Class CodonTables

java.lang.Object
org.snpeff.codons.CodonTables
All Implemented Interfaces:
Iterable<CodonTable>

public class CodonTables extends Object implements 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
  • Field Details

  • Method Details

    • getInstance

      public static CodonTables getInstance()
    • aa

      public String aa(String codon, Genome genome, String chromosome)
      Translate a codon into an amino acid for a given genome+chromosome
    • add

      public void add(CodonTable codonTable)
      Add a codon table
    • codon

      public List<String> codon(String aa, Genome genome, String chromosome)
      Translate an amino acid into a codon for a given genome+chromosome
    • getTable

      public CodonTable getTable(Genome genome)
      Get default genome-wide codon table
    • getTable

      public CodonTable getTable(Genome genome, String chromosome)
      Get a codon table WARNING: It will return the standard codon table if nothing if found
    • getTable

      public CodonTable getTable(String codonTableName)
      Get a codon table by name
    • iterator

      public Iterator<CodonTable> iterator()
      Specified by:
      iterator in interface Iterable<CodonTable>
    • set

      public void set(Genome genome, Chromosome chr, CodonTable codonTable)
      Set a codon table for a given genome invalid input: '&' chromosome
    • set

      public void set(Genome genome, CodonTable codonTable)
      Set a codon table for a all chromosomes in a genome I.e.: Default genome-wide chromosome table