- textField - Variable in class gui.FileComponent
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- textField - Variable in class gui.StringComponent
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- thread - package thread
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- threadFactory - Variable in class general.Bind
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To create the right type of thread.
- ThreadFactory - Class in thread
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Class to create the right type of thread.
- ThreadFactory(List<Constraint>, Map<BioEntity, Constraint>, InteractionNetwork) - Constructor for class thread.ThreadFactory
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- ThreadFactoryCPLEX - Class in thread
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CPLEX version of the Thread factory.
- ThreadFactoryCPLEX(List<Constraint>, Map<BioEntity, Constraint>, InteractionNetwork) - Constructor for class thread.ThreadFactoryCPLEX
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- ThreadFactoryGLPK - Class in thread
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GLPK version of the Thread factory.
- ThreadFactoryGLPK(List<Constraint>, Map<BioEntity, Constraint>, InteractionNetwork) - Constructor for class thread.ThreadFactoryGLPK
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- ThreadFVA - Class in thread
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Thread to perform an FVA analysis.
- ThreadFVA(Bind, Queue<BioEntity>, Queue<BioEntity>, FVAResult) - Constructor for class thread.ThreadFVA
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- ThreadKO - Class in thread
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Thread to perform an FVA analysis.
- ThreadKO(Bind, Queue<BioEntity>, KOResult, Objective) - Constructor for class thread.ThreadKO
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- ThreadReac - Class in thread
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Thread to perform an analysis with a varying flux.
- ThreadReac(Bind, Queue<Double>, Map<BioEntity, Double>, ReacAnalysisResult, Objective) - Constructor for class thread.ThreadReac
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- threads - Variable in class analyses.DRAnalysis
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- threads - Variable in class analyses.FVAAnalysis
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List containing the threads that will maximize and minimize each entity.
- threads - Variable in class analyses.KOAnalysis
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List containing the threads that will knock out each entity.
- threads - Variable in class analyses.ReacAnalysis
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- threads - Variable in class analyses.TwoReacsAnalysis
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- ThreadTwoReacs - Class in thread
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Thread to perform an analysis with two varying fluxes.
- ThreadTwoReacs(Bind, Queue<double[]>, TwoReacsAnalysisResult, Map<BioEntity, Double>, Map<BioEntity, Double>, Objective) - Constructor for class thread.ThreadTwoReacs
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- threeDResults - Variable in class analyses.result.ParetoAnalysisResult
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List of all the 3D results associated to their scores.
- times - Variable in class analyses.result.RFBAResult
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All times.
- timeToString(double) - Method in class analyses.RFBAAnalysis
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- todo - Variable in class thread.ThreadFVA
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Number of entities to treat.
- todo - Variable in class thread.ThreadKO
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Number of entities to treat.
- toPlot - Variable in class analyses.RFBAAnalysis
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List of entities names to plot.
- toString() - Method in class general.Constraint
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- toString() - Method in class general.Objective
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- toString() - Method in class interaction.And
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- toString() - Method in class interaction.EqInteraction
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- toString() - Method in class interaction.IfThenInteraction
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- toString() - Method in class interaction.InversedRelation
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- toString() - Method in class interaction.Or
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- toString() - Method in class interaction.Relation
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- toString() - Method in class interaction.Unique
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- toString() - Method in class interaction.UniqueProbability
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- toString() - Method in class operation.Operation
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- toString() - Method in class operation.OperationEq
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- toString() - Method in class operation.OperationGe
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- toString() - Method in class operation.OperationGt
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- toString() - Method in class operation.OperationLe
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- toString() - Method in class operation.OperationLt
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- toString() - Method in class operation.OperationNotEq
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- transform(double, double, RelationFactory, OperationFactory) - Method in class interaction.UniqueProbability
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Transforms the relation into an AND interaction with two constraints.
- transformation - Variable in class interaction.UniqueProbability
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- twoDResults - Variable in class analyses.result.ParetoAnalysisResult
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List of all the 2D results associated to their scores.
- TwoReacsAnalysis - Class in analyses
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Class to run an analysis with two varying fluxes.
- TwoReacsAnalysis(Bind, String, Map<BioEntity, Double>, Map<BioEntity, Double>, double, double, double, String, double, double, double, boolean) - Constructor for class analyses.TwoReacsAnalysis
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- TwoReacsAnalysisResult - Class in analyses.result
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Class representing the result of an analysis with two varying fluxes.
- TwoReacsAnalysisResult(String, String, String, int, double, double, double, double, double, double) - Constructor for class analyses.result.TwoReacsAnalysisResult
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- TwoReacsAnalysisResult.MyPlot - Class in analyses.result
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Class to create a personalized grid plot.
- TwoReacsAnalysisResult.MyPlot(String, Color, double[], double[], double[][]) - Constructor for class analyses.result.TwoReacsAnalysisResult.MyPlot
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