org.ginsim.core.graph.regulatorygraph.perturbation

Interface Perturbation

All Superinterfaces:

org.colomoto.biolqm.modifier.perturbation.LogicalModelPerturbation

All Known Implementing Classes:

PerturbationFixed, PerturbationMultiple, PerturbationRange, PerturbationRegulator

public interface Perturbation
extends org.colomoto.biolqm.modifier.perturbation.LogicalModelPerturbation

A perturbation is a (series of) change that can be applied to a regulatory graph. Applying the perturbation leads to a new set of logical functions. This interface extends the base perturbations provided by LogicalModel and adds some convenience methods

Author:

Aurelien Naldi

Method Summary

Modifier and Type	Method and Description
Perturbation	clone(ListOfPerturbations manager, Map<org.colomoto.biolqm.NodeInfo,org.colomoto.biolqm.NodeInfo> m_nodes, Map<Perturbation,Perturbation> m_perturbations) Copy the perturbation to a new graph (in particular to a reduced version of the current graph)
String	getDescription() Get a human-readable description of the perturbation
void	toXML(XMLWriter out) Save the perturbation definition to XML (to save in zginml)

Methods inherited from interface org.colomoto.biolqm.modifier.perturbation.LogicalModelPerturbation

affectsNode, apply, getStringRepresentation, restrictValues, update

Method Detail

toXML

void toXML(XMLWriter out)
    throws IOException

Save the perturbation definition to XML (to save in zginml)

Parameters:

out -

Throws:

IOException

clone

Perturbation clone(ListOfPerturbations manager,
                   Map<org.colomoto.biolqm.NodeInfo,org.colomoto.biolqm.NodeInfo> m_nodes,
                   Map<Perturbation,Perturbation> m_perturbations)

Copy the perturbation to a new graph (in particular to a reduced version of the current graph)

Parameters:

manager -

m_nodes -

m_perturbations -

Returns:

getDescription

String getDescription()

Get a human-readable description of the perturbation

Returns:

a string describing the changes