Examples of KineticLaw


Examples of org.sbml.jsbml.KineticLaw

  @Test
  public void test_read_l1v1_branch() throws XMLStreamException, InvalidPropertiesFormatException, IOException, ClassNotFoundException {
    SBMLDocument d;
    Model m;
    Compartment c;
    KineticLaw kl;
    LocalParameter p;
    Reaction r;
    Species s;
    SpeciesReference sr;
    UnitDefinition ud;
    String filename = DATA_FOLDER + "/libsbml-test-data/l1v1-branch.xml";
    d = new SBMLReader().readSBML(filename);
    if (d == null)
      ;
    {
    }
    assertTrue(d.getLevel() == 1);
    assertTrue(d.getVersion() == 1);
    m = d.getModel();
    assertTrue(m.getName().equals("Branch"));
    assertTrue(m.getCompartmentCount() == 1);
    c = m.getCompartment(0);
    assertTrue(c.getName().equals("compartmentOne"));
    assertTrue(c.getVolume() == 1);
    ud = c.getDerivedUnitDefinition();
    assertTrue(ud.getUnitCount() == 1);

    // assertTrue(ud.getUnit(0).getKind() == Unit.Kind.LITRE); // getDerivedUnitDefinition not working properly
    assertTrue(m.getSpeciesCount() == 4);
    s = m.getSpecies(0);
    assertTrue(s.getName().equals("S1"));
    assertTrue(s.getCompartment().equals("compartmentOne"));
    assertTrue(s.getInitialAmount() == 0);
    assertTrue(s.getBoundaryCondition() == false);

    //    ud = s.getDerivedUnitDefinition(); // getDerivedUnitDefinition not working properly
//    assertTrue(ud.getUnitCount() == 2);
//    assertTrue(ud.getUnit(0).getKind() == Unit.Kind.MOLE);
//    assertTrue(ud.getUnit(0).getExponent() == 1);
//    assertTrue(ud.getUnit(1).getKind() == Unit.Kind.LITRE);
//    assertTrue(ud.getUnit(1).getExponent() == -1);
   
    s = m.getSpecies(1);
    assertTrue(s.getName().equals("X0"));
    assertTrue(s.getCompartment().equals("compartmentOne"));
    assertTrue(s.getInitialAmount() == 0);
    assertTrue(s.getBoundaryCondition() == true);
    s = m.getSpecies(2);
    assertTrue(s.getName().equals("X1"));
    assertTrue(s.getCompartment().equals("compartmentOne"));
    assertTrue(s.getInitialAmount() == 0);
    assertTrue(s.getBoundaryCondition() == true);
    s = m.getSpecies(3);
    assertTrue(s.getName().equals("X2"));
    assertTrue(s.getCompartment().equals("compartmentOne"));
    assertTrue(s.getInitialAmount() == 0);
    assertTrue(s.getBoundaryCondition() == true);
    assertTrue(m.getReactionCount() == 3);
    r = m.getReaction(0);
    assertTrue(r.getName().equals("reaction_1"));
    assertTrue(r.getReversible() == false);
    assertTrue(r.getFast() == false);
    ud = r.getKineticLaw().getDerivedUnitDefinition();

    //    assertTrue(ud.getUnitCount() == 2);
//    assertTrue(ud.getUnit(0).getKind() == Unit.Kind.MOLE);
//    assertTrue(ud.getUnit(0).getExponent() == 1);
//    assertTrue(ud.getUnit(1).getKind() == Unit.Kind.LITRE);
//    assertTrue(ud.getUnit(1).getExponent() == -1);
   
    assertTrue(r.getKineticLaw().containsUndeclaredUnits() == true);
    r = m.getReaction(1);
    assertTrue(r.getName().equals("reaction_2"));
    assertTrue(r.getReversible() == false);
    assertTrue(r.getFast() == false);
    r = m.getReaction(2);
    assertTrue(r.getName().equals("reaction_3"));
    assertTrue(r.getReversible() == false);
    assertTrue(r.getFast() == false);
    r = m.getReaction(0);
    assertTrue(r.getReactantCount() == 1);
    assertTrue(r.getProductCount() == 1);
    sr = r.getReactant(0);
    assertTrue(sr.getSpecies().equals("X0"));
    assertTrue(sr.getStoichiometry() == 1);
    assertTrue(sr.getDenominator() == 1);
    sr = r.getProduct(0);
    assertTrue(sr.getSpecies().equals("S1"));
    assertTrue(sr.getStoichiometry() == 1);
    assertTrue(sr.getDenominator() == 1);
    kl = r.getKineticLaw();
    assertTrue(kl.getFormula().equals("k1*X0")); // We are not putting the same space in the formula
    assertTrue(kl.getLocalParameterCount() == 1);
    p = kl.getParameter(0);
    assertTrue(p.getName().equals("k1"));
    assertTrue(p.getValue() == 0);
    r = m.getReaction(1);
    assertTrue(r.getReactantCount() == 1);
    assertTrue(r.getProductCount() == 1);
    sr = r.getReactant(0);
    assertTrue(sr.getSpecies().equals("S1"));
    assertTrue(sr.getStoichiometry() == 1);
    assertTrue(sr.getDenominator() == 1);
    sr = r.getProduct(0);
    assertTrue(sr.getSpecies().equals("X1"));
    assertTrue(sr.getStoichiometry() == 1);
    assertTrue(sr.getDenominator() == 1);
    kl = r.getKineticLaw();
    assertTrue(kl.getFormula().equals("k2*S1")); // equals("k2 * S1")
    assertTrue(kl.getLocalParameterCount() == 1);
    p = kl.getParameter(0);
    assertTrue(p.getName().equals("k2"));
    assertTrue(p.getValue() == 0);
    r = m.getReaction(2);
    assertTrue(r.getReactantCount() == 1);
    assertTrue(r.getProductCount() == 1);
    sr = r.getReactant(0);
    assertTrue(sr.getSpecies().equals("S1"));
    assertTrue(sr.getStoichiometry() == 1);
    assertTrue(sr.getDenominator() == 1);
    sr = r.getProduct(0);
    assertTrue(sr.getSpecies().equals("X2"));
    assertTrue(sr.getStoichiometry() == 1);
    assertTrue(sr.getDenominator() == 1);
    kl = r.getKineticLaw();
    assertTrue(kl.getFormula().equals("k3*S1")); // equals("k3 * S1")
    assertTrue(kl.getLocalParameterCount() == 1);
    p = kl.getParameter(0);
    assertTrue(p.getName().equals("k3"));
    assertTrue(p.getValue() == 0);
    d = null;
  }
View Full Code Here

Examples of org.sbml.jsbml.KineticLaw

   
    /*
     * Local Parameters
     */
    logger.debug("==== LocalParameters ====");
    KineticLaw kl = r1.createKineticLaw();
    LocalParameter parameter = kl.createLocalParameter("lp1");
    parameter.setValue(2d);
    kl.getListOfLocalParameters().add(new LocalParameter("lp2"));
    try {
      kl.createLocalParameter("lp1");
      fail();
    } catch (IllegalArgumentException exc) {
      logger.debug(exc.getLocalizedMessage());
      assertTrue(kl.getListOfLocalParameters()
                   .filterList(new NameFilter(parameter.getId())).size() == 1);
    }
    kl.removeLocalParameter(parameter);
    assertTrue(kl.getListOfLocalParameters()
               .filterList(new NameFilter(parameter.getId())).size() == 0);
    assertTrue(kl.getLocalParameter(parameter.getId()) == null);
    // remove ListOfLocalParameters
    ListOf<LocalParameter> listOfLP = kl.getListOfLocalParameters();
    kl.unsetListOfLocalParameters();
    assertTrue(!listOfLP.contains(parameter));
    assertTrue(kl.getLocalParameter("lp2") == null);
    // add ListOfLocalParameters
    listOfLP.add(parameter);
    kl.setListOfLocalParameters(listOfLP);
    assertTrue(kl.getLocalParameter(parameter.getId()) != null);
   
