[Biojava-dev] Some words about documentation in Biojava1 and other aspects to Biojava2

[Maximilian Haeussler]

>
>
>Program execution
>-----------------
>Maybe this is a bit offtopic and I know that many things have been told
>about external program execution (blast, clustalw...). But it is a reality
>that many people use Biojava to execute such programs and parse its
>results... and for applications at that level. I've developed already a
>solution for this situation that can be improved of course... It is just
>some general parameters... for instance, I have and object BlastParameters
>that implement a Parameters interface, that is executed by a
>SimpleExecutor class... and the results are a SimpleExecutionReport etc...
>in that BlastParameters object I have accessor methods to blast
>parameters... I know that this is then platform dependent some extent, but
>could'nt be a subproject, or module, or whatever?
>
Me too, I've just written AlgorithmRunner-classes that encapsulate 
algorithm execution, parameter setting,
storing in xml, command line building and returning the results. Anyone 
else here with something similar?
I'd be interesting in sharing code so we can  copy from each other. My 
current problems include  starting many processes (workers) in parallel 
for multiprocessor machines... not completely trivial, as I'm gradually 
finding out.

The second general way that you can use to start algorithms is to pass 
parameters to html-forms and parse the results. I know this is crazy but 
sometimes it is the only way to get hold of databases, especially 
commercial ones. Has anyone here already done something like that? I am 
starting to look at http API from Apache Jakarta Commons. Any other 
suggestions on finding a good library to play "browser" via http?

Max