edu.uconn.mcb.lineageevolver
Class Genome

java.lang.Object
  edu.uconn.mcb.lineageevolver.Genome

All Implemented Interfaces:

java.lang.Cloneable, Visitable

public class Genome

extends java.lang.Object

implements java.lang.Cloneable, Visitable

Model of Genomes, composed of a collection of Genes.

Author:

Hasan Khalil, Lina Pezzella

Nested Class Summary

class

Genome.NoHGTProcessed Exception thrown when hgt was not processed within a reasonable timeframe.

Field Summary

private Gene[]	_gneGenes The collection of genes in this genome.
private int[]	_intParalogs The number of paralogs per gene in this genome.
private float[]	_lakeCategories The values for Lake's ten categories.
static int	DEFAULT_REVERSAL_DIST_MEAN Default mean of the distance from the origin of replication of a reversal event.
static int	DEFAULT_REVERSAL_DIST_STDEV Default standard deviation of the distance from the origin of replication of a reversal event.
static int	DEFAULT_REVERSAL_MEAN Default mean of the number of genes to be reversed.
static int	DEFAULT_REVERSAL_STDEV Default standard deviation of the number of genes to be reversed.
static float	DUPE_KILL_FREQ The number of substitutions to process before calling duplicate or kill gene.
static float[]	LAKE_MUTATION_MEAN The mean (per category) percentages of mutation used when Lake Categories are mutated.
static float[]	LAKE_MUTATION_STDEV The standard deviations (per category) for mutation percentages used when Lake Categories are mutated.
static float[]	LAKE_PROBABILITIES The probability that each rate category will affect horizontal gene transfer.
static java.util.Random	randomNumberGenerator Random number generator shared by all genomes.
private int	totalSubs The age of this genome, including the age of its ancestors, in the number of substitutions it has undergone.

Constructor Summary

Genome(java.lang.String[] sequences, float[][] substitutionProbabilities, float[] lakeCategories)

Genome(java.lang.String[] sequences, float[] evolutionSpeeds, float[][] substitutionProbabilities, float[] lakeCategories)
Constructor for objects of type Genome.

Method Summary

protected java.lang.Object	clone()
Gene	duplicateGene() Duplicates the given gene within this genome and inserts it into this genome.
void	evolve(int intDistance) Induces evolution in this Genome by causing genes selected according to random calculations on the evolution speed of each gene to undergo 'evolution'.
Gene	getGene(int index) Returns the Gene at a given index in this Genome.
float[]	getGeneEvolutionSpeeds() Returns an array containing the evolution speeds for each gene in this Genome.
float	getLakeCategory(int index) Returns the lake category value specified.
int	getSize() Returns the number of genes in this genome.
void	hgt(Genome gnmSource) Selects the genes on which horizontal transfer will occur within this genome.
void	killGene(int intGeneIndex) Kills the given gene within this genome.
static void	main(java.lang.String[] args) Driver for debugging/testing.
private static float[]	makeEvolutionSpeeds(int count) Generates random evolution speeds between 0 and 1 (uniform distribution).
private void	mutateRateCategories() Mutate each of Lake's categories by adding a random value (positive or negative) to each.
void	printString() Similar to toString(), but also details each gene recursively, all printing to System.out as oppose to returning a string.
void	reversal() Processes reversal in this genome from either the origin or terminus of replication (applicable only to circular prokaryotic genomes).
void	symmetricReversal() Processes a reversal event such that the reversal is symmetric about the origin or terminus of replication.
java.lang.String	toString()
void	visit(Visitor v) Method to visit this visitable object with a visitor.

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

randomNumberGenerator

public static final java.util.Random randomNumberGenerator

Random number generator shared by all genomes.

_gneGenes

private Gene[] _gneGenes

The collection of genes in this genome.

_intParalogs

private int[] _intParalogs

The number of paralogs per gene in this genome.

LAKE_PROBABILITIES

public static final float[] LAKE_PROBABILITIES

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

LAKE_MUTATION_MEAN

public static final float[] LAKE_MUTATION_MEAN

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

LAKE_MUTATION_STDEV

public static final float[] LAKE_MUTATION_STDEV

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

DUPE_KILL_FREQ

public static final float DUPE_KILL_FREQ

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

See Also:

Constant Field Values

totalSubs

private int totalSubs

The age of this genome, including the age of its ancestors, in the number of substitutions it has undergone.

_lakeCategories

private float[] _lakeCategories

The values for Lake's ten categories.

DEFAULT_REVERSAL_MEAN

public static final int DEFAULT_REVERSAL_MEAN

Default mean of the number of genes to be reversed.

See Also:

Constant Field Values

DEFAULT_REVERSAL_STDEV

public static final int DEFAULT_REVERSAL_STDEV

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

See Also:

Constant Field Values

DEFAULT_REVERSAL_DIST_MEAN

public static final int DEFAULT_REVERSAL_DIST_MEAN

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

See Also:

Constant Field Values

DEFAULT_REVERSAL_DIST_STDEV

public static final int DEFAULT_REVERSAL_DIST_STDEV

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

See Also:

Constant Field Values

Constructor Detail

Genome

public Genome(java.lang.String[] sequences,
              float[] evolutionSpeeds,
              float[][] substitutionProbabilities,
              float[] lakeCategories)

Constructor for objects of type Genome.

Parameters:

sequences - An array containing sequences for each gene in this genome.

evolutionSpeeds - An array of evolution speeds corresponding to each of the genes in this genome.

substitutionProbabilities - An array of arrays of substitution probabilities for each site specified by the above sequences.

lakeCategories - An array containing each lake category float value, in order.

Genome

public Genome(java.lang.String[] sequences,
              float[][] substitutionProbabilities,
              float[] lakeCategories)

Parameters:

sequences -

substitutionProbabilities -

lakeCategories -

Method Detail

makeEvolutionSpeeds

private static float[] makeEvolutionSpeeds(int count)

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

Parameters:

count - the number of speeds to generate.

Returns:

an array containing each generated speed.

evolve

public void evolve(int intDistance)

Induces evolution in this Genome by causing genes selected according to random calculations on the evolution speed of each gene to undergo 'evolution'. 'Evolution' consists of substitutions and mutation of Lake Categories.

Parameters:

intDistance - the number of substitutions along this branch.

mutateRateCategories

private void mutateRateCategories()

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

killGene

public void killGene(int intGeneIndex)

Kills the given gene within this genome.

Parameters:

intGeneIndex - the index of the gene to kill.

duplicateGene

public Gene duplicateGene()

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

Returns:

the duplicate gene.

reversal

public void reversal()

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

symmetricReversal

public void symmetricReversal()

Processes a reversal event such that the reversal is symmetric about the origin or terminus of replication.

hgt

public void hgt(Genome gnmSource)
         throws Genome.NoHGTProcessed

Selects the genes on which horizontal transfer will occur within this genome. TODO: Comment heavily here.

Parameters:

gnmSource - the source genome for horizontal transfer.

Throws:

Genome.NoHGTProcessed - If HGT was not processed.

getGeneEvolutionSpeeds

public float[] getGeneEvolutionSpeeds()

Returns an array containing the evolution speeds for each gene in this Genome.

Returns:

an array containing the evolution speeds for each gene in this Genome.

getGene

public Gene getGene(int index)

Returns the Gene at a given index in this Genome.

Parameters:

index - the index of the Gene to be returned.

Returns:

the Gene to be returned.

getLakeCategory

public float getLakeCategory(int index)

Returns the lake category value specified.

Parameters:

index - the numerical index of the category to return.

Returns:

the specified category value.

getSize

public int getSize()

Returns the number of genes in this genome.

Returns:

the number of genes in this genome.

clone

protected java.lang.Object clone()

See Also:

Object.clone()

toString

public java.lang.String toString()

See Also:

TODO: Comment exactly which details get outputted here.

main

public static void main(java.lang.String[] args)

Driver for debugging/testing.

Parameters:

args - Arguments are not used for this driver.

visit

public void visit(Visitor v)

Description copied from interface: Visitable

Method to visit this visitable object with a visitor.

Specified by:

visit in interface Visitable

Parameters:

v - the visitor with which to visit this visitable object.

See Also:

Visitable.visit(edu.uconn.mcb.lineageevolver.misc.Visitor)

printString

public void printString()

Similar to toString(), but also details each gene recursively, all printing to System.out as oppose to returning a string.