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Revision 1.251 - (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: 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_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 1.250: +4 -7 lines
Diff to previous 1.250 , to selected 1.123
Changed to use the SEED Viewer if invoked in NMPDR mode.

Revision 1.250 - (view) (download) (annotate) - [select for diffs]
Mon May 5 21:41:27 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_07_21, rast_rel_2008_08_07
Changes since 1.249: +17 -7 lines
Diff to previous 1.249 , to selected 1.123
Changed to redirect search engines to the seed viewer.

Revision 1.249 - (view) (download) (annotate) - [select for diffs]
Tue Apr 29 08:12:27 2008 UTC (11 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.248: +3 -2 lines
Diff to previous 1.248 , to selected 1.123
Upgraded tracing.

Revision 1.248 - (view) (download) (annotate) - [select for diffs]
Wed Jan 2 01:45:39 2008 UTC (12 years, 3 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.247: +20 -17 lines
Diff to previous 1.247 , to selected 1.123
Change the implimentation of the similarities navigation buttons
'previous PEG' and 'next PEG' so that they really work on location
information.  Uses new next_feature() and previous_feature() functions
added to FIG.pm.

Revision 1.247 - (view) (download) (annotate) - [select for diffs]
Thu Dec 6 14:27:33 2007 UTC (12 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.246: +5 -11 lines
Diff to previous 1.246 , to selected 1.123
Added sim support to NMPDR mode.

Revision 1.246 - (view) (download) (annotate) - [select for diffs]
Fri Nov 30 21:47:57 2007 UTC (12 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.245: +6 -2 lines
Diff to previous 1.245 , to selected 1.123
we think we're fixing an obscure sims bug ... bruce??

Revision 1.245 - (view) (download) (annotate) - [select for diffs]
Thu Nov 15 21:06:50 2007 UTC (12 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.244: +9 -8 lines
Diff to previous 1.244 , to selected 1.123
fix to FF.pm

Revision 1.244 - (view) (download) (annotate) - [select for diffs]
Mon Jul 16 19:48:52 2007 UTC (12 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.243: +6 -0 lines
Diff to previous 1.243 , to selected 1.123
Implemented performance improvements for compare-regions.

Revision 1.243 - (view) (download) (annotate) - [select for diffs]
Tue Apr 10 04:01:55 2007 UTC (12 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.242: +3 -6 lines
Diff to previous 1.242 , to selected 1.123
Fixed so some of the annotation links will still display if no user is logged in.

Revision 1.242 - (view) (download) (annotate) - [select for diffs]
Fri Feb 23 03:10:33 2007 UTC (13 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.241: +2 -0 lines
Diff to previous 1.241 , to selected 1.123
Fixed so that riboswitches display on an "NMPDR RiboSwitch Page" instead of an "NMPDR BS Page".

Revision 1.241 - (view) (download) (annotate) - [select for diffs]
Thu Feb 8 15:31:22 2007 UTC (13 years, 1 month ago) by paczian
Branch: MAIN
Changes since 1.240: +5 -1 lines
Diff to previous 1.240 , to selected 1.123
added check for annotation links not to be shown when there is no user present

Revision 1.240 - (view) (download) (annotate) - [select for diffs]
Tue Feb 6 16:27:47 2007 UTC (13 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.239: +2 -0 lines
Diff to previous 1.239 , to selected 1.123
Fixed an error in the title for the chromosome context table.

Revision 1.239 - (view) (download) (annotate) - [select for diffs]
Wed Jan 24 18:35:59 2007 UTC (13 years, 2 months ago) by paczian
Branch: MAIN
Changes since 1.238: +3 -0 lines
Diff to previous 1.238 , to selected 1.123
fixed cgi object passing bug

Revision 1.238 - (view) (download) (annotate) - [select for diffs]
Fri Jan 19 18:22:34 2007 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.237: +0 -1 lines
Diff to previous 1.237 , to selected 1.123
take out the fix to clear request; it did not work; Tobi or Daniel must handle it

Revision 1.237 - (view) (download) (annotate) - [select for diffs]
Fri Jan 19 18:05:34 2007 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.236: +1 -0 lines
Diff to previous 1.236 , to selected 1.123
fix fast_assignment bug; request needed to be cleared

Revision 1.236 - (view) (download) (annotate) - [select for diffs]
Fri Nov 3 18:22:09 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.235: +6 -4 lines
Diff to previous 1.235 , to selected 1.123
Fixed missing headers in SEED mode.

Revision 1.235 - (view) (download) (annotate) - [select for diffs]
Tue Oct 17 12:53:32 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.234: +3 -0 lines
Diff to previous 1.234 , to selected 1.123
Enhanced so that the template can detect whether or not a protein is being displayed.

Revision 1.234 - (view) (download) (annotate) - [select for diffs]
Tue Oct 17 11:38:03 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.233: +5 -1 lines
Diff to previous 1.233 , to selected 1.123
Added tracing.

Revision 1.233 - (view) (download) (annotate) - [select for diffs]
Tue Oct 3 02:33:37 2006 UTC (13 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.232: +1 -1 lines
Diff to previous 1.232 , to selected 1.123
Upgraded to the new tracing technology.

Revision 1.232 - (view) (download) (annotate) - [select for diffs]
Mon Oct 2 03:05:46 2006 UTC (13 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.231: +10 -4 lines
Diff to previous 1.231 , to selected 1.123
Changed to use the new tracing system. Added a show/hide button for BBHs.

Revision 1.231 - (view) (download) (annotate) - [select for diffs]
Fri Aug 25 19:44:40 2006 UTC (13 years, 7 months ago) by paczian
Branch: MAIN
Changes since 1.230: +12 -1 lines
Diff to previous 1.230 , to selected 1.123
catched the exception of an invalid peg id being passed

Revision 1.230 - (view) (download) (annotate) - [select for diffs]
Thu Aug 24 22:58:03 2006 UTC (13 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.229: +70 -42 lines
Diff to previous 1.229 , to selected 1.123
Enhanced for use with non-PEG features.

Revision 1.229 - (view) (download) (annotate) - [select for diffs]
Mon Aug 14 16:12:08 2006 UTC (13 years, 7 months ago) by paczian
Branch: MAIN
Changes since 1.228: +66 -28 lines
Diff to previous 1.228 , to selected 1.123
updated to use new backend

Revision 1.228 - (view) (download) (annotate) - [select for diffs]
Thu Aug 3 22:18:50 2006 UTC (13 years, 7 months ago) by paczian
Branch: MAIN
Changes since 1.227: +7 -0 lines
Diff to previous 1.227 , to selected 1.123
added the support for non fig ids which was lost in the translation

Revision 1.227 - (view) (download) (annotate) - [select for diffs]
Thu Aug 3 05:27:30 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.226: +5 -1 lines
Diff to previous 1.226 , to selected 1.123
Fixed compare_regions and BBHs.

Revision 1.226 - (view) (download) (annotate) - [select for diffs]
Thu Aug 3 03:00:04 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.225: +2 -7 lines
Diff to previous 1.225 , to selected 1.123
Enhanced to display protein families in Sprout using the new family tables.

Revision 1.225 - (view) (download) (annotate) - [select for diffs]
Wed Aug 2 14:46:24 2006 UTC (13 years, 8 months ago) by paczian
Branch: MAIN
Changes since 1.224: +17 -0 lines
Diff to previous 1.224 , to selected 1.123
added a missing block to support next and previous peg navigation via the according buttons.

Revision 1.224 - (view) (download) (annotate) - [select for diffs]
Fri Jul 28 02:52:43 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.223: +2 -2 lines
Diff to previous 1.223 , to selected 1.123
*** empty log message ***

Revision 1.223 - (view) (download) (annotate) - [select for diffs]
Fri Jul 28 02:13:42 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.222: +81 -79 lines
Diff to previous 1.222 , to selected 1.123
Converted for NMPDR compatability.

