Пример #1
0
 public void test_SBMLConvertStrict_convertNonStrictSBO()
 {
     SBMLDocument d = new  SBMLDocument(2,4);
       Model m = d.createModel();
       Compartment c = m.createCompartment();
       c.setId( "c");
       c.setConstant(false);
       (c).setSBOTerm(64);
       assertTrue( d.setLevelAndVersion(2,3,true) == false );
       assertTrue( d.getLevel() == 2 );
       assertTrue( d.getVersion() == 4 );
       assertTrue( d.setLevelAndVersion(2,2,true) == false );
       assertTrue( d.getLevel() == 2 );
       assertTrue( d.getVersion() == 4 );
       assertTrue( d.setLevelAndVersion(2,1,true) == true );
       assertTrue( d.getLevel() == 2 );
       assertTrue( d.getVersion() == 1 );
       Compartment c1 = d.getModel().getCompartment(0);
       assertTrue( (c1).getSBOTerm() == -1 );
       assertTrue( d.setLevelAndVersion(1,2,true) == true );
       assertTrue( d.getLevel() == 1 );
       assertTrue( d.getVersion() == 2 );
       Compartment c2 = d.getModel().getCompartment(0);
       assertTrue( (c2).getSBOTerm() == -1 );
       d = null;
 }
Пример #2
0
 public void test_SBMLDocument_createWith()
 {
     SBMLDocument d = new  SBMLDocument(1,2);
       assertTrue( d.getTypeCode() == libsbml.SBML_DOCUMENT );
       assertTrue( d.getNotes() == null );
       assertTrue( d.getAnnotation() == null );
       assertTrue( d.getLevel() == 1 );
       assertTrue( d.getVersion() == 2 );
       assertTrue( d.getNumErrors() == 0 );
       d = null;
 }
Пример #3
0
 public void test_SBMLConvertStrict_convertL1ParamRule()
 {
     SBMLDocument d = new  SBMLDocument(1,2);
       Model m = d.createModel();
       Compartment c = m.createCompartment();
       c.setId( "c");
       Parameter p = m.createParameter();
       p.setId( "p");
       Parameter p1 = m.createParameter();
       p1.setId( "p1");
       ASTNode math = libsbml.parseFormula("p");
       Rule ar = m.createAssignmentRule();
       ar.setVariable( "p1");
       ar.setMath(math);
       ar.setUnits( "mole");
       assertTrue( d.setLevelAndVersion(2,1,true) == true );
       assertTrue( d.getLevel() == 2 );
       assertTrue( d.getVersion() == 1 );
       Rule r1 = d.getModel().getRule(0);
       assertTrue( r1.getUnits() == "" );
       d = null;
 }
Пример #4
0
 public void test_SBMLConvert_addModifiersToReaction()
 {
     SBMLDocument d = new  SBMLDocument(1,2);
       Model m = d.createModel();
       Reaction r = m.createReaction();
       KineticLaw kl = r.createKineticLaw();
       kl.setFormula( "k1*S1*S2*S3*S4*S5");
       SimpleSpeciesReference ssr1;
       SimpleSpeciesReference ssr2;
       Species s1 = m.createSpecies();
       s1.setId( "S1" );
       Species s2 = m.createSpecies();
       s2.setId( "S2");
       Species s3 = m.createSpecies();
       s3.setId( "S3");
       Species s4 = m.createSpecies();
       s4.setId( "S4");
       Species s5 = m.createSpecies();
       s5.setId( "S5");
       SpeciesReference sr1 = r.createReactant();
       SpeciesReference sr2 = r.createReactant();
       SpeciesReference sr3 = r.createProduct();
       sr1.setSpecies( "S1");
       sr2.setSpecies( "S2");
       sr3.setSpecies( "S5");
       assertTrue( r.getNumModifiers() == 0 );
       assertTrue( d.setLevelAndVersion(2,1,false) == true );
       assertTrue( d.getLevel() == 2 );
       assertTrue( d.getVersion() == 1 );
       assertTrue( m.getReaction(0).getNumModifiers() == 2 );
       ssr1 = m.getReaction(0).getModifier(0);
       ssr2 = m.getReaction(0).getModifier(1);
       assertTrue((  "S3" == ssr1.getSpecies() ));
       assertTrue((  "S4" == ssr2.getSpecies() ));
       d = null;
 }
Пример #5
0
 public void test_SBMLConvert_convertToL1_SBMLDocument()
 {
     SBMLDocument d = new  SBMLDocument(2,1);
       assertTrue( d.setLevelAndVersion(1,2,false) == true );
       assertTrue( d.getLevel() == 1 );
       assertTrue( d.getVersion() == 2 );
       d = null;
 }
Пример #6
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 public void test_SBMLConvert_convertToL2v4_DuplicateAnnotations_model()
 {
     SBMLDocument d = new  SBMLDocument(2,1);
       Model m = d.createModel();
       string annotation =  "<rdf/>\n<rdf/>";
       int i = (m).setAnnotation(annotation);
       assertTrue( d.getLevel() == 2 );
