edu.uconn.mcb.lineageevolver
Class ASRVByteAAGene

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

All Implemented Interfaces:

java.lang.Cloneable, Gene

public class ASRVByteAAGene

extends java.lang.Object

implements Gene

Gene implementation using ByteAminoAcid and Simple Among Site Rate Variation (ASRV).

Author:

Hasan Khalil, Lina Pezzella

Field Summary

private ByteAminoAcid[]	_aaAminoAcid The sequence of amino acids that make up this gene.
private float	_fltEvolutionSpeed The speed with which this gene evolves.
int	_id The ID number for this gene.
int	_paralogID The paralog ID number for this gene.
private static SubstitutionMatrix	_smtrx The currently employed substitution matrix for this gene.
private int	_totalSubs The number of substitutions processed in this gene.
static int	ASRV_MUT_FREQ The number of substitutions undergone before each ASRV mutation.
static int	ASRV_MUTLENGTH_MEAN The average length of sites that mutate their substitution rates in a given mutation event.
static int	ASRV_MUTLENGTH_STDEV The standard deviation of sites that mutate their substitution rates in a given mutation event.
static int	DEFAULT_GENESIZE Default size for a gene in number of amino acids.
static float	DUPLICATE_EVOLSPEED_FACTOR The factor by which to increase the fltEvolutionSpeed of a newly duplicated gene.
static float	EVOLRATE_MUTATION_MEAN The average rate at which this gene's fltEvolutionSpeed mutations.
static float	EVOLRATE_MUTATION_STDEV The standard deviation for this gene's fltEvolutionSpeed mutation.
static java.util.Random	randomNumberGenerator Random number generator shared by all gen1es.

Constructor Summary

	ASRVByteAAGene() Default constructor for objects of type ASRVByteAAGene.
private	ASRVByteAAGene(float fltEvolutionSpeed, int id, int paralogID) Constructor for objects of type ASRVByteAAGene that sets characteristic properties of gene instances.
	ASRVByteAAGene(float fltEvolutionSpeed, int id, int paralogID, float[] subProbabilities, byte[] sequence) Constructor for objects of type ASRVByteAAGene that generates a new gene given a byte sequence.
	ASRVByteAAGene(float fltEvolutionSpeed, int id, int paralogID, float[] subProbabilities, java.lang.String sequence) Constructor for objects of type ASRVByteAAGene that generates a new gene given a character sequence in the form of a String.

Method Summary

java.lang.Object	clone() All genes must be cloneable.
Gene	duplicate(int paralogID) Generates an paralog of this gene.
boolean	equals(java.lang.Object obj) Checks for equality between two ASRVByteAAGenes.
AminoAcid	getAminoAcid(int index) Returns the AminoAcid at the given index.
float	getEvolutionSpeed() Returns the currently employed evolution speed for this Gene
int	getID() Return the ID number for this gene.
int	getParalogID() Returns the paralog number for this gene.
int	getSize() Returns the number of AminoAcids in this Gene.
static void	main(java.lang.String[] args) Generic driver for ASRVByteAAGenes.
void	mutateASRV() Mutate the ASRV by swapping randomly selected regions.
void	mutateEvolutionSpeed() Mutates the evolution speed of this Gene randomly up or down from the current evolution speed.
void	reverse() Reverses the amino acid positions in this gene.
void	setEvolutionSpeed(float fltNewEvolutionSpeed) Sets the evolution speed for this Gene.
void	substitute() Processes substitution according to the currently employed substitution matrix for this Gene.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

randomNumberGenerator

public static final java.util.Random randomNumberGenerator

Random number generator shared by all gen1es.

DEFAULT_GENESIZE

public static final int DEFAULT_GENESIZE

Default size for a gene in number of amino acids.

See Also:

Constant Field Values

_id

public final int _id

The ID number for this gene.

_paralogID

public final int _paralogID

The paralog ID number for this gene.

_smtrx

private static final SubstitutionMatrix _smtrx

The currently employed substitution matrix for this gene.

_aaAminoAcid

private ByteAminoAcid[] _aaAminoAcid

The sequence of amino acids that make up this gene.

_fltEvolutionSpeed

private float _fltEvolutionSpeed

The speed with which this gene evolves.

_totalSubs

private int _totalSubs

The number of substitutions processed in this gene.

EVOLRATE_MUTATION_MEAN

public static final float EVOLRATE_MUTATION_MEAN

The average rate at which this gene's fltEvolutionSpeed mutations.

See Also:

Constant Field Values

EVOLRATE_MUTATION_STDEV

public static final float EVOLRATE_MUTATION_STDEV

The standard deviation for this gene's fltEvolutionSpeed mutation.

See Also:

Constant Field Values

DUPLICATE_EVOLSPEED_FACTOR

public static final float DUPLICATE_EVOLSPEED_FACTOR

The factor by which to increase the fltEvolutionSpeed of a newly duplicated gene.

See Also:

Constant Field Values

ASRV_MUTLENGTH_MEAN

public static final int ASRV_MUTLENGTH_MEAN

The average length of sites that mutate their substitution rates in a given mutation event.

See Also:

Constant Field Values

ASRV_MUTLENGTH_STDEV

public static final int ASRV_MUTLENGTH_STDEV

The standard deviation of sites that mutate their substitution rates in a given mutation event.

See Also:

Constant Field Values

ASRV_MUT_FREQ

public static final int ASRV_MUT_FREQ

The number of substitutions undergone before each ASRV mutation.

See Also:

Constant Field Values

Constructor Detail

ASRVByteAAGene

public ASRVByteAAGene()

Default constructor for objects of type ASRVByteAAGene.

ASRVByteAAGene

public ASRVByteAAGene(float fltEvolutionSpeed,
                      int id,
                      int paralogID,
                      float[] subProbabilities,
                      java.lang.String sequence)

Constructor for objects of type ASRVByteAAGene that generates a new gene given a character sequence in the form of a String.

Parameters:

fltEvolutionSpeed - the speed with which this ASRVByteAAGene evolves.

id - the ID number for this ASRVByteAAGene.

paralogID - the paralogID number for this ASRVByteAAGene.

subProbabilities - the ASRV probabilities for the amino acids in this ASRVByteAAGene.

sequence - the sequence of amino acids in this ASRVByteAAGene.

ASRVByteAAGene

public ASRVByteAAGene(float fltEvolutionSpeed,
                      int id,
                      int paralogID,
                      float[] subProbabilities,
                      byte[] sequence)

Constructor for objects of type ASRVByteAAGene that generates a new gene given a byte sequence.

Parameters:

fltEvolutionSpeed - the speed with which this ASRVByteAAGene evolves.

id - the ID number for this ASRVByteAAGene.

paralogID - the paralogID number for this ASRVByteAAGene.

subProbabilities - the ASRV probabilities for the amino acids in this ASRVByteAAGene.

sequence - the sequence of amino acids in this ASRVByteAAGene.

ASRVByteAAGene

private ASRVByteAAGene(float fltEvolutionSpeed,
                       int id,
                       int paralogID)

Constructor for objects of type ASRVByteAAGene that sets characteristic properties of gene instances.

Parameters:

fltEvolutionSpeed - the speed with which this ASRVByteAAGene evolves.

id - the ID number for this ASRVByteAAGene.

paralogID - the paralogID number for this ASRVByteAAGene.

Method Detail

getEvolutionSpeed

public float getEvolutionSpeed()

Description copied from interface: Gene

Returns the currently employed evolution speed for this Gene

Specified by:

getEvolutionSpeed in interface Gene

Returns:

the currently employed evolution speed for this gene

See Also:

Gene.getEvolutionSpeed()

setEvolutionSpeed

public void setEvolutionSpeed(float fltNewEvolutionSpeed)

Description copied from interface: Gene

Sets the evolution speed for this Gene.

Specified by:

setEvolutionSpeed in interface Gene

Parameters:

fltNewEvolutionSpeed - the new evolution speed for this gene

See Also:

Gene.setEvolutionSpeed(float)

mutateEvolutionSpeed

public void mutateEvolutionSpeed()

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

substitute

public void substitute()

Description copied from interface: Gene

Processes substitution according to the currently employed substitution matrix for this Gene. Calculates overall substitution probabilities on the amino acid level on the fly from specific amino acid substitution probabilities and the currently employed Among Site Rate Variation (ASRV) distrubtion curve for this Gene.

Specified by:

substitute in interface Gene

See Also:

Gene.substitute()

mutateASRV

public void mutateASRV()

Mutate the ASRV by swapping randomly selected regions.

getAminoAcid

public AminoAcid getAminoAcid(int index)

Description copied from interface: Gene

Returns the AminoAcid at the given index.

Specified by:

getAminoAcid in interface Gene

Parameters:

index - the index of the AminoAcid to return.

Returns:

the AminoAcid at the given index.

See Also:

Gene.getAminoAcid(int)

getSize

public int getSize()

Description copied from interface: Gene

Returns the number of AminoAcids in this Gene.

Specified by:

getSize in interface Gene

Returns:

the number of AminoAcids in this Gene.

See Also:

Gene.getSize()

getID

public int getID()

Description copied from interface: Gene

Return the ID number for this gene.

Specified by:

getID in interface Gene

Returns:

the ID number for this gene.

See Also:

Gene.getID()

getParalogID

public int getParalogID()

Description copied from interface: Gene

Returns the paralog number for this gene.

Specified by:

getParalogID in interface Gene

Returns:

the paralog number for this gene.

See Also:

Gene.getParalogID()

duplicate

public Gene duplicate(int paralogID)

Description copied from interface: Gene

Generates an paralog of this gene.

Specified by:

duplicate in interface Gene

Parameters:

paralogID - the paralog ID for the duplicated gene.

Returns:

the generated paralog of this gene.

See Also:

Gene.duplicate(int)

reverse

public void reverse()

Description copied from interface: Gene

Reverses the amino acid positions in this gene.

Specified by:

reverse in interface Gene

See Also:

Gene.reverse()

clone

public java.lang.Object clone()

Description copied from interface: Gene

All genes must be cloneable.

Specified by:

clone in interface Gene

See Also:

Object.clone()

equals

public boolean equals(java.lang.Object obj)

Checks for equality between two ASRVByteAAGenes. Only performs checks on evolution speed, and amino acids (count, type, etc.).

See Also:

Object.equals(java.lang.Object)

toString

public java.lang.String toString()

See Also:

Object.toString()

main

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

Generic driver for ASRVByteAAGenes.

Parameters:

args - Arguments are not used in this driver.