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Revision 1.309 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 12 14:34:14 2005 UTC (14 years, 5 months ago) by redwards
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CVS Tags: merge-trunktag-bodev_news-3
Changes since 1.308: +91 -40 lines
Diff to previous 1.308
Changing attributes and modifying protein.cgi with show/hides

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Tue Jul 12 00:34:32 2005 UTC (14 years, 5 months ago) by overbeek
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Changes since 1.307: +16 -16 lines
Diff to previous 1.307
updates to build protein families

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Sun Jul 10 04:59:11 2005 UTC (14 years, 5 months ago) by redwards
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Changes since 1.306: +8 -1 lines
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making index_subsystems work

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Sat Jul 9 21:46:15 2005 UTC (14 years, 5 months ago) by redwards
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Changes since 1.305: +17 -0 lines
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added index subsystems to subsys.cgi

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Fri Jul 1 02:09:16 2005 UTC (14 years, 5 months ago) by redwards
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Changes since 1.304: +46 -26 lines
Diff to previous 1.304
Changed proteinfamilies.cgi

Revision 1.304 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 29 15:06:12 2005 UTC (14 years, 5 months ago) by olson
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CVS Tags: merge-trunktag-bobdev_news-2
Changes since 1.303: +2 -2 lines
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Tweak tracing.

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Wed Jun 29 00:28:01 2005 UTC (14 years, 5 months ago) by redwards
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Changes since 1.302: +88 -5 lines
Diff to previous 1.302
Initial release of proteinfamilies.cgi into the wild

Revision 1.302 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 28 17:25:04 2005 UTC (14 years, 5 months ago) by redwards
Branch: MAIN
Changes since 1.301: +20 -0 lines
Diff to previous 1.301
commiting FIG.pm::clean_spaces to remove leading, trailing, and extra spaces. Please use it

Revision 1.301 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 24 21:39:14 2005 UTC (14 years, 5 months ago) by parrello
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CVS Tags: merge-trunktag-bobdev_news-1
Changes since 1.300: +16 -17 lines
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Fixed the environment-variable tracing so that it does not override previous tracing options if they were set.

Revision 1.300 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 23 21:24:48 2005 UTC (14 years, 5 months ago) by overbeek
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Changes since 1.299: +5 -0 lines
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finally

Revision 1.299 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 23 19:35:07 2005 UTC (14 years, 5 months ago) by olson
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Changes since 1.298: +33 -2 lines
Diff to previous 1.298
Add some more gene  name mapping stuff.

Add Tracer environment variable for affecting tracing.

Fix typo in invocation of load_coupling.

Revision 1.298 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 22 21:00:24 2005 UTC (14 years, 5 months ago) by parrello
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Changes since 1.297: +514 -531 lines
Diff to previous 1.297
Replaced tabs with spaces to make indenting device-independent.
Moved "Open" and "OpenDir" to the Tracer.pm module.
Added more POD documentation.

Revision 1.297 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 20 21:58:56 2005 UTC (14 years, 5 months ago) by olson
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Changes since 1.296: +63 -0 lines
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Add genome/peg id mapping routines. (For functional coupling support).

Revision 1.296 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 20 17:08:32 2005 UTC (14 years, 5 months ago) by overbeek
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Changes since 1.295: +1 -1 lines
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add new protein family routines

Revision 1.295 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 20 17:04:45 2005 UTC (14 years, 5 months ago) by overbeek
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Changes since 1.294: +72 -11 lines
Diff to previous 1.294
add new protein family routines

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Mon Jun 20 04:03:44 2005 UTC (14 years, 5 months ago) by overbeek
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Changes since 1.293: +6 -1 lines
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disable old protein families

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Mon Jun 13 16:43:48 2005 UTC (14 years, 5 months ago) by overbeek
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CVS Tags: Root-bobdev_news
Branch point for: Branch-bobdev_news
Changes since 1.292: +20 -33 lines
Diff to previous 1.292
Ross change commit after cleanup

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Mon Jun 13 09:32:09 2005 UTC (14 years, 5 months ago) by parrello
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Changes since 1.291: +160 -2 lines
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Added Open and OpenDir methods for streamlining file and directory operations.

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Fri Jun 10 16:08:52 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.290: +7 -7 lines
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fixes to cached pin displays

Revision 1.290 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 10 15:36:37 2005 UTC (14 years, 6 months ago) by redwards
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Changes since 1.289: +7 -9 lines
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adding correspondence.cgi

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Thu Jun 9 20:03:15 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.288: +95 -1 lines
Diff to previous 1.288
re-add couipling routines

Revision 1.288 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 9 18:39:05 2005 UTC (14 years, 6 months ago) by parrello
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Changes since 1.287: +39 -28 lines
Diff to previous 1.287
*** empty log message ***

Revision 1.287 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 9 05:36:30 2005 UTC (14 years, 6 months ago) by parrello
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Changes since 1.286: +2333 -1628 lines
Diff to previous 1.286
*** empty log message ***

Revision 1.286 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 8 23:05:21 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.285: +7 -30 lines
Diff to previous 1.285
major change to BBHs (use precomputed)

Revision 1.285 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 7 16:41:23 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.284: +2 -1 lines
Diff to previous 1.284
Fixed typo in &hypo(), and added new rule. -- /gdp

Revision 1.284 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 1 01:18:50 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.283: +91 -12 lines
Diff to previous 1.283
install precomputed functional coupling data

Revision 1.283 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 29 13:33:56 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.282: +24 -0 lines
Diff to previous 1.282
add test for existence of relation that works only under Postgres

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Wed May 25 18:58:27 2005 UTC (14 years, 6 months ago) by redwards
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Changes since 1.281: +39 -0 lines
Diff to previous 1.281
added subsystems_roles method to FIG.pm

Revision 1.281 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 25 16:07:23 2005 UTC (14 years, 6 months ago) by olson
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Changes since 1.280: +92 -0 lines
Diff to previous 1.280
Code for similarity request export.

Revision 1.280 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 20 11:23:07 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.279: +1 -1 lines
Diff to previous 1.279
fix bug in search_indexes

Revision 1.279 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 17 16:04:08 2005 UTC (14 years, 6 months ago) by olson
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Changes since 1.278: +307 -19 lines
Diff to previous 1.278
Bundle of misc bob changes, including sim computation code and search-for-substring.

Revision 1.278 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 10 12:03:39 2005 UTC (14 years, 7 months ago) by overbeek
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Changes since 1.277: +4 -1 lines
Diff to previous 1.277
fixes to using trees under subsystems

Revision 1.277 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 5 17:43:03 2005 UTC (14 years, 7 months ago) by overbeek
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Changes since 1.276: +5 -3 lines
Diff to previous 1.276
fix indexing search code

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Tue May 3 21:03:38 2005 UTC (14 years, 7 months ago) by overbeek
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Changes since 1.275: +1 -1 lines
Diff to previous 1.275
add css generation modules

Revision 1.275 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 29 16:43:29 2005 UTC (14 years, 7 months ago) by overbeek
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Changes since 1.274: +1 -0 lines
Diff to previous 1.274
add assign_to_close_strains

Revision 1.274 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 18 18:29:31 2005 UTC (14 years, 7 months ago) by mkubal
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Changes since 1.273: +2 -3 lines
Diff to previous 1.273
revised on Monday

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Mon Apr 18 06:26:04 2005 UTC (14 years, 7 months ago) by redwards
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Changes since 1.272: +1 -1 lines
Diff to previous 1.272
minor fix to select tag/values

Revision 1.272 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 18 06:19:40 2005 UTC (14 years, 7 months ago) by redwards
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Changes since 1.271: +3 -1 lines
Diff to previous 1.271
minor fix to select tag/values

Revision 1.271 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Apr 17 16:30:19 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.270: +2 -0 lines
Diff to previous 1.270
handle missing annotations file gracefully

Revision 1.270 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 15 23:23:13 2005 UTC (14 years, 7 months ago) by golsen
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Changes since 1.269: +7 -27 lines
Diff to previous 1.269
Fix bunged index search

Revision 1.269 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 14 18:52:19 2005 UTC (14 years, 7 months ago) by mkubal
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Changes since 1.268: +2 -1 lines
Diff to previous 1.268
search_index now returns attributes

Revision 1.268 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 13 15:37:30 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.267: +30 -21 lines
Diff to previous 1.267
changed genome stats to show attributes

Revision 1.267 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Apr 10 03:32:30 2005 UTC (14 years, 8 months ago) by golsen
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Changes since 1.266: +1 -1 lines
Diff to previous 1.266
Re-enable "duplicates" in sims.  Multiple regions of matching is common
in eukaryotic sequences, and only seeing one is disorienting.

Revision 1.266 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 8 20:22:23 2005 UTC (14 years, 8 months ago) by redwards
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Changes since 1.265: +10 -15 lines
Diff to previous 1.265
changed tag/value pairs completely. Ooops!

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Thu Apr 7 19:16:10 2005 UTC (14 years, 8 months ago) by redwards
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Changes since 1.264: +30 -15 lines
Diff to previous 1.264
many changes to key/value pairs to make them work

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Sun Apr 3 19:43:41 2005 UTC (14 years, 8 months ago) by redwards
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Changes since 1.263: +5 -2 lines
Diff to previous 1.263
changing pir corresepondence

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Sun Apr 3 19:11:11 2005 UTC (14 years, 8 months ago) by redwards
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Changes since 1.262: +97 -8 lines
Diff to previous 1.262
Added a script to load pir superfamilies in the background. This will download all the data and install it. Changed pir.cgi to background this job as it takes a while.

Revision 1.262 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 2 11:56:12 2005 UTC (14 years, 8 months ago) by overbeek
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Changes since 1.261: +2 -0 lines
Diff to previous 1.261
add update_subsys_conflicts to fig.pl

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Thu Mar 31 18:05:28 2005 UTC (14 years, 8 months ago) by overbeek
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Changes since 1.260: +3 -0 lines
Diff to previous 1.260
fix to asses_completeness

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Wed Mar 30 19:58:20 2005 UTC (14 years, 8 months ago) by olson
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Changes since 1.259: +27 -0 lines
Diff to previous 1.259
Add genome_with_md5sum.

Warn on FigGFF errors only if you're bob.

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Wed Mar 30 15:53:37 2005 UTC (14 years, 8 months ago) by redwards
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Changes since 1.258: +4 -4 lines
Diff to previous 1.258
changing attributes returned back to variables

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Tue Mar 29 20:41:17 2005 UTC (14 years, 8 months ago) by redwards
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Changes since 1.257: +7 -5 lines
Diff to previous 1.257
minor changes to rae.cgi

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Tue Mar 29 19:29:39 2005 UTC (14 years, 8 months ago) by overbeek
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Changes since 1.256: +3 -2 lines
Diff to previous 1.256
add make_pu from ids and seqs

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Tue Mar 29 18:42:26 2005 UTC (14 years, 8 months ago) by overbeek
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Changes since 1.255: +7 -0 lines
Diff to previous 1.255
broaden set of acceptable aliases as dbxrefs

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Wed Mar 23 18:54:39 2005 UTC (14 years, 8 months ago) by golsen
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Changes since 1.254: +1 -1 lines
Diff to previous 1.254
Removed constraint that sims request had to be by a fig ID.  Ross seems to
have solved the orginal problem that names that could not be mapped
returned a representitive ID with undefined length, which crashed sims().
Now failure to map a name returns an empty list, and sims graceful returns
an empty list of similarities.

Revision 1.254 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 21 22:01:22 2005 UTC (14 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.253: +0 -1 lines
Diff to previous 1.253
A few similarities tweeks.  Move the submit button on the default protein
page (to shorten the line slightly).  Remove a debug statement that was
writing to the error log.

Revision 1.253 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 21 21:39:32 2005 UTC (14 years, 8 months ago) by golsen
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Changes since 1.252: +7 -4 lines
Diff to previous 1.252
Add options to Similarities to override Max expand when asking for FIG IDs.
It gets annoying to have to constantly increase the value, and it is not
predictable how many sims will need to be expanded to get any desired
number of FIG IDs.

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Mon Mar 21 18:33:49 2005 UTC (14 years, 8 months ago) by overbeek
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Changes since 1.251: +1 -1 lines
Diff to previous 1.251
fix to best_bbh_candidates and added fill_subsys

Revision 1.251 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 20 22:26:16 2005 UTC (14 years, 8 months ago) by golsen
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Changes since 1.250: +36 -2 lines
Diff to previous 1.250
When sorting similarities by percent identity or bit score per position,
include a penalty for very sort sequences, so that they do not randomly
appear much higher in the similaries list than they should.  The current
treatment for this is roughly a two standard deviation penalty.

The original behavior is still available as non-star versions.
The "help" information has been updated (and other aspects clarified
as well).

Revision 1.250 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Mar 19 01:27:13 2005 UTC (14 years, 8 months ago) by overbeek
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Changes since 1.249: +4 -0 lines
Diff to previous 1.249
update hypo

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Wed Mar 16 17:56:22 2005 UTC (14 years, 8 months ago) by golsen
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Changes since 1.248: +2 -2 lines
Diff to previous 1.248
Fix end condition test on expand_raw_sims to promptly return.

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Wed Mar 16 15:17:45 2005 UTC (14 years, 8 months ago) by overbeek
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Changes since 1.247: +1 -0 lines
Diff to previous 1.247
remove ddd: in front of some organisms (mostly uniprot)

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Wed Mar 16 15:11:56 2005 UTC (14 years, 8 months ago) by overbeek
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Changes since 1.246: +2 -1 lines
Diff to previous 1.246
change spaces to _s in subsystem names

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Wed Mar 16 00:18:09 2005 UTC (14 years, 8 months ago) by olson
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Changes since 1.245: +1 -1 lines
Diff to previous 1.245
make the gff stuff work again.

