Uses of Package
edu.uconn.mcb.lineageevolver

Packages that use edu.uconn.mcb.lineageevolver
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. 
 

Classes in edu.uconn.mcb.lineageevolver used by edu.uconn.mcb.lineageevolver
AATranslator.InvalidAminoAcid
          Base class for exceptions generated during amino acid encoding/decoding.
AminoAcid
          Common interface for models of amino acids.
ByteAminoAcid
          Amino Acid implementation using byte datatype.
Gene
          Common interface for models of genes.
Genome
          Model of Genomes, composed of a collection of Genes.
Genome.NoHGTProcessed
          Exception thrown when hgt was not processed within a reasonable timeframe.
GenomeVisitor
          Abstract class for all visitors meant exclusively for Genomes.
Lineage.HGTDenied
          Exception thrown when HGT failed a reasonable number of times.
LineageVisitor
          Abstract base class for all Visitors intended specifically to visit Lineages.
Recombiner
          Intermediary class encapsulating the recombination process between two genes.
Recombiner.NoRecombineRegion
          Exception thrown when no region suitable for recombination could be found.
Substitutable
          Common interface for modelling substitutable elements.
SubstitutionMatrix
          Common interface for all substitution matrices.
 

Classes in edu.uconn.mcb.lineageevolver used by edu.uconn.mcb.lineageevolver.config
Genome
          Model of Genomes, composed of a collection of Genes.
 

Classes in edu.uconn.mcb.lineageevolver used by edu.uconn.mcb.lineageevolver.graph
Genome
          Model of Genomes, composed of a collection of Genes.
GenomeVisitor
          Abstract class for all visitors meant exclusively for Genomes.
Lineage
          Model of Lineages comprised of a collection of Genomes.
LineageVisitor
          Abstract base class for all Visitors intended specifically to visit Lineages.