Package org.biojava.bio.program.ssbind

Class AlphabetResolver

java.lang.Object
org.biojava.bio.program.ssbind.AlphabetResolver
public class AlphabetResolver extends 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

  • Constructor Details

  • Method Details

    • resolveAlphabet

      public static FiniteAlphabet resolveAlphabet(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.