- savePng(Plot3DPanel, File) - Method in class analyses.result.TwoReacsAnalysisResult
-
Save the plot as a PBG image file.
- sbmlFile - Variable in class applications.FlexfluxCompFVA
-
- sbmlFile - Variable in class applications.FlexfluxDR
-
- sbmlFile - Variable in class applications.FlexfluxFBA
-
- sbmlFile - Variable in class applications.FlexfluxFVA
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- sbmlFile - Variable in class applications.FlexfluxKO
-
- sbmlFile - Variable in class applications.FlexfluxPareto
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- sbmlFile - Variable in class applications.FlexfluxReac
-
- sbmlFile - Variable in class applications.FlexfluxRFBA
-
- sbmlFile - Variable in class applications.FlexfluxTwoReacs
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- score - Variable in class analyses.result.ReacAnalysisResult
-
- score - Variable in class analyses.result.TwoReacsAnalysisResult
-
- searchField - Variable in class analyses.result.CompFVAResult
-
Field to search for entities in the plot.
- searchField - Variable in class analyses.result.FBAResult
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Field to search for entities in the plot.
- searchField - Variable in class analyses.result.FVAResult
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Field to search for entities in the plot.
- searchField - Variable in class analyses.result.KOResult
-
Field to search for entities in the plot.
- setBioNet(BioNetwork) - Method in class thread.ThreadFactory
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- setComparator(PhenotypicPhaseComparator) - Method in class analyses.result.ReacAnalysisResult
-
- setComparator(PhenotypicPhaseComparator) - Method in class analyses.result.TwoReacsAnalysisResult
-
- setConstraintsToAdd(Map<Constraint, Boolean>) - Method in class thread.ResolveThread
-
- setLb(double) - Method in class general.Constraint
-
- setLoadObjective(boolean) - Method in class general.Bind
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- setMax(BioEntity, double) - Method in class analyses.result.FVAResult
-
Set the maximum value of an entity.
- setMin(BioEntity, double) - Method in class analyses.result.FVAResult
-
Set the minimum value of an entity.
- setMIPStart() - Method in class general.CplexBind
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- setNetwork(BioNetwork, boolean) - Method in class general.Bind
-
Sets the problem's network and adds constraints and interactions included
in it.
- setObjective(Objective) - Method in class general.Bind
-
Sets the objective.
- setObjSense(boolean) - Method in class general.Bind
-
Sets the sense of the objective function.
- setObjSense(boolean) - Method in class general.CplexBind
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- setObjSense(boolean) - Method in class general.GLPKBind
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- setObjValue(double) - Method in class analyses.result.FBAResult
-
- setOverWritesBounds(boolean) - Method in class general.Constraint
-
- setProbabilityRelation(boolean) - Method in class interaction.Relation
-
- setReactionsBounds() - Method in class general.Bind
-
Sets the bounds of reaction entities from the bioNetwork values.
- setRightEntityType(BioEntity, boolean, boolean) - Method in class general.Bind
-
Changes the type of an entity to a new one.
- setShadowPriceGroups(Map<Double, List<Double>>) - Method in class analyses.result.ReacAnalysisResult
-
Orders the phenotype phases.
- setShadowPriceGroups(Map<Double, List<double[]>>) - Method in class analyses.result.TwoReacsAnalysisResult
-
Orders the phenotype phases.
- setShadowPriceGroups() - Method in class thread.ThreadReac
-
- setShadowPriceGroups() - Method in class thread.ThreadTwoReacs
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- setUb(double) - Method in class general.Constraint
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- shadowPriceGroups - Variable in class analyses.result.ReacAnalysisResult
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phenotype phases sorted by shadow-price value.
- shadowPriceGroups - Variable in class analyses.result.TwoReacsAnalysisResult
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phenotype phases sorted by shadow-price value.
- shadowPriceGroups - Variable in class analyses.TwoReacsAnalysis
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phenotype phases sorted by shadow-price value.
- shadowPriceGroups - Static variable in class thread.ThreadReac
-
Groups of phenotype phases.
- shadowPriceGroups - Static variable in class thread.ThreadTwoReacs
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Groups of phenotype phases.
- simpleConstraints - Variable in class general.Bind
-
Contains the constraints of just one entity and with coeff = 1, it make
it easier to get and change them.
- simpleConstraints - Variable in class thread.ThreadFactory
-
Bind simple constraints to copy.
- solver - Variable in class applications.FlexfluxCompFVA
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- solver - Variable in class applications.FlexfluxDR
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- solver - Variable in class applications.FlexfluxFBA
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- solver - Variable in class applications.FlexfluxFVA
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- solver - Variable in class applications.FlexfluxKO
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- solver - Variable in class applications.FlexfluxPareto
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- solver - Variable in class applications.FlexfluxReac
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- solver - Variable in class applications.FlexfluxRFBA
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- solver - Variable in class applications.FlexfluxTwoReacs
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- solverPrepared - Variable in class general.Bind
-
If false the fba cannot strat.
- solvers - Variable in class gui.MainFrame
-
- solverSimpleConstraints - Variable in class general.Bind
-
The solver constraint objcet corresponding to an entity.
- sorter - Variable in class analyses.result.CompFVAResult
-
- sorter - Variable in class analyses.result.FVAResult
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- steadyStateConstraints - Variable in class general.Bind
-
Contains all the constraints caused by the steady state assumption.
- StringComponent - Class in gui
-
- StringComponent(String) - Constructor for class gui.StringComponent
-