Package org.sbml.jsbml

Examples of org.sbml.jsbml.Reaction

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  /**
   *
   */
  @Test public void testUnRegister2() {
   
    Reaction r1 = model.removeReaction("R1");

    assertTrue(r1.getReactant("SP1") != null);

    assertTrue(model.findNamedSBase("LP1") == null);
   
    // creating a product with the same id as a species
    r1.createProduct("S1");
  }
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    assertTrue(x1.getName().equals("X1"));
    assertTrue(x1.getInitialAmount() == 0);
    assertTrue(x1.getBoundaryCondition() == true);
   
   
    Reaction r1 = model.getReaction(0);
   
    assertTrue(r1 != null);
   
    assertTrue(r1.getName().equals("reaction_1"));
    assertTrue(r1.getListOfReactants().size() == 1);
    assertTrue(r1.getListOfProducts().size() == 1);
    assertTrue(r1.getNumModifiers() == 0);
    assertTrue(r1.getReversible() == false);
   
    assertTrue(r1.getListOfReactants().get(0).getSpecies().equals("X0"));
    assertTrue(r1.getListOfProducts().get(0).getSpecies().equals("S1"));
   
    KineticLaw rdClkKL = r1.getKineticLaw();

    assertTrue(rdClkKL != null);
    assertTrue(rdClkKL.getListOfLocalParameters().size() == 1);
    assertTrue(rdClkKL.getListOfLocalParameters().get(0).getName().equals("k1"));
   
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        if (unitDefinition.isSetListOfUnits()) {
          listOfElementsToWrite = new ArrayList<Object>();
          listOfElementsToWrite.add(unitDefinition.getListOfUnits());
        }
      } else if (sbase instanceof Reaction) {
        Reaction reaction = (Reaction) sbase;
        listOfElementsToWrite = new ArrayList<Object>();

        if (reaction.isSetListOfReactants()) {
          listOfElementsToWrite.add(reaction.getListOfReactants());
        }
        if (reaction.isSetListOfProducts()) {
          listOfElementsToWrite.add(reaction.getListOfProducts());
        }
        if (reaction.isSetListOfModifiers()) {
          listOfElementsToWrite.add(reaction.getListOfModifiers());
        }
        if (reaction.isSetKineticLaw()) {
          listOfElementsToWrite.add(reaction.getKineticLaw());
        }

        if (listOfElementsToWrite.isEmpty()) {
          listOfElementsToWrite = null;
        }
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          }
        }
      }
      if (model.isSetListOfReactions()) {
        for (int i = 0; i < model.getNumReactions(); i++) {
          Reaction reaction = model.getReaction(i);
          if (reaction.isSetCompartment()
              && !reaction.isSetCompartmentInstance()) {
            log4jLogger.warn("No Compartment matches the compartmentID of reaction.");
          }

          if (reaction.isSetListOfReactants()) {
            for (int j = 0; j < reaction.getNumReactants(); j++) {
              SpeciesReference speciesReference = reaction
                  .getReactant(j);

              if (speciesReference.isSetSpecies()
                  && !speciesReference.isSetSpeciesInstance()) {
                log4jLogger.warn(String.format("No Species matches the speciesID '%s' of %s.",
                    speciesReference.getId(), speciesReference.getElementName()));
              }
            }
          }
          if (reaction.isSetListOfProducts()) {
            for (int j = 0; j < reaction.getNumProducts(); j++) {
              SpeciesReference speciesReference = reaction
                  .getProduct(j);

              if (speciesReference.isSetSpecies()
                  && !speciesReference.isSetSpeciesInstance()) {
                log4jLogger.warn(String.format("No Species matches the speciesID '%s' of %s.",
                    speciesReference.getId(), speciesReference.getElementName()));
              }
            }
          }
          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();
            if (kineticLaw.isSetTimeUnits()
                && !kineticLaw.isSetTimeUnitsInstance()) {
              log4jLogger.warn("No UnitDefinition matches the timeUnitsID of kineticLaw.");
            }
            if (kineticLaw.isSetSubstanceUnits()
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              return constraint;
            } else if (elementName.equals("reaction")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfReactions)) {
              Reaction reaction = (Reaction) newContextObject;
              model.addReaction(reaction);
              reaction.initDefaults();

              return reaction;
            } else if (elementName.equals("event")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfEvents)
                && model.getLevel() > 1) {
              Event event = (Event) newContextObject;
              model.addEvent(event);
              event.initDefaults();

