On Tue, Feb 12, 2002 at 01:44:34PM -0500, Ratiba Terbaoui wrote: > > hello, > > I'm a new user of Biojava and i want to know if i can run Blast using > Biojava, which classes i have tu use
Hi... BioJava includes some a fairly advanced parser for output from the `blast' family of programs. There's some tutorial documentation about this on the website: http://www.biojava.org/tutorials/blastlikeParsingCookBook/cookbook.html You might also like to look at the javadoc documentation for the packages: org.biojava.bio.program.sax org.biojava.bio.program.ssbind What this code /doesn't/ do for you is run the blast program itself. At the moment, the best way to do this is to use the Java Process API. Look at the classes java.lang.Runtime and java.lang.Process in the Java API. It might be nice to have a wrapper within BioJava for launching blast, but this potentially leads to awkward questions, like where to find blast executables, how to set command line options, etc... Hope you find this a good starting point -- mail me or the list if you have any trouble, Thomas. _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
