Package org.snpeff.codons
Class FindRareAaIntervals
- java.lang.Object
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- org.snpeff.codons.FindRareAaIntervals
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public class FindRareAaIntervals extends java.lang.Object
Find intervals where rare amino acids occur- Author:
- pablocingolani
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Field Summary
Fields Modifier and Type Field Description static double
RARE_THRESHOLD
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Constructor Summary
Constructors Constructor Description FindRareAaIntervals(Genome genome)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.Collection<RareAminoAcid>
findRareAa(java.lang.String proteinFastaFile)
Find all sites having rare amino acidsdouble
getRareThreshold()
void
setRareThreshold(double rareThreshold)
void
setVerbose(boolean verbose)
java.lang.String
toString()
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Field Detail
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RARE_THRESHOLD
public static final double RARE_THRESHOLD
- See Also:
- Constant Field Values
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Constructor Detail
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FindRareAaIntervals
public FindRareAaIntervals(Genome genome)
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Method Detail
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findRareAa
public java.util.Collection<RareAminoAcid> findRareAa(java.lang.String proteinFastaFile)
Find all sites having rare amino acids- Parameters:
proteinFastaFile
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getRareThreshold
public double getRareThreshold()
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setRareThreshold
public void setRareThreshold(double rareThreshold)
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setVerbose
public void setVerbose(boolean verbose)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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