              return event;
            } else if (elementName.equals("compartmentType")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfCompartmentTypes)
                && (model.getLevel() == 2 && model.getVersion() > 1)) {
              CompartmentType compartmentType = (CompartmentType) newContextObject;
              model.addCompartmentType(compartmentType);

              return compartmentType;
            } else if (elementName.equals("speciesType")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfSpeciesTypes)
                && (model.getLevel() == 2 && model.getVersion() > 1)) {
              SpeciesType speciesType = (SpeciesType) newContextObject;
              model.addSpeciesType(speciesType);

              return speciesType;
            } else {
              log4jLogger.warn("The element " + elementName + " is not recognized");
            }
          } else if (list.getParentSBMLObject() instanceof UnitDefinition) {
            UnitDefinition unitDefinition = (UnitDefinition) list
                .getParentSBMLObject();

            if (elementName.equals("unit")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfUnits)) {
              Unit unit = (Unit) newContextObject;
              unit.initDefaults();
              unitDefinition.addUnit(unit);

              return unit;
            } else {
              log4jLogger.warn("The element " + elementName + " is not recognized");
            }
          } else if (list.getParentSBMLObject() instanceof Reaction) {
            Reaction reaction = (Reaction) list
                .getParentSBMLObject();

            if (elementName.equals("speciesReference")
                && (reaction.getLevel() > 1 || (reaction
                    .getLevel() == 1 && reaction
                    .getVersion() == 2))) {
              SpeciesReference speciesReference = (SpeciesReference) newContextObject;
              speciesReference.initDefaults();

              if (list.getSBaseListType().equals(
                  ListOf.Type.listOfReactants)) {
                reaction.addReactant(speciesReference);

                return speciesReference;
              } else if (list.getSBaseListType().equals(
                  ListOf.Type.listOfProducts)) {
                reaction.addProduct(speciesReference);

                return speciesReference;
              } else {
                log4jLogger.warn("The element " + elementName + " is not recognized");
              }
            } else if (elementName.equals("specieReference")
                && reaction.getLevel() == 1) {
              SpeciesReference speciesReference = (SpeciesReference) newContextObject;
              speciesReference.initDefaults();

              if (list.getSBaseListType().equals(
                  ListOf.Type.listOfReactants)) {
                reaction.addReactant(speciesReference);

                return speciesReference;
              } else if (list.getSBaseListType().equals(
                  ListOf.Type.listOfProducts)) {
                reaction.addProduct(speciesReference);

                return speciesReference;
              } else {
                log4jLogger.warn("The element " + elementName + " is not recognized");
              }
            } 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");
            }
          } else if (list.getParentSBMLObject() instanceof KineticLaw) {
            KineticLaw kineticLaw = (KineticLaw) list
                .getParentSBMLObject();
            // Level 3 : parameter and listOfParameters =>
            // localParameter and listOfLocalParameter
            if (elementName.equals("localParameter")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfLocalParameters)
                && kineticLaw.getLevel() >= 3) {
              LocalParameter localParameter = (LocalParameter) newContextObject;
              kineticLaw.addParameter(localParameter);

              return localParameter;
            } else if (elementName.equals("parameter")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfLocalParameters)
                && kineticLaw.isSetLevel()
                && kineticLaw.getLevel() < 3) {
              LocalParameter localParameter = new LocalParameter(
                  (Parameter) newContextObject);
              kineticLaw.addParameter(localParameter);

              return localParameter;
            } else {
              log4jLogger.warn("The element " + elementName + " is not recognized");
            }
          } else if (list.getParentSBMLObject() instanceof Event) {
            Event event = (Event) list.getParentSBMLObject();

            if (elementName.equals("eventAssignment")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfEventAssignments)
                && event.getLevel() > 1) {
              EventAssignment eventAssignment = (EventAssignment) newContextObject;
              event.addEventAssignment(eventAssignment);

              return eventAssignment;
            } else {
              log4jLogger.warn("The element " + elementName + " is not recognized");
            }
          } else {
            log4jLogger.warn("The element " + elementName + " is not recognized");
          }
        } else if (contextObject instanceof UnitDefinition) {
          UnitDefinition unitDefinition = (UnitDefinition) contextObject;

          if (elementName.equals("listOfUnits")) {
            ListOf<Unit> listOfUnits = (ListOf<Unit>) newContextObject;
            unitDefinition.setListOfUnits(listOfUnits);