Revision 1.222 - (view) (download) (annotate) - [select for diffs]
Wed Jul 26 21:10:41 2006 UTC (13 years, 8 months ago) by paczian
Branch: MAIN
Changes since 1.221: +3 -0 lines
Diff to previous 1.221 , to selected 1.123
added annotate / negate annotation, view annotation, view all realted annotations

Revision 1.221 - (view) (download) (annotate) - [select for diffs]
Tue Jul 25 21:33:05 2006 UTC (13 years, 8 months ago) by hwang
Branch: MAIN
Changes since 1.220: +2 -1 lines
Diff to previous 1.220 , to selected 1.123
Added hr line

Revision 1.220 - (view) (download) (annotate) - [select for diffs]
Tue Jul 25 20:55:56 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.219: +124 -122 lines
Diff to previous 1.219 , to selected 1.123
Turned off protein families for Sprout.

Revision 1.219 - (view) (download) (annotate) - [select for diffs]
Tue Jul 25 20:44:53 2006 UTC (13 years, 8 months ago) by hwang
Branch: MAIN
Changes since 1.218: +1 -0 lines
Diff to previous 1.218 , to selected 1.123
Added the line to see the changes to get pubmed journals

Revision 1.218 - (view) (download) (annotate) - [select for diffs]
Tue Jul 25 19:58:08 2006 UTC (13 years, 8 months ago) by paczian
Branch: MAIN
Changes since 1.217: +157 -3297 lines
Diff to previous 1.217 , to selected 1.123
total redo

Revision 1.217 - (view) (download) (annotate) - [select for diffs]
Tue Jul 25 19:22:57 2006 UTC (13 years, 8 months ago) by hwang
Branch: MAIN
Changes since 1.216: +30 -1 lines
Diff to previous 1.216 , to selected 1.123
Moved the pubmed link from the bottom to the middle of the page. Reserve bottom links for tools

Revision 1.216 - (view) (download) (annotate) - [select for diffs]
Mon Jul 24 18:22:14 2006 UTC (13 years, 8 months ago) by hwang
Branch: MAIN
Changes since 1.215: +4 -2 lines
Diff to previous 1.215 , to selected 1.123
Added line to see pubmed links

Revision 1.215 - (view) (download) (annotate) - [select for diffs]
Thu Jul 20 20:13:45 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.214: +1 -1 lines
Diff to previous 1.214 , to selected 1.123
Changed external templates to php.

Revision 1.214 - (view) (download) (annotate) - [select for diffs]
Thu Jul 20 19:00:47 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.213: +730 -727 lines
Diff to previous 1.213 , to selected 1.123
Fixed to choose the correct template even if the request parameter is modified by the code.

Revision 1.213 - (view) (download) (annotate) - [select for diffs]
Thu Jul 20 18:44:11 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.212: +2 -1 lines
Diff to previous 1.212 , to selected 1.123
More tracing.

Revision 1.212 - (view) (download) (annotate) - [select for diffs]
Thu Jul 20 18:37:52 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.211: +1 -0 lines
Diff to previous 1.211 , to selected 1.123
Added tracing.

Revision 1.211 - (view) (download) (annotate) - [select for diffs]
Tue Jul 18 18:27:21 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.210: +15 -1 lines
Diff to previous 1.210 , to selected 1.123
Updated so that each service will use a different template if URL-specified templates are enabled.

Revision 1.210 - (view) (download) (annotate) - [select for diffs]
Wed Jul 12 22:21:35 2006 UTC (13 years, 8 months ago) by hwang
Branch: MAIN
Changes since 1.209: +9 -2 lines
Diff to previous 1.209 , to selected 1.123
Changed the cgi to only show the general tools and organism specific tools.

Revision 1.209 - (view) (download) (annotate) - [select for diffs]
Wed Jul 12 03:13:52 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.208: +2 -2 lines
Diff to previous 1.208 , to selected 1.123
Fix to the new alternate-template code.

Revision 1.208 - (view) (download) (annotate) - [select for diffs]
Wed Jul 12 02:52:50 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.207: +6 -1 lines
Diff to previous 1.207 , to selected 1.123
Added the capability of specifying an alternate location for the protein template in the FIG_Config file.

Revision 1.207 - (view) (download) (annotate) - [select for diffs]
Tue Jun 27 22:40:49 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.206: +17 -13 lines
Diff to previous 1.206 , to selected 1.123
updates to Toby's new interface

Revision 1.206 - (view) (download) (annotate) - [select for diffs]
Tue Jun 27 17:21:04 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.205: +32 -8 lines
Diff to previous 1.205 , to selected 1.123
establish a means of separating old and new protein.cgi

Revision 1.205 - (view) (download) (annotate) - [select for diffs]
Wed Jun 21 23:59:48 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.204: +2 -2 lines
Diff to previous 1.204 , to selected 1.123
RAE: compare regionsa and num genomes

Revision 1.204 - (view) (download) (annotate) - [select for diffs]
Tue Jun 6 03:34:22 2006 UTC (13 years, 9 months ago) by hwang
Branch: MAIN
Changes since 1.203: +2 -2 lines
Diff to previous 1.203 , to selected 1.123
fixed syntax error.

Revision 1.203 - (view) (download) (annotate) - [select for diffs]
Tue Jun 6 03:25:01 2006 UTC (13 years, 9 months ago) by hwang
Branch: MAIN
Changes since 1.202: +40 -3 lines
Diff to previous 1.202 , to selected 1.123
For other external tools that doesn't use post/get and need preprocessing, if method is internal, then call internal script.

Revision 1.202 - (view) (download) (annotate) - [select for diffs]
Wed May 24 16:16:57 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.201: +2 -3 lines
Diff to previous 1.201 , to selected 1.123
RAE: restoring base url

Revision 1.201 - (view) (download) (annotate) - [select for diffs]
Mon May 22 01:23:28 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.200: +0 -1 lines
Diff to previous 1.200 , to selected 1.123
RAE: Deleting a STDERR

Revision 1.200 - (view) (download) (annotate) - [select for diffs]
Mon May 22 00:41:03 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.199: +39 -15 lines
Diff to previous 1.199 , to selected 1.123
RAE: correcting links to tools

Revision 1.199 - (view) (download) (annotate) - [select for diffs]
Mon May 8 21:48:57 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.198: +3 -1 lines
Diff to previous 1.198 , to selected 1.123
avoid losing user when showing FC evidence

Revision 1.198 - (view) (download) (annotate) - [select for diffs]
Tue Apr 25 17:18:42 2006 UTC (13 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.197: +14 -13 lines
Diff to previous 1.197 , to selected 1.123
*** empty log message ***

Revision 1.197 - (view) (download) (annotate) - [select for diffs]
Tue Apr 25 16:50:45 2006 UTC (13 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.196: +14 -12 lines
Diff to previous 1.196 , to selected 1.123
Removed extra columns per request by Leslie.

Revision 1.196 - (view) (download) (annotate) - [select for diffs]
Wed Apr 12 20:25:50 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.195: +0 -7 lines
Diff to previous 1.195 , to selected 1.123
minor changes to eliminate master:

Revision 1.195 - (view) (download) (annotate) - [select for diffs]
Mon Mar 20 03:06:35 2006 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.194: +7 -2 lines
Diff to previous 1.194 , to selected 1.123
RAE: Adding BUT NOT to protein.cgi

Revision 1.194 - (view) (download) (annotate) - [select for diffs]
Fri Mar 10 22:19:24 2006 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.193: +1 -1 lines
Diff to previous 1.193 , to selected 1.123
fix commentary called from protein.cgi -- I think that someone altered the format of GG output

Revision 1.193 - (view) (download) (annotate) - [select for diffs]
Fri Mar 3 23:09:29 2006 UTC (14 years, 1 month ago) by golsen
Branch: MAIN
Changes since 1.192: +2 -1 lines
Diff to previous 1.192 , to selected 1.123
Minor change in information displayed on contig abbreviation mouse-over.

Revision 1.192 - (view) (download) (annotate) - [select for diffs]
Fri Mar 3 22:36:37 2006 UTC (14 years, 1 month ago) by golsen
Branch: MAIN
Changes since 1.191: +18 -8 lines
Diff to previous 1.191 , to selected 1.123
Add genome name pop-up on mouse-over of title abbreviations to chromosomal
cluster and pinned region views.  Added infrastructure for links and
context menus, too.  Changes to GenoGraphics also adjust left margin
of the diagrams to match the actual title lengths.

