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