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Revision 1.62 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 23 23:39:22 2008 UTC (11 years, 7 months ago) by golsen
Branch: MAIN
CVS Tags: mgrast_dev_02212011, mgrast_dev_02222011, mgrast_dev_03252011, mgrast_dev_03312011, mgrast_dev_04012011, mgrast_dev_04052011, mgrast_dev_04082011, mgrast_dev_04132011, mgrast_dev_05262011, mgrast_dev_06072011, mgrast_rel_2008_0625, mgrast_rel_2008_0806, mgrast_rel_2008_0917, mgrast_rel_2008_0919, mgrast_rel_2008_0923, mgrast_rel_2008_0924, mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_4, mgrast_release_3_1_0, myrast_33, rast_2008_0924, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_rel_2008_10_09, rast_rel_2008_10_29, rast_rel_2008_11_24, rast_rel_2008_12_18, rast_rel_2009_02_05, rast_rel_2009_03_26, rast_rel_2009_05_18, rast_rel_2009_07_09, rast_rel_2009_0925, rast_rel_2010_0118, rast_rel_2010_0526, rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119, rast_release_2008_09_29
Changes since 1.61: +26 -20 lines
Diff to previous 1.61 , to selected 1.31
Move writing of assignment annotation from a case-by-case basis (and it
was missing in several key places) to the FIG::assign_function.

Modify the code in each of the calling locations to not make duplicate
annotations.

At the same time, remove (most) of the instances of making different
calls to assign_function depending on the user name.  assign_function
treats everyone as master (but writes an annotation with the real user
name).

Revision 1.61 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 5 02:02:29 2008 UTC (12 years, 1 month ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_04_23, rast_rel_2008_06_16, rast_rel_2008_06_18, rast_rel_2008_07_21, rast_rel_2008_08_07
Changes since 1.60: +19 -17 lines
Diff to previous 1.60 , to selected 1.31
Changed POD heading levels.

Revision 1.60 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 8 21:55:29 2007 UTC (12 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.59: +1 -1 lines
Diff to previous 1.59 , to selected 1.31
Fix diagram update bug on isntall of existing subystem.

Revision 1.59 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 13 16:45:29 2007 UTC (13 years ago) by olson
Branch: MAIN
Changes since 1.58: +20 -1 lines
Diff to previous 1.58 , to selected 1.31
non-peg ss install fix

Revision 1.58 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 22 22:44:31 2007 UTC (13 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.57: +7 -2 lines
Diff to previous 1.57 , to selected 1.31
other part of this

Revision 1.57 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 13 20:22:39 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.56: +12 -6 lines
Diff to previous 1.56 , to selected 1.31
fixes to deleted_features, replace_features_with, etc

Revision 1.56 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 5 19:06:30 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.55: +17 -0 lines
Diff to previous 1.55 , to selected 1.31
Added license words.

Revision 1.55 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 6 18:52:35 2005 UTC (14 years, 6 months ago) by olson
Branch: MAIN
CVS Tags: caBIG-00-00-00, caBIG-dataload-0
Changes since 1.54: +2 -5 lines
Diff to previous 1.54 , to selected 1.31
Make annotations_made_fast return new Annotation objects instead of arrays of data.

Add the Annotation object.

Revision 1.54 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 1 19:23:49 2005 UTC (14 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.53: +3 -0 lines
Diff to previous 1.53 , to selected 1.31
Add FIG::by_genome_id for sorting genome ID lists.

Add $fig->extract_assignments_from_annoatations to transform the output of annotations_made_fast
to a list of the current assignments (per the annotations data).

Revision 1.53 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 1 18:23:49 2005 UTC (14 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.52: +23 -28 lines
Diff to previous 1.52 , to selected 1.31
Add fast= flag to package_annotations, and the %options array in P2Pupdate::pacakge_annotations
to support it. (skip_aliases and skip_sequences support). Makes export of annotations to a
SEED that you know has the same data for the same ID *MUCH* faster.

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 1 18:14:53 2005 UTC (14 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.51: +77 -0 lines
Diff to previous 1.51 , to selected 1.31
make package_annotations use $fig->annotations_made_fast.

Add date parsing to FIG.pm ($fig->parse_date) using Date::Parse if available.

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 8 21:54:39 2005 UTC (14 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.50: +5 -5 lines
Diff to previous 1.50 , to selected 1.31
More diagram changes.

Add new simple start page.

Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 3 17:40:42 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.49: +184 -9 lines
Diff to previous 1.49 , to selected 1.31
Add support for creating and parsing diagram data as part of subsystem clearinghouse packages.

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 29 22:39:49 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.48: +28 -0 lines
Diff to previous 1.48 , to selected 1.31
Reactions support for subsystem downloads.

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 17 18:41:48 2005 UTC (14 years, 9 months ago) by olson
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-1, merge-trunktag-bobdev_news-2, merge-trunktag-bodev_news-3
Changes since 1.47: +2 -2 lines
Diff to previous 1.47 , to selected 1.31
Fix number  of spaces in annotation.

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 29 17:03:32 2005 UTC (14 years, 11 months ago) by olson
Branch: MAIN
CVS Tags: Root-bobdev_news
Branch point for: Branch-bobdev_news
Changes since 1.46: +59 -1 lines
Diff to previous 1.46 , to selected 1.31
Add install-anno-from gff routine (first cut).

Fix mismatched brace.

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 26 15:08:26 2005 UTC (14 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.45: +7 -0 lines
Diff to previous 1.45 , to selected 1.31
document importing external protein sequences

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 19 03:01:45 2005 UTC (14 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.44: +5 -1 lines
Diff to previous 1.44 , to selected 1.31
various fixes to package/install annotations

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 18 17:45:40 2005 UTC (14 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.43: +4 -2 lines
Diff to previous 1.43 , to selected 1.31
fix evil bug in install_assignments

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Apr 17 15:29:47 2005 UTC (14 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.42: +1 -1 lines
Diff to previous 1.42 , to selected 1.31
Fix bad bug in install annotations

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 7 18:53:40 2005 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.41: +11 -1 lines
Diff to previous 1.41 , to selected 1.31
support skipping assignments in p2p subsystem install

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 17 23:20:56 2004 UTC (15 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.40: +41 -4 lines
Diff to previous 1.40 , to selected 1.31
More subsystem/p2p fixes.

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 17 21:33:11 2004 UTC (15 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.39: +45 -3 lines
Diff to previous 1.39 , to selected 1.31
Some changes for subsystem import analysis.

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 6 18:26:56 2004 UTC (15 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.38: +503 -42 lines
Diff to previous 1.38 , to selected 1.31
Add subsystem install stuff.

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 17 15:39:59 2004 UTC (15 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.37: +0 -1 lines
Diff to previous 1.37 , to selected 1.31
Fix parsing bug.

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 16 15:15:57 2004 UTC (15 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.36: +135 -3 lines
Diff to previous 1.36 , to selected 1.31
remove inappropriate setting of g+s bit

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 9 14:38:55 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.35: +9 -4 lines
Diff to previous 1.35 , to selected 1.31
export only current assignments (not all that were made)

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 25 21:48:15 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.34: +36 -7 lines
Diff to previous 1.34 , to selected 1.31
sort links

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 29 14:15:57 2004 UTC (15 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.33: +11 -11 lines
Diff to previous 1.33 , to selected 1.31
Fix

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 28 20:10:11 2004 UTC (15 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.32: +400 -11 lines
Diff to previous 1.32 , to selected 1.31
Fixes needed to run with 'use strict'.
Add analysis code for new subsystem import.

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 16 14:13:35 2004 UTC (15 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.31: +6 -0 lines
Diff to previous 1.31
Put ext-bin in the path for swithc_to_release.

Revision 1.31 - (view) (download) (as text) (annotate) - [selected]
Thu Apr 1 22:07:31 2004 UTC (16 years ago) by disz
Branch: MAIN
Changes since 1.30: +6 -6 lines
Diff to previous 1.30
More P2P fixes.
Add setgid to the mkdir/chmod's.

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 31 18:39:15 2004 UTC (16 years ago) by overbeek
Branch: MAIN
Changes since 1.29: +14 -10 lines
Diff to previous 1.29 , to selected 1.31
p2p changes

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 31 16:32:22 2004 UTC (16 years ago) by overbeek
Branch: MAIN
Changes since 1.28: +136 -37 lines
Diff to previous 1.28 , to selected 1.31
attempt to fix package/install for p2p

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 31 11:14:47 2004 UTC (16 years ago) by overbeek
Branch: MAIN
Changes since 1.27: +8 -0 lines
Diff to previous 1.27 , to selected 1.31
move PEG translation into FIG.pm

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 31 10:52:25 2004 UTC (16 years ago) by overbeek
Branch: MAIN
Changes since 1.26: +18 -5 lines
Diff to previous 1.26 , to selected 1.31
updates relating to p2p and installing new releases

