Class CodonPrefTools

Method Details

• getCodonPreference

  public static CodonPref getCodonPreference(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

• writeToXML

  public static void writeToXML(CodonPref codonPref, PrintWriter writer) throws NullPointerException, IOException, IllegalSymbolException, BioException

  write out a specified CodonPref object in XML format.

  Throws:

  NullPointerException

  IOException

  IllegalSymbolException

  BioException

• readFromXML

  public static CodonPref readFromXML(InputStream prefStream, String name) throws BioException

  reads a specified CodonPref from an file.

  Parameters:

  name - name of organism

  Throws:

  BioException

• readFromXML

  public static CodonPref[] readFromXML(InputStream prefStream) throws BioException

  Throws:

  BioException

• readFromXML

  public static void readFromXML(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(InputStream input, OutputStream output) throws 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:

  IOException