Uses of Interface
edu.uconn.mcb.lineageevolver.Gene

Packages that use Gene

edu.uconn.mcb.lineageevolver

Provides all basic, universal LineageEvolver classes directly, and serves as a parent for all other LineageEvolver packages.

Uses of Gene in edu.uconn.mcb.lineageevolver

Classes in edu.uconn.mcb.lineageevolver that implement Gene

class

ASRVByteAAGene Gene implementation using ByteAminoAcid and Simple Among Site Rate Variation (ASRV).

Fields in edu.uconn.mcb.lineageevolver declared as Gene

(package private) Gene	Recombiner._gneSource The gene from which recombined material will be copied.
(package private) Gene	Recombiner._gneDestination The gene into which recombined material will be copied.
(package private) Gene	Recombiner.NoRecombineRegion.gneDestination The destination Gene for which recombination failed.
(package private) Gene	Recombiner.NoRecombineRegion.gneSource The source Gene for which recombination failed.
private Gene[]	Genome._gneGenes The collection of genes in this genome.

Methods in edu.uconn.mcb.lineageevolver that return Gene

Gene	Genome.duplicateGene() Duplicates the given gene within this genome and inserts it into this genome.
Gene	Genome.getGene(int index) Returns the Gene at a given index in this Genome.
Gene	Gene.duplicate(int paralogID) Generates an paralog of this gene.
Gene	ASRVByteAAGene.duplicate(int paralogID)

Constructors in edu.uconn.mcb.lineageevolver with parameters of type Gene

Recombiner(Gene gneSource, Gene gneDestination)
Default constructor for objects of type Recombiner.

Recombiner.NoRecombineRegion(Gene gneSource, Gene gneDestination)
Constructor for objects of type NoRecombineRegion, provided source and destination Genes on which recombination failed.

DiagonalRecombiner(Gene gneSource, Gene gneDestination)
Default constructor for objects of type DiagonalRecombiner.