public void setUp()
{
S = new Species(3,1);
if (S == null);
{
}
}
public void test_ListOf_clear()
{
ListOf lo = new ListOf();
SBase sp = new Species(2,4);
lo.append(sp);
lo.append(sp);
lo.append(sp);
lo.append(sp);
lo.append(sp);
assertTrue( lo.size() == 5 );
lo.clear(true);
assertTrue( lo.size() == 0 );
lo.append(sp);
lo.append(sp);
lo.append(sp);
lo.append(sp);
lo.appendAndOwn(sp);
assertTrue( lo.size() == 5 );
SBase elem;
elem = lo.get(0);
elem = null;
elem = lo.get(1);
elem = null;
elem = lo.get(2);
elem = null;
elem = lo.get(3);
elem = null;
elem = lo.get(4);
elem = null;
lo.clear(false);
assertTrue( lo.size() == 0 );
lo = null;
}
public void setUp()
{
C = new Species(1,2);
if (C == null);
{
}
}
public void test_Species_setCharge2()
{
Species c = new Species(2,2);
int i = c.setCharge(4);
assertTrue( i == libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE );
assertEquals( false, c.isSetCharge() );
c = null;
}
/**
* Adds the given species as a reactant with the given stoichiometry
*
* @param species the species to be added as reactant
*
* @param stoichiometry an optional parameter specifying the
* stoichiometry of the product (defaulting to 1)
*
* @param id an optional id to be given to the species reference that will
* be created. (defaulting to empty string, i.e. not set)
*
* @param constant an attribute specifying whether the species reference is
* constant or not (defaulting to true)
*
*
* @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_INVALID_OBJECT LIBSBML_INVALID_OBJECT@endlink
* @li @link libsbml#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE@endlink
* @li @link libsbml#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID@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.
*
*
*
* @note the Species object itself is NOT added to the model
*
* @see createProduct()
*/
public int addReactant(Species species, double stoichiometry, string id, bool constant)
{
int ret = libsbmlPINVOKE.Reaction_addReactant__SWIG_1(swigCPtr, Species.getCPtr(species), stoichiometry, id, constant);
return ret;
}
/**
* Adds the given species as a product with the given stoichiometry
*
* @param species the species to be added as product
*
* @param stoichiometry an optional parameter specifying the
* stoichiometry of the product (defaulting to 1)
*
* @param id an optional id to be given to the species reference that will
* be created. (defaulting to empty string, i.e. not set)
*
* @param constant an attribute specifying whether the species reference is
* constant or not (defaulting to true)
*
*
* @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_INVALID_OBJECT LIBSBML_INVALID_OBJECT@endlink
* @li @link libsbml#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE@endlink
* @li @link libsbml#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID@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.
*
*
*
* @note the Species object itself is NOT added to the model
*
* @see createProduct()
*/
public int addProduct(Species species, double stoichiometry, string id)
{
int ret = libsbmlPINVOKE.Reaction_addProduct__SWIG_2(swigCPtr, Species.getCPtr(species), stoichiometry, id);
return ret;
}
public void test_Model_getNumSpeciesWithBoundaryCondition()
{
Species s1 = new Species(2,4);
Species s2 = new Species(2,4);
Species s3 = new Species(2,4);
s1.setId( "s1");
s2.setId( "s2");
s3.setId( "s3");
s1.setCompartment( "c1");
s2.setCompartment( "c2");
