I don't think this is a troll at all. This seems to be a common complaint with BioJava and Java itself. Are resources problems in BioJava occuring in general or only when large sequences are being analyzed? Can we pinpoint instances where BioJava is being a pig or is this a typical problem when doing bioinformatics with Java?
I know... this is a troll.... but it sort of resonates with me about the
way Java development works - people have to fix on a JVM version to get
real like-a-rock stability and work about bugs in that release, and Java is just dreadful in resource management (in particular memory
footprint) meaning you have to give it really beefy machines to run on.
http://www.internalmemos.com/memos/memodetails.php?memo_id=1321
Another Slashdot faithful. :-)
This is why I think i have alot of reluctance to move to Java; C is by farNothing wrong with that, C is an excellent language and there is still plenty of C development going on. If C is the right tool for the job, then by all means use it.
my prefered strongly-typed, "non-scripting" language. But I am a
dinosaur...
Speaking of C, I was wondering if anybody has done any experimenting with using C/C++ and JNI for computational and/or resource intensive tasks. Since BioJava is based on interfaces, it seems you could replace sequence implementations and objects that perform calculations on sequences with C implementations.
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