Examples of org.sbml.jsbml.Rule

org.sbml.jsbml.Rule
The base class for the {@link AlgebraicRule}, {@link RateRule}, {@link AssignmentRule}. @author Andreas Dräger @since 0.8 @version $Rev: 1531 $

    assertTrue(M.getReactionCount() == 1);
  }


  @Test
  public void test_Model_addRules() throws ParseException {
    Rule r1 = new AlgebraicRule(2, 4);
    AssignmentRule r2 = new AssignmentRule(2, 4);
    RateRule r3 = new RateRule(2, 4);
    r2.setVariable("r2");
    r3.setVariable("r3");
    r1.setMath(ASTNode.parseFormula("2"));
    r2.setMath(ASTNode.parseFormula("2"));
    r3.setMath(ASTNode.parseFormula("2"));
    M.addRule(r1);
    M.addRule(r2);
    M.addRule(r3);

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    assertTrue(M.getReactionCount() == 0);
  }


  @Test
  public void test_Model_createAlgebraicRule() {
    Rule ar = M.createAlgebraicRule();
    assertTrue(ar != null);
    assertTrue(M.getRuleCount() == 1);
    assertEquals(M.getRule(0), ar);
  }

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    assertEquals(M.getRule(0), ar);
  }


  @Test
  public void test_Model_createAssignmentRule() {
    Rule ar = M.createAssignmentRule();
    assertTrue(ar != null);
    assertTrue(M.getRuleCount() == 1);
    assertEquals(M.getRule(0), ar);
  }

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    assertTrue(M.createProduct() == null);
  }


  @Test
  public void test_Model_createRateRule() {
    Rule rr = M.createRateRule();
    assertTrue(rr != null);
    assertTrue(M.getRuleCount() == 1);
    assertEquals(M.getRule(0), rr);
  }

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  // TODO: API changes, setVariable function is not in the Rule Class.


  @Test
  public void test_Model_getRules() throws ParseException {
    Rule ar = new AlgebraicRule(2, 4);
    AssignmentRule scr = new AssignmentRule(2, 4);
    AssignmentRule cvr = new AssignmentRule(2, 4);
    AssignmentRule pr = new AssignmentRule(2, 4);
    scr.setVariable("r2");
    cvr.setVariable("r3");
    pr.setVariable("r4");
    ar.setFormula("x + 1");
    scr.setFormula("k * t/(1 + k)");
    cvr.setFormula("0.10 * t");
    pr.setFormula("k3/k2");
    M.addRule(ar);
    M.addRule(scr);
    M.addRule(cvr);
    M.addRule(pr);
    assertTrue(M.getRuleCount() == 4);
    ar = M.getRule(0);
    scr = (AssignmentRule) M.getRule(1);
    cvr = (AssignmentRule) M.getRule(2);
    pr = (AssignmentRule) M.getRule(3);
    assertTrue(ar.getFormula().equals("x+1")); // .equals("x + 1")
    assertTrue(scr.getFormula().equals("k*t/(1+k)")); // .equals("k * t/(1 + k)"));
    assertTrue(cvr.getFormula().equals("0.1*t")); // .equals("0.10 * t"));
    assertTrue(pr.getFormula().equals("k3/k2"));
  }

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    o3 = null;
  }


  @Test
  public void test_Model_removeRule() {
    Rule o1, o2;
    RateRule o3;
    o1 = M.createAssignmentRule();
    o2 = M.createAlgebraicRule();
    o3 = M.createRateRule();
    o3.setVariable("test");

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    }


    // Create vertices and edges for assignment and rate rules
    for (i = 0; i < model.getRuleCount(); i++) {
      equation = new InnerNode<SBase>(model.getRule(i));
      Rule r = model.getRule(i);
      if (r instanceof RateRule) {
        equations.add(equation);
        variable = variableHash.get(((RateRule) r)
            .getVariableInstance());
        // link
        variable.addNode(equation);
        equation.addNode(variable);


      }


      else if (r instanceof AssignmentRule) {
        variable = variableHash.get(((AssignmentRule) r)
            .getVariableInstance());
        // link
        if (variable!=null) {
          equations.add(equation);
          variable.addNode(equation);
          equation.addNode(variable);
        }


      }
    }


    // Create vertices and edges for algebraic rules
    for (i = 0; i < model.getRuleCount(); i++) {
      equation = new InnerNode<SBase>(model.getRule(i));
      Rule r = model.getRule(i);
      if (r instanceof AlgebraicRule) {
        equations.add(equation);
        // all identifiers withn the MathML of this AlgebraicRule
        svariables.clear();
        getVariables(null, model.getRule(i).getMath(), svariables, model.getLevel());

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          log4jLogger.debug("Transformed SBMLLevel1Rule: processEndDocument: model is level 1");


          int i = 0;
          for (Rule rule : model.getListOfRules().clone()) {
            if (rule instanceof SBMLLevel1Rule) {
              Rule realRule;
              
              if (((SBMLLevel1Rule) rule).isScalar()) {
                realRule = ((SBMLLevel1Rule) rule).cloneAsAssignmentRule();
                log4jLogger.debug("Transformed SBMLLevel1Rule: " + ((SBMLLevel1Rule) rule).getVariable() + " into AssignmentRule.");
              } else {
                realRule = ((SBMLLevel1Rule) rule).cloneAsRateRule();
                log4jLogger.debug("Transformed SBMLLevel1Rule: " + ((SBMLLevel1Rule) rule).getVariable() + " into RateRule.");
              }
              
              log4jLogger.debug("Transformed SBMLLevel1Rule: realRule = " + realRule);


              model.getListOfRules().remove(i);
              model.getListOfRules().add(i, realRule);
            }
            i++;
          }
        }
        
        for (int i = 0; i < model.getRuleCount(); i++) {
          Rule rule = model.getRule(i);
          if (rule instanceof AssignmentRule) {
            AssignmentRule assignmentRule = (AssignmentRule) rule;
            if (assignmentRule.isSetVariable()
                && !assignmentRule.isSetVariableInstance()) {
              log4jLogger.warn("No Symbol matches the variableID of AssignmentRule.");

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    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"));
    
    SBMLDocument doc2 = doc1.clone();
    try {
      (new SBMLWriter()).write(doc1, System.out);
      System.out.println("\n==================");

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    if (sbmlDocument.isSetModel()) {
      Model model = sbmlDocument.getModel();


      if (model.isSetListOfRules()) {
        for (int i = 0; i < model.getRuleCount(); i++) {
          Rule rule = model.getRule(i);
          if (rule instanceof AssignmentRule) {
            AssignmentRule assignmentRule = (AssignmentRule) rule;
            setAssignmentRuleVariable(assignmentRule, model);
          } else if (rule instanceof RateRule) {
            RateRule rateRule = (RateRule) rule;

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org.sbml.jsbml.test.HashCodeTest

org.sbml.jsbml.test.sbml.TestModel

org.sbml.jsbml.validator.OverdeterminationValidator

org.sbml.jsbml.xml.parsers.SBMLCoreParser

org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser

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