Class CodonTables

  • All Implemented Interfaces:
    java.lang.Iterable<CodonTable>

    public class CodonTables
    extends java.lang.Object
    implements java.lang.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
    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.lang.String aa​(java.lang.String codon, Genome genome, java.lang.String chromosome)
      Translate a codon into an amino acid for a given genome+chromosome
      void add​(CodonTable codonTable)
      Add a codon table
      java.util.List<java.lang.String> codon​(java.lang.String aa, Genome genome, java.lang.String chromosome)
      Translate an amino acid into a codon for a given genome+chromosome
      static CodonTables getInstance()  
      CodonTable getTable​(java.lang.String codonTableName)
      Get a codon table by name
      CodonTable getTable​(Genome genome)
      Get default genome-wide codon table
      CodonTable getTable​(Genome genome, java.lang.String chromosome)
      Get a codon table WARNING: It will return the standard codon table if nothing if found
      java.util.Iterator<CodonTable> iterator()  
      void set​(Genome genome, CodonTable codonTable)
      Set a codon table for a all chromosomes in a genome I.e.: Default genome-wide chromosome table
      void set​(Genome genome, Chromosome chr, CodonTable codonTable)
      Set a codon table for a given genome & chromosome
      • Methods 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
    • Method Detail

      • getInstance

        public static CodonTables getInstance()
      • aa

        public java.lang.String aa​(java.lang.String codon,
                                   Genome genome,
                                   java.lang.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 java.util.List<java.lang.String> codon​(java.lang.String aa,
                                                      Genome genome,
                                                      java.lang.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,
                                   java.lang.String chromosome)
        Get a codon table WARNING: It will return the standard codon table if nothing if found
      • getTable

        public CodonTable getTable​(java.lang.String codonTableName)
        Get a codon table by name
      • iterator

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

        public void set​(Genome genome,
                        Chromosome chr,
                        CodonTable codonTable)
        Set a codon table for a given genome & 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