Package org.sbml.jsbml

Examples of org.sbml.jsbml.SpeciesReference

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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);

        if (species == null) {
          parameter = model.getParameter(variableID);

          if (parameter == null) {
            if (model.isSetListOfReactions()) {

              int i = 0;
              SpeciesReference sr = null;

              while (i <= model.getNumReactions() - 1
                  && sr == null) {
                Reaction reaction = model.getReaction(i);
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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);

        if (species == null) {
          parameter = model.getParameter(variableID);

          if (parameter == null) {
            if (model.isSetListOfReactions()) {

              int i = 0;
              SpeciesReference sr = null;

              while (i <= model.getNumReactions() - 1
                  && sr == null) {
                Reaction reaction = model.getReaction(i);
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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);

        if (species == null) {
          parameter = model.getParameter(variableID);

          if (parameter == null) {
            if (model.isSetListOfReactions()) {

              int i = 0;
              SpeciesReference sr = null;

              while (i <= model.getNumReactions() - 1
                  && sr == null) {
                Reaction reaction = model.getReaction(i);
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    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));
    math = ASTNode.times(math, new ASTNode(3.7, 8, kl));
    kl.setMath(math);
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    /*
     * Reactions
     */
    logger.debug("==== Reactions ====");
    Reaction r2 = new Reaction(level, version);
    SpeciesReference sr1 = r2.createReactant(s1);
    sr1.setId("sr1");
    r2.createModifier(p1);
    r2.setId("r2");
    model.addReaction(r2);
   
    /*
 
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Related Classes of org.sbml.jsbml.SpeciesReference

  • org.sbml.jsbml.test.IdRegistrationTest
  • org.sbml.jsbml.test.sbml.TestModel
  • org.sbml.jsbml.test.sbml.TestReaction
  • org.sbml.jsbml.test.sbml.TestReadFromFile1
  • org.sbml.jsbml.test.sbml.TestReadFromFile5
  • org.sbml.jsbml.test.TestClone
  • org.sbml.jsbml.test.TreeSearchTest
  • org.sbml.jsbml.xml.parsers.SBMLCoreParser
  • org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
  • org.sbml.jsbml.xml.test.MathMLTest
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