Examples of Reaction

it.freedomotic.reactions.Reaction
@author enrico
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 $
reaction.Reaction
@author akpinar @questions How do you change k?

Examples of org.sbml.jsbml.Reaction

    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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Examples of org.sbml.jsbml.Reaction

    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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Examples of org.sbml.jsbml.Reaction

    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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Examples of org.sbml.jsbml.Reaction

    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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Examples of org.sbml.jsbml.Reaction

    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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Examples of org.sbml.jsbml.Reaction

    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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Examples of org.sbml.jsbml.Reaction

    assertEquals(M.getParameter("Km3"), null);
  }


  @Test
  public void test_Model_getReaction() {
    Reaction r1 = new Reaction(2, 4);
    Reaction r2 = new Reaction(2, 4);
    r1.setId("reaction_1");
    r2.setId("reaction_2");
    M.addReaction(r1);
    M.addReaction(r2);
    assertTrue(M.getReactionCount() == 2);
    r1 = M.getReaction(0);
    r2 = M.getReaction(1);
    assertTrue(r1.getId().equals("reaction_1"));
    assertTrue(r2.getId().equals("reaction_2"));
  }

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Examples of org.sbml.jsbml.Reaction

    assertTrue(r2.getId().equals("reaction_2"));
  }


  @Test
  public void test_Model_getReactionById() {
    Reaction r1 = new Reaction(2, 4);
    Reaction r2 = new Reaction(2, 4);
    r1.setId("reaction_1");
    r2.setId("reaction_2");
    M.addReaction(r1);
    M.addReaction(r2);
    assertTrue(M.getReactionCount() == 2);
    // assertNotEquals(M.getReaction("reaction_1"), r1);
    // assertNotEquals(M.getReaction("reaction_2"), r2);

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Examples of org.sbml.jsbml.Reaction

    o3 = null;
  }


  @Test
  public void test_Model_removeReaction() {
    Reaction o1, o2, o3;
    o1 = M.createReaction();
    o2 = M.createReaction();
    o3 = M.createReaction();
    o3.setId("test");
    assertTrue(M.removeReaction(0).equals(o1));

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Examples of org.sbml.jsbml.Reaction

    math.addChild(pieces);
    fd.setMath(math);
    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 {
      new SBMLWriter().write(doc, System.out);

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