org.colomoto.biolqm.io.petrinet

Class AbstractPNEncoder

java.lang.Object

java.lang.Thread

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

org.colomoto.biolqm.io.BaseExporter

org.colomoto.biolqm.io.petrinet.AbstractPNEncoder

All Implemented Interfaces:

Runnable, Callable<Boolean>, ModelExporter, Task<Boolean>

Direct Known Subclasses:

PNEncoderAPNN, PNEncoderINA, PNEncoderPNML

public abstract class AbstractPNEncoder
extends BaseExporter

Export a regulatory graph to petri net (shared methods).

translating a regulatory graph to a petri net is done as follow:

• each node will be represented by two places, a negative one and a positive one. Markers in the positive place represent it's level. if it is not at it's maximum missing marker(s) will be in it's negative place: the number of markers in the petri net is constant
• each logical parameter will be represented by transition(s) with "test" arcs to non-modified places and "normal" arcs to the positive and negative place of the modified place.

with some simplifications:

• work on the tree representation of logical parameters and use ranges instead of exact values as precondition of transitions
• "input" nodes are specials: no transition will affect them and their basal value will be used as initial markup
• autoregulation can trigger some cases where a transition can't be fired, these are not created

references:

• Simao, E., Remy, E., Thieffry, D. and Chaouiya, C.: Qualitative modelling of Regulated Metabolic Pathways: Application to the Tryptophan biosynthesis in E. Coli.
• Chaouiya, C., Remy, E. and Thieffry, D.: Petri Net Modelling of Biological Regulatory Networks

Nested Class Summary

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

Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field and Description
org.colomoto.mddlib.MDDManager	ddmanager
int[]	functions
int	len
List<NodeInfo>	nodeOrder

Fields inherited from class org.colomoto.biolqm.io.BaseExporter

model, streams

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
AbstractPNEncoder(LogicalModel model)

Method Summary

Modifier and Type	Method and Description
protected abstract void	doExport(String netName, List<NodeInfo> nodes, List[] t_transition, byte[][] t_markup, OutputStreamWriter out)
void	export()
byte[]	getInitialstate()
void	setInitialState(byte[] init)

Methods inherited from class org.colomoto.biolqm.io.BaseExporter

performTask, setDestination

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.biolqm.io.ModelExporter

setDestination, setDestination

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

background, cancel, getResult, getStatus, setParameter, setParameters, setParameters

Methods inherited from interface java.util.concurrent.Callable

call

Field Detail

nodeOrder

public final List<NodeInfo> nodeOrder

ddmanager

public final org.colomoto.mddlib.MDDManager ddmanager

functions

public final int[] functions

len

public final int len

Constructor Detail

AbstractPNEncoder

public AbstractPNEncoder(LogicalModel model)

Method Detail

doExport

protected abstract void doExport(String netName,
                                 List<NodeInfo> nodes,
                                 List[] t_transition,
                                 byte[][] t_markup,
                                 OutputStreamWriter out)
                          throws IOException

Throws:

IOException

export

public void export()
            throws IOException

Specified by:

export in class BaseExporter

Throws:

IOException

setInitialState

public void setInitialState(byte[] init)

getInitialstate

public byte[] getInitialstate()