org.colomoto.biolqm

Class ConnectivityMatrix

java.lang.Object

org.colomoto.biolqm.ConnectivityMatrix

public class ConnectivityMatrix
extends Object

Build and consult regulatory relations between variables in a Logical Model. This will assemble for each component, the list of its regulators, and for each core components the list of its targets.

Author:

Aurelien Naldi

Constructor Summary

Constructors

Constructor and Description
ConnectivityMatrix(LogicalModel model)

Method Summary

Modifier and Type	Method and Description
int[]	getCoreTargets(int idx, boolean extra) Get the list of components regulated by a given core component.
org.colomoto.mddlib.VariableEffect[][]	getRegulatorEffects(int idx, boolean extra) Get sign information about the regulators of a node.
int[]	getRegulators(int idx, boolean extra) Get the list of core components regulating a given component.

Methods inherited from class java.lang.Object

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

Constructor Detail

ConnectivityMatrix

public ConnectivityMatrix(LogicalModel model)

Method Detail

getRegulators

public int[] getRegulators(int idx,
                           boolean extra)

Get the list of core components regulating a given component.

Parameters:

idx - index of the component

extra - if true the considered component is an extra component, otherwise it is part of the core

Returns:

indices of its regulators (all are core components)

getCoreTargets

public int[] getCoreTargets(int idx,
                            boolean extra)

Get the list of components regulated by a given core component.

Parameters:

idx - index of the considered core component

extra - if true, it will give regulated extra components, otherwise core components

Returns:

indices of regulated components either in the core or in extra

getRegulatorEffects

public org.colomoto.mddlib.VariableEffect[][] getRegulatorEffects(int idx,
                                                                  boolean extra)

Get sign information about the regulators of a node. All regulators are extracted from the MDD, thus all should have an effect. Each position in the returned array denotes the sign of the regulator at the same position in the list of regulators returned by getRegulators(int, boolean).

Parameters:

idx - the component index

extra - if true, consider extra components instead of core

Returns:

a list of regulation signs.