[Biojava-l] library for running blast and formatdb

Tue, 14 Jan 2003 11:20:28 -0500 (EST)

Other designs to consider

Configurable/Configuration

> http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/Configurable.html
> http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/Configuration.html

Parameterizable/Parameters

> http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/Parameterizable.html
> http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/Parameters.html

I find the Apache Avalon project to be completely full of good ideas
and full of completely unusable implementation.

   michael

On Tue, 14 Jan 2003, Patrick McConnell wrote:

>
> What I have written provides two essential base classes: Program and
> Parameters.  The Program class provides the functionality for launching a
> program and capturing output.  I should also put in hooks for handling the
> input and output as streams as an alternative to capturing it in memory.
> The Parameters class builds command arguments based on the fields of the
> extending class using reflection.  It provides some flexibility for
> determining what the flags and delimitters look like.  There has been
> discussion to change the implementation somewhat to use jakarta's CLI
> library, and I think a hybrid of the two would be appropriate.
>
> I have written Program and Parameters implementations for NCBI's blastall
> and formatdb programs.  Now, after chatting with Jason Stajich here at
> Duke, I am working on a flexible queueing system for Programs.  This code
> isn't complete yet, though.
>
> So, if everyone likes this framework for launching programs, I'd be glad to
> donate it to BioJava.  If people don't like it, I'll change it based on
> suggestions.  Whomever is interested, please check out:
> http://www.dbsr.duke.edu/software/blast . My code is fully documented, and
> I have added a couple examples that demonstrate the ease of launching
> blast.
>
> As to the XML description of program parameters, I think that is a good
> idea, and can be a factory method in my Parameters class.  The method takes
> in the XML somehow (File or Stream or whatever) and returns a Parameters
> object.  But, I know that some people would prefer to handle the Parameters
> internally with code instead of externally in a File.  So, we should not
> limit ourselves to a single approach.
>
> Thanks!
>
> -Patrick
>
>
>
>
>
> "Schreiber, Mark" <mark.schreiber@agresearch.co.nz>@biojava.org on
> 01/13/2003 03:08:08 PM
>
> Sent by:    biojava-l-admin@biojava.org
>
>
> To:    "Patrick McConnell" <MCCon012@mc.duke.edu>
> cc:    <biojava-l@biojava.org>
>
> Subject:    RE: [Biojava-l] library for running blast and formatdb
>
> One thing sorely missing from BioJava is the ability to launch and
> capture the results of common bioinformatics programs. I know Java isn't
> the best at this but it's not that bad. It's also needed if you want to
> develop pipeline type applications.
>
> Would it be possible to get some kind of over-arching interface based
> API so that services can be made available with similar interfaces.
>
> Possibly a Service or Program interface a Paramater list or map, some
> kind of result stream?
>
> Just my $0.02
>
> - Mark
>
> > -----Original Message-----
> > From: Patrick McConnell [mailto:MCCon012@mc.duke.edu]
> > Sent: Tuesday, 14 January 2003 4:15 a.m.
> > To: biojava-l@biojava.org
> > Subject: Re: [Biojava-l] library for running blast and formatdb
> >
> >
> >
> >
> > >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
> > >
> > >
> > > _______________________________________________
> > > Biojava-l mailing list  -  Biojava-l@biojava.org
> > > http://biojava.org/mailman/listinfo/biojava-l
> > >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> >
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