utils.list

Class BinnedList

java.lang.Object

utils.list.AbstractList

utils.list.BinnedList

All Implemented Interfaces:

IProbabilityHolder

public class BinnedList
extends AbstractList
implements IProbabilityHolder

Author:

N. Ferrando, J. Alberdi-Rodriguez

Field Summary

Fields

Modifier and Type	Field and Description
private static float	BIN_DIFFERENCE_FACTOR
private AbstractList[]	bins
private boolean	clean Stores if the current totalProbability and the probability calculated from the list are the same.
private int	currentBin

Fields inherited from class utils.list.AbstractList

EVENTS_PER_CLEANUP

Constructor Summary

Constructors

Constructor and Description
BinnedList(Parser parser, int binAmount, int extraBinLevels)

Method Summary

Modifier and Type	Method and Description
void	addAtom(AbstractAtom atom)
void	addDiffusionProbability(double probabilityChange) Updates the total probability
int	cleanup()
void	deleteAtom(AbstractAtom atom) Not tested.
AbstractAtom	getAtomAt(int position)
AbstractList[]	getBins()
double	getDiffusionProbabilityFromList()
java.util.ListIterator	getIterator()
int	getSize()
AbstractAtom	nextEvent()
void	reset()
void	traceSizes(java.lang.String separator)
private void	updateCurrentList()

Methods inherited from class utils.list.AbstractList

addRemovalsSinceLastCleanup, addTime, addTime, autoCleanup, autoCleanup, getDeltaTime, getDepositionProbability, getDiffusionProbability, getGlobalProbability, getLevel, getParent, getRemovalsSinceLastCleanup, getTime, getTotalAtoms, nextReaction, resetRemovalsSinceLastCleanup, resetTime, setDepositionProbability, setDiffusionProbability, setLevel, setParent, setRates, setTotalAtoms

Methods inherited from class java.lang.Object

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

Field Detail

BIN_DIFFERENCE_FACTOR

private static final float BIN_DIFFERENCE_FACTOR

See Also:

Constant Field Values

bins

private final AbstractList[] bins

currentBin

private int currentBin

clean

private boolean clean

Stores if the current totalProbability and the probability calculated from the list are the same.

Constructor Detail

BinnedList

public BinnedList(Parser parser,
                  int binAmount,
                  int extraBinLevels)

Method Detail

updateCurrentList

private void updateCurrentList()

addAtom

public void addAtom(AbstractAtom atom)

Specified by:

addAtom in class AbstractList

deleteAtom

public void deleteAtom(AbstractAtom atom)

Not tested. Might fail.There might be a problem between selected bin and current atom.

Specified by:

deleteAtom in class AbstractList

Parameters:

atom - atom to be deleted.

addDiffusionProbability

public void addDiffusionProbability(double probabilityChange)

Updates the total probability

Specified by:

addDiffusionProbability in interface IProbabilityHolder

Parameters:

probabilityChange - probability change

nextEvent

public AbstractAtom nextEvent()

Specified by:

nextEvent in class AbstractList

cleanup

public int cleanup()

Specified by:

cleanup in class AbstractList

getDiffusionProbabilityFromList

public double getDiffusionProbabilityFromList()

Specified by:

getDiffusionProbabilityFromList in class AbstractList

reset

public void reset()

Overrides:

reset in class AbstractList

getAtomAt

public AbstractAtom getAtomAt(int position)

Specified by:

getAtomAt in class AbstractList

getSize

public int getSize()

Specified by:

getSize in class AbstractList

traceSizes

public void traceSizes(java.lang.String separator)

getBins

public AbstractList[] getBins()

getIterator

public java.util.ListIterator getIterator()

Specified by:

getIterator in class AbstractList