Examples of org.sbml.jsbml.ModifierSpeciesReference

org.sbml.jsbml.ModifierSpeciesReference
Represents the modifierSpeciesReference XML element of a SBML file. @author Andreas Dräger @since 0.8 @version $Rev: 1524 $

              setSpeciesReferenceSpecies(speciesReference, model);
            }
          }
          if (reaction.isSetListOfModifiers()) {
            for (int j = 0; j < reaction.getNumModifiers(); j++) {
              ModifierSpeciesReference modifierSpeciesReference = reaction
                  .getModifier(j);


              setSpeciesReferenceSpecies(
                  modifierSpeciesReference, model);
            }

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  }


  @Test
  public void test_Model_createModifier() {
    Reaction r;
    ModifierSpeciesReference msr;
    M.createReaction();
    M.createReaction();
    msr = M.createModifier();
    assertTrue(msr != null);
    assertTrue(M.getNumReactions() == 2);

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              }
            }
          }
          if (reaction.isSetListOfModifiers()) {
            for (int j = 0; j < reaction.getNumModifiers(); j++) {
              ModifierSpeciesReference modifierSpeciesReference = reaction
                  .getModifier(j);


              if (modifierSpeciesReference.isSetSpecies()
                  && !modifierSpeciesReference
                      .isSetSpeciesInstance()) {
                log4jLogger.warn(String.format("No Species matches the speciesID '%s' of %s.", 
                    modifierSpeciesReference.getId(), modifierSpeciesReference.getElementName()));
              }
            }
          }
          if (reaction.isSetKineticLaw()) {
            KineticLaw kineticLaw = reaction.getKineticLaw();

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            } else if (elementName
                .equals("modifierSpeciesReference")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfModifiers)
                && reaction.getLevel() > 1) {
              ModifierSpeciesReference modifierSpeciesReference = (ModifierSpeciesReference) newContextObject;
              reaction.addModifier(modifierSpeciesReference);


              return modifierSpeciesReference;
            } else {
              log4jLogger.warn("The element " + elementName + " is not recognized");

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              setSpeciesReferenceSpecies(speciesReference, model);
            }
          }
          if (reaction.isSetListOfModifiers()) {
            for (int j = 0; j < reaction.getNumModifiers(); j++) {
              ModifierSpeciesReference modifierSpeciesReference = reaction
                  .getModifier(j);


              setSpeciesReferenceSpecies(
                  modifierSpeciesReference, model);
            }

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Related Classes of org.sbml.jsbml.ModifierSpeciesReference

org.sbml.jsbml.test.sbml.TestModel

org.sbml.jsbml.test.sbml.TestReaction

org.sbml.jsbml.test.TreeSearchTest

org.sbml.jsbml.xml.parsers.SBMLCoreParser

org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser

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