/// <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);
}
public void setUp()
{
R = new Reaction(2,4);
if (R == null);
{
}
}
/// <summary>
/// Saves products of a SBML reaction into a dictionary, containing their compartment and SpeciesReference.
/// </summary>
private Dictionary <string, List <SpeciesReference> > ComputeProducts(Reaction sbmlReaction, Model model)
{
var productCompartmentMoleculeDictionary = new Dictionary <string, List <SpeciesReference> >();
for (long i = 0; i < sbmlReaction.getNumProducts(); i++)
{
var product = sbmlReaction.getProduct(i);
var productSpecies = GetSpeciesById(product.getSpecies(), model);
var compartment = productSpecies.getCompartment();
if (_sbmlInformation.MoleculeInformation.All(info => info.SpeciesIds.TrueForAll(s => s != productSpecies.getId())))
{
continue;
}
if (!productCompartmentMoleculeDictionary.ContainsKey(compartment))
{
productCompartmentMoleculeDictionary[compartment] = new List <SpeciesReference> {
product
}
}
;
else
{
productCompartmentMoleculeDictionary[compartment].Add(product);
}
}
return(productCompartmentMoleculeDictionary);
}
/// <summary>
/// Creates the Local Parameters of the MoBi Reaction by the given local Parameters
/// of the SBML Reaction.
/// </summary>
private List <IParameter> CreateLocalParameters(Reaction sbmlReaction)
{
if (sbmlReaction.getKineticLaw() == null)
{
return(null);
}
if (sbmlReaction.getKineticLaw().getNumLocalParameters() <= 0)
{
return(null);
}
var parameter = new List <IParameter>();
for (long i = 0; i < sbmlReaction.getKineticLaw().getNumLocalParameters(); i++)
{
var p = sbmlReaction.getKineticLaw().getLocalParameter(i);
var formula = ObjectBaseFactory.Create <ConstantFormula>()
.WithValue(p.getValue());
var localParameter = ObjectBaseFactory.Create <IParameter>()
.WithName(p.getId())
.WithDescription(p.getNotesString())
.WithFormula(formula);
var dim = GetDimension(p);
if (dim != null)
{
localParameter.Dimension = dim;
}
if (localParameter != null)
{
parameter.Add(localParameter);
}
}
return(parameter);
}
/// <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);
}
}
/// <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);
}
public void test_KineticLaw_getParameterById()
{
Parameter k1 = new Parameter(2,4);
Parameter k2 = new Parameter(2,4);
k1.setId( "k1");
k2.setId( "k2");
k1.setValue(3.14);
k2.setValue(2.72);
M.addParameter(k1);
M.addParameter(k2);
Reaction r1 = new Reaction(2,4);
r1.setId( "reaction_1" );
KineticLaw kl = new KineticLaw(2,4);
kl.setFormula( "k1 * X0");
Parameter k3 = new Parameter(2,4);
Parameter k4 = new Parameter(2,4);
k3.setId( "k1");
k4.setId( "k2");
k3.setValue(2.72);
k4.setValue(3.14);
kl.addParameter(k3);
kl.addParameter(k4);
r1.setKineticLaw(kl);
M.addReaction(r1);
KineticLaw kl1 = M.getReaction(0).getKineticLaw();
assertNotEquals(kl1.getParameter( "k1" ),k3);
assertNotEquals(kl1.getParameter( "k1" ),k1);
assertNotEquals(kl1.getParameter( "k2" ),k4);
assertEquals(kl1.getParameter( "k3" ),null);
}
/// <summary>
/// Creates the Educts of the MoBi reaction.
/// </summary>
private void CreateEducts(Reaction sbmlReaction, IReactionBuilder reactionBuilder, Model model)
{
for (long i = 0; i < sbmlReaction.getNumReactants(); i++)
{
var educt = CreateReactionPartner(sbmlReaction.getReactant(i), model);
if (educt != null)
{
reactionBuilder.AddEduct(educt);
}
}
}
/// <summary>
/// Creates the Products of the MoBi reaction.
/// </summary>
private void CreateProducts(Reaction sbmlReaction, IReactionBuilder reactionBuilder, Model model)
{
for (long i = 0; i < sbmlReaction.getNumProducts(); i++)
{
var product = CreateReactionPartner(sbmlReaction.getProduct(i), model);
if (product != null)
{
reactionBuilder.AddProduct(product);
}
}
}
/// <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);
}
}
/// <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_Reaction_addProduct2()
{
Reaction m = new Reaction(2,2);
SpeciesReference p = new SpeciesReference(2,1);
p.setSpecies( "k");
int i = m.addProduct(p);
assertTrue( i == libsbml.LIBSBML_VERSION_MISMATCH );
assertTrue( m.getNumProducts() == 0 );
p = null;
m = null;
}
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"));
}
/// <summary>
/// Imports the SBML Modifiers to MoBi Modifiers.
/// </summary>
private void CreateModifiers(Reaction sbmlReaction, IReactionBuilder reactionBuilder, string reactionCompartment, Model model)
{
for (long i = 0; i < sbmlReaction.getNumModifiers(); i++)
{
var modifier = sbmlReaction.getModifier(i);
if (ModifierInDifferentCompartment(reactionCompartment, modifier, model))
{
continue;
}
var modifierMolecule = _sbmlInformation.GetMoleculeBySBMLId(modifier.getSpecies());
if (modifierMolecule != null)
{
reactionBuilder.AddModifier(modifierMolecule.Name);
}
}
}
/// <summary>
/// Creates the Kinetic Formula for a passive Transport.
/// </summary>
private void CreateKinetic(Reaction sbmlReaction, ITransportBuilder passiveTransport)
{
_astHandler.NeedAbsolutePath = true;
var formula = sbmlReaction.getKineticLaw() == null
? ObjectBaseFactory.Create <ExplicitFormula>().WithFormulaString(String.Empty)
: _astHandler.Parse(sbmlReaction.getKineticLaw().getMath(), sbmlReaction.getId(), _sbmlProject, _sbmlInformation);
if (formula == null)
{
passiveTransport.Formula = ObjectBaseFactory.Create <ExplicitFormula>()
.WithFormulaString(String.Empty)
.WithName(SBMLConstants.DEFAULT_FORMULA_NAME);
}
else
{
passiveTransport.Formula = formula;
_passiveTransportBuildingBlock.FormulaCache.Add(formula);
}
}
public void test_Reaction_addProduct1()
{
Reaction m = new Reaction(2,2);
SpeciesReference p = new SpeciesReference(2,2);
SpeciesReference p1 = new SpeciesReference(2,2);
p1.setSpecies( "k");
p1.setId( "k1");
int i = m.addProduct(p);
assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT );
p.setSpecies( "k");
p.setId( "k1");
i = m.addProduct(p);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( m.getNumProducts() == 1 );
i = m.addProduct(p1);
assertTrue( i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID );
assertTrue( m.getNumProducts() == 1 );
p = null;
p1 = null;
m = null;
}
/// <summary>
/// Checks if all reaction partners are in the same compartment.
/// </summary>
private bool IsMultiCompartmentReaction(Reaction sbmlReaction, Model model)
{
var compartment = String.Empty;
for (long i = 0; i < sbmlReaction.getNumReactants(); i++)
{
var x = sbmlReaction.getReactant(i).getSpecies();
var species = GetSpeciesById(x, model);
if (compartment == String.Empty)
{
compartment = species.getCompartment();
}
else
{
if (compartment != species.getCompartment())
{
return(true);
}
}
}
for (long i = 0; i < sbmlReaction.getNumProducts(); i++)
{
var x = sbmlReaction.getProduct(i).getSpecies();
var species = GetSpeciesById(x, model);
if (compartment == String.Empty)
{
compartment = species.getCompartment();
}
else
{
if (compartment != species.getCompartment())
{
return(true);
}
}
}
return(false);
}
public void test_SpeciesReference_Reactant_parent_create()
{
Reaction r = new Reaction(2,4);
SpeciesReference sr = r.createReactant();
ListOf lo = r.getListOfReactants();
assertTrue( lo == r.getReactant(0).getParentSBMLObject() );
assertTrue( lo == sr.getParentSBMLObject() );
assertTrue( r == lo.getParentSBMLObject() );
}
public void test_SpeciesReference_Reactant_parent_add()
{
SpeciesReference sr = new SpeciesReference(2,4);
Reaction r = new Reaction(2,4);
sr.setSpecies("s");
r.addReactant(sr);
sr = null;
ListOf lo = r.getListOfReactants();
assertTrue( lo == r.getReactant(0).getParentSBMLObject() );
assertTrue( r == lo.getParentSBMLObject() );
}
public void test_SpeciesReference_Modifier_parent_create()
{
Reaction r = new Reaction(2,4);
ModifierSpeciesReference sr = r.createModifier();
ListOf lo = r.getListOfModifiers();
assertTrue( lo == sr.getParentSBMLObject() );
assertTrue( lo == r.getModifier(0).getParentSBMLObject() );
assertTrue( r == lo.getParentSBMLObject() );
}
/// <summary>
/// Imports a SBML Reaction by creating a passive Transport.
/// </summary>
private void CreatePassiveTransport(Reaction sbmlReaction, Model model)
{
var reactant = sbmlReaction.getReactant(0).getSpecies();
var product = sbmlReaction.getProduct(0).getSpecies();
var reactantSpecies = GetSpeciesById(reactant, model);
var productSpecies = GetSpeciesById(product, model);
if (_sbmlInformation.MoleculeInformation.All(info => info.SpeciesIds.TrueForAll(s => s != reactant)))
{
return;
}
if (_sbmlInformation.MoleculeInformation.All(info => info.SpeciesIds.TrueForAll(s => s != product)))
{
return;
}
var molInfoReactant = _sbmlInformation.MoleculeInformation.FirstOrDefault(info => info.SpeciesIds.Contains(reactant));
var molInfoProduct = _sbmlInformation.MoleculeInformation.FirstOrDefault(info => info.SpeciesIds.Contains(product));
if (molInfoProduct == null)
{
return;
}
if (molInfoReactant == null)
{
return;
}
//must be the same Molecule
if (molInfoReactant.GetMoleculeBuilder() != molInfoProduct.GetMoleculeBuilder())
{
CreateErrorMessage();
}
var passiveTransport = ObjectBaseFactory.Create <ITransportBuilder>().WithName(sbmlReaction.getId());
passiveTransport.ForAll = false;
if (molInfoReactant.GetMoleculeBuilderName() == null)
{
return;
}
passiveTransport.MoleculeList.AddMoleculeName(molInfoReactant.GetMoleculeBuilderName());
var reactantCompartment = GetContainerFromCompartment_(molInfoReactant.GetCompartment(reactantSpecies));
var productCompartment = GetContainerFromCompartment_(molInfoProduct.GetCompartment(productSpecies));
if (reactantCompartment != null && productCompartment != null)
{
var reactantMatchTag = new MatchTagCondition(reactantCompartment.Name);
var productMatchTag = new MatchTagCondition(productCompartment.Name);
passiveTransport.SourceCriteria.Add(reactantMatchTag);
passiveTransport.TargetCriteria.Add(productMatchTag);
}
var parameters = CreateLocalParameters(sbmlReaction);
if (parameters != null)
{
parameters.ForEach(passiveTransport.AddParameter);
}
CreateKinetic(sbmlReaction, passiveTransport);
AddNeighbourhood(reactantCompartment, productCompartment, model);
_passiveTransportBuildingBlock.Add(passiveTransport);
}
public void test_Reaction_setName3()
{
Reaction p = new Reaction(2,2);
int i = p.setName("");
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertEquals( false, p.isSetName() );
p = null;
}
public void test_Reaction_createReactant()
{
Reaction m = new Reaction(2,2);
SpeciesReference p = m.createReactant();
assertTrue( m.getNumReactants() == 1 );
assertTrue( (p).getLevel() == 2 );
assertTrue( (p).getVersion() == 2 );
m = null;
}
public void test_Reaction_addReactant4()
{
Reaction m = new Reaction(2,2);
SpeciesReference p = null;
int i = m.addReactant(p);
assertTrue( i == libsbml.LIBSBML_OPERATION_FAILED );
assertTrue( m.getNumReactants() == 0 );
m = null;
}
public void test_KineticLaw_parent_add()
{
KineticLaw kl = new KineticLaw(2,4);
Reaction r = new Reaction(2,4);
r.setKineticLaw(kl);
assertTrue( r == r.getKineticLaw().getParentSBMLObject() );
r = null;
}
public void test_SpeciesReference_Reactant_ancestor_add()
{
SpeciesReference sr = new SpeciesReference(2,4);
Reaction r = new Reaction(2,4);
sr.setSpecies("s");
r.addReactant(sr);
sr = null;
ListOf lo = r.getListOfReactants();
SpeciesReference obj = r.getReactant(0);
assertTrue( obj.getAncestorOfType(libsbml.SBML_REACTION) == r );
assertTrue( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo );
assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
assertTrue( obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null );
}
public void test_Reaction_ancestor_add()
{
Reaction ia = new Reaction(2,4);
Model m = new Model(2,4);
ia.setId("k");
m.addReaction(ia);
ia = null;
ListOf lo = m.getListOfReactions();
Reaction obj = m.getReaction(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_Reaction_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,1);
sbmlns.addNamespaces(xmlns);
Reaction object1 = new Reaction(sbmlns);
assertTrue( object1.getTypeCode() == libsbml.SBML_REACTION );
assertTrue( object1.getMetaId() == "" );
assertTrue( object1.getNotes() == null );
assertTrue( object1.getAnnotation() == null );
assertTrue( object1.getLevel() == 2 );
assertTrue( object1.getVersion() == 1 );
assertTrue( object1.getNamespaces() != null );
assertTrue( object1.getNamespaces().getLength() == 2 );
object1 = null;
}
public void test_SpeciesReference_Reactant_ancestor_create()
{
Reaction r = new Reaction(2,4);
SpeciesReference sr = r.createReactant();
ListOf lo = r.getListOfReactants();
assertTrue( sr.getAncestorOfType(libsbml.SBML_REACTION) == r );
assertTrue( sr.getAncestorOfType(libsbml.SBML_LIST_OF) == lo );
assertTrue( sr.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
assertTrue( sr.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null );
SpeciesReference obj = r.getReactant(0);
assertTrue( obj.getAncestorOfType(libsbml.SBML_REACTION) == r );
assertTrue( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo );
assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
assertTrue( obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null );
}
/// <summary>
/// Creates for each compartment of the SBML Reaction one "Ghostreaction" to import multicompartment reactions.
/// </summary>
private void CreateGhostReactions(Reaction sbmlReaction, Dictionary <string, List <SpeciesReference> > eductCompartmentMoleculeDictionary, Dictionary <string, List <SpeciesReference> > productCompartmentMoleculeDictionary, Model model)
{
var usedProducts = new List <string>();
foreach (var keyValuePair in eductCompartmentMoleculeDictionary)
{
var reactionBuilder = ObjectBaseFactory.Create <IReactionBuilder>()
.WithName(sbmlReaction.getId() + "_" + keyValuePair.Key + "_ghostReaction")
.WithDescription(sbmlReaction.getNotesString());
CreateModifiers(sbmlReaction, reactionBuilder, keyValuePair.Key, model);
var parameters = CreateLocalParameters(sbmlReaction);
if (parameters != null)
{
parameters.ForEach(reactionBuilder.AddParameter);
}
CreateKineticLaw(sbmlReaction.getKineticLaw(), reactionBuilder, true);
var compartmentName = keyValuePair.Key;
if (!_sbmlInformation.DummyNameContainerDictionary.ContainsValue(compartmentName))
{
return;
}
var dummyMolecule = _sbmlInformation.DummyNameContainerDictionary.FirstOrDefault(x => x.Value == compartmentName).Key;
reactionBuilder.AddModifier(dummyMolecule);
foreach (var species in keyValuePair.Value)
{
var reactionPartner = CreateReactionPartner(species, model);
if (reactionPartner != null)
{
reactionBuilder.AddEduct(reactionPartner);
}
}
if (productCompartmentMoleculeDictionary.ContainsKey(keyValuePair.Key))
{
usedProducts.Add(keyValuePair.Key);
var productsInThisCompartment = productCompartmentMoleculeDictionary[keyValuePair.Key];
foreach (var product in productsInThisCompartment)
{
var reactionPartner = CreateReactionPartner(product, model);
if (reactionPartner != null)
{
reactionBuilder.AddProduct(reactionPartner);
}
}
}
ReactionBuilderList.Add(reactionBuilder);
}
foreach (var keyValuePair in productCompartmentMoleculeDictionary)
{
if (usedProducts.Contains(keyValuePair.Key))
{
continue;
}
var reactionBuilder = ObjectBaseFactory.Create <IReactionBuilder>()
.WithName(sbmlReaction.getId() + "_" + keyValuePair.Key + "_ghostReaction")
.WithDescription(sbmlReaction.getNotesString());
CreateModifiers(sbmlReaction, reactionBuilder, keyValuePair.Key, model);
var parameters = CreateLocalParameters(sbmlReaction);
if (parameters != null)
{
parameters.ForEach(reactionBuilder.AddParameter);
}
CreateKineticLaw(sbmlReaction.getKineticLaw(), reactionBuilder, true);
var compartmentName = keyValuePair.Key;
if (!_sbmlInformation.DummyNameContainerDictionary.ContainsValue(compartmentName))
{
return;
}
var dummyMolecule = _sbmlInformation.DummyNameContainerDictionary.FirstOrDefault(x => x.Value == compartmentName).Key;