s3.setCompartment( "c3");
s1.setBoundaryCondition(true);
s2.setBoundaryCondition(false);
s3.setBoundaryCondition(true);
assertTrue( M.getNumSpecies() == 0 );
assertTrue( M.getNumSpeciesWithBoundaryCondition() == 0 );
M.addSpecies(s1);
assertTrue( M.getNumSpecies() == 1 );
assertTrue( M.getNumSpeciesWithBoundaryCondition() == 1 );
M.addSpecies(s2);
assertTrue( M.getNumSpecies() == 2 );
assertTrue( M.getNumSpeciesWithBoundaryCondition() == 1 );
M.addSpecies(s3);
assertTrue( M.getNumSpecies() == 3 );
assertTrue( M.getNumSpeciesWithBoundaryCondition() == 2 );
}
public void test_L3_Species_hasRequiredAttributes()
{
Species s = new Species(3,1);
assertEquals( false, s.hasRequiredAttributes() );
s.setId( "id");
assertEquals( false, s.hasRequiredAttributes() );
s.setCompartment( "cell");
assertEquals( false, s.hasRequiredAttributes() );
s.setHasOnlySubstanceUnits(false);
assertEquals( false, s.hasRequiredAttributes() );
s.setBoundaryCondition(false);
assertEquals( false, s.hasRequiredAttributes() );
s.setConstant(false);
assertEquals( true, s.hasRequiredAttributes() );
s = null;
}
public void test_Model_addSpecies5()
{
Model m = new Model(2,2);
Species s = new Species(2,2);
s.setId( "s");
s.setCompartment( "c");
Species s1 = new Species(2,2);
s1.setId( "s");
s1.setCompartment( "c");
int i = m.addSpecies(s);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( m.getNumSpecies() == 1 );
i = m.addSpecies(s1);
assertTrue( i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID );
assertTrue( m.getNumSpecies() == 1 );
s = null;
s1 = null;
m = null;
}
public void test_Model_addSpecies2()
{
Model m = new Model(2,2);
Species s = new Species(2,1);
s.setId( "s");
s.setCompartment( "c");
int i = m.addSpecies(s);
assertTrue( i == libsbml.LIBSBML_VERSION_MISMATCH );
assertTrue( m.getNumSpecies() == 0 );
s = null;
m = null;
}
public void test_SBMLConvert_convertToL1_Species_Concentration()
{
SBMLDocument d = new SBMLDocument(2,1);
Model m = d.createModel();
string sid = "C";
Compartment c = new Compartment(2,1);
Species s = new Species(2,1);
c.setId(sid);
c.setSize(1.2);
m.addCompartment(c);
s.setId( "s" );
s.setCompartment(sid);
s.setInitialConcentration(2.34);
m.addSpecies(s);
assertTrue( d.setLevelAndVersion(1,2,true) == true );
Species s1 = m.getSpecies(0);
assertTrue( s1 != null );
assertTrue(( "C" == s1.getCompartment() ));
assertTrue( m.getCompartment( "C").getSize() == 1.2 );
assertTrue( s1.getInitialConcentration() == 2.34 );
assertTrue( s1.isSetInitialConcentration() == true );
d = null;
}
public void test_SBMLConvert_convertToL1_Species_Amount()
{
SBMLDocument d = new SBMLDocument(2,1);
Model m = d.createModel();
string sid = "C";
Compartment c = new Compartment(2,4);
Species s = new Species(2,4);
c.setId(sid);
m.addCompartment(c);
s.setCompartment(sid);
s.setInitialAmount(2.34);
m.addSpecies(s);
assertTrue( d.setLevelAndVersion(1,2,true) == true );
assertTrue( s.getInitialAmount() == 2.34 );
d = null;
}
public void test_Species_copyConstructor()
{
Species o1 = new Species(2,4);
o1.setId("c");
o1.setSpeciesType("c1");
assertTrue( o1.getId() == "c" );
assertEquals(o1.getSpeciesType(), "c1");
Species o2 = new Species(o1);
assertTrue( o2.getId() == "c" );
assertEquals(o2.getSpeciesType(), "c1");
assertTrue( o2.getParentSBMLObject() == o1.getParentSBMLObject() );
o2 = null;
o1 = null;
}
public void test_ListOf_copyConstructor()
{
ListOf o1 = new ListOf();
Species s = new Species(2,1);
