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

M

main(String[]) - Static method in class edu.uconn.mcb.lineageevolver.ASRVByteAAGene

Generic driver for ASRVByteAAGenes.

main(String[]) - Static method in class edu.uconn.mcb.lineageevolver.ByteAminoAcid

Simple driver for ByteAminoAcid testing/debugging.

main(String[]) - Static method in class edu.uconn.mcb.lineageevolver.Genome

Driver for debugging/testing.

main(String[]) - Static method in class edu.uconn.mcb.lineageevolver.Lineage

Main driver for LineageEvolver - runs the simulation and outputs results.

main(String[]) - Static method in class edu.uconn.mcb.lineageevolver.parsing.FASTAParser

Test driver.

main(String[]) - Static method in class edu.uconn.mcb.lineageevolver.parsing.LECParser

Test driver.

makeEvolutionSpeeds(int) - Static method in class edu.uconn.mcb.lineageevolver.Genome

Generates random evolution speeds between 0 and 1 (uniform distribution).

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

Mutate the ASRV by swapping randomly selected regions.

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

Mutates the evolution speed of this Gene randomly up or down from the current evolution speed.

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

Mutate each of Lake's categories by adding a random value (positive or negative) to each.