neurord.numeric.grid

Class NextEventQueue.NextEvent

java.lang.Object

neurord.numeric.grid.NextEventQueue.NextEvent

All Implemented Interfaces:

IGridCalc.Event, NextEventQueue.Node

Direct Known Subclasses:

NextEventQueue.NextDiffusion, NextEventQueue.NextReaction, NextEventQueue.NextStimulation

Enclosing class:

NextEventQueue

public abstract class NextEventQueue.NextEvent
extends Object
implements NextEventQueue.Node, IGridCalc.Event

Field Summary

Fields

Modifier and Type	Field and Description
protected int	extent extent: how many "instances" of this event are scheduled to occur.
protected boolean	leap leap: when the event was generated as an "exact" event (false), or "leap" event (true).
protected double	original_wait time: original wait time.
protected NextEventQueue.NextEvent	reverse
protected boolean	reverse_is_leaping
protected List<neurord.numeric.grid.NextEventQueue.ScoeffElem>	scoeff_ki
protected double	time time: when the event is scheduled to occur.

Method Summary

Modifier and Type	Method and Description
protected void	addDependent(NextEventQueue.NextEvent ev, String[] species, boolean verbose)
abstract void	addRelations(HashMap<Integer,ArrayList<NextEventQueue.NextEvent>> map, String[] species, boolean verbose)
void	addReverse(NextEventQueue.NextEvent other)
Collection<IGridCalc.Event>	dependent()
String	description()
int	element() "source" voxel number
int	event_number() Index in the sequential numbering of all events
abstract IGridCalc.EventType	event_type()
int	index()
int[]	reactant_stoichiometry()
protected int[]	reactantPopulation()
int[]	reactants()
protected void	setEvent(int extent, boolean leap, double wait_start, double time)
void	setIndex(int index)
String	stat_index_description()
int	stat_index()
abstract int[]	substrate_stoichiometry() Stoichiometries of species, negative on the lhs, positive on the rhs
abstract Map<Integer,int[][]>	substrates_by_voxel()
abstract int[]	substrates() Indices of species on both sides of the reaction
double	time()
protected void	updateStatistics(int[][] eventStatistics, int firings)

Methods inherited from class java.lang.Object

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

Methods inherited from interface neurord.numeric.grid.IGridCalc.Event

element2

Field Detail

scoeff_ki

protected List<neurord.numeric.grid.NextEventQueue.ScoeffElem> scoeff_ki

time

protected double time

time: when the event is scheduled to occur. Absolute time.

original_wait

protected double original_wait

time: original wait time. This is only used when logging individual events.

extent

protected int extent

extent: how many "instances" of this event are scheduled to occur. Must be greater than 0.

leap

protected boolean leap

leap: when the event was generated as an "exact" event (false), or "leap" event (true). In the first case, extent must be 1. If this.reverse is non-null, a leap is always bidirecational.

reverse

protected NextEventQueue.NextEvent reverse

reverse_is_leaping

protected boolean reverse_is_leaping

Method Detail

event_type

public abstract IGridCalc.EventType event_type()

Specified by:

event_type in interface IGridCalc.Event

setEvent

protected void setEvent(int extent,
                        boolean leap,
                        double wait_start,
                        double time)

event_number

public int event_number()

Description copied from interface: IGridCalc.Event

Index in the sequential numbering of all events

Specified by:

event_number in interface IGridCalc.Event

stat_index

public int stat_index()

Specified by:

stat_index in interface IGridCalc.Event

stat_index_description

public String stat_index_description()

Specified by:

stat_index_description in interface IGridCalc.Event

index

public int index()

Specified by:

index in interface NextEventQueue.Node

element

public int element()

Description copied from interface: IGridCalc.Event

"source" voxel number

Specified by:

element in interface IGridCalc.Event

description

public String description()

Specified by:

description in interface IGridCalc.Event

setIndex

public void setIndex(int index)

Specified by:

setIndex in interface NextEventQueue.Node

time

public double time()

Specified by:

time in interface NextEventQueue.Node

substrates

public abstract int[] substrates()

Description copied from interface: IGridCalc.Event

Indices of species on both sides of the reaction

Specified by:

substrates in interface IGridCalc.Event

substrate_stoichiometry

public abstract 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

substrates_by_voxel

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

addReverse

public void addReverse(NextEventQueue.NextEvent other)

reactantPopulation

protected int[] reactantPopulation()

dependent

public Collection<IGridCalc.Event> dependent()

Specified by:

dependent in interface IGridCalc.Event

reactants

public int[] reactants()

reactant_stoichiometry

public int[] reactant_stoichiometry()

addDependent

protected void addDependent(NextEventQueue.NextEvent ev,
                            String[] species,
                            boolean verbose)

addRelations

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

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.

species: - species names by index

verbose: - print status info

updateStatistics

protected void updateStatistics(int[][] eventStatistics,
                                int firings)