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

D

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

Default size for a gene in number of amino acids.

DEFAULT_RECOMBINE_MEAN - Static variable in class edu.uconn.mcb.lineageevolver.Recombiner

Default mean of recombination sequence length.

DEFAULT_RECOMBINE_PADDING - Static variable in class edu.uconn.mcb.lineageevolver.Recombiner

Default padding of acceptable recombination sequence.

DEFAULT_RECOMBINE_STDEV - Static variable in class edu.uconn.mcb.lineageevolver.Recombiner

Default standard deviation of recombination sequence length.

DEFAULT_REVERSAL_DIST_MEAN - Static variable in class edu.uconn.mcb.lineageevolver.Genome

Default mean of the distance from the origin of replication of a reversal event.

DEFAULT_REVERSAL_DIST_STDEV - Static variable in class edu.uconn.mcb.lineageevolver.Genome

Default standard deviation of the distance from the origin of replication of a reversal event.

DEFAULT_REVERSAL_MEAN - Static variable in class edu.uconn.mcb.lineageevolver.Genome

Default mean of the number of genes to be reversed.

DEFAULT_REVERSAL_STDEV - Static variable in class edu.uconn.mcb.lineageevolver.Genome

Default standard deviation of the number of genes to be reversed.

DUPE_KILL_FREQ - Static variable in class edu.uconn.mcb.lineageevolver.Genome

The number of substitutions to process before calling duplicate or kill gene.

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

The factor by which to increase the fltEvolutionSpeed of a newly duplicated gene.

DiagonalRecombiner - class edu.uconn.mcb.lineageevolver.DiagonalRecombiner.

Description of type goes here.

DiagonalRecombiner(Gene, Gene) - Constructor for class edu.uconn.mcb.lineageevolver.DiagonalRecombiner

Default constructor for objects of type DiagonalRecombiner.

DirectedGraph - interface edu.uconn.mcb.lineageevolver.graph.DirectedGraph.

Common interface for all graph objects.

data - Variable in class edu.uconn.mcb.lineageevolver.graph.EdgeListEdge

The data stored in this edge.

data - Variable in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology.EdgeData

The data stored in this edge.

data - Variable in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology.NodeData

An extra data parameter for storing anything else in a Node.

data - Variable in class edu.uconn.mcb.lineageevolver.graph.EdgeListNode

The data stored in this node.

destination - Variable in class edu.uconn.mcb.lineageevolver.graph.EdgeListEdge

The node towards which this edge goes.

duplicate(int) - Method in class edu.uconn.mcb.lineageevolver.ASRVByteAAGene

duplicate(int) - Method in interface edu.uconn.mcb.lineageevolver.Gene

Generates an paralog of this gene.

duplicateGene() - Method in class edu.uconn.mcb.lineageevolver.Genome

Duplicates the given gene within this genome and inserts it into this genome.