Revision 1.191 - (view) (download) (annotate) - [select for diffs]
Fri Mar 3 20:14:56 2006 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.190: +9 -1 lines
Diff to previous 1.190 , to selected 1.123
Fix for bug 322

Revision 1.190 - (view) (download) (annotate) - [select for diffs]
Fri Mar 3 18:07:56 2006 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.189: +23 -1 lines
Diff to previous 1.189 , to selected 1.123
Add javascript-check in protein tools. If there is some, and we're sprout, don't try to put the NMPDR
header on the page.

Revision 1.189 - (view) (download) (annotate) - [select for diffs]
Thu Feb 23 22:00:32 2006 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.188: +83 -2 lines
Diff to previous 1.188 , to selected 1.123
fixes to compare region to move between contigs

Revision 1.188 - (view) (download) (annotate) - [select for diffs]
Tue Feb 21 22:48:23 2006 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.187: +6 -7 lines
Diff to previous 1.187 , to selected 1.123
RAE: allowing add links when no links were present

Revision 1.187 - (view) (download) (annotate) - [select for diffs]
Mon Feb 13 22:10:34 2006 UTC (14 years, 1 month ago) by efrank
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.186: +10 -0 lines
Diff to previous 1.186 , to selected 1.123
           # caBIG insists on explicitly displaying the taxon ID rather
           # than learning how to read the figID, so display it.
           # ...please don't delete this without consulting with Ed

           my $taxon;
           if ($prot =~ /^fig\|(\d+)\.(\d+)/) {
               push(@{$html->{general}},"<h2>Taxon=$1 (NCBI TaxonId, if one exists)</h2>\n");
           }

Revision 1.186 - (view) (download) (annotate) - [select for diffs]
Fri Feb 3 19:54:00 2006 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.185: +2 -1 lines
Diff to previous 1.185 , to selected 1.123
RAE: minor fix to FigWebServices/protein.cgi dna_sequence_adjacent

Revision 1.185 - (view) (download) (annotate) - [select for diffs]
Fri Feb 3 17:20:51 2006 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.184: +0 -2 lines
Diff to previous 1.184 , to selected 1.123
remove debug

Revision 1.184 - (view) (download) (annotate) - [select for diffs]
Fri Feb 3 17:20:40 2006 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.183: +9 -3 lines
Diff to previous 1.183 , to selected 1.123
add BasicLocation fix to the flanking-dna code.

Revision 1.183 - (view) (download) (annotate) - [select for diffs]
Fri Feb 3 02:36:24 2006 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.182: +1 -1 lines
Diff to previous 1.182 , to selected 1.123
RAE: Corrected DNA-sequence adjacent for Sprout

Revision 1.182 - (view) (download) (annotate) - [select for diffs]
Fri Feb 3 02:32:34 2006 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.181: +6 -1 lines
Diff to previous 1.181 , to selected 1.123
RAE: Corrected DNA-sequence adjacent for Sprout

Revision 1.181 - (view) (download) (annotate) - [select for diffs]
Thu Feb 2 18:30:59 2006 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.180: +9 -2 lines
Diff to previous 1.180 , to selected 1.123
Remove edit controlled vocab link for NMPDR version.

Revision 1.180 - (view) (download) (annotate) - [select for diffs]
Wed Jan 25 17:50:37 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.179: +1 -1 lines
Diff to previous 1.179 , to selected 1.123
RAE: Changing identical proteins to be on first

Revision 1.179 - (view) (download) (annotate) - [select for diffs]
Tue Jan 24 20:48:02 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.178: +1 -1 lines
Diff to previous 1.178 , to selected 1.123
RAE: Shortening colors explained for VV

Revision 1.178 - (view) (download) (annotate) - [select for diffs]
Tue Jan 24 20:44:06 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.177: +2 -2 lines
Diff to previous 1.177 , to selected 1.123
RAE: Shortening colors explained for VV

Revision 1.177 - (view) (download) (annotate) - [select for diffs]
Tue Jan 24 20:39:51 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.176: +2 -2 lines
Diff to previous 1.176 , to selected 1.123
RAE: Shortening colors explained for VV

Revision 1.176 - (view) (download) (annotate) - [select for diffs]
Tue Jan 24 20:36:48 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.175: +2 -2 lines
Diff to previous 1.175 , to selected 1.123
RAE: Shortening colors explained for VV

Revision 1.175 - (view) (download) (annotate) - [select for diffs]
Mon Jan 16 18:02:11 2006 UTC (14 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.174: +84 -17 lines
Diff to previous 1.174 , to selected 1.123
Nearly total rewrite of dna_sequence_adjacent:
   Fixed off-by-one errors in the end of coloring (which started it all).
   Modified to detect end of contig (it used to fail if it ran off end).
   Modified to handle multisegment locations.

Revision 1.174 - (view) (download) (annotate) - [select for diffs]
Mon Jan 9 18:02:22 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.173: +0 -7 lines
Diff to previous 1.173 , to selected 1.123
correct protein families link

Revision 1.173 - (view) (download) (annotate) - [select for diffs]
Wed Jan 4 04:46:12 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.172: +32 -1 lines
Diff to previous 1.172 , to selected 1.123
RAE: Add link for getting adjacent sequences

Revision 1.172 - (view) (download) (annotate) - [select for diffs]
Fri Dec 23 18:13:45 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.171: +2 -2 lines
Diff to previous 1.171 , to selected 1.123
clean up help for abstract functional coupling

Revision 1.171 - (view) (download) (annotate) - [select for diffs]
Tue Dec 20 17:59:09 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.170: +22 -0 lines
Diff to previous 1.170 , to selected 1.123
add abstract functional coupling

Revision 1.170 - (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 1.169: +17 -0 lines
Diff to previous 1.169 , to selected 1.123
add license words

Revision 1.169 - (view) (download) (annotate) - [select for diffs]
Wed Nov 23 21:31:14 2005 UTC (14 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.168: +7 -7 lines
Diff to previous 1.168 , to selected 1.123
Explicitly pass $cgi through set_ec_and_tc_links to set_ec_to_maps,
rather than picking it up as a global in set_ec_to_maps.

Revision 1.168 - (view) (download) (annotate) - [select for diffs]
Wed Nov 23 20:34:59 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.167: +12 -9 lines
Diff to previous 1.167 , to selected 1.123
major changes to attributes and protein families. There are changes to several modules to deal with new attributes database, and simultaneous updates to protein families

Revision 1.167 - (view) (download) (annotate) - [select for diffs]
Fri Nov 11 19:55:27 2005 UTC (14 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.166: +3 -1 lines
Diff to previous 1.166 , to selected 1.123
Added trace messages for the EC problem in Sprout.

Revision 1.166 - (view) (download) (annotate) - [select for diffs]
Wed Oct 26 18:31:07 2005 UTC (14 years, 5 months ago) by mkubal
Branch: MAIN
CVS Tags: caBIG-00-00-00
Changes since 1.165: +11 -4 lines
Diff to previous 1.165 , to selected 1.123
removed check for is_eukaryotic

Revision 1.165 - (view) (download) (annotate) - [select for diffs]
Tue Oct 25 17:41:32 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.164: +5 -3 lines
Diff to previous 1.164 , to selected 1.123
more more more proteinfamily stuff

Revision 1.164 - (view) (download) (annotate) - [select for diffs]
Tue Oct 25 14:28:48 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.163: +3 -4 lines
Diff to previous 1.163 , to selected 1.123
fixing link into proteinfamilies.cgi

Revision 1.163 - (view) (download) (annotate) - [select for diffs]
Mon Oct 24 21:48:48 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.162: +1 -1 lines
Diff to previous 1.162 , to selected 1.123
Don't show xxx id's in the identical protien list.

Revision 1.162 - (view) (download) (annotate) - [select for diffs]
Sat Oct 22 17:43:49 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.161: +4 -4 lines
Diff to previous 1.161 , to selected 1.123
changing the format of attribute_keys

Revision 1.161 - (view) (download) (annotate) - [select for diffs]
Wed Oct 12 21:03:16 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.160: +32 -22 lines
Diff to previous 1.160 , to selected 1.123
Broad minor fixes to make the SEED use relative paths throughout.

