Examples of org.sbml.jsbml.Compartment

org.sbml.jsbml.Compartment
Represents the compartment in a model, i.e., a variable element with name, identifier, unit, and value that may change during a simulation. This is the container for reacting species. @author Andreas Dräger @author Nicolas Rodriguez @author Marine Dumousseau @since 0.8 @version $Rev: 1531 $

  @BeforeClass
  public static void setUpBeforeClass() throws Exception {
    doc = new SBMLDocument(3, 1);
    Model m = doc.createModel("test_model");
    
    Compartment c = m.createCompartment("default");
    c.setSpatialDimensions(3d);
    
    Species s1 = m.createSpecies("s1", "species1", c);
    Species s2 = m.createSpecies("s2", "species2", c);
    Species s3 = m.createSpecies("s3", "species3", c);
    Species s4 = m.createSpecies("s4", "species4", c);

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  @SuppressWarnings("deprecation")
  @Test
  public void test_read_l1v1_branch() throws XMLStreamException, InvalidPropertiesFormatException, IOException, ClassNotFoundException {
    SBMLDocument d;
    Model m;
    Compartment c;
    KineticLaw kl;
    LocalParameter p;
    Reaction r;
    Species s;
    SpeciesReference sr;
    UnitDefinition ud;
    String filename = DATA_FOLDER + "/libsbml-test-data/l1v1-branch.xml";
    d = new SBMLReader().readSBML(filename);
    if (d == null)
      ;
    {
    }
    assertTrue(d.getLevel() == 1);
    assertTrue(d.getVersion() == 1);
    m = d.getModel();
    assertTrue(m.getName().equals("Branch"));
    assertTrue(m.getCompartmentCount() == 1);
    c = m.getCompartment(0);
    assertTrue(c.getName().equals("compartmentOne"));
    assertTrue(c.getVolume() == 1);
    ud = c.getDerivedUnitDefinition();
    assertTrue(ud.getUnitCount() == 1);


    // assertTrue(ud.getUnit(0).getKind() == Unit.Kind.LITRE); // getDerivedUnitDefinition not working properly
    assertTrue(m.getSpeciesCount() == 4);
    s = m.getSpecies(0);

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    /*
     * Compartments
     */
    logger.debug("==== Compartments ====");
    Compartment c1 = model.createCompartment("c1");
    c1.setSize(2d);
    Compartment c2 = model.createCompartment("c2");
    try {
      c2.setId(c1.getId());
      fail();
    } catch (IllegalArgumentException exc) {
      System.err.println(exc.getLocalizedMessage());
      assertTrue(!c2.getId().equals(c1.getId()));
    }
    // remove ListOfCompartments
    ListOf<Compartment> listOfC = model.getListOfCompartments();
    model.unsetListOfCompartments();
    // add ListOfCompartments
    model.setListOfCompartments(listOfC);
    Compartment c3 = new Compartment(level, version);
    c3.setId("c3");
    model.addCompartment(c3);
    c3.setId("c4");
    
    /*
     * Species and Species References
     */
    logger.debug("==== Species ====");

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public class TestCompartment {
  private Compartment C;


  @Before public void setUp() throws Exception
  {
    C = new  Compartment(2,4);
    if (C == null);
    {
    }
  }

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    assertEquals( false, C.isSetOutside() );
  }


  @Test public void test_Compartment_createWith()
  {
    Compartment c = new  Compartment(2,4);
    c.setId( "A");
//    assertTrue( c.getTypeCode() == libsbml.SBML_COMPARTMENT );
    assertTrue( c.getMetaId().equals("") == true );
    assertTrue( c.getNotes() == null );
    // assertTrue( c.getAnnotation() == null );
    assertTrue( c.getName().equals("") == true );
    assertTrue( c.getSpatialDimensions() == 3d );
    assertTrue(c.getId().equals( "A"     ));
    assertTrue( c.getConstant() == true );
    assertEquals( true, c.isSetId() );
    assertEquals( false, c.isSetName() );
    c = null;
  }

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  }


  @SuppressWarnings("deprecation")
@Test public void test_Compartment_initDefaults()
  {
    Compartment c = new  Compartment(2,4);
    c.setId( "A");
    c.initDefaults();
    assertTrue(c.getId().equals( "A"));
    assertTrue( c.getName().equals("") == true );
    assertTrue( c.getUnits().equals("") == true );
    assertTrue( c.getOutside().equals("") == true );
    assertTrue( c.getSpatialDimensions() == 3d );
    // assertTrue( c.getVolume() == 1.0 ); // There is no default for the volume/size in L2 !!
    assertTrue( Double.isNaN(c.getVolume()));
    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() );
    c = null;
  }

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@Test public void test_read_l2v1_assignment()
  {
    SBMLReader reader = new SBMLReader();
    SBMLDocument d = null;
    Model m;
    Compartment c;
    Species s;
    Parameter gp;
    LocalParameter lp;
    AssignmentRule ar;
    Reaction r;
    SpeciesReference sr;
    KineticLaw kl;
    UnitDefinition ud;
    Reaction r1;
    ListOf<Compartment> loc;
    Compartment c1;
    ListOf<Rule> lor;
    AssignmentRule ar1;
    ListOf<Parameter> lop;
    Parameter p1;
    ListOf<Species> los;
    Species s1;
    String filename = new String( DATA_FOLDER + "/libsbml-test-data/" );
    filename += "l2v1-assignment.xml";
    try {
    d = reader.readSBML(filename);
  } catch (IOException e) {
    e.printStackTrace();
    assert(false);
  } catch (XMLStreamException e) {
    e.printStackTrace();
    assert(false);
  }


  System.out.println(" TestReadFromFile 5: reading done.");
  
  assertTrue( d.getLevel() == 2 );
    assertTrue( d.getVersion() == 1 );
    m = d.getModel();
    assertTrue( m != null );
    assertTrue( m.getCompartmentCount() == 1 );
    c = m.getCompartment(0);
    assertTrue( c != null );
    assertTrue( c.getId().equals( "cell") );
/*    ud = c.getDerivedUnitDefinition();
    assertTrue( ud.getUnitCount() == 1 );
    assertTrue( ud.getUnit(0).getKind() == Kind.LITRE );
    */
    loc = m.getListOfCompartments();
    c1 = loc.get(0);
    assertTrue( c1.equals(c) );
    c1 = loc.get("cell");
    assertTrue( c1.equals(c) );
    assertTrue( m.getSpeciesCount() == 5 );
    s = m.getSpecies(0);
    assertTrue( s != null );
    assertTrue( s.getId().equals( "X0"  ) );
    assertTrue( s.getCompartment().equals( "cell") );

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   */
  @Before public void setUp() { 
    doc = new SBMLDocument(2, 4);
    model = doc.createModel("model");
    
    Compartment comp = model.createCompartment("cell");
    comp.setMetaId("cell");
    
    Species s1 = model.createSpecies("S1", comp);
    s1.setMetaId("S1");
    
    Species s2 = model.createSpecies("S2", comp);

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    Model model = doc.createModel("test_model");
    Parameter p1 = model.createParameter("p1");
    p1.setId("p2");
    model.removeParameter(p1);


    Compartment c = model.createCompartment("c");
    c.setSize(4.3);
    c.setSBOTerm(SBO.getPhysicalCompartment());


    Species s1 = model.createSpecies("s1", c);
    s1.addCVTerm(new CVTerm(CVTerm.Type.BIOLOGICAL_QUALIFIER,
        Qualifier.BQB_IS, "urn:miriam:kegg.compound:C12345"));
    s1.setValue(23.7);

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    assertEquals(kl1.getParameter("k3"), null);
  }


  @Test
  public void test_Model_addCompartment() {
    Compartment c = new Compartment(2, 4);
    c.setId("c");
    M.addCompartment(c);
    assertTrue(M.getCompartmentCount() == 1);
  }

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