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Tue Mar 15 23:56:53 2005 UTC (14 years, 8 months ago) by olson
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Changes since 1.244: +76 -1 lines
Diff to previous 1.244
Put the FigGFF code in a require for now.

Add fast anno lookup.

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Mon Mar 14 19:17:37 2005 UTC (14 years, 8 months ago) by olson
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Changes since 1.243: +13 -0 lines
Diff to previous 1.243
Add general-purpose GFF writing stuff.

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Mon Mar 14 02:04:44 2005 UTC (14 years, 8 months ago) by golsen
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Changes since 1.242: +3 -3 lines
Diff to previous 1.242
Minor fix in expand_raw_sims so that it stops when it should

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Sun Mar 13 00:55:21 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.241: +59 -17 lines
Diff to previous 1.241
Initial commit of organisms.cgi which allows separate entry pages for different groups of organisms

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Fri Mar 11 22:03:13 2005 UTC (14 years, 9 months ago) by overbeek
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Changes since 1.240: +10 -2 lines
Diff to previous 1.240
fix for mapped_prot_ids

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Fri Mar 11 04:11:30 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.239: +4 -5 lines
Diff to previous 1.239
Making tag/value pairs work

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Fri Mar 11 03:04:32 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.238: +12 -5 lines
Diff to previous 1.238
Making tag/value pairs work

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Fri Mar 11 01:04:32 2005 UTC (14 years, 9 months ago) by golsen
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Changes since 1.237: +247 -122 lines
Diff to previous 1.237
Many new options for similarities

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Tue Mar 8 21:14:53 2005 UTC (14 years, 9 months ago) by olson
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Changes since 1.236: +19 -1 lines
Diff to previous 1.236
Add contig_md5sum.

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Tue Mar 8 21:06:04 2005 UTC (14 years, 9 months ago) by olson
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Changes since 1.235: +30 -0 lines
Diff to previous 1.235
Add support for computing MD5 checksums for contigs and genomes.

The checksum of a genome is defined as the checksum of its signature file. The signature
file consists of tab-separated lines, one for each contig, ordered by the contig id.
Each line contains the contig ID, the length of the contig in nucleotides, and the
MD5 checksum of the nucleotide data, with uppercase letters forced to lower case.

The signature file is written by index_contigs to
The genome's md5 checksum is written by index_contigs to <genomedir>/MD5SUM.

The md5.c code here is extracted from the Perl Digest::MD5 module. We use the perl
configuration to build it so that it will work correctly on 64-bit architectures.

Revision 1.235 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 6 15:10:02 2005 UTC (14 years, 9 months ago) by overbeek
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Changes since 1.234: +1 -0 lines
Diff to previous 1.234
disconnect get_attributes until I can talk to Rob

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Sat Mar 5 04:29:59 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.233: +10 -2 lines
Diff to previous 1.233
added highlight by peg attribute to subsystem

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Fri Mar 4 23:16:42 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.232: +23 -17 lines
Diff to previous 1.232
tweaks to coloring ss by oa

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Fri Mar 4 22:37:06 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.231: +128 -13 lines
Diff to previous 1.231
Added color by organism attributes to subsystems page

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Fri Mar 4 18:29:21 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.230: +3 -0 lines
Diff to previous 1.230
Added attribute editing to the protein.cgi page

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Fri Mar 4 06:22:10 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.229: +204 -18 lines
Diff to previous 1.229
Big updates to FIG.pm for the addition of methods to properly handle attributes. Also modified genome_statistics to take advantage of these new methods. load_attributes will load genomes and other attributes but doesn't not yet use the new methods (but should), and Attributes.html is some docs.

Revision 1.229 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 27 01:39:55 2005 UTC (14 years, 9 months ago) by overbeek
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Changes since 1.228: +51 -3 lines
Diff to previous 1.228
major changes in notion of function and load_attributes

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Sat Feb 26 19:49:59 2005 UTC (14 years, 9 months ago) by overbeek
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Changes since 1.227: +4 -0 lines
Diff to previous 1.227
filters for data mining

Revision 1.227 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 26 11:01:13 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.226: +20 -3 lines
Diff to previous 1.226
add reset_curator.cgi

Revision 1.226 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 16 18:59:20 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.225: +3 -1 lines
Diff to previous 1.225
highlight subsystems with no genomes attached

Revision 1.225 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 18:41:04 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.224: +1 -1 lines
Diff to previous 1.224
Fix subsystem_classification in FIG.pm

Revision 1.224 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 18:18:14 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.223: +8 -17 lines
Diff to previous 1.223
Moved the subsystem_classification getting/setting into subsys.pm where it belongs, and so I ammended FIG.pm. Also added the boxes on the subsystem page so you can see the classifications.

Revision 1.223 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 17:20:43 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.222: +6 -5 lines
Diff to previous 1.222
minor change to FIG::subsystem_classification

Revision 1.222 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 06:49:27 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.221: +3 -3 lines
Diff to previous 1.221
Initial addition of subsys_summary.cgi and minor modification of FIG.pm

Revision 1.221 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 05:38:43 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.220: +6 -3 lines
Diff to previous 1.220
changes to subsystem_classification

Revision 1.220 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 04:51:47 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.219: +9 -14 lines
Diff to previous 1.219
fix routine for locating candidates for a role in a genome

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Sat Feb 12 04:08:00 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.218: +35 -0 lines
Diff to previous 1.218
Minor changes to pir.cgi and added subsystem_classification to FIG.pm

Revision 1.218 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 04:01:01 2005 UTC (14 years, 9 months ago) by overbeek
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Changes since 1.217: +20 -72 lines
Diff to previous 1.217
many fixes to extending subsystems

Revision 1.217 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 03:50:04 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.216: +26 -0 lines
Diff to previous 1.216
Add some pod to FIG.pm

Revision 1.216 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 03:00:57 2005 UTC (14 years, 9 months ago) by mkubal
Branch: MAIN
Changes since 1.215: +19 -15 lines
Diff to previous 1.215
update

Revision 1.215 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 11 06:34:05 2005 UTC (14 years, 10 months ago) by mkubal
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Changes since 1.214: +85 -3 lines
Diff to previous 1.214
added all_for_genome, etc

Revision 1.214 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 10 13:33:37 2005 UTC (14 years, 10 months ago) by olson
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Changes since 1.213: +26 -0 lines
Diff to previous 1.213
Add subsystems_for_genome.

