[Biojava-l] status? Blast parser?

[Simon Brocklehurst]

> Ah, you called my bluff!
>
> I wasn't thinking of anything too complicated, actually.  I'm working on a
> Web application in which HTML output from a Blast parser would be part of a
> larger page containing other data, navigation info, links, look-n-feel etc.
> The body of the document (ie. HTML blast output) is nested within several
> outer tables that help with layout and positioning.
>
> Within this context, some desirable areas over which to exert control would
> be:
>
>         - get the output as a table only, not a standalone html document.
>         - simple formatting such as table width, cell spacing, cell padding,
>
>           alignment, borders on/off and so forth.  Basically the ability to
> set
>           arguments to the <table> tag.
>         - some rudimentary control over font size and color, just so the
> table
>           doesn't clash too badly with the look of the rest of the page.
>         - maybe some simple control over the content of the output.  Course
> settings
>           like 'terse', 'verbose', 'summary' or the ability to selectively
>           include/exclude certain columns in a table would be interesting,
> but not
>         essential.

So... you don't want much then ;-)   You know, <pre> tags are quite cool...
(just kidding!)... Seriously,  I think that in reality we could produce many of
the effects you want at the level of most HTML user agents by being a bit clever
about HTML fragment output.  Thanks for responding with what you're looking for,
it's appreciated.

> I'd like to be able to include hyperlinks back to the original datasources
> in the table, but at that level I'm thinking the easiest way to do that
> would be to pull out the raw data and build the table myself.

To be honest, this is pretty important for almost any application I can think
of. I'd think we had failed to some extent if we didn't deal with this
relatively cleanly.

S.
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
mailto:simon.brocklehurst@CambridgeAntibody.com