(The motivation this is to fully enable hiding the actual location of a running SEED system behind a web proxy so that things like NMPDR protein page references can be made stable across multiple releases).

This involved things like the following:

Changing $cgi->url() to $cgi->url(-relative => 1)
Changing $cgi->self_url() to $cgi->url(-relative => 1, -query => 1, -path_info => 1)

Changing the definition of FIG::cgi_url() to return "." (this may break something, but I haven't found it yet).

Revision 1.160 - (view) (download) (annotate) - [select for diffs]
Tue Oct 11 01:09:31 2005 UTC (14 years, 5 months ago) by redwards
Branch: MAIN
Changes since 1.159: +41 -5 lines
Diff to previous 1.159 , to selected 1.123
adding popup windows to explain evidence codes

Revision 1.159 - (view) (download) (annotate) - [select for diffs]
Mon Oct 10 16:56:16 2005 UTC (14 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.158: +1 -1 lines
Diff to previous 1.158 , to selected 1.123
update TCDB web link

Revision 1.158 - (view) (download) (annotate) - [select for diffs]
Thu Oct 6 17:09:49 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.157: +11 -2 lines
Diff to previous 1.157 , to selected 1.123
Adding JS popups for the subsystems

Revision 1.157 - (view) (download) (annotate) - [select for diffs]
Wed Oct 5 20:34:02 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.156: +2 -1 lines
Diff to previous 1.156 , to selected 1.123
fixes to update_uniq_id_data

Revision 1.156 - (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 1.155: +4 -2 lines
Diff to previous 1.155 , to selected 1.123
fixes on showing subsystems

Revision 1.155 - (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 1.154: +3 -3 lines
Diff to previous 1.154 , to selected 1.123
fixes to display_subsys.cgi

Revision 1.154 - (view) (download) (annotate) - [select for diffs]
Thu Sep 15 20:45:22 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.153: +10 -3 lines
Diff to previous 1.153 , to selected 1.123
Only show the subsystem numbers in the contig context if we're in SEED (not sprout).

Revision 1.153 - (view) (download) (annotate) - [select for diffs]
Sat Sep 10 18:13:00 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.152: +3 -2 lines
Diff to previous 1.152 , to selected 1.123
minor changes for help on compare_regions

Revision 1.152 - (view) (download) (annotate) - [select for diffs]
Sat Sep 10 17:52:09 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.151: +13 -10 lines
Diff to previous 1.151 , to selected 1.123
on compare_regions fix inclusion of pinned orgs

Revision 1.151 - (view) (download) (annotate) - [select for diffs]
Sat Sep 10 15:10:24 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.150: +60 -48 lines
Diff to previous 1.150 , to selected 1.123
fixes to compare regions

Revision 1.150 - (view) (download) (annotate) - [select for diffs]
Thu Sep 8 15:38:23 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.149: +10 -1 lines
Diff to previous 1.149 , to selected 1.123
Remove help message for annotations when in sprout mode.

Revision 1.149 - (view) (download) (annotate) - [select for diffs]
Tue Sep 6 21:13:48 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.148: +19 -2 lines
Diff to previous 1.148 , to selected 1.123
Make user can_user not set to empty when going into subsys.cgi.

Revision 1.148 - (view) (download) (annotate) - [select for diffs]
Tue Aug 30 21:11:26 2005 UTC (14 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.147: +25 -1 lines
Diff to previous 1.147 , to selected 1.123
Instead of just showing a count of subsystems the pegs are in (in the context),
assign unique numbers to them and show the numbers each peg particpates in.

Revision 1.147 - (view) (download) (annotate) - [select for diffs]
Wed Aug 17 01:20:14 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.146: +4 -3 lines
Diff to previous 1.146 , to selected 1.123
show curator of subsystem on protein page

Revision 1.146 - (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 1.145: +21 -10 lines
Diff to previous 1.145 , to selected 1.123
NMPDR updates.

Revision 1.145 - (view) (download) (annotate) - [select for diffs]
Mon Aug 1 18:52:58 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.144: +9 -0 lines
Diff to previous 1.144 , to selected 1.123
update stuff relating to protein families

Revision 1.144 - (view) (download) (annotate) - [select for diffs]
Fri Jul 29 21:27:33 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.143: +0 -1 lines
Diff to previous 1.143 , to selected 1.123
removing one instance of FIG.js

Revision 1.143 - (view) (download) (annotate) - [select for diffs]
Thu Jul 28 21:01:09 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.142: +6 -6 lines
Diff to previous 1.142 , to selected 1.123
correcting ev_link in protein.cgi by Rob

Revision 1.142 - (view) (download) (annotate) - [select for diffs]
Wed Jul 27 16:55:16 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.141: +1 -1 lines
Diff to previous 1.141 , to selected 1.123
details on supporting evidence codes

Revision 1.141 - (view) (download) (annotate) - [select for diffs]
Wed Jul 27 15:46:25 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.140: +26 -5 lines
Diff to previous 1.140 , to selected 1.123
add evidence codes to protein.cgi

Revision 1.140 - (view) (download) (annotate) - [select for diffs]
Fri Jul 22 21:50:44 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.139: +10 -10 lines
Diff to previous 1.139 , to selected 1.123
minor tweaks by Rob to make nmpdr work

Revision 1.139 - (view) (download) (annotate) - [select for diffs]
Fri Jul 22 15:31:50 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.138: +10 -6 lines
Diff to previous 1.138 , to selected 1.123
fixing relative urls

Revision 1.138 - (view) (download) (annotate) - [select for diffs]
Sun Jul 17 19:04:27 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.137: +7 -7 lines
Diff to previous 1.137 , to selected 1.123
Making attributes interface work

Revision 1.137 - (view) (download) (annotate) - [select for diffs]
Thu Jul 14 15:53:54 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.136: +3 -2 lines
Diff to previous 1.136 , to selected 1.123
Fixed lost username in protein.cgi and removed Bound/Find uncalled gene from FIGGenDB.pm

Revision 1.136 - (view) (download) (annotate) - [select for diffs]
Wed Jul 13 04:16:28 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.135: +7 -2 lines
Diff to previous 1.135 , to selected 1.123
Changes to proteinfamilies representations

Revision 1.135 - (view) (download) (annotate) - [select for diffs]
Wed Jul 13 03:57:22 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.134: +1 -1 lines
Diff to previous 1.134 , to selected 1.123
putting a line break back in for vv

Revision 1.134 - (view) (download) (annotate) - [select for diffs]
Tue Jul 12 14:34:15 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
CVS Tags: merge-trunktag-bodev_news-3
Changes since 1.133: +66 -25 lines
Diff to previous 1.133 , to selected 1.123
Changing attributes and modifying protein.cgi with show/hides

Revision 1.133 - (view) (download) (annotate) - [select for diffs]
Sat Jul 9 20:22:02 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.132: +2 -1 lines
Diff to previous 1.132 , to selected 1.123
adding help links

Revision 1.132 - (view) (download) (annotate) - [select for diffs]
Thu Jul 7 20:08:11 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.131: +0 -1 lines
Diff to previous 1.131 , to selected 1.123
remove debug.

Revision 1.131 - (view) (download) (annotate) - [select for diffs]
Thu Jul 7 19:32:19 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.130: +1 -1 lines
Diff to previous 1.130 , to selected 1.123
Changed name of button on compare region

Revision 1.130 - (view) (download) (annotate) - [select for diffs]
Thu Jul 7 14:38:46 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.129: +14 -3 lines
Diff to previous 1.129 , to selected 1.123
Added new column, nummber of subsystems, to protein.cgi

Revision 1.129 - (view) (download) (annotate) - [select for diffs]
Wed Jul 6 04:17:38 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.128: +36 -1 lines
Diff to previous 1.128 , to selected 1.123
Changes to index on property values, display properties in search output, and
display properties in protien page.

Revision 1.128 - (view) (download) (annotate) - [select for diffs]
Fri Jul 1 02:09:16 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.127: +7 -4 lines
Diff to previous 1.127 , to selected 1.123
Changed proteinfamilies.cgi

Revision 1.127 - (view) (download) (annotate) - [select for diffs]
Wed Jun 29 14:48:27 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-2
Changes since 1.126: +5 -0 lines
Diff to previous 1.126 , to selected 1.123
fix bug in SFXlate.pm

Revision 1.126 - (view) (download) (annotate) - [select for diffs]
Wed Jun 29 04:33:02 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.125: +33 -0 lines
Diff to previous 1.125 , to selected 1.123
Changes to javascript to externalize everything into FIG.js and clean up the code

Revision 1.125 - (view) (download) (annotate) - [select for diffs]
Wed Jun 29 00:28:01 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.124: +33 -2 lines
Diff to previous 1.124 , to selected 1.123
Initial release of proteinfamilies.cgi into the wild

Revision 1.124 - (view) (download) (annotate) - [select for diffs]
Wed Jun 29 00:06:24 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.123: +2 -1 lines
Diff to previous 1.123
minor fixes to print_context in protein.cgi

Revision 1.123 - (view) (download) (annotate) - [selected]
Tue Jun 28 18:46:43 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.122: +1 -0 lines
Diff to previous 1.122
add tigr links

Revision 1.122 - (view) (download) (annotate) - [select for diffs]
Tue Jun 28 02:30:40 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.121: +33 -5 lines
Diff to previous 1.121 , to selected 1.123
fixes to Sprout in protein.cgi

Revision 1.121 - (view) (download) (annotate) - [select for diffs]
Mon Jun 27 20:00:55 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.120: +22 -1 lines
Diff to previous 1.120 , to selected 1.123
after Sprout runs

Revision 1.120 - (view) (download) (annotate) - [select for diffs]
Fri Jun 24 21:21:42 2005 UTC (14 years, 9 months ago) by parrello
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-1
Changes since 1.119: +21 -21 lines
Diff to previous 1.119 , to selected 1.123
Fixed some tabs.
Changed so that fancier tracing can be turned on.

Revision 1.119 - (view) (download) (annotate) - [select for diffs]
Thu Jun 23 21:24:49 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.118: +22 -7 lines
Diff to previous 1.118 , to selected 1.123
finally

Revision 1.118 - (view) (download) (annotate) - [select for diffs]
Mon Jun 20 04:03:44 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.117: +1 -7 lines
Diff to previous 1.117 , to selected 1.123
disable old protein families

Revision 1.117 - (view) (download) (annotate) - [select for diffs]
Mon Jun 13 19:44:32 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: Root-bobdev_news
Branch point for: Branch-bobdev_news
Changes since 1.116: +2 -433 lines
Diff to previous 1.116 , to selected 1.123
interface routines hack

Revision 1.116 - (view) (download) (annotate) - [select for diffs]
Mon Jun 13 16:44:04 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.115: +48 -17 lines
Diff to previous 1.115 , to selected 1.123
Ross change commit after cleanup

Revision 1.115 - (view) (download) (annotate) - [select for diffs]
Fri Jun 10 16:08:52 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.114: +8 -4 lines
Diff to previous 1.114 , to selected 1.123
fixes to cached pin displays

Revision 1.114 - (view) (download) (annotate) - [select for diffs]
Mon Jun 6 13:25:16 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.113: +1 -1 lines
Diff to previous 1.113 , to selected 1.123
add find_maximal_clusters

Revision 1.113 - (view) (download) (annotate) - [select for diffs]
Fri Jun 3 23:09:10 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.112: +1 -0 lines
Diff to previous 1.112 , to selected 1.123
fix bug in compare_regions

Revision 1.112 - (view) (download) (annotate) - [select for diffs]
Fri Jun 3 00:27:44 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.111: +16 -4 lines
Diff to previous 1.111 , to selected 1.123
start removing trash in filtering automated assignments

Revision 1.111 - (view) (download) (annotate) - [select for diffs]
Wed Jun 1 11:32:26 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.110: +2 -11 lines
Diff to previous 1.110 , to selected 1.123
cleanup

Revision 1.110 - (view) (download) (annotate) - [select for diffs]
Wed Jun 1 02:59:52 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.109: +5 -1 lines
Diff to previous 1.109 , to selected 1.123
fixes to chromosomal_clusters.cgi

Revision 1.109 - (view) (download) (annotate) - [select for diffs]
Wed Jun 1 01:18:50 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.108: +36 -23 lines
Diff to previous 1.108 , to selected 1.123
install precomputed functional coupling data

Revision 1.108 - (view) (download) (annotate) - [select for diffs]
Wed May 4 03:17:43 2005 UTC (14 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.107: +21 -21 lines
Diff to previous 1.107 , to selected 1.123
*** empty log message ***

Revision 1.107 - (view) (download) (annotate) - [select for diffs]
Thu Apr 28 19:56:10 2005 UTC (14 years, 11 months ago) by golsen
Branch: MAIN
Changes since 1.106: +3 -1 lines
Diff to previous 1.106 , to selected 1.123
URI escape the subsystem name on links to subsystems with protein.

Revision 1.106 - (view) (download) (annotate) - [select for diffs]
Tue Apr 12 20:35:12 2005 UTC (14 years, 11 months ago) by golsen
Branch: MAIN
Changes since 1.105: +1 -0 lines
Diff to previous 1.105 , to selected 1.123
Add "get sequences" button to similarities.

Revision 1.105 - (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 1.104: +11 -10 lines
Diff to previous 1.104 , to selected 1.123
changed tag/value pairs completely. Ooops!

Revision 1.104 - (view) (download) (annotate) - [select for diffs]
Fri Apr 8 18:36:29 2005 UTC (14 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.103: +18 -8 lines
Diff to previous 1.103 , to selected 1.123
Hack to expand display-region for euks. -- /gdp

Revision 1.103 - (view) (download) (annotate) - [select for diffs]
Mon Mar 21 22:01:22 2005 UTC (15 years ago) by golsen
Branch: MAIN
Changes since 1.102: +2 -2 lines
Diff to previous 1.102 , to selected 1.123
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 1.102 - (view) (download) (annotate) - [select for diffs]
Mon Mar 21 21:39:32 2005 UTC (15 years ago) by golsen
Branch: MAIN
Changes since 1.101: +32 -21 lines
Diff to previous 1.101 , to selected 1.123
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.

Revision 1.101 - (view) (download) (annotate) - [select for diffs]
Sun Mar 20 22:26:16 2005 UTC (15 years ago) by golsen
Branch: MAIN
Changes since 1.100: +9 -3 lines
Diff to previous 1.100 , to selected 1.123
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 1.100 - (view) (download) (annotate) - [select for diffs]
Mon Mar 14 01:22:32 2005 UTC (15 years ago) by golsen
Branch: MAIN
Changes since 1.99: +44 -39 lines
Diff to previous 1.99 , to selected 1.123
Minor fixes on similarities

Revision 1.99 - (view) (download) (annotate) - [select for diffs]
Fri Mar 11 03:04:32 2005 UTC (15 years ago) by redwards
Branch: MAIN
Changes since 1.98: +47 -15 lines
Diff to previous 1.98 , to selected 1.123
Making tag/value pairs work

Revision 1.98 - (view) (download) (annotate) - [select for diffs]
Fri Mar 11 01:04:32 2005 UTC (15 years ago) by golsen
Branch: MAIN
Changes since 1.97: +91 -81 lines
Diff to previous 1.97 , to selected 1.123
Many new options for similarities

Revision 1.97 - (view) (download) (annotate) - [select for diffs]
Wed Mar 9 07:34:49 2005 UTC (15 years ago) by golsen
Branch: MAIN
Changes since 1.96: +63 -29 lines
Diff to previous 1.96 , to selected 1.123
Color-code functions in similarities table.  Fix filter for environmental sequences.

