[Bio] / FigWebServices / subsys.cgi Repository:
ViewVC logotype

Log of /FigWebServices/subsys.cgi

Parent Directory Parent Directory


Links to HEAD: (view) (download) (annotate)
Sticky Tag:

Revision 1.218 - (view) (download) (annotate) - [select for diffs]
Mon May 6 23:02:50 2013 UTC (6 years, 6 months ago) by redwards
Branch: MAIN
CVS Tags: HEAD, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.217: +14 -6 lines
Diff to previous 1.217
adding a column for the number of genomes associated with each role

Revision 1.217 - (view) (download) (annotate) - [select for diffs]
Fri May 3 23:09:55 2013 UTC (6 years, 6 months ago) by redwards
Branch: MAIN
Changes since 1.216: +17 -2 lines
Diff to previous 1.216
adding a set variants box

Revision 1.216 - (view) (download) (annotate) - [select for diffs]
Fri Jan 4 19:16:51 2013 UTC (6 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.215: +23 -5 lines
Diff to previous 1.215
change the globals to use "our" instead of "my" to support the plack-cgi compilation.

Revision 1.215 - (view) (download) (annotate) - [select for diffs]
Thu Nov 13 21:58:38 2008 UTC (11 years ago) by dejongh
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_dev_08022011, mgrast_dev_08112011, mgrast_dev_10262011, mgrast_dev_12152011, 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_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
Changes since 1.214: +2 -7 lines
Diff to previous 1.214
get the kegg map names from the database

Revision 1.214 - (view) (download) (annotate) - [select for diffs]
Wed Apr 2 19:36:44 2008 UTC (11 years, 7 months ago) by overbeek
Branch: MAIN
CVS Tags: 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, rast_2008_0924, 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, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_rel_2008_10_09, rast_rel_2008_10_29, rast_release_2008_09_29
Changes since 1.213: +1 -1 lines
Diff to previous 1.213
allow non-numeric variant codes

Revision 1.213 - (view) (download) (annotate) - [select for diffs]
Mon Feb 11 17:35:24 2008 UTC (11 years, 9 months ago) by bartels
Branch: MAIN
Changes since 1.212: +8 -2 lines
Diff to previous 1.212
removed typing error

Revision 1.212 - (view) (download) (annotate) - [select for diffs]
Tue Jan 29 20:55:54 2008 UTC (11 years, 9 months ago) by bartels
Branch: MAIN
Changes since 1.211: +26 -2 lines
Diff to previous 1.211
(hopefully) solved the description / notes issue

Revision 1.211 - (view) (download) (annotate) - [select for diffs]
Fri Nov 2 19:13:21 2007 UTC (12 years ago) by dejongh
Branch: MAIN
Changes since 1.210: +27 -31 lines
Diff to previous 1.210
Hope College updates

Revision 1.210 - (view) (download) (annotate) - [select for diffs]
Mon Sep 10 21:42:49 2007 UTC (12 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.209: +2 -1 lines
Diff to previous 1.209
move scenario data in subsys.cgi

Revision 1.209 - (view) (download) (annotate) - [select for diffs]
Tue Aug 21 13:12:23 2007 UTC (12 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.208: +1 -1 lines
Diff to previous 1.208
add spaces after seqs when displayed from subsys.cgi

Revision 1.208 - (view) (download) (annotate) - [select for diffs]
Mon Aug 20 12:38:20 2007 UTC (12 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.207: +3 -1 lines
Diff to previous 1.207
add org and func on displayed seqs in col of subsystem

Revision 1.207 - (view) (download) (annotate) - [select for diffs]
Fri May 18 15:18:48 2007 UTC (12 years, 5 months ago) by dejongh
Branch: MAIN
Changes