fern.simulation.algorithm

Class DependencyGraph

java.lang.Object

fern.simulation.algorithm.DependencyGraph

public class DependencyGraph
extends Object

Implements a dependency graph. It is a directed graph whose vertices are the reactions of a network. From vertex i to vertex j is an edge iff i=j or there is at least one species that changes quantity when reaction i fires and is reactant of reaction j.

This definition implies that if a reaction i fires, the propensities of each descendant in the dependency graph has to be recalculated and no other.

For reference see M.A.Gibson and J.Bruck, Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels, J.Phys.Chem.A., Vol 104, no 9, 2000

Author:

Florian Erhard

See Also:

GillespieEnhanced, GibsonBruckSimulator

Constructor Summary

Constructors

Constructor and Description
DependencyGraph(Network net) Creates the dependency graph for a given network

Method Summary

Modifier and Type	Method and Description
LinkedList<Integer>	getDependent(int reaction) Gets the descendants of a reaction in the dependency graph

Methods inherited from class java.lang.Object

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

Constructor Detail

DependencyGraph

public DependencyGraph(Network net)

Creates the dependency graph for a given network

Parameters:

net - the network

Method Detail

getDependent

public LinkedList<Integer> getDependent(int reaction)

Gets the descendants of a reaction in the dependency graph

Parameters:

reaction - index of the reaction

Returns:

list of dependent reactions