org.colomoto.biolqm.io.petrinet

Class AbstractPNEncoder

java.lang.Object

org.colomoto.biolqm.io.petrinet.AbstractPNEncoder

Direct Known Subclasses:

PNEncoderAPNN, PNEncoderINA, PNEncoderPNML

public abstract class AbstractPNEncoder
extends Object

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

Field Summary

Fields

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

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(PNConfig config, OutputStreamProvider out)

Methods inherited from class java.lang.Object

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

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(PNConfig config,
                   OutputStreamProvider out)
            throws IOException

Throws:

IOException