s.setId("species_1");
o1.append(s);
s = null;
ListOf o2 = new ListOf(o1);
assertTrue( o2.size() == 1 );
assertTrue( ((Species) o2.get(0)).getId() == "species_1" );
assertTrue( o2.getParentSBMLObject() == o1.getParentSBMLObject() );
o2 = null;
o1 = null;
}
public void test_Species()
{
Species s = new Species(2,4);
assertEquals( true, s.hasRequiredElements() );
s = null;
}
public void test_Model_getSpeciesById()
{
Species s1 = new Species(2,4);
Species s2 = new Species(2,4);
s1.setId( "Glucose" );
s2.setId( "Glucose_6_P" );
s1.setCompartment( "c");
s2.setCompartment( "c");
M.addSpecies(s1);
M.addSpecies(s2);
assertTrue( M.getNumSpecies() == 2 );
assertTrue( M.getSpecies( "Glucose" ) != s1 );
assertTrue( M.getSpecies( "Glucose_6_P") != s2 );
assertTrue( M.getSpecies( "Glucose2" ) == null );
}
public void test_Model_getSpecies()
{
Species s1 = new Species(2,4);
Species s2 = new Species(2,4);
s1.setId( "Glucose" );
s2.setId( "Glucose_6_P" );
s1.setCompartment( "c");
s2.setCompartment( "c");
M.addSpecies(s1);
M.addSpecies(s2);
assertTrue( M.getNumSpecies() == 2 );
s1 = M.getSpecies(0);
s2 = M.getSpecies(1);
assertTrue(( "Glucose" == s1.getId() ));
assertTrue(( "Glucose_6_P" == s2.getId() ));
}
/**
* Adds the given species as a reactant with the given stoichiometry
*
* @param species the species to be added as reactant
*
* @param stoichiometry an optional parameter specifying the
* stoichiometry of the product (defaulting to 1)
*
* @param id an optional id to be given to the species reference that will
* be created. (defaulting to empty string, i.e. not set)
*
* @param constant an attribute specifying whether the species reference is
* constant or not (defaulting to true)
*
*
* @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_INVALID_OBJECT LIBSBML_INVALID_OBJECT@endlink
* @li @link libsbml#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE@endlink
* @li @link libsbml#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID@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.
*
*
*
* @note the Species object itself is NOT added to the model
*
* @see createProduct()
*/
public int addReactant(Species species, double stoichiometry)
{
int ret = libsbmlPINVOKE.Reaction_addReactant__SWIG_3(swigCPtr, Species.getCPtr(species), stoichiometry);
return ret;
}
/**
* Adds the given species as a reactant with the given stoichiometry
*
* @param species the species to be added as reactant
*
* @param stoichiometry an optional parameter specifying the
* stoichiometry of the product (defaulting to 1)
*
* @param id an optional id to be given to the species reference that will
* be created. (defaulting to empty string, i.e. not set)
*
* @param constant an attribute specifying whether the species reference is
* constant or not (defaulting to true)
*
*
* @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_INVALID_OBJECT LIBSBML_INVALID_OBJECT@endlink
* @li @link libsbml#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE@endlink
* @li @link libsbml#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID@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.
*
*
*
* @note the Species object itself is NOT added to the model
*
* @see createProduct()
*/
public int addReactant(Species species)
{
int ret = libsbmlPINVOKE.Reaction_addReactant__SWIG_4(swigCPtr, Species.getCPtr(species));
return ret;
}
/**
* Adds a copy of the given Species object to this Model.
