public void setUp()
{
C = new Compartment(2,4);
if (C == null);
{
}
}
public void setUp()
{
string filename = "../../sbml/annotation/test/test-data/annotationL3.xml";
d = libsbml.readSBML(filename);
m = d.getModel();
c = m.getCompartment(0);
}
public void test_Compartment()
{
Compartment c = new Compartment(2,4);
assertEquals( false, (c.hasRequiredAttributes()) );
c.setId("c");
assertEquals( true, c.hasRequiredAttributes() );
c = null;
}
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;
}
public void test_Compartment_setCompartmentType2()
{
Compartment c = new Compartment(2,2);
int i = c.setCompartmentType( "1cell");
assertTrue( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE );
assertEquals( false, c.isSetCompartmentType() );
i = c.unsetCompartmentType();
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertEquals( false, c.isSetCompartmentType() );
c = null;
}
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;
}
public void test_Compartment_assignmentOperator()
{
Compartment o1 = new Compartment(2,4);
o1.setId("c");
o1.setOutside("c2");
assertTrue( o1.getId() == "c" );
assertTrue( o1.getOutside() == "c2" );
Compartment o2 = new Compartment(2,4);
o2 = o1;
assertTrue( o2.getId() == "c" );
assertTrue( o2.getOutside() == "c2" );
assertTrue( o2.getParentSBMLObject() == o1.getParentSBMLObject() );
o2 = null;
o1 = null;
}
public void test_Compartment_createWith()
{
Compartment c = new Compartment(2,4);
c.setId( "A");
assertTrue( c.getTypeCode() == libsbml.SBML_COMPARTMENT );
assertTrue( c.getMetaId() == "" );
assertTrue( c.getNotes() == null );
assertTrue( c.getAnnotation() == null );
assertTrue( c.getName() == "" );
assertTrue( c.getSpatialDimensions() == 3 );
assertTrue(( "A" == c.getId() ));
assertTrue( c.getConstant() == true );
assertEquals( true, c.isSetId() );
assertEquals( false, c.isSetName() );
c = null;
}
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;
}
public void test_Compartment_initDefaults()
{
Compartment c = new Compartment(2,4);
c.setId( "A");
c.initDefaults();
assertTrue(( "A" == c.getId() ));
assertTrue( c.getName() == "" );
assertTrue( c.getUnits() == "" );
assertTrue( c.getOutside() == "" );
assertTrue( c.getSpatialDimensions() == 3 );
assertTrue( c.getVolume() == 1.0 );
assertTrue( c.getConstant() == true );
assertEquals( true, c.isSetId() );
assertEquals( false, c.isSetName() );
assertEquals( false, c.isSetSize() );
assertEquals( false, c.isSetVolume() );
assertEquals( false, c.isSetUnits() );
assertEquals( false, c.isSetOutside() );
assertEquals( true, c.isSetSpatialDimensions() );
assertEquals( true, c.isSetConstant() );
c = null;
}
public void test_internal_consistency_check_99903()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Compartment c = new Compartment(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
c.setConstant(true);
c.setId("c");
m.addCompartment(c);
Rule r = m.createAssignmentRule();
r.setVariable("c");
r.setFormula("2*3");
errors = d.checkInternalConsistency();
assertTrue( errors == 3 );
d = null;
}
public void test_SBMLConvert_convertToL1_Species_Amount()
{
SBMLDocument d = new SBMLDocument(2,4);
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_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_Model_getCompartmentById()
{
Compartment c1 = new Compartment(2,4);
Compartment c2 = new Compartment(2,4);
c1.setId( "A" );
c2.setId( "B" );
M.addCompartment(c1);
M.addCompartment(c2);
assertTrue( M.getNumCompartments() == 2 );
assertTrue( M.getCompartment( "A" ) != c1 );
assertTrue( M.getCompartment( "B" ) != c2 );
assertTrue( M.getCompartment( "C" ) == 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() );
}
public void test_Compartment_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,1);
sbmlns.addNamespaces(xmlns);
Compartment c = new Compartment(sbmlns);
assertTrue( c.getTypeCode() == libsbml.SBML_COMPARTMENT );
assertTrue( c.getMetaId() == "" );
assertTrue( c.getNotes() == null );
assertTrue( c.getAnnotation() == null );
assertTrue( c.getLevel() == 2 );
