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_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_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 test_Model_addCompartment()
{
Compartment c = new Compartment(2,4);
c.setId( "c");
M.addCompartment(c);
assertTrue( M.getNumCompartments() == 1 );
}
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_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_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_Compartment_setId4()
{
Compartment c = new Compartment(2,2);
int i = c.setId("");
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertEquals( false, c.isSetId() );
c = null;
}
public void test_Compartment_setId2()
{
Compartment c = new Compartment(2,2);
int i = c.setId( "1cell");
assertTrue( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE );
assertEquals( false, c.isSetId() );
c = null;
}
public void test_L3_Compartment_hasRequiredAttributes()
{
Compartment c = new Compartment(3,1);
assertEquals( false, c.hasRequiredAttributes() );
c.setId( "id");
assertEquals( false, c.hasRequiredAttributes() );
c.setConstant(false);
assertEquals( true, c.hasRequiredAttributes() );
c = null;
}
public void test_SyncAnnotation_stringChangesMetaid()
{
Compartment c = new Compartment(3,1);
c.setMetaId("_000005");
c.setId("A");
string addedAnn =
" <annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n" +
" <rdf:Description rdf:about=\"#_000003\">\n" +
" <dc:creator>\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:parseType=\"Resource\">\n" +
" <vCard:N rdf:parseType=\"Resource\">\n" +
" <vCard:Family>Le Novere</vCard:Family>\n" +
" <vCard:Given>Nicolas</vCard:Given>\n" +
" </vCard:N>\n" +
" <vCard:EMAIL>[email protected]</vCard:EMAIL>\n" +
" <vCard:ORG rdf:parseType=\"Resource\">\n" +
" <vCard:Orgname>EMBL-EBI</vCard:Orgname>\n" +
" </vCard:ORG>\n" +
" </rdf:li>\n" +
" </rdf:Bag>\n" +
" </dc:creator>\n" +
" <dcterms:created rdf:parseType=\"Resource\">\n" +
" <dcterms:W3CDTF>2005-02-02T14:56:11Z</dcterms:W3CDTF>\n" +
" </dcterms:created>\n" +
" <dcterms:modified rdf:parseType=\"Resource\">\n" +
" <dcterms:W3CDTF>2006-05-30T10:46:02Z</dcterms:W3CDTF>\n" +
" </dcterms:modified>\n" +
" <bqbiol:is>\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0007274\"/>\n" +
" </rdf:Bag>\n" +
" </bqbiol:is>\n" +
" </rdf:Description>\n" +
" </rdf:RDF>\n" +
" </annotation>";
c.setAnnotation(addedAnn);
string expected =
"<compartment metaid=\"_000005\" id=\"A\">\n" +
" <annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n" +
" <rdf:Description rdf:about=\"#_000005\">\n" +
" <dc:creator>\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:parseType=\"Resource\">\n" +
" <vCard:N rdf:parseType=\"Resource\">\n" +
" <vCard:Family>Le Novere</vCard:Family>\n" +
" <vCard:Given>Nicolas</vCard:Given>\n" +
" </vCard:N>\n" +
" <vCard:EMAIL>[email protected]</vCard:EMAIL>\n" +
" <vCard:ORG rdf:parseType=\"Resource\">\n" +
" <vCard:Orgname>EMBL-EBI</vCard:Orgname>\n" +
" </vCard:ORG>\n" +
" </rdf:li>\n" +
" </rdf:Bag>\n" +
" </dc:creator>\n" +
" <dcterms:created rdf:parseType=\"Resource\">\n" +
" <dcterms:W3CDTF>2005-02-02T14:56:11Z</dcterms:W3CDTF>\n" +
" </dcterms:created>\n" +
" <dcterms:modified rdf:parseType=\"Resource\">\n" +
" <dcterms:W3CDTF>2006-05-30T10:46:02Z</dcterms:W3CDTF>\n" +
" </dcterms:modified>\n" +
" <bqbiol:is>\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0007274\"/>\n" +
" </rdf:Bag>\n" +
" </bqbiol:is>\n" +
" </rdf:Description>\n" +
" </rdf:RDF>\n" +
" </annotation>\n" +
"</compartment>";
assertEquals( true, equals(expected,c.toSBML()) );
}
public void test_SyncAnnotation_stringChangesMetaid2()
{
Compartment c = new Compartment(2, 3);
c.setMetaId("_000005");
c.setId("A");
string addedAnn =
" <annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n" +
" <rdf:Description rdf:about=\"#_000003\">\n" +
" <bqbiol:is>\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0007274\"/>\n" +
" </rdf:Bag>\n" +
" </bqbiol:is>\n" +
" </rdf:Description>\n" +
" </rdf:RDF>\n" +
" </annotation>";
c.setAnnotation(addedAnn);
string expected =
"<compartment metaid=\"_000005\" id=\"A\">\n" +
" <annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n" +
" <rdf:Description rdf:about=\"#_000005\">\n" +
" <bqbiol:is>\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0007274\"/>\n" +
" </rdf:Bag>\n" +
" </bqbiol:is>\n" +
" </rdf:Description>\n" +
" </rdf:RDF>\n" +
" </annotation>\n" +
"</compartment>";
assertEquals(true, equals(expected, c.toSBML()));
}
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 );
}
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_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_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_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() ));
}
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_copyConstructor()
{
Compartment o1 = new Compartment(2,4);
o1.setId("c");
o1.setOutside("c2");
assertTrue( o1.getId() == "c" );
assertTrue( o1.getOutside() == "c2" );
Compartment o2 = new Compartment(o1);
assertTrue( o2.getId() == "c" );
assertTrue( o2.getOutside() == "c2" );
assertTrue( o2.getParentSBMLObject() == o1.getParentSBMLObject() );
o2 = null;
o1 = null;
}
