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

L

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

The mean (per category) percentages of mutation used when Lake Categories are mutated.

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

The standard deviations (per category) for mutation percentages used when Lake Categories are mutated.

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

The probability that each rate category will affect horizontal gene transfer.

LECParser - class edu.uconn.mcb.lineageevolver.parsing.LECParser.

Parser for the XML-formatted ELECT output files.

LECParser() - Constructor for class edu.uconn.mcb.lineageevolver.parsing.LECParser

Defualt constructor for objects of type LECParser.

Lineage - class edu.uconn.mcb.lineageevolver.Lineage.

Model of Lineages comprised of a collection of Genomes.

Lineage(Configuration) - Constructor for class edu.uconn.mcb.lineageevolver.Lineage

Default constructor for objects of type lineage.

Lineage.HGTDenied - exception edu.uconn.mcb.lineageevolver.Lineage.HGTDenied.

Exception thrown when HGT failed a reasonable number of times.

Lineage.HGTDenied() - Constructor for class edu.uconn.mcb.lineageevolver.Lineage.HGTDenied

LineageFork - class edu.uconn.mcb.lineageevolver.LineageFork.

LineageVisitor subclass encapsulating the n-furcation process.

LineageFork(GraphEdge) - Constructor for class edu.uconn.mcb.lineageevolver.LineageFork

Constructor for Objects of type LineageFork provided an edge on which to fork.

LineageVisitor - class edu.uconn.mcb.lineageevolver.LineageVisitor.

Abstract base class for all Visitors intended specifically to visit Lineages.

LineageVisitor() - Constructor for class edu.uconn.mcb.lineageevolver.LineageVisitor