Package org.sbml.jsbml

Examples of org.sbml.jsbml.Parameter

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    //Model libsbmlAdapterModel = libSBMLAdapterReader.readModel(libsbmlDoc.getModel());
   
    // System.out.println("nb global parameters = " + libsbmlDoc.getModel().getParameters());
   
    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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    SBMLReader reader = new SBMLReader();
    SBMLDocument d = null;
    Model m;
    Compartment c;
    Species s;
    Parameter gp;
    LocalParameter lp;
    AssignmentRule ar;
    Reaction r;
    SpeciesReference sr;
    KineticLaw kl;
    UnitDefinition ud;
    Reaction r1;
    ListOf<Compartment> loc;
    Compartment c1;
    ListOf<Rule> lor;
    AssignmentRule ar1;
    ListOf<Parameter> lop;
    Parameter p1;
    ListOf<Species> los;
    Species s1;
    String filename = new String( DATA_FOLDER + "/libsbml-test-data/" );
    filename += "l2v1-assignment.xml";
    try {
    d = reader.readSBML(filename);
  } catch (IOException e) {
    e.printStackTrace();
    assert(false);
  } catch (XMLStreamException e) {
    e.printStackTrace();
    assert(false);
  }

  System.out.println(" TestReadFromFile 5: reading done.");
 
  assertTrue( d.getLevel() == 2 );
    assertTrue( d.getVersion() == 1 );
    m = d.getModel();
    assertTrue( m != null );
    assertTrue( m.getCompartmentCount() == 1 );
    c = m.getCompartment(0);
    assertTrue( c != null );
    assertTrue( c.getId().equals( "cell") );
/*    ud = c.getDerivedUnitDefinition();
    assertTrue( ud.getUnitCount() == 1 );
    assertTrue( ud.getUnit(0).getKind() == Kind.LITRE );
    */
    loc = m.getListOfCompartments();
    c1 = loc.get(0);
    assertTrue( c1.equals(c) );
    c1 = loc.get("cell");
    assertTrue( c1.equals(c) );
    assertTrue( m.getSpeciesCount() == 5 );
    s = m.getSpecies(0);
    assertTrue( s != null );
    assertTrue( s.getId().equals( "X0"  ) );
    assertTrue( s.getCompartment().equals( "cell") );
    assertTrue( s.getInitialConcentration() == 1.0 );
    los = m.getListOfSpecies();
    s1 = los.get(0);
    assertTrue( s1.equals(s) );
    s1 = los.get("X0");
    assertTrue( s1.equals(s) );
    s = m.getSpecies(1);
    assertTrue( s != null );
    assertTrue( s.getId().equals( "X1"  ) );
    assertTrue( s.getCompartment().equals( "cell") );
    assertTrue( s.getInitialConcentration() == 0.0 );
    s = m.getSpecies(2);
    assertTrue( s != null );
    assertTrue( s.getId().equals( "T"   ) );
    assertTrue( s.getCompartment().equals( "cell") );
    assertTrue( s.getInitialConcentration() == 0.0 );
    s = m.getSpecies(3);
    assertTrue( s != null );
    assertTrue( s.getId().equals( "S1"  ) );
    assertTrue( s.getCompartment().equals( "cell") );
    assertTrue( s.getInitialConcentration() == 0.0 );
    s = m.getSpecies(4);
    assertTrue( s != null );
    assertTrue( s.getId().equals( "S2"  ) );
    assertTrue( s.getCompartment().equals( "cell") );
    assertTrue( s.getInitialConcentration() == 0.0 );
    assertTrue( m.getParameterCount() == 1 );
    gp = m.getParameter(0);
    assertTrue( gp != null );
    assertTrue( gp.getId().equals( "Keq") );
    assertTrue( gp.getValue() == 2.5 );
    lop = m.getListOfParameters();
    p1 = lop.get(0);
    assertTrue( p1.equals(gp) );
    p1 = lop.get("Keq");
    assertTrue( p1.equals(gp) );
    /*
    ud = gp.getDerivedUnitDefinition();
    assertTrue( ud.getUnitCount() == 0 );
    assertTrue( m.getRuleCount() == 2 );
    */
 
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  public ListenerTest() {
    SBMLDocument doc = new SBMLDocument(2, 2);
    doc.addTreeNodeChangeListener(this);
    Model model = doc.createModel("test_model");
    Parameter p1 = model.createParameter("p1");
    p1.setId("p2");
    model.removeParameter(p1);

    Compartment c = model.createCompartment("c");
    c.setSize(4.3);
    c.setSBOTerm(SBO.getPhysicalCompartment());
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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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    M = null;
  }

  @Test
  public void test_KineticLaw_getParameterById() throws ParseException {
    Parameter k1 = new Parameter(2, 4);
    Parameter k2 = new Parameter(2, 4);
    k1.setId("k1");
    k2.setId("k2");
    k1.setValue(3.14);
    k2.setValue(2.72);
    M.addParameter(k1);
    M.addParameter(k2);
    Reaction r1 = new Reaction(2, 4);
    r1.setId("reaction_1");
    KineticLaw kl = new KineticLaw(2, 4);
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    assertTrue(M.getCompartmentCount() == 1);
  }

  @Test
  public void test_Model_addParameter() {
    Parameter p = new Parameter(2, 4);
    p.setId("p");
    M.addParameter(p);
    assertTrue(M.getParameterCount() == 1);
  }
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    assertTrue(M.createModifier() == null);
  }

  @Test
  public void test_Model_createParameter() {
    Parameter p = M.createParameter();
    assertTrue(p != null);
    assertTrue(M.getParameterCount() == 1);
    assertEquals(M.getParameter(0), p); // TODO: check why this failing
  }
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    assertTrue(M.getSpeciesWithBoundaryConditionCount() == 2);
  }

  @Test
  public void test_Model_getParameter() {
    Parameter p1 = new Parameter(2, 4);
    Parameter p2 = new Parameter(2, 4);
    p1.setId("Km1");
    p2.setId("Km2");
    M.addParameter(p1);
    M.addParameter(p2);
    assertTrue(M.getParameterCount() == 2);
    p1 = M.getParameter(0);
    p2 = M.getParameter(1);
    assertTrue(p1.getId().equals("Km1"));
    assertTrue(p2.getId().equals("Km2"));
  }
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    assertTrue(p2.getId().equals("Km2"));
  }

  @Test
  public void test_Model_getParameterById() {
    Parameter p1 = new Parameter(2, 4);
    Parameter p2 = new Parameter(2, 4);
    p1.setId("Km1");
    p2.setId("Km2");
    M.addParameter(p1);
    M.addParameter(p2);
    assertTrue(M.getParameterCount() == 2);
    // assertNotEquals(M.getParameter("Km1"), p1);
    // assertNotEquals(M.getParameter("Km2"), p2);
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    o3 = null;
  }

  @Test
  public void test_Model_removeParameter() {
    Parameter o1, o2, o3;
    o1 = M.createParameter();
    o2 = M.createParameter();
    o3 = M.createParameter();
    o3.setId("test");
    assertTrue(M.removeParameter(0).equals(o1));
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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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