BioJava: ExternalProcess class

The BioWeka project committed a set of Java classes to the BioJava project to execute external programs within Java programs.

The ExternalProcess class is intended for applications that call an external program many times, e.g. in a loop, with varying command line arguments and that need high performance throughput, i.e. the program's input and output should not be written to disk, but directly written/read to/from its standard input, output and error streams. Therefore, it provides input/output handling in multiple threads and the threads are managed by a thread pool.