org.colomoto.biolqm.helper.inferinteraction

Class InteractionSearcher

java.lang.Object

org.colomoto.biolqm.helper.inferinteraction.InteractionSearcher

public class InteractionSearcher
extends Object

Extract detailed interactions from a logical model. If you only need lists of regulators, you can use ConnectivityMatrix, this searcher will also provide thresholds and signs.

Basic idea: for each function, unfold the list of leaves and use this "full" list to look for the effects of each regulator.

Usage: it will be needed to infer interactions for the GINML export and correct signs for the SBML export

Author:

Duncan Berenguier, Aurelien Naldi

Field Summary

Fields

Modifier and Type	Field and Description
protected static byte	FUNC_DUAL
protected static byte	FUNC_NEGATIVE
protected static byte	FUNC_NON
protected static byte	FUNC_POSITIVE

Constructor Summary

Constructors

Constructor and Description
InteractionSearcher(LogicalModel model)

Method Summary

Modifier and Type	Method and Description
void	run()

Methods inherited from class java.lang.Object

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

Field Detail

FUNC_NON

protected static final byte FUNC_NON

See Also:

Constant Field Values

FUNC_POSITIVE

protected static final byte FUNC_POSITIVE

See Also:

Constant Field Values

FUNC_NEGATIVE

protected static final byte FUNC_NEGATIVE

See Also:

Constant Field Values

FUNC_DUAL

protected static final byte FUNC_DUAL

See Also:

Constant Field Values

Constructor Detail

InteractionSearcher

public InteractionSearcher(LogicalModel model)

Method Detail

run

public void run()