[Biojava-l] status? Blast parser?

Simon Brocklehurst simon.brocklehurst@CambridgeAntibody.com
Wed, 16 Feb 2000 19:54:37 +0000

> 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.

Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK