Package org.snpeff.codons
Class CodonTables
java.lang.Object
org.snpeff.codons.CodonTables
- All Implemented Interfaces:
Iterable<CodonTable>
All codon tables are stored here. Mapping for genome/chromosome to codon table are also stored here
Note: This object is a singleton
- Author:
- pcingola
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Field Summary
Fields -
Method Summary
Modifier and TypeMethodDescriptionTranslate a codon into an amino acid for a given genome+chromosomevoid
add
(CodonTable codonTable) Add a codon tableTranslate an amino acid into a codon for a given genome+chromosomestatic CodonTables
Get a codon table by nameGet default genome-wide codon tableGet a codon table WARNING: It will return the standard codon table if nothing if founditerator()
void
set
(Genome genome, CodonTable codonTable) Set a codon table for a all chromosomes in a genome I.e.: Default genome-wide chromosome tablevoid
set
(Genome genome, Chromosome chr, CodonTable codonTable) Set a codon table for a given genome invalid input: '&' chromosomeMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Field Details
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STANDARD_TABLE
- See Also:
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STANDARD_TABLE_NAME
- See Also:
-
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Method Details
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getInstance
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aa
Translate a codon into an amino acid for a given genome+chromosome -
add
Add a codon table -
codon
Translate an amino acid into a codon for a given genome+chromosome -
getTable
Get default genome-wide codon table -
getTable
Get a codon table WARNING: It will return the standard codon table if nothing if found -
getTable
Get a codon table by name -
iterator
- Specified by:
iterator
in interfaceIterable<CodonTable>
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set
Set a codon table for a given genome invalid input: '&' chromosome -
set
Set a codon table for a all chromosomes in a genome I.e.: Default genome-wide chromosome table
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