[Biojava-l] SeqIOTools.readXXXXFields() method??

Roy Park RPark@lexgen.com
Fri, 26 Jul 2002 11:16:06 -0500

Hello everyone.

I deal with a number of pseudo EMBL/GenBank formatted sequences, and it
would be extremely nice (?) to have methods that only attempt to parse out
specified fields.

The primary reason for this is that, right now, the format.readSequence()
throws BioException way too frequently for my purpose - i.e. although I only
need the fields X, Y and Z from each sequence definition, the readSequence()
throws exception where it finds the field W to be mal-formed, etc.

I see that modified versions of the StreamReader class, the SequenceFormat
implementing classes, etc. has to be written, which I can do.  I'm wondering
if anyone could suggest a preferred way of passing the desired fields to be

readXXXXFields(BufferedReader _br, ArrayList(of String) _fieldsToBeParsed)..
readXXXXFields(BufferedReader _br, String[] _fieldsToBeParsed)..etc.

(I think the readXXXXX(BufferedReader) should be called if the second
argument is null.)

Any input would be greatly appreciated.  (what about the naming of the
methods - readXXXXPartial()??)

Roy K. Park
Bioinformatics Data Analyst
Lexicon Genetics Incorporated

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