Examples of KineticLaw

org.sbml.jsbml.KineticLaw
Represents the kineticLaw XML element of a SBML file. @author Andreas Dräger @author Marine Dumousseau @since 0.8 @version $Rev: 1531 $

Examples of org.sbml.jsbml.KineticLaw

          setRDFAbout(reaction);
          logger.warn("The reaction element '" + reaction.getId() + "' has an invalid rdf:about inside his annotation.");
        }


        if (reaction.isSetKineticLaw()){
          KineticLaw kineticLaw = reaction.getKineticLaw();


          if (!kineticLaw.hasValidAnnotation()){
            setRDFAbout(kineticLaw);
            logger.warn("The kineticLaw element '" + kineticLaw.getMetaId() + "' has an invalid rdf:about inside his annotation.");
          }


          if (kineticLaw.isSetListOfParameters()){
            for (LocalParameter parameter : kineticLaw.getListOfLocalParameters()){
              if (!parameter.hasValidAnnotation()){
                setRDFAbout(parameter);
                logger.warn("The local parameter element '" + parameter.getId() + "' has an invalid rdf:about inside his annotation.");
              }
            }

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Examples of org.sbml.jsbml.KineticLaw

    System.out.println(math.toMathML());
    
    Species species = m.createSpecies("spec");
    Reaction r = m.createReaction("r");
    r.addReactant(new SpeciesReference(species));
    KineticLaw kl = new KineticLaw(level, version);
    math = new ASTNode(fd, kl);
    math.addChild(new ASTNode(species, kl));
    math = ASTNode.times(math, new ASTNode(3.7, 8, kl));
    kl.setMath(math);
    r.setKineticLaw(kl);
    
    System.out.println(math.toMathML());


    try {

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Examples of org.sbml.jsbml.KineticLaw

    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);
    kl.setFormula("k1 * X0");
    LocalParameter k3 = new LocalParameter(2, 4);
    LocalParameter k4 = new LocalParameter(2, 4);
    k3.setId("k1");
    k4.setId("k2");
    k3.setValue(2.72);
    k4.setValue(3.14);
    kl.addParameter(k3);
    kl.addParameter(k4);
    r1.setKineticLaw(kl);
    M.addReaction(r1);
    KineticLaw kl1 = M.getReaction(0).getKineticLaw();
    // assertTrue(!kl1.getParameter("k1").equals(k3)); // TODO : compare Parameter and LocalParameter
    // assertTrue(!kl1.getParameter("k1").equals(k1)); // We are not doinga clone of the object and even it will return true
    // assertTrue(!kl1.getParameter("k2").equals(k4)); // TODO : compare Parameter and LocalParameter
    assertEquals(kl1.getParameter("k3"), null);
  }

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Examples of org.sbml.jsbml.KineticLaw

  }


  @Test
  public void test_Model_createKineticLaw() {
    Reaction r;
    KineticLaw kl;
    M.createReaction();
    M.createReaction();
    kl = M.createKineticLaw();
    assertTrue(kl != null);
    assertTrue(M.getNumReactions() == 2);

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Examples of org.sbml.jsbml.KineticLaw

  }


  @Test
  public void test_Model_createKineticLawParameter() {
    Reaction r;
    KineticLaw kl;
    LocalParameter p;
    M.createReaction();
    M.createReaction();
    M.createKineticLaw();
    p = M.createKineticLawParameter();
    assertTrue(M.getNumReactions() == 2);
    r = M.getReaction(0);
    assertEquals(r.getKineticLaw(), null);
    r = M.getReaction(1);
    assertTrue(r.getKineticLaw() != null);
    kl = r.getKineticLaw();
    assertTrue(kl.getNumParameters() == 1);
    assertEquals(kl.getParameter(0), p);
  }

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Examples of org.sbml.jsbml.KineticLaw

  }


  @Test
  public void test_Model_createKineticLaw_alreadyExists() {
    Reaction r;
    KineticLaw kl;
    r = M.createReaction();
    kl = M.createKineticLaw();
    assertEquals(r.getKineticLaw(), kl);
  }

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Examples of org.sbml.jsbml.KineticLaw

   */
  @Test public void testRegister3() {
    
    Reaction r2 = new Reaction(2,4);
    r2.setId("R2");
    KineticLaw k = r2.createKineticLaw();
    
    k.createLocalParameter("LP1");
    
    // We should not be allowed to register an other local parameter with the same id
    try {
      k.createLocalParameter("LP1");
      // fail("We should not be able to add a local parameter with the same id as an other local parameter in the same kineticLaw.");
    } catch (IdentifierException e) {
      // success
    } catch (IllegalArgumentException e) {
      // success (this the exception returned often, IdentifierException would be better)
    }


    assertTrue(k.getLocalParameterCount() == 1);
    
    try {
      model.addReaction(r2);
    } catch (IllegalArgumentException e) {
      // failure

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Examples of org.sbml.jsbml.KineticLaw

    // Creating a new reaction without id
    Reaction r2 = model.createReaction();


    assertTrue(model.getNumReactions() == 2);


    KineticLaw k = r2.createKineticLaw();
    
    k.createLocalParameter("LP1");
    
    k.getLocalParameter("LP1").setMetaId("LP1_2");
    k.getLocalParameter(0).setName("LP1_2");
    
    assertTrue(k.getLocalParameterCount() == 1);
    
    assertTrue(model.findLocalParameters("LP1").size() == 2);
    assertTrue(model.findReactionsForLocalParameter("LP1").size() == 1);
    
    r2.setId("R2");

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Examples of org.sbml.jsbml.KineticLaw

   * If this {@link ReactionRule} had a previous KineticLaw, it will be destroyed.
   * 
   * @return the new {@link KineticLaw} object
   */
  public KineticLaw createKineticLaw() {
    KineticLaw kl = new KineticLaw(getLevel(), getVersion());
    setKineticLaw(kl);


    return kl;
  }

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Examples of org.sbml.jsbml.KineticLaw

   * @return {@code true} if calling this method changed the properties
   *         of this element.
   */
  public boolean unsetKineticLaw() {
    if (kineticLaw != null) {
      KineticLaw oldKinticLaw = kineticLaw;
      kineticLaw = null;
      oldKinticLaw.fireNodeRemovedEvent();
      return true;
    }
    return false;
  }

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