Package de.uni_halle.informatik.biodata.mp.polishing.ext.fbc

Class StrictnessPredicate

java.lang.Object
de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate
All Implemented Interfaces:
Predicate<org.sbml.jsbml.Model>
public class StrictnessPredicate extends Object implements Predicate<org.sbml.jsbml.Model>
From ...:

The following restrictions are in effect if an “fbc” model object has a value of 'true' for the attribute 'strict' on Model: 1) Each Reaction in a Model must define values for the attributes 'lowerFluxBound' and 'upperFluxBound', with each attribute pointing to a valid Parameter object defined in the current Model. (implemented via reactionHasValidBounds(org.sbml.jsbml.Reaction)) 2) Each Parameter object referred to by the Reaction attributes 'lowerFluxBound' and 'upperFluxBound' must have its 'constant' attribute set to the value 'true' and its 'value' attribute set to a value of type double. This value may not be 'NaN'. (implemented via reactionHasValidBounds(org.sbml.jsbml.Reaction)) 3) SpeciesReference objects in Reaction objects must have their 'stoichiometry' attribute set to a double value that is not 'NaN', nor '-INF', nor 'INF'. In addition, the value of their 'constant' attribute must be set to 'true'. (implemented via reactionSpeciesReferencesHaveValidAttributes(org.sbml.jsbml.Reaction)) 4) InitialAssignment objects may not target the Parameter objects referenced by the Reaction attributes 'lowerFluxBound' and 'upperFluxBound', nor any SpeciesReference objects. (implemented via initialAssignmentDoesNotReferenceBoundParameters(org.sbml.jsbml.InitialAssignment) and initialAssignmentDoesNotReferenceSpeciesReferences(org.sbml.jsbml.InitialAssignment)) 5) All defined FluxObjective objects must have their coefficient attribute set to a double value that is not 'NaN', nor '-INF', nor 'INF'. (implemented via fluxObjectiveHasValidCoefficients(org.sbml.jsbml.ext.fbc.FluxObjective)) 6) A Reaction 'lowerFluxBound' attribute may not point to a Parameter object that has a value of 'INF'. (implemented via reactionHasValidBounds(org.sbml.jsbml.Reaction)) 7) A Reaction 'upperFluxBound' attribute may not point to a Parameter object that has a value of '-INF'. (implemented via reactionHasValidBounds(org.sbml.jsbml.Reaction)) 8) For all Reaction objects, the value of a 'lowerFluxBound' attribute must be less than or equal to the value of the 'upperFluxBound' attribute. (implemented via reactionHasValidBounds(org.sbml.jsbml.Reaction))

  • Constructor Details

    • StrictnessPredicate

      public StrictnessPredicate()

  • Method Details

    • test

      public boolean test(org.sbml.jsbml.Model model)
      Specified by:
      test in interface Predicate<org.sbml.jsbml.Model>

    • reactionHasValidBounds

      public boolean reactionHasValidBounds(org.sbml.jsbml.Reaction r)
      1) Each Reaction in a Model must define values for the attributes 'lowerFluxBound' and 'upperFluxBound', with each attribute pointing to a valid Parameter object defined in the current Model. 2) Each Parameter object referred to by the Reaction attributes 'lowerFluxBound' and 'upperFluxBound' must have its 'constant' attribute set to the value 'true' and its 'value' attribute set to a value of type double. This value may not be 'NaN'. 6) A Reaction 'lowerFluxBound' attribute may not point to a Parameter object that has a value of 'INF'. 7) A Reaction 'upperFluxBound' attribute may not point to a Parameter object that has a value of '-INF'. 8) For all Reaction objects, the value of a 'lowerFluxBound' attribute must be less than or equal to the value of the 'upperFluxBound' attribute.

    • isBoundSet

      public boolean isBoundSet(org.sbml.jsbml.Parameter bound)

    • reactionSpeciesReferencesHaveValidAttributes

      public boolean reactionSpeciesReferencesHaveValidAttributes(org.sbml.jsbml.Reaction r)
      see strictnessOfSpeciesReferences(org.sbml.jsbml.ListOf<org.sbml.jsbml.SpeciesReference>)

    • strictnessOfSpeciesReferences

      public boolean strictnessOfSpeciesReferences(org.sbml.jsbml.ListOf<org.sbml.jsbml.SpeciesReference> listOfSpeciesReference)
      3) SpeciesReference objects in Reaction objects must have their 'stoichiometry' attribute set to a double value that is not 'NaN', nor '-INF', nor 'INF'. In addition, the value of their 'constant' attribute must be set to 'true'.

    • initialAssignmentDoesNotReferenceBoundParameters

      public boolean initialAssignmentDoesNotReferenceBoundParameters(org.sbml.jsbml.InitialAssignment ia)
      4) InitialAssignment objects may not target the Parameter objects referenced by the Reaction attributes 'lowerFluxBound' and 'upperFluxBound', nor any SpeciesReference objects.

    • initialAssignmentDoesNotReferenceSpeciesReferences

      public boolean initialAssignmentDoesNotReferenceSpeciesReferences(org.sbml.jsbml.InitialAssignment ia)
      4) InitialAssignment objects may not target the Parameter objects referenced by the Reaction attributes 'lowerFluxBound' and 'upperFluxBound', nor any SpeciesReference objects.

    • fluxObjectiveHasValidCoefficients

      public Boolean fluxObjectiveHasValidCoefficients(org.sbml.jsbml.ext.fbc.FluxObjective fo)
      5) All defined FluxObjective objects must have their coefficient attribute set to a double value that is not 'NaN', nor '-INF', nor 'INF'.