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Revision 1.56 - (view) (download) (annotate) - [select for diffs]
Tue Sep 16 18:22:29 2008 UTC (11 years, 6 months ago) by parrello
Branch: MAIN
CVS Tags: HEAD, 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_dev_08022011, mgrast_dev_08112011, mgrast_dev_10262011, mgrast_dev_12152011, mgrast_rel_2008_0625, 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, mgrast_release_3_1_1, mgrast_release_3_1_2, mgrast_version_3_2, myrast_33, myrast_rel40, 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_rel_2011_0928, rast_rel_2014_0729, rast_rel_2014_0912, rast_release_2008_09_29
Changes since 1.55: +93 -88 lines
Diff to previous 1.55 , to selected 1.38
Changed to use the SEED Viewer if invoked in NMPDR mode.

Revision 1.55 - (view) (download) (annotate) - [select for diffs]
Fri May 16 08:35:30 2008 UTC (11 years, 10 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806, rast_rel_2008_06_16, rast_rel_2008_06_18, rast_rel_2008_08_07
Changes since 1.54: +7 -34 lines
Diff to previous 1.54 , to selected 1.38
Converted to use FIG_CGI, so that it does robot tracking automatically.

Revision 1.54 - (view) (download) (annotate) - [select for diffs]
Wed May 23 02:16:35 2007 UTC (12 years, 10 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_04_23, rast_rel_2008_07_21
Changes since 1.53: +6 -2 lines
Diff to previous 1.53 , to selected 1.38
Removed the contig display for Sprout.

Revision 1.53 - (view) (download) (annotate) - [select for diffs]
Thu Apr 19 00:03:18 2007 UTC (12 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.52: +5 -2 lines
Diff to previous 1.52 , to selected 1.38
Disabled a confusing link for NMPDR.

Revision 1.52 - (view) (download) (annotate) - [select for diffs]
Wed Feb 28 23:49:44 2007 UTC (13 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.51: +7 -3 lines
Diff to previous 1.51 , to selected 1.38
Adding the contig lengths tables that Veronika wanted

Revision 1.51 - (view) (download) (annotate) - [select for diffs]
Fri Nov 3 00:27:25 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.50: +92 -77 lines
Diff to previous 1.50 , to selected 1.38
Added an organism search box for Sprout. Turned off attribute display for Sprout.

Revision 1.50 - (view) (download) (annotate) - [select for diffs]
Sat Oct 21 06:55:45 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.49: +9 -7 lines
Diff to previous 1.49 , to selected 1.38
Added a display of the genome name.

Revision 1.49 - (view) (download) (annotate) - [select for diffs]
Thu Sep 14 07:58:14 2006 UTC (13 years, 6 months ago) by redwards
Branch: MAIN
Changes since 1.48: +7 -5 lines
Diff to previous 1.48 , to selected 1.38
correcting reactions in genome_statistics.cgi

Revision 1.48 - (view) (download) (annotate) - [select for diffs]
Tue Aug 15 21:54:51 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.47: +1 -1 lines
Diff to previous 1.47 , to selected 1.38
RAE: updating genome-statistics.cgi

Revision 1.47 - (view) (download) (annotate) - [select for diffs]
Tue Aug 15 18:16:38 2006 UTC (13 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.46: +1 -0 lines
Diff to previous 1.46 , to selected 1.38
Added missing use statement.

Revision 1.46 - (view) (download) (annotate) - [select for diffs]
Thu Aug 10 07:32:17 2006 UTC (13 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.45: +431 -482 lines
Diff to previous 1.45 , to selected 1.38
Added Sprout capability.

Revision 1.45 - (view) (download) (annotate) - [select for diffs]
Thu Jun 29 16:50:29 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.44: +18 -1 lines
Diff to previous 1.44 , to selected 1.38
RAE: Adding search box

Revision 1.44 - (view) (download) (annotate) - [select for diffs]
Mon Jun 26 19:30:23 2006 UTC (13 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.43: +1 -1 lines
Diff to previous 1.43 , to selected 1.38
Fixed bug in subsystem processing. The method used was SEED-only, but this script is used by NMPDR.

Revision 1.43 - (view) (download) (annotate) - [select for diffs]
Tue Jun 13 23:32:15 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.42: +1 -1 lines
Diff to previous 1.42 , to selected 1.38
RAE: moving PIRSF to links

Revision 1.42 - (view) (download) (annotate) - [select for diffs]
Wed Apr 26 20:23:46 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.41: +2 -1 lines
Diff to previous 1.41 , to selected 1.38
RAE: Adding complete to genome statistics page

Revision 1.41 - (view) (download) (annotate) - [select for diffs]
Thu Mar 23 04:51:55 2006 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.40: +19 -10 lines
Diff to previous 1.40 , to selected 1.38
RAE: Yummy attributes

Revision 1.40 - (view) (download) (annotate) - [select for diffs]
Mon Mar 6 16:51:27 2006 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.39: +8 -1 lines
Diff to previous 1.39 , to selected 1.38
Ensure SPROUT=1 gets passed properly from subsystem_summary to genome_statistics to display_subsys.

