Examples of org.sbml.jsbml.Model

org.sbml.jsbml.Model

JSBML implementation of SBML's {@link Model} construct.

In an SBML model definition, a single object of class {@link Model} serves asthe overall container for the lists of the various model components. All of the lists are optional, but if a given list container is present within the model, the list must not be empty; that is, it must have length one or more.
@author Andreas Dräger @author Marine Dumousseau @author Nicolas Rodriguez @since 0.8 @version $Rev: 1525 $

   */
  @Test public void readL1V1Units() throws XMLStreamException, InvalidPropertiesFormatException, IOException, ClassNotFoundException {
    String fileName = DATA_FOLDER + "/libsbml-test-data/l1v1-units.xml";
    
    SBMLDocument doc = new SBMLReader().readSBMLFile(fileName);
    Model model = doc.getModel();
    
    assertTrue(doc.getLevel() == 1 && doc.getVersion() == 1);
    
    assertTrue(model.getLevel() == 1 && model.getVersion() == 1);
    
    assertTrue(model.getId().equals(""));
    assertTrue(model.getName().equals(""));
    
    Species s1 = model.getSpecies("s1");
    
    assertTrue(s1 != null);
    
    assertTrue(s1.getName().equals("s1"));
    assertTrue(s1.getId().equals("s1")); // changed, was :  assertTrue(s1.getId().equals(""));
    assertTrue(s1.getNumCVTerms() == 0);
    
    assertTrue(s1.getInitialAmount() == 1);
    
    
    UnitDefinition mls = model.getUnitDefinition(1);
    
    assertTrue(mls != null);
    assertTrue(mls.getNumUnits() == 3);
    assertTrue(mls.getName().equals("mls"));
    assertTrue(mls.getUnit(0).getScale() == -3);
    assertTrue(mls.getUnit(0).getKind().getName().equals("mole"));
    
    assertTrue(mls.getUnit(2).getExponent() == -1);
    assertTrue(mls.getUnit(2).getKind().getName().equals("second"));
    assertTrue(mls.getUnit(2).getKind().equals(Kind.SECOND));


    Parameter vm = model.getParameter(0);
    
    assertTrue(vm != null);
    assertTrue(vm.getUnits().equals("mls"));


  }

View Full Code Here

   */
  public static void main(String[] args) throws XMLStreamException,
      SBMLException {
    SBMLDocument doc = new SBMLDocument(2, 4);
    doc.addTreeNodeChangeListener(new SimpleTreeNodeChangeListener());
    Model model = doc.createModel("test_model");
    
    Parameter k1 = model.createParameter("k1");
    Parameter k2 = model.createParameter("k2");


    k1.addCVTerm(new CVTerm(CVTerm.Qualifier.BQB_IS, "test"));
    
    k1.setConstant(false);
    k2.setConstant(false);
    
    Event event = model.createEvent("test_event");
    
    Trigger trigger = event.createTrigger();
    trigger.setMath(ASTNode.geq(new ASTNode(ASTNode.Type.NAME_TIME),
        new ASTNode(10)));

View Full Code Here

  @Test public void readL1V1Rules() throws XMLStreamException, InvalidPropertiesFormatException, IOException, ClassNotFoundException {


    String fileName = DATA_FOLDER + "/libsbml-test-data/l1v1-rules.xml";
    
    SBMLDocument doc = new SBMLReader().readSBMLFile(fileName);
    Model model = doc.getModel();
    
    assertTrue(doc.getLevel() == 1 && doc.getVersion() == 1);
    
    assertTrue(model.getLevel() == 1 && model.getVersion() == 1);
    
    assertTrue(model.getId().equals(""));
    assertTrue(model.getName().equals(""));
    
    int nbRateRules = model.getListOfRules().filterList(new Filter() {
      
      /*
       * (non-Javadoc)
       * @see org.sbml.jsbml.util.filters.Filter#accepts(java.lang.Object)
       */
      public boolean accepts(Object o) {
        if (o instanceof RateRule) {
          return true;
        }
        
        return false;
      }
    }).size();


    int nbAssignmentRules = model.getListOfRules().filterList(new Filter() {
      
      /*
       * (non-Javadoc)
       * @see org.sbml.jsbml.util.filters.Filter#accepts(java.lang.Object)
       */
      public boolean accepts(Object o) {
        if (o instanceof AssignmentRule) {
          return true;
        }
        
        return false;
      }
    }).size();
    
    assertTrue(model.getListOfRules().size() == 4);
    assertTrue(nbRateRules == 1);
    assertTrue(nbAssignmentRules == 3);
  }

View Full Code Here

  public void processEndDocument(SBMLDocument sbmlDocument) {


    log4jLogger.debug("SBMLCoreParser : processEndDocument");
    
    if (sbmlDocument.isSetModel()) {
      Model model = sbmlDocument.getModel();


      if (model.isSetAreaUnits() && !model.isSetAreaUnitsInstance()) {
        log4jLogger.warn("No unitDefinition matches the areaUnitsID of Model.");
      }
      if (model.isSetConversionFactor()
          && !model.isSetConversionFactorInstance()) {
        log4jLogger.warn("No parameter matches the conversionFactorID of Model.");
      }
      if (model.isSetExtentUnits() && !model.isSetExtentUnitsInstance()) {
        log4jLogger.warn("No unitDefinition matches the extentUnitsID of Model.");
      }
      if (model.isSetLengthUnits() && !model.isSetLengthUnitsInstance()) {
        log4jLogger.warn("No unitDefinition matches the lengthUnitsID of Model.");
      }
      if (model.isSetSubstanceUnits()
          && !model.isSetSubstanceUnitsInstance()) {
        log4jLogger.warn("No unitDefinition matches the substanceUnitsID of Model.");
      }
      if (model.isSetTimeUnits() && !model.isSetTimeUnitsInstance()) {
        log4jLogger.warn("No unitDefinition matches the timeUnitsID of Model.");
      }
      if (model.isSetVolumeUnits() && !model.isSetVolumeUnitsInstance()) {
        log4jLogger.warn("No unitDefinition matches the volumeUnitsID of Model.");
      }


      if (model.isSetListOfRules()) {
        
        if (model.getLevel() == 1) {


          log4jLogger.debug("Transformed SBMLLevel1Rule : processEndDocument : model is level 1");


          int i = 0;
          for (Rule rule : model.getListOfRules().clone()) {
            if (rule instanceof SBMLLevel1Rule) {
              Rule realRule;
              
              if (((SBMLLevel1Rule) rule).isScalar()) {
                realRule = ((SBMLLevel1Rule) rule).cloneAsAssignmentRule();
                log4jLogger.debug("Transformed SBMLLevel1Rule : " + ((SBMLLevel1Rule) rule).getVariable() + " into AssignmentRule.");
              } else {
                realRule = ((SBMLLevel1Rule) rule).cloneAsRateRule();
                log4jLogger.debug("Transformed SBMLLevel1Rule : " + ((SBMLLevel1Rule) rule).getVariable() + " into RateRule.");
              }
              
              log4jLogger.debug("Transformed SBMLLevel1Rule : realRule = " + realRule);


              model.getListOfRules().remove(i);
              model.getListOfRules().add(i, realRule);
            }
            i++;
          }
        }
        
        for (int i = 0; i < model.getNumRules(); i++) {
          Rule rule = model.getRule(i);
          if (rule instanceof AssignmentRule) {
            AssignmentRule assignmentRule = (AssignmentRule) rule;
            if (assignmentRule.isSetVariable()
                && !assignmentRule.isSetVariableInstance()) {
              log4jLogger.warn("No Symbol matches the variableID of AssignmentRule.");
            }
            if (assignmentRule.isSetUnits()
                && !assignmentRule.isSetUnitsInstance()
                && assignmentRule.isParameter()) {
              log4jLogger.warn("No UnitDefinition matches the unitsID of AssignmentRule.");
            }
          } else if (rule instanceof RateRule) {
            RateRule rateRule = (RateRule) rule;
            if (rateRule.isSetVariable()
                && !rateRule.isSetVariableInstance()) {
              log4jLogger.warn("No Symbol matches the variableID of RateRule.");
            }
          }
        }
      }
      if (model.isSetListOfCompartments()) {
        for (int i = 0; i < model.getNumCompartments(); i++) {
          Compartment compartment = model.getCompartment(i);
          if (compartment.isSetCompartmentType()
              && !compartment.isSetCompartmentTypeInstance()) {
            log4jLogger.warn("No CompartmentType matches the compartmentTypeID of compartment.");
          }
          if (compartment.isSetOutside()
              && !compartment.isSetOutsideInstance()) {
            log4jLogger.warn("No Compartment matches the outsideID of compartment.");
          }
          if (compartment.isSetUnits()
              && !compartment.isSetUnitsInstance()) {
            log4jLogger.warn("No UnitDefinition matches the unitsID of compartment.");
          }
        }
      }
      if (model.isSetListOfEvents()) {
        for (int i = 0; i < model.getNumEvents(); i++) {
          Event event = model.getEvent(i);


