Class CodonTable


  • public class CodonTable
    extends java.lang.Object
    A codon translation table
    Author:
    pcingola
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.lang.String DEFAULT_START_CODON
      All start codons are translated as "M".
    • Constructor Summary

      Constructors 
      Constructor Description
      CodonTable​(java.lang.String name, java.lang.String table)  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.lang.String aa​(java.lang.String codons)
      Translate codons to an amino acid sequence
      java.lang.String aa​(java.lang.String codons, boolean fullProteinSequence)  
      java.lang.String aaThreeLetterCode​(char aa)  
      java.lang.String aaThreeLetterCode​(java.lang.String aa)
      Convert 1-letter code to 3-letter code (amino acids) Reference: http://www.hgvs.org/mutnomen/standards.html#aalist
      java.lang.String codon​(java.lang.String aa)
      Translate an amino acid into a codon
      int degenerate​(java.lang.String codon, int pos)
      Degree of "degenerate site" What is a "degenerate site"? Here is an explanation form Stephen Wright (Univ.
      java.lang.String getName()  
      boolean isStart​(java.lang.String codon)
      Is 'codon' a start codon in this table?
      boolean isStartFirst​(java.lang.String codon)
      Is the first codon a 'start' codon?
      boolean isStop​(java.lang.String codon)
      Is 'codon' a stop codon in this table?
      boolean isStopAa​(java.lang.String aas)
      Is there a stop codon in this amino acid sequence
      java.lang.String toString()  
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
    • Field Detail

      • DEFAULT_START_CODON

        public static final java.lang.String DEFAULT_START_CODON
        All start codons are translated as "M". Reference: https://en.wikipedia.org/wiki/Start_codon Alternative start codons are different from the standard AUG codon and are found in both prokaryotes (bacteria) and eukaryotes. Alternate start codons are still translated as Met when they are at the start of a protein (even if the codon encodes a different amino acid otherwise). This is because a separate transfer RNA (tRNA) is used for initiation.
        See Also:
        Constant Field Values
    • Constructor Detail

      • CodonTable

        public CodonTable​(java.lang.String name,
                          java.lang.String table)
    • Method Detail

      • aa

        public java.lang.String aa​(java.lang.String codons)
        Translate codons to an amino acid sequence
      • aa

        public java.lang.String aa​(java.lang.String codons,
                                   boolean fullProteinSequence)
      • aaThreeLetterCode

        public java.lang.String aaThreeLetterCode​(char aa)
      • aaThreeLetterCode

        public java.lang.String aaThreeLetterCode​(java.lang.String aa)
        Convert 1-letter code to 3-letter code (amino acids) Reference: http://www.hgvs.org/mutnomen/standards.html#aalist
        Parameters:
        Amino - acid in three letter code
      • codon

        public java.lang.String codon​(java.lang.String aa)
        Translate an amino acid into a codon
      • degenerate

        public int degenerate​(java.lang.String codon,
                              int pos)
        Degree of "degenerate site" What is a "degenerate site"? Here is an explanation form Stephen Wright (Univ. Toronto), who requested to add this feature "...a fourfold degenerate site would be a site where any change is synonymous. So the third codon position for the arginine CGN, is a fourfold degenerate site, as is the third codon position for valine, alanine, etc. Similarly, all second positions of a codon are zerofold degenerate, since any change is nonsynonymous. Many first codon positions are also zerofold degenerate, however, for example, the first codon position of AGG is NOT zerofold, because a shift to CGG is a synonymous change."
        Parameters:
        codon -
        pos -
        Returns:
        Degenracy level, or '-1' if not available
      • getName

        public java.lang.String getName()
      • isStart

        public boolean isStart​(java.lang.String codon)
        Is 'codon' a start codon in this table?
      • isStartFirst

        public boolean isStartFirst​(java.lang.String codon)
        Is the first codon a 'start' codon?
      • isStop

        public boolean isStop​(java.lang.String codon)
        Is 'codon' a stop codon in this table?
      • isStopAa

        public boolean isStopAa​(java.lang.String aas)
        Is there a stop codon in this amino acid sequence
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object