com.rubecula.darwin.domain.helper
Interface Expresser

All Known Implementing Classes:

Expresser_, Expresser_Direct, Expresser_Function, Expresser_Mendelian, Expresser_Sex, Expresser_TS

public interface Expresser

Defines the operations supported by an "expresser", that is an object that can take a Gene (or Genome) and express that gene(s) in the context of an environment.

Author:

Robin Hillyard

Method Summary

java.util.Collection<Expression>	express(Colony colony, Gene... genes) Express the gene in the context of the environment, potentially resulting in several expressions, each of which may be either a Trait or an ExPhen.
Trait	express(Gene... genes) Express the genes.
Pharacter	getCharacter()
java.lang.String	getComplement(Locus locus, java.lang.String allele) Get the complementary allele key, such that isComplementary(Locus, String, String) will be true.
boolean	isComplementary(Locus locus, java.lang.String allele1, java.lang.String allele2)

Method Detail

express

java.util.Collection<Expression> express(Colony colony,
                                         Gene... genes)

Express the gene in the context of the environment, potentially resulting in several expressions, each of which may be either a Trait or an ExPhen. This is the more general form of expression and typically will invoke the more specific form -- express(Gene...) -- (colony is ignored and always returns a Trait). This method supports both polygeny (where several genes act together) and pleiotropy (where one or more genes results in more than one trait).

Parameters:

colony - (which may be null)

genes - one gene or a set of polygenic genes.

Returns:

a collection of objects which are either a Trait or an ExPhen

express

Trait express(Gene... genes)

Express the genes.

Parameters:

genes -

Returns:

a Trait

getCharacter

Pharacter getCharacter()

Returns:

the character which the expressed trait will exhibit.

getComplement

java.lang.String getComplement(Locus locus,
                               java.lang.String allele)

Get the complementary allele key, such that isComplementary(Locus, String, String) will be true.

Parameters:

locus -

allele -

Returns:

the complementary allele key.

isComplementary

boolean isComplementary(Locus locus,
                        java.lang.String allele1,
                        java.lang.String allele2)

Parameters:

locus -

allele1 -

allele2 -

Returns:

true if the alleles are complementary, i.e. if expressed sequentially, the result would be the same as if they had not been expressed at all.