       assertTrue( d.getVersion() == 1 );
       assertTrue( (m).getAnnotation().getNumChildren() == 2 );
       assertTrue( d.setLevelAndVersion(2,4,true) == true );
       assertTrue( d.getLevel() == 2 );
       assertTrue( d.getVersion() == 4 );
       m = d.getModel();
       assertTrue( (m).getAnnotation().getNumChildren() == 1 );
       d = null;
 }
Пример #7
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 public void test_SBMLDocument_copyConstructor()
 {
     SBMLDocument o1 = new SBMLDocument();
       o1.setLevelAndVersion(2,1,false);
       assertTrue( o1.getLevel() == 2 );
       assertTrue( o1.getVersion() == 1 );
       SBMLDocument o2 = new SBMLDocument(o1);
       assertTrue( o2.getLevel() == 2 );
       assertTrue( o2.getVersion() == 1 );
       o2 = null;
       o1 = null;
 }
Пример #8
0
 public void test_SBMLDocument_clone()
 {
     SBMLDocument o1 = new SBMLDocument();
       o1.setLevelAndVersion(1,1,false);
       Model m = new Model(1,1);
       m.setId("foo");
       o1.setModel(m);
       assertTrue( o1.getLevel() == 1 );
       assertTrue( o1.getVersion() == 1 );
       assertTrue( o1.getModel().getId() ==  "foo" );
       assertTrue( o1.getModel().getLevel() == 1 );
       assertTrue( o1.getModel().getVersion() == 1 );
       assertTrue( o1.getModel().getSBMLDocument() == o1 );
       SBMLDocument o2 = o1.clone();
       assertTrue( o2.getLevel() == 1 );
       assertTrue( o2.getVersion() == 1 );
       assertTrue( o2.getModel().getId() ==  "foo" );
       assertTrue( o2.getModel().getLevel() == 1 );
       assertTrue( o2.getModel().getVersion() == 1 );
       assertTrue( o2.getModel().getSBMLDocument() == o2 );
       o2 = null;
       o1 = null;
 }
Пример #9
0
 public void test_SBMLDocument_assignmentOperator()
 {
     SBMLDocument o1 = new SBMLDocument();
       o1.setLevelAndVersion(2,1,false);
       assertTrue( o1.getLevel() == 2 );
       assertTrue( o1.getVersion() == 1 );
       SBMLDocument o2 = new SBMLDocument();
       o2 = o1;
       assertTrue( o2.getLevel() == 2 );
       assertTrue( o2.getVersion() == 1 );
       o2 = null;
       o1 = null;
 }
Пример #10
0
 public void test_SBMLConvertStrict_convertNonStrictUnits()
 {
     SBMLDocument d = new  SBMLDocument(2,4);
       Model m = d.createModel();
       Compartment c = m.createCompartment();
       c.setId( "c");
       c.setConstant(false);
       Parameter p = m.createParameter();
       p.setId( "p");
       p.setUnits( "mole");
       ASTNode math = libsbml.parseFormula("p");
       Rule ar = m.createAssignmentRule();
       ar.setVariable( "c");
       ar.setMath(math);
       assertTrue( d.setLevelAndVersion(2,1,true) == false );
       assertTrue( d.getLevel() == 2 );
       assertTrue( d.getVersion() == 4 );
       assertTrue( d.setLevelAndVersion(2,2,true) == false );
       assertTrue( d.getLevel() == 2 );
       assertTrue( d.getVersion() == 4 );
       assertTrue( d.setLevelAndVersion(2,3,true) == false );
       assertTrue( d.getLevel() == 2 );
       assertTrue( d.getVersion() == 4 );
       assertTrue( d.setLevelAndVersion(1,2,true) == false );
       assertTrue( d.getLevel() == 2 );
       assertTrue( d.getVersion() == 4 );
       d = null;
 }
Пример #11
0
 public void test_SBMLConvertStrict_convertToL1()
 {
     SBMLDocument d = new  SBMLDocument(2,4);
       Model m = d.createModel();
       (m).setMetaId( "_m");
       Compartment c = m.createCompartment();
       c.setId( "c");
       (c).setSBOTerm(240);
       Species s = m.createSpecies();
       s.setId( "s");
       s.setCompartment( "c");
       s.setHasOnlySubstanceUnits(true);
       assertTrue( d.setLevelAndVersion(1,2,true) == true );
       assertTrue( d.getLevel() == 1 );
       assertTrue( d.getVersion() == 2 );
       Model m1 = d.getModel();
       assertTrue( (m1).getMetaId() == "" );
       Compartment c1 = m1.getCompartment(0);
       assertTrue( (c1).getSBOTerm() == -1 );
       Species s1 = m1.getSpecies(0);
       assertTrue( s1.getHasOnlySubstanceUnits() == false );
       d = null;
 }
Пример #12
0
 public void test_ReadSBML_SBML()
 {
     string s = wrapXML("<sbml level='1' version='1'> </sbml>");
       D = libsbml.readSBMLFromString(s);
       assertTrue( D.getLevel() == 1 );
       assertTrue( D.getVersion() == 1 );
 }