Revision 1.213 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 7 00:27:34 2005 UTC (14 years, 10 months ago) by parrello
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Changes since 1.212: +76 -14 lines
Diff to previous 1.212
no message

Revision 1.212 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 5 04:12:35 2005 UTC (14 years, 10 months ago) by overbeek
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Changes since 1.211: +1 -1 lines
Diff to previous 1.211
head -1 should be head -n 1

Revision 1.211 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 31 14:01:07 2005 UTC (14 years, 10 months ago) by overbeek
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Changes since 1.210: +2 -1 lines
Diff to previous 1.210
add pegs_in_subsystems

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Thu Jan 27 00:31:21 2005 UTC (14 years, 10 months ago) by parrello
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Changes since 1.209: +133 -68 lines
Diff to previous 1.209
no message

Revision 1.209 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 26 18:37:58 2005 UTC (14 years, 10 months ago) by overbeek
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Changes since 1.208: +8 -10 lines
Diff to previous 1.208
fix bugs introduced into by_alias function

Revision 1.208 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 23 00:38:22 2005 UTC (14 years, 10 months ago) by golsen
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Changes since 1.207: +3 -2 lines
Diff to previous 1.207
Time stamp individual load steps

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Tue Jan 18 21:06:41 2005 UTC (14 years, 10 months ago) by olson
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Changes since 1.206: +1 -1 lines
Diff to previous 1.206
fix dumb typo.

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Tue Jan 18 21:02:45 2005 UTC (14 years, 10 months ago) by olson
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Changes since 1.205: +15 -0 lines
Diff to previous 1.205
Add peg_in_gendb and genome_in_gendb

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Tue Jan 18 20:55:32 2005 UTC (14 years, 10 months ago) by olson
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Changes since 1.204: +6 -0 lines
Diff to previous 1.204
add get_system_name() call.

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Sun Jan 16 16:05:20 2005 UTC (14 years, 10 months ago) by overbeek
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Changes since 1.203: +16 -2 lines
Diff to previous 1.203
fix to scoring fc

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Thu Jan 13 17:32:51 2005 UTC (14 years, 10 months ago) by olson
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Changes since 1.202: +1 -1 lines
Diff to previous 1.202
More fixes for Sprout integration.

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Wed Jan 12 21:22:08 2005 UTC (14 years, 10 months ago) by olson
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Changes since 1.201: +2 -1 lines
Diff to previous 1.201
sprout debugging

Revision 1.201 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 12 20:18:56 2005 UTC (14 years, 10 months ago) by parrello
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Changes since 1.200: +13 -12 lines
Diff to previous 1.200
no message

Revision 1.200 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 12 20:08:30 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.199: +297 -301 lines
Diff to previous 1.199
no message

Revision 1.199 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 11 18:59:39 2005 UTC (14 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.198: +1 -1 lines
Diff to previous 1.198
I ran into a bug today where I was using by_alias to look up aliases
for the peg-mapping code, and one of the aliases was DR6', with a
single-quote. Because the code in by_alias doesn't quote its argument,
the SQL failed with a syntax error.

The perl DBI library has a mechanism designed to solve this
problem. If you use ? in a sql string where you want to substitute an
argument from code, DBI will do the appropriate quoting for you. I've
made this accessible via the SQL method in the DBrtns module, so the
by_alias code now looks like this:

    if (($relational_db_response = $rdbH->SQL("SELECT id FROM ext_alias WHERE ( alias = ? )", undef, $alias))

and works properly in the face of $alias having a single-quote in
it. I believe this mechanism is also more efficient. Note the second
argument of SQL is a verbose flag, which means that any bound
variables (to replace ?s in the query) have to start at the third
argument.

I've also made a change in the SQL method such that the query is done
inside an eval{} block, and if it fails, the error is reraised using
confess so that it is possible to see the full backtrace so you can
find in the source where the bad query was.

Revision 1.198 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 9 17:15:12 2005 UTC (14 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.197: +1 -1 lines
Diff to previous 1.197
fix disambiguating maps

Revision 1.197 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 8 18:22:00 2005 UTC (14 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.196: +1 -1 lines
Diff to previous 1.196
add check to assign_function

Revision 1.196 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 7 18:55:21 2005 UTC (14 years, 11 months ago) by olson
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Changes since 1.195: +2 -2 lines
Diff to previous 1.195
add option to not create a release info file to get_release_info()

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Wed Jan 5 16:19:44 2005 UTC (14 years, 11 months ago) by olson
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Changes since 1.194: +78 -4 lines
Diff to previous 1.194
p2p changes.

Revision 1.194 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 3 02:23:12 2005 UTC (14 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.193: +0 -1 lines
Diff to previous 1.193
fix stupid error in cleaning up aliases

Revision 1.193 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 3 02:21:08 2005 UTC (14 years, 11 months ago) by overbeek
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Changes since 1.192: +4 -27 lines
Diff to previous 1.192
automatically generate aliases from mapped IDs

Revision 1.192 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 29 17:59:36 2004 UTC (14 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.191: +1 -1 lines
Diff to previous 1.191
minor fix to FIG.pm and addition of generate_kegg_map_ec_tables

Revision 1.191 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 16 22:57:43 2004 UTC (14 years, 11 months ago) by overbeek
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Changes since 1.190: +2 -1 lines
Diff to previous 1.190
fixes to assigned_function

Revision 1.190 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 15 02:04:34 2004 UTC (14 years, 11 months ago) by overbeek
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Changes since 1.189: +9 -5 lines
Diff to previous 1.189
allow set of seeks to cores for bbhs

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Mon Dec 13 19:24:15 2004 UTC (14 years, 11 months ago) by redwards
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Changes since 1.188: +4 -4 lines
Diff to previous 1.188
Minor changes to FIG.pm POD

Revision 1.188 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 10 07:04:39 2004 UTC (15 years ago) by redwards
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Changes since 1.187: +18 -0 lines
Diff to previous 1.187
Changes to subsys.cgi that warn if a subsystem doesn't exist

Revision 1.187 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 8 21:28:10 2004 UTC (15 years ago) by overbeek
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Changes since 1.186: +9 -2 lines
Diff to previous 1.186
raw time for annotations

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Mon Dec 6 18:25:18 2004 UTC (15 years ago) by olson
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Changes since 1.185: +1 -1 lines
Diff to previous 1.185
fix a comment

Revision 1.185 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 5 16:35:15 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.184: +2 -2 lines
Diff to previous 1.184
add checking for subsystems

Revision 1.184 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 3 18:55:20 2004 UTC (15 years ago) by olson
Branch: MAIN
Changes since 1.183: +39 -2 lines
Diff to previous 1.183
Add subsystem_roles() method.
Add status callback to translate_pegs.
Remove setting of sticky bit in verify_dir.

