com.rubecula.darwin.domain.helper
Interface Genotype

All Superinterfaces:

Basic, CacheSignature, Censusible, java.util.Collection<Gene>, Genes, net.sf.tostring0.Identifiable, java.lang.Iterable<Gene>, net.sf.tostring0.IToString, java.util.List<Gene>, Ploidy

All Known Subinterfaces:

Genome

All Known Implementing Classes:

Genome_, Genome_Linear, Genotype_

public interface Genotype
extends net.sf.tostring0.IToString, Ploidy, Genes, Censusible, net.sf.tostring0.Identifiable

A Genotype is a (diploid or haploid) set of genes which can be manipulated. TODO consider defining a Genotype as a haploid set of genes.

Author:

Robin Hillyard

Field Summary

Fields inherited from interface net.sf.tostring0.IToString

ANGBR_OPEN, ANGBRA_CLSE, BRA_CLSE, BRA_OPEN, BRCE_OPEN, BRCS_CLSE, COLON, LIST_SEPARATOR, MAX_ELEMENTS_DEFAULT, S_MT, S_PERCENT, SEPARATOR, SPACE

Fields inherited from interface com.rubecula.darwin.domain.helper.Ploidy

DIPLOID, HAPLOID

Method Summary

boolean	addGene(Gene gene) Add gene to this Genotype at its end.
void	addGene(int locus, Gene gene) Add a Gene to this Genotype at a specific index.
void	addGenes(Genes genes) Add the given genes to this Genotype.
void	doCensus(FrequencyMap<Allele> alleleFrequencies)

Methods inherited from interface net.sf.tostring0.IToString

toString, toStringBrief, toStringId

Methods inherited from interface com.rubecula.darwin.domain.helper.Ploidy

getPloidy

Methods inherited from interface com.rubecula.darwin.domain.helper.Genes

getGene

Methods inherited from interface java.util.List

add, add, addAll, addAll, clear, contains, containsAll, equals, get, hashCode, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, retainAll, set, size, subList, toArray, toArray

Methods inherited from interface com.rubecula.darwin.domain.helper.Basic

getBases

Methods inherited from interface com.rubecula.darwin.domain.helper.CacheSignature

getSignature

Methods inherited from interface com.rubecula.darwin.domain.helper.Censusible

censusMe, getCensusibleChildren

Methods inherited from interface net.sf.tostring0.Identifiable

getIdentifier

Method Detail

addGene

boolean addGene(Gene gene)

Add gene to this Genotype at its end.

Parameters:

gene - an implementer of Gene.

Returns:

true if successful.

addGene

void addGene(int locus,
             Gene gene)

Add a Gene to this Genotype at a specific index.

Parameters:

locus - the locus of the gene.

gene - the gene to be added.

addGenes

void addGenes(Genes genes)

Add the given genes to this Genotype. The new genes will be located at the end of the current set.

Parameters:

genes -

doCensus

void doCensus(FrequencyMap<Allele> alleleFrequencies)

Parameters:

alleleFrequencies -