assertTrue( c.getVersion() == 1 );
assertTrue( c.getNamespaces() != null );
assertTrue( c.getNamespaces().getLength() == 2 );
assertTrue( c.getName() == "" );
assertTrue( c.getSpatialDimensions() == 3 );
assertTrue( c.getConstant() == true );
c = null;
}
public void test_Compartment()
{
Compartment c = new Compartment(2,4);
assertEquals( true, c.hasRequiredElements() );
c = null;
}
public void test_Model_addCompartment5()
{
Model m = new Model(2,2);
Compartment c = new Compartment(2,2);
c.setId( "c");
Compartment c1 = new Compartment(2,2);
c1.setId( "c");
int i = m.addCompartment(c);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( m.getNumCompartments() == 1 );
i = m.addCompartment(c1);
assertTrue( i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID );
assertTrue( m.getNumCompartments() == 1 );
c = null;
c1 = null;
m = null;
}
public void tearDown()
{
C = null;
}
public void test_RDFAnnotation_parseCVTerms()
{
XMLNode node = RDFAnnotationParser.parseCVTerms(m.getCompartment(0));
assertTrue( node.getNumChildren() == 1 );
XMLNode rdf = node.getChild(0);
assertTrue(( "RDF" == rdf.getName() ));
assertTrue(( "rdf" == rdf.getPrefix() ));
assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI() ));
assertTrue( rdf.getNumChildren() == 1 );
XMLNode desc = rdf.getChild(0);
assertTrue(( "Description" == desc.getName() ));
assertTrue(( "rdf" == desc.getPrefix() ));
assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI() ));
assertTrue( desc.getNumChildren() == 1 );
XMLNode is1 = desc.getChild(0);
assertTrue(( "is" == is1.getName() ));
assertTrue(( "bqbiol" == is1.getPrefix() ));
assertTrue( is1.getNumChildren() == 1 );
XMLNode Bag = is1.getChild(0);
assertTrue(( "Bag" == Bag.getName() ));
assertTrue(( "rdf" == Bag.getPrefix() ));
assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == Bag.getURI() ));
assertTrue( Bag.getNumChildren() == 4 );
XMLNode li = Bag.getChild(0);
assertTrue(( "li" == li.getName() ));
assertTrue(( "rdf" == li.getPrefix() ));
assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI() ));
assertTrue( li.getNumChildren() == 0 );
XMLNode li1 = Bag.getChild(1);
assertTrue(( "li" == li1.getName() ));
assertTrue(( "rdf" == li1.getPrefix() ));
assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li1.getURI() ));
assertTrue( li1.getNumChildren() == 0 );
XMLNode li2 = Bag.getChild(2);
assertTrue(( "li" == li2.getName() ));
assertTrue(( "rdf" == li2.getPrefix() ));
assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li2.getURI() ));
assertTrue( li2.getNumChildren() == 0 );
XMLNode li3 = Bag.getChild(3);
assertTrue(( "li" == li3.getName() ));
assertTrue(( "rdf" == li3.getPrefix() ));
assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li3.getURI() ));
assertTrue( li3.getNumChildren() == 0 );
node = null;
XMLNode node1 = RDFAnnotationParser.parseCVTerms(null);
assertTrue( node1 == null );
node1 = RDFAnnotationParser.createCVTerms(null);
assertTrue( node1 == null );
node1 = RDFAnnotationParser.parseCVTerms(m.getCompartment(2));
assertTrue( node1 == null );
node1 = RDFAnnotationParser.createCVTerms(m.getCompartment(2));
assertTrue( node1 == null );
node1 = RDFAnnotationParser.parseCVTerms(m);
assertTrue( node1 == null );
node1 = RDFAnnotationParser.createCVTerms(m);
assertTrue( node1 == null );
Compartment c = new Compartment(3,1);
c.setMetaId("_002");
node1 = RDFAnnotationParser.parseCVTerms(c);
assertTrue( node1 == null );
node1 = RDFAnnotationParser.createCVTerms(c);
assertTrue( node1 == null );
CVTerm cv = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv.setBiologicalQualifierType(23);
cv.addResource("http://myres");
c.addCVTerm(cv);
node1 = RDFAnnotationParser.createCVTerms(c);
assertTrue( node1 == null );
c = null;
Model m1 = new Model(3,1);
m1.setMetaId("_002");
cv = new CVTerm(libsbml.MODEL_QUALIFIER);
cv.setModelQualifierType(23);
cv.addResource("http://myres");
m1.addCVTerm(cv);
node1 = RDFAnnotationParser.createCVTerms(m1);
assertTrue( node1 == null );
}
/**
* Copy constructor; creates a copy of a Compartment.
