Package org.biojava.bio.program.ssbind
Class AlphabetResolver
java.lang.Object
org.biojava.bio.program.ssbind.AlphabetResolver
AlphabetResolver
s 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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic FiniteAlphabet
resolveAlphabet
(String identifier) resolveAlphabet
returns an appropriateAlphabet
for an arbitrary identifier.
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Constructor Details
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AlphabetResolver
public AlphabetResolver()
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Method Details
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resolveAlphabet
resolveAlphabet
returns an appropriateAlphabet
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
- aString
identifier (recognised are BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX, DNA and PROTEIN).- Returns:
- a
FiniteAlphabet
. - Throws:
BioException
- if the identifier is not known.
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