org.biojavax.ga.util

Class WeightedSet

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractSet

org.biojavax.ga.util.WeightedSet

All Implemented Interfaces:

java.io.Serializable, java.lang.Iterable, java.util.Collection, java.util.Set

public class WeightedSet
extends java.util.AbstractSet
implements java.io.Serializable

Inspred by the BioJava Distribution objects the WeightedSet is a map from a Key to a Weight. Unlike Distributions the Keys do not have to be Symbols. In the GA package the WeightedMap is useful for sampling Organisms according to their fitness.

When Symbols are added or their weights are set then the weights are internally normalized to 1

Since:

1.5

Version:

1.0

Author:

Mark Schreiber

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
WeightedSet()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	add(java.lang.Object o) Adds a new Object with a weight of zero.
boolean	addAll(java.util.Collection c)
java.util.Map	asMap() Converts the Set to a map from key Objects to Double weights.
void	clear()
boolean	contains(java.lang.Object o)
boolean	containsAll(java.util.Collection c)
protected double	getTotalWeight() The total weight that has been added to this Set.
double	getWeight(java.lang.Object o) Determines the normalized weight for o
boolean	isEmpty()
java.util.Iterator	iterator() Returns an unmodifiable iterator over the keys of the set.
boolean	remove(java.lang.Object o)
boolean	retainAll(java.util.Collection c)
java.lang.Object	sample() Randomly samples an Object from the Set according to its weight.
void	setWeight(java.lang.Object o, double w) Sets the weight of an Object.
int	size()
java.lang.Object[]	toArray()

Methods inherited from class java.util.AbstractSet

equals, hashCode, removeAll

Methods inherited from class java.util.AbstractCollection

toArray, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Set

toArray

Constructor Detail

WeightedSet

public WeightedSet()

Method Detail

asMap

public java.util.Map asMap()

Converts the Set to a map from key Objects to Double weights.

Returns:

a Map with all the key-weight mappings. Weights are not normalized in this map.

sample

public java.lang.Object sample()

Randomly samples an Object from the Set according to its weight.

Returns:

the Object sampled.

getWeight

public double getWeight(java.lang.Object o)
                 throws java.util.NoSuchElementException

Determines the normalized weight for o

Parameters:

o - the Object you want to know the weight of

Returns:

the normalized weight

Throws:

java.util.NoSuchElementException - if o is not found in this set

getTotalWeight

protected double getTotalWeight()

The total weight that has been added to this Set.

Returns:

the total weight (the value that can be used for normalizing)

setWeight

public void setWeight(java.lang.Object o,
             double w)

Sets the weight of an Object. If the Object is not in this Set then it is added.

Parameters:

o - the Object

w - the weight.

Throws:

java.lang.IllegalArgumentException - if w is < 0.0

contains

public boolean contains(java.lang.Object o)

Specified by:

contains in interface java.util.Collection

Specified by:

contains in interface java.util.Set

Overrides:

contains in class java.util.AbstractCollection

remove

public boolean remove(java.lang.Object o)

Specified by:

remove in interface java.util.Collection

Specified by:

remove in interface java.util.Set

Overrides:

remove in class java.util.AbstractCollection

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface java.util.Collection

Specified by:

isEmpty in interface java.util.Set

Overrides:

isEmpty in class java.util.AbstractCollection

retainAll

public boolean retainAll(java.util.Collection c)

Specified by:

retainAll in interface java.util.Collection

Specified by:

retainAll in interface java.util.Set

Overrides:

retainAll in class java.util.AbstractCollection

add

public boolean add(java.lang.Object o)

Adds a new Object with a weight of zero. Equivalent to setWeight(o, 0.0);

Specified by:

add in interface java.util.Collection

Specified by:

add in interface java.util.Set

Overrides:

add in class java.util.AbstractCollection

Parameters:

o - the object to add.

Returns:

true if this Object has not been added before.

size

public int size()

Specified by:

size in interface java.util.Collection

Specified by:

size in interface java.util.Set

Specified by:

size in class java.util.AbstractCollection

containsAll

public boolean containsAll(java.util.Collection c)

Specified by:

containsAll in interface java.util.Collection

Specified by:

containsAll in interface java.util.Set

Overrides:

containsAll in class java.util.AbstractCollection

toArray

public java.lang.Object[] toArray()

Specified by:

toArray in interface java.util.Collection

Specified by:

toArray in interface java.util.Set

Overrides:

toArray in class java.util.AbstractCollection

clear

public void clear()

Specified by:

clear in interface java.util.Collection

Specified by:

clear in interface java.util.Set

Overrides:

clear in class java.util.AbstractCollection

iterator

public java.util.Iterator iterator()

Returns an unmodifiable iterator over the keys of the set.

Specified by:

iterator in interface java.lang.Iterable

Specified by:

iterator in interface java.util.Collection

Specified by:

iterator in interface java.util.Set

Specified by:

iterator in class java.util.AbstractCollection

Returns:

an Iterator

addAll

public boolean addAll(java.util.Collection c)

Specified by:

addAll in interface java.util.Collection

Specified by:

addAll in interface java.util.Set

Overrides:

addAll in class java.util.AbstractCollection