Serialized Form

Package edu.uconn.mcb.lineageevolver.config

Class edu.uconn.mcb.lineageevolver.config.Configuration extends java.lang.Object implements Serializable

Serialized Fields

_tree

GraphTopology _tree

The topology.

_hgtCounts

int[] _hgtCounts

Our breakpoints for HGT.

_totalTime

int _totalTime

The total time to process evolution.

_rootGenome

Genome _rootGenome

The root genome.

Package edu.uconn.mcb.lineageevolver

Class edu.uconn.mcb.lineageevolver.AATranslator.InvalidAminoAcid extends java.lang.RuntimeException implements Serializable

Class edu.uconn.mcb.lineageevolver.AATranslator.InvalidAminoAcid.InvalidAminoAcidByte extends AATranslator.InvalidAminoAcid implements Serializable

Serialized Fields

aa

byte aa

The bad byte that was used as an encoded AminoAcid.

Class edu.uconn.mcb.lineageevolver.AATranslator.InvalidAminoAcid.InvalidAminoAcidChar extends AATranslator.InvalidAminoAcid implements Serializable

Serialized Fields

aa

char aa

The bad character that was used as an encoded AminoAcid.

Class edu.uconn.mcb.lineageevolver.AATranslator.InvalidAminoAcid.InvalidAminoAcidInt extends AATranslator.InvalidAminoAcid implements Serializable

Serialized Fields

aa

int aa

The bad integer that was used as an encoded AminoAcid.

Class edu.uconn.mcb.lineageevolver.Genome.NoHGTProcessed extends java.lang.RuntimeException implements Serializable

Class edu.uconn.mcb.lineageevolver.Lineage.HGTDenied extends java.lang.RuntimeException implements Serializable

Class edu.uconn.mcb.lineageevolver.Recombiner.NoRecombineRegion extends java.lang.RuntimeException implements Serializable

Serialized Fields

gneDestination

Gene gneDestination

The destination Gene for which recombination failed.

gneSource

Gene gneSource

The source Gene for which recombination failed.