Uses of Class
edu.uconn.mcb.lineageevolver.Genome

Packages that use Genome

edu.uconn.mcb.lineageevolver	Provides all basic, universal LineageEvolver classes directly, and serves as a parent for all other LineageEvolver packages.
edu.uconn.mcb.lineageevolver.config	This package provides configuration interfaces and classes.
edu.uconn.mcb.lineageevolver.graph	Provides graph data structure interface and implementation.

Uses of Genome in edu.uconn.mcb.lineageevolver

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

Genome[]

Lineage.getTopLevel() Returns the top level of genomes in this lineage.

Methods in edu.uconn.mcb.lineageevolver with parameters of type Genome

private float	Lineage.getCategoryDifference(Genome gnm1, Genome gnm2) Returns the weighted difference in Lake's categories between two Genomes.
abstract void	GenomeVisitor.applyToGenome(Genome g) Applies this visitor to the given Genome.
void	GenomeRearranger.applyToGenome(Genome g) Applies rearrangement on the given genome.
void	GenomeEvolver.applyToGenome(Genome g) Induces 'evolution' on the given genome.
void	Genome.hgt(Genome gnmSource) Selects the genes on which horizontal transfer will occur within this genome.
void	GeneKiller.applyToGenome(Genome g) Processes gene death on the provided genome.
void	GeneDuplicator.applyToGenome(Genome g) Processes gene duplication on the provided genome.

Uses of Genome in edu.uconn.mcb.lineageevolver.config

Fields in edu.uconn.mcb.lineageevolver.config declared as Genome

protected Genome

Configuration._rootGenome The root genome.

Methods in edu.uconn.mcb.lineageevolver.config that return Genome

Genome

Configuration.getRootGenome() Returns the root Genome.

Methods in edu.uconn.mcb.lineageevolver.config with parameters of type Genome

void	Configuration.setRootGenome(Genome genome) Sets the root genome.

Uses of Genome in edu.uconn.mcb.lineageevolver.graph

Fields in edu.uconn.mcb.lineageevolver.graph declared as Genome

(package private) Genome

EdgeListGraphTopology.NodeData.genome The genome residing in this node.

Methods in edu.uconn.mcb.lineageevolver.graph that return Genome

Genome	GraphTopology.getGenome(GraphNode v) Returns genome stored in the given node.
Genome	EdgeListGraphTopology.getGenome(GraphNode v)

Methods in edu.uconn.mcb.lineageevolver.graph with parameters of type Genome

void	GraphTopology.setGenome(GraphNode v, Genome g) Sets the genome for a given node.
void	EdgeListGraphTopology.setGenome(GraphNode v, Genome g)

Constructors in edu.uconn.mcb.lineageevolver.graph with parameters of type Genome

EdgeListGraphTopology.NodeData(java.lang.String name, Genome genome, java.lang.Object data, EdgeListNode node)
Default constructor for objects of type NodeData.