[Biojava-l] library for running blast and formatdb

[Patrick McConnell]

>I suppose it's a matter of another external dependency vs. reinvented
>utility code in biojava . . .  Would it make sense to merge the better
>qualities of the two?

The CLI project looks like it is quite flexible and robust.  But, with
this, it is somewhat complex.  This is in contrast to the simplicity of
creating parameters via reflection.  I think that these two methods could
be effectively combined so that we gain the simplicty of reflection with
the flexibility of CLI.  The base parameters class can use CLI to build its
parameters.  As an option, it can build CLI options via reflection for
simplicity.  When users extend the base class, they can utilize the
flexibility of CLI if they need it, otherwise they can use reflection for a
quick and dirty parameter parsing.  The base class could even extend the
Options class, so we are really working with a hybrid of the two.  What
does everyone think?

-Patrick






"Michael L. Heuer" <heuermh@acm.org>@shell3.shore.net> on 01/10/2003
05:18:52 PM

Sent by:    Michael Heuer <heuermh@shell3.shore.net>


To:    Patrick McConnell <MCCon012@mc.duke.edu>
cc:    biojava-l@biojava.org

Subject:    Re: [Biojava-l] library for running blast and formatdb


On Fri, 10 Jan 2003, Patrick McConnell wrote:

> In the process, I developed some useful and flexible base classes for
> formatting parameters and running programs.  Parameters are automatically
> converted to an argument array via reflection and reading of standard out
> and standard error in separate threads is handled automatically.

The base classes are nice, but I prefer the design of

> http://jakarta.apache.org/commons/cli

a lot better for handling parameters.

I suppose it's a matter of another external dependency vs. reinvented
utility code in biojava . . .  Would it make sense to merge the better
qualities of the two?

I also have a few simple classes for oneoff scripts with command line &
logging facade support that I use all the time, see

> http://www.shore.net/~heuermh/oneoff.tar.gz

but they don't have any extra support for external programs.

   michael

>
> Check it out if you are interested:
> http://www.dbsr.duke.edu/software/blast/default.htm .  The full source,
> javadocs, and binary class files are available.  Also, if this seems
> appropriate for BioJava, I have no problem donating it to the cause.  I
> think that at least the base classes, or some modification of them, would
> be useful to others.
>
> Please email me with suggestions/comments,
>
> -Patrick McConnell
> Duke Bioinformatics Shared Resource
> mccon012@mc.duke.edu
>
>
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