Package org.sbml.jsbml

Examples of org.sbml.jsbml.Parameter

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      String variableID = rule.getVariable();

      Compartment compartment = model.getCompartment(variableID);
      Species species = null;
      SpeciesReference speciesReference = null;
      Parameter parameter = null;

      if (compartment == null) {
        species = model.getSpecies(variableID);

        if (species == null) {
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      String variableID = eventAssignment.getVariable();

      Compartment compartment = model.getCompartment(variableID);
      Species species = null;
      SpeciesReference speciesReference = null;
      Parameter parameter = null;

      if (compartment == null) {
        species = model.getSpecies(variableID);

        if (species == null) {
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      String variableID = initialAssignment.getVariable();

      Compartment compartment = model.getCompartment(variableID);
      Species species = null;
      SpeciesReference speciesReference = null;
      Parameter parameter = null;

      if (compartment == null) {
        species = model.getSpecies(variableID);

        if (species == null) {
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      String variableID = rule.getVariable();

      Compartment compartment = model.getCompartment(variableID);
      Species species = null;
      SpeciesReference speciesReference = null;
      Parameter parameter = null;

      if (compartment == null) {
        species = model.getSpecies(variableID);

        if (species == null) {
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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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    return Double.isNaN(x);
  }

  @Before public void setUp() throws Exception
  {
    P = new  Parameter(3,1);
  }
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    @Test public void test_L3_Parameter_hasRequiredAttributes()
    {
      assertTrue(false); // TODO : we need to implement the method sbase.hasRequiredAttributes() for all element
     
      Parameter p = new  Parameter(3,1);
//      assertEquals( false, p.hasRequiredAttributes() );
      p.setId( "id");
//      assertEquals( false, p.hasRequiredAttributes() );
      p.setConstant(false);
//      assertEquals( true, p.hasRequiredAttributes() );
      p = null;
    }
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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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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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