- FBA(boolean, boolean) - Method in class general.Bind
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Checks the interactions if it has to, and performs the FBA.
- FBAAnalysis - Class in analyses
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Class to run a simple FBA analysis.
- FBAAnalysis(Bind) - Constructor for class analyses.FBAAnalysis
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- FBAResult - Class in analyses.result
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Class representing the result of a simple FBA analysis.
- FBAResult(Bind) - Constructor for class analyses.result.FBAResult
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- FBAWithConstraints(List<Constraint>, boolean, boolean) - Method in class general.Bind
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Takes constraints, checks interactions for those constraints, and
performs FBA.
- fc - Variable in class gui.FileComponent
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- FileComponent - Class in gui
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- FileComponent(String) - Constructor for class gui.FileComponent
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- filePath - Variable in class analyses.ParetoAnalysis
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Path to the file containing the objectives and experimental values
- fillExecList() - Method in class gui.MainFrame
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- findClasses(File, String) - Static method in class applications.gui.GraphicalFlexflux
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Recursive method used to find all classes in a given directory and
subdirs.
- flag - Variable in class general.DoubleResult
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Flag giving information about the solve. 0 means an optimal solution was
found, 1 means the problem was unfeasible.
- FlexfluxCompFVA - Class in applications
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Compares the results of two FVA analyses given a metabolic network, an
objective function and two different set of constraints.
- FlexfluxCompFVA() - Constructor for class applications.FlexfluxCompFVA
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- FlexfluxDR - Class in applications
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Finds dead reactions in a given metabolic network.
- FlexfluxDR() - Constructor for class applications.FlexfluxDR
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- FlexfluxFBA - Class in applications
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Computes an FBA analysis given a metabolic network, an objective function and constraints.
- FlexfluxFBA() - Constructor for class applications.FlexfluxFBA
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- FlexfluxFVA - Class in applications
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Computes an FVA analysis given a metabolic network, an objective function and
constraints.
- FlexfluxFVA() - Constructor for class applications.FlexfluxFVA
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- FlexfluxKO - Class in applications
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Computes an KO analysis given a metabolic network, an objective function and
constraints.
- FlexfluxKO() - Constructor for class applications.FlexfluxKO
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- FlexfluxPareto - Class in applications
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The goal of this analysis is to determine what objective (or set of
objectives) an organism is optimizing.
- FlexfluxPareto() - Constructor for class applications.FlexfluxPareto
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- FlexfluxReac - Class in applications
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Computes different FBA analysis given a metabolic network, an objective
function and constraints, by making a reaction flux change.
- FlexfluxReac() - Constructor for class applications.FlexfluxReac
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- FlexfluxRFBA - Class in applications
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Computes a time dependent analysis given a metabolic network, an objective
function and constraints.
- FlexfluxRFBA() - Constructor for class applications.FlexfluxRFBA
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- FlexfluxTest - Class in applications
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Tests the solvers
- FlexfluxTest() - Constructor for class applications.FlexfluxTest
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- FlexfluxTwoReacs - Class in applications
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Computes different FBA analysis given a metabolic network, an objective
function and constraints, by making two reactions fluxes change.
- FlexfluxTwoReacs() - Constructor for class applications.FlexfluxTwoReacs
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- fluxesQueue - Variable in class thread.ThreadReac
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Contains all fluxes to treat.
- fluxesQueue - Variable in class thread.ThreadTwoReacs
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Contains all fluxes to treat.
- FluxSumKeyWord - Static variable in class general.Vars
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Keyword for the sum of all fluxes.
- fluxValues - Variable in class analyses.result.ReacAnalysisResult
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All flux values.
- fva - Variable in class analyses.ReacAnalysis
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Determines if FVA's must be performed on each phenotype phase.
- fva - Variable in class analyses.TwoReacsAnalysis
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Determines if FVA's must be performed on each phenotype phase.
- FVAAnalysis - Class in analyses
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Class to run an FVA analysis.
- FVAAnalysis(Bind, Map<String, BioEntity>, List<Constraint>) - Constructor for class analyses.FVAAnalysis
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- FVAResult - Class in analyses.result
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Class representing the result of an FVA analysis.
- FVAResult(double) - Constructor for class analyses.result.FVAResult
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- FVAResult.MyDocumentListener - Class in analyses.result
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- FVAResult.MyDocumentListener() - Constructor for class analyses.result.FVAResult.MyDocumentListener
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