alun.gchap
Class GeneticTrait

java.lang.Object
  alun.gchap.GeneticTrait

Direct Known Subclasses:

Marker, MultiLocusTrait

public abstract class GeneticTrait
extends java.lang.Object

A genetic trait links together a locus with phenotypes.

Constructor Summary

GeneticTrait(Locus loc)
Creates a new genetic trait for the given locus.

Method Summary

void	downCode() Removes from the locus any alleles that have zero frequency.
void	downCode(double tol)
void	geneCount(int n) Runs n iterations of the gene counting algorithm for the trait.
Locus	getLocus() Returns the asssociated locus.
int	nPhenotypes() Returns the number of phenotype for the trait at this locus.
void	parsDownCode() Removes from the locus any alleles that have frequency less than the the given value.
java.lang.String	toString() Returns a string representation of the trait.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

GeneticTrait

public GeneticTrait(Locus loc)

Creates a new genetic trait for the given locus.

Method Detail

nPhenotypes

public int nPhenotypes()

Returns the number of phenotype for the trait at this locus.

getLocus

public Locus getLocus()

Returns the asssociated locus.

downCode

public void downCode()

Removes from the locus any alleles that have zero frequency.

parsDownCode

public void parsDownCode()

Removes from the locus any alleles that have frequency less than the the given value.

downCode

public void downCode(double tol)

geneCount

public void geneCount(int n)

Runs n iterations of the gene counting algorithm for the trait.

toString

public java.lang.String toString()

Returns a string representation of the trait.

Overrides:

toString in class java.lang.Object