Package org.sbml.jsbml

Examples of org.sbml.jsbml.Parameter

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  @SuppressWarnings("deprecation")
  public static void main(String[] args) throws ParseException,
      XMLStreamException, SBMLException {
    SBMLDocument doc = new SBMLDocument(3, 1);
    Model model = doc.createModel("test_model");
    Parameter p = model.createParameter("p1");
    p.setValue(1d);
    Event e = model.createEvent("e1");
    Priority prior = e.createPriority();
    prior.setMath(new ASTNode(1));
    Trigger t = e.createTrigger();
    t.setFormula("time == 1");
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          }
        }
      }
      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.");
          }
        }
      }
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              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(
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    //Model libsbmlAdapterModel = libSBMLAdapterReader.readModel(libsbmlDoc.getModel());
   
    // System.out.println("nb global parameters = " + libsbmlDoc.getModel().getNumParameters());
   
    Parameter J18 = model.getParameter("J18");
   
    assertTrue(J18 != null);
    assertTrue(J18.getValue() == 0.6);
   
    Reaction pRB_synthesis = model.getReaction("pRB_synthesis");
   
    assertTrue(pRB_synthesis != null);
    System.out.println("pRB_synthesis additional annotation : " + pRB_synthesis.getAnnotation().getNonRDFannotation());
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          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 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(
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      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) {
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      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) {
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      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) {
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      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) {
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Related Classes of org.sbml.jsbml.Parameter

  • org.sbml.jsbml.test.ListenerTest
  • org.sbml.jsbml.test.PriorityTest
  • org.sbml.jsbml.test.RemoveFromModelTest
  • org.sbml.jsbml.test.sbml.TestIncompatibilities
  • org.sbml.jsbml.test.sbml.TestL3Parameter
  • org.sbml.jsbml.test.sbml.TestModel
  • org.sbml.jsbml.test.sbml.TestParameter
  • org.sbml.jsbml.test.sbml.TestReadFromFile5
  • org.sbml.jsbml.test.Test
  • org.sbml.jsbml.test.ToyModelTest
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