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Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 23 22:19:44 2004 UTC (15 years, 8 months ago) by olson
Branch: MAIN
CVS Tags: HEAD, Root-bobdev_news, caBIG-00-00-00, caBIG-05Apr06-00, caBIG-13Feb06-00, merge-bobdev_news-1, merge-bobdev_news-2, merge-bodev_news-3, merge-trunktag-bobdev_news-1, merge-trunktag-bobdev_news-2, merge-trunktag-bodev_news-3, myrast_33
Branch point for: Branch-bobdev_news
Changes since 1.2: +28 -14 lines
Diff to previous 1.2
Fix from bill:

In the prolog code, I have changed the subsystem parsing so that
it uses far less stack, and this allows Conserved_tRNAs (the
subsystem that failed for Rick) to get parsed and going.  (I didn't
run the whole job.)

Only one file needs to be replaced (billogix does not need to be recompiled).
It is (on seed-mac-1)

   /Users/mccune/Billogix2/parse.pl

More detail, in case you're interested ...

We were parsing the whole subsystem into a detailed data structure,
including the parts we aren't using.  The sequence section, e.g.

>fig|188.1.peg.1567 COG: COG1384,Magn1649,ZP_00049059.1,gi|23006995
MGGAVGLHPPLRAAGRPETHPKLAGLVTRALAYYRDFVRPQKQYRAPTEEEAAALRDLSE
TLAEHEGSTDPEALQAIVYEVGRRHFPDLSGKAKSPDGRPGVSKTWFASIYNVLFGEAQG
PRFGSFIALYGVGGTRALIEKALSGALVAEHEAFLASRKAAAE

is the vast majority of the data, and is not currently used by
billogix.  The fix is to accept any strings as sequences rather
than parsing them.  So this problem might up again if we
ever want the prolog code to use those sequences.

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 14 22:04:49 2004 UTC (15 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.1: +13 -8 lines
Diff to previous 1.1
Make integration chagnes

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 7 15:30:08 2004 UTC (15 years, 9 months ago) by mkubal
Branch: MAIN
Branch point for: bill
Initial revision

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