Revision 1.96 - (view) (download) (annotate) - [select for diffs]
Sun Mar 6 15:30:20 2005 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.95: +2 -1 lines
Diff to previous 1.95 , to selected 1.123
turn off print_kv_pairs in protein.cgi

Revision 1.95 - (view) (download) (annotate) - [select for diffs]
Fri Mar 4 18:38:12 2005 UTC (15 years ago) by redwards
Branch: MAIN
Changes since 1.94: +35 -37 lines
Diff to previous 1.94 , to selected 1.123
Tweaks to attribute editing to the protein.cgi page

Revision 1.94 - (view) (download) (annotate) - [select for diffs]
Fri Mar 4 18:29:21 2005 UTC (15 years ago) by redwards
Branch: MAIN
Changes since 1.93: +79 -7 lines
Diff to previous 1.93 , to selected 1.123
Added attribute editing to the protein.cgi page

Revision 1.93 - (view) (download) (annotate) - [select for diffs]
Thu Mar 3 23:54:03 2005 UTC (15 years, 1 month ago) by golsen
Branch: MAIN
Changes since 1.92: +32 -16 lines
Diff to previous 1.92 , to selected 1.123
When similarities are grouped by genome, merge the Organism cells to show the grouping

Revision 1.92 - (view) (download) (annotate) - [select for diffs]
Tue Mar 1 13:13:52 2005 UTC (15 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.91: +3 -3 lines
Diff to previous 1.91 , to selected 1.123
Remove warning about missing sprout.

Revision 1.91 - (view) (download) (annotate) - [select for diffs]
Sat Feb 26 11:01:13 2005 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.90: +5 -6 lines
Diff to previous 1.90 , to selected 1.123
add reset_curator.cgi

Revision 1.90 - (view) (download) (annotate) - [select for diffs]
Sat Feb 26 00:50:37 2005 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.89: +38 -12 lines
Diff to previous 1.89 , to selected 1.123
add group_by_genome to displaying sims in protein.cgi

Revision 1.89 - (view) (download) (annotate) - [select for diffs]
Fri Feb 25 17:20:42 2005 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.88: +3 -1 lines
Diff to previous 1.88 , to selected 1.123
set links to subsystems from protein.cgi with can_alter set

Revision 1.88 - (view) (download) (annotate) - [select for diffs]
Wed Feb 23 12:10:28 2005 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.87: +1 -1 lines
Diff to previous 1.87 , to selected 1.123
fix closest_pegs

Revision 1.87 - (view) (download) (annotate) - [select for diffs]
Wed Feb 23 12:07:10 2005 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.86: +1 -1 lines
Diff to previous 1.86 , to selected 1.123
fix closest_pegs

Revision 1.86 - (view) (download) (annotate) - [select for diffs]
Tue Feb 22 17:16:36 2005 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.85: +1 -1 lines
Diff to previous 1.85 , to selected 1.123
relax bound used on determining closest pegs

Revision 1.85 - (view) (download) (annotate) - [select for diffs]
Tue Feb 22 13:43:16 2005 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.84: +4 -1 lines
Diff to previous 1.84 , to selected 1.123
turn off GenDB link in SPROUT code

Revision 1.84 - (view) (download) (annotate) - [select for diffs]
Mon Feb 21 18:13:43 2005 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.83: +21 -4 lines
Diff to previous 1.83 , to selected 1.123
add links to TC numbers

Revision 1.83 - (view) (download) (annotate) - [select for diffs]
Wed Feb 9 20:43:27 2005 UTC (15 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.82: +25 -6 lines
Diff to previous 1.82 , to selected 1.123
Use icons instead of letters for sprout/seed links.

Revision 1.82 - (view) (download) (annotate) - [select for diffs]
Fri Feb 4 06:59:46 2005 UTC (15 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.81: +0 -2 lines
Diff to previous 1.81 , to selected 1.123
more changes to genomebrowser.cgi to make it work really well

Revision 1.81 - (view) (download) (annotate) - [select for diffs]
Thu Feb 3 22:45:38 2005 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.80: +26 -12 lines
Diff to previous 1.80 , to selected 1.123
fixes to region context

Revision 1.80 - (view) (download) (annotate) - [select for diffs]
Mon Jan 31 07:29:39 2005 UTC (15 years, 2 months ago) by redwards
Branch: MAIN
Changes since 1.79: +20 -3 lines
Diff to previous 1.79 , to selected 1.123
Minor change to formatting on subsys.cgi. Changed protein tools in protein.cgi to give either a long view with descriptions or just the short view

Revision 1.79 - (view) (download) (annotate) - [select for diffs]
Sat Jan 29 16:54:05 2005 UTC (15 years, 2 months ago) by redwards
Branch: MAIN
Changes since 1.78: +1 -0 lines
Diff to previous 1.78 , to selected 1.123
Changed protein.cgi so only those attributes whose last column begins http are displayed

Revision 1.78 - (view) (download) (annotate) - [select for diffs]
Sat Jan 29 03:41:49 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.77: +2 -2 lines
Diff to previous 1.77 , to selected 1.123
fixes to extract_genome

Revision 1.77 - (view) (download) (annotate) - [select for diffs]
Fri Jan 28 21:42:40 2005 UTC (15 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.76: +57 -24 lines
Diff to previous 1.76 , to selected 1.123
Optionally filter sims by percent identity and percent coverage

Revision 1.76 - (view) (download) (annotate) - [select for diffs]
Fri Jan 28 19:30:02 2005 UTC (15 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.75: +292 -97 lines
Diff to previous 1.75 , to selected 1.123
Commit some changes in how the SEED similarities HTML form is created, and localization of the filtering of the sims (moved out of display loop).  This is support for new filters, not yet installed.

Revision 1.75 - (view) (download) (annotate) - [select for diffs]
Thu Jan 27 18:28:29 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.74: +2 -3 lines
Diff to previous 1.74 , to selected 1.123
fix extend_subsys.cgi

Revision 1.74 - (view) (download) (annotate) - [select for diffs]
Thu Jan 27 17:36:25 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.73: +13 -5 lines
Diff to previous 1.73 , to selected 1.123
fix null values in some tables in protein.cgi

Revision 1.73 - (view) (download) (annotate) - [select for diffs]
Tue Jan 25 21:30:55 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.72: +39 -12 lines
Diff to previous 1.72 , to selected 1.123
set links to SEED and GBrowse from NMPDR

Revision 1.72 - (view) (download) (annotate) - [select for diffs]
Tue Jan 25 19:14:40 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.71: +7 -1 lines
Diff to previous 1.71 , to selected 1.123
put show_tools fixes back

Revision 1.71 - (view) (download) (annotate) - [select for diffs]
Tue Jan 25 18:04:35 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.70: +2 -7 lines
Diff to previous 1.70 , to selected 1.123
fixes to Sprout annotation

Revision 1.70 - (view) (download) (annotate) - [select for diffs]
Tue Jan 25 08:40:10 2005 UTC (15 years, 2 months ago) by redwards
Branch: MAIN
Changes since 1.69: +7 -1 lines
Diff to previous 1.69 , to selected 1.123
Changes to protein.cgi to allow comments in FIGdisk/FIG/Data/Global/LinksToTools and nicer tables

Revision 1.69 - (view) (download) (annotate) - [select for diffs]
Tue Jan 25 03:16:42 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.68: +2 -1 lines
Diff to previous 1.68 , to selected 1.123
fixes to protein.cgi

Revision 1.68 - (view) (download) (annotate) - [select for diffs]
Tue Jan 25 03:00:30 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.67: +158 -62 lines
Diff to previous 1.67 , to selected 1.123
radical fixes to prot.cgi

Revision 1.67 - (view) (download) (annotate) - [select for diffs]
Mon Jan 24 21:02:41 2005 UTC (15 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.66: +8 -7 lines
Diff to previous 1.66 , to selected 1.123
Minor changes to SEED sims code in anticipation of something a little more radical

Revision 1.66 - (view) (download) (annotate) - [select for diffs]
Sun Jan 23 15:43:49 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.65: +1 -1 lines
Diff to previous 1.65 , to selected 1.123
fixes to index.cgi

Revision 1.65 - (view) (download) (annotate) - [select for diffs]
Sun Jan 23 14:50:38 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.64: +18 -10 lines
Diff to previous 1.64 , to selected 1.123
fixes to protein.cgi

Revision 1.64 - (view) (download) (annotate) - [select for diffs]
Fri Jan 21 01:44:55 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.63: +2 -1 lines
Diff to previous 1.63 , to selected 1.123
add links to aliases on similarities

