I would love to see this placed in the biojava core... Might switch me back from bioperl ;-)
-Mat > -----Original Message----- > From: Patrick McConnell [mailto:[EMAIL PROTECTED]] > Sent: Friday, January 10, 2003 3:12 PM > To: [EMAIL PROTECTED] > Subject: [Biojava-l] library for running blast and formatdb > > > > In the past, there have been quite a few requests on how to > run blast from > a Java program. I have developed some classes for running > NCBI blastall > and formatdb. All of the parameters for the respective programs are > implemented, and everything is reasonably well documented. > Also useful is > an option to run blast without input and output files, > utilizing standard > input and output. > > 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. > > 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 > [EMAIL PROTECTED] > > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
