Uses of Class
general.Bind

Packages that use Bind

Package	Description
analyses
analyses.result
general
interaction
interaction.cplex
thread

Uses of Bind in analyses

Fields in analyses declared as Bind

Modifier and Type	Field and Description
protected Bind	Analysis.b The Bind from witch the analysis will use the data.

Constructors in analyses with parameters of type Bind

Constructor and Description
Analysis(Bind b)
CompFVAAnalysis(Bind b, FVAResult res1, FVAResult res2) It is constructed with two FVA results and then compares them.
DRAnalysis(Bind b, double d)
FBAAnalysis(Bind b)
FVAAnalysis(Bind b, java.util.Map<java.lang.String,parsebionet.biodata.BioEntity> mapEntities, java.util.List<Constraint> constraints)
KOAnalysis(Bind b, int mode, java.util.Map<java.lang.String,parsebionet.biodata.BioEntity> entities)
ParetoAnalysis(Bind b, java.lang.String filePath, boolean plotAll)
ReacAnalysis(Bind bind, java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities, java.lang.String name, double init, double end, double deltaF, boolean fva)
RFBAAnalysis(Bind b, java.lang.String biomassReac, double X, double deltaT, int iterations, java.util.List<java.lang.String> toPlot)
TwoReacsAnalysis(Bind bind, java.lang.String reac, java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities1, java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities2, double init, double end, double deltaF, java.lang.String reac2, double init2, double end2, double deltaF2, boolean fva)

Uses of Bind in analyses.result

Fields in analyses.result declared as Bind

Modifier and Type	Field and Description
private Bind	FBAResult.bind

Constructors in analyses.result with parameters of type Bind

Constructor and Description
DRResult(double objValue, Bind b)
FBAResult(Bind b)

Uses of Bind in general

Subclasses of Bind in general

Modifier and Type	Class and Description
class	CplexBind CPLEX version of Bind.
class	GLPKBind GLPK version of Bind.

Uses of Bind in interaction

Methods in interaction with parameters of type Bind

Modifier and Type	Method and Description
abstract java.lang.Object	Interaction.makeInteraction(Bind bind) Creates the interaction.
java.lang.Object	IfThenInteraction.makeInteraction(Bind bind) Only used when interactions in solver.
java.lang.Object	EqInteraction.makeInteraction(Bind bind) Only used when interactions in solver.
abstract java.lang.Object	Relation.runThrough(Bind b) Used when interactions are in the solver.
java.lang.Object	Unique.runThrough(Bind b) Only used when interaction are in the solver.
java.lang.Object	Or.runThrough(Bind b) Only used when interaction are in the solver.
java.lang.Object	UniqueProbability.runThrough(Bind b)
java.lang.Object	And.runThrough(Bind b) Only used when interaction are in the solver.
java.lang.Object	InversedRelation.runThrough(Bind b) Only used when interaction are in the solver.

Uses of Bind in interaction.cplex

Methods in interaction.cplex with parameters of type Bind

Modifier and Type	Method and Description
java.lang.Object	IfThenInteractionCplex.makeInteraction(Bind b)
java.lang.Object	EqInteractionCplex.makeInteraction(Bind b)
java.lang.Object	InversedRelationCplex.runThrough(Bind bind)
java.lang.Object	OrCPLEX.runThrough(Bind b) Return an IloConstraint
java.lang.Object	AndCPLEX.runThrough(Bind b) returns an IloConstraint
java.lang.Object	UniqueCPLEX.runThrough(Bind bind)

Uses of Bind in thread

Fields in thread declared as Bind

Modifier and Type	Field and Description
protected Bind	ResolveThread.bind The bind to copy.

Constructors in thread with parameters of type Bind

Constructor and Description
ResolveThread(Bind b) Creates a thread without an objective function.
ResolveThread(Bind b, Objective obj) Creates a thread with an objective function.
ThreadFVA(Bind b, java.util.Queue<parsebionet.biodata.BioEntity> ents, java.util.Queue<parsebionet.biodata.BioEntity> entsCopy, FVAResult result)
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)