Hi guys :
The following code snippet, for two 150 amino acid proteins, is taking a
somewhat long time, that is, well over 4 minutes, ....
long t=(System.currentTimeMillis());
StructurePairAligner aligner = new StructurePairAligner();
aligner.align(s1, s2);
aligner.setDebug(false);
System.out.println("time = " + (System.currentTimeMillis()-t)/1000+"
sec");
Strangely, Im running biojava on a 2x28 GHz Quad Core Intel Xeon chip, Mac
OS 10.5.8, with aggressiveheap enabled, and 6 Gigs of RAM.
This suprises me since the tests on the biojava wiki page for structural
alignments seem to be quite efficient.
--
Jay Vyas
MMSB/UCHC
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