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

R

RandomSelection - class edu.uconn.mcb.lineageevolver.RandomSelection.

Class used for weighted random selection of an element in a set, given discrete relative probabilities (weights) between elements in the set.

RandomSelection(float[]) - Constructor for class edu.uconn.mcb.lineageevolver.RandomSelection

Default constructor for objects of type RandomSelection.

Recombiner - class edu.uconn.mcb.lineageevolver.Recombiner.

Intermediary class encapsulating the recombination process between two genes.

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

Default constructor for objects of type Recombiner.

Recombiner.NoRecombineRegion - exception edu.uconn.mcb.lineageevolver.Recombiner.NoRecombineRegion.

Exception thrown when no region suitable for recombination could be found.

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

Constructor for objects of type NoRecombineRegion, provided source and destination Genes on which recombination failed.

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

Random number generator shared by all gen1es.

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

Random number generator shared by all genomes.

randomNumberGenerator - Static variable in class edu.uconn.mcb.lineageevolver.RandomSelection

Random number generator shared amongst all RandomSelection classes.

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

Random number generator shared by all Recombiners.

rate - Static variable in class edu.uconn.mcb.lineageevolver.JTT

The actual matrix data.

recombine() - Method in class edu.uconn.mcb.lineageevolver.DiagonalRecombiner

recombine() - Method in class edu.uconn.mcb.lineageevolver.Recombiner

Processes recombination between the source and destination genes.

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

Processes reversal in this genome from either the origin or terminus of replication (applicable only to circular prokaryotic genomes).

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

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

Reverses the amino acid positions in this gene.