            return listOfUnits;
          }
        } else if (contextObject instanceof Event) {
          Event event = (Event) contextObject;

          if (elementName.equals("listOfEventAssignments")) {
            ListOf<EventAssignment> listOfEventAssignments = (ListOf<EventAssignment>) newContextObject;
            event.setListOfEventAssignments(listOfEventAssignments);

            return listOfEventAssignments;
          } else if (elementName.equals("trigger")) {
            Trigger trigger = (Trigger) newContextObject;
            event.setTrigger(trigger);

            return trigger;
          } else if (elementName.equals("delay")) {
            Delay delay = (Delay) newContextObject;
            event.setDelay(delay);

            return delay;
          } else if (elementName.equals("priority")) {
            Priority priority = (Priority) newContextObject;
            event.setPriority(priority);

            return priority;
          } else {
            log4jLogger.warn("The element " + elementName + " is not recognized");
          }
        } else if (contextObject instanceof Reaction) {
          Reaction reaction = (Reaction) contextObject;
          if (elementName.equals("listOfReactants")) {
            ListOf<SpeciesReference> listOfReactants = (ListOf<SpeciesReference>) newContextObject;
            reaction.setListOfReactants(listOfReactants);

            return listOfReactants;
          } else if (elementName.equals("listOfProducts")) {
            ListOf<SpeciesReference> listOfProducts = (ListOf<SpeciesReference>) newContextObject;
            reaction.setListOfProducts(listOfProducts);

            return listOfProducts;
          } else if (elementName.equals("listOfModifiers")
              && reaction.getLevel() > 1) {
            ListOf<ModifierSpeciesReference> listOfModifiers = (ListOf<ModifierSpeciesReference>) newContextObject;
            reaction.setListOfModifiers(listOfModifiers);

            return listOfModifiers;
          } else if (elementName.equals("kineticLaw")) {
            KineticLaw kineticLaw = (KineticLaw) newContextObject;
            reaction.setKineticLaw(kineticLaw);

            return kineticLaw;
          } else {
            log4jLogger.warn("The element " + elementName + " is not recognized");
          }
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        if (unitDefinition.isSetListOfUnits()) {
          listOfElementsToWrite = new ArrayList<Object>();
          listOfElementsToWrite.add(unitDefinition.getListOfUnits());
        }
      } else if (sbase instanceof Reaction) {
        Reaction reaction = (Reaction) sbase;
        listOfElementsToWrite = new ArrayList<Object>();

        if (reaction.isSetListOfReactants()) {
          listOfElementsToWrite.add(reaction.getListOfReactants());
        }
        if (reaction.isSetListOfProducts()) {
          listOfElementsToWrite.add(reaction.getListOfProducts());
        }
        if (reaction.isSetKineticLaw()) {
          listOfElementsToWrite.add(reaction.getKineticLaw());
        }

        if (listOfElementsToWrite.isEmpty()) {
          listOfElementsToWrite = null;
        }
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          setInitialAssignmentSymbol(initialAssignment, model);
        }
      }
      if (model.isSetListOfReactions()) {
        for (int i = 0; i < model.getNumReactions(); i++) {
          Reaction reaction = model.getReaction(i);

          setReactionCompartment(reaction, model);

          if (reaction.isSetListOfReactants()) {
            for (int j = 0; j < reaction.getNumReactants(); j++) {
              SpeciesReference speciesReference = reaction
                  .getReactant(j);

              setSpeciesReferenceSpecies(speciesReference, model);
            }
          }
          if (reaction.isSetListOfProducts()) {
            for (int j = 0; j < reaction.getNumProducts(); j++) {
              SpeciesReference speciesReference = reaction
                  .getProduct(j);

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

              setSpeciesReferenceSpecies(
                  modifierSpeciesReference, model);
            }
          }
          if (reaction.isSetKineticLaw()) {
            KineticLaw kineticLaw = reaction.getKineticLaw();
            if (kineticLaw.isSetListOfParameters()) {
              for (int j = 0; j < kineticLaw.getNumParameters(); j++) {
                LocalParameter parameter = kineticLaw
                    .getParameter(j);
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              return rule;
            } else if (elementName.equals("reaction")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfReactions)) {
              Reaction reaction = (Reaction) newContextObject;
              model.addReaction(reaction);

              return reaction;
            } else {
              // TODO : SBML syntax error, throw an exception?
            }
          } else if (list.getParentSBMLObject() instanceof UnitDefinition) {
            UnitDefinition unitDefinition = (UnitDefinition) list
                .getParentSBMLObject();

            if (elementName.equals("unit")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfUnits)) {
              Unit unit = (Unit) newContextObject;
              unitDefinition.addUnit(unit);

              return unit;
            } else {
              // TODO : SBML syntax error, throw an exception?
            }
          } else if (list.getParentSBMLObject() instanceof Reaction) {
            Reaction reaction = (Reaction) list
                .getParentSBMLObject();

            if (elementName.equals("specieReference")) {
              SpeciesReference speciesReference = (SpeciesReference) newContextObject;

              if (list.getSBaseListType().equals(
                  ListOf.Type.listOfReactants)) {
                reaction.addReactant(speciesReference);

                return speciesReference;
              } else if (list.getSBaseListType().equals(
                  ListOf.Type.listOfProducts)) {
                reaction.addProduct(speciesReference);

                return speciesReference;
              } else {
                // TODO : SBML syntax error, throw an exception?
              }
            } else {
              // TODO : SBML syntax error, throw an exception?
            }
          } else if (list.getParentSBMLObject() instanceof KineticLaw) {
            KineticLaw kineticLaw = (KineticLaw) list
                .getParentSBMLObject();

            if (elementName.equals("parameter")
                && list.getSBaseListType().equals(
                    ListOf.Type.listOfParameters)) {
              LocalParameter localParameter = (LocalParameter) newContextObject;
              kineticLaw.addParameter(localParameter);

              return localParameter;
            } else {
              // TODO : SBML syntax error, throw an exception?
            }
          } else {
            // TODO : SBML syntax error, throw an exception?
          }
        } else if (contextObject instanceof UnitDefinition) {
          UnitDefinition unitDefinition = (UnitDefinition) contextObject;

          if (elementName.equals("listOfUnits")) {
            ListOf<Unit> listOfUnits = (ListOf<Unit>) newContextObject;
            unitDefinition.setListOfUnits(listOfUnits);

            return listOfUnits;
          }
        } else if (contextObject instanceof Reaction) {
          Reaction reaction = (Reaction) contextObject;

          if (elementName.equals("listOfReactants")) {
            ListOf listOfReactants = (ListOf) newContextObject;
            reaction.setListOfReactants(listOfReactants);
            listOfReactants
                .setSBaseListType(ListOf.Type.listOfReactants);

            return listOfReactants;
          } else if (elementName.equals("listOfProducts")) {
            ListOf listOfProducts = (ListOf) newContextObject;
            reaction.setListOfProducts(listOfProducts);
            listOfProducts
                .setSBaseListType(ListOf.Type.listOfProducts);

            return listOfProducts;
          } else if (elementName.equals("kineticLaw")) {
            KineticLaw kineticLaw = (KineticLaw) newContextObject;
            reaction.setKineticLaw(kineticLaw);

            return kineticLaw;
          } else {
            // TODO : SBML syntax error, throw an exception?
          }
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              int i = 0;
              SpeciesReference sr = null;

              while (i <= model.getNumReactions() - 1
                  && sr == null) {
                Reaction reaction = model.getReaction(i);

                if (reaction != null) {
                  sr = reaction.getReactant(variableID);
                  if (sr == null) {
                    sr = reaction.getProduct(variableID);
                  }
                }
              }

              speciesReference = sr;
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              int i = 0;
              SpeciesReference sr = null;

              while (i <= model.getNumReactions() - 1
                  && sr == null) {
                Reaction reaction = model.getReaction(i);

                if (reaction != null) {
                  sr = reaction.getReactant(variableID);
                  if (sr == null) {
                    sr = reaction.getProduct(variableID);
                  }
                }
              }

              speciesReference = sr;
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  • org.sbml.jsbml.test.IdRegistrationTest
  • org.sbml.jsbml.test.MathMLTest
  • org.sbml.jsbml.test.RemoveFromModelTest
  • org.sbml.jsbml.test.RemoveFromParentTest
  • org.sbml.jsbml.test.sbml.TestModel
  • org.sbml.jsbml.test.sbml.TestReaction
  • org.sbml.jsbml.test.sbml.TestReadFromFile1
  • org.sbml.jsbml.test.sbml.TestReadFromFile5
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