org.ginsim.service.tool.modelreduction

Class ReconstructionTask

java.lang.Object

java.lang.Thread

org.colomoto.common.task.AbstractTask<RegulatoryGraph>

org.ginsim.service.tool.modelreduction.ReconstructionTask

All Implemented Interfaces:

Runnable, Callable<RegulatoryGraph>, org.colomoto.common.task.Task<RegulatoryGraph>, ViewCopyHelper<Graph<RegulatoryNode,RegulatoryMultiEdge>,RegulatoryNode,RegulatoryMultiEdge>

public class ReconstructionTask
extends org.colomoto.common.task.AbstractTask<RegulatoryGraph>
implements ViewCopyHelper<Graph<RegulatoryNode,RegulatoryMultiEdge>,RegulatoryNode,RegulatoryMultiEdge>

Reconstruct a Regulatory Graph from a Logical model and restore layout, comments and metadata from an original graph. This is used by the reduction tool to show the reduced graph.

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
ReconstructionTask(org.colomoto.biolqm.LogicalModel reducedModel, RegulatoryGraph graph)
ReconstructionTask(org.colomoto.biolqm.LogicalModel reducedModel, RegulatoryGraph graph, ReductionConfig config)

Method Summary

Modifier and Type	Method and Description
Dimension	getOffset() Offset to move the last copied element.
RegulatoryMultiEdge	getSourceEdge(RegulatoryMultiEdge me) Retrieve the equivalent edge from the source graph.
RegulatoryNode	getSourceNode(RegulatoryNode node) Retrieve the equivalent node from the source graph.
RegulatoryGraph	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

ReconstructionTask

public ReconstructionTask(org.colomoto.biolqm.LogicalModel reducedModel,
                          RegulatoryGraph graph)

ReconstructionTask

public ReconstructionTask(org.colomoto.biolqm.LogicalModel reducedModel,
                          RegulatoryGraph graph,
                          ReductionConfig config)

Method Detail

performTask

public RegulatoryGraph performTask()

Specified by:

performTask in class org.colomoto.common.task.AbstractTask<RegulatoryGraph>

getSourceNode

public RegulatoryNode getSourceNode(RegulatoryNode node)

Description copied from interface: ViewCopyHelper

Retrieve the equivalent node from the source graph.

Specified by:

getSourceNode in interface ViewCopyHelper<Graph<RegulatoryNode,RegulatoryMultiEdge>,RegulatoryNode,RegulatoryMultiEdge>

Returns:

getSourceEdge

public RegulatoryMultiEdge getSourceEdge(RegulatoryMultiEdge me)

Description copied from interface: ViewCopyHelper

Retrieve the equivalent edge from the source graph.

Specified by:

getSourceEdge in interface ViewCopyHelper<Graph<RegulatoryNode,RegulatoryMultiEdge>,RegulatoryNode,RegulatoryMultiEdge>

Returns:

getOffset

public Dimension getOffset()

Description copied from interface: ViewCopyHelper

Offset to move the last copied element.

Specified by:

getOffset in interface ViewCopyHelper<Graph<RegulatoryNode,RegulatoryMultiEdge>,RegulatoryNode,RegulatoryMultiEdge>

Returns:

an offset (will be updated by calls to getSourceNode) or null