Examples of org.sbml.jsbml.Compartment

org.sbml.jsbml.Compartment
Represents the compartment in a model, i.e., a variable element with name, identifier, unit, and value that may change during a simulation. This is the container for reacting species. @author Andreas Dräger @author Nicolas Rodriguez @author Marine Dumousseau @since 0.8 @version $Rev: 1531 $

  private void setAssignmentRuleVariable(AssignmentRule 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) {

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  private void setCompartmentOutside(Compartment compartment, Model model) {


    if (compartment.isSetOutside()) {
      String outsideID = compartment.getOutside();


      Compartment outside = model.getCompartment(outsideID);


      if (outside != null) {
        compartment.setOutside(outside);
      } else {
        // TODO : the compartment ID doesn't match a compartment, throw

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      Model model) {


    if (eventAssignment.isSetVariable()) {
      String variableID = eventAssignment.getVariable();


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


      if (compartment == null) {

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      InitialAssignment initialAssignment, Model model) {


    if (initialAssignment.isSetVariable()) {
      String variableID = initialAssignment.getVariable();


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


      if (compartment == null) {

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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) {

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  private void setReactionCompartment(Reaction reaction, Model model) {


    if (reaction.isSetCompartment()) {
      String compartmentID = reaction.getCompartment();


      Compartment compartment = model.getCompartment(compartmentID);


      if (compartment != null) {
        reaction.setCompartment(compartment);
      } else {
        // TODO : the compartment ID doesn't match a compartment, throw

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  private void setSpeciesCompartment(Species species, Model model) {


    if (species.isSetCompartment()) {
      String compartmentID = species.getCompartment();


      Compartment compartment = model.getCompartment(compartmentID);


      if (compartment != null) {
        species.setCompartment(compartment);
      } else {
        // TODO : the compartment ID doesn't match a compartment, throw

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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"));

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    assertTrue(doc.getLevel() == 2 && doc.getVersion() == 4);
    
    assertTrue(model.getId().equals(""));
    assertTrue(model.getName().equals("Swat2004_Mammalian_G1_S_Transition"));


    Compartment cell = model.getCompartment(0);
    
    assertTrue(cell.getSize() == 1);
    
    assertTrue(model.getListOfUnitDefinitions().size() == 3);    
    assertTrue(model.getListOfUnitDefinitions().get(1).getMetaId().equals("metaid_0000004"));
    
    Species pRBp = model.getSpecies("pRBp");

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  @SuppressWarnings("deprecation")
  @Test
  public void test_read_l1v1_branch() throws XMLStreamException, InvalidPropertiesFormatException, IOException, ClassNotFoundException {
    SBMLDocument d;
    Model m;
    Compartment c;
    KineticLaw kl;
    LocalParameter p;
    Reaction r;
    Species s;
    SpeciesReference sr;
    UnitDefinition ud;
    String filename = DATA_FOLDER + "/libsbml-test-data/l1v1-branch.xml";
    d = new SBMLReader().readSBML(filename);
    if (d == null)
      ;
    {
    }
    assertTrue(d.getLevel() == 1);
    assertTrue(d.getVersion() == 1);
    m = d.getModel();
    assertTrue(m.getName().equals("Branch"));
    assertTrue(m.getNumCompartments() == 1);
    c = m.getCompartment(0);
    assertTrue(c.getName().equals("compartmentOne"));
    assertTrue(c.getVolume() == 1);
    ud = c.getDerivedUnitDefinition();
    assertTrue(ud.getNumUnits() == 1);


    // assertTrue(ud.getUnit(0).getKind() == Unit.Kind.LITRE); // getDerivedUnitDefinition not working properly
    assertTrue(m.getNumSpecies() == 4);
    s = m.getSpecies(0);

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org.sbml.jsbml.ext.qual.BuildToyModelTest

org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin

org.sbml.jsbml.test.EventTest

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.TestCompartment

org.sbml.jsbml.test.sbml.TestIncompatibilities

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