Package fern.simulation.algorithm

Class Summary

Class	Description
AbstractBaseTauLeaping	Base class for all tau leaping procedures (which are different in the methods choosing the timestep candidates for critical and noncritical reactions).
AbstractTauLeapingPropensityBoundSimulator	There are some possibilities to bind the expected change of the propensities by a value epsilon in order to fulfill the leap condition.
CompositionRejection	This is an enhanced version of the original Direct method developed by Gillespie.
DependencyGraph	Implements a dependency graph.
GibsonBruckSimulator	Implementation of the algorithm of Gibson and Bruck.
GillespieEnhanced	This is an enhanced version of the original Direct method developed by Gillespie.
GillespieSimple	Implementation of Gillespie's Direct method.
GroupContainer
HybridMaximalTimeStep	This is an modified version of Maximal Time Step Method by Puchalka and Kierzec.
IndexedPriorityQueue	Implements an indexed priority queue.
TauLeapingAbsoluteBoundSimulator	There are some possibilities to bind the expected change of the propensities by a value epsilon in order to fulfill the leap condition.
TauLeapingRelativeBoundSimulator	There are some possibilities to bind the expected change of the propensities by a value epsilon in order to fulfill the leap condition.
TauLeapingSpeciesPopulationBoundSimulator	There are some possibilities to bind the expected change of the propensities by a value epsilon in order to fulfill the leap condition.