Package org.biojava.bio.symbol

Class CodonPrefTools

  • public class CodonPrefTools
extends java.lang.Object
    An utility class for codon preferences
    Since:
    1.3
    Author:
    David Huen, Mark Schreiber

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.lang.String CEREVISIAE_NUCLEAR
      Saccharomyces cerevisiae codon preferences
      static java.lang.String DROSOPHILA_MELANOGASTER_NUCLEAR
      Drosophila melanogaster codon preferences
      static java.lang.String ECOLI
      Escherichia coli codon preferences
      static java.lang.String FUGU_NUCLEAR
      Takifugu rubripes codon preferences
      static java.lang.String MAN_NUCLEAR
      Homo sapiens codon preferences
      static java.lang.String MOUSE_NUCLEAR
      Mus musculus codon preferences
      static java.lang.String POMBE_NUCLEAR
      Schizosaccharomyces pombe codon preferences
      static java.lang.String RAT_NUCLEAR
      Rattus norvegicus codon preferences
      static java.lang.String WORM_NUCLEAR
      Caenorhabditis elegans codon preferences

    • Constructor Summary

      Constructors 
      Constructor Description
      CodonPrefTools()  

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static CodonPref getCodonPreference​(java.lang.String id)
      get the specified codon preference.
      static FiniteAlphabet getDinucleotideAlphabet()
      returns an RNA dinucleotide alphabet.
      static CodonPref[] readFromXML​(java.io.InputStream prefStream)  
      static CodonPref readFromXML​(java.io.InputStream prefStream, java.lang.String name)
      reads a specified CodonPref from an file.
      static void readFromXML​(java.io.InputStream prefStream, CodonPrefFilter filter)
      read an CodonPref XML stream and handle it with a CodonPrefFilter object.
      static void translateCUD​(java.io.InputStream input, java.io.OutputStream output)
      reads in a file in Codon Usage Database format and translate it into our XML format These can be obtained from the Codon Usage Database.
      static void writeToXML​(CodonPref codonPref, java.io.PrintWriter writer)
      write out a specified CodonPref object in XML format.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • DROSOPHILA_MELANOGASTER_NUCLEAR

        public static java.lang.String DROSOPHILA_MELANOGASTER_NUCLEAR
        Drosophila melanogaster codon preferences

      • MAN_NUCLEAR

        public static java.lang.String MAN_NUCLEAR
        Homo sapiens codon preferences

      • MOUSE_NUCLEAR

        public static java.lang.String MOUSE_NUCLEAR
        Mus musculus codon preferences

      • RAT_NUCLEAR

        public static java.lang.String RAT_NUCLEAR
        Rattus norvegicus codon preferences

      • FUGU_NUCLEAR

        public static java.lang.String FUGU_NUCLEAR
        Takifugu rubripes codon preferences

      • WORM_NUCLEAR

        public static java.lang.String WORM_NUCLEAR
        Caenorhabditis elegans codon preferences

      • CEREVISIAE_NUCLEAR

        public static java.lang.String CEREVISIAE_NUCLEAR
        Saccharomyces cerevisiae codon preferences

      • POMBE_NUCLEAR

        public static java.lang.String POMBE_NUCLEAR
        Schizosaccharomyces pombe codon preferences

      • ECOLI

        public static java.lang.String ECOLI
        Escherichia coli codon preferences

    • Constructor Detail

      • CodonPrefTools

        public CodonPrefTools()

    • Method Detail

      • getCodonPreference

        public static CodonPref getCodonPreference​(java.lang.String id)
        get the specified codon preference.

      • getDinucleotideAlphabet

        public static FiniteAlphabet getDinucleotideAlphabet()
        returns an RNA dinucleotide alphabet. Used to represent the non-wobble bases in WobbleDistribution

      • readFromXML

        public static CodonPref readFromXML​(java.io.InputStream prefStream,
                                    java.lang.String name)
                             throws BioException
        reads a specified CodonPref from an file.
        Parameters:
        name - name of organism
        Throws:
        BioException

      • readFromXML

        public static void readFromXML​(java.io.InputStream prefStream,
                               CodonPrefFilter filter)
                        throws BioException
        read an CodonPref XML stream and handle it with a CodonPrefFilter object.
        Throws:
        BioException

      • translateCUD

        public static void translateCUD​(java.io.InputStream input,
                                java.io.OutputStream output)
                         throws java.io.IOException
        reads in a file in Codon Usage Database format and translate it into our XML format These can be obtained from the Codon Usage Database.

        Note that the output assumes that the universal genetic code is used as that is not encoded in the CUD files. Edit the output appropriately to modify the genetic code if necessary.

        Throws:
        java.io.IOException