          if (event.isSetTimeUnits()
              && !event.isSetTimeUnitsInstance()) {
            log4jLogger.warn("No UnitDefinition matches the timeUnitsID of event.");
          }


          if (event.isSetListOfEventAssignments()) {


            for (int j = 0; j < event.getNumEventAssignments(); j++) {
              EventAssignment eventAssignment = event
                  .getEventAssignment(j);


              if (eventAssignment.isSetVariable()
                  && !eventAssignment.isSetVariableInstance()) {
                log4jLogger.warn("No Symbol matches the variableID of eventAssignment.");
              }
            }
          }
        }
      }
      if (model.isSetListOfInitialAssignments()) {
        for (int i = 0; i < model.getNumInitialAssignments(); i++) {
          InitialAssignment initialAssignment = model
              .getInitialAssignment(i);


          if (initialAssignment.isSetVariable()
              && !initialAssignment.isSetVariableInstance()) {
            log4jLogger.warn("No Symbol matches the symbolID of initialAssignment.");
          }
        }
      }
      if (model.isSetListOfReactions()) {
        for (int i = 0; i < model.getNumReactions(); i++) {
          Reaction reaction = model.getReaction(i);
          if (reaction.isSetCompartment()
              && !reaction.isSetCompartmentInstance()) {
            log4jLogger.warn("No Compartment matches the compartmentID of reaction.");
          }


          if (reaction.isSetListOfReactants()) {
            for (int j = 0; j < reaction.getNumReactants(); j++) {
              SpeciesReference speciesReference = reaction
                  .getReactant(j);


              if (speciesReference.isSetSpecies()
                  && !speciesReference.isSetSpeciesInstance()) {
                log4jLogger.warn(String.format("No Species matches the speciesID '%s' of %s.", 
                    speciesReference.getId(), speciesReference.getElementName()));
              }
            }
          }
          if (reaction.isSetListOfProducts()) {
            for (int j = 0; j < reaction.getNumProducts(); j++) {
              SpeciesReference speciesReference = reaction
                  .getProduct(j);


              if (speciesReference.isSetSpecies()
                  && !speciesReference.isSetSpeciesInstance()) {
                log4jLogger.warn(String.format("No Species matches the speciesID '%s' of %s.", 
                    speciesReference.getId(), speciesReference.getElementName()));
              }
            }
          }
          if (reaction.isSetListOfModifiers()) {
            for (int j = 0; j < reaction.getNumModifiers(); j++) {
              ModifierSpeciesReference modifierSpeciesReference = reaction
                  .getModifier(j);


