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 $

   */
  @Before
  public void init() {
    int level = 3, version = 1;
    SBMLDocument doc = new SBMLDocument(level, version);
    Model model = doc.createModel("test_model");
    sbase = model.createParameter("test_param");
    kind = Unit.Kind.AMPERE;
    assertTrue(!sbase.isSetUnits());
  }

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          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();
            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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  @SuppressWarnings("deprecation")
  @Test public void readL1V2Branch() throws XMLStreamException, InvalidPropertiesFormatException, IOException, ClassNotFoundException {
    String fileName = DATA_FOLDER + "/libsbml-test-data/l1v2-branch.xml";
    
    SBMLDocument doc = new SBMLReader().readSBMLFile(fileName);
    Model model = doc.getModel();
    
    assertTrue(doc.getLevel() == 1 && doc.getVersion() == 2);
    
    assertTrue(model.getLevel() == 1 && model.getVersion() == 2);
    
    // assertTrue(model.getId().equals("")); // TODO : document. Different behavior than libsbml, we set the id as the name for SBML level 1 models.
    assertTrue(model.getId().equals("Branch"));
    assertTrue(model.getName().equals("Branch"));
    
    Species s1 = model.getSpecies("S1");
    
    assertTrue(s1 != null);
    
    assertTrue(s1.getName().equals("S1"));
    assertTrue(s1.getId().equals("S1")); // changed, was assertTrue(s1.getId().equals("")); cf comment above.
    assertTrue(s1.getNumCVTerms() == 0);
    
    assertTrue(s1.getInitialAmount() == 0);
    assertTrue(s1.getBoundaryCondition() == false);
    
    Species x1 = model.getSpecies("X1");
    
    assertTrue(x1 != null);
    
    assertTrue(x1.getName().equals("X1"));
    assertTrue(x1.getInitialAmount() == 0);
    assertTrue(x1.getBoundaryCondition() == true);
    
    
    Reaction r1 = model.getReaction(0);
    
    assertTrue(r1 != null);
    
    assertTrue(r1.getName().equals("reaction_1"));
    assertTrue(r1.getListOfReactants().size() == 1);

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   */
  @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"));


  }

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  @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);
  }

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          listOfElementsToWrite = new ArrayList<Object>();
          listOfElementsToWrite.add(sbmlDocument.getModel());
        }
      } else if (sbase instanceof Model) {


        Model model = (Model) sbase;
        listOfElementsToWrite = new ArrayList<Object>();
        if (model.isSetListOfUnitDefinitions()) {
          listOfElementsToWrite.add(model.getListOfUnitDefinitions());
        }
        if (model.isSetListOfCompartments()) {
          listOfElementsToWrite.add(model.getListOfCompartments());
        }
        if (model.isSetListOfSpecies()) {
          listOfElementsToWrite.add(model.getListOfSpecies());
        }
        if (model.isSetListOfParameters()) {
          listOfElementsToWrite.add(model.getListOfParameters());
        }
        if (model.isSetListOfRules()) {
          listOfElementsToWrite.add(model.getListOfRules());
        }
        if (model.isSetListOfReactions()) {
          listOfElementsToWrite.add(model.getListOfReactions());
        }


        if (listOfElementsToWrite.isEmpty()) {
          listOfElementsToWrite = null;
        }

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  public Map<String, String> writeXMLAttributes() {
    return super.writeXMLAttributes();
  }


  public Model getModel() {
    Model model = getSBMLDocument().getModel();
    return model != null ? model : null;
  }

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   * .SBMLDocument)
   */
  public void processEndDocument(SBMLDocument sbmlDocument) {


    if (sbmlDocument.isSetModel()) {
      Model model = sbmlDocument.getModel();


      if (model.isSetListOfRules()) {
        for (int i = 0; i < model.getNumRules(); i++) {
          Rule rule = model.getRule(i);
          if (rule instanceof AssignmentRule) {
            AssignmentRule assignmentRule = (AssignmentRule) rule;
            setAssignmentRuleVariable(assignmentRule, model);
          } else if (rule instanceof RateRule) {
            RateRule rateRule = (RateRule) rule;
            setRateRuleVariable(rateRule, model);
          }
        }
      }
      if (model.isSetListOfCompartments()) {
        for (int i = 0; i < model.getNumCompartments(); i++) {
          Compartment compartment = model.getCompartment(i);


          setCompartmentCompartmentType(compartment, model);
          setCompartmentOutside(compartment, model);
          setCompartmentUnits(compartment, model);
        }
      }
      if (model.isSetListOfEvents()) {
        for (int i = 0; i < model.getNumEvents(); i++) {
          Event event = model.getEvent(i);


