AbstractList (Morphokinetics)

java.lang.Object
- utils.list.AbstractList

All Implemented Interfaces:: IProbabilityHolder

Direct Known Subclasses:: BinnedList, LinearList

public abstract class AbstractList
extends java.lang.Object
implements IProbabilityHolder

Field Summary

Fields
Modifier and Type	Field and Description
`private boolean`	`autoCleanup`
`private boolean`	`computeTime`
`private double`	`deltaTime`
`private int`	`diffusionIndex`
`protected static int`	`EVENTS_PER_CLEANUP`
`private int`	`level`
`private IProbabilityHolder`	`parent`
`private double[]`	`rates`
`private int`	`ratesLength`
`private int`	`removalsSinceLastCleanup`
`private double`	`time`
`private int`	`totalAtoms`

Constructor Summary

Constructors
Constructor and Description

AbstractList(Parser parser)

Constructors
Constructor and Description
`AbstractList(Parser parser)`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`abstract void`	`addAtom(AbstractAtom a)`
`void`	`addRemovalsSinceLastCleanup()`
`void`	`addTime()`
`void`	`addTime(double time)`
`boolean`	`autoCleanup()`
`AbstractList`	`autoCleanup(boolean auto)`
`abstract int`	`cleanup()`
`abstract void`	`deleteAtom(AbstractAtom a)`
`abstract AbstractAtom`	`getAtomAt(int pos)`
`double`	`getDeltaTime(boolean compute)`
`(package private) double`	`getDepositionProbability()`
`double`	`getDiffusionProbability()` Total hops probability.
`abstract double`	`getDiffusionProbabilityFromList()`
`double`	`getGlobalProbability()` Total hops probability plus deposition probability plus desorption probability plus reaction probability.
`abstract java.util.ListIterator`	`getIterator()`
`int`	`getLevel()`
`IProbabilityHolder`	`getParent()`
`int`	`getRemovalsSinceLastCleanup()`
`abstract int`	`getSize()`
`double`	`getTime()`
`int`	`getTotalAtoms()`
`abstract AbstractAtom`	`nextEvent()`
`byte`	`nextReaction()` Equivalent to nextEvent, but only valid for catalysis.
`void`	`reset()`
`void`	`resetRemovalsSinceLastCleanup()`
`void`	`resetTime()` Method to set time to zero.
`void`	`setDepositionProbability(double depositionProbability)`
`(package private) void`	`setDiffusionProbability(double probability)`
`void`	`setLevel(int level)`
`void`	`setParent(IProbabilityHolder parent)`
`void`	`setRates(double[] rates)`
`void`	`setTotalAtoms(int totalAtoms)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface utils.list.IProbabilityHolder
addDiffusionProbability

Field Detail

EVENTS_PER_CLEANUP
```
protected static final int EVENTS_PER_CLEANUP
```
See Also:

Constant Field Values

removalsSinceLastCleanup
```
private int removalsSinceLastCleanup
```

autoCleanup
```
private boolean autoCleanup
```

time
```
private double time
```

rates
```
private double[] rates
```

totalAtoms
```
private int totalAtoms
```

parent
```
private IProbabilityHolder parent
```

level
```
private int level
```

computeTime
```
private boolean computeTime
```

deltaTime
```
private double deltaTime
```

ratesLength
```
private final int ratesLength
```

diffusionIndex
```
private final int diffusionIndex
```

Constructor Detail
- AbstractList
```
public AbstractList(Parser parser)
```

Method Detail

addAtom

public abstract void addAtom(AbstractAtom a)

deleteAtom

public abstract void deleteAtom(AbstractAtom a)

nextEvent

public abstract AbstractAtom nextEvent()

getTime
```
public double getTime()
```

addTime
```
public void addTime(double time)
```

addTime
```
public void addTime()
```

getDeltaTime

public double getDeltaTime(boolean compute)

cleanup
```
public abstract int cleanup()
```

autoCleanup

public AbstractList autoCleanup(boolean auto)

getDepositionProbability
```
double getDepositionProbability()
```

setDepositionProbability

public void setDepositionProbability(double depositionProbability)

setRates
```
public void setRates(double[] rates)
```

getRemovalsSinceLastCleanup

public int getRemovalsSinceLastCleanup()

resetRemovalsSinceLastCleanup

public void resetRemovalsSinceLastCleanup()

addRemovalsSinceLastCleanup

public void addRemovalsSinceLastCleanup()

setDiffusionProbability

void setDiffusionProbability(double probability)

setParent

public void setParent(IProbabilityHolder parent)

getParent
```
public IProbabilityHolder getParent()
```

autoCleanup
```
public boolean autoCleanup()
```

getDiffusionProbabilityFromList

public abstract double getDiffusionProbabilityFromList()

getDiffusionProbability
```
public double getDiffusionProbability()
```
Total hops probability.

Returns:

total probability (always >= 0)

getGlobalProbability
```
public double getGlobalProbability()
```
Total hops probability plus deposition probability plus desorption probability plus reaction probability.

Returns:

total movement + deposition + desorption + reaction.

reset
```
public void reset()
```

resetTime
```
public void resetTime()
```
Method to set time to zero. Useful for catalysis to measure TOF.

getAtomAt

public abstract AbstractAtom getAtomAt(int pos)

getSize
```
public abstract int getSize()
```

getIterator

public abstract java.util.ListIterator getIterator()

getTotalAtoms
```
public int getTotalAtoms()
```

setTotalAtoms

public void setTotalAtoms(int totalAtoms)

getLevel
```
public int getLevel()
```
Returns:

the level

setLevel
```
public final void setLevel(int level)
```
Parameters:

level - the level to set

nextReaction
```
public byte nextReaction()
```
Equivalent to nextEvent, but only valid for catalysis.

Returns:

next reaction type that should be executed.

Class AbstractList

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface utils.list.IProbabilityHolder

Field Detail

EVENTS_PER_CLEANUP

removalsSinceLastCleanup

autoCleanup

time

rates

totalAtoms

parent

level

computeTime

deltaTime

ratesLength

diffusionIndex

Constructor Detail

AbstractList

Method Detail

addAtom

deleteAtom

nextEvent

getTime

addTime

addTime

getDeltaTime

cleanup

autoCleanup

getDepositionProbability

setDepositionProbability

setRates

getRemovalsSinceLastCleanup

resetRemovalsSinceLastCleanup

addRemovalsSinceLastCleanup

setDiffusionProbability

setParent

getParent

autoCleanup

getDiffusionProbabilityFromList

getDiffusionProbability

getGlobalProbability

reset

resetTime

getAtomAt

getSize

getIterator

getTotalAtoms

setTotalAtoms

getLevel

setLevel

nextReaction