org.ginsim.service.tool.circuit

Class CircuitAlgo

java.lang.Object

org.ginsim.service.tool.circuit.CircuitAlgo

public class CircuitAlgo
extends Object

analyse circuits to detect their functionality/functional range.

on circuits:

• a circuit is non-functional if any of it's edge is inactive
• a circuit is negative if it contains 2k+1 negative interactions

on interactions:

• an interaction is non-functional if the main range is non-functional
• an interaction is negative if the negative range is wider than the positive one

about interaction's contexts:

• a context is non-functional if in this context, the activation of the interaction (considering min and max of it's activation range) has no effect on the activity of the target interaction
• a context is functional, positive (resp negative) if in this context, the activation of the interaction triggers (resp inhibits) the activation of the target interaction

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	CircuitAlgo.subReport

Constructor Summary

Constructors

Constructor and Description
CircuitAlgo(RegulatoryGraph graph, boolean do_cleanup)
CircuitAlgo(RegulatoryGraph graph, Perturbation mutant, boolean do_cleanup)

Method Summary

Modifier and Type	Method and Description
int	checkEdge(RegulatoryEdge ei, int[] t_circuit, int nextmin, int nextmax)
int	cleanupContext(int context, int[] t_circuit) Remove constraint on the members from a functionality context.
org.colomoto.mddlib.MDDManager	getManager()
int	mergeContexts(int context, int node) Merge functionality contexts.
long[]	score(int node) compute a score for the context.

Methods inherited from class java.lang.Object

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

Constructor Detail

CircuitAlgo

public CircuitAlgo(RegulatoryGraph graph,
                   boolean do_cleanup)

CircuitAlgo

public CircuitAlgo(RegulatoryGraph graph,
                   Perturbation mutant,
                   boolean do_cleanup)

Parameters:

graph - the studied graph

t_constraint - constraints on the nodes

Method Detail

checkEdge

public int checkEdge(RegulatoryEdge ei,
                     int[] t_circuit,
                     int nextmin,
                     int nextmax)

Parameters:

ei - the edge to test

t_circuit - members of the circuit

nextmin -

nextmax -

Returns:

the functionality context for this edge

score

public long[] score(int node)

compute a score for the context. higher is better (score increases with the size of the phase space region) return: [score, sign] sign can be: FALSE, POSITIVE, NEGATIVE or DUAL This method is _NOT_ thread safe

Parameters:

node -

Returns:

a score along with a sign indication

mergeContexts

public int mergeContexts(int context,
                         int node)

Merge functionality contexts.

Parameters:

context -

node -

Returns:

cleanupContext

public int cleanupContext(int context,
                          int[] t_circuit)

Remove constraint on the members from a functionality context.

Parameters:

context -

t_circuit -

Returns:

getManager

public org.colomoto.mddlib.MDDManager getManager()