[Biojava-l] structure alignment seems slow ...

[Jay Vyas]

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