              if (modifierSpeciesReference.isSetSpecies()
                  && !modifierSpeciesReference
                      .isSetSpeciesInstance()) {
                log4jLogger.warn(String.format("No Species matches the speciesID '%s' of %s.", 
                    modifierSpeciesReference.getId(), modifierSpeciesReference.getElementName()));
              }
            }
          }
          if (reaction.isSetKineticLaw()) {
            KineticLaw kineticLaw = reaction.getKineticLaw();
            if (kineticLaw.isSetTimeUnits()
                && !kineticLaw.isSetTimeUnitsInstance()) {
              log4jLogger.warn("No UnitDefinition matches the timeUnitsID of kineticLaw.");
            }
            if (kineticLaw.isSetSubstanceUnits()
                && !kineticLaw.isSetSubstanceUnitsInstance()) {
              log4jLogger.warn("No UnitDefinition matches the substanceUnitsID of kineticLaw.");
            }
            if (kineticLaw.isSetListOfLocalParameters()) {
              for (int j = 0; j < kineticLaw.getNumLocalParameters(); j++) {
                LocalParameter parameter = kineticLaw
                    .getLocalParameter(j);
                if (parameter.isSetUnits()
                    && !parameter.isSetUnitsInstance()) {
                  log4jLogger.warn(String.format(
                    "No UnitDefinition matches the unitsID '%s'of the parameter %s.",
                    parameter.getUnits(), parameter.getId()));
                }
              }
            }
          }
        }
      }
      if (model.isSetListOfSpecies()) {
        for (int i = 0; i < model.getNumSpecies(); i++) {
          Species species = model.getSpecies(i);


          if (species.isSetSubstanceUnits()
              && !species.isSetSubstanceUnitsInstance()) {
            log4jLogger.warn("No UnitDefinition matches the subtsanceUnitsID of species.");
          }
          if (species.isSetSpeciesType()
              && !species.isSetSpeciesTypeInstance()) {
            log4jLogger.warn("No SpeciesType matches the speciesTypeID of species.");
          }
          if (species.isSetConversionFactor()
              && !species.isSetConversionFactorInstance()) {
            log4jLogger.warn("No Parameter matches the conversionFactorID of species.");
          }
          if (species.isSetCompartment()
              && !species.isSetCompartmentInstance()) {
            log4jLogger.warn("No Compartment matches the compartmentID of species.");
          }
          if (species.isSetSpatialSizeUnits()
              && !species.isSetSpatialSizeUnitsInstance()) {
            log4jLogger.warn("No UnitDefinition matches the spatialSizeUnitsID of species.");
          }
        }
      }
      if (model.isSetListOfParameters()) {
        for (int i = 0; i < model.getNumParameters(); i++) {
          Parameter parameter = model.getParameter(i);
          if (parameter.isSetUnits()
              && !parameter.isSetUnitsInstance()) {
            log4jLogger.warn("No UnitDefinition matches the unitsID of parameter.");
          }
        }

View Full Code Here


  public static void main(String args[]) {
    SBMLDocument doc = new SBMLDocument(2, 4);
    doc.setNotes("<body>Senseless test commentar</body>");


    Model m = doc.createModel("model");


    CVTerm term = new CVTerm();
    term.setQualifierType(Type.MODEL_QUALIFIER);
    term.setModelQualifierType(Qualifier.BQM_IS);
    term.addResource("urn:miriam:kegg.pathway:hsa00010");
    m.addCVTerm(term);


    History history = new History();
    Creator creator = new Creator();
    creator.setFamilyName("Dr\u00e4ger");
    creator.setGivenName("Andreas");
    creator.setEmail("andreas.draeger@uni-tuebingen.de");
    creator.setOrganization("Universit\u00e4t T\u00fcbingen");
    history.addCreator(creator);
    history.setCreatedDate(Calendar.getInstance().getTime());
    history.addModifiedDate(Calendar.getInstance().getTime());
    m.setHistory(history);


    m
        .setNotes("<body>A senseless test model with a senseless notes element.</body>");


    m.getUnitDefinition("substance").getUnit(0).setScale(-3);


    try {
      new SBMLWriter().write(doc, new BufferedOutputStream(System.out),
          "SBMLWriterTest", "");
    } catch (XMLStreamException e) {

View Full Code Here

      System.out.printf("[IN]:\t%s\n", formula);
      System.out.printf("[OUT]:\t%s\n", testNode.toFormula());
      System.out.printf("[LTX]:\t%s\n", testNode.toLaTeX());


//      AssignmentRule as = new AssignmentRule(2, 4);
      Model m = new Model(2, 4);
      FunctionDefinition fd = new FunctionDefinition("f", 2, 4);
      m.addFunctionDefinition(fd);
      //as.setMath(ASTNode.parseFormula("f(a, b, c, d)"));
      //m.addRule(as);
      //System.out.println(as.getMath().toString());


    }

View Full Code Here

   * @throws SBMLException
   */
  @SuppressWarnings("deprecation")
  public static void main(String args[]) throws ParseException, XMLStreamException, SBMLException {
    SBMLDocument doc = new SBMLDocument(1, 2);
    Model m = doc.createModel();
    Compartment c = m.createCompartment("c1");
    Species s1 = m.createSpecies("s1", c);
    Species s2 = m.createSpecies("s2", c);
    Reaction r = m.createReaction("r1");
    r.createReactant(null, s1);
    r.createProduct(null, s2);
    KineticLaw kl = r.createKineticLaw();
    kl.setFormula("s1 * 3");
    SBMLWriter.write(doc, System.out, ' ', (short) 2);

View Full Code Here

public class SpeciesAnnotationTest extends SimpleTreeNodeChangeListener {


  public SpeciesAnnotationTest() throws XMLStreamException, SBMLException {
    SBMLDocument doc = new SBMLDocument(2, 4);
    doc.addTreeNodeChangeListener(this);
    Model model = doc.createModel("model_test");
    Species s1 = model.createSpecies("s1", model.createCompartment("c1"));
    s1.setMetaId("meta_" + s1.getId());
    // Not necessary anymore.
    // s1.getAnnotation().addRDFAnnotationNamespace("bqbiol", "",
    // "http://biomodels.net/biology-qualifiers/");
    s1.addCVTerm(new CVTerm(CVTerm.Type.BIOLOGICAL_QUALIFIER,

View Full Code Here

   */
  @SuppressWarnings("deprecation")
  @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.getNumCompartments() == 1);
    c = m.getCompartment(0);
    assertTrue(c.getName().equals("compartmentOne"));
    assertTrue(c.getVolume() == 1);
    ud = c.getDerivedUnitDefinition();
    assertTrue(ud.getNumUnits() == 1);


    // assertTrue(ud.getUnit(0).getKind() == Unit.Kind.LITRE); // getDerivedUnitDefinition not working properly
    assertTrue(m.getNumSpecies() == 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.getNumUnits() == 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.getNumReactions() == 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.getNumUnits() == 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.getNumReactants() == 1);
    assertTrue(r.getNumProducts() == 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.getNumParameters() == 1);
    p = kl.getParameter(0);
    assertTrue(p.getName().equals("k1"));
    assertTrue(p.getValue() == 0);
    r = m.getReaction(1);
    assertTrue(r.getNumReactants() == 1);
    assertTrue(r.getNumProducts() == 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.getNumParameters() == 1);
    p = kl.getParameter(0);
    assertTrue(p.getName().equals("k2"));
    assertTrue(p.getValue() == 0);
    r = m.getReaction(2);
    assertTrue(r.getNumReactants() == 1);
    assertTrue(r.getNumProducts() == 1);
    sr = r.getReactant(0);
    assertTrue(sr.getSpecies().equals("S1"));
    assertTrue(sr.getStoichiometry() == 1);

View Full Code Here


          return annotation;
        } else if (contextObject instanceof SBMLDocument) {
          SBMLDocument sbmlDocument = (SBMLDocument) contextObject;
          if (elementName.equals("model")) {
            Model model = (Model) newContextObject;
            model.setLevel(sbmlDocument.getLevel());
            model.setVersion(sbmlDocument.getVersion());
            model.initDefaults();
            model.setParentSBML(sbmlDocument);
            sbmlDocument.setModel(model);


            return model;
          }
        } else if (contextObject instanceof Model) {


          Model model = (Model) contextObject;
          if (newContextObject instanceof ListOf<?>) {
            if (elementName.equals("listOfFunctionDefinitions")
                && model.getLevel() > 1) {
              ListOf<FunctionDefinition> listOfFunctionDefinitions = (ListOf<FunctionDefinition>) newContextObject;
              model.setListOfFunctionDefinitions(listOfFunctionDefinitions);


              return listOfFunctionDefinitions;
            } else if (elementName.equals("listOfUnitDefinitions")) {
              ListOf<UnitDefinition> listOfUnitDefinitions = (ListOf<UnitDefinition>) newContextObject;
              model.setListOfUnitDefinitions(listOfUnitDefinitions);


              return listOfUnitDefinitions;
            } else if (elementName.equals("listOfCompartments")) {
              ListOf<Compartment> listOfCompartments = (ListOf<Compartment>) newContextObject;
              model.setListOfCompartments(listOfCompartments);


              return listOfCompartments;
            } else if (elementName.equals("listOfSpecies")) {
              ListOf<Species> listOfSpecies = (ListOf<Species>) newContextObject;
              model.setListOfSpecies(listOfSpecies);


              return listOfSpecies;
            } else if (elementName.equals("listOfParameters")) {
              ListOf<Parameter> listOfParameters = (ListOf<Parameter>) newContextObject;
              model.setListOfParameters(listOfParameters);


              return listOfParameters;
            } else if (elementName.equals("listOfInitialAssignments")
                && ((model.getLevel() == 2 && model.getVersion() > 1) 
                    || model.getLevel() >= 3)) {
              ListOf<InitialAssignment> listOfInitialAssignments = (ListOf<InitialAssignment>) newContextObject;
              model.setListOfInitialAssignments(listOfInitialAssignments);


              return listOfInitialAssignments;
            } else if (elementName.equals("listOfRules")) {
              ListOf<Rule> listOfRules = (ListOf<Rule>) newContextObject;
              model.setListOfRules(listOfRules);


              return listOfRules;
            } else if (elementName.equals("listOfConstraints")
                && ((model.getLevel() == 2 && model.getVersion() > 1) 
                    || model.getLevel() >= 3)) {
              ListOf<Constraint> listOfConstraints = (ListOf<Constraint>) newContextObject;
              model.setListOfConstraints(listOfConstraints);


              return listOfConstraints;
            } else if (elementName.equals("listOfReactions")) {
              ListOf<Reaction> listOfReactions = (ListOf<Reaction>) newContextObject;
              model.setListOfReactions(listOfReactions);


              return listOfReactions;
            } else if (elementName.equals("listOfEvents")
                && model.getLevel() > 1) {
              ListOf<Event> listOfEvents = (ListOf<Event>) newContextObject;
              model.setListOfEvents(listOfEvents);


              return listOfEvents;
            } else if (elementName.equals("listOfCompartmentTypes")
                && (model.getLevel() == 2 && model.getVersion() > 1)) {
              ListOf<CompartmentType> listOfCompartmentTypes = (ListOf<CompartmentType>) newContextObject;
              model.setListOfCompartmentTypes(listOfCompartmentTypes);


              return listOfCompartmentTypes;
            } else if (elementName.equals("listOfSpeciesTypes")
                && (model.getLevel() == 2 && model.getVersion() > 1)) {
              ListOf<SpeciesType> listOfSpeciesTypes = (ListOf<SpeciesType>) newContextObject;
              model.setListOfSpeciesTypes(listOfSpeciesTypes);


              return listOfSpeciesTypes;
            } else {
              log4jLogger.warn("The element " + elementName + " is not recognized");
            }
          } else {
            log4jLogger.warn("The element " + elementName + " is not recognized");
          }
        } else if (contextObject instanceof ListOf<?>) {
          ListOf<?> list = (ListOf<?>) contextObject;
          if (list.getParentSBMLObject() instanceof Model) {


            Model model = (Model) list.getParentSBMLObject();
            if (elementName.equals("functionDefinition")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfFunctionDefinitions)
                && model.getLevel() > 1) {
              FunctionDefinition functionDefinition = (FunctionDefinition) newContextObject;
              model.addFunctionDefinition(functionDefinition);


              return functionDefinition;
            } else if (elementName.equals("unitDefinition")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfUnitDefinitions)) {
              UnitDefinition unitDefinition = (UnitDefinition) newContextObject;
              model.addUnitDefinition(unitDefinition);


              return unitDefinition;
            } else if (elementName.equals("compartment")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfCompartments)) {
              Compartment compartment = (Compartment) newContextObject;
              compartment.initDefaults();
              model.addCompartment(compartment);


              return compartment;
            } else if (elementName.equals("species")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfSpecies)
                && ((model.getLevel() == 1 && model
                    .getVersion() > 1) || model.getLevel() > 1)) {
              Species species = (Species) newContextObject;
              species.initDefaults();
              model.addSpecies(species);


              return species;
            }
            // level 1 : species => specie
            else if (elementName.equals("specie")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfSpecies)
                && model.getLevel() == 1
                && model.getVersion() == 1) {
              Species species = (Species) newContextObject;
              species.initDefaults();
              model.addSpecies(species);


              return species;
            } else if (elementName.equals("parameter")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfParameters)) {
              Parameter parameter = (Parameter) newContextObject;
              parameter.initDefaults();
              model.addParameter(parameter);


              return parameter;
            } else if (elementName.equals("initialAssignment")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfInitialAssignments)
                && ((model.getLevel() == 2 && model
                    .getVersion() > 1) || model.getLevel() >= 3)) {
              InitialAssignment initialAssignment = (InitialAssignment) newContextObject;
              model.addInitialAssignment(initialAssignment);


              return initialAssignment;
            } else if (elementName.equals("algebraicRule")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfRules)) {
              AlgebraicRule rule = (AlgebraicRule) newContextObject;
              model.addRule(rule);


              return rule;
            } else if (elementName.equals("assignmentRule")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfRules)
                && model.getLevel() > 1) {
              AssignmentRule rule = (AssignmentRule) newContextObject;
              model.addRule(rule);


              return rule;
            } else if (elementName.equals("parameterRule")
                && list.getSBaseListType().equals(ListOf.Type.listOfRules)
                && model.getLevel() == 1) 
            {
              ExplicitRule rule = (ExplicitRule) newContextObject;
              model.addRule(rule);


              return rule;
            } else if (elementName.equals("specieConcentrationRule")
                && list.getSBaseListType().equals(ListOf.Type.listOfRules)
                && model.getLevel() == 1
                && model.getVersion() == 1) 
            {
              ExplicitRule rule = (ExplicitRule) newContextObject;
              model.addRule(rule);


              return rule;
            } else if (elementName.equals("speciesConcentrationRule")
                && list.getSBaseListType().equals(ListOf.Type.listOfRules)
                && model.getLevel() == 1
                && model.getVersion() == 2) 
            {
              ExplicitRule rule = (ExplicitRule) newContextObject;
              model.addRule(rule);


              return rule;
            } else if (elementName.equals("compartmentVolumeRule")
                && list.getSBaseListType().equals(ListOf.Type.listOfRules)
                && model.getLevel() == 1) 
            {
              ExplicitRule rule = (ExplicitRule) newContextObject;
              model.addRule(rule);


              return rule;
            } else if (elementName.equals("rateRule")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfRules)) {
              RateRule rule = (RateRule) newContextObject;
              model.addRule(rule);


              return rule;
            } else if (elementName.equals("constraint")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfConstraints)
                && ((model.getLevel() == 2 && model
                    .getVersion() > 1) || model.getLevel() >= 3)) {
              Constraint constraint = (Constraint) newContextObject;
              model.addConstraint(constraint);


              return constraint;
            } else if (elementName.equals("reaction")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfReactions)) {
              Reaction reaction = (Reaction) newContextObject;
              model.addReaction(reaction);
              reaction.initDefaults();


              return reaction;
            } else if (elementName.equals("event")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfEvents)
                && model.getLevel() > 1) {
              Event event = (Event) newContextObject;
              model.addEvent(event);
              event.initDefaults();


              return event;
            } else if (elementName.equals("compartmentType")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfCompartmentTypes)
                && (model.getLevel() == 2 && model.getVersion() > 1)) {
              CompartmentType compartmentType = (CompartmentType) newContextObject;
              model.addCompartmentType(compartmentType);


              return compartmentType;
            } else if (elementName.equals("speciesType")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfSpeciesTypes)
                && (model.getLevel() == 2 && model.getVersion() > 1)) {
              SpeciesType speciesType = (SpeciesType) newContextObject;
              model.addSpeciesType(speciesType);


              return speciesType;
            } else {
              log4jLogger.warn("The element " + elementName + " is not recognized");
            }

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