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

[Chad Matsalla]

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