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java.lang.Objectfern.simulation.algorithm.DependencyGraph
public class DependencyGraph
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
GillespieEnhanced
,
GibsonBruckSimulator
Constructor Summary | |
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DependencyGraph(Network net)
Creates the dependency graph for a given network |
Method Summary | |
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LinkedList<Integer> |
getDependent(int reaction)
Gets the descendants of a reaction in the dependency graph |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public DependencyGraph(Network net)
net
- the networkMethod Detail |
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public LinkedList<Integer> getDependent(int reaction)
reaction
- index of the reaction
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