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 $

    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.getNumReactions() == 2);
    // assertNotEquals(M.getReaction("reaction_1"), r1);
    // assertNotEquals(M.getReaction("reaction_2"), r2);

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    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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  private Reaction R;


  @Before public void setUp() throws Exception
  {
    R = new  Reaction(2,4);
    if (R == null);
    {
    }
  }

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    Compartment c;
    Species s;
    Parameter gp;
    LocalParameter lp;
    AssignmentRule ar;
    Reaction r;
    SpeciesReference sr;
    KineticLaw kl;
    UnitDefinition ud;
    Reaction r1;
    ListOf<Compartment> loc;
    Compartment c1;
    ListOf<Rule> lor;
    AssignmentRule ar1;
    ListOf<Parameter> lop;
    Parameter p1;
    ListOf<Species> los;
    Species s1;
    String filename = new String( DATA_FOLDER + "/libsbml-test-data/" );
    filename += "l2v1-assignment.xml";
    try {
    d = reader.readSBML(filename);
  } catch (IOException e) {
    e.printStackTrace();
    assert(false);
  } catch (XMLStreamException e) {
    e.printStackTrace();
    assert(false);
  }


  System.out.println(" TestReadFromFile 5 : reading done.");
  
  assertTrue( d.getLevel() == 2 );
    assertTrue( d.getVersion() == 1 );
    m = d.getModel();
    assertTrue( m != null );
    assertTrue( m.getNumCompartments() == 1 );
    c = m.getCompartment(0);
    assertTrue( c != null );
    assertTrue( c.getId().equals( "cell") );
/*    ud = c.getDerivedUnitDefinition();
    assertTrue( ud.getNumUnits() == 1 );
    assertTrue( ud.getUnit(0).getKind() == Kind.LITRE );
    */
    loc = m.getListOfCompartments();
    c1 = loc.get(0);
    assertTrue( c1.equals(c) );
    c1 = loc.get("cell");
    assertTrue( c1.equals(c) );
    assertTrue( m.getNumSpecies() == 5 );
    s = m.getSpecies(0);
    assertTrue( s != null );
    assertTrue( s.getId().equals( "X0"  ) );
    assertTrue( s.getCompartment().equals( "cell") );
    assertTrue( s.getInitialConcentration() == 1.0 );
    los = m.getListOfSpecies();
    s1 = los.get(0);
    assertTrue( s1.equals(s) );
    s1 = los.get("X0");
    assertTrue( s1.equals(s) );
    s = m.getSpecies(1);
    assertTrue( s != null );
    assertTrue( s.getId().equals( "X1"  ) );
    assertTrue( s.getCompartment().equals( "cell") );
    assertTrue( s.getInitialConcentration() == 0.0 );
    s = m.getSpecies(2);
    assertTrue( s != null );
    assertTrue( s.getId().equals( "T"   ) );
    assertTrue( s.getCompartment().equals( "cell") );
    assertTrue( s.getInitialConcentration() == 0.0 );
    s = m.getSpecies(3);
    assertTrue( s != null );
    assertTrue( s.getId().equals( "S1"  ) );
    assertTrue( s.getCompartment().equals( "cell") );
    assertTrue( s.getInitialConcentration() == 0.0 );
    s = m.getSpecies(4);
    assertTrue( s != null );
    assertTrue( s.getId().equals( "S2"  ) );
    assertTrue( s.getCompartment().equals( "cell") );
    assertTrue( s.getInitialConcentration() == 0.0 );
    assertTrue( m.getNumParameters() == 1 );
    gp = m.getParameter(0);
    assertTrue( gp != null );
    assertTrue( gp.getId().equals( "Keq") );
    assertTrue( gp.getValue() == 2.5 );
    lop = m.getListOfParameters();
    p1 = lop.get(0);
    assertTrue( p1.equals(gp) );
    p1 = lop.get("Keq");
    assertTrue( p1.equals(gp) );
    /*
    ud = gp.getDerivedUnitDefinition();
    assertTrue( ud.getNumUnits() == 0 );
    assertTrue( m.getNumRules() == 2 );
    */
    ar = (AssignmentRule)  m.getRule(0);
    assertTrue( ar != null );
    assertTrue( ar.getVariable().equals( "S1"           ) );
    assertTrue( ar.getFormula().equals( "T/(1+Keq)") );
    /*
    ud = ar.getDerivedUnitDefinition();
    assertTrue( ud.getNumUnits() == 2 );
    assertTrue( ud.getUnit(0).getKind() == Kind.MOLE );
    assertTrue( ud.getUnit(0).getExponent() == 1 );
    assertTrue( ud.getUnit(1).getKind() == Kind.LITRE );
    assertTrue( ud.getUnit(1).getExponent() == -1 );
    */
    assertTrue( ar.containsUndeclaredUnits() == true );
    lor = m.getListOfRules();
    ar1 = (AssignmentRule) lor.get(0);
    assertTrue( ar1.equals(ar) );
    ar1 = (AssignmentRule) lor.get("S1");
    assertTrue( ar1.equals(ar) );
    ar = (AssignmentRule)  m.getRule(1);
    assertTrue( ar != null );
    assertTrue( ar.getVariable().equals( "S2"      ) );
    assertTrue( ar.getFormula().equals( "Keq*S1") );
    assertTrue( m.getNumReactions() == 2 );
    r = m.getReaction(0);
    assertTrue( r != null );
    assertTrue( r.getId().equals( "in") );
    assertTrue( r.getNumReactants() == 1 );
    assertTrue( r.getNumProducts() == 1 );
    sr = r.getReactant(0);
    assertTrue( sr != null );
    assertTrue( sr.getSpecies().equals( "X0") );
    sr = r.getProduct(0);
    assertTrue( sr != null );
    assertTrue( sr.getSpecies().equals( "T" ) );
    kl = r.getKineticLaw();
    assertTrue( kl != null );
    assertTrue( kl.getFormula().equals( "k1*X0") );
    assertTrue( kl.getLocalParameterCount() == 1 );
    r1 = (Reaction) kl.getParentSBMLObject();
    assertTrue( r1 != null );
    assertTrue( r1.getId().equals( "in") );
    assertTrue( r1.getNumReactants() == 1 );
    assertTrue( r1.getNumProducts() == 1 );
    lp = kl.getLocalParameter(0);
    assertTrue( lp != null );
    assertTrue( lp.getId().equals( "k1") );
    assertTrue( lp.getValue() == 0.1 );
    kl = (KineticLaw) lp.getParentSBMLObject().getParentSBMLObject();

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        spatialSpecies = new SpatialSpeciesPlugin(species);
        species.addExtension(SpatialConstants.namespaceURI, spatialSpecies);
      }
      contextObject = spatialSpecies;
    } else if (contextObject instanceof Reaction) {
      Reaction reaction = (Reaction) contextObject;
      SpatialReactionPlugin spatialReaction = null;
      if (reaction.getExtension(SpatialConstants.namespaceURI) != null) {
        spatialReaction = (SpatialReactionPlugin) reaction.getExtension(SpatialConstants.namespaceURI);
      } else {
        spatialReaction = new SpatialReactionPlugin(reaction);
        reaction.addExtension(SpatialConstants.namespaceURI, spatialReaction);
      }
      contextObject = spatialReaction;
    }


    super.processAttribute(elementName, attributeName, value, uri, prefix,

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  /**
   * 
   */
  @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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  /**
   * 
   */
  @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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  /**
   * 
   */
  @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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  /**
   * 
   */
  @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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   * 
   */
  @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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