SpeciesReference clone()
{
SpeciesReference ret
= (SpeciesReference)libsbml.DowncastSBase(libsbmlPINVOKE.SpeciesReference_clone(swigCPtr), true);
return(ret);
}
SpeciesReference(SpeciesReference orig) : this(libsbmlPINVOKE.new_SpeciesReference__SWIG_2(SpeciesReference.getCPtr(orig)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
public void setUp()
{
SR = new SpeciesReference(3,1);
if (SR == null);
{
}
}
SpeciesReference clone()
{
IntPtr cPtr = libsbmlPINVOKE.SpeciesReference_clone(swigCPtr);
SpeciesReference ret = (cPtr == IntPtr.Zero) ? null : new SpeciesReference(cPtr, true);
return(ret);
}
public void setUp()
{
sr = new SpeciesReference(2,4);
if (sr == null);
{
}
}
public void test_SpeciesReference_setDenominator2()
{
SpeciesReference c = new SpeciesReference(2,2);
int i = c.setDenominator(4);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( c.getDenominator() == 4 );
c = null;
}
public void test_Reaction_addReactant()
{
SpeciesReference sr = new SpeciesReference(2,4);
sr.setSpecies( "s");
R.addReactant(sr);
assertTrue( R.getNumReactants() == 1 );
assertTrue( R.getNumProducts() == 0 );
assertTrue( R.getNumModifiers() == 0 );
sr = null;
}
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;
}
internal static HandleRef getCPtrAndDisown(SpeciesReference obj)
{
HandleRef ptr = new HandleRef(null, IntPtr.Zero);
if (obj != null)
{
ptr = obj.swigCPtr;
obj.swigCMemOwn = false;
}
return(ptr);
}
public void test_SpeciesReference_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,1);
sbmlns.addNamespaces(xmlns);
SpeciesReference object1 = new SpeciesReference(sbmlns);
assertTrue( object1.getTypeCode() == libsbml.SBML_SPECIES_REFERENCE );
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_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_SpeciesReference_setId3()
{
SpeciesReference c = new SpeciesReference(2,1);
int i = c.setId( "cell");
assertTrue( i == libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE );
assertEquals( false, c.isSetId() );
c = null;
}
public void test_L3_SpeciesReference_hasRequiredAttributes()
{
SpeciesReference sr = new SpeciesReference(3,1);
assertEquals( false, sr.hasRequiredAttributes() );
sr.setSpecies( "id");
assertEquals( false, sr.hasRequiredAttributes() );
sr.setConstant(false);
assertEquals( true, sr.hasRequiredAttributes() );
sr = 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;
}
/**
* Adds a given SpeciesReference object as a product in this Reaction.
*
* The SpeciesReference instance in @p sr is copied.
*
* @param sr a SpeciesReference object referring to a Species in the
* enclosing Model
*
*
* @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_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 createProduct()
*/
public int addProduct(SpeciesReference sr)
{
int ret = libsbmlPINVOKE.Reaction_addProduct__SWIG_0(swigCPtr, SpeciesReference.getCPtr(sr));
return ret;
}
public void test_StoichiometryMath_parent_add()
{
StoichiometryMath m = new StoichiometryMath(2,4);
SpeciesReference sr = new SpeciesReference(2,4);
sr.setStoichiometryMath(m);
m = null;
assertTrue( sr == sr.getStoichiometryMath().getParentSBMLObject() );
sr = null;
}
public void test_SpeciesReference()
{
SpeciesReference sr = new SpeciesReference(2,4);
assertEquals( false, (sr.hasRequiredAttributes()) );
sr.setSpecies("sr");
assertEquals( true, sr.hasRequiredAttributes() );
sr = null;
}
public void test_Reaction_getReactant()
{
SpeciesReference sr1 = new SpeciesReference(2,4);
SpeciesReference sr2 = new SpeciesReference(2,4);
sr1.setSpecies( "R1");
sr2.setSpecies( "R2");
R.addReactant(sr1);
R.addReactant(sr2);
sr1 = null;
sr2 = null;