*
* @param s the Species object to add
*
* @return integer value indicating success/failure of the
* function. 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
* @li @link libsbmlcs.libsbml.LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
* @li @link libsbmlcs.libsbml.LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
* @li @link libsbmlcs.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 createSpecies()
*/
public int addSpecies(Species s)
{
int ret = libsbmlPINVOKE.Model_addSpecies(swigCPtr, Species.getCPtr(s));
return ret;
}
public void test_Model_addSpecies3()
{
Model m = new Model(2,2);
Species s = new Species(1,2);
s.setId( "s");
s.setCompartment( "c");
s.setInitialAmount(2);
int i = m.addSpecies(s);
assertTrue( i == libsbml.LIBSBML_LEVEL_MISMATCH );
assertTrue( m.getNumSpecies() == 0 );
s = null;
m = null;
}
public void test_internal_consistency_check_99916_reaction()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Species s = new Species(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
Reaction r = m.createReaction();
r.setId("r");
SpeciesReference sr = r.createReactant();
s.setId("s");
s.setCompartment("c");
s.setConstant(true);
sr.setSpecies("s");
m.addSpecies(s);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_L3_Species_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3,1);
sbmlns.addNamespaces(xmlns);
Species s = new Species(sbmlns);
assertTrue( s.getTypeCode() == libsbml.SBML_SPECIES );
assertTrue( s.getMetaId() == "" );
assertTrue( s.getNotes() == null );
assertTrue( s.getAnnotation() == null );
assertTrue( s.getLevel() == 3 );
assertTrue( s.getVersion() == 1 );
assertTrue( s.getNamespaces() != null );
assertTrue( s.getNamespaces().getLength() == 2 );
assertTrue( s.getId() == "" );
assertTrue( s.getName() == "" );
assertTrue( s.getCompartment() == "" );
assertEquals( true, isnan(s.getInitialAmount()) );
assertEquals( true, isnan(s.getInitialConcentration()) );
assertTrue( s.getSubstanceUnits() == "" );
assertTrue( s.getHasOnlySubstanceUnits() == false );
assertTrue( s.getBoundaryCondition() == false );
assertTrue( s.getConstant() == false );
assertTrue( s.getConversionFactor() == "" );
assertEquals( false, s.isSetId() );
assertEquals( false, s.isSetName() );
assertEquals( false, s.isSetCompartment() );
assertEquals( false, s.isSetInitialAmount() );
assertEquals( false, s.isSetInitialConcentration() );
assertEquals( false, s.isSetSubstanceUnits() );
assertEquals( false, s.isSetHasOnlySubstanceUnits() );
assertEquals( false, s.isSetBoundaryCondition() );
assertEquals( false, s.isSetConstant() );
assertEquals( false, s.isSetConversionFactor() );
s = null;
}
public void tearDown()
{
S = null;
}
public void test_internal_consistency_check_99916_rule()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Species s = new Species(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
s.setId("s");
s.setCompartment("c");
s.setConstant(true);
m.addSpecies(s);
Rule r = m.createAssignmentRule();
r.setVariable("s");
r.setFormula("2");
errors = d.checkInternalConsistency();
assertTrue( errors == 2 );
d = null;
}
internal static HandleRef getCPtrAndDisown(Species obj)
{
HandleRef ptr = new HandleRef(null, IntPtr.Zero);
if (obj != null)
{
ptr = obj.swigCPtr;
obj.swigCMemOwn = false;
}
return ptr;
}
internal static HandleRef getCPtr(Species obj)
{
return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
}
public void test_internal_consistency_check_99919()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Species s = new Species(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
s.setId("s");
s.setCompartment("c");
s.setHasOnlySubstanceUnits(true);
m.addSpecies(s);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
/**
* Copy constructor; creates a copy of this Species object.
*
* @param orig the object to copy.
*/
public Species(Species orig)
: this(libsbmlPINVOKE.new_Species__SWIG_2(Species.getCPtr(orig)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
/**
* Adds the given species as a modifier to this reaction
*
* @param species the species to be added as modifier
*
* @param id an optional id to be given to the species reference that will
* be created. (defaulting to empty string, i.e. not set)
*
*
* @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_INVALID_OBJECT LIBSBML_INVALID_OBJECT@endlink
* @li @link libsbml#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE@endlink
* @li @link libsbml#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID@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.
*
*
*
* @note the Species object itself is NOT added to the model
*
* @see createModifier()
*/
public int addModifier(Species species)
{
int ret = libsbmlPINVOKE.Reaction_addModifier__SWIG_2(swigCPtr, Species.getCPtr(species));
return ret;
}