- main(String[]) - Static method in class applications.FlexfluxCompFVA
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- main(String[]) - Static method in class applications.FlexfluxDR
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- main(String[]) - Static method in class applications.FlexfluxFBA
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- main(String[]) - Static method in class applications.FlexfluxFVA
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- main(String[]) - Static method in class applications.FlexfluxKO
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- main(String[]) - Static method in class applications.FlexfluxPareto
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- main(String[]) - Static method in class applications.FlexfluxReac
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- main(String[]) - Static method in class applications.FlexfluxRFBA
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- main(String[]) - Static method in class applications.FlexfluxTest
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- main(String[]) - Static method in class applications.FlexfluxTwoReacs
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- main(String[]) - Static method in class applications.gui.GraphicalFlexflux
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- MainFrame - Class in gui
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FlexFlux GUI frame
- MainFrame(List<String>, List<Class>) - Constructor for class gui.MainFrame
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- makeAnd() - Method in class interaction.cplex.RelationFactoryCPLEX
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- makeAnd() - Method in class interaction.RelationFactory
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- makeConstraint(BioEntity, double) - Method in class operation.Operation
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Make constraint from an entity and a value.
- makeConstraint(BioEntity, double) - Method in class operation.OperationEq
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- makeConstraint(BioEntity, double) - Method in class operation.OperationGe
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- makeConstraint(BioEntity, double) - Method in class operation.OperationGt
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- makeConstraint(BioEntity, double) - Method in class operation.OperationLe
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- makeConstraint(BioEntity, double) - Method in class operation.OperationLt
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- makeConstraint(BioEntity, double) - Method in class operation.OperationNotEq
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- makeConstraints() - Method in class interaction.And
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- makeConstraints() - Method in class interaction.InversedRelation
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- makeConstraints() - Method in class interaction.Or
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- makeConstraints() - Method in class interaction.Relation
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Creates the constraints corresponding to the relation.
- makeConstraints() - Method in class interaction.Unique
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- makeConstraints() - Method in class interaction.UniqueProbability
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- makeEq() - Method in class operation.OperationFactory
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- makeEq() - Method in class operation.OperationFactoryCPLEX
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- makeEqInteraction(Relation, Relation) - Method in class interaction.cplex.RelationFactoryCPLEX
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- makeEqInteraction(Relation, Relation) - Method in class interaction.RelationFactory
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- makeFormulaFromString(String) - Method in class general.Bind
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Creates an equation from a string.
- makeFVAThread(boolean, Queue<BioEntity>, Queue<BioEntity>, FVAResult) - Method in class thread.ThreadFactory
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Makes a thread for an FVA analysis.
- makeFVAThread(boolean, Queue<BioEntity>, Queue<BioEntity>, FVAResult) - Method in class thread.ThreadFactoryCPLEX
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- makeFVAThread(boolean, Queue<BioEntity>, Queue<BioEntity>, FVAResult) - Method in class thread.ThreadFactoryGLPK
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- makeGe() - Method in class operation.OperationFactory
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- makeGe() - Method in class operation.OperationFactoryCPLEX
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- makeGt() - Method in class operation.OperationFactory
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- makeGt() - Method in class operation.OperationFactoryCPLEX
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- makeIfThenInteraction(Relation, Relation) - Method in class interaction.cplex.RelationFactoryCPLEX
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- makeIfThenInteraction(Relation, Relation) - Method in class interaction.RelationFactory
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- makeInteraction(Bind) - Method in class interaction.cplex.EqInteractionCplex
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- makeInteraction(Bind) - Method in class interaction.cplex.IfThenInteractionCplex
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- makeInteraction(Bind) - Method in class interaction.EqInteraction
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Only used when interactions in solver.
- makeInteraction(Bind) - Method in class interaction.IfThenInteraction
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Only used when interactions in solver.
- makeInteraction(Bind) - Method in class interaction.Interaction
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Creates the interaction.
- makeInversedRelation(Relation) - Method in class interaction.cplex.RelationFactoryCPLEX
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- makeInversedRelation(Relation) - Method in class interaction.RelationFactory
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- makeKOThread(boolean, Queue<BioEntity>, KOResult, Objective) - Method in class thread.ThreadFactory
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Makes a thread for a KO analysis.
- makeKOThread(boolean, Queue<BioEntity>, KOResult, Objective) - Method in class thread.ThreadFactoryCPLEX
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- makeKOThread(boolean, Queue<BioEntity>, KOResult, Objective) - Method in class thread.ThreadFactoryGLPK
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- makeLe() - Method in class operation.OperationFactory
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- makeLe() - Method in class operation.OperationFactoryCPLEX
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- makeLt() - Method in class operation.OperationFactory
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- makeLt() - Method in class operation.OperationFactoryCPLEX
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- makeNotEq() - Method in class operation.OperationFactory
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- makeNotEq() - Method in class operation.OperationFactoryCPLEX
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- makeObjectiveFromString(String, boolean, String) - Method in class general.Bind
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* creates an objective from a string.
- makeObjsPairs() - Method in class analyses.ParetoAnalysis
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- makeObjsTriplets() - Method in class analyses.ParetoAnalysis
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- makeOperation(IloNumExpr, double) - Method in interface operation.OperationCPLEX
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Creates a CPLEX constraint corresponding to a entity and a value.