    /*
     * Compartments
     */
    logger.debug("==== Compartments ====");
View Full Code Here

Examples of org.sbml.jsbml.KineticLaw

    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.getCompartmentCount() == 1 );
    c = m.getCompartment(0);
    assertTrue( c != null );
    assertTrue( c.getId().equals( "cell") );
/*    ud = c.getDerivedUnitDefinition();
    assertTrue( ud.getUnitCount() == 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.getSpeciesCount() == 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.getParameterCount() == 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.getUnitCount() == 0 );
    assertTrue( m.getRuleCount() == 2 );
    */
    ar = (AssignmentRulem.getRule(0);
    assertTrue( ar != null );
    assertTrue( ar.getVariable().equals( "S1"           ) );
    assertTrue( ar.getFormula().equals( "T/(1+Keq)") );
    /*
    ud = ar.getDerivedUnitDefinition();
    assertTrue( ud.getUnitCount() == 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 = (AssignmentRulem.getRule(1);
    assertTrue( ar != null );
    assertTrue( ar.getVariable().equals( "S2"      ) );
    assertTrue( ar.getFormula().equals( "Keq*S1") );
    assertTrue( m.getReactionCount() == 2 );
    r = m.getReaction(0);
    assertTrue( r != null );
    assertTrue( r.getId().equals( "in") );
    assertTrue( r.getReactantCount() == 1 );
    assertTrue( r.getProductCount() == 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.getReactantCount() == 1 );
    assertTrue( r1.getProductCount() == 1 );
    lp = kl.getLocalParameter(0);
    assertTrue( lp != null );
    assertTrue( lp.getId().equals( "k1") );
    assertTrue( lp.getValue() == 0.1 );
    kl = (KineticLaw) lp.getParentSBMLObject().getParentSBMLObject();
    assertTrue( kl != null );
    assertTrue( kl.getFormula().equals( "k1*X0") );
    assertTrue( kl.getLocalParameterCount() == 1 );
    r = m.getReaction(1);
    assertTrue( r != null );
    assertTrue( r.getId().equals( "out") );
    assertTrue( r.getReactantCount() == 1 );
    assertTrue( r.getProductCount() == 1 );
    sr = r.getReactant(0);
    assertTrue( sr != null );
    assertTrue( sr.getSpecies().equals( "T" ) );
    sr = r.getProduct(0);
    assertTrue( sr != null );
    assertTrue( sr.getSpecies().equals( "X1") );
    kl = r.getKineticLaw();
    assertTrue( kl != null );
    assertTrue( kl.getFormula().equals( "k2*T") );
    assertTrue( kl.getLocalParameterCount() == 1 );
    lp = kl.getLocalParameter(0);
    assertTrue( lp != null );
    assertTrue( lp.getId().equals( "k2") );
    assertTrue( lp.getValue() == 0.15 );
    d = null;
  }
View Full Code Here

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
View Full Code Here

Examples of org.sbml.jsbml.KineticLaw

    // 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");
View Full Code Here

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);
  }
View Full Code Here

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.getReactionCount() == 2);
View Full Code Here

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.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);
  }
View Full Code Here

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);
  }
View Full Code Here

Examples of org.sbml.jsbml.KineticLaw

        if (listOfElementsToWrite.isEmpty()) {
          listOfElementsToWrite = null;
        }
      } else if (sbase instanceof KineticLaw) {
        KineticLaw kineticLaw = (KineticLaw) sbase;

        if (kineticLaw.isSetListOfParameters()) {
          listOfElementsToWrite = new ArrayList<Object>();
          listOfElementsToWrite.add(kineticLaw.getListOfParameters());
        }
      }
    }
    return listOfElementsToWrite;
  }
View Full Code Here
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