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
