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

  /**
   * 
   */
  @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 {

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Examples of org.sbml.jsbml.Reaction

   * 
   */
  @Test public void testRegister3_1() {
    
    // Creating a new reaction without id
    Reaction r2 = model.createReaction();


    assertTrue(model.getReactionCount() == 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");
    
    assertTrue(model.findReactionsForLocalParameter("LP1").size() == 2);
    
    assertTrue(doc.findSBase("LP1_2") != null);
  
    r2.unsetKineticLaw();


    assertTrue(doc.findSBase("LP1_2") == null);


    assertTrue(model.findLocalParameters("LP1").size() == 1);

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Examples of org.sbml.jsbml.Reaction

    // Using a List instead of a Set to store the Reaction associated with a local Parameter as
    // if the object HashCode change, it is not possible anymore to remove the element !!!
    
    // http://stackoverflow.com/questions/254441/hashset-remove-and-iterator-remove-not-working


    Reaction r2 = model.createReaction("R2");
    Reaction r3 = model.createReaction("R3");
    
    HashSet<Reaction> reactionSet = new HashSet<Reaction>();
    
    reactionSet.add(r2);
    reactionSet.add(r3);

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Examples of org.sbml.jsbml.Reaction

   * 
   */
  @Test public void testRegister3_3() {
    
    // Creating a new reaction without id
    Reaction r2 = model.createReaction();


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


    KineticLaw k = r2.createKineticLaw();
    
    // Creating a new local parameter without id 
    LocalParameter lp = k.createLocalParameter();
    
    lp.setMetaId("LP1_2");
    lp.setName("LP1_2");
    lp.setId("LP1");
    
    assertTrue(k.getLocalParameterCount() == 1);
    
    assertTrue(doc.findSBase("LP1_2") != null);


    assertTrue(k.getLocalParameter("LP1") != null);
    assertTrue(model.findLocalParameters("LP1").size() == 2);
    assertTrue(model.findReactionsForLocalParameter("LP1").size() == 1); // because r2 has no ID yet !!
    
    lp.setId("LP1_2"); // changing the id of the localParameter !!
    
    assertTrue(k.getLocalParameter("LP1") == null);
    assertTrue(k.getLocalParameter("LP1_2") != null);
    
    assertTrue(model.findLocalParameters("LP1_2").size() == 1);
    
    assertTrue(model.findLocalParameters("LP1").size() == 1);
    
    assertTrue(model.findReactionsForLocalParameter("LP1_2").size() == 0);  // because r2 has no ID yet !!


    r2.setId("R2");
    
    assertTrue(model.findReactionsForLocalParameter("LP1_2").size() == 1);
    assertTrue(model.findReactionsForLocalParameter("LP1").size() == 1);
    
    assertTrue(doc.findSBase("LP1_2") != null);
    assertTrue(model.getReaction("R2") != null);
    assertTrue(model.findNamedSBase("R2") != null);
    
    r2.unsetKineticLaw();


    assertTrue(doc.findSBase("LP1_2") == null);


    assertTrue(model.findLocalParameters("LP1_2").size() == 0);

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Examples of org.sbml.jsbml.Reaction

  /**
   * 
   */
  @Test public void testRegister5_2() {
    
    Reaction r2 = new Reaction();
    r2.setId("R2");
    
    // Setting the same id as an existing Species    
    r2.createReactant("S1");
    
    try {
      model.addReaction(r2);
      
      fail("We should not be able to register twice the same id.");

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Examples of org.sbml.jsbml.Reaction

  /**
   * 
   */
  @Test public void testRegister5_3() {
    
    Reaction r2 = new Reaction();
    r2.setId("R2");
    
    // Setting the same id as an existing Species    
    r2.createReactant("S1");
    
    // Setting the parent by hand !!  // TODO: should we limit the access of SBase.setParentSBML and TreeNode.setParent (should be possible) ??    
    // r2.setParentSBML(new ListOf<Reaction>(2, 4));
    // r2.getParent().setParentSBML(model); // This will make the registration of the reaction non recursive

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Examples of org.sbml.jsbml.Reaction

  /**
   * 
   */
  @Test public void testRegister7() {
    
    Reaction r2 = model.createReaction("R2");
    
    r2.createReactant("SR3");
    
    r2.createKineticLaw().createLocalParameter("LP1");
    
    Reaction clonedR2 = r2.clone();


    assertTrue(clonedR2.getKineticLaw().getLocalParameterCount() == 1);


    try {
      clonedR2.getKineticLaw().createLocalParameter("LP1");
      
      fail("We should not be able to register twice the same id.");
    } catch (IllegalArgumentException e) {
      assertTrue(true);
      // success
    }


    try {
      clonedR2.getKineticLaw().createLocalParameter("LP2");
      assertTrue(true);
      // success      
    } catch (IllegalArgumentException e) {
      fail("We should be able to register a new local parameter on a cloned reaction.");
    }
    
    assertTrue(clonedR2.getKineticLaw().getLocalParameterCount() == 2);
  }

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Examples of org.sbml.jsbml.Reaction

  /**
   * 
   */
  @Test public void testRegister8() {
    
    Reaction r2 = model.createReaction("R2");
    
    KineticLaw kl = r2.createKineticLaw();


    ListOf<LocalParameter> listOfLP = new ListOf<LocalParameter>(2, 4);
    listOfLP.add(new LocalParameter("LP1"));
    listOfLP.add(new LocalParameter("LP2"));
    listOfLP.add(new LocalParameter("LP3"));

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Examples of org.sbml.jsbml.Reaction

   * 
   */
  @Test public void testUnRegister() {
    
    
    Reaction r1 = model.removeReaction("R1");
    
    assertTrue(model.getReaction("R1") == null);    
    assertTrue(model.getReaction(0) == null);
    assertTrue(model.findNamedSBase("SP1") == null);
    assertTrue(model.findNamedSBase("SP2") == null);
    // assertTrue(model.findNamedSBase("LP1") == null);
    assertTrue(doc.findSBase("SP1") == null);
    assertTrue(doc.findSBase("R1") == null);
    assertTrue(doc.findSBase("LP1") == null);
    
    Species s3 = new Species();
    
    // Setting the same id as a removed SpeciesReference
    s3.setId("SP1");


    // Setting the same metaid as a removed LocalParameter
    try {
      s3.setMetaId("LP1");
      assertTrue(true);
    } catch (IdentifierException e) {
      fail("We should be able to put any metaId to a Species not linked to a model.");
    }


    try {
      model.addSpecies(s3);
      assertTrue(true);
    } catch (IllegalArgumentException e) {
      fail("We should be able to register an id or metaid from a removed element.");
      // success
    }
    
    try {
      SpeciesReference reactant = r1.createReactant("S1");
      reactant.setMetaId("S1");
    } catch (IllegalArgumentException e) {
      fail("We should be able to put any id to an element removed from a model.");
    } catch (IdentifierException e) {
      fail("We should be able to put any id to an element removed from a model.");

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Examples of org.sbml.jsbml.Reaction

  /**
   * 
   */
  @Test public void testUnRegister2() {
    
    Reaction r1 = model.removeReaction("R1");


    assertTrue(r1.getReactant("SP1") != null);


    assertTrue(model.findNamedSBase("LP1") == null);
    
    // creating a product with the same id as a species
    r1.createProduct("S1");
  }

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