thread

Class ThreadFactoryGLPK

java.lang.Object

thread.ThreadFactory

thread.ThreadFactoryGLPK

public class ThreadFactoryGLPK
extends ThreadFactory

GLPK version of the Thread factory.

Author:

lmarmiesse 10 avr. 2013

Field Summary

Fields inherited from class thread.ThreadFactory

bioNet, constraints, intNet, simpleConstraints

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
ThreadFVA	makeFVAThread(boolean interactionInSolver, java.util.Queue<parsebionet.biodata.BioEntity> ents, java.util.Queue<parsebionet.biodata.BioEntity> entsCopy, FVAResult result) Makes a thread for an FVA analysis.
ThreadKO	makeKOThread(boolean interactionInSolver, java.util.Queue<parsebionet.biodata.BioEntity> entities, KOResult result, Objective obj) Makes a thread for a KO analysis.
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.
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.

Methods inherited from class thread.ThreadFactory

setBioNet

Methods inherited from class java.lang.Object

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

Constructor Detail

ThreadFactoryGLPK

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

Method Detail

makeFVAThread

public ThreadFVA makeFVAThread(boolean interactionInSolver,
                      java.util.Queue<parsebionet.biodata.BioEntity> ents,
                      java.util.Queue<parsebionet.biodata.BioEntity> entsCopy,
                      FVAResult result)

Description copied from class: ThreadFactory

Makes a thread for an FVA analysis.

Specified by:

makeFVAThread in class ThreadFactory

Parameters:

interactionInSolver - Whether or not interactions are in the solver.

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

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

result - An empty FVA result.

Returns:

A FVA thread.

makeKOThread

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

Description copied from class: ThreadFactory

Makes a thread for a KO analysis.

Specified by:

makeKOThread in class ThreadFactory

Parameters:

interactionInSolver - Whether or not interactions are in the solver.

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

result - An empty KO result.

obj - The objective function.

Returns:

A KO thread

makeReacThread

public 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)

Description copied from class: ThreadFactory

Makes a thread for an analysis with a varying variable.

Specified by:

makeReacThread in class ThreadFactory

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 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)

Description copied from class: ThreadFactory

Makes a thread for an analysis with two varying variables.

Specified by:

makeTwoReacsThread in class ThreadFactory

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.