assertTrue( R.getNumReactants() == 2 );
assertTrue( R.getNumProducts() == 0 );
assertTrue( R.getNumModifiers() == 0 );
sr1 = R.getReactant(0);
sr2 = R.getReactant(1);
assertTrue(( "R1" == sr1.getSpecies() ));
assertTrue(( "R2" == sr2.getSpecies() ));
}
internal static HandleRef getCPtr(SpeciesReference obj)
{
return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
}
public void test_SpeciesReference()
{
SpeciesReference sr = new SpeciesReference(2,4);
assertEquals( true, sr.hasRequiredElements() );
sr = null;
}
private static int Main(string[] args)
{
var retval = 0;
var sbmlns = new SBMLNamespaces(3, 1, "comp", 1);
// create the document
var document = new SBMLDocument(sbmlns);
//Create our submodel
var compdoc = (CompSBMLDocumentPlugin) (document.getPlugin("comp"));
compdoc.setRequired(true);
var mod1 = compdoc.createModelDefinition();
mod1.setId("enzyme");
mod1.setName("enzyme");
var comp = mod1.createCompartment();
comp.setSpatialDimensions(3);
comp.setConstant(true);
comp.setId("comp");
comp.setSize(1L);
var spec = new Species(3, 1);
spec.setCompartment("comp");
spec.setHasOnlySubstanceUnits(false);
spec.setConstant(false);
spec.setBoundaryCondition(false);
spec.setId("S");
mod1.addSpecies(spec);
spec.setId("E");
mod1.addSpecies(spec);
spec.setId("D");
mod1.addSpecies(spec);
spec.setId("ES");
mod1.addSpecies(spec);
var rxn = new Reaction(3, 1);
rxn.setReversible(true);
rxn.setFast(false);
var rxn2 = new Reaction(rxn);
rxn.setId("J0");
rxn2.setId("J1");
var sr = new SpeciesReference(3, 1);
sr.setConstant(true);
sr.setStoichiometry(1);
sr.setSpecies("S");
rxn.addReactant(sr);
sr.setSpecies("E");
rxn.addReactant(sr);
rxn2.addProduct(sr);
sr.setSpecies("ES");
rxn.addProduct(sr);
rxn2.addReactant(sr);
sr.setSpecies("D");
rxn2.addProduct(sr);
mod1.addReaction(rxn);
mod1.addReaction(rxn2);
// create the Model
var model = document.createModel();
model.setId("aggregate");
// Create a submodel
var mplugin = (CompModelPlugin) (model.getPlugin("comp"));
var submod1 = mplugin.createSubmodel();
submod1.setId("submod1");
submod1.setModelRef("enzyme");
var submod2 = new Submodel();
submod2.setId("submod2");
submod2.setModelRef("enzyme");
mplugin.addSubmodel(submod2);
libsbml.writeSBMLToFile(document, "enzyme_model.xml");
document = libsbml.readSBMLFromFile("enzyme_model.xml");
if (document == null)
{
Console.WriteLine("Error reading back in file.");
retval = -1;
}
else
{
document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false);
document.checkConsistency();
if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 ||
document.getErrorLog().getNumFailsWithSeverity(3) > 0)
{
var stream = new OStringStream();
document.printErrors(stream);
Console.WriteLine("Errors encoutered when round-tripping SBML file: \n" +
stream.str());
retval = -1;
}
libsbml.writeSBMLToFile(document, "enzyme_model_rt.xml");
}
return retval;
}
private static int Main(string[] args)
{
var retval = 0;
var sbmlns = new SBMLNamespaces(3, 1, "comp", 1);
// create the document
var document = new SBMLDocument(sbmlns);
//Define the external model definition
var compdoc = (CompSBMLDocumentPlugin)(document.getPlugin("comp"));
compdoc.setRequired(true);
var extmod = compdoc.createExternalModelDefinition();
extmod.setId("ExtMod1");
extmod.setSource("enzyme_model.xml");
extmod.setModelRef("enzyme");
//Define the 'simple' model
var mod1 = compdoc.createModelDefinition();
mod1.setId("simple");
var comp = mod1.createCompartment();
comp.setSpatialDimensions(3);
comp.setConstant(true);
comp.setId("comp");
comp.setSize(1L);
var spec = new Species(sbmlns);
//We have to construct it this way because we get the comp plugin from it later.
