A B C D E F G H I J K L M N O P R S T V _

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_aaAminoAcid - Variable in class edu.uconn.mcb.lineageevolver.ASRVByteAAGene

The sequence of amino acids that make up this gene.

_byteType - Variable in class edu.uconn.mcb.lineageevolver.ByteAminoAcid

The type of this amino acid.

_currentTime - Variable in class edu.uconn.mcb.lineageevolver.Lineage

The amount of time that has passed since the beginning of evolution.

_edge - Variable in class edu.uconn.mcb.lineageevolver.LineageFork

The node to fork

_edges - Variable in class edu.uconn.mcb.lineageevolver.Lineage

The edges we are currently processing.

_edges - Variable in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraph

Our list of edges.

_fltEvolutionSpeed - Variable in class edu.uconn.mcb.lineageevolver.ASRVByteAAGene

The speed with which this gene evolves.

_fltSubstitutionProbability - Variable in class edu.uconn.mcb.lineageevolver.ByteAminoAcid

The probability that this amino acid will undergo substitution.

_gneDestination - Variable in class edu.uconn.mcb.lineageevolver.Recombiner

The gene into which recombined material will be copied.

_gneGenes - Variable in class edu.uconn.mcb.lineageevolver.Genome

The collection of genes in this genome.

_gneSource - Variable in class edu.uconn.mcb.lineageevolver.Recombiner

The gene from which recombined material will be copied.

_hgtCounts - Variable in class edu.uconn.mcb.lineageevolver.Lineage

The amount of substitions before horizontal gene transfer is to be processed.

_hgtCounts - Variable in class edu.uconn.mcb.lineageevolver.config.Configuration

Our breakpoints for HGT.

_id - Variable in class edu.uconn.mcb.lineageevolver.ASRVByteAAGene

The ID number for this gene.

_intParalogs - Variable in class edu.uconn.mcb.lineageevolver.Genome

The number of paralogs per gene in this genome.

_intToChar - Static variable in class edu.uconn.mcb.lineageevolver.AATranslator

Provides mapping between char and int encodings for AminoAcids.

_lakeCategories - Variable in class edu.uconn.mcb.lineageevolver.Genome

The values for Lake's ten categories.

_nodes - Variable in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraph

Our list of nodes.

_paralogID - Variable in class edu.uconn.mcb.lineageevolver.ASRVByteAAGene

The paralog ID number for this gene.

_parser - Variable in class edu.uconn.mcb.lineageevolver.parsing.LECParser

The actual parser used to parse the XML document.

_probabilities - Variable in class edu.uconn.mcb.lineageevolver.RandomSelection

The probability of selection per element in the n-tuple.

_rootGenome - Variable in class edu.uconn.mcb.lineageevolver.config.Configuration

The root genome.

_smtrx - Static variable in class edu.uconn.mcb.lineageevolver.ASRVByteAAGene

The currently employed substitution matrix for this gene.

_substitutions - Variable in class edu.uconn.mcb.lineageevolver.GenomeEvolver

The length of evolution that this visitor will process.

_total - Variable in class edu.uconn.mcb.lineageevolver.RandomSelection

The sum of all probabilities in the provided array.

_totalSubs - Variable in class edu.uconn.mcb.lineageevolver.ASRVByteAAGene

The number of substitutions processed in this gene.

_totalTime - Variable in class edu.uconn.mcb.lineageevolver.Lineage

The total time to process evolution.

_totalTime - Variable in class edu.uconn.mcb.lineageevolver.config.Configuration

The total time to process evolution.

_tree - Variable in class edu.uconn.mcb.lineageevolver.Lineage

The tree topology to follow for this lineage.

_tree - Variable in class edu.uconn.mcb.lineageevolver.config.Configuration

The topology.