utils.list

Class LinearList

java.lang.Object

utils.list.AbstractList

utils.list.LinearList

All Implemented Interfaces:

IProbabilityHolder

public class LinearList
extends AbstractList
implements IProbabilityHolder

Linked list basic implementation.

Author:

N. Ferrando, J. Alberdi-Rodriguez

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	clean Stores if the current totalProbability and the probability calculated from the list are the same.
private double	Ri_DeltaI
private java.util.ArrayList<AbstractAtom>	surface

Fields inherited from class utils.list.AbstractList

EVENTS_PER_CLEANUP

Constructor Summary

Constructors

Constructor and Description
LinearList(Parser parser)

Method Summary

Modifier and Type	Method and Description
void	addAtom(AbstractAtom atom)
void	addDiffusionProbability(double probabilityChange) Updates the diffusion probability.
int	cleanup()
void	deleteAtom(AbstractAtom atom)
AbstractAtom	getAtomAt(int position)
double	getDiffusionProbabilityFromList()
java.util.ListIterator<AbstractAtom>	getIterator()
double	getRi_DeltaI()
int	getSize()
AbstractAtom	nextEvent()
void	reset()

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

surface

private final java.util.ArrayList<AbstractAtom> surface

clean

private boolean clean

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

Ri_DeltaI

private double Ri_DeltaI

Constructor Detail

LinearList

public LinearList(Parser parser)

Method Detail

getDiffusionProbabilityFromList

public double getDiffusionProbabilityFromList()

Specified by:

getDiffusionProbabilityFromList in class AbstractList

addDiffusionProbability

public void addDiffusionProbability(double probabilityChange)

Updates the diffusion probability.

Specified by:

addDiffusionProbability in interface IProbabilityHolder

Parameters:

probabilityChange - probability change.

reset

public void reset()

Overrides:

reset in class AbstractList

cleanup

public int cleanup()

Specified by:

cleanup in class AbstractList

addAtom

public void addAtom(AbstractAtom atom)

Specified by:

addAtom in class AbstractList

deleteAtom

public void deleteAtom(AbstractAtom atom)

Specified by:

deleteAtom in class AbstractList

nextEvent

public AbstractAtom nextEvent()

Specified by:

nextEvent in class AbstractList

getSize

public int getSize()

Specified by:

getSize in class AbstractList

getAtomAt

public AbstractAtom getAtomAt(int position)

Specified by:

getAtomAt in class AbstractList

getIterator

public java.util.ListIterator<AbstractAtom> getIterator()

Specified by:

getIterator in class AbstractList

getRi_DeltaI

public double getRi_DeltaI()