[Bioperl-l] Re: [Bioperl-l] [Bioperl-l] Pushing towards 1.0

[Steve Chervitz]

Yes, Jason and I are using the same SearchIO system, but different Bio::Search::
interfaces. At present, they co-exist but we should boil them down to just
one set before the release. The implementations of these interfaces will
likely remain since Jason's are generic whereas mine have more Blast-specific
functionality. This is an area where employing Hilmar's factory pattern
suggestion makes alot of sense.

Funny you should mention HTML input/output, since I haven't yet added this
to my new SearchIO objects either. For outputting, I have this Bio::SearchIO::Writer
system that plugs into SearchIO which I am using for generating tabular
output. It should be easy enough to add a HTML writer object. For HTML-formatted
input, I have some ideas, but nothing firm yet.

Another thing that's not in Jason's or my Bio::Search:: stuff is any sort
of functionality related to running new search jobs. As Ewan mentioned before
(http://bioperl.org/pipermail/bioperl-l/2001-July/006020.html), it would
be good to tie into a novella-like system. (I believe Martin mentioned to
me the possibility of contributing novella to Bioperl. Don't know what the
current thinking here is).

Steve

>Steve and I talked about it and it should be the same thing - note that
I
>did commit a blast text parser which may be superceded by Steve's if it
>does a better job (need the from/to HTML features at some point).  It
>seems to me (without seeing code) Steve wants to provide something
>slightly more robust for the Bio::Search objects as well.  I'm not exactly
>clear what direction that will mean but hopefully we're all on the same
>page here.  I am actively using my SearchIO stuff so I think it is as
>least getting a workout to try and track down any missing features.
>
>> This might be a stupid question, but how does this work with Jason's
>> SearchIO Blast stuff. Is it the same? different? if so, how so?
>>
>>
>> Just confused slightly...
>>
>>
>>
>>
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>
>--
>Jason Stajich
>Duke University
>jason@cgt.mc.duke.edu
>
>