[Owl-devel] How to organize 'runner' classes?

Henning Stehr stehr at molgen.mpg.de
Tue Mar 16 10:31:39 EDT 2010

Dear developers,

We have quite a few classes whose main purpose is to run some external
program, parse the output and return results as a java object. They
are usually called SomethingRunner.

The examples that I could find are : DaliRunner, PolyposeRunner,
MaxClusterRunner, BlastRunner and TCoffeeRunner.
In addition there is the Tinker related stuff which has its own
package owl.tinker and the interface to paul in the obscure package

Shall we group all these together in some package? If so, how should
this package be named? Some ideas would be: owl.runners,
The main intention would be to make them easier to find and to make it
obvious that everything in the package will depend on some external
executable which needs to be installed seperately.

Or, shall we keep them in the proteinstructure and sequence package as
it is the case now? The argument here would be that e.g. Blast is
strictly sequence related while Dali only deals with structures.

Any opinions?


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