org.biojava.bio.program.ssbind
Class AlphabetResolver

java.lang.Object
  |
  +--org.biojava.bio.program.ssbind.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

Constructor Summary

AlphabetResolver()

Method Summary

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.