jenes.chromosome

Class GenericAlleleSet<T>

java.lang.Object

jenes.chromosome.GenericAlleleSet<T>

Type Parameters:

T -

All Implemented Interfaces:

AlleleSet<T>

Direct Known Subclasses:

DoubleAlleleSet, DoubleAlleleSet, IntegerAlleleSet, IntegerAlleleSet

public class GenericAlleleSet<T>
extends java.lang.Object
implements AlleleSet<T>

A GenericAlleleSet represents a concrete allele set implementation. It is usefull to instantiate a new AlleleSet when the allele values are contained by a list, by an array or by a Set. At creation time, the aplhabet objects are not cloned so:

Note that this implementation is not synchronized. If multiple threads access a GenericAlleleSet concurrently, and at least one of the threads modifies the set, it must be synchronized externally or wrapped using the Collections.synchronizedSet(Set) method.

Note that if values are modified externally, the allele set object also change according at that modification.

Some examples of code are provided below.

    Set s = Collections.synchronizedSet(new HashSet(...));
    GenericAlleleSet geneticAlleleSet = new GenericAlleleSet(s);
 

to build a generic allele set with the object value accesses synchronized.

    GenericAlleleSet generic alleleSet = new GenericAlleleSet(true, false),
 

to build a generic allele set with the boolean values as allele object values.

    GenericAlleleSet generic alleleSet = new GenericAlleleSet(AnyJavaEnum.values()) );
 

to build a generic allele set with the enum values.

Since:

1.0

Version:

2.0

See Also:

ObjectChromosome

Constructor Summary

Constructors

Constructor and Description
GenericAlleleSet(java.util.List<T> list) Creates a new AlleleSet instance with the alphabet values contained by the specified list
GenericAlleleSet(java.util.Set<T> set) Creates a new AlleleSet instance with the alphabet values contained by the specified set
GenericAlleleSet(T... values) Creates a new AlleleSet instance with the alphabet values contained by the specified array

Method Summary

Methods

Modifier and Type	Method and Description
double	difference(T a0, T a1) Provides the genetic difference between two alleles.
double[][]	getDefaultDifferences() Returns the default difference matrix as given by the difference of allele positions in the set.
T	getElementAt(int pos) Returns the allele at a given positition.
int	getIndexOf(T a) Returns the index of element a.
T	getRandomValue() Returns an allele randomly chosen.
void	setDifferences(double[][] diff) Sets the difference matrix between alleles.
int	size() Returns the number of alleles held by the allele set.

Methods inherited from class java.lang.Object

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

Constructor Detail

GenericAlleleSet

public GenericAlleleSet(java.util.Set<T> set)

Creates a new AlleleSet instance with the alphabet values contained by the specified set

Parameters:

set - the set with the alphabet allele values

GenericAlleleSet

public GenericAlleleSet(T... values)

Creates a new AlleleSet instance with the alphabet values contained by the specified array

Parameters:

values - the alphabet values array

GenericAlleleSet

public GenericAlleleSet(java.util.List<T> list)

Creates a new AlleleSet instance with the alphabet values contained by the specified list

Parameters:

list - the alphabet values list

Method Detail

getElementAt

public final T getElementAt(int pos)

Returns the allele at a given positition.

Specified by:

getElementAt in interface AlleleSet<T>

Parameters:

pos -

Returns:

the element

getIndexOf

public final int getIndexOf(T a)

Returns the index of element a.

Parameters:

a - - the allele to find

Returns:

the allele index

getRandomValue

public final T getRandomValue()

Returns an allele randomly chosen.

Specified by:

getRandomValue in interface AlleleSet<T>

Returns:

a value

size

public final int size()

Returns the number of alleles held by the allele set.

Specified by:

size in interface AlleleSet<T>

Returns:

the number of alleles

setDifferences

public void setDifferences(double[][] diff)

Sets the difference matrix between alleles. It is expected that diff is a square matrix according to set size, with diff(i,i) = 0 and diff(i,j) = -diff(j,i).

Parameters:

diff - - the difference matrix

getDefaultDifferences

public double[][] getDefaultDifferences()

Returns the default difference matrix as given by the difference of allele positions in the set.

Returns:

the allele difference matrix.

difference

public double difference(T a0,
                T a1)

Description copied from interface: AlleleSet

Provides the genetic difference between two alleles.

Specified by:

difference in interface AlleleSet<T>

Parameters:

a0 - - first allele

a1 - - second allele

Returns:

- the genetic difeerence