Ewan> For guys who do run Java as part of their production code in Ewan> bioinformatics,
Ewan> (a) do you have versioning problems over time? Versioning with Java is a pain in the ass. We seem to get repeated problems with different versions both in terms of point releases, and versions on different OS'es. There is no intrinsic reason relating to java, why this should be the case, at least not as far as I can see. It just seems to happen. Also libraries seem to expand massively and in duplicate, and often in multiple versions. Part of the problem here is that (for redhat users anyway) the RPM's they ship do not advertise their dependencies correctly, and there is no standard installation scheme. If Sun took on board the work done by jpackage.org things would be much better. Sadly building jpackage RPM's for the JDK is a pain, and jpackage can not release these directly as binaries because of silly licensing issues. Ewan> (b) are there resource problems or not? Ewan> If so, how do you deal with these? I have found this to be much less of an issue, or rather, I have found this to be much less of an issue as time has gone on. You can set up a swing GUI app now, without flooring the OS (which wasn't the case when I started using swing in 1.2 beta days). And you can do reasonable amounts of computation. The problem comes if you try and use Java like perl. Setting up a JVM is expensive. If you have lots of little scripts, as is common with perl, and run each in its own JVM you are going to have problems. My experience with perl (using bioperl, and the go database API) was that running a database, and blast at the same time, took up far more resource than perl did. If I had used java instead, then this would still have been the case. I only used perl because there was no replacement for go API. Perl is a nice language in some ways, but I just hate coding in a language whose syntax looks like Snoopy swearing..... Cheers Phil _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
