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 read. readXXXXFields(BufferedReader _br, ArrayList(of String) _fieldsToBeParsed).. or 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 *************************************************************************** The contents of this communication are intended only for the addressee and may contain confidential and/or privileged material. If you are not the intended recipient, please do not read, copy, use or disclose this communication and notify the sender. Opinions, conclusions and other information in this communication that do not relate to the official business of my company shall be understood as neither given nor endorsed by it. *************************************************************************** _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
