Class AlphabetResolver


  • public class AlphabetResolver
    extends java.lang.Object
    AlphabetResolvers are helpers which determine which type of sequence Alphabet to expect from a search result. Now public to allow use by anyone making custom handlers.
    Since:
    1.2
    Author:
    Keith James
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static FiniteAlphabet resolveAlphabet​(java.lang.String identifier)
      resolveAlphabet returns an appropriate Alphabet for an arbitrary identifier.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • AlphabetResolver

        public AlphabetResolver()
    • Method Detail

      • resolveAlphabet

        public static FiniteAlphabet resolveAlphabet​(java.lang.String identifier)
                                              throws BioException
        resolveAlphabet returns an appropriate Alphabet for an arbitrary identifier. The protein alphabet returned will include the termination character as e.g. BLASTX 6-frame translations are likely to include stops.
        Parameters:
        identifier - a String identifier (recognised are BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX, DNA and PROTEIN).
        Returns:
        a FiniteAlphabet.
        Throws:
        BioException - if the identifier is not known.