org.ginsim.service.tool.interactionanalysis

Class InteractionAnalysisAlgo

java.lang.Object

org.ginsim.service.tool.interactionanalysis.InteractionAnalysisAlgo

public class InteractionAnalysisAlgo
extends Object

Search all the non functional interactions in the graph 'regGraph' and do some actions on them depending on the options (opt_*).

Author:

Duncan Berenguier

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
InteractionAnalysisAlgo()

Method Summary

Modifier and Type	Method and Description
protected InteractionAnalysisAlgoResult	run(RegulatoryGraph regGraph, Perturbation mutant, List<RegulatoryNode> selectedNodes) Search all the non functional interactions in the graph 'g' and do some actions on them depending on the options (opt_*).

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

InteractionAnalysisAlgo

public InteractionAnalysisAlgo()

Method Detail

run

protected InteractionAnalysisAlgoResult run(RegulatoryGraph regGraph,
                                            Perturbation mutant,
                                            List<RegulatoryNode> selectedNodes)

Search all the non functional interactions in the graph 'g' and do some actions on them depending on the options (opt_*). For each vertices, scan the reduced Omdd representation of the node logical function to know which vertices are effective (<=>present). If an edge source vertex incoming on this vertex is not in the Omdd, then its non functional.

Parameters:

regGraph - the graph where to search the non functional interactions.

mutant - the mutant definition

selectedNodes - the set of selected nodes to run the analysis on.

Returns:

an object with functionality conditions for all interactions