[Biojava-dev] no need for LENGTH_TYPE_TERM

[mark.schreiber at novartis.com]

I think this sounds sensible. Having another term for something that can 
be derived from the alphabet is redundant.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com

phone +65 6722 2973
fax  +65 6722 2910





"george waldon" <gwaldon at geneinfinity.org>
Sent by: biojava-dev-bounces at lists.open-bio.org
04/20/2007 05:05 AM
Please respond to george waldon

 
        To:     biojava-dev at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-dev] no need for LENGTH_TYPE_TERM


LENGTH_TYPE_TERM is a RichSequence term that is used to distinguish 
between "aa" and "bp" during the write operation in uniprot format and in 
genbank format.

This code is error-prone. For instance, converting a protein sequence from 
a fasta file to a genbank formatted file still write "bp". Indeed, the 
sequence annotation for this term should be generated during the 
enrichment of sequence. 

I don't think the extra-work is really necessary. Is-there any objection 
that I remove this term and rely instead on the alphabet (either PROTEIN 
or PROTEIN_TERM) during the writing operations?

Thanks,
George
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