- makeOperation(IloNumExpr, double) - Method in class operation.OperationEqCPLEX
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- makeOperation(IloNumExpr, double) - Method in class operation.OperationGeCPLEX
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- makeOperation(IloNumExpr, double) - Method in class operation.OperationGtCPLEX
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- makeOperation(IloNumExpr, double) - Method in class operation.OperationLeCPLEX
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- makeOperation(IloNumExpr, double) - Method in class operation.OperationLtCPLEX
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- makeOperation(IloNumVar, double) - Method in class operation.OperationNotEq
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- makeOperation(IloNumExpr, double) - Method in class operation.OperationNotEqCPLEX
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- makeOperationFromString(String) - Method in class operation.OperationFactory
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Create the right type of Operation given a string.
- makeOr() - Method in class interaction.cplex.RelationFactoryCPLEX
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- makeOr() - Method in class interaction.RelationFactory
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- makeReacThread(boolean, Queue<Double>, Map<BioEntity, Double>, ReacAnalysisResult, Objective) - Method in class thread.ThreadFactory
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Makes a thread for an analysis with a varying variable.
- makeReacThread(boolean, Queue<Double>, Map<BioEntity, Double>, ReacAnalysisResult, Objective) - Method in class thread.ThreadFactoryCPLEX
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- makeReacThread(boolean, Queue<Double>, Map<BioEntity, Double>, ReacAnalysisResult, Objective) - Method in class thread.ThreadFactoryGLPK
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- makeRelationFromString(String, int) - Method in class general.Bind
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Creates a Relation from a string.
- makeSolverConstraint(Constraint, List<Object>, Map<String, double[]>) - Method in class general.Bind
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Creates a constraint for the solver.
- makeSolverConstraint(Constraint, List<Object>, Map<String, double[]>) - Method in class general.CplexBind
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- makeSolverConstraint(Constraint, List<Object>, Map<String, double[]>) - Method in class general.GLPKBind
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- makeSolverObjective() - Method in class general.Bind
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Transforms the porblem's objective into a solver objective.
- makeSolverObjective() - Method in class general.CplexBind
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- makeSolverObjective() - Method in class general.GLPKBind
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- makeSteadyStateConstraints() - Method in class general.Bind
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Adds steady-state constraints to the problem from the metabolic network.
- makeTwoReacsThread(boolean, Queue<double[]>, TwoReacsAnalysisResult, Map<BioEntity, Double>, Map<BioEntity, Double>, Objective) - Method in class thread.ThreadFactory
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Makes a thread for an analysis with two varying variables.
- makeTwoReacsThread(boolean, Queue<double[]>, TwoReacsAnalysisResult, Map<BioEntity, Double>, Map<BioEntity, Double>, Objective) - Method in class thread.ThreadFactoryCPLEX
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- makeTwoReacsThread(boolean, Queue<double[]>, TwoReacsAnalysisResult, Map<BioEntity, Double>, Map<BioEntity, Double>, Objective) - Method in class thread.ThreadFactoryGLPK
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- makeUnique(BioEntity, Operation, double) - Method in class interaction.cplex.RelationFactoryCPLEX
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- makeUnique(BioEntity, Operation, double) - Method in class interaction.RelationFactory
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- makeUniqueFromCondition(String, int) - Method in class general.Bind
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Creates a Unique from a string.
- map - Variable in class analyses.result.CompFVAResult
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Map containing each entity and the results ofr both FVA's.
- map - Variable in class analyses.result.FVAResult
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Map containig all result values.
- map - Variable in class analyses.result.KOResult
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Map containing the result for each knocked out entity.
- mapEntities - Variable in class analyses.FVAAnalysis
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Entities to run the FVA analysis on.
- maxField - Variable in class analyses.result.CompFVAResult
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Field to search for entities in the plot.
- maxField - Variable in class analyses.result.FVAResult
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Field to search for entities in the plot.
- maximize - Variable in class general.Objective
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If true, it maximizes the function, if false it minimizes.
- maxThread - Static variable in class general.Vars
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Maximum number of threads created.
- message - Variable in class applications.FlexfluxCompFVA
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- message - Variable in class applications.FlexfluxDR
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- message - Variable in class applications.FlexfluxFBA
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- message - Variable in class applications.FlexfluxFVA
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- message - Variable in class applications.FlexfluxKO
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- message - Variable in class applications.FlexfluxPareto
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- message - Variable in class applications.FlexfluxReac
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- message - Variable in class applications.FlexfluxRFBA
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- message - Variable in class applications.FlexfluxTest
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- message - Variable in class applications.FlexfluxTwoReacs
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- minField - Variable in class analyses.result.CompFVAResult
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Field to search for entities in the plot.
- minField - Variable in class analyses.result.FVAResult
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Field to search for entities in the plot.
- minGrpsSize - Variable in class analyses.ReacAnalysis
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Minimal group size to consider it is a phenotype phase.
- minGrpsSize - Variable in class analyses.result.ReacAnalysisResult
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Minimal group size to consider it is a phenotype phase.
- minGrpsSize - Variable in class analyses.result.TwoReacsAnalysisResult
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Minimal group size to consider it is a phenotype phase.
- minGrpsSize - Variable in class analyses.TwoReacsAnalysis
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Minimal group size to consider it is a phenotype phase.
- minValue - Variable in class analyses.DRAnalysis
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Maximal flux value to consider a reaction dead.
- mipParm - Variable in class general.GLPKBind
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- mode - Variable in class analyses.KOAnalysis
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0 : the KO is performed on reactions. 1 : the KO is performed on genes.
- mode - Variable in class applications.FlexfluxDR
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- mode - Variable in class applications.FlexfluxKO
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- model - Variable in class general.CplexBind
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- model - Variable in class general.GLPKBind
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- MyTableModel - Class in analyses.result
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Table model used for plots.
- MyTableModel(Object[][], Object[]) - Constructor for class analyses.result.MyTableModel
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