Package org.sbml.jsbml

Examples of org.sbml.jsbml.Species

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            } 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(
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   */
  @Test public void checkHashCode() throws ParseException {
    SBMLDocument doc1 = new SBMLDocument(3, 1);
    Model model = doc1.createModel("test_model");
    Compartment c = model.createCompartment("c1");
    Species s = model.createSpecies("s1", c);
    s.addCVTerm(new CVTerm(CVTerm.Qualifier.BQB_IS, "urn:miriam:kegg.compound:C00001"));
    Rule r = model.createAlgebraicRule();
    r.setMath(ASTNode.parseFormula("sin(3) + 1"));
   
    SBMLDocument doc2 = doc1.clone();
    assertTrue(doc1.hashCode() == doc2.hashCode());
    assertTrue(model.hashCode() != doc2.hashCode());
    assertTrue(s.getCVTerm(0).equals(new CVTerm(CVTerm.Qualifier.BQB_IS, "urn:miriam:kegg.compound:C00001")));
    assertTrue(s.getCVTerm(0).hashCode() == (new CVTerm(CVTerm.Qualifier.BQB_IS, "urn:miriam:kegg.compound:C00001")).hashCode());
    assertTrue(doc1.equals(doc2));
    assertTrue(doc2.equals(doc1));
  }
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        new ASTNode(16, fd)));
    math.addChild(pieces);
    fd.setMath(math);
    System.out.println(math.toMathML());
   
    Species species = m.createSpecies("spec");
    Reaction r = m.createReaction("r");
    r.addReactant(new SpeciesReference(species));
    KineticLaw kl = new KineticLaw(level, version);
    math = new ASTNode(fd, kl);
    math.addChild(new ASTNode(species, kl));
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          }
        }
      }
      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);
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              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(
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    if (rule.isSetVariable()) {
      String variableID = rule.getVariable();

      Compartment compartment = model.getCompartment(variableID);
      Species species = null;
      SpeciesReference speciesReference = null;
      Parameter parameter = null;

      if (compartment == null) {
        species = model.getSpecies(variableID);
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    if (eventAssignment.isSetVariable()) {
      String variableID = eventAssignment.getVariable();

      Compartment compartment = model.getCompartment(variableID);
      Species species = null;
      SpeciesReference speciesReference = null;
      Parameter parameter = null;

      if (compartment == null) {
        species = model.getSpecies(variableID);
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    if (initialAssignment.isSetVariable()) {
      String variableID = initialAssignment.getVariable();

      Compartment compartment = model.getCompartment(variableID);
      Species species = null;
      SpeciesReference speciesReference = null;
      Parameter parameter = null;

      if (compartment == null) {
        species = model.getSpecies(variableID);
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  private void setRateRuleVariable(RateRule rule, Model model) {
    if (rule.isSetVariable()) {
      String variableID = rule.getVariable();

      Compartment compartment = model.getCompartment(variableID);
      Species species = null;
      SpeciesReference speciesReference = null;
      Parameter parameter = null;

      if (compartment == null) {
        species = model.getSpecies(variableID);
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      SimpleSpeciesReference speciesReference, Model model) {

    if (speciesReference.isSetSpecies()) {
      String speciesID = speciesReference.getSpecies();

      Species species = model.getSpecies(speciesID);

      if (species != null) {
        speciesReference.setSpecies(species);
      } else {
        // TODO : the species ID doesn't match a species, throw an
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Related Classes of org.sbml.jsbml.Species

  • org.mcisb.ontology.drugbank.DrugBankUtils
  • org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin
  • org.sbml.jsbml.test.HashCodeTest
  • org.sbml.jsbml.test.IdRegistrationTest
  • org.sbml.jsbml.test.ListenerTest
  • org.sbml.jsbml.test.MathMLTest
  • org.sbml.jsbml.test.RemoveFromModelTest
  • org.sbml.jsbml.test.sbml.TestModel
  • org.sbml.jsbml.test.sbml.TestReadFromFile1
  • org.sbml.jsbml.test.sbml.TestReadFromFile5
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