[Biojava-l] Preparation for a 1.1 release?

[Keith James]

>>>>> "Thomas" == Thomas Down <td2@sanger.ac.uk> writes:

    Thomas> I/O:

    Thomas>    - We're currently without a working GENBANK parser (our
    Thomas> only major regression since 1.0).  I guess this is my
    Thomas> responsibility, but if there is anyone out there who uses
    Thomas> GENBANK files more than I do, please have a go at this.

I was thinking about Swissprot/Trembl parsing, but I heard that the
Swissprot team have XML plans. A chance that I can get my hands on
Swissprot as XML is enough to put me off this idea.

    Thomas> Sequence searching:

    Thomas>    - It would be good to have some tests for this.  Does
    Thomas> anyone feel like glueing the current BLAST parser to
    Thomas> Gerald's org.biojava.bio.search interfaces?

I'm working on Fasta now, but Blast was going to be my next job. If
someone else gets there first, no problem. (Code suggestions on the
other thread duly noted, by the way).

    Thomas>    - Does anyone have any comments about the current set
    Thomas> of tutorials?

Both the 'Symbols & SymbolLists ' and 'Sequences & Features' ones were
absolutely vital for me to get started. If they hadn't been there I
might have given up (or at least put it off until later). Working code
snippets are a great way of pulling together the (somewhat abstract)
concepts applied in the various packages and saying "here's how these
fit together in a useful way".

    Thomas>    - More tutorials would be great.  In particular:

    Thomas>       + SequenceDBs + The search packages (if we get this
    Thomas> hooked up to BLAST and/or FASTA).

I admit it, I'm a documentation facist. I'll do the Fasta search
docs/tutorial when the code is working. Is there going to be a common
format (DocBook, or something?)

cheers,

-- 

-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA