fern.simulation.algorithm

Class IndexedPriorityQueue

java.lang.Object

fern.simulation.algorithm.IndexedPriorityQueue

public class IndexedPriorityQueue
extends Object

Implements an indexed priority queue. It is a data structure to manage the absolute taus of the Gibson-Bruck algorithm in an efficient way. It is composed of a binary heap (the taus are the keys) and an index for fast access to a node of the heap. The fast access is necessary to update unused taus in the queue.

For reference see M.A.Gibson and J.Bruck, Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels, J.Phys.Chem.A., Vol 104, no 9, 2000

Author:

Florian Erhard

See Also:

GibsonBruckSimulator

Field Summary

Fields

Modifier and Type	Field and Description
static Random	RND

Constructor Summary

Constructors

Constructor and Description
IndexedPriorityQueue(double[] t) Creates a IndexedPriorityQueue from the given taus

Method Summary

Modifier and Type	Method and Description
double	getKey(int i) Gets the tau of a reaction by lookup in the index
int	getMin() Gets the index of the minimal tau in the queue.
double	getMinKey() Gets the minimal tau in the queue.
int	size() Gets the number of nodes in the binary heap.
String	toString()
void	update(int i, double value) Updates the tau of a reaction to a given value

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

RND

public static final Random RND

Constructor Detail

IndexedPriorityQueue

public IndexedPriorityQueue(double[] t)

Creates a IndexedPriorityQueue from the given taus

Parameters:

t - taus

Method Detail

toString

public String toString()

Overrides:

toString in class Object

size

public int size()

Gets the number of nodes in the binary heap.

Returns:

number of nodes in the binary heap.

getMin

public int getMin()

Gets the index of the minimal tau in the queue.

Returns:

index of the minimal tau

getMinKey

public double getMinKey()

Gets the minimal tau in the queue.

Returns:

minimal tau

update

public void update(int i,
                   double value)

Updates the tau of a reaction to a given value

Parameters:

i - index of the reaction

value - new tau

getKey

public double getKey(int i)

Gets the tau of a reaction by lookup in the index

Parameters:

i - index of the reaction

Returns:

tau of the reaction