spec.setCompartment("comp");
spec.setHasOnlySubstanceUnits(false);
spec.setConstant(false);
spec.setBoundaryCondition(false);
spec.setId("S");
spec.setInitialConcentration(5);
mod1.addSpecies(spec);
spec.setId("D");
spec.setInitialConcentration(10);
mod1.addSpecies(spec);
var rxn = new Reaction(3, 1);
rxn.setReversible(true);
rxn.setFast(false);
rxn.setId("J0");
var sr = new SpeciesReference(3, 1);
sr.setConstant(true);
sr.setStoichiometry(1);
sr.setSpecies("S");
rxn.addReactant(sr);
sr.setSpecies("D");
rxn.addProduct(sr);
mod1.addReaction(rxn);
var mod1plug = (CompModelPlugin)(mod1.getPlugin("comp"));
var port = new Port();
port.setId("S_port");
port.setIdRef("S");
mod1plug.addPort(port);
var port2 = mod1plug.createPort();
port2.setId("D_port");
port2.setIdRef("D");
port.setId("comp_port");
port.setIdRef("comp");
mod1plug.addPort(port);
port.setId("J0_port");
port.setIdRef("J0");
mod1plug.addPort(port);
// create the Model
var model = document.createModel();
model.setId("complexified");
// Set the submodels
var mplugin = (CompModelPlugin)(model.getPlugin("comp"));
var submod1 = mplugin.createSubmodel();
submod1.setId("A");
submod1.setModelRef("ExtMod1");
var submod2 = mplugin.createSubmodel();
submod2.setId("B");
submod2.setModelRef("simple");
var del = submod2.createDeletion();
del.setPortRef("J0_port");
// Synchronize the compartments
var mcomp = model.createCompartment();
mcomp.setSpatialDimensions(3);
mcomp.setConstant(true);
mcomp.setId("comp");
mcomp.setSize(1L);
var compartplug = (CompSBasePlugin)(mcomp.getPlugin("comp"));
var re = new ReplacedElement();
re.setIdRef("comp");
re.setSubmodelRef("A");
compartplug.addReplacedElement(re);
re.setSubmodelRef("B");
re.unsetIdRef();
re.setPortRef("comp_port");
compartplug.addReplacedElement(re);
//Synchronize the species
spec.setId("S");
spec.setInitialConcentration(5);
var specplug = (CompSBasePlugin)(spec.getPlugin("comp"));
var sre = specplug.createReplacedElement();
sre.setSubmodelRef("A");
sre.setIdRef("S");
var sre2 = specplug.createReplacedElement();
sre2.setSubmodelRef("B");
sre2.setPortRef("S_port");
model.addSpecies(spec);
spec.setId("D");
spec.setInitialConcentration(10);
sre.setIdRef("D");
sre2.setPortRef("D_port");
model.addSpecies(spec);
libsbml.writeSBMLToFile(document, "spec_example3.xml");
document = libsbml.readSBMLFromFile("spec_example3.xml");
if (document == null)
{
Console.WriteLine("Error reading back in file.");
retval = -1;
}
else
{
document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false);
document.checkConsistency();
if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 ||
document.getErrorLog().getNumFailsWithSeverity(3) > 0)
{
var stream = new OStringStream();
document.printErrors(stream);
Console.WriteLine("Errors encoutered when round-tripping SBML file: \n" +
stream.str());
retval = -1;
}
libsbml.writeSBMLToFile(document, "spec_example3_rt.xml");
}
return retval;
}
public void test_internal_consistency_check_99921()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
SpeciesReference sr = new SpeciesReference(2,4);
d.setLevelAndVersion(2,1,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
Species s = m.createSpecies();
s.setId("s");
Reaction r = m.createReaction();
r.setId("r");
s.setCompartment("c");
sr.setSpecies("s");
sr.setName("mmm");
r.addReactant(sr);
errors = d.checkInternalConsistency();
assertTrue( errors == 1 );
assertTrue( d.getError(0).getErrorId() == 21101 );
d = null;
}
public void tearDown()
{
SR = null;
}
public void test_StoichiometryMath_ancestor_create()
{
SpeciesReference sr = new SpeciesReference(2,4);
StoichiometryMath sm = sr.createStoichiometryMath();
assertTrue( sm.getAncestorOfType(libsbml.SBML_SPECIES_REFERENCE) == sr );
assertTrue( sm.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
assertTrue( sm.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null );
StoichiometryMath obj = sr.getStoichiometryMath();
assertTrue( obj.getAncestorOfType(libsbml.SBML_SPECIES_REFERENCE) == sr );
assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
assertTrue( obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null );
