general

Class CplexBind

java.lang.Object

general.Bind

general.CplexBind

public class CplexBind
extends Bind

CPLEX version of Bind. It transforms porblem's variables, constraints and interactions into Objects usable by the CPLEX solver.

Author:

lmarmiesse 6 mars 2013

Field Summary

Fields

Modifier and Type	Field and Description
private ilog.cplex.IloCplex	cplex
private ilog.concert.IloObjective	cplexObj
private ilog.cplex.IloCplexModeler	model
java.util.Map<java.lang.String,ilog.concert.IloNumVar>	vars Map to match entities names to a CPLEX variable.

Fields inherited from class general.Bind

bioNet, constraintObjectives, constraints, deadReactions, exchangeInteractions, interactionInSolver, interactionsEntitiesCause, interactionsEntitiesConsequence, intNet, intToConstraint, lastSolve, obj, operationFactory, reactionToActiveGPR, relationFactory, simpleConstraints, solverSimpleConstraints, steadyStateConstraints, threadFactory

Constructor Summary

Constructors

Constructor and Description
CplexBind(boolean interactionInSolver)
CplexBind(java.util.List<Constraint> constraints, java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints, InteractionNetwork intNet, parsebionet.biodata.BioNetwork bioNet, boolean interactionInSolver)

Method Summary

Methods

Modifier and Type	Method and Description
void	changeObjVarValue(parsebionet.biodata.BioEntity e, double value) Changes the coefficient of an entity in the objective.
protected void	changeVarBounds(java.lang.String entity, double[] bounds) Changes the bounds of an entity.
void	clear() Clears the solver's model.
protected void	deleteConstraints(java.util.List<java.lang.Object> solverConstraints) Deletes solver constraints.
void	end()
void	entitiesToSolverVars() Transforms problem entities into the right solver variables.
DoubleResult	go(boolean saveResults) Make the solver perform the solves.
void	init() Initialization of CPLEX parameters and of the right factories.
protected void	interactionsToSolverConstraints(java.util.List<Interaction> interactions) Transforms problem interactions into solver constraints.
boolean	isMIP()
void	makeSolverConstraint(Constraint constraint, java.util.List<java.lang.Object> toRemoveFromModel, java.util.Map<java.lang.String,double[]> oldBounds) Creates a constraint for the solver.
void	makeSolverObjective() Transforms the porblem's objective into a solver objective.
void	setMIPStart()
void	setObjSense(boolean maximize) Sets the sense of the objective function.

Methods inherited from class general.Bind

checkInteractions, checkInteractionsForEntities, clearSolver, constraintsToSolverConstraints, createFluxesSummation, displayConstraints, FBA, FBAWithConstraints, getBioNetwork, getConstraints, getDeadReactions, getExchangeInteractions, getInteractionNetwork, getInteractionsEntities, getInteractionsEntitiesCause, getIntToConstraint, getObjective, getSimpleConstraints, getSolvedValue, getThreadFactory, isInteractionInSolver, isLastSolveEmpty, loadConditionsFile, loadInteractionsFile, loadSbmlNetwork, makeObjectiveFromString, prepareSolver, setLoadObjective, setNetwork, setObjective

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

model

private ilog.cplex.IloCplexModeler model

cplex

private ilog.cplex.IloCplex cplex

cplexObj

private ilog.concert.IloObjective cplexObj

vars

public java.util.Map<java.lang.String,ilog.concert.IloNumVar> vars

Map to match entities names to a CPLEX variable.

Constructor Detail

CplexBind

public CplexBind(boolean interactionInSolver)

CplexBind

public CplexBind(java.util.List<Constraint> constraints,
         java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints,
         InteractionNetwork intNet,
         parsebionet.biodata.BioNetwork bioNet,
         boolean interactionInSolver)

Method Detail

init

public void init()

Initialization of CPLEX parameters and of the right factories.

entitiesToSolverVars

public void entitiesToSolverVars()

Description copied from class: Bind

Transforms problem entities into the right solver variables.

Specified by:

entitiesToSolverVars in class Bind

makeSolverConstraint

public void makeSolverConstraint(Constraint constraint,
                        java.util.List<java.lang.Object> toRemoveFromModel,
                        java.util.Map<java.lang.String,double[]> oldBounds)

Description copied from class: Bind

Creates a constraint for the solver.

Specified by:

makeSolverConstraint in class Bind

Parameters:

constraint - Constraint to create

toRemoveFromModel - is used to come back to how it was before.

oldBounds - is used to come back to how it was before.

interactionsToSolverConstraints

protected void interactionsToSolverConstraints(java.util.List<Interaction> interactions)

Description copied from class: Bind

Transforms problem interactions into solver constraints.

Specified by:

interactionsToSolverConstraints in class Bind

makeSolverObjective

public void makeSolverObjective()

Description copied from class: Bind

Transforms the porblem's objective into a solver objective.

Specified by:

makeSolverObjective in class Bind

changeObjVarValue

public void changeObjVarValue(parsebionet.biodata.BioEntity e,
                     double value)

Description copied from class: Bind

Changes the coefficient of an entity in the objective.

Specified by:

changeObjVarValue in class Bind

Parameters:

e - The entity

value - The coefficient

setObjSense

public void setObjSense(boolean maximize)

Description copied from class: Bind

Sets the sense of the objective function.

Specified by:

setObjSense in class Bind

Parameters:

maximize - if true : maximize, if false : minimize

go

public DoubleResult go(boolean saveResults)

Description copied from class: Bind

Make the solver perform the solves.

Specified by:

go in class Bind

Returns:

An object containing the objective value and a flag that says if the problem was feasible or not.

clear

public void clear()

Description copied from class: Bind

Clears the solver's model.

Specified by:

clear in class Bind

end

public void end()

Specified by:

end in class Bind

setMIPStart

public void setMIPStart()

isMIP

public boolean isMIP()

Specified by:

isMIP in class Bind

Returns:

true : the problem is a MIP, false : it is not

deleteConstraints

protected void deleteConstraints(java.util.List<java.lang.Object> solverConstraints)

Description copied from class: Bind

Deletes solver constraints.

Specified by:

deleteConstraints in class Bind

changeVarBounds

protected void changeVarBounds(java.lang.String entity,
                   double[] bounds)

Description copied from class: Bind

Changes the bounds of an entity.

Specified by:

changeVarBounds in class Bind

Parameters:

entity - The entity to change

bounds - New bounds