Revision 1.39 - (view) (download) (annotate) - [select for diffs]
Mon Feb 6 20:33:56 2006 UTC (14 years, 1 month ago) by disz
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.38: +2 -2 lines
Diff to previous 1.38
sorted table by taxonomy

Revision 1.38 - (view) (download) (annotate) - [selected]
Tue Jan 31 21:04:06 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.37: +3 -3 lines
Diff to previous 1.37
Fixed links in tables

Revision 1.37 - (view) (download) (annotate) - [select for diffs]
Tue Jan 31 20:58:26 2006 UTC (14 years, 2 months ago) by disz
Branch: MAIN
Changes since 1.36: +5 -1 lines
Diff to previous 1.36 , to selected 1.38
Added Links

Revision 1.36 - (view) (download) (annotate) - [select for diffs]
Tue Jan 31 20:56:20 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.35: +3 -3 lines
Diff to previous 1.35 , to selected 1.38
Table Formatting

Revision 1.35 - (view) (download) (annotate) - [select for diffs]
Tue Jan 31 20:22:03 2006 UTC (14 years, 2 months ago) by disz
Branch: MAIN
Changes since 1.34: +82 -6 lines
Diff to previous 1.34 , to selected 1.38
formatted genome table

Revision 1.34 - (view) (download) (annotate) - [select for diffs]
Sun Jan 22 00:15:25 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.33: +7 -0 lines
Diff to previous 1.33 , to selected 1.38
RAE: Adding subsys counts

Revision 1.33 - (view) (download) (annotate) - [select for diffs]
Mon Dec 5 19:12:12 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.32: +17 -0 lines
Diff to previous 1.32 , to selected 1.38
add license words

Revision 1.32 - (view) (download) (annotate) - [select for diffs]
Fri Nov 4 21:51:41 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-00-00-00
Changes since 1.31: +22 -3 lines
Diff to previous 1.31 , to selected 1.38
inactivating attributes

Revision 1.31 - (view) (download) (annotate) - [select for diffs]
Tue Oct 18 23:33:30 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.30: +9 -9 lines
Diff to previous 1.30 , to selected 1.38
minor fix to genome_statistics.cgi

Revision 1.30 - (view) (download) (annotate) - [select for diffs]
Mon Oct 10 19:28:45 2005 UTC (14 years, 5 months ago) by efrank
Branch: MAIN
Changes since 1.29: +15 -5 lines
Diff to previous 1.29 , to selected 1.38
Don't assume there are any assignments for an organism.  This fixes
a divide by zero error.

Revision 1.29 - (view) (download) (annotate) - [select for diffs]
Sun Sep 18 14:11:22 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.28: +2 -1 lines
Diff to previous 1.28 , to selected 1.38
fixes on showing subsystems

Revision 1.28 - (view) (download) (annotate) - [select for diffs]
Sun Sep 18 01:20:28 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.27: +1 -1 lines
Diff to previous 1.27 , to selected 1.38
fixes to display_subsys.cgi

Revision 1.27 - (view) (download) (annotate) - [select for diffs]
Thu Sep 15 19:13:20 2005 UTC (14 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.26: +29 -2 lines
Diff to previous 1.26 , to selected 1.38
Make genome_statistics ignore subsystem entries that have variant=-1.

Revision 1.26 - (view) (download) (annotate) - [select for diffs]
Sun Sep 11 17:02:41 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.25: +5 -2 lines
Diff to previous 1.25 , to selected 1.38
fixes to display of reactions

Revision 1.25 - (view) (download) (annotate) - [select for diffs]
Sun Sep 11 16:34:41 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.24: +5 -1 lines
Diff to previous 1.24 , to selected 1.38
add functiontion to FIG.pm to get active subsystems for a genome

Revision 1.24 - (view) (download) (annotate) - [select for diffs]
Tue Aug 16 19:40:15 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.23: +33 -0 lines
Diff to previous 1.23 , to selected 1.38
NMPDR updates.

Revision 1.23 - (view) (download) (annotate) - [select for diffs]
Wed Aug 10 17:13:45 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.22: +9 -0 lines
Diff to previous 1.22 , to selected 1.38
fixes to displaying reactions and status of models

Revision 1.22 - (view) (download) (annotate) - [select for diffs]
Wed Aug 10 16:17:52 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.21: +4 -4 lines
Diff to previous 1.21 , to selected 1.38
fixes to showing reactions

Revision 1.21 - (view) (download) (annotate) - [select for diffs]
Tue Aug 9 18:12:16 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.20: +67 -1 lines
Diff to previous 1.20 , to selected 1.38
added show_reactions

Revision 1.20 - (view) (download) (annotate) - [select for diffs]
Tue Aug 9 14:44:58 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.19: +14 -3 lines
Diff to previous 1.19 , to selected 1.38
improvements to showing subsystems for an organism

