org.colomoto.biolqm.modifier.perturbation

Class InteractionPerturbation

java.lang.Object

org.colomoto.biolqm.modifier.perturbation.InteractionPerturbation

All Implemented Interfaces:

LogicalModelPerturbation

public class InteractionPerturbation
extends Object
implements LogicalModelPerturbation

A perturbation which removes the effect of a component on another (i.e. removes an interaction). The target component will behave as if this regulator had a fixed value.

Author:

Aurelien Naldi

Field Summary

Fields

Modifier and Type	Field and Description
NodeInfo	regulator
int	regValue
NodeInfo	target

Constructor Summary

Constructors

Constructor and Description
InteractionPerturbation(NodeInfo regulator, NodeInfo target, int regValue)

Method Summary

Modifier and Type	Method and Description
boolean	affectsNode(NodeInfo node) Test if the perturbation affects the function of a specific node
boolean	equals(Object o)
String	getStringRepresentation()
void	restrictValues(byte[] state, List<NodeInfo> nodeOrder) Apply the perturbation(s) directly to a state, i.e., restricts the values of the state in the valid range of the perturbation(s).
String	toString()
void	update(LogicalModel model) Apply the perturbation to a model directly (do not create a modified model).

Methods inherited from class java.lang.Object

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

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

apply

Field Detail

regValue

public final int regValue

target

public final NodeInfo target

regulator

public final NodeInfo regulator

Constructor Detail

InteractionPerturbation

public InteractionPerturbation(NodeInfo regulator,
                               NodeInfo target,
                               int regValue)

Method Detail

restrictValues

public void restrictValues(byte[] state,
                           List<NodeInfo> nodeOrder)

Description copied from interface: LogicalModelPerturbation

Apply the perturbation(s) directly to a state, i.e., restricts the values of the state in the valid range of the perturbation(s).

Specified by:

restrictValues in interface LogicalModelPerturbation

Parameters:

state - the state to be restricted

nodeOrder - the ordered list of components in the state

update

public void update(LogicalModel model)

Description copied from interface: LogicalModelPerturbation

Apply the perturbation to a model directly (do not create a modified model). This can be used directly when we do not need to preserve the original model. It is also convenient for multiple perturbations, to avoid creating intermediate models.

Specified by:

update in interface LogicalModelPerturbation

Parameters:

model - the modified model

toString

public String toString()

Overrides:

toString in class Object

getStringRepresentation

public String getStringRepresentation()

Specified by:

getStringRepresentation in interface LogicalModelPerturbation

Returns:

a simple serialised description of the perturbation

equals

public boolean equals(Object o)

Overrides:

equals in class Object

affectsNode

public boolean affectsNode(NodeInfo node)

Description copied from interface: LogicalModelPerturbation

Test if the perturbation affects the function of a specific node

Specified by:

affectsNode in interface LogicalModelPerturbation

Parameters:

node - a component of the model

Returns:

true if component is affected by this perturbation