neurord.numeric.grid

Class NextEventQueue.NextReaction

java.lang.Object

neurord.numeric.grid.NextEventQueue.NextEvent

neurord.numeric.grid.NextEventQueue.NextReaction

All Implemented Interfaces:

IGridCalc.Event, NextEventQueue.Node

Enclosing class:

NextEventQueue

public class NextEventQueue.NextReaction
extends NextEventQueue.NextEvent

Field Summary

Fields inherited from class neurord.numeric.grid.NextEventQueue.NextEvent

extent, leap, original_wait, reverse, reverse_is_leaping, scoeff_ki, time

Method Summary

Modifier and Type	Method and Description
void	addRelations(HashMap<Integer,ArrayList<NextEventQueue.NextEvent>> map, String[] species, boolean verbose)
double	calcPropensity() Calculate propensity of this event.
int	element2() "target" voxel number (different from source only for diffusion)
IGridCalc.EventType	event_type()
int	leap_count(double current, double time, boolean bidirectional) Calculate the (randomized) extent of the reaction based in the time given.
double	leap_time(double current) Calculate the time for which this reaction changes the population of products by ɛ.
protected int[]	productPopulation()
protected double	self_leap_limit(int[] X) Make sure that the propensity of *this* reaction does not change too much.
int[]	substrate_stoichiometry() Stoichiometries of species, negative on the lhs, positive on the rhs
Map<Integer,int[][]>	substrates_by_voxel()
int[]	substrates() Indices of species on both sides of the reaction
String	toString()

Methods inherited from class neurord.numeric.grid.NextEventQueue.NextEvent

addDependent, addReverse, dependent, description, element, event_number, index, reactant_stoichiometry, reactantPopulation, reactants, setEvent, setIndex, stat_index_description, stat_index, time, updateStatistics

Methods inherited from class java.lang.Object

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

Method Detail

event_type

public IGridCalc.EventType event_type()

Specified by:

event_type in interface IGridCalc.Event

Specified by:

event_type in class NextEventQueue.NextEvent

productPopulation

protected int[] productPopulation()

self_leap_limit

protected double self_leap_limit(int[] X)

Make sure that the propensity of *this* reaction does not change too much. Based on the equation: da/dX_i / a = n_i / X_i

leap_time

public double leap_time(double current)

Description copied from class: NextEventQueue.NextEvent

Calculate the time for which this reaction changes the population of products by ɛ. Propensity is not recalculated, so must be brought up-to-date externally.

leap_count

public int leap_count(double current,
                      double time,
                      boolean bidirectional)

Description copied from class: NextEventQueue.NextEvent

Calculate the (randomized) extent of the reaction based in the time given.

addRelations

public void addRelations(HashMap<Integer,ArrayList<NextEventQueue.NextEvent>> map,
                         String[] species,
                         boolean verbose)

Specified by:

addRelations in class NextEventQueue.NextEvent

Parameters:

map - contains, for every voxel, a list of events which depend on the state of that voxel. Subsequently, if this event should look at events attached to any voxel it modifies, and maybe add them as its relation.

calcPropensity

public double calcPropensity()

Description copied from class: NextEventQueue.NextEvent

Calculate propensity of this event.

substrates

public int[] substrates()

Description copied from interface: IGridCalc.Event

Indices of species on both sides of the reaction

Specified by:

substrates in interface IGridCalc.Event

Specified by:

substrates in class NextEventQueue.NextEvent

substrate_stoichiometry

public int[] substrate_stoichiometry()

Description copied from interface: IGridCalc.Event

Stoichiometries of species, negative on the lhs, positive on the rhs

Specified by:

substrate_stoichiometry in interface IGridCalc.Event

Specified by:

substrate_stoichiometry in class NextEventQueue.NextEvent

substrates_by_voxel

public Map<Integer,int[][]> substrates_by_voxel()

Specified by:

substrates_by_voxel in class NextEventQueue.NextEvent

element2

public int element2()

Description copied from interface: IGridCalc.Event

"target" voxel number (different from source only for diffusion)

toString

public String toString()

Overrides:

toString in class Object