Uses of Class
general.Objective

Packages that use Objective

Package	Description
analyses
analyses.result
general
thread

Uses of Objective in analyses

Fields in analyses with type parameters of type Objective

Modifier and Type	Field and Description
(package private) java.util.List<java.util.Map<Objective,java.lang.Double>>	ParetoAnalysis.experimentalValues List containing all experimental values for each objective.
(package private) java.util.List<Objective>	ParetoAnalysis.objectives List of objectives.
(package private) java.util.Map<Objective,double[]>	ParetoAnalysis.objectivesBounds key : an objective, value : its lower and upper bounds

Uses of Objective in analyses.result

Fields in analyses.result with type parameters of type Objective

Modifier and Type	Field and Description
(package private) java.util.Map<Objective,java.util.List<java.lang.Double>>	ParetoAnalysisResult.oneDResults 1D results for all the objectives.

Constructor parameters in analyses.result with type arguments of type Objective

Constructor and Description
ParetoAnalysisResult(java.util.Map<Objective,java.util.List<java.lang.Double>> oneDResults, java.util.Map<ReacAnalysisResult,java.lang.Double> twoDResults, java.util.Map<TwoReacsAnalysisResult,java.lang.Double> threeDResults)

Uses of Objective in general

Fields in general declared as Objective

Modifier and Type	Field and Description
protected Objective	Bind.obj Objective of the problem.

Fields in general with type parameters of type Objective

Modifier and Type	Field and Description
protected java.util.List<Objective>	Bind.constraintObjectives List used when several objectives are given in the condition file.

Methods in general that return Objective

Modifier and Type	Method and Description
Objective	Bind.getObjective()
Objective	Bind.makeObjectiveFromString(java.lang.String expr, boolean maximize, java.lang.String name) * creates an objective from a string.

Methods in general with parameters of type Objective

Modifier and Type	Method and Description
void	Bind.setObjective(Objective obj) Sets the objective.

Uses of Objective in thread

Methods in thread with parameters of type Objective

Modifier and Type	Method and Description
ThreadKO	ThreadFactoryCPLEX.makeKOThread(boolean interactionInSolver, java.util.Queue<parsebionet.biodata.BioEntity> entities, KOResult result, Objective obj)
ThreadKO	ThreadFactoryGLPK.makeKOThread(boolean interactionInSolver, java.util.Queue<parsebionet.biodata.BioEntity> entities, KOResult result, Objective obj)
abstract ThreadKO	ThreadFactory.makeKOThread(boolean interactionInSolver, java.util.Queue<parsebionet.biodata.BioEntity> reacsQueue, KOResult koResult, Objective obj) Makes a thread for a KO analysis.
ThreadReac	ThreadFactoryCPLEX.makeReacThread(boolean interactionInSolver, java.util.Queue<java.lang.Double> fluxesQueue, java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities, ReacAnalysisResult result, Objective obj)
ThreadReac	ThreadFactoryGLPK.makeReacThread(boolean interactionInSolver, java.util.Queue<java.lang.Double> fluxesQueue, java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities, ReacAnalysisResult result, Objective obj)
abstract ThreadReac	ThreadFactory.makeReacThread(boolean interactionInSolver, java.util.Queue<java.lang.Double> fluxesQueue, java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities, ReacAnalysisResult result, Objective obj) Makes a thread for an analysis with a varying variable.
ResolveThread	ThreadFactoryCPLEX.makeTwoReacsThread(boolean interactionInSolver, java.util.Queue<double[]> fluxesQueue, TwoReacsAnalysisResult result, java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities1, java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities2, Objective obj)
ResolveThread	ThreadFactoryGLPK.makeTwoReacsThread(boolean interactionInSolver, java.util.Queue<double[]> fluxesQueue, TwoReacsAnalysisResult result, java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities1, java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities2, Objective obj)
abstract ResolveThread	ThreadFactory.makeTwoReacsThread(boolean interactionInSolver, java.util.Queue<double[]> fluxesQueue, TwoReacsAnalysisResult result, java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities1, java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities2, Objective obj) Makes a thread for an analysis with two varying variables.

Constructors in thread with parameters of type Objective

Constructor and Description
ResolveThread(Bind b, Objective obj) Creates a thread with an objective function.
ThreadKO(Bind b, java.util.Queue<parsebionet.biodata.BioEntity> entities, KOResult result, Objective obj)
ThreadReac(Bind b, java.util.Queue<java.lang.Double> fluxesQueue, java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities, ReacAnalysisResult result, Objective obj)
ThreadTwoReacs(Bind b, java.util.Queue<double[]> fluxesQueue, TwoReacsAnalysisResult result, java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities1, java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities2, Objective obj)