com.milaboratory.core.alignment.blast

Class BlastAlignerParameters

java.lang.Object

com.milaboratory.core.alignment.blast.BlastAlignerParameters

public class BlastAlignerParameters
extends Object

Constructor Summary

Constructors

Constructor and Description
BlastAlignerParameters()

Method Summary

Methods

Modifier and Type	Method and Description
void	addArgumentsTo(List<String> cmd)
void	addEnvVariablesTo(ProcessBuilder processBuilder)
void	chechAlphabet(Alphabet<?> alphabet)
int	getBatchSize()
BlastTask	getBlastTask()
double	getEValue()
int	getGapExtend()
int	getGapOpen()
String	getMatrix()
int	getNumAlignments()
int	getNumThreads()
int	getPenalty()
int	getReward()
int	getWordSize()
void	setBatchSize(int batchSize)
void	setBlastTask(BlastTask blastTask)
void	setEValue(double eValue)
void	setGapExtend(int gapExtend)
void	setGapOpen(int gapOpen)
void	setMatrix(String matrix)
void	setNumAlignments(int numAlignments)
void	setNumThreads(int numThreads)
void	setPenalty(int penalty)
void	setReward(int reward)
void	setWordSize(int wordSize)

Methods inherited from class java.lang.Object

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

Constructor Detail

BlastAlignerParameters

public BlastAlignerParameters()

Method Detail

getNumThreads

public int getNumThreads()

setNumThreads

public void setNumThreads(int numThreads)

getNumAlignments

public int getNumAlignments()

setNumAlignments

public void setNumAlignments(int numAlignments)

getBatchSize

public int getBatchSize()

setBatchSize

public void setBatchSize(int batchSize)

getBlastTask

public BlastTask getBlastTask()

setBlastTask

public void setBlastTask(BlastTask blastTask)

getEValue

public double getEValue()

setEValue

public void setEValue(double eValue)

getWordSize

public int getWordSize()

setWordSize

public void setWordSize(int wordSize)

getGapOpen

public int getGapOpen()

setGapOpen

public void setGapOpen(int gapOpen)

getGapExtend

public int getGapExtend()

setGapExtend

public void setGapExtend(int gapExtend)

getMatrix

public String getMatrix()

setMatrix

public void setMatrix(String matrix)

getPenalty

public int getPenalty()

setPenalty

public void setPenalty(int penalty)

getReward

public int getReward()

setReward

public void setReward(int reward)

chechAlphabet

public void chechAlphabet(Alphabet<?> alphabet)

addEnvVariablesTo

public void addEnvVariablesTo(ProcessBuilder processBuilder)

addArgumentsTo

public void addArgumentsTo(List<String> cmd)