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 30 16:44:51 2004 UTC (16 years ago) by olson
Branch: MAIN
Changes since 1.25: +6 -4 lines
Diff to previous 1.25 , to selected 1.31
fix cmdline argument to install_annotations

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 24 00:05:40 2004 UTC (16 years ago) by overbeek
Branch: MAIN
Changes since 1.24: +6 -1 lines
Diff to previous 1.24 , to selected 1.31
export subsystems stuff

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 23 23:50:58 2004 UTC (16 years ago) by overbeek
Branch: MAIN
Changes since 1.23: +4 -4 lines
Diff to previous 1.23 , to selected 1.31
fix exportable -> exchangable

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 17 18:17:34 2004 UTC (16 years ago) by overbeek
Branch: MAIN
Changes since 1.22: +17 -0 lines
Diff to previous 1.22 , to selected 1.31
basic export of subsystems stuff

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 10 22:33:42 2004 UTC (16 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.21: +24 -0 lines
Diff to previous 1.21 , to selected 1.31
we need to find the architecture for this seed; since configure doesn't
save it, we go grunking in the generated config/fig-user-env.sh script.

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 21 20:23:55 2004 UTC (16 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.20: +1 -1 lines
Diff to previous 1.20 , to selected 1.31
fix format

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 21 18:27:29 2004 UTC (16 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.19: +28 -200 lines
Diff to previous 1.19 , to selected 1.31
from the Penn trip

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 7 03:34:13 2004 UTC (16 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.18: +1 -1 lines
Diff to previous 1.18 , to selected 1.31
make Assignments files have readable names

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 7 03:12:44 2004 UTC (16 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.17: +6 -7 lines
Diff to previous 1.17 , to selected 1.31
make p2p assignments get written to Assignments

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 3 14:13:48 2004 UTC (16 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.16: +16 -55 lines
Diff to previous 1.16 , to selected 1.31
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 (16 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.15: +1 -1 lines
Diff to previous 1.15 , to selected 1.31
changes to annotations to allow extraction of assignments

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 23 22:17:56 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
Changes since 1.14: +16 -1 lines
Diff to previous 1.14 , to selected 1.31
handle null length annotation exchanges

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 23 21:29:02 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
Changes since 1.13: +1 -1 lines
Diff to previous 1.13 , to selected 1.31
fix quote

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 23 21:10:26 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
Changes since 1.12: +4 -0 lines
Diff to previous 1.12 , to selected 1.31
reject genomes that we do not have here on p2p updates

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 23 20:21:31 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
Changes since 1.11: +1 -1 lines
Diff to previous 1.11 , to selected 1.31
add who from on install_annotations

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 23 19:48:53 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
Changes since 1.10: +1 -0 lines
Diff to previous 1.10 , to selected 1.31
File Permissions

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 23 17:38:35 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
Changes since 1.9: +3 -4 lines
Diff to previous 1.9 , to selected 1.31
fixes to p2p

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 22 21:34:15 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
Changes since 1.8: +5 -5 lines
Diff to previous 1.8 , to selected 1.31
Added full path for commands like "merge_annotations"

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 22 08:59:04 2003 UTC (16 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +13 -4 lines
Diff to previous 1.7 , to selected 1.31
added logging for p2p assignment exchanges

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 22 08:42:00 2003 UTC (16 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +15 -24 lines
Diff to previous 1.6 , to selected 1.31
fixes to package_assignments

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 22 03:37:42 2003 UTC (16 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +10 -2 lines
Diff to previous 1.5 , to selected 1.31
corrections to package assignments

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 22 02:56:46 2003 UTC (16 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.4: +32 -9 lines
Diff to previous 1.4 , to selected 1.31
corrections to package assignments

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 20 15:19:21 2003 UTC (16 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +21 -17 lines
Diff to previous 1.3 , to selected 1.31
for incremental additions to the DB, delete old versions of things

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 19 20:04:52 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
Changes since 1.2: +2 -2 lines
Diff to previous 1.2 , to selected 1.31
P2P Stuff

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 19 17:19:58 2003 UTC (16 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.1: +39 -21 lines
Diff to previous 1.1 , to selected 1.31
fixes to p2p updates

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 1 16:54:26 2003 UTC (16 years, 4 months ago) by efrank
Branch: MAIN
Branch point for: initial
Diff to selected 1.31
Initial revision

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