public void setUp()
{
R = new Reaction(2,4);
if (R == null);
{
}
}
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);
}
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;
}
public void test_Model_addReaction()
{
Reaction r = new Reaction(2,4);
r.setId( "r");
M.addReaction(r);
assertTrue( M.getNumReactions() == 1 );
}
public void test_Model_addReaction3()
{
Model m = new Model(2,2);
Reaction r = new Reaction(1,2);
r.setId( "r");
int i = m.addReaction(r);
assertTrue( i == libsbml.LIBSBML_LEVEL_MISMATCH );
assertTrue( m.getNumReactions() == 0 );
r = null;
m = null;
}
/**
* Copy constructor; creates a copy of this Reaction.
*
* @param orig the object to copy.
*/
public Reaction(Reaction orig)
: this(libsbmlPINVOKE.new_Reaction__SWIG_2(Reaction.getCPtr(orig)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
internal static HandleRef getCPtr(Reaction obj)
{
return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
}
public void test_internal_consistency_check_99904_react()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Reaction r = new Reaction(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("cc");
r.setId("r");
r.setMetaId("mmm");
m.addReaction(r);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_Reaction_copyConstructor()
{
Reaction o1 = new Reaction(2,4);
o1.setId("c");
assertTrue( o1.getId() == "c" );
KineticLaw kl = new KineticLaw(2,4);
o1.setKineticLaw(kl);
kl = null;
assertTrue( o1.isSetKineticLaw() == true );
assertNotEquals(o1.getKineticLaw(),null);
Reaction o2 = new Reaction(o1);
assertTrue( o2.getId() == "c" );
assertTrue( o2.isSetKineticLaw() == true );
assertNotEquals(o2.getKineticLaw(),null);
assertTrue( o2.getParentSBMLObject() == o1.getParentSBMLObject() );
o2 = null;
o1 = null;
}
public void test_Reaction()
{
Reaction r = new Reaction(2,4);
assertEquals( true, r.hasRequiredElements() );
r = null;
}
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;
}
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_Model_getSpeciesReferenceById()
{
Reaction r1 = new Reaction(2,4);
r1.setId( "r1");
SpeciesReference sr = r1.createReactant();
sr.setId( "s1");
M.addReaction(r1);
assertTrue( M.getNumReactions() == 1 );
assertNotEquals(M.getSpeciesReference( "s1" ),sr);
}
public void test_Model_getReactionById()
{
Reaction r1 = new Reaction(2,4);
Reaction r2 = new Reaction(2,4);
r1.setId( "reaction_1" );
r2.setId( "reaction_2" );
M.addReaction(r1);
M.addReaction(r2);
assertTrue( M.getNumReactions() == 2 );
assertNotEquals(M.getReaction( "reaction_1" ),r1);
assertNotEquals(M.getReaction( "reaction_2" ),r2);
assertEquals(M.getReaction( "reaction_3" ),null);
}
public void test_Model_getReaction()
{
Reaction r1 = new Reaction(2,4);
Reaction r2 = new Reaction(2,4);
r1.setId( "reaction_1");
r2.setId( "reaction_2");
M.addReaction(r1);
M.addReaction(r2);
assertTrue( M.getNumReactions() == 2 );
r1 = M.getReaction(0);
r2 = M.getReaction(1);
assertTrue(( "reaction_1" == r1.getId() ));
assertTrue(( "reaction_2" == r2.getId() ));
}
public void test_Reaction_addProduct3()
{
Reaction m = new Reaction(2,2);
SpeciesReference p = new SpeciesReference(1,2);
p.setSpecies( "k");
int i = m.addProduct(p);
assertTrue( i == libsbml.LIBSBML_LEVEL_MISMATCH );
assertTrue( m.getNumProducts() == 0 );
p = null;
m = 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_Reaction_addReactant2()
{
Reaction m = new Reaction(2,2);
SpeciesReference p = new SpeciesReference(2,1);
p.setSpecies( "k");
int i = m.addReactant(p);
assertTrue( i == libsbml.LIBSBML_VERSION_MISMATCH );
assertTrue( m.getNumReactants() == 0 );
p = null;
m = null;
}
public void tearDown()
{
R = 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;
}
/**
* 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. 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 createReaction()
*/
public int addReaction(Reaction r)
{
int ret = libsbmlPINVOKE.Model_addReaction(swigCPtr, Reaction.getCPtr(r));
return ret;
}
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_internal_consistency_check_99911_react()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Model m = d.createModel();
Reaction r = new Reaction(2,4);
d.setLevelAndVersion(2,1,false);
r.setId("r");
r.setSBOTerm(2);
m.addReaction(r);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = 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;
}
internal static HandleRef getCPtrAndDisown(Reaction obj)
{
HandleRef ptr = new HandleRef(null, IntPtr.Zero);
if (obj != null)
{
ptr = obj.swigCPtr;
obj.swigCMemOwn = false;
}
return ptr;
}
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_Model_addReaction1()
{
Model m = new Model(2,2);
Reaction r = new Reaction(2,2);
int i = m.addReaction(r);
assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT );
r.setId( "r");
i = m.addReaction(r);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( m.getNumReactions() == 1 );
r = null;
m = null;
}
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_Model_addReaction5()
{
Model m = new Model(2,2);
Reaction r = new Reaction(2,2);
r.setId( "r");
Reaction r1 = new Reaction(2,2);
r1.setId( "r");
int i = m.addReaction(r);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( m.getNumReactions() == 1 );
i = m.addReaction(r1);
assertTrue( i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID );
assertTrue( m.getNumReactions() == 1 );
r = null;
r1 = null;
m = 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(SN11);
s = new Reaction(SN12);
s = new Reaction(SN21);
s = new Reaction(SN22);
s = new Reaction(SN23);
s = new Reaction(SN24);
}
catch (SBMLConstructorException e)
{
s = null;
}
assertTrue(s != null);
string msg = "";
try
{
s = new Reaction(99,99);
}
catch (SBMLConstructorException e)
{
msg = e.Message;
}
assertTrue(msg == ErrMsg);
}