[Biojava-l] Alphabet issues

[Saif Ur-Rehman]

Dear Concerned,

I am attempting to read in a Fasta file of amino acid sequences using the
Alphabet "PROTEIN-TERM" and I am sporadically getting an Illegalsymbolexception
which states

"This tokenization doesn't contain character: 'M'"

The code causing the exception is as follows

BufferedInputStream is = new BufferedInputStream(new FileInputStream(filename));

Alphabet alpha= ProteinTools.getTAlphabet();
SequenceDB db = SeqIOTools.readFasta(is, alpha);


Thanking you in advance

Saif

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Saif Ur-Rehman
Research Student
Phone: +44 (0)1334 46 3362
Email:su24 at st-andrews.ac.uk
http://bio.st-andrews.ac.uk/staff/su24.htm
The Centre for Evolution, Genes & Genomics (CEGG), University of St Andrews


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