Examples of RateRule

org.sbml.jsbml.RateRule
Represents the rateRule XML element of a SBML file. @author Andreas Dräger @author Marine Dumousseau @since 0.8 @version $Rev: 1531 $

Examples of org.sbml.jsbml.RateRule


  @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);
    assertTrue(M.getRuleCount() == 3);
  }

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Examples of org.sbml.jsbml.RateRule

  }


  @Test
  public void test_Model_removeRule() {
    Rule o1, o2;
    RateRule o3;
    o1 = M.createAssignmentRule();
    o2 = M.createAlgebraicRule();
    o3 = M.createRateRule();
    o3.setVariable("test");
    assertTrue(M.removeRule(0).equals(o1));
    assertTrue(M.getRuleCount() == 2);
    assertTrue(M.removeRule(0).equals(o2));
    assertTrue(M.getRuleCount() == 1);
    assertTrue( M.removeRule("test").equals(o3) );

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Examples of org.sbml.jsbml.RateRule

  /**
   * 
   * @return
   */
  public RateRule cloneAsRateRule() {
    return new RateRule(this);
  }

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Examples of org.sbml.jsbml.RateRule

                && !assignmentRule.isSetUnitsInstance()
                && assignmentRule.isParameter()) {
              log4jLogger.warn("No UnitDefinition matches the unitsID of AssignmentRule.");
            }
          } else if (rule instanceof RateRule) {
            RateRule rateRule = (RateRule) rule;
            if (rateRule.isSetVariable()
                && !rateRule.isSetVariableInstance()) {
              log4jLogger.warn("No Symbol matches the variableID of RateRule.");
            }
          }
        }
      }

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Examples of org.sbml.jsbml.RateRule


              return rule;
            } else if (elementName.equals("rateRule")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfRules)) {
              RateRule rule = (RateRule) newContextObject;
              model.addRule(rule);


              return rule;
            } else if (elementName.equals("constraint")
                && list.getSBaseListType().equals(

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Examples of org.sbml.jsbml.RateRule

          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;
            setRateRuleVariable(rateRule, model);
          }
        }
      }
      if (model.isSetListOfCompartments()) {

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Examples of org.sbml.jsbml.RateRule


  @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);
    assertTrue(M.getNumRules() == 3);
  }

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Examples of org.sbml.jsbml.RateRule

  }


  @Test
  public void test_Model_removeRule() {
    Rule o1, o2;
    RateRule o3;
    o1 = M.createAssignmentRule();
    o2 = M.createAlgebraicRule();
    o3 = M.createRateRule();
    o3.setVariable("test");
    assertTrue(M.removeRule(0).equals(o1));
    assertTrue(M.getNumRules() == 2);
    assertTrue(M.removeRule(0).equals(o2));
    assertTrue(M.getNumRules() == 1);
    assertTrue( M.removeRule("test").equals(o3) );

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Examples of org.sbml.jsbml.RateRule

  /**
   * 
   * @return
   */
  public RateRule cloneAsRateRule() {
    return new RateRule(this);
  }

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Examples of org.sbml.jsbml.RateRule

                && !assignmentRule.isSetUnitsInstance()
                && assignmentRule.isParameter()) {
              log4jLogger.warn("No UnitDefinition matches the unitsID of AssignmentRule.");
            }
          } else if (rule instanceof RateRule) {
            RateRule rateRule = (RateRule) rule;
            if (rateRule.isSetVariable()
                && !rateRule.isSetVariableInstance()) {
              log4jLogger.warn("No Symbol matches the variableID of RateRule.");
            }
          }
        }
      }

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