}
public void test_L3_SpeciesReference_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3,1);
sbmlns.addNamespaces(xmlns);
SpeciesReference sr = new SpeciesReference(sbmlns);
assertTrue( sr.getTypeCode() == libsbml.SBML_SPECIES_REFERENCE );
assertTrue( sr.getMetaId() == "" );
assertTrue( sr.getNotes() == null );
assertTrue( sr.getAnnotation() == null );
assertTrue( sr.getLevel() == 3 );
assertTrue( sr.getVersion() == 1 );
assertTrue( sr.getNamespaces() != null );
assertTrue( sr.getNamespaces().getLength() == 2 );
assertTrue( sr.getId() == "" );
assertTrue( sr.getName() == "" );
assertTrue( sr.getSpecies() == "" );
assertEquals( true, isnan(sr.getStoichiometry()) );
assertTrue( sr.getConstant() == false );
assertEquals( false, sr.isSetId() );
assertEquals( false, sr.isSetName() );
assertEquals( false, sr.isSetSpecies() );
assertEquals( false, sr.isSetStoichiometry() );
assertEquals( false, sr.isSetConstant() );
sr = null;
}
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_Reaction_getReactantById()
{
SpeciesReference sr1 = new SpeciesReference(2,4);
sr1.setSpecies( "R1");
SpeciesReference sr2 = new SpeciesReference(2,4);
sr2.setSpecies( "R2");
R.addReactant(sr1);
R.addReactant(sr2);
assertTrue( R.getNumReactants() == 2 );
assertTrue( R.getNumProducts() == 0 );
assertTrue( R.getNumModifiers() == 0 );
assertNotEquals(R.getReactant( "R1"),sr1);
assertNotEquals(R.getReactant( "R2"),sr2);
assertEquals(R.getReactant( "R3"),null);
sr1 = null;
sr2 = null;
}
internal static HandleRef getCPtr(SpeciesReference obj)
{
return((obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr);
}
/**
* Copy constructor; creates a copy of this SpeciesReference.
*
* @param orig the SpeciesReference instance to copy.
*
* @throws @if python ValueError @else SBMLConstructorException @endif
* Thrown if the argument @p orig is @c null.
*/
public SpeciesReference(SpeciesReference orig)
: this(libsbmlPINVOKE.new_SpeciesReference__SWIG_2(SpeciesReference.getCPtr(orig)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
/**
* Adds a given SpeciesReference object as a reactant in this Reaction.
*
* The SpeciesReference instance in @p sr is copied.
*
* @param sr a SpeciesReference object referring to a Species in the
* enclosing Model
*
* @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
* @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 createReactant()
*/
public int addReactant(SpeciesReference sr)
{
int ret = libsbmlPINVOKE.Reaction_addReactant(swigCPtr, SpeciesReference.getCPtr(sr));
return ret;
}
internal static HandleRef getCPtrAndDisown(SpeciesReference obj)
{
HandleRef ptr = new HandleRef(null, IntPtr.Zero);
if (obj != null)
{
ptr = obj.swigCPtr;
obj.swigCMemOwn = false;
}
return ptr;
}
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_SpeciesReference_constructor()
{
SBase s;
try
{
s = new SpeciesReference(1,1);
s = new SpeciesReference(1,2);
s = new SpeciesReference(2,1);
s = new SpeciesReference(2,2);
s = new SpeciesReference(2,3);
s = new SpeciesReference(2,4);
s = new SpeciesReference(3,1);
s = new SpeciesReference(SN11);
s = new SpeciesReference(SN12);
s = new SpeciesReference(SN21);
s = new SpeciesReference(SN22);
s = new SpeciesReference(SN23);
s = new SpeciesReference(SN24);
s = new SpeciesReference(SN31);
}
catch (SBMLConstructorException e)
{
s = null;
}
assertTrue(s != null);
string msg = "";
try
{
s = new SpeciesReference(9,9);
}
catch (SBMLConstructorException e)
{
msg = e.Message;
}
assertTrue(msg == ErrMsg);
msg = "";
try
{
s = new SpeciesReference(SN99);
}
catch (SBMLConstructorException e)
{
msg = e.Message;
}
assertTrue(msg == ErrMsg);
}
public void test_StoichiometryMath_ancestor_add()
{
StoichiometryMath m = new StoichiometryMath(2,4);
SpeciesReference sr = new SpeciesReference(2,4);
sr.setStoichiometryMath(m);
m = null;
StoichiometryMath obj = sr.getStoichiometryMath();
assertTrue( obj.getAncestorOfType(libsbml.SBML_SPECIES_REFERENCE) == sr );
assertTrue( obj.getAncestorOfType(libsbml.SBML_MODEL) == null );
assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
sr = null;
}