Revision 1.19 - (view) (download) (annotate) - [select for diffs]
Tue Aug 9 14:25:11 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.18: +32 -68 lines
Diff to previous 1.18 , to selected 1.38
improvements to showing subsystems for an organism

Revision 1.18 - (view) (download) (annotate) - [select for diffs]
Thu Aug 4 22:35:28 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.17: +37 -13 lines
Diff to previous 1.17 , to selected 1.38
Counting subsystems

Revision 1.17 - (view) (download) (annotate) - [select for diffs]
Thu Aug 4 21:06:05 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.16: +28 -0 lines
Diff to previous 1.16 , to selected 1.38
subsys by genomes

Revision 1.16 - (view) (download) (annotate) - [select for diffs]
Sun Jul 10 18:17:42 2005 UTC (14 years, 8 months ago) by golsen
Branch: MAIN
CVS Tags: merge-trunktag-bodev_news-3
Changes since 1.15: +48 -19 lines
Diff to previous 1.15 , to selected 1.38
Add project description to genome statistics report.
Format PEG statistics as a table (easier to read).
Add title to "Statistics Page" when no genome is selected.
Some minor code clean up.

Revision 1.15 - (view) (download) (annotate) - [select for diffs]
Wed Apr 13 16:38:11 2005 UTC (14 years, 11 months ago) by redwards
Branch: MAIN
CVS Tags: Root-bobdev_news, merge-bobdev_news-1, merge-bobdev_news-2, merge-trunktag-bobdev_news-1, merge-trunktag-bobdev_news-2
Branch point for: Branch-bobdev_news
Changes since 1.14: +2 -1 lines
Diff to previous 1.14 , to selected 1.38
better stats

Revision 1.14 - (view) (download) (annotate) - [select for diffs]
Wed Apr 13 15:37:30 2005 UTC (14 years, 11 months ago) by redwards
Branch: MAIN
Changes since 1.13: +15 -0 lines
Diff to previous 1.13 , to selected 1.38
changed genome stats to show attributes

Revision 1.13 - (view) (download) (annotate) - [select for diffs]
Fri Apr 8 20:22:23 2005 UTC (14 years, 11 months ago) by redwards
Branch: MAIN
Changes since 1.12: +13 -13 lines
Diff to previous 1.12 , to selected 1.38
changed tag/value pairs completely. Ooops!

Revision 1.12 - (view) (download) (annotate) - [select for diffs]
Sat Mar 5 00:31:36 2005 UTC (15 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.11: +8 -3 lines
Diff to previous 1.11 , to selected 1.38
minor changes to oa in genome stats

Revision 1.11 - (view) (download) (annotate) - [select for diffs]
Fri Mar 4 18:29:21 2005 UTC (15 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.10: +1 -0 lines
Diff to previous 1.10 , to selected 1.38
Added attribute editing to the protein.cgi page

Revision 1.10 - (view) (download) (annotate) - [select for diffs]
Fri Mar 4 06:22:10 2005 UTC (15 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.9: +117 -0 lines
Diff to previous 1.9 , to selected 1.38
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 1.9 - (view) (download) (annotate) - [select for diffs]
Fri Jan 14 13:56:37 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +41 -1 lines
Diff to previous 1.8 , to selected 1.38
additional statistics

Revision 1.8 - (view) (download) (annotate) - [select for diffs]
Mon Jan 10 13:09:01 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +71 -24 lines
Diff to previous 1.7 , to selected 1.38
add some statistics capabilities

Revision 1.7 - (view) (download) (annotate) - [select for diffs]
Sat Dec 18 13:03:01 2004 UTC (15 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.6: +2 -2 lines
Diff to previous 1.6 , to selected 1.38
Fix typo in page title.

Revision 1.6 - (view) (download) (annotate) - [select for diffs]
Wed Oct 27 02:51:43 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +111 -19 lines
Diff to previous 1.5 , to selected 1.38
genome_statistics.cgi is completed

Revision 1.5 - (view) (download) (annotate) - [select for diffs]
Tue Oct 26 14:01:00 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.4: +71 -2 lines
Diff to previous 1.4 , to selected 1.38
minor advances in genome_statistics.cgi

Revision 1.4 - (view) (download) (annotate) - [select for diffs]
Sun Oct 24 02:45:41 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +33 -7 lines
Diff to previous 1.3 , to selected 1.38
minor additions to genome statistics

Revision 1.3 - (view) (download) (annotate) - [select for diffs]
Sat Oct 23 21:41:38 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.2: +27 -2 lines
Diff to previous 1.2 , to selected 1.38
stupid error in FIG.pm

Revision 1.2 - (view) (download) (annotate) - [select for diffs]
Sat Oct 23 21:28:54 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.1: +1 -1 lines
Diff to previous 1.1 , to selected 1.38
minor fix

Revision 1.1 - (view) (download) (annotate) - [select for diffs]
Sat Oct 23 19:51:41 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Diff to selected 1.38
introduce genome statistics

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