Uses of Class
org.snpeff.codons.CodonTable

Packages that use CodonTable

Package	Description
org.snpeff.codons
org.snpeff.interval
org.snpeff.snpEffect
org.snpeff.snpEffect.testCases.unity

Uses of CodonTable in org.snpeff.codons

Methods in org.snpeff.codons that return CodonTable

Modifier and Type	Method	Description
CodonTable	CodonTables.getTable(java.lang.String codonTableName)	Get a codon table by name
CodonTable	CodonTables.getTable(Genome genome)	Get default genome-wide codon table
CodonTable	CodonTables.getTable(Genome genome, java.lang.String chromosome)	Get a codon table WARNING: It will return the standard codon table if nothing if found

Methods in org.snpeff.codons that return types with arguments of type CodonTable

Modifier and Type	Method	Description
java.util.Iterator<CodonTable>	CodonTables.iterator()

Methods in org.snpeff.codons with parameters of type CodonTable

Modifier and Type	Method	Description
void	CodonTables.add(CodonTable codonTable)	Add a codon table
void	CodonTables.set(Genome genome, CodonTable codonTable)	Set a codon table for a all chromosomes in a genome I.e.: Default genome-wide chromosome table
void	CodonTables.set(Genome genome, Chromosome chr, CodonTable codonTable)	Set a codon table for a given genome & chromosome

Uses of CodonTable in org.snpeff.interval

Methods in org.snpeff.interval that return CodonTable

Modifier and Type	Method	Description
CodonTable	Marker.codonTable()	Get a suitable codon table
CodonTable	Chromosome.getCodonTable()

Uses of CodonTable in org.snpeff.snpEffect

Constructors in org.snpeff.snpEffect with parameters of type CodonTable

Constructor	Description
PurityChange(CodonTable codonTable)

Uses of CodonTable in org.snpeff.snpEffect.testCases.unity

Fields in org.snpeff.snpEffect.testCases.unity declared as CodonTable

Modifier and Type	Field	Description
protected CodonTable	TestCasesBase.codonTable