- reac - Variable in class applications.FlexfluxReac
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- reac - Variable in class applications.FlexfluxTwoReacs
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- reac2 - Variable in class applications.FlexfluxTwoReacs
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- ReacAnalysis - Class in analyses
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Class to run an analysis with one varying flux value.
- ReacAnalysis(Bind, Map<BioEntity, Double>, String, double, double, double, boolean) - Constructor for class analyses.ReacAnalysis
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- ReacAnalysisResult - Class in analyses.result
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Class representing the result of an analysis with a varying flux.
- ReacAnalysisResult(String, String, List<Double>, Map<Double, Double>, int, double, double, double) - Constructor for class analyses.result.ReacAnalysisResult
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- ReacAnalysisResult.MyRenderer - Class in analyses.result
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Class used to set the right colors and sized for the plot.
- ReacAnalysisResult.MyRenderer(boolean, boolean, Map<Integer, Integer>) - Constructor for class analyses.result.ReacAnalysisResult.MyRenderer
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- reacName - Variable in class analyses.result.ReacAnalysisResult
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- reacName - Variable in class analyses.result.TwoReacsAnalysisResult
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- reacName - Variable in class analyses.TwoReacsAnalysis
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Names of the varying variables.
- reacName2 - Variable in class analyses.result.TwoReacsAnalysisResult
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- reacName2 - Variable in class analyses.TwoReacsAnalysis
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Names of the varying variables.
- reactionToActiveGPR - Variable in class general.Bind
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Link a reaction to it's GPR interaction.
- rel - Variable in class interaction.InversedRelation
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Relation that is the opposite.
- Relation - Class in interaction
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Base class for all relations.
- Relation() - Constructor for class interaction.Relation
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- relationFactory - Variable in class general.Bind
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To create the right relations.
- RelationFactory - Class in interaction
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Class used to create the right type of relation.
- RelationFactory() - Constructor for class interaction.RelationFactory
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- RelationFactoryCPLEX - Class in interaction.cplex
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CPLEX version of the Relation Factory.
- RelationFactoryCPLEX() - Constructor for class interaction.cplex.RelationFactoryCPLEX
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- RelationWithList - Class in interaction
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Class corresponding to relations that can contain other relations.
- RelationWithList() - Constructor for class interaction.RelationWithList
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- removeNotTransformedUnique() - Method in class interaction.InteractionNetwork
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- removeNumEntity(BioEntity) - Method in class interaction.InteractionNetwork
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- removeUpdate(DocumentEvent) - Method in class analyses.result.CompFVAResult.MyDocumentListener
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- removeUpdate(DocumentEvent) - Method in class analyses.result.FVAResult.MyDocumentListener
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- requiredArgsPanel - Variable in class gui.MainFrame
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- requiredOptions - Variable in class gui.MainFrame
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- res1 - Variable in class analyses.CompFVAAnalysis
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First FVA result.
- res2 - Variable in class analyses.CompFVAAnalysis
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Second FVA result.
- ResolveThread - Class in thread
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Superclass of all FlexFlux threads.
- ResolveThread(Bind, Objective) - Constructor for class thread.ResolveThread
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Creates a thread with an objective function.
- ResolveThread(Bind) - Constructor for class thread.ResolveThread
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Creates a thread without an objective function.
- result - Variable in class general.DoubleResult
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Value of the objective function calculated by the solver.
- result - Variable in class thread.ThreadFVA
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The FVA result.
- result - Variable in class thread.ThreadKO
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The KO result.
- result - Variable in class thread.ThreadReac
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The result.
- result - Variable in class thread.ThreadTwoReacs
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The result.
- resultMap - Variable in class analyses.result.RFBAResult
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Map with key : time and value : map of entities and their values
- results - Variable in class analyses.result.TwoReacsAnalysisResult
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Each double[] is a point x,y,z with x : reac1 flux value, y = reac2 flux
value and z = objective value.
- resultTable - Variable in class analyses.result.CompFVAResult
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Table containing all results.
- resultTable - Variable in class analyses.result.FBAResult
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Table with all results.
- resultTable - Variable in class analyses.result.FVAResult
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Table with all results.
- resultTable - Variable in class analyses.result.KOResult
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Table with all results.
- resultValues - Variable in class analyses.result.ReacAnalysisResult
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results.
- RFBAAnalysis - Class in analyses
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Class to run a time dependent FBA.
- RFBAAnalysis(Bind, String, double, double, int, List<String>) - Constructor for class analyses.RFBAAnalysis
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- RFBAResult - Class in analyses.result
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Class representing the result of a time dependent FBA analysis.
- RFBAResult() - Constructor for class analyses.result.RFBAResult
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- round(double) - Static method in class general.Vars
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Rounds number to the decimal precision.
- run() - Method in class gui.GuiRunAnalysis
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- run() - Method in class gui.MainFrame
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- run() - Method in class thread.ThreadFVA
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Starts the thread.
- run() - Method in class thread.ThreadKO
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- run() - Method in class thread.ThreadReac
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- run() - Method in class thread.ThreadTwoReacs
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- runAnalysis() - Method in class analyses.Analysis
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Runs the analysis.
- runAnalysis() - Method in class analyses.CompFVAAnalysis
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- runAnalysis() - Method in class analyses.DRAnalysis
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- runAnalysis() - Method in class analyses.FBAAnalysis
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- runAnalysis() - Method in class analyses.FVAAnalysis
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- runAnalysis() - Method in class analyses.KOAnalysis
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- runAnalysis() - Method in class analyses.ParetoAnalysis
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- runAnalysis() - Method in class analyses.ReacAnalysis
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- runAnalysis() - Method in class analyses.RFBAAnalysis
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- runAnalysis() - Method in class analyses.TwoReacsAnalysis
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- runThrough(Bind) - Method in class interaction.And
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Only used when interaction are in the solver.
- runThrough(Bind) - Method in class interaction.cplex.AndCPLEX
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returns an IloConstraint
- runThrough(Bind) - Method in class interaction.cplex.InversedRelationCplex
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- runThrough(Bind) - Method in class interaction.cplex.OrCPLEX
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Return an IloConstraint
- runThrough(Bind) - Method in class interaction.cplex.UniqueCPLEX
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- runThrough(Bind) - Method in class interaction.InversedRelation
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Only used when interaction are in the solver.
- runThrough(Bind) - Method in class interaction.Or
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Only used when interaction are in the solver.
- runThrough(Bind) - Method in class interaction.Relation
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Used when interactions are in the solver.
- runThrough(Bind) - Method in class interaction.Unique
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Only used when interaction are in the solver.
- runThrough(Bind) - Method in class interaction.UniqueProbability
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