[Bioperl-l] arbitrary hashes, blast, statistics, parameters, and java interoperability

[Jason Stajich]

Chad - I think you forgot to commit
Bio/Search/BlastStatistics.pm in your new Statistics module commits.

-jason

On Fri, 14 May 2004, Chad Matsalla wrote:

>
> On Fri, 14 May 2004, Aaron J. Mackey wrote:
> > I'd be happy to see the statistics and parameters turn into full
> > objects, and could even imagine some useful functions that a
> > Bio::Search::Statistics::BLAST object might provide:
>
> <snip good ideas>
>
> > I realize you (and 99.9% of the world) only care about BLAST statistics
> > and parameters
>
> At this time, yes.
>
> > but I really do think you should subclass these things
> > so that we can plug in others when/if necessary.  I would think that
> > all an interface should gaurantee are generic data access methods
> > (get_param, set_param, etc).
>
> So I will create:
> Bio::Tools::Run::ParameterI
> with no attributes, inherits from root, and two procedures:
> get_param(key)
> set_param(key,value)
> and
> Bio::Search::StatisticsI
> with no attributes, inherits from root, and two procedures:
> get_statistic(key)
> set_statistic(key,value)
>
> Then I will create:
> Bio::Tools::Run::BlastParameters
> with these attibutes:
> expect,filter,gapext,gapopen,include,match,matrix,mismatch
> and
> Bio::Search::Result::BlastStatistics
> with these attributes:
> <sigh> Yes, a whole bunch of attributes.
>
>
> The elimination of arbitrary hashes, in this case, completely fixes my
> Java<->Perl interoperability 'issues'.
>
> Chad Matsalla
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu