);
m.createCompartment();
ListOf loc = m.getListOfCompartments();
assertTrue( loc.size() == 1 );
SBase c = new Compartment(2,4);
int i = loc.append(c);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( loc.size() == 2 );
SBase sp = new Species(2,4);
i = loc.append(sp);
assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT );
assertTrue( loc.size() == 2 );
m = null;
sp = null;
}
/// <summary>
/// Checks if the given Initial Assignment wants to assign a stoichiometry (species Reference).
/// This is not supported and causes a Notification.
/// </summary>
public void CheckSpeciesReferences(string assignmentId, string paramName, Model model)
{
foreach (var sp in _sbmlInformation.SpeciesReferences)
{
if (sp.getId() != paramName)
{
continue;
}
var msg = new NotificationMessage(GetMainSpatialStructure(model), MessageOrigin.All, null,
NotificationType.Warning)
{
Message = SBMLConstants.SBML_FEATURE_NOT_SUPPORTED + ": Stoichiometry of " + assignmentId +
" was set to default value: " + SBMLConstants.SBML_STOICHIOMETRY_DEFAULT
};
_sbmlInformation.NotificationMessages.Add(msg);
}
}
public void test_SBMLDocument_setLevelAndVersion_Error()
{
SBMLDocument d = new SBMLDocument();
d.setLevelAndVersion(2,1,true);
Model m1 = new Model(2,1);
Unit u = new Unit(2,1);
u.setKind(libsbml.UnitKind_forName("mole"));
u.setOffset(3.2);
UnitDefinition ud = new UnitDefinition(2,1);
ud.setId( "ud");
ud.addUnit(u);
m1.addUnitDefinition(ud);
d.setModel(m1);
assertTrue( d.setLevelAndVersion(2,2,true) == false );
assertTrue( d.setLevelAndVersion(2,3,true) == false );
assertTrue( d.setLevelAndVersion(1,2,true) == false );
assertTrue( d.setLevelAndVersion(1,1,true) == false );
d = null;
}
protected override void Import(Model model)
{
for (long i = 0; i < model.getNumRules(); i++)
{
var rule = model.getRule(i);
if (rule.isAssignment())
{
CreateAssignmentRule(rule, model);
}
if (rule.isRate())
{
CreateRateRule(rule, model);
}
if (rule.isAlgebraic())
{
CreateAlgebraicRule(model);
}
}
AddToProject();
}
/// <summary>
/// Gets the dimension of a species. It is set by it's one substanceUnits attribute
/// or by the substanceUnits definition of the Model.
/// </summary>
private IDimension GetDimension(Species s, Model model)
{
var substanceUnits = s.isSetSubstanceUnits() ? s.getSubstanceUnits() : model.getSubstanceUnits();
IDimension amountDimension = null;
if (_sbmlInformation.MobiDimension.ContainsKey(substanceUnits))
{
amountDimension = _sbmlInformation.MobiDimension[substanceUnits];
}
if (amountDimension == null)
{
return(null);
}
if (_moBiDimensionFactory.Dimensions.All(dim => dim.Name != amountDimension.Name))
{
_moBiDimensionFactory.AddDimension(amountDimension);
}
return(amountDimension);
}
public void test_Model_L1V2()
{
Model m = new Model(1,2);
assertEquals( false, (m.hasRequiredElements()) );
m.createCompartment();
assertEquals( true, m.hasRequiredElements() );
m = null;
}
public void test_Model_L1V1()
{
Model m = new Model(1,1);
assertEquals( false, (m.hasRequiredElements()) );
m.createCompartment();
assertEquals( false, (m.hasRequiredElements()) );
m.createSpecies();
assertEquals( false, (m.hasRequiredElements()) );
m.createReaction();
assertEquals( true, m.hasRequiredElements() );
m = null;
}
public void test_Model()
{
Model m = new Model(2,4);
assertEquals( true, m.hasRequiredElements() );
m = null;
}
/**
* Copy constructor; creates a (deep) copy of the given Model object.
*
* @param orig the object to copy.
*/
public Model(Model orig)
: this(libsbmlPINVOKE.new_Model__SWIG_2(Model.getCPtr(orig)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
internal static HandleRef getCPtrAndDisown(Model obj)
{
HandleRef ptr = new HandleRef(null, IntPtr.Zero);
if (obj != null)
{
ptr = obj.swigCPtr;
obj.swigCMemOwn = false;
}
return ptr;
}
internal static HandleRef getCPtr(Model obj)
{
return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
}
/**
* Copies a given Model object's subcomponents and appends the copies to
* the appropriate places in this Model.
*
* This method also calls the <code>appendFrom</code> method on all libSBML
* plug-in objects.
*
*
*
* SBML Level 3 consists of a <em>Core</em> definition that can be extended
* via optional SBML Level 3 <em>packages</em>. A given model may indicate
* that it uses one or more SBML packages, and likewise, a software tool may be
* able to support one or more packages. LibSBML does not come preconfigured
* with all possible packages included and enabled, in part because not all
* package specifications have been finalized. To support the ability for
* software systems to enable support for the Level 3 packages they choose,
* libSBML features a <em>plug-in</em> mechanism. Each SBML Level 3
* package is implemented in a separate code plug-in that can be enabled by the
* application to support working with that SBML package. A given SBML model
* may thus contain not only objects defined by SBML Level 3 Core, but also
* objects created by libSBML plug-ins supporting additional Level 3
* packages.
*
*
*
* @param model the Model to merge with this one.
*
*/
public new int appendFrom(Model model)
{
int ret = libsbmlPINVOKE.Model_appendFrom(swigCPtr, Model.getCPtr(model));
return ret;
}
public void test_Model_constructor()
{
SBase s;
try
{
s = new Model(1,1);
s = new Model(1,2);
s = new Model(2,1);
s = new Model(2,2);
s = new Model(2,3);
s = new Model(2,4);
s = new Model(3,1);
s = new Model(SN11);
s = new Model(SN12);
s = new Model(SN21);
s = new Model(SN22);
s = new Model(SN23);
s = new Model(SN24);
s = new Model(SN31);
}
catch (SBMLConstructorException e)
{
s = null;
}
assertTrue(s != null);
string msg = "";
try
{
s = new Model(9,9);
}
catch (SBMLConstructorException e)
{
msg = e.Message;
}
assertTrue(msg == ErrMsg);
msg = "";
try
{
s = new Model(SN99);
}
catch (SBMLConstructorException e)
{
msg = e.Message;
}
assertTrue(msg == ErrMsg);
}
public void test_create_l1v1_units()
{
SBMLDocument d;
Model m;
Compartment c;
KineticLaw kl;
Parameter p;
Reaction r;
Species s;
SpeciesReference sr;
Unit u;
UnitDefinition ud;
d = new SBMLDocument();
m = new Model(2,4);
d.setModel(m);
ud = m.createUnitDefinition();
ud.setName( "substance");
u = m.createUnit();
u.setKind(libsbml.UNIT_KIND_MOLE);
u.setScale(-3);
ud = m.createUnitDefinition();
ud.setName( "mls");
u = m.createUnit();
u.setKind(libsbml.UNIT_KIND_MOLE);
u.setScale(-3);
u = m.createUnit();
u.setKind(libsbml.UNIT_KIND_LITER);
u.setExponent(-1);
u = m.createUnit();
u.setKind(libsbml.UNIT_KIND_SECOND);
u.setExponent(-1);
c = m.createCompartment();
c.setName( "cell");
s = m.createSpecies();
s.setName( "x0");
s.setCompartment( "cell");
s.setInitialAmount(1);
s = m.createSpecies();
s.setName( "x1");
s.setCompartment( "cell");
s.setInitialAmount(1);
s = m.createSpecies();
s.setName( "s1");
s.setCompartment( "cell");
s.setInitialAmount(1);
s = m.createSpecies();
s.setName( "s2");
s.setCompartment( "cell");
s.setInitialAmount(1);
p = m.createParameter();
p.setName( "vm");
p.setUnits( "mls");
p.setValue(2);
p = m.createParameter();
p.setName( "km");
p.setValue(2);
r = m.createReaction();
r.setName( "v1");
sr = m.createReactant();
sr.setSpecies( "x0");
sr = m.createProduct();
sr.setSpecies( "s1");
kl = m.createKineticLaw();
kl.setFormula( "(vm * s1)/(km + s1)");
r = m.createReaction();
r.setName( "v2");
sr = m.createReactant();
sr.setSpecies( "s1");
sr = m.createProduct();
sr.setSpecies( "s2");
kl = m.createKineticLaw();
kl.setFormula( "(vm * s2)/(km + s2)");
r = m.createReaction();
r.setName( "v3");
sr = m.createReactant();
sr.setSpecies( "s2");
sr = m.createProduct();
sr.setSpecies( "x1");
kl = m.createKineticLaw();
kl.setFormula( "(vm * s1)/(km + s1)");
d = null;
}
/**
* Creates a new L3ParserSettings object with specific values for all
* possible settings.
*
* @param model a Model object to be used for disambiguating identifiers
*
* @param parselog a flag that controls how the parser will handle
* the symbol @c log in formulas
*
* @param collapseminus a flag that controls how the parser will handle
* minus signs
*
* @param parseunits a flag that controls how the parser will handle
* apparent references to units of measurement associated with raw
* numbers in a formula
*
* @param avocsymbol a flag that controls how the parser will handle
* the appearance of the symbol @c avogadro in a formula
*
* @see getModel()
* @see setModel(@if java Model model@endif)
* @see unsetModel()
* @see getParseLog()
* @see setParseLog(@if java int type@endif)
* @see getParseUnits()
* @see setParseUnits(@if java bool units@endif)
* @see getParseCollapseMinus()
* @see setParseCollapseMinus(@if java bool collapseminus@endif)
* @see getParseAvogadroCsymbol()
* @see setParseAvogadroCsymbol(@if java bool l2only@endif)
*/
public L3ParserSettings(Model model, int parselog, bool collapseminus, bool parseunits, bool avocsymbol)
: this(libsbmlPINVOKE.new_L3ParserSettings__SWIG_1(Model.getCPtr(model), parselog, collapseminus, parseunits, avocsymbol), true)
{
}
public static IdList mapComponentValues(Model m)
{
IdList ret = new IdList(libsbmlPINVOKE.SBMLTransforms_mapComponentValues(Model.getCPtr(m)), true);
return ret;
}
/** */
/* libsbml-internal */
public static bool expandInitialAssignments(Model m)
{
bool ret = libsbmlPINVOKE.SBMLTransforms_expandInitialAssignments(Model.getCPtr(m));
return ret;
}
/** */
/* libsbml-internal */
public static double evaluateASTNode(ASTNode node, Model m)
{
double ret = libsbmlPINVOKE.SBMLTransforms_evaluateASTNode__SWIG_0(ASTNode.getCPtr(node), Model.getCPtr(m));
return ret;
}
/**
* Sets the model reference in this L3ParserSettings object.
*
* When a Model object is provided, identifiers (values of type @c SId)
* from that model are used in preference to pre-defined MathML
* definitions. More precisely, the Model entities whose identifiers will
* shadow identical symbols in the mathematical formula are: Species,
* Compartment, Parameter, Reaction, and SpeciesReference. For instance,
* if the parser is given a Model containing a Species with the identifier
* "<code>pi</code>", and the formula to be parsed is
* "<code>3*pi</code>", the MathML produced will contain the
* construct <code><ci> pi </ci></code> instead of the
* construct <code><pi/></code>.
* Similarly, when a Model object is provided, @c SId values of
* user-defined functions present in the Model will be used preferentially
* over pre-defined MathML functions. For example, if the passed-in Model
* contains a FunctionDefinition with the identifier
* "<code>sin</code>", that function will be used instead of the
* predefined MathML function <code><sin/></code>.
*
* @param model a Model object to be used for disambiguating identifiers
*
* @warning <span class='warning'>This does @em not copy the Model object.
* This means that modifications made to the object after invoking this
* method may affect parsing behavior.</span>
*
* @see getModel()
* @see unsetModel()
*/
public void setModel(Model model)
{
libsbmlPINVOKE.L3ParserSettings_setModel(swigCPtr, Model.getCPtr(model));
}
public void test_L3_Model_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3,1);
sbmlns.addNamespaces(xmlns);
Model m = new Model(sbmlns);
assertTrue( m.getTypeCode() == libsbml.SBML_MODEL );
assertTrue( m.getMetaId() == "" );
assertTrue( m.getNotes() == null );
assertTrue( m.getAnnotation() == null );
assertTrue( m.getLevel() == 3 );
assertTrue( m.getVersion() == 1 );
assertTrue( m.getNamespaces() != null );
assertTrue( m.getNamespaces().getLength() == 2 );
assertTrue( m.getId() == "" );
assertTrue( m.getName() == "" );
assertTrue( m.getSubstanceUnits() == "" );
assertTrue( m.getTimeUnits() == "" );
assertTrue( m.getVolumeUnits() == "" );
assertTrue( m.getAreaUnits() == "" );
assertTrue( m.getLengthUnits() == "" );
assertTrue( m.getConversionFactor() == "" );
assertEquals( false, m.isSetId() );
assertEquals( false, m.isSetName() );
assertEquals( false, m.isSetSubstanceUnits() );
assertEquals( false, m.isSetTimeUnits() );
assertEquals( false, m.isSetVolumeUnits() );
assertEquals( false, m.isSetAreaUnits() );
assertEquals( false, m.isSetLengthUnits() );
assertEquals( false, m.isSetConversionFactor() );
m = null;
}
/**
* Sets the Model for this SBMLDocument to a copy of the given Model.
*
* @param m the new Model to use.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif The possible values
* returned by this function are:
* @li @link libsbmlcs.libsbml.LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link libsbmlcs.libsbml.LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
* @li @link libsbmlcs.libsbml.LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
*
* @see createModel()
* @see getModel()
*/
public int setModel(Model m)
{
int ret = libsbmlPINVOKE.SBMLDocument_setModel(swigCPtr, Model.getCPtr(m));
return ret;
}
public void tearDown()
{
M = null;
}
public void test_Compartment_parent_add()
{
Compartment c = new Compartment(2,4);
c.setId("c");
Model m = new Model(2,4);
m.addCompartment(c);
c = null;
ListOf lo = m.getListOfCompartments();
assertTrue( lo == m.getCompartment(0).getParentSBMLObject() );
assertTrue( m == lo.getParentSBMLObject() );
}
