public class NextEventQueue extends Object
Modifier and Type | Class and Description |
---|---|
class |
NextEventQueue.Happening |
class |
NextEventQueue.NextDiffusion |
class |
NextEventQueue.NextEvent |
class |
NextEventQueue.NextReaction |
class |
NextEventQueue.NextStimulation |
static interface |
NextEventQueue.Node |
static class |
NextEventQueue.Numbering |
class |
NextEventQueue.PriorityTree<T extends NextEventQueue.Node> |
Modifier and Type | Field and Description |
---|---|
static org.apache.logging.log4j.Logger |
log |
static int[] |
MINUS_ONE |
static int[] |
MINUS_ONE_PLUS_ONE |
static int[] |
PLUS_ONE |
Constructor and Description |
---|
NextEventQueue(RandomGenerator random,
StepGenerator stepper,
int[][] particles,
boolean adaptive,
double tolerance,
double leap_min_jump)
Use create() instead, this is public only for testing.
|
Modifier and Type | Method and Description |
---|---|
double |
advance(double time,
double tstop,
double timelimit,
int[][] eventStatistics,
List<IGridCalc.Happening> events)
Execute an event if the next event is before tstop.
|
static NextEventQueue |
create(int[][] particles,
RandomGenerator random,
StepGenerator stepper,
VolumeGrid grid,
ReactionTable rtab,
StimulationTable stimtab,
boolean adaptive,
double tolerance,
double leap_min_jump,
boolean verbose,
String statistics) |
Collection<IGridCalc.Event> |
getEvents() |
int |
stat_count(String statistics,
String[] species) |
static int[][] |
stoichiometry(int[] ri,
int[] rs,
int[] pi,
int[] ps)
Calculates a joint array of stoichiometries from reactants @ri, @rs and products @pi, @ps.
|
int |
updatePopulation(int element,
int specie,
int count,
NextEventQueue.NextEvent event) |
public static final org.apache.logging.log4j.Logger log
public static final int[] PLUS_ONE
public static final int[] MINUS_ONE
public static final int[] MINUS_ONE_PLUS_ONE
public NextEventQueue(RandomGenerator random, StepGenerator stepper, int[][] particles, boolean adaptive, double tolerance, double leap_min_jump)
public static int[][] stoichiometry(int[] ri, int[] rs, int[] pi, int[] ps)
public int updatePopulation(int element, int specie, int count, NextEventQueue.NextEvent event)
public static NextEventQueue create(int[][] particles, RandomGenerator random, StepGenerator stepper, VolumeGrid grid, ReactionTable rtab, StimulationTable stimtab, boolean adaptive, double tolerance, double leap_min_jump, boolean verbose, String statistics)
public double advance(double time, double tstop, double timelimit, int[][] eventStatistics, List<IGridCalc.Happening> events)
timelimit
- is the maximum time that leap events are allowed to extend to.
Normally this would either be either tstop or the simulation time.eventStatistics
- is an array to store event counts in as {firings, extent}.events
- will be used to store all Hapennings, unless null.public Collection<IGridCalc.Event> getEvents()
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