Examples of org.sbml.jsbml.Reaction

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

    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);
    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

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    assertTrue(M.getParameterCount() == 1);
  }


  @Test
  public void test_Model_addReaction() {
    Reaction r = new Reaction(2, 4);
    r.setId("r");
    M.addReaction(r);
    assertTrue(M.getReactionCount() == 1);
  }

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    assertEquals(M.getInitialAssignment(0), c);
  }


  @Test
  public void test_Model_createKineticLaw() {
    Reaction r;
    KineticLaw kl;
    M.createReaction();
    M.createReaction();
    kl = M.createKineticLaw();
    assertTrue(kl != null);
    assertTrue(M.getReactionCount() == 2);
    r = M.getReaction(0);
    assertEquals(r.getKineticLaw(), null);
    r = M.getReaction(1);
    assertEquals(r.getKineticLaw(), kl);
  }

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    assertEquals(r.getKineticLaw(), kl);
  }


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

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    assertEquals(kl.getLocalParameter(0), p);
  }


  @Test
  public void test_Model_createKineticLawParameter_noKineticLaw() {
    Reaction r;
    r = M.createReaction();
    assertEquals(r.getKineticLaw(), null);
    assertTrue(M.createKineticLawParameter() == null);
  }

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    assertTrue(M.createKineticLawParameter() == null);
  }


  @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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    assertTrue(M.createKineticLaw() == null);
  }


  @Test
  public void test_Model_createModifier() {
    Reaction r;
    ModifierSpeciesReference msr;
    M.createReaction();
    M.createReaction();
    msr = M.createModifier();
    assertTrue(msr != null);
    assertTrue(M.getReactionCount() == 2);
    r = M.getReaction(1);
    assertTrue(r.getModifierCount() == 1);
    assertEquals(r.getModifier(0), msr);
  }

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    assertEquals(M.getParameter(0), p); // TODO: check why this failing
  }


  @Test
  public void test_Model_createProduct() {
    Reaction r;
    SpeciesReference sr;
    M.createReaction();
    M.createReaction();
    sr = M.createProduct();
    assertTrue(sr != null);
    assertTrue(M.getReactionCount() == 2);
    r = M.getReaction(1);
    assertTrue(r.getProductCount() == 1);
    assertEquals(r.getProduct(0), sr);
  }

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    assertEquals(M.getRule(0), rr);
  }


  @Test
  public void test_Model_createReactant() {
    Reaction r;
    SpeciesReference sr;
    M.createReaction();
    M.createReaction();
    sr = M.createReactant();
    assertTrue(sr != null);
    assertTrue(M.getReactionCount() == 2);
    r = M.getReaction(1);
    assertTrue(r.getReactantCount() == 1);
    assertEquals(r.getReactant(0), sr);
  }

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    assertTrue(M.createReactant() == null);
  }


  @Test
  public void test_Model_createReaction() {
    Reaction r = M.createReaction();
    assertTrue(r != null);
    assertTrue(M.getReactionCount() == 1);
    assertEquals(M.getReaction(0), r);
  }

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