experiments
Class Genome

java.lang.Object
  experiments.Genome

public class Genome
extends java.lang.Object

This class represents a genome. It contains variables for genome file, genome sequence (string and char array), genome length, gc rate, number of each nucleotide type and related frequency.

Constructor Summary

Genome()
Generates an empty genome

Genome(java.io.File f)
Generates an empty genome

Method Summary

double	getfA()
double	getfC()
double	getfG()
double	getfT()
double	getGcContent()
char[]	getGenArr()
java.io.File	getGenFile()
java.lang.String	getGenFileName()
int	getGenLen()
java.lang.String	getGenStr()
int	getnA()
int	getnC()
int	getnG()
int	getnT()
boolean	isBasicIndexeAlreadyComputed()
void	loadGenFile() Loads genome from a fasta file into string genStr, array genArr and sets genLen
void	loadGenFileStr() Loads genome from a fasta file into string genStr
char[]	permuteGen() Generates a permutation of this genome
void	setBasicIndexeAlreadyComputed(boolean basicIndexeAlreadyComputed)
void	setfA(double fA)
void	setfC(double fC)
void	setfG(double fG)
void	setfT(double fT)
void	setGcContent(double gcContent)
void	setGenArr(char[] genArr)
void	setGenFile(java.io.File genFile)
void	setGenFileName(java.lang.String genFileName)
void	setGenLen(int genLen)
void	setGenStr(java.lang.String genStr)
void	setnA(int nA)
void	setnC(int nC)
void	setnG(int nG)
void	setnT(int nT)

Methods inherited from class java.lang.Object

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

Constructor Detail

Genome

public Genome()

Generates an empty genome

Genome

public Genome(java.io.File f)

Generates an empty genome

Method Detail

loadGenFile

public void loadGenFile()

Loads genome from a fasta file into string genStr, array genArr and sets genLen

loadGenFileStr

public void loadGenFileStr()

Loads genome from a fasta file into string genStr

permuteGen

public char[] permuteGen()

Generates a permutation of this genome

getGenFile

public java.io.File getGenFile()

Returns:

the genFile

setGenFile

public void setGenFile(java.io.File genFile)

Parameters:

genFile - the genFile to set

getGenFileName

public java.lang.String getGenFileName()

Returns:

the genFileName

setGenFileName

public void setGenFileName(java.lang.String genFileName)

Parameters:

genFileName - the genFileName to set

getGenStr

public java.lang.String getGenStr()

Returns:

the genStr

setGenStr

public void setGenStr(java.lang.String genStr)

Parameters:

genStr - the genStr to set

getGenArr

public char[] getGenArr()

Returns:

the genArr

setGenArr

public void setGenArr(char[] genArr)

Parameters:

genArr - the genArr to set

getGenLen

public int getGenLen()

Returns:

the genLen

setGenLen

public void setGenLen(int genLen)

Parameters:

genLen - the genLen to set

getGcContent

public double getGcContent()

Returns:

the gcContent

setGcContent

public void setGcContent(double gcContent)

Parameters:

gcContent - the gcContent to set

getnA

public int getnA()

Returns:

the nA

setnA

public void setnA(int nA)

Parameters:

nA - the nA to set

getnT

public int getnT()

Returns:

the nT

setnT

public void setnT(int nT)

Parameters:

nT - the nT to set

getnC

public int getnC()

Returns:

the nC

setnC

public void setnC(int nC)

Parameters:

nC - the nC to set

getnG

public int getnG()

Returns:

the nG

setnG

public void setnG(int nG)

Parameters:

nG - the nG to set

getfA

public double getfA()

Returns:

the fA

setfA

public void setfA(double fA)

Parameters:

fA - the fA to set

getfT

public double getfT()

Returns:

the fT

setfT

public void setfT(double fT)

Parameters:

fT - the fT to set

getfC

public double getfC()

Returns:

the fC

setfC

public void setfC(double fC)

Parameters:

fC - the fC to set

getfG

public double getfG()

Returns:

the fG

setfG

public void setfG(double fG)

Parameters:

fG - the fG to set

isBasicIndexeAlreadyComputed

public boolean isBasicIndexeAlreadyComputed()

Returns:

the basicIndexeAlreadyComputed

setBasicIndexeAlreadyComputed

public void setBasicIndexeAlreadyComputed(boolean basicIndexeAlreadyComputed)

Parameters:

basicIndexeAlreadyComputed - the basicIndexeAlreadyComputed to set