[Biojava-l] DNATools broken (AbstractMethodError)

[Keith James]

Anyone know what's happened here? DNATools constructor is falling over
because AbstractAlphabet method getAlphabets() is being called. This
method does not exist:

java.lang.AbstractMethodError: org.biojava.bio.symbol.Alphabet.getAlphabets()
        at org.biojava.bio.symbol.AbstractAlphabet.getGapSymbol (AbstractAlphabet.java:257) (pc 1)
        at org.biojava.bio.symbol.AbstractAlphabet.getAmbiguity (AbstractAlphabet.java:121) (pc 10)
        at org.biojava.bio.symbol.AlphabetManager.characterTokenizationFromXML (AlphabetManager.java:994) (pc 187)
        at org.biojava.bio.symbol.AlphabetManager.alphabetFromXML (AlphabetManager.java:954) (pc 318)
        at org.biojava.bio.symbol.AlphabetManager.<clinit> (AlphabetManager.java:785) (pc 429)
        at org.biojava.bio.seq.DNATools.<clinit> (DNATools.java:52) (pc 2)
rethrown as org.biojava.bio.BioError: Unable to initialize DNATools
        at org.biojava.bio.seq.DNATools.<clinit> (DNATools.java:83) (pc 279)
        at org.biojava.bio.seq.io.SeqIOTools.getDNAParser (SeqIOTools.java:49) (pc 0)
        at org.biojava.bio.seq.io.SeqIOTools.readEmbl (SeqIOTools.java:80) (pc 12)
        at uk.ac.sanger.psu.gemini.DataHandler.readSequenceFromFile (DataHandler.java:227) (pc 111)


I've scanned a few files for recent changes, but can't find the source
of the problem.

ta,

Keith

-- 

-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK