thread

Class ThreadFactory

java.lang.Object

thread.ThreadFactory

Direct Known Subclasses:

ThreadFactoryCPLEX, ThreadFactoryGLPK

public abstract class ThreadFactory
extends java.lang.Object

Class to create the right type of thread. To create the right Bind for the solver, this class must be extended for each solver.

Author:

lmarmiesse 8 mars 2013

Field Summary

Fields

Modifier and Type	Field and Description
protected parsebionet.biodata.BioNetwork	bioNet Bind bioNetwork to copy.
protected java.util.List<Constraint>	constraints Bind constraints to copy.
protected InteractionNetwork	intNet Bind interaction network to copy.
protected java.util.Map<parsebionet.biodata.BioEntity,Constraint>	simpleConstraints Bind simple constraints to copy.

Constructor Summary

Constructors

Constructor and Description
ThreadFactory(java.util.List<Constraint> constraints, java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints, InteractionNetwork intNet)

Method Summary

Methods

Modifier and Type	Method and Description
abstract ThreadFVA	makeFVAThread(boolean interactionInSolver, java.util.Queue<parsebionet.biodata.BioEntity> entQueue, java.util.Queue<parsebionet.biodata.BioEntity> entQueueCopy, FVAResult result) Makes a thread for an FVA analysis.
abstract ThreadKO	makeKOThread(boolean interactionInSolver, java.util.Queue<parsebionet.biodata.BioEntity> reacsQueue, KOResult koResult, Objective obj) Makes a thread for a KO analysis.
abstract ThreadReac	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.
abstract ResolveThread	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.
void	setBioNet(parsebionet.biodata.BioNetwork bioNet)

Methods inherited from class java.lang.Object

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

Field Detail

constraints

protected java.util.List<Constraint> constraints

Bind constraints to copy.

simpleConstraints

protected java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints

Bind simple constraints to copy.

intNet

protected InteractionNetwork intNet

Bind interaction network to copy.

bioNet

protected parsebionet.biodata.BioNetwork bioNet

Bind bioNetwork to copy.

Constructor Detail

ThreadFactory

public ThreadFactory(java.util.List<Constraint> constraints,
             java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints,
             InteractionNetwork intNet)

Method Detail

makeFVAThread

public abstract ThreadFVA makeFVAThread(boolean interactionInSolver,
                      java.util.Queue<parsebionet.biodata.BioEntity> entQueue,
                      java.util.Queue<parsebionet.biodata.BioEntity> entQueueCopy,
                      FVAResult result)

Makes a thread for an FVA analysis.

Parameters:

interactionInSolver - Whether or not interactions are in the solver.

entQueue - The queue of entities to perform the FVA on for maximization.

entQueueCopy - entQueue The queue of entities to perform the FVA on for minimization.

result - An empty FVA result.

Returns:

A FVA thread.

makeKOThread

public abstract ThreadKO makeKOThread(boolean interactionInSolver,
                    java.util.Queue<parsebionet.biodata.BioEntity> reacsQueue,
                    KOResult koResult,
                    Objective obj)

Makes a thread for a KO analysis.

Parameters:

interactionInSolver - Whether or not interactions are in the solver.

reacsQueue - The queue of entities to perform the KO on.

koResult - An empty KO result.

obj - The objective function.

Returns:

A KO thread

setBioNet

public void setBioNet(parsebionet.biodata.BioNetwork bioNet)

makeReacThread

public abstract ThreadReac 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.

Parameters:

interactionInSolver - Whether or not interactions are in the solver.

fluxesQueue - The queue of fluxes.

entities - Map containing the entity to make vary.

result - an empty ReacAnalysis result.

obj - The objective function.

Returns:

A Thread for an analysis with a varying variable.

makeTwoReacsThread

public abstract ResolveThread 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.

Parameters:

interactionInSolver - Whether or not interactions are in the solver.

fluxesQueue - The queue of fluxes.

result - an empty TwoReacsAnalysis result.

entities1 - Map containing the first entity to make vary.

entities2 - Map containing the second entity to make vary.

obj - The objective function.

Returns:

A thread for an analysis with two varying variables.