Package org.sbml.jsbml

Examples of org.sbml.jsbml.Parameter

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  private void setSpeciesConversionFactor(Species species, Model model) {

    if (species.isSetConversionFactor()) {
      String conversionFactorID = species.getConversionFactor();

      Parameter parameter = model.getParameter(conversionFactorID);

      if (parameter != null) {
        species.setConversionFactor(parameter);
      } else {
        // TODO : the parameter ID doesn't match a parameter, throw an
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      SBMLException {
    SBMLDocument doc = new SBMLDocument(2, 4);
    doc.addTreeNodeChangeListener(new SimpleTreeNodeChangeListener());
    Model model = doc.createModel("test_model");
   
    Parameter k1 = model.createParameter("k1");
    Parameter k2 = model.createParameter("k2");

    k1.addCVTerm(new CVTerm(CVTerm.Qualifier.BQB_IS, "test"));
   
    k1.setConstant(false);
    k2.setConstant(false);
   
    Event event = model.createEvent("test_event");
   
    Trigger trigger = event.createTrigger();
    trigger.setMath(ASTNode.geq(new ASTNode(ASTNode.Type.NAME_TIME),
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    assertTrue(mls.getUnit(2).getExponent() == -1);
    assertTrue(mls.getUnit(2).getKind().getName().equals("second"));
    assertTrue(mls.getUnit(2).getKind().equals(Kind.SECOND));

    Parameter vm = model.getParameter(0);
   
    assertTrue(vm != null);
    assertTrue(vm.getUnits().equals("mls"));

  }
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    M = null;
  }

  @Test
  public void test_KineticLaw_getParameterById() throws ParseException {
    Parameter k1 = new Parameter(2, 4);
    Parameter k2 = new Parameter(2, 4);
    k1.setId("k1");
    k2.setId("k2");
    k1.setValue(3.14);
    k2.setValue(2.72);
    M.addParameter(k1);
    M.addParameter(k2);
    Reaction r1 = new Reaction(2, 4);
    r1.setId("reaction_1");
    KineticLaw kl = new KineticLaw(2, 4);
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    assertTrue(M.getNumCompartments() == 1);
  }

  @Test
  public void test_Model_addParameter() {
    Parameter p = new Parameter(2, 4);
    p.setId("p");
    M.addParameter(p);
    assertTrue(M.getNumParameters() == 1);
  }
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    assertTrue(M.createModifier() == null);
  }

  @Test
  public void test_Model_createParameter() {
    Parameter p = M.createParameter();
    assertTrue(p != null);
    assertTrue(M.getNumParameters() == 1);
    assertEquals(M.getParameter(0), p); // TODO : check why this failing
  }
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    assertTrue(M.getNumSpeciesWithBoundaryCondition() == 2);
  }

  @Test
  public void test_Model_getParameter() {
    Parameter p1 = new Parameter(2, 4);
    Parameter p2 = new Parameter(2, 4);
    p1.setId("Km1");
    p2.setId("Km2");
    M.addParameter(p1);
    M.addParameter(p2);
    assertTrue(M.getNumParameters() == 2);
    p1 = M.getParameter(0);
    p2 = M.getParameter(1);
    assertTrue(p1.getId().equals("Km1"));
    assertTrue(p2.getId().equals("Km2"));
  }
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    assertTrue(p2.getId().equals("Km2"));
  }

  @Test
  public void test_Model_getParameterById() {
    Parameter p1 = new Parameter(2, 4);
    Parameter p2 = new Parameter(2, 4);
    p1.setId("Km1");
    p2.setId("Km2");
    M.addParameter(p1);
    M.addParameter(p2);
    assertTrue(M.getNumParameters() == 2);
    // assertNotEquals(M.getParameter("Km1"), p1);
    // assertNotEquals(M.getParameter("Km2"), p2);
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    o3 = null;
  }

  @Test
  public void test_Model_removeParameter() {
    Parameter o1, o2, o3;
    o1 = M.createParameter();
    o2 = M.createParameter();
    o3 = M.createParameter();
    o3.setId("test");
    assertTrue(M.removeParameter(0).equals(o1));
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  public ListenerTest() {
    SBMLDocument doc = new SBMLDocument(2, 2);
    doc.addTreeNodeChangeListener(this);
    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());
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Related Classes of org.sbml.jsbml.Parameter

  • org.sbml.jsbml.test.ListenerTest
  • org.sbml.jsbml.test.PriorityTest
  • org.sbml.jsbml.test.RemoveFromModelTest
  • org.sbml.jsbml.test.sbml.TestIncompatibilities
  • org.sbml.jsbml.test.sbml.TestL3Parameter
  • org.sbml.jsbml.test.sbml.TestModel
  • org.sbml.jsbml.test.sbml.TestParameter
  • org.sbml.jsbml.test.sbml.TestReadFromFile5
  • org.sbml.jsbml.test.Test
  • org.sbml.jsbml.test.ToyModelTest
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