[Biojava-l] RES: external processes

[Dickson S. Guedes]

Hi All,

Sorry, I don't have many time in this week but, I did see many question in
list about
MultAlign using Biojava, but Biojava DON'T have a Class to make MultAlign.
So In my
teses I´d want to use a set of pre-aligned sequences, then I create a Class
to do it
calling ClustalW as a external executable.

A Simple Example founds at:

http://biojava.org/wiki/BioJava:Tutorial:MultiAlignClustalW

Sorry, I don't make any comments and any comments or javadoc in that class,
but I'll do, for now I have other things to do at this week and don't have
much time :(

I accept sugestions too, and thanks for all.

[]s
--
Dickson S. Guedes
/*
 * UNISUL - Universidade do Sul de Santa Catarina
 * ATI - Assessoria de Tecnologia da Informação
 * Tubarão - Santa Catarina - Brasil
 * (0xx48) 621-3200 - http://www.unisul.br
 *
 *    "Quis custodiet ipsos custodes?"
 */  

> -----Mensagem original-----
> De: biojava-l-bounces at lists.open-bio.org 
> [mailto:biojava-l-bounces at lists.open-bio.org] Em nome de 
> mark.schreiber at novartis.com
> Enviada em: quarta-feira, 17 de maio de 2006 02:44
> Para: biojava-l at biojava.org
> Assunto: [Biojava-l] external processes
> 
> Hi all -
> 
> I noticed that someone has posted a tutorial to the wiki page
> (http://biojava.org/wiki/BioJava:Tutorial:MultiAlignClustalW) 
> showing how to launch ClustalW from biojava which is very 
> much appreciated. The tutorial makes use of the standard Java 
> Runtime and Process classes. 
> Developers may also be interested in the ExecRunner class 
> that is in the utils package of biojava1.4.
> 
> There is also an entire API for handelling external processes 
> in the CVS version of biojava (org.biojava.utils.process) 
> which makes handling of external processes much simpler.
> 
> - Mark
> 
> Mark Schreiber
> Research Investigator (Bioinformatics)
> 
> Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road
> #05-01 Chromos
> Singapore 138670
> www.nitd.novartis.com
> 
> phone +65 6722 2973
> fax  +65 6722 2910
> 
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