reactionBuilder.AddModifier(dummyMolecule);
foreach (var species in keyValuePair.Value)
{
var reactionPartner = CreateReactionPartner(species, model);
if (reactionPartner != null)
{
reactionBuilder.AddProduct(reactionPartner);
}
}
ReactionBuilderList.Add(reactionBuilder);
}
}
public void test_SpeciesReference_Modifier_ancestor_add()
{
ModifierSpeciesReference sr = new ModifierSpeciesReference(2,4);
sr.setSpecies("s");
Reaction r = new Reaction(2,4);
r.addModifier(sr);
sr = null;
ListOf lo = r.getListOfModifiers();
ModifierSpeciesReference obj = r.getModifier(0);
assertTrue( obj.getAncestorOfType(libsbml.SBML_REACTION) == r );
assertTrue( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo );
assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
assertTrue( obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null );
}
public void test_Reaction_addReactant3()
{
Reaction m = new Reaction(2,2);
SpeciesReference p = new SpeciesReference(1,2);
p.setSpecies( "k");
int i = m.addReactant(p);
assertTrue( i == libsbml.LIBSBML_LEVEL_MISMATCH );
assertTrue( m.getNumReactants() == 0 );
p = null;
m = null;
}
public void test_KineticLaw_parent_create()
{
Reaction r = new Reaction(2,4);
KineticLaw kl = r.createKineticLaw();
assertTrue( r == kl.getParentSBMLObject() );
r = null;
}
public void test_Reaction_createKineticLaw()
{
Reaction r = new Reaction(2,2);
KineticLaw kl = r.createKineticLaw();
assertTrue( r.isSetKineticLaw() == true );
assertTrue( (kl).getLevel() == 2 );
assertTrue( (kl).getVersion() == 2 );
r = null;
}
public void test_KineticLaw_parent_NULL()
{
Reaction r = new Reaction(2,4);
KineticLaw kl = r.createKineticLaw();
Parameter p = kl.createParameter();
assertTrue( r == kl.getParentSBMLObject() );
assertTrue( r == p.getAncestorOfType(libsbml.SBML_REACTION) );
assertTrue( kl == p.getAncestorOfType(libsbml.SBML_KINETIC_LAW) );
KineticLaw kl1 = kl.clone();
assertTrue( kl1.getParentSBMLObject() == null );
assertTrue( kl1.getParameter(0).getAncestorOfType(libsbml.SBML_REACTION) == null );
assertTrue( kl1 == kl1.getParameter(0).getAncestorOfType(libsbml.SBML_KINETIC_LAW) );
r = null;
}
public void test_Reaction_setFast2()
{
Reaction R1 = new Reaction(2,4);
int i = R1.unsetFast();
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( R1.getFast() == false );
assertEquals( false, R1.isSetFast() );
}
public void test_Reaction_parent_add()
{
Reaction ia = new Reaction(2,4);
Model m = new Model(2,4);
ia.setId("k");
m.addReaction(ia);
ia = null;
ListOf lo = m.getListOfReactions();
assertTrue( lo == m.getReaction(0).getParentSBMLObject() );
assertTrue( m == lo.getParentSBMLObject() );
}
public void tearDown()
{
R = null;
}
public void test_SpeciesReference_Modifier_parent_add()
{
ModifierSpeciesReference sr = new ModifierSpeciesReference(2,4);
sr.setSpecies("s");
Reaction r = new Reaction(2,4);
r.addModifier(sr);
sr = null;
ListOf lo = r.getListOfModifiers();
assertTrue( lo == r.getModifier(0).getParentSBMLObject() );
assertTrue( r == lo.getParentSBMLObject() );
}
public void test_Reaction()
{
Reaction r = new Reaction(2,4);
assertEquals( true, r.hasRequiredElements() );
r = null;
}
public void test_KineticLaw_ancestor_create()
{
Reaction r = new Reaction(2,4);
KineticLaw kl = r.createKineticLaw();
assertTrue( kl.getAncestorOfType(libsbml.SBML_REACTION) == r );
assertTrue( kl.getAncestorOfType(libsbml.SBML_DELAY) == null );
assertTrue( kl.getAncestorOfType(libsbml.SBML_MODEL) == null );
assertTrue( kl.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
KineticLaw obj = r.getKineticLaw();
assertTrue( obj.getAncestorOfType(libsbml.SBML_REACTION) == r );
assertTrue( obj.getAncestorOfType(libsbml.SBML_MODEL) == null );
assertTrue( obj.getAncestorOfType(libsbml.SBML_DELAY) == null );
assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
r = null;
}
/**
* Adds a copy of the given Reaction object to this Model.
*
* @param r the Reaction object to add
*
*
* @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 libsbml#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink
* @li @link libsbml#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH@endlink
* @li @link libsbml#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH@endlink
* @li @link libsbml#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID@endlink
* @li @link libsbml#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT@endlink
* @li @link libsbml#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED@endlink
*
*
* @note This method should be used with some caution. The fact that this
* method @em copies the object passed to it means that the caller will be
* left holding a physically different object instance than the one contained
* inside this object. Changes made to the original object instance (such as
* resetting attribute values) will <em>not affect the instance in this
* object</em>. In addition, the caller should make sure to free the
* original object if it is no longer being used, or else a memory leak will
* result. Please see other methods on this class (particularly a
* corresponding method whose name begins with the word <code>create</code>)
* for alternatives that do not lead to these issues.
*
*
*
* @see createReaction()
*/
public int addReaction(Reaction r)
{
int ret = libsbmlPINVOKE.Model_addReaction(swigCPtr, Reaction.getCPtr(r));
return ret;
}
public void test_L3_Reaction_hasRequiredAttributes()
{
Reaction r = new Reaction(3,1);
assertEquals( false, r.hasRequiredAttributes() );
r.setId( "id");
assertEquals( false, r.hasRequiredAttributes() );
r.setFast(false);
assertEquals( false, r.hasRequiredAttributes() );
r.setReversible(false);
assertEquals( true, r.hasRequiredAttributes() );
r = null;
}
public void test_Reaction_constructor()
{
SBase s;
try
{
s = new Reaction(1,1);
s = new Reaction(1,2);
s = new Reaction(2,1);
s = new Reaction(2,2);
s = new Reaction(2,3);
s = new Reaction(2,4);
s = new Reaction(3,1);
s = new Reaction(SN11);
s = new Reaction(SN12);
s = new Reaction(SN21);
s = new Reaction(SN22);
s = new Reaction(SN23);
s = new Reaction(SN24);
s = new Reaction(SN31);
}
catch (SBMLConstructorException e)
{
s = null;
}
assertTrue(s != null);
string msg = "";
try
{
s = new Reaction(9,9);
}
catch (SBMLConstructorException e)
{
msg = e.Message;
}
assertTrue(msg == ErrMsg);
msg = "";
try
{
s = new Reaction(SN99);
}
catch (SBMLConstructorException e)
{
msg = e.Message;
}
assertTrue(msg == ErrMsg);
}
public void test_L3_Reaction_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3,1);
sbmlns.addNamespaces(xmlns);
Reaction r = new Reaction(sbmlns);
assertTrue( r.getTypeCode() == libsbml.SBML_REACTION );
assertTrue( r.getMetaId() == "" );
assertTrue( r.getNotes() == null );
assertTrue( r.getAnnotation() == null );
assertTrue( r.getLevel() == 3 );
assertTrue( r.getVersion() == 1 );
assertTrue( r.getNamespaces() != null );
assertTrue( r.getNamespaces().getLength() == 2 );
assertTrue( r.getId() == "" );
assertTrue( r.getName() == "" );
assertTrue( r.getCompartment() == "" );
assertTrue( r.getFast() == false );
assertTrue( r.getReversible() == true );
assertEquals( false, r.isSetId() );
assertEquals( false, r.isSetName() );
assertEquals( false, r.isSetCompartment() );
assertEquals( false, r.isSetFast() );
assertEquals( false, r.isSetReversible() );
r = null;
}