[Bioperl-l] joining BioPerl and Java

Dr. Christoph Gille christoph.gille at charite.de
Fri Jan 6 14:18:49 EST 2006

I am planing to bring BioPerl and BioJava/STRAP together.  Motivation:
I think that this might be useful because BioPerl allows to write
Bioinformatics programs in a very comfortable way and BioJava and
STRAP provide visualization tools for sequences, alignments and
structures. Further Java is fast enough for computational intensive
calculations.  As a positive side effect STRAP users may benefit from
additional modules.

Implementation: The plan is to provide a Java wrapper class for BioPerl
programs.This wrapper class should be as simple as possible so that even
PERL programmers without Java experience are able to embed their PERL

Initially, this class should manage installation of PERL, Cygwin (DOS
computers) and BioPerl.  At first invokation it will download the
respective PERL program as a zip archive.
It will create a working directory and
will start the PERL program.  After the PERL program has terminated it
will parse and evaluate the output and perform the required action.

Communication between the PERL and Java layer will be possible via
stdin/stdout streams and with local files.

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