- calculateScore() - Method in class analyses.result.ReacAnalysisResult
-
Adds up all the distance of the experimental values to the calculated
line.
- calculateScore() - Method in class analyses.result.TwoReacsAnalysisResult
-
Adds up all the distance of the experimental values to the calculated
surface.
- centerPanel - Variable in class gui.MainFrame
-
- changedUpdate(DocumentEvent) - Method in class analyses.result.CompFVAResult.MyDocumentListener
-
- changedUpdate(DocumentEvent) - Method in class analyses.result.FVAResult.MyDocumentListener
-
- changeObjVarValue(BioEntity, double) - Method in class general.Bind
-
Changes the coefficient of an entity in the objective.
- changeObjVarValue(BioEntity, double) - Method in class general.CplexBind
-
- changeObjVarValue(BioEntity, double) - Method in class general.GLPKBind
-
- changeVarBounds(String, double[]) - Method in class general.Bind
-
Changes the bounds of an entity.
- changeVarBounds(String, double[]) - Method in class general.CplexBind
-
- changeVarBounds(String, double[]) - Method in class general.GLPKBind
-
- cheat - Static variable in class general.Vars
-
Determines if FlexFlux uses epsilon.
- checkbox - Variable in class gui.BooleanComponent
-
- checkInteractions() - Method in class general.Bind
-
Checks all interactions.
- checkInteractionsForEntities(Map<BioEntity, double[]>) - Method in class general.Bind
-
Returns list of true interactions when setting the given entities to the
given values. double[0]=lb, double[1]=ub.
- choice - Variable in class gui.MainFrame
-
- ChoiceComponent - Class in gui
-
- ChoiceComponent(String) - Constructor for class gui.ChoiceComponent
-
- choices - Variable in class gui.ChoiceComponent
-
- chooserButton - Variable in class gui.FileComponent
-
- clean(double) - Method in class analyses.result.DRResult
-
Removes all reaction that are not considered dead.
- clear() - Method in class general.Bind
-
Clears the solver's model.
- clear() - Method in class general.CplexBind
-
- clear() - Method in class general.GLPKBind
-
- clear() - Method in class interaction.InteractionNetwork
-
Clears all lists.
- clearSolver() - Method in class general.Bind
-
Clears the solver.
- coeffs - Variable in class general.Objective
-
Their coefficients.
- COLORLIST - Static variable in class analyses.result.ReacAnalysisResult
-
- COLORLIST - Variable in class analyses.result.ReacAnalysisResult.MyRenderer
-
- COLORLIST - Static variable in class analyses.result.TwoReacsAnalysisResult
-
- columnNames - Variable in class gui.MainFrame
-
- commandArray - Variable in class gui.GuiRunAnalysis
-
- comparator - Variable in class analyses.result.ReacAnalysisResult
-
Comparator between phenotype phases.
- comparator - Variable in class analyses.result.TwoReacsAnalysisResult
-
Comparator between phenotype phases.
- CompFVAAnalysis - Class in analyses
-
Class to perform a comparison of two FVA's.
- CompFVAAnalysis(Bind, FVAResult, FVAResult) - Constructor for class analyses.CompFVAAnalysis
-
It is constructed with two FVA results and then compares them.
- CompFVAResult - Class in analyses.result
-
Class representing the result of a comparison between two FVA's.
- CompFVAResult(Map<String, double[]>, double, double) - Constructor for class analyses.result.CompFVAResult
-
- CompFVAResult.MyDocumentListener - Class in analyses.result
-
- CompFVAResult.MyDocumentListener() - Constructor for class analyses.result.CompFVAResult.MyDocumentListener
-
- CompFVAResult.MyTableCellRenderer - Class in analyses.result
-
Class to set the right colors foe the two last columns of the FVA
comparison plot.
- CompFVAResult.MyTableCellRenderer() - Constructor for class analyses.result.CompFVAResult.MyTableCellRenderer
-
- condFile - Variable in class applications.FlexfluxCompFVA
-
- condFile - Variable in class applications.FlexfluxDR
-
- condFile - Variable in class applications.FlexfluxFBA
-
- condFile - Variable in class applications.FlexfluxFVA
-
- condFile - Variable in class applications.FlexfluxKO
-
- condFile - Variable in class applications.FlexfluxPareto
-
- condFile - Variable in class applications.FlexfluxReac
-
- condFile - Variable in class applications.FlexfluxRFBA
-
- condFile - Variable in class applications.FlexfluxTwoReacs
-
- condFile2 - Variable in class applications.FlexfluxCompFVA
-
- condition - Variable in class interaction.Interaction
-
condition Relation.
- consequence - Variable in class interaction.Interaction
-
consequence Relation.
- Constraint - Class in general
-
This class represents a constraints for the problem.
- Constraint(Map<BioEntity, Double>, Double, Double) - Constructor for class general.Constraint
-
Creates a constraint;
- Constraint(Map<BioEntity, Double>, Double, boolean) - Constructor for class general.Constraint
-
Creates an inequality constraint.
- constraintObjectives - Variable in class general.Bind
-
List used when several objectives are given in the condition file.
- constraints - Variable in class analyses.FVAAnalysis
-
List of contraints to add before the FVA.
- constraints - Variable in class general.Bind
-
All problem's constraints.
- constraints - Variable in class interaction.Relation
-
Constraints corresponding to the relation.
- constraints - Variable in class thread.ThreadFactory
-
Bind constraints to copy.
- constraintsToAdd - Variable in class thread.ResolveThread
-
Constraints to add.
- constraintsToSolverConstraints() - Method in class general.Bind
-
Transforms all problem's constraints into solver constraints.
- correspGroup - Variable in class analyses.result.ReacAnalysisResult.MyRenderer
-
- cplex - Variable in class general.CplexBind
-
- CplexBind - Class in general
-
CPLEX version of Bind.
- CplexBind(boolean) - Constructor for class general.CplexBind
-
- CplexBind(List<Constraint>, Map<BioEntity, Constraint>, InteractionNetwork, BioNetwork, boolean) - Constructor for class general.CplexBind
-
- cplexObj - Variable in class general.CplexBind
-
- createConstraints() - Method in class interaction.Relation
-
Used when interaction are not in the solver
- createFluxesSummation() - Method in class general.Bind
-