Package edu.uconn.mcb.lineageevolver

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

See:
Description

Interface Summary

AminoAcid	Common interface for models of amino acids.
Gene	Common interface for models of genes.
Substitutable	Common interface for modelling substitutable elements.
SubstitutionMatrix	Common interface for all substitution matrices.

Class Summary

AATranslator	Serves as a translator between AminoAcid naming schemes.
ASRVByteAAGene	Gene implementation using ByteAminoAcid and Simple Among Site Rate Variation (ASRV).
ByteAminoAcid	Amino Acid implementation using byte datatype.
DiagonalRecombiner	Description of type goes here.
GeneDuplicator	GenomeVisitor subclass encapsulating gene duplication functionality.
GeneKiller	GenomeVisitor subclass encapsulating gene death functionality.
Genome	Model of Genomes, composed of a collection of Genes.
GenomeEvolver	GenomeVisitor subclass encapsulating generic 'evolution'.
GenomeRearranger	GenomeVisitor subclass encapsulating the rearrangement process.
GenomeVisitor	Abstract class for all visitors meant exclusively for Genomes.
JTT	JTT Substitution Matrix.
Lineage	Model of Lineages comprised of a collection of Genomes.
LineageFork	LineageVisitor subclass encapsulating the n-furcation process.
LineageVisitor	Abstract base class for all Visitors intended specifically to visit Lineages.
RandomSelection	Class used for weighted random selection of an element in a set, given discrete relative probabilities (weights) between elements in the set.
Recombiner	Intermediary class encapsulating the recombination process between two genes.

Exception Summary

AATranslator.InvalidAminoAcid	Base class for exceptions generated during amino acid encoding/decoding.
AATranslator.InvalidAminoAcid.InvalidAminoAcidByte	Exception thrown when a byte value outside the AminoAcid range was used as an encoded AminoAcid.
AATranslator.InvalidAminoAcid.InvalidAminoAcidChar	Exception thrown when a character value outside the AminoAcid range was used as an encoded AminoAcid.
AATranslator.InvalidAminoAcid.InvalidAminoAcidInt	Exception thrown when an integer value outside the AminoAcid range (0-19) was used as an encoded AminoAcid.

Package edu.uconn.mcb.lineageevolver Description

Provides all basic, universal LineageEvolver classes directly, and serves as a parent for all other LineageEvolver packages. This package directly provides all of the basic interfaces and implementing classes for each level of abstraction within the LineageEvolver design, as well as associated visitors.