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 $

   */
  @SuppressWarnings("deprecation")
  public static void main(String args[]) throws ParseException, XMLStreamException, SBMLException {
    SBMLDocument doc = new SBMLDocument(1, 2);
    Model m = doc.createModel();
    Compartment c = m.createCompartment("c1");
    Species s1 = m.createSpecies("s1", c);
    Species s2 = m.createSpecies("s2", c);
    Reaction r = m.createReaction("r1");
    r.createReactant(null, s1);
    r.createProduct(null, s2);

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   * 
   */
  @Test public void checkHashCode() throws ParseException {
    SBMLDocument doc1 = new SBMLDocument(3, 1);
    Model model = doc1.createModel("test_model");
    Compartment c = model.createCompartment("c1");
    Species s = model.createSpecies("s1", c);
    s.addCVTerm(new CVTerm(CVTerm.Qualifier.BQB_IS, "urn:miriam:kegg.compound:C00001"));
    Rule r = model.createAlgebraicRule();
    r.setMath(ASTNode.parseFormula("sin(3) + 1"));

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   */
  public EventTest() throws ParseException, XMLStreamException, SBMLException {
    SBMLDocument doc = new SBMLDocument(3, 1);
    doc.addTreeNodeChangeListener(this);
    Model model = doc.createModel("event_model");
    Compartment c = model.createCompartment("compartment");
    model.createSpecies("s1", c);
    model.createSpecies("s2", c);
    Event ev = model.createEvent();
    Trigger trigger = ev.createTrigger(false, true, ASTNode.parseFormula("3 >= 2"));
    trigger.setMath(ASTNode.geq(new ASTNode(ASTNode.Type.NAME_TIME),

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    assertTrue(c2.getId().equals("B"));
  }


  @Test
  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").equals(c1)); // would be the same in jsbml
    // assertTrue(!M.getCompartment("B").equals(c2));

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    assertEquals(M.getUnitDefinition("rototillers"), null);
  }


  @Test
  public void test_Model_removeCompartment() {
    Compartment o1, o2, o3;
    o1 = M.createCompartment();
    o2 = M.createCompartment();
    o3 = M.createCompartment();
    o3.setId("test");
    assertTrue(M.removeCompartment(0).equals(o1));

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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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          }
        }
      }
      if (model.isSetListOfCompartments()) {
        for (int i = 0; i < model.getNumCompartments(); i++) {
          Compartment compartment = model.getCompartment(i);
          if (compartment.isSetCompartmentType()
              && !compartment.isSetCompartmentTypeInstance()) {
            log4jLogger.warn("No CompartmentType matches the compartmentTypeID of compartment.");
          }
          if (compartment.isSetOutside()
              && !compartment.isSetOutsideInstance()) {
            log4jLogger.warn("No Compartment matches the outsideID of compartment.");
          }
          if (compartment.isSetUnits()
              && !compartment.isSetUnitsInstance()) {
            log4jLogger.warn("No UnitDefinition matches the unitsID of compartment.");
          }
        }
      }
      if (model.isSetListOfEvents()) {

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              return unitDefinition;
            } else if (elementName.equals("compartment")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfCompartments)) {
              Compartment compartment = (Compartment) newContextObject;
              compartment.initDefaults();
              model.addCompartment(compartment);


              return compartment;
            } else if (elementName.equals("species")
                && list.getSBaseListType().equals(

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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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    /*
     * 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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Related Classes of org.sbml.jsbml.Compartment

org.sbml.jsbml.ext.qual.BuildToyModelTest

org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin

org.sbml.jsbml.test.EventTest

org.sbml.jsbml.test.HashCodeTest

org.sbml.jsbml.test.IdRegistrationTest

org.sbml.jsbml.test.ListenerTest

org.sbml.jsbml.test.MathMLTest

org.sbml.jsbml.test.RemoveFromModelTest

org.sbml.jsbml.test.sbml.TestCompartment

org.sbml.jsbml.test.sbml.TestIncompatibilities

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