Revision 1.63 - (view) (download) (annotate) - [select for diffs]
Fri Jan 21 01:24:00 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.62: +218 -31 lines
Diff to previous 1.62 , to selected 1.123
protein.cgi for Sprout

Revision 1.62 - (view) (download) (annotate) - [select for diffs]
Wed Jan 19 19:54:03 2005 UTC (15 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.61: +1 -2 lines
Diff to previous 1.61 , to selected 1.123
no message

Revision 1.61 - (view) (download) (annotate) - [select for diffs]
Wed Jan 19 18:48:21 2005 UTC (15 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.60: +1 -1 lines
Diff to previous 1.60 , to selected 1.123
no message

Revision 1.60 - (view) (download) (annotate) - [select for diffs]
Tue Jan 18 08:16:13 2005 UTC (15 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.59: +880 -1078 lines
Diff to previous 1.59 , to selected 1.123
no message

Revision 1.59 - (view) (download) (annotate) - [select for diffs]
Fri Jan 14 23:06:47 2005 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.58: +11 -9 lines
Diff to previous 1.58 , to selected 1.123
Misc sprout-related fixes

Revision 1.58 - (view) (download) (annotate) - [select for diffs]
Wed Jan 12 21:54:52 2005 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.57: +14 -0 lines
Diff to previous 1.57 , to selected 1.123
Trap errors and show them on the webpage.

Revision 1.57 - (view) (download) (annotate) - [select for diffs]
Wed Jan 12 21:50:10 2005 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.56: +11 -2 lines
Diff to previous 1.56 , to selected 1.123
Fix up Sprout protein page template stuff

Revision 1.56 - (view) (download) (annotate) - [select for diffs]
Wed Jan 12 21:22:08 2005 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.55: +23 -4 lines
Diff to previous 1.55 , to selected 1.123
sprout debugging

Revision 1.55 - (view) (download) (annotate) - [select for diffs]
Sun Jan 9 17:15:12 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.54: +2 -22 lines
Diff to previous 1.54 , to selected 1.123
fix disambiguating maps

Revision 1.54 - (view) (download) (annotate) - [select for diffs]
Thu Jan 6 10:53:18 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.53: +1 -1 lines
Diff to previous 1.53 , to selected 1.123
take reference to SproutFIG.pm out of protein.cgi

Revision 1.53 - (view) (download) (annotate) - [select for diffs]
Thu Jan 6 00:47:45 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.52: +764 -278 lines
Diff to previous 1.52 , to selected 1.123
introduce rewritten protein.cgi

Revision 1.52 - (view) (download) (annotate) - [select for diffs]
Fri Dec 17 14:53:32 2004 UTC (15 years, 3 months ago) by heiko
Branch: MAIN
Changes since 1.51: +4 -4 lines
Diff to previous 1.51 , to selected 1.123
fixed javascript code for the popup menu
heiko neuweger

Revision 1.51 - (view) (download) (annotate) - [select for diffs]
Fri Dec 10 18:32:49 2004 UTC (15 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.50: +8 -2 lines
Diff to previous 1.50 , to selected 1.123
preserve translation in resubmit

Revision 1.50 - (view) (download) (annotate) - [select for diffs]
Wed Nov 24 19:28:29 2004 UTC (15 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.49: +16 -1 lines
Diff to previous 1.49 , to selected 1.123
add number subs to sim display

Revision 1.49 - (view) (download) (annotate) - [select for diffs]
Wed Nov 17 21:59:19 2004 UTC (15 years, 4 months ago) by redwards
Branch: MAIN
Changes since 1.48: +10 -1 lines
Diff to previous 1.48 , to selected 1.123
Modified protein.cgi so that you can affect chromosomal clustering with the three cgi parameters
fcbound fcsim fccoup (for bound, sim_cutoff and coupling_cutoff). Note that you have to know what
these are and what they do as I didn't provide any interface to change the values, but you can
easily add them to the URL

Revision 1.48 - (view) (download) (annotate) - [select for diffs]
Thu Nov 11 04:25:47 2004 UTC (15 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.47: +34 -11 lines
Diff to previous 1.47 , to selected 1.123
GenDB changes

Revision 1.47 - (view) (download) (annotate) - [select for diffs]
Tue Nov 2 18:57:54 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.46: +8 -2 lines
Diff to previous 1.46 , to selected 1.123
Show the gendb link if the gendb directory has been set up.

Revision 1.46 - (view) (download) (annotate) - [select for diffs]
Wed Oct 27 19:19:19 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.45: +1 -1 lines
Diff to previous 1.45 , to selected 1.123
COmment out linking line for now.

Revision 1.45 - (view) (download) (annotate) - [select for diffs]
Fri Oct 22 20:37:46 2004 UTC (15 years, 5 months ago) by heiko
Branch: MAIN
Changes since 1.44: +3 -0 lines
Diff to previous 1.44 , to selected 1.123
added Link to GenDB

Revision 1.44 - (view) (download) (annotate) - [select for diffs]
Sun Oct 17 16:40:13 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.43: +13 -3 lines
Diff to previous 1.43 , to selected 1.123
added homologs_in_clusters.cgi

Revision 1.43 - (view) (download) (annotate) - [select for diffs]
Fri Sep 24 19:35:58 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.42: +2 -2 lines
Diff to previous 1.42 , to selected 1.123
fix bug in chromosomal_clusters causing lines not aligned on red

Revision 1.42 - (view) (download) (annotate) - [select for diffs]
Wed Sep 22 20:24:20 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.41: +5 -5 lines
Diff to previous 1.41 , to selected 1.123
minor fixes

Revision 1.41 - (view) (download) (annotate) - [select for diffs]
Wed Sep 22 17:25:38 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.40: +17 -3 lines
Diff to previous 1.40 , to selected 1.123
restructured code for presenting chromosomal clusters

Revision 1.40 - (view) (download) (annotate) - [select for diffs]
Mon Sep 20 13:35:25 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.39: +48 -3 lines
Diff to previous 1.39 , to selected 1.123
add some comments to assignment1

Revision 1.39 - (view) (download) (annotate) - [select for diffs]
Fri Sep 17 20:53:05 2004 UTC (15 years, 6 months ago) by golsen
Branch: MAIN
Changes since 1.38: +1 -1 lines
Diff to previous 1.38 , to selected 1.123
Put space in alias list for peg context table so that the alias will wrap in the talbe

Revision 1.38 - (view) (download) (annotate) - [select for diffs]
Mon Sep 13 02:12:21 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.37: +13 -19 lines
Diff to previous 1.37 , to selected 1.123
add attributes as key-value pairs attached to fids

Revision 1.37 - (view) (download) (annotate) - [select for diffs]
Mon Aug 23 21:46:44 2004 UTC (15 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.36: +13 -2 lines
Diff to previous 1.36 , to selected 1.123
Added javascript buttons for check all/none
Added color for annotations that are not the same as the primary annotations

Revision 1.36 - (view) (download) (annotate) - [select for diffs]
Thu Aug 19 23:53:17 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.35: +18 -11 lines
Diff to previous 1.35 , to selected 1.123
in protein.cgi, show a reasonable message if the ID is not real

Revision 1.35 - (view) (download) (annotate) - [select for diffs]
Sat Aug 14 13:15:49 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.34: +77 -1 lines
Diff to previous 1.34 , to selected 1.123
add commentary to displayed regions in protein.cgi

Revision 1.34 - (view) (download) (annotate) - [select for diffs]
Sun Aug 8 05:25:31 2004 UTC (15 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.33: +62 -23 lines
Diff to previous 1.33 , to selected 1.123
Add "previous PEG" and "next PEG" buttons to similarities; and minor interface enhancements

Revision 1.33 - (view) (download) (annotate) - [select for diffs]
Sat Aug 7 17:55:16 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.32: +1 -1 lines
Diff to previous 1.32 , to selected 1.123
set RefSeq links

Revision 1.32 - (view) (download) (annotate) - [select for diffs]
Mon Aug 2 20:02:29 2004 UTC (15 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.31: +17 -3 lines
Diff to previous 1.31 , to selected 1.123
Colorize organisms by domain in similarities list.  Changes protein.cgi and FIG.pm