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Wed Nov 10 22:10:22 2004 UTC (15 years, 1 month ago) by olson
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Changes since 1.182: +46 -0 lines
Diff to previous 1.182
add higher-level construct support

Revision 1.182 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 5 14:57:59 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.181: +0 -1 lines
Diff to previous 1.181
untested changes to extract_genomes - copy-all-but in Global

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Thu Nov 4 18:27:29 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.180: +4 -1 lines
Diff to previous 1.180
allow external IDs on subsystem displays

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Wed Nov 3 17:46:17 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.179: +7 -0 lines
Diff to previous 1.179
add is_complete function to FIG.pm

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Tue Nov 2 14:45:31 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.178: +81 -1 lines
Diff to previous 1.178
fix bug in subsys.cgi and add Literature to Global

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Mon Oct 25 20:59:34 2004 UTC (15 years, 1 month ago) by redwards
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Changes since 1.177: +8 -0 lines
Diff to previous 1.177
Adding  some pod

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Sat Oct 23 21:41:38 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.176: +1 -1 lines
Diff to previous 1.176
stupid error in FIG.pm

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Sat Oct 23 19:58:28 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.175: +2 -2 lines
Diff to previous 1.175
fix bound in find_role_in_org

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Fri Oct 22 19:30:37 2004 UTC (15 years, 1 month ago) by heiko
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Changes since 1.174: +23 -0 lines
Diff to previous 1.174
added function
all_features_detailed
will return fig_id, location, type as array

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Fri Oct 22 16:55:42 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.173: +7 -7 lines
Diff to previous 1.173
fill_in_cell for Heiko

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Sun Oct 17 16:40:13 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.172: +9 -7 lines
Diff to previous 1.172
added homologs_in_clusters.cgi

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Sun Oct 17 00:05:17 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.171: +4 -0 lines
Diff to previous 1.171
fix to by_alias

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Sun Oct 17 00:02:34 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.170: +21 -6 lines
Diff to previous 1.170
fixes to UniProt IDs on chromosomal_clusters.cgi

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Sat Oct 16 20:42:28 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.169: +22 -2 lines
Diff to previous 1.169
fixes to generalize chromosomal_clusters.cgi for UniProt

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Fri Oct 15 17:04:09 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.168: +97 -48 lines
Diff to previous 1.168
peg links generalized to fid links

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Fri Oct 15 00:38:11 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.167: +15 -4 lines
Diff to previous 1.167
fixes to subsystem code

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Mon Oct 11 23:55:40 2004 UTC (15 years, 2 months ago) by overbeek
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Changes since 1.166: +1 -0 lines
Diff to previous 1.166
remove extra EOLs on changed locations

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Mon Oct 11 21:38:58 2004 UTC (15 years, 2 months ago) by overbeek
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Changes since 1.165: +7 -2 lines
Diff to previous 1.165
fixes to change_location_of_feature

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Mon Oct 11 18:46:45 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.164: +10 -44 lines
Diff to previous 1.164
More fixes for sprout support.

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Fri Oct 8 22:04:48 2004 UTC (15 years, 2 months ago) by redwards
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Changes since 1.163: +1 -1 lines
Diff to previous 1.163
Added number of contigs to menu

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Tue Oct 5 22:06:28 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.162: +55 -0 lines
Diff to previous 1.162
more DAS fixes

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Mon Oct 4 15:56:10 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.161: +29 -0 lines
Diff to previous 1.161
Changes for DAS integration

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Fri Oct 1 19:48:37 2004 UTC (15 years, 2 months ago) by overbeek
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Changes since 1.160: +5 -5 lines
Diff to previous 1.160
minor fixes to exporting sets

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Fri Sep 24 20:27:22 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.159: +20 -1 lines
Diff to previous 1.159
doc fix

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Fri Sep 24 18:58:42 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.158: +7 -4 lines
Diff to previous 1.158
Possible fix for beg_of and contig_of
More p2p stuff

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Fri Sep 24 18:34:32 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.157: +165 -1 lines
Diff to previous 1.157
Some contig manipulation stuff, more p2p stuff.

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Thu Sep 23 20:04:04 2004 UTC (15 years, 2 months ago) by redwards
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Changes since 1.156: +16 -2 lines
Diff to previous 1.156
$fig->adjacent_genes was not returning adjacent genes

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Wed Sep 22 19:32:29 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.155: +0 -2 lines
Diff to previous 1.155
remove print

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Wed Sep 22 19:29:51 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.154: +134 -1 lines
Diff to previous 1.154
Mods for P2P update stuff.

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Mon Sep 20 21:16:02 2004 UTC (15 years, 2 months ago) by overbeek
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Changes since 1.153: +6 -3 lines
Diff to previous 1.153
subsystem_genomes should return just genomes with an operational variant

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Thu Sep 16 15:15:57 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.152: +4 -4 lines
Diff to previous 1.152
remove inappropriate setting of g+s bit

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Thu Sep 16 04:35:03 2004 UTC (15 years, 2 months ago) by overbeek
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Changes since 1.151: +4 -4 lines
Diff to previous 1.151
Fixed errors in POD documentation. -- /gdp

Revision 1.151 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 13 02:12:20 2004 UTC (15 years, 2 months ago) by overbeek
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Changes since 1.150: +19 -0 lines
Diff to previous 1.150
add attributes as key-value pairs attached to fids

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Sat Sep 11 00:46:49 2004 UTC (15 years, 3 months ago) by golsen
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Changes since 1.149: +9 -3 lines
Diff to previous 1.149
Add domain-based selection to genomes function.  Used to generate domain-specfic genome lists.

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Thu Sep 9 00:00:09 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.148: +0 -1 lines
Diff to previous 1.148
minor fixes

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Tue Sep 7 02:54:16 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.147: +17 -2 lines
Diff to previous 1.147
add new subsystem interface

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Fri Aug 27 21:55:57 2004 UTC (15 years, 3 months ago) by mkubal
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Changes since 1.146: +81 -2 lines
Diff to previous 1.146
added adjacent_genes() and supporting methods

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Fri Aug 27 18:32:07 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.145: +14 -0 lines
Diff to previous 1.145
set current user

Revision 1.145 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 24 22:12:17 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.144: +6 -4 lines
Diff to previous 1.144
minor changes to indexing translations

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Mon Aug 23 18:58:54 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.143: +1 -1 lines
Diff to previous 1.143
sort sims into the correct order

Revision 1.143 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 23 18:51:34 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.142: +3 -3 lines
Diff to previous 1.142
fix evil bug in index searches

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Mon Aug 23 18:35:51 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.141: +17 -2 lines
Diff to previous 1.141
sort sims by bit score

Revision 1.141 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 23 03:34:32 2004 UTC (15 years, 3 months ago) by golsen
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Changes since 1.140: +200 -2 lines
Diff to previous 1.140
Fix a typo in annotations_made and start adding infrastructure to fix genes_in_region issues

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Sun Aug 22 21:36:42 2004 UTC (15 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.139: +1 -0 lines
Diff to previous 1.139
have function_of append to end of lines

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Fri Aug 20 17:37:58 2004 UTC (15 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.138: +70 -89 lines
Diff to previous 1.138
update feature alterations

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Fri Aug 20 00:42:54 2004 UTC (15 years, 3 months ago) by golsen
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Changes since 1.137: +8 -8 lines
Diff to previous 1.137
Fixed major error in org_of

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Thu Aug 19 23:45:58 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.136: +31 -0 lines
Diff to previous 1.136
handle changes to feature locations

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Wed Aug 18 15:46:51 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.135: +179 -22 lines
Diff to previous 1.135
add abilities to add, delete and update features

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Mon Aug 16 22:10:55 2004 UTC (15 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.134: +160 -60 lines
Diff to previous 1.134
straighten out FIG.pm

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Fri Aug 13 14:04:20 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.133: +126 -0 lines
Diff to previous 1.133
interface for Bielefeld in FIG.pm

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Thu Aug 12 11:39:44 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.132: +1 -1 lines
Diff to previous 1.132
fix errors relating to read_annotations

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Mon Aug 9 13:36:18 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.131: +2 -2 lines
Diff to previous 1.131
major fix in read_annotations in FIG.pm

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Sat Aug 7 18:48:39 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.130: +1 -1 lines
Diff to previous 1.130
fixes to aliases_of

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Mon Aug 2 20:02:29 2004 UTC (15 years, 4 months ago) by golsen
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Changes since 1.129: +81 -0 lines
Diff to previous 1.129
Colorize organisms by domain in similarities list.  Changes protein.cgi and FIG.pm

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Sun Aug 1 11:50:25 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.128: +1 -2 lines
Diff to previous 1.128
fix order on genes returned in a region

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Sun Jul 25 21:48:15 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.127: +3 -1 lines
Diff to previous 1.127
sort links

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Sun Jul 18 22:58:36 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.126: +41 -6 lines
Diff to previous 1.126
handle bug that lost notes for subsystems

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Fri Jul 16 21:58:03 2004 UTC (15 years, 4 months ago) by gdpusch
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Changes since 1.125: +19 -5 lines
Diff to previous 1.125
Added out-of-bounds checks to &extract_seq(), plus debugging information for loci whose sequences could not be extracted.

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Fri Jul 16 20:41:26 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.124: +4 -0 lines
Diff to previous 1.124
updates to ssa2.cgi and warnings when assignments fail

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Mon Jul 12 21:14:53 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.123: +6 -0 lines
Diff to previous 1.123
Add "umask 0" to fig.pm to ensure all new files are world writable.

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Thu Jul 1 21:17:53 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.122: +282 -45 lines
Diff to previous 1.122
More sim/askfor/pool stuff.

Make fig load_all show progress.

Fix run_in_background to do the right thing with an open db handle.

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Mon Jun 28 20:11:14 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.121: +42 -2 lines
Diff to previous 1.121
Add assignments_made_for_protein
expand some code for readability.

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Sun Jun 27 22:49:49 2004 UTC (15 years, 5 months ago) by overbeek
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Changes since 1.120: +9 -1 lines
Diff to previous 1.120
handle names of subsystems just a bit better

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Wed Jun 23 21:33:43 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.119: +58 -10 lines
Diff to previous 1.119
Add assignments_made_full, which returns the date and id of person who made the assignment.
assignments_made now just maps the result of assignments_made.

Add some comments.

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Wed Jun 16 16:52:10 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.118: +1 -0 lines
Diff to previous 1.118
Modifications to fix & finish up the automated subsystem extension.

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Wed Jun 16 14:25:36 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.117: +1 -0 lines
Diff to previous 1.117
New map support.

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Wed Jun 16 14:04:40 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.116: +98 -0 lines
Diff to previous 1.116
add background job support.

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Mon Jun 14 22:04:24 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.115: +96 -0 lines
Diff to previous 1.115
Add background job support

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Thu Jun 10 14:00:36 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.114: +5 -5 lines
Diff to previous 1.114
Add scalar decl to is_bacterial and friends.

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Thu Jun 10 13:39:55 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.113: +30 -0 lines
Diff to previous 1.113
add more funcs for tutorials

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Tue Jun 8 20:26:23 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.112: +159 -4 lines
Diff to previous 1.112
add some scalar annotations; add find_role_in_org

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Tue Jun 8 17:19:43 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.111: +16 -2 lines
Diff to previous 1.111
Guard the rquire of figrpc in case we don't have the necessary modules installed for it.

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Tue Jun 8 15:02:14 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.110: +70 -14 lines
Diff to previous 1.110
Add capability for :scalar :list :remote annotations to FIG interface. This works with
modules that are declared as subclasses of FIGAttributes.

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Thu Jun 3 20:58:04 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.109: +1 -1 lines
Diff to previous 1.109
reorder load of databases just slightly

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Thu Jun 3 08:12:44 2004 UTC (15 years, 6 months ago) by gdpusch
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Changes since 1.108: +1 -1 lines
Diff to previous 1.108
Fixed typo in pod-documentation

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Wed Jun 2 09:45:16 2004 UTC (15 years, 6 months ago) by gdpusch
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Changes since 1.107: +30 -29 lines
Diff to previous 1.107
Added check for "defined" status of filehandle reads from <SSA>; removed various "masking" redefinitions of "my" variables.

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Wed Jun 2 09:23:35 2004 UTC (15 years, 6 months ago) by gdpusch
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Changes since 1.106: +46 -16 lines
Diff to previous 1.106
Fixed typos in various $fig->genome_*() accessor functions.

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Tue Jun 1 20:45:39 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.105: +1 -1 lines
Diff to previous 1.105
fix typo.

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Tue Jun 1 20:40:55 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.104: +2 -2 lines
Diff to previous 1.104
Add $force_load argument to get_subsystem; results in the discarding
of the cached subsystem if there is one.

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Tue Jun 1 20:21:44 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.103: +20 -0 lines
Diff to previous 1.103
add subsystems_for_peg

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Tue Jun 1 19:06:17 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.102: +3 -2 lines
Diff to previous 1.102
fix the call to figrpc

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Tue Jun 1 19:02:37 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.101: +13 -0 lines
Diff to previous 1.101
added redirect in FIG constructor to create a FIGrpc if the FIG_URL environment variable is set

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Tue Jun 1 00:45:38 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.100: +5 -2 lines
Diff to previous 1.100
make bbhs sensitive to lengths of match - watch out for fused proteins

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Sun May 30 15:04:26 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.99: +21 -9 lines
Diff to previous 1.99
precomputed BBHs

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Sat May 29 14:08:58 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.98: +1 -1 lines
Diff to previous 1.98
untested changes to extract_genomes

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Fri May 28 19:27:00 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.97: +21 -5 lines
Diff to previous 1.97
attempt to change FIG.pm to keep mac-1 up

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Thu May 27 18:22:11 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.96: +0 -1 lines
Diff to previous 1.96
doh, had left a debug print in there

Revision 1.96 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 26 22:34:17 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.95: +19 -0 lines
Diff to previous 1.95
add genome_and_peg_of

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Mon May 24 22:02:47 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.94: +10 -3 lines
Diff to previous 1.94
Factor out the subsystem caching.

Revision 1.94 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 24 21:59:32 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.93: +8 -1 lines
Diff to previous 1.93
cache subsystem objects, since they can be expensive to create.

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Mon May 24 21:55:18 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.92: +196 -34 lines
Diff to previous 1.92
Beginning of sim queueing stuff.
First implementation of Subsystem object, with FIG::peg_in_subsystem_cell
implemented in terms of it.

Revision 1.92 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 24 21:14:16 2004 UTC (15 years, 6 months ago) by gdpusch
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Changes since 1.91: +60 -3 lines
Diff to previous 1.91
Changed name of genome-size access method to \&genome_szdna($genome_id) to match the SQL keyword; added \&genome_pegs($genome) and \&genome_rnas($genome) to return number of PEGs and RNAs, resp.

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Mon May 24 21:03:39 2004 UTC (15 years, 6 months ago) by gdpusch
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Changes since 1.90: +28 -0 lines
Diff to previous 1.90
Added access method \&genome_size($genome_id) to return the number of base-pairs in an organism\'s contig files.

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Mon May 24 19:32:36 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.89: +47 -0 lines
Diff to previous 1.89
add file_head and file_read

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Sat May 22 11:43:00 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.88: +6 -0 lines
Diff to previous 1.88
fix error in tutorial

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Fri May 21 18:05:55 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.87: +6 -2 lines
Diff to previous 1.87
fixes to similarities

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Thu May 20 12:26:47 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.86: +14 -2 lines
Diff to previous 1.86
make aliases include external aliases

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Wed May 19 15:54:10 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.85: +3 -0 lines
Diff to previous 1.85
allow comma-separated contiguous regions in dna_seq argument list

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Wed May 19 14:15:57 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.84: +25 -0 lines
Diff to previous 1.84
add all_contigs

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Wed May 19 13:17:39 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.83: +25 -9 lines
Diff to previous 1.83
fixes on memory leak and genome version

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Tue May 18 00:44:54 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.82: +1 -1 lines
Diff to previous 1.82
set max open files to 50

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Mon May 17 09:22:50 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.81: +91 -8 lines
Diff to previous 1.81
support addition of links to pegs

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Fri May 14 18:06:51 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.80: +41 -1 lines
Diff to previous 1.80
fixed up links

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Thu May 13 20:59:56 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.79: +1 -2 lines
Diff to previous 1.79
fix add_genome

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Tue May 4 16:27:23 2004 UTC (15 years, 7 months ago) by olson
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Changes since 1.78: +43 -3 lines
Diff to previous 1.78
more protection around the code that pokes at the clearing house, in case xmlrpc libs are missing

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Mon May 3 17:16:50 2004 UTC (15 years, 7 months ago) by olson
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Changes since 1.77: +11 -0 lines
Diff to previous 1.77
Add comment.

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Sat May 1 02:56:38 2004 UTC (15 years, 7 months ago) by olson
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Changes since 1.76: +3 -2 lines
Diff to previous 1.76
Comment out import of Clearinghouse until we get the env updated.

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Thu Apr 29 16:41:16 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.75: +9 -0 lines
Diff to previous 1.75
tools for query

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Wed Apr 28 21:59:32 2004 UTC (15 years, 7 months ago) by olson
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Changes since 1.74: +184 -0 lines
Diff to previous 1.74
Clearinghouse publishing stuff

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Wed Apr 28 04:34:52 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.73: +4 -1 lines
Diff to previous 1.73
fix to definition of bbh

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Tue Apr 27 15:41:28 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.72: +22 -0 lines
Diff to previous 1.72
basic query tools

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Sat Apr 24 23:27:05 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.71: +4 -3 lines
Diff to previous 1.71
make sure that external_calls produces one function for each peg

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Sat Apr 24 15:02:08 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.70: +34 -6 lines
Diff to previous 1.70
tools for McCune to build expert automated assignments

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Fri Apr 23 21:51:15 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.69: +1 -0 lines
Diff to previous 1.69
make load_all build blast dbs for fig proteins

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Fri Apr 23 21:49:02 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.68: +1 -1 lines
Diff to previous 1.68
fixes to index.cgi to blast against all complete

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Fri Apr 23 17:23:40 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.67: +2 -2 lines
Diff to previous 1.67
fixes to best_candidates

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Fri Apr 23 16:59:40 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.66: +9 -5 lines
Diff to previous 1.66
fixes to best_bbh_candidates

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Mon Apr 19 11:36:39 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.65: +4 -2 lines
Diff to previous 1.65
fix a bad bug in assignment permissions

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Fri Apr 9 15:26:05 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.64: +17 -3 lines
Diff to previous 1.64
pass back more detailed data for candidates for a role

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Fri Apr 9 14:55:36 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.63: +85 -0 lines
Diff to previous 1.63
more intelligent candidates for function

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Thu Apr 8 11:49:33 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.62: +11 -0 lines
Diff to previous 1.62
fixes in auto assignments

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Thu Apr 1 22:58:44 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.61: +8 -0 lines
Diff to previous 1.61
allow p2p to send me epoch dates, rather than readable dates

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Thu Apr 1 22:10:34 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.60: +1 -1 lines
Diff to previous 1.60
turn off warning messages for translation failures when translating PEG ids

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Thu Apr 1 22:07:31 2004 UTC (15 years, 8 months ago) by disz
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Changes since 1.59: +4 -4 lines
Diff to previous 1.59
More P2P fixes.
Add setgid to the mkdir/chmod's.

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Thu Apr 1 14:54:57 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.58: +66 -0 lines
Diff to previous 1.58
fixes to candidates for a role

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Wed Mar 31 19:20:24 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.57: +11 -1 lines
Diff to previous 1.57
p2p for updating release

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Wed Mar 31 18:39:15 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.56: +3 -3 lines
Diff to previous 1.56
p2p changes

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Wed Mar 31 16:32:22 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.55: +52 -0 lines
Diff to previous 1.55
attempt to fix package/install for p2p

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Wed Mar 31 11:14:47 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.54: +148 -0 lines
Diff to previous 1.54
move PEG translation into FIG.pm

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Mon Mar 29 23:13:14 2004 UTC (15 years, 8 months ago) by mkubal
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Changes since 1.53: +2 -2 lines
Diff to previous 1.53
removes ## markers in FIG.pm

Revision 1.53 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 29 23:12:40 2004 UTC (15 years, 8 months ago) by mkubal
Branch: MAIN
Changes since 1.52: +7 -104 lines
Diff to previous 1.52
removes ## markers in FIG.pm and fixed Blast.pm

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 26 21:38:38 2004 UTC (15 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.51: +18 -0 lines
Diff to previous 1.51
Make get_local_hostname check for a FIGdisk/config/hostname file and use
that as the local hostname if present.

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 26 13:01:46 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.50: +11 -2 lines
Diff to previous 1.50
better peg mapping when importing spreadsheets

Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 25 17:10:50 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.49: +11 -0 lines
Diff to previous 1.49
includes errors

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 25 13:48:27 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.48: +3 -1 lines
Diff to previous 1.48
improvements on importing subsystems

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 24 00:05:40 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.47: +1 -1 lines
Diff to previous 1.47
export subsystems stuff

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 23 21:54:03 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.46: +7 -1 lines
Diff to previous 1.46
Broke a semicolon-chained set of commands in &delete_genomes() into separate &run() invocations, so that if any of them fail, the delete operation will abort. -- /gdp

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 22 02:33:57 2004 UTC (15 years, 8 months ago) by gdpusch
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Changes since 1.45: +1 -1 lines
Diff to previous 1.45
Fixed failure to declare two variables in routine &read_fasta_record(). -- /gdp

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 22 01:51:30 2004 UTC (15 years, 8 months ago) by gdpusch
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Changes since 1.44: +58 -1 lines
Diff to previous 1.44
Added routine &read_fasta_record(). -- /gdp

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 19 21:58:31 2004 UTC (15 years, 8 months ago) by golsen
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Changes since 1.43: +24 -13 lines
Diff to previous 1.43
Relative base address support and cgi_url() based on current http request

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 19 18:45:36 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.42: +39 -22 lines
Diff to previous 1.42
fixes to coupling and protein.cgi

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Thu Mar 18 16:02:32 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.41: +19 -0 lines
Diff to previous 1.41
add versions to spreadsheets

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 18 13:16:40 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.40: +1 -1 lines
Diff to previous 1.40
exchangable flags on spreadsheet

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 17 20:18:22 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.39: +105 -6 lines
Diff to previous 1.39
for Gordon and Mike

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 17 18:17:34 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.38: +107 -0 lines
Diff to previous 1.38
basic export of subsystems stuff

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 15 23:06:47 2004 UTC (15 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.37: +33 -0 lines
Diff to previous 1.37
Add get_seed_id()

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 15 04:37:50 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.36: +2 -4 lines
Diff to previous 1.36
new spreadsheet

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 14 03:46:16 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.35: +298 -188 lines
Diff to previous 1.35
fixes

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 9 23:19:23 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.34: +97 -0 lines
Diff to previous 1.34
fixed distances and spreadsheet

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 5 22:17:16 2004 UTC (15 years, 9 months ago) by overbeek
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Changes since 1.33: +25 -0 lines
Diff to previous 1.33
support gi and NP numbers for access to fig IDs

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 3 14:56:43 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.32: +48 -1 lines
Diff to previous 1.32
add merged annotations

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 3 12:49:23 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.31: +4 -2 lines
Diff to previous 1.31
fixes from DOE meeting

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 19 12:55:35 2004 UTC (15 years, 9 months ago) by overbeek
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Changes since 1.30: +1 -1 lines
Diff to previous 1.30
fix bug due to change in sims

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 17 22:23:36 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.29: +9 -5 lines
Diff to previous 1.29
preserve translation through similarities

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Sun Feb 15 17:12:54 2004 UTC (15 years, 9 months ago) by overbeek
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Changes since 1.28: +7 -4 lines
Diff to previous 1.28
added Gary Olsen changes

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Tue Feb 10 22:35:57 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.27: +19 -1 lines
Diff to previous 1.27
in get_local_hostname, ensure that we get a FQDN. If we don't, just bail and
use our IP address.

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 3 16:45:57 2004 UTC (15 years, 10 months ago) by overbeek
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Changes since 1.26: +9 -0 lines
Diff to previous 1.26
minor fixes

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 26 22:51:32 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.25: +12 -4 lines
Diff to previous 1.25
fixes

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 21 18:27:29 2004 UTC (15 years, 10 months ago) by overbeek
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Changes since 1.24: +1 -0 lines
Diff to previous 1.24
from the Penn trip

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 16 19:37:40 2004 UTC (15 years, 10 months ago) by overbeek
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Changes since 1.23: +2 -2 lines
Diff to previous 1.23
chop delimiter off annotations

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 14 20:20:32 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.22: +9 -99 lines
Diff to previous 1.22
synch up Ross

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 8 16:31:59 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.21: +8 -0 lines
Diff to previous 1.21
handle loops in translation

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 7 03:34:13 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.20: +9 -0 lines
Diff to previous 1.20
make Assignments files have readable names

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 6 23:08:26 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.19: +1 -1 lines
Diff to previous 1.19
fix in extract_genomes

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 6 18:14:48 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.18: +14 -4 lines
Diff to previous 1.18
fix stick behavior for checked sims

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 5 12:26:58 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.17: +2 -1 lines
Diff to previous 1.17
minor bugs

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 3 14:13:48 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.16: +41 -1 lines
Diff to previous 1.16
fix P2P to use get_assignments

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 3 06:03:43 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.15: +25 -20 lines
Diff to previous 1.15
changes to annotations to allow extraction of assignments

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 30 05:21:24 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.14: +2 -2 lines
Diff to previous 1.14
fix order of database loads

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 29 02:22:37 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.13: +17 -12 lines
Diff to previous 1.13
numerous performance issues

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 28 17:11:29 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.12: +55 -18 lines
Diff to previous 1.12
cleanup issues relating to large numbers of partial genomes

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 23 22:38:31 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.11: +1 -1 lines
Diff to previous 1.11
make plugging URLs more robust

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 23 22:29:51 2003 UTC (15 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.10: +5 -5 lines
Diff to previous 1.10
remove prints

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 23 22:28:10 2003 UTC (15 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.9: +207 -0 lines
Diff to previous 1.9
Add IP-determination logic.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 22 01:24:22 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +14 -5 lines
Diff to previous 1.8
add pins and clusters properly

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 21 01:20:59 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +0 -1 lines
Diff to previous 1.7
allow multiple sims files in update_sims

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 20 21:08:43 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +26 -3 lines
Diff to previous 1.6
fixed issues relating to addition/deletion of genomes

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 19 20:09:34 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +0 -18 lines
Diff to previous 1.5
get rid of set_urls, since it will not work anymore

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 5 14:31:23 2003 UTC (16 years ago) by overbeek
Branch: MAIN
CVS Tags: delong-01, delong-02
Changes since 1.4: +1 -1 lines
Diff to previous 1.4
fix permissions on added genome

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 4 21:49:02 2003 UTC (16 years ago) by overbeek
Branch: MAIN
Changes since 1.3: +6 -2 lines
Diff to previous 1.3
fix bug in function translation

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 3 21:24:31 2003 UTC (16 years ago) by overbeek
Branch: MAIN
Changes since 1.2: +4 -3 lines
Diff to previous 1.2
*** empty log message ***

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 3 19:39:29 2003 UTC (16 years ago) by efrank
Branch: MAIN
Changes since 1.1: +25 -5 lines
Diff to previous 1.1

fixed a bunch of changes

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 1 16:54:26 2003 UTC (16 years ago) by efrank
Branch: MAIN
Branch point for: initial
Initial revision

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