Examples of Species

Examples of org.sbml.jsbml.Species

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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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Examples of org.sbml.jsbml.Species

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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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Examples of org.sbml.jsbml.Species

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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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Examples of org.sbml.jsbml.Species

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  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,
        CVTerm.Qualifier.BQB_HAS_PART, "urn:miriam:obo.chebi:CHEBI:15422"));
    System.out.println("==================================");
    new SBMLWriter().write(doc, System.out);
    new JTreeOfSBML(doc);
  }
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