Revision 1.31 - (view) (download) (annotate) - [select for diffs]
Thu Jul 22 15:43:53 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.30: +11 -3 lines
Diff to previous 1.30 , to selected 1.123
make multiple columns for links

Revision 1.30 - (view) (download) (annotate) - [select for diffs]
Tue Jul 20 20:59:37 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.29: +5 -4 lines
Diff to previous 1.29 , to selected 1.123
add %identity to similarities and fix a bug in extract_genomes

Revision 1.29 - (view) (download) (annotate) - [select for diffs]
Tue Jun 8 16:08:55 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.28: +5 -1 lines
Diff to previous 1.28 , to selected 1.123
fix very ugly bug in assignments from protein.cgi

Revision 1.28 - (view) (download) (annotate) - [select for diffs]
Tue Jun 1 20:22:35 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.27: +24 -15 lines
Diff to previous 1.27 , to selected 1.123
add links to subsystems

Revision 1.27 - (view) (download) (annotate) - [select for diffs]
Tue May 18 12:50:43 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.26: +1 -1 lines
Diff to previous 1.26 , to selected 1.123
put contig name on context table

Revision 1.26 - (view) (download) (annotate) - [select for diffs]
Mon May 17 09:22:50 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.25: +6 -1 lines
Diff to previous 1.25 , to selected 1.123
support addition of links to pegs

Revision 1.25 - (view) (download) (annotate) - [select for diffs]
Fri May 14 18:06:51 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.24: +11 -2 lines
Diff to previous 1.24 , to selected 1.123
fixed up links

Revision 1.24 - (view) (download) (annotate) - [select for diffs]
Tue May 4 14:43:01 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.23: +2 -2 lines
Diff to previous 1.23 , to selected 1.123
require score of 2 for coupling

Revision 1.23 - (view) (download) (annotate) - [select for diffs]
Mon May 3 17:04:11 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.22: +22 -0 lines
Diff to previous 1.22 , to selected 1.123
fixes to links in HTML.pm, code to sync systems after an update, and fixes to index.cgi and protein.cgi

Revision 1.22 - (view) (download) (annotate) - [select for diffs]
Fri Apr 23 21:49:03 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.21: +3 -1 lines
Diff to previous 1.21 , to selected 1.123
fixes to index.cgi to blast against all complete

Revision 1.21 - (view) (download) (annotate) - [select for diffs]
Wed Apr 7 21:24:25 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.20: +2 -2 lines
Diff to previous 1.20 , to selected 1.123
set looser bounds for computing coupling evidence

Revision 1.20 - (view) (download) (annotate) - [select for diffs]
Fri Apr 2 18:02:20 2004 UTC (16 years ago) by overbeek
Branch: MAIN
Changes since 1.19: +1 -1 lines
Diff to previous 1.19 , to selected 1.123
add a new version of the spreadsheet software

Revision 1.19 - (view) (download) (annotate) - [select for diffs]
Sun Mar 21 02:20:55 2004 UTC (16 years ago) by golsen
Branch: MAIN
Changes since 1.18: +11 -0 lines
Diff to previous 1.18 , to selected 1.123
Add HTML structuring tags in HTML.pm; Add titles to some pages in index.cgi and protein.cgi; Pretty-up the HTML produced for tables (add newlines and indents)

Revision 1.18 - (view) (download) (annotate) - [select for diffs]
Sat Mar 20 02:10:23 2004 UTC (16 years ago) by golsen
Branch: MAIN
Changes since 1.17: +206 -135 lines
Diff to previous 1.17 , to selected 1.123
Sticky just_fig checkbox; simplify print_similarities parameter gathering; minor sims GUI changes; redo sim table drawing; colorize sim regions; hide aliases option

Revision 1.17 - (view) (download) (annotate) - [select for diffs]
Fri Mar 19 18:45:37 2004 UTC (16 years ago) by overbeek
Branch: MAIN
Changes since 1.16: +4 -0 lines
Diff to previous 1.16 , to selected 1.123
fixes to coupling and protein.cgi

Revision 1.16 - (view) (download) (annotate) - [select for diffs]
Fri Mar 5 22:17:16 2004 UTC (16 years ago) by overbeek
Branch: MAIN
Changes since 1.15: +14 -0 lines
Diff to previous 1.15 , to selected 1.123
support gi and NP numbers for access to fig IDs

Revision 1.15 - (view) (download) (annotate) - [select for diffs]
Wed Mar 3 14:56:43 2004 UTC (16 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.14: +32 -2 lines
Diff to previous 1.14 , to selected 1.123
add merged annotations

Revision 1.14 - (view) (download) (annotate) - [select for diffs]
Mon Feb 23 23:03:59 2004 UTC (16 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.13: +4 -1 lines
Diff to previous 1.13 , to selected 1.123
allow just fig ids

Revision 1.13 - (view) (download) (annotate) - [select for diffs]
Mon Feb 23 21:04:27 2004 UTC (16 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.12: +1 -1 lines
Diff to previous 1.12 , to selected 1.123
fix gene order on compare regions

Revision 1.12 - (view) (download) (annotate) - [select for diffs]
Tue Feb 17 22:23:36 2004 UTC (16 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.11: +7 -2 lines
Diff to previous 1.11 , to selected 1.123
preserve translation through similarities

Revision 1.11 - (view) (download) (annotate) - [select for diffs]
Sun Feb 15 17:12:54 2004 UTC (16 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.10: +186 -104 lines
Diff to previous 1.10 , to selected 1.123
added Gary Olsen changes

Revision 1.10 - (view) (download) (annotate) - [select for diffs]
Sat Feb 7 17:41:30 2004 UTC (16 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.9: +13 -5 lines
Diff to previous 1.9 , to selected 1.123
make fc show up without refresh

Revision 1.9 - (view) (download) (annotate) - [select for diffs]
Sat Jan 31 17:06:07 2004 UTC (16 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +1 -1 lines
Diff to previous 1.8 , to selected 1.123
fix formatting annotations

Revision 1.8 - (view) (download) (annotate) - [select for diffs]
Tue Jan 6 18:22:18 2004 UTC (16 years, 2 months ago) by efrank
Branch: MAIN
Changes since 1.7: +1 -0 lines
Diff to previous 1.7 , to selected 1.123
try to fix overrides on radio

Revision 1.7 - (view) (download) (annotate) - [select for diffs]
Tue Jan 6 18:14:48 2004 UTC (16 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +2 -2 lines
Diff to previous 1.6 , to selected 1.123
fix stick behavior for checked sims

Revision 1.6 - (view) (download) (annotate) - [select for diffs]
Mon Jan 5 12:26:58 2004 UTC (16 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +1 -1 lines
Diff to previous 1.5 , to selected 1.123
minor bugs

Revision 1.5 - (view) (download) (annotate) - [select for diffs]
Mon Dec 29 02:22:37 2003 UTC (16 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.4: +4 -4 lines
Diff to previous 1.4 , to selected 1.123
numerous performance issues

Revision 1.4 - (view) (download) (annotate) - [select for diffs]
Tue Dec 16 16:59:42 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
Changes since 1.3: +0 -14 lines
Diff to previous 1.3 , to selected 1.123
Removed stray tool_hdr content that got copied in here

Revision 1.3 - (view) (download) (annotate) - [select for diffs]
Sat Dec 6 01:35:57 2003 UTC (16 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.2: +1 -1 lines
Diff to previous 1.2 , to selected 1.123
get rid of duplicate in comparing regions

Revision 1.2 - (view) (download) (annotate) - [select for diffs]
Wed Dec 3 21:24:31 2003 UTC (16 years, 4 months ago) by overbeek
Branch: MAIN
CVS Tags: delong-01, delong-02
Changes since 1.1: +285 -1 lines
Diff to previous 1.1 , to selected 1.123
*** empty log message ***

Revision 1.1 - (view) (download) (annotate) - [select for diffs]
Mon Dec 1 16:57:09 2003 UTC (16 years, 4 months ago) by efrank
Branch: MAIN
Branch point for: initial
Diff to selected 1.123
Initial revision

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