general

Class GLPKBind

java.lang.Object

general.Bind

general.GLPKBind

public class GLPKBind
extends Bind

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

Author:

lmarmiesse 9 avr. 2013

Field Summary

Fields

Modifier and Type	Field and Description
private org.gnu.glpk.glp_iocp	mipParm
private org.gnu.glpk.glp_prob	model
private org.gnu.glpk.glp_smcp	parm
private java.util.Map<java.lang.String,java.lang.Integer>	vars Map to match entities names to a GLPK column index.

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
GLPKBind(boolean interactionInSolver)
GLPKBind(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 d) Changes the coefficient of an entity in the objective.
protected void	changeVarBounds(java.lang.String entity, double[] bounds) Changes the bounds of an entity.
protected void	clear() Clears the solver's model.
protected void	deleteConstraints(java.util.List<java.lang.Object> constraints) Deletes solver constraints.
void	end()
void	entitiesToSolverVars() Transforms problem entities into the right solver variables.
protected DoubleResult	go(boolean saveResults) Make the solver perform the solves.
void	init() Initialization of GLPK parameters and of the right factories.
protected void	interactionsToSolverConstraints(java.util.List<Interaction> interactions) Not used.
boolean	isMIP()
protected 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	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 org.gnu.glpk.glp_prob model

parm

private org.gnu.glpk.glp_smcp parm

mipParm

private org.gnu.glpk.glp_iocp mipParm

vars

private java.util.Map<java.lang.String,java.lang.Integer> vars

Map to match entities names to a GLPK column index.

Constructor Detail

GLPKBind

public GLPKBind(boolean interactionInSolver)

GLPKBind

public GLPKBind(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 GLPK 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

interactionsToSolverConstraints

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

Not used. This solver does not support interactions.

Specified by:

interactionsToSolverConstraints in class Bind

makeSolverConstraint

protected 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.

deleteConstraints

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

Description copied from class: Bind

Deletes solver constraints.

Specified by:

deleteConstraints 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 d)

Description copied from class: Bind

Changes the coefficient of an entity in the objective.

Specified by:

changeObjVarValue in class Bind

Parameters:

e - The entity

d - 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

clear

protected void clear()

Description copied from class: Bind

Clears the solver's model.

Specified by:

clear in class Bind

isMIP

public boolean isMIP()

Specified by:

isMIP in class Bind

Returns:

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

go

protected 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.

end

public void end()

Specified by:

end 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