*
* @param orig the Compartment instance to copy.
*
* @throws @if python ValueError @else SBMLConstructorException @endif
* Thrown if the argument @p orig is @c null.
*/
public Compartment(Compartment orig)
: this(libsbmlPINVOKE.new_Compartment__SWIG_2(Compartment.getCPtr(orig)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
internal static HandleRef getCPtrAndDisown(Compartment obj)
{
HandleRef ptr = new HandleRef(null, IntPtr.Zero);
if (obj != null)
{
ptr = obj.swigCPtr;
obj.swigCMemOwn = false;
}
return ptr;
}
internal static HandleRef getCPtr(Compartment obj)
{
return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
}
public void test_Model_addCompartment()
{
Compartment c = new Compartment(2,4);
c.setId( "c");
M.addCompartment(c);
assertTrue( M.getNumCompartments() == 1 );
}
public void test_internal_consistency_check_99904()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Compartment c = new Compartment(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
c.setId("c");
c.setMetaId("mmm");
m.addCompartment(c);
errors = d.checkInternalConsistency();
assertTrue( errors == 1 );
assertTrue( d.getError(0).getErrorId() == 10103 );
d = null;
}
public void test_Compartment_ancestor_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();
Compartment obj = m.getCompartment(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 );
}
/**
* Adds a copy of the given Compartment object to this Model.
*
* @param c the Compartment object to add
*
* @return integer value indicating success/failure of the
* function. 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 createCompartment()
*/
public int addCompartment(Compartment c)
{
int ret = libsbmlPINVOKE.Model_addCompartment(swigCPtr, Compartment.getCPtr(c));
return ret;
}
public void test_SBase_setSBOTerm1()
{
SBase c = new Compartment(1,2);
int i = c.setSBOTerm(2);
assertTrue( i == libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE );
assertEquals( false, c.isSetSBOTerm() );
c = null;
}
public void test_Compartment_constructor()
{
SBase s;
try
{
s = new Compartment(1,1);
s = new Compartment(1,2);
s = new Compartment(2,1);
s = new Compartment(2,2);
s = new Compartment(2,3);
s = new Compartment(2,4);
s = new Compartment(3,1);
s = new Compartment(SN11);
s = new Compartment(SN12);
s = new Compartment(SN21);
s = new Compartment(SN22);
s = new Compartment(SN23);
s = new Compartment(SN24);
s = new Compartment(SN31);
}
catch (SBMLConstructorException e)
{
s = null;
}
assertTrue(s != null);
string msg = "";
try
{
s = new Compartment(9,9);
}
catch (SBMLConstructorException e)
{
msg = e.Message;
}
assertTrue(msg == ErrMsg);
msg = "";
try
{
s = new Compartment(SN99);
}
catch (SBMLConstructorException e)
{
msg = e.Message;
}
assertTrue(msg == ErrMsg);
msg = "";
try
{
s = new Compartment(SN99);
}
catch (SBMLConstructorException e)
{
msg = e.Message;
}
assertTrue(msg == ErrMsg);
}
public void test_Model_getCompartment()
{
Compartment c1 = new Compartment(2,4);
Compartment c2 = new Compartment(2,4);
c1.setId( "A");
c2.setId( "B");
M.addCompartment(c1);
M.addCompartment(c2);
assertTrue( M.getNumCompartments() == 2 );
c1 = M.getCompartment(0);
c2 = M.getCompartment(1);
assertTrue(( "A" == c1.getId() ));
assertTrue(( "B" == c2.getId() ));
}
