Hi Henning<br><br>That makes a lot of sense indeed. I would go for the solution of grouping them all in one single package, owl.runners sounds good to me. Also all the stuff in the tinker package should go in there too. Actually at the moment the tinker package is also misnamed as it contains gromacs related stuff too. <br>
<br>Jose<br><br><br><br><br><br><div class="gmail_quote">On 16 March 2010 15:31, Henning Stehr <span dir="ltr"><<a href="mailto:stehr@molgen.mpg.de">stehr@molgen.mpg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear developers,<br>
<br>
We have quite a few classes whose main purpose is to run some external<br>
program, parse the output and return results as a java object. They<br>
are usually called SomethingRunner.<br>
<br>
The examples that I could find are : DaliRunner, PolyposeRunner,<br>
MaxClusterRunner, BlastRunner and TCoffeeRunner.<br>
In addition there is the Tinker related stuff which has its own<br>
package owl.tinker and the interface to paul in the obscure package<br>
actionTools.<br>
<br>
Shall we group all these together in some package? If so, how should<br>
this package be named? Some ideas would be: owl.runners,<br>
owl.externalprograms<br>
The main intention would be to make them easier to find and to make it<br>
obvious that everything in the package will depend on some external<br>
executable which needs to be installed seperately.<br>
<br>
Or, shall we keep them in the proteinstructure and sequence package as<br>
it is the case now? The argument here would be that e.g. Blast is<br>
strictly sequence related while Dali only deals with structures.<br>
<br>
Any opinions?<br>
<br>
Cheers,<br>
Henning<br>
<br>
_______________________________________________<br>
Owl-devel mailing list<br>
<a href="mailto:Owl-devel@bioinformatics.org">Owl-devel@bioinformatics.org</a><br>
<a href="http://www.bioinformatics.org/mailman/listinfo/owl-devel" target="_blank">http://www.bioinformatics.org/mailman/listinfo/owl-devel</a><br>
</blockquote></div><br>