Package org.snpeff.codons

Class FindRareAaIntervals

java.lang.Object

org.snpeff.codons.FindRareAaIntervals

public class FindRareAaIntervals
extends java.lang.Object

Find intervals where rare amino acids occur

Author:

pablocingolani

Field Summary

Fields

Modifier and Type	Field	Description
static double	RARE_THRESHOLD

Constructor Summary

Constructors

Constructor	Description
FindRareAaIntervals(Genome genome)

Method Summary

Modifier and Type	Method	Description
java.util.Collection<RareAminoAcid>	findRareAa(java.lang.String proteinFastaFile)	Find all sites having rare amino acids
double	getRareThreshold()
void	setRareThreshold(double rareThreshold)
void	setVerbose(boolean verbose)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

RARE_THRESHOLD

public static final double RARE_THRESHOLD

See Also:

Constant Field Values

Constructor Detail

FindRareAaIntervals

public FindRareAaIntervals(Genome genome)

Method Detail

findRareAa

public java.util.Collection<RareAminoAcid> findRareAa(java.lang.String proteinFastaFile)

Find all sites having rare amino acids

Parameters:

proteinFastaFile -

getRareThreshold

public double getRareThreshold()

setRareThreshold

public void setRareThreshold(double rareThreshold)

setVerbose

public void setVerbose(boolean verbose)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object