- IfThenInteraction - Class in interaction
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Class representing ifThen interactions.
- IfThenInteraction(Relation, Relation) - Constructor for class interaction.IfThenInteraction
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- IfThenInteractionCplex - Class in interaction.cplex
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CPLEX version of the IfTheninteraction.
- IfThenInteractionCplex(Relation, Relation) - Constructor for class interaction.cplex.IfThenInteractionCplex
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- init - Variable in class analyses.ReacAnalysis
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Initial value
- init - Variable in class analyses.result.ReacAnalysisResult
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Parameters of the varying variable.
- init - Variable in class analyses.result.TwoReacsAnalysisResult
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Parameters of the varying variables.
- init - Variable in class analyses.TwoReacsAnalysis
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Initial values.
- init - Variable in class applications.FlexfluxReac
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- init - Variable in class applications.FlexfluxTwoReacs
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- init() - Method in class general.CplexBind
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Initialization of CPLEX parameters and of the right factories.
- init() - Method in class general.GLPKBind
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Initialization of GLPK parameters and of the right factories.
- init(String[]) - Method in class gui.ArgumentComponent
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- init(String) - Method in class gui.ArgumentComponent
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- init(String[]) - Method in class gui.BooleanComponent
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- init(String) - Method in class gui.BooleanComponent
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- init(String[]) - Method in class gui.ChoiceComponent
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- init(String) - Method in class gui.ChoiceComponent
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- init(String[]) - Method in class gui.FileComponent
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- init(String) - Method in class gui.FileComponent
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- init(String[]) - Method in class gui.StringComponent
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- init(String) - Method in class gui.StringComponent
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- init2 - Variable in class analyses.result.TwoReacsAnalysisResult
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Parameters of the varying variables.
- init2 - Variable in class analyses.TwoReacsAnalysis
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Initial values.
- init2 - Variable in class applications.FlexfluxTwoReacs
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- initX - Variable in class analyses.RFBAAnalysis
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- insertUpdate(DocumentEvent) - Method in class analyses.result.CompFVAResult.MyDocumentListener
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- insertUpdate(DocumentEvent) - Method in class analyses.result.FVAResult.MyDocumentListener
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- intEntities - Variable in class interaction.InteractionNetwork
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List of entities with interger values.
- interaction - package interaction
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- Interaction - Class in interaction
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Interaction is the base class to all interactions.
- Interaction(Relation, Relation) - Constructor for class interaction.Interaction
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- interaction.cplex - package interaction.cplex
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- interactionInSolver - Variable in class general.Bind
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Decides if the interactions will be treated in ther solver or before.
- InteractionNetwork - Class in interaction
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Class containing all entities and all interactions of the problem.
- InteractionNetwork() - Constructor for class interaction.InteractionNetwork
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- interactionsEntitiesCause - Variable in class general.Bind
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- interactionsEntitiesConsequence - Variable in class general.Bind
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To handle time dependent interactions. the Relation is true if the
bioEntity is > 0 . double[0] corresponds to how long it takes for the
interactions to become active and double[1] corresponds to how long it
stays active.
- interactionsToCheck - Variable in class interaction.InteractionNetwork
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- interactionsToSolverConstraints(List<Interaction>) - Method in class general.Bind
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Transforms problem interactions into solver constraints.
- interactionsToSolverConstraints(List<Interaction>) - Method in class general.CplexBind
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- interactionsToSolverConstraints(List<Interaction>) - Method in class general.GLPKBind
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Not used.
- intFile - Variable in class applications.FlexfluxCompFVA
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- intFile - Variable in class applications.FlexfluxDR
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- intFile - Variable in class applications.FlexfluxFBA
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- intFile - Variable in class applications.FlexfluxFVA
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- intFile - Variable in class applications.FlexfluxKO
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- intFile - Variable in class applications.FlexfluxPareto
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- intFile - Variable in class applications.FlexfluxReac
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- intFile - Variable in class applications.FlexfluxRFBA
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- intFile - Variable in class applications.FlexfluxTwoReacs
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- intNet - Variable in class general.Bind
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The interaction network of the problem.
- intNet - Variable in class thread.ThreadFactory
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Bind interaction network to copy.
- intToConstraint - Variable in class general.Bind
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Links an interactions to a list of constraints to check if the
interaction is true.
- InversedRelation - Class in interaction
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Class representing an inversed Relation.
- InversedRelation(Relation) - Constructor for class interaction.InversedRelation
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- InversedRelationCplex - Class in interaction.cplex
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CPLEX version of an inversed relation.
- InversedRelationCplex(Relation) - Constructor for class interaction.cplex.InversedRelationCplex
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- Irrev1 - Static variable in class general.Vars
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- Irrev2 - Static variable in class general.Vars
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- isInteractionInSolver() - Method in class general.Bind
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- isLastSolveEmpty() - Method in class general.Bind
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- isMIP() - Method in class general.Bind
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- isMIP() - Method in class general.CplexBind
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- isMIP() - Method in class general.GLPKBind
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- isNotTransformedUnique() - Method in class interaction.InteractionNetwork
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- isProbabilityInteraction() - Method in class interaction.Interaction
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- isProbabilityRelation() - Method in class interaction.Relation
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- isTrue(Map<BioEntity, Constraint>) - Method in class interaction.And
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- isTrue(Map<BioEntity, Constraint>) - Method in class interaction.InversedRelation
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Return the opposite of the isTrue function of rel.
- isTrue(Map<BioEntity, Constraint>) - Method in class interaction.Or
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- isTrue(Map<BioEntity, Constraint>) - Method in class interaction.Relation
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- isTrue(Map<BioEntity, Constraint>) - Method in class interaction.Unique
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- isTrue(Constraint, double) - Method in class operation.Operation
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Checks if the combination of the constraint, the operation and the value
is true or not.
- isTrue(Constraint, double) - Method in class operation.OperationEq
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- isTrue(Constraint, double) - Method in class operation.OperationGe
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- isTrue(Constraint, double) - Method in class operation.OperationGt
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- isTrue(Constraint, double) - Method in class operation.OperationLe
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- isTrue(Constraint, double) - Method in class operation.OperationLt
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- isTrue(Constraint, double) - Method in class operation.OperationNotEq
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- iterations - Variable in class analyses.RFBAAnalysis
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Number of iterations.
- iterations - Variable in class applications.FlexfluxRFBA
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