          setEventTimeUnits(event, model);


          if (event.isSetListOfEventAssignments()) {


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


              setEventAssignmentVariable(eventAssignment, model);
            }
          }
        }
      }
      if (model.isSetListOfInitialAssignments()) {
        for (int i = 0; i < model.getNumInitialAssignments(); i++) {
          InitialAssignment initialAssignment = model
              .getInitialAssignment(i);


          setInitialAssignmentSymbol(initialAssignment, model);
        }
      }
      if (model.isSetListOfReactions()) {
        for (int i = 0; i < model.getNumReactions(); i++) {
          Reaction reaction = model.getReaction(i);


          setReactionCompartment(reaction, model);


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


              setSpeciesReferenceSpecies(speciesReference, model);
            }
          }
          if (reaction.isSetListOfProducts()) {
            for (int j = 0; j < reaction.getNumProducts(); j++) {
              SpeciesReference speciesReference = reaction
                  .getProduct(j);


              setSpeciesReferenceSpecies(speciesReference, model);
            }
          }
          if (reaction.isSetListOfModifiers()) {
            for (int j = 0; j < reaction.getNumModifiers(); j++) {
              ModifierSpeciesReference modifierSpeciesReference = reaction
                  .getModifier(j);


              setSpeciesReferenceSpecies(
                  modifierSpeciesReference, model);
            }
          }
          if (reaction.isSetKineticLaw()) {
            KineticLaw kineticLaw = reaction.getKineticLaw();
            if (kineticLaw.isSetListOfParameters()) {
              for (int j = 0; j < kineticLaw.getNumParameters(); j++) {
                LocalParameter parameter = kineticLaw
                    .getParameter(j);


                setParameterUnits(parameter, model);
              }
            }
          }
        }
      }
      if (model.isSetListOfSpecies()) {
        for (int i = 0; i < model.getNumSpecies(); i++) {
          Species species = model.getSpecies(i);


          setSpeciesSubstanceUnits(species, model);
          setSpeciesSpeciesType(species, model);
          setSpeciesConversionFactor(species, model);
          setSpeciesCompartment(species, model);
        }
      }
      if (model.isSetListOfParameters()) {
        for (int i = 0; i < model.getNumParameters(); i++) {
          Parameter parameter = model.getParameter(i);


          setParameterUnits(parameter, model);
        }
      }

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


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


          Model model = (Model) contextObject;
          if (newContextObject instanceof ListOf<?>) {
            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("listOfRules")) {
              ListOf<Rule> listOfRules = (ListOf<Rule>) newContextObject;
              model.setListOfRules(listOfRules);


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


              return listOfReactions;
            } else {
              // TODO : SBML syntax error, throw an exception?
            }
          } else {
            // TODO : SBML syntax error, throw an exception?
          }
        } else if (contextObject instanceof ListOf<?>) {
          ListOf<?> list = (ListOf<?>) contextObject;
          if (list.getParentSBMLObject() instanceof Model) {


            Model model = (Model) list.getParentSBMLObject();
            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;
              model.addCompartment(compartment);


              return compartment;
            } else if (elementName.equals("specie")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfSpecies)) {
              Species species = (Species) newContextObject;
              model.addSpecies(species);


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


              return parameter;
            } 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") // TODO : wrong, there are no assignmentRule element, only more specialize rule
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfRules)) {
              AssignmentRule rule = (AssignmentRule) newContextObject;
              model.addRule(rule);


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


              return reaction;
            } else {
              // TODO : SBML syntax error, throw an exception?
            }

View Full Code Here

      ClassNotFoundException, InstantiationException,
      IllegalAccessException, UnsupportedLookAndFeelException {


    UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());


    Model m = new Model("test", 2, 4);
    m.createFunctionDefinition("f");
    m.createRateRule();
    FormulaParser parser;


    for (int i = 0; i < testCases.length; i++) {
      System.out.printf("%d.\treading:\t%s\n", i, testCases[i]);
      parser = new FormulaParser(new StringReader(testCases[i]));

View Full Code Here

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cysbml.layout.CytoscapeLayoutTools

cysbml.layout.LayoutExtension

cysbml.layout.NetworkLayout

cysbml.mapping.NavigationTree

cysbml.SBMLGraphReader

cysbml.SBMLLayoutGraphReader

cysbmlexample.CySBMLExample

org.sbml.jsbml.ext.groups.Member

org.sbml.jsbml.ext.groups.TestL3groups

org.sbml.jsbml.ext.layout.AbstractReferenceGlyph

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