[Biojava-l] Java Resource Management [a semi troll...]

[Dave Keller]

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>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.
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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?

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>http://www.internalmemos.com/memos/memodetails.php?memo_id=1321
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Another Slashdot faithful. :-)

>This is why I think i have alot of reluctance to move to Java; C is by far
>my prefered strongly-typed, "non-scripting" language. But I am a
>dinosaur...
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Nothing 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.

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.