org.ginsim.service.tool.modelreduction

Class ReductionTask

java.lang.Object

java.lang.Thread

org.colomoto.common.task.AbstractTask<org.colomoto.biolqm.LogicalModel>

org.ginsim.service.tool.modelreduction.ReductionTask

All Implemented Interfaces:

Runnable, Callable<org.colomoto.biolqm.LogicalModel>, org.colomoto.common.task.Task<org.colomoto.biolqm.LogicalModel>

public class ReductionTask
extends org.colomoto.common.task.AbstractTask<org.colomoto.biolqm.LogicalModel>

Build a simplified model, based on a complete one, by removing some nodes. The first step is to build new MDD for the targets of the removed nodes. If this succeeded (no circuit was removed...), a new regulatory graph is created and all non-removed nodes are copied into it, as well as all remaining interactions. Then the logical parameters of the unaffected nodes are restored. For the affected nodes, some work is required, using the newly built MDD for their logical function:

• new edges are added if needed (coming from the regulators of their deleted regulators)
• new logical parameters are extracted from the MDD

Author:

Aurelien Naldi

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields inherited from class org.colomoto.common.task.AbstractTask

canceled

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor and Description
ReductionTask(org.colomoto.biolqm.LogicalModel model, ReductionConfig config)
ReductionTask(org.colomoto.biolqm.LogicalModel model, ReductionConfig config, ReductionLauncher launcher)
ReductionTask(RegulatoryGraph graph, ReductionConfig config)
ReductionTask(RegulatoryGraph graph, ReductionConfig config, ReductionLauncher launcher)

Method Summary

Modifier and Type	Method and Description
org.colomoto.biolqm.LogicalModel	performTask()

Methods inherited from class org.colomoto.common.task.AbstractTask

background, call, cancel, getResult, getStatus, run

Methods inherited from class java.lang.Thread

activeCount, checkAccess, clone, countStackFrames, currentThread, destroy, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, stop, suspend, toString, yield

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.colomoto.common.task.Task

setParameter, setParameters, setParameters

Constructor Detail

ReductionTask

public ReductionTask(RegulatoryGraph graph,
                     ReductionConfig config)

ReductionTask

public ReductionTask(org.colomoto.biolqm.LogicalModel model,
                     ReductionConfig config)

ReductionTask

public ReductionTask(RegulatoryGraph graph,
                     ReductionConfig config,
                     ReductionLauncher launcher)

ReductionTask

public ReductionTask(org.colomoto.biolqm.LogicalModel model,
                     ReductionConfig config,
                     ReductionLauncher launcher)

Method Detail

performTask

public org.colomoto.biolqm.LogicalModel performTask()

Specified by:

performTask in class org.colomoto.common.task.AbstractTask<org.colomoto.biolqm.LogicalModel>