public class NextEventQueue.NextDiffusion extends NextEventQueue.NextEvent
extent, leap, original_wait, reverse, reverse_is_leaping, scoeff_ki, time
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 leap_time based on the limit on variance and expected extents.
|
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() |
addDependent, addReverse, dependent, description, element, event_number, index, reactant_stoichiometry, reactantPopulation, reactants, setEvent, setIndex, stat_index_description, stat_index, time, updateStatistics
public IGridCalc.EventType event_type()
event_type
in interface IGridCalc.Event
event_type
in class NextEventQueue.NextEvent
public double calcPropensity()
NextEventQueue.NextEvent
public int[] substrates()
IGridCalc.Event
substrates
in interface IGridCalc.Event
substrates
in class NextEventQueue.NextEvent
public int[] substrate_stoichiometry()
IGridCalc.Event
substrate_stoichiometry
in interface IGridCalc.Event
substrate_stoichiometry
in class NextEventQueue.NextEvent
public int element2()
IGridCalc.Event
public Map<Integer,int[][]> substrates_by_voxel()
substrates_by_voxel
in class NextEventQueue.NextEvent
public double leap_time(double current)
public int leap_count(double current, double time, boolean bidirectional)
NextEventQueue.NextEvent
public void addRelations(HashMap<Integer,ArrayList<NextEventQueue.NextEvent>> map, String[] species, boolean verbose)
addRelations
in class NextEventQueue.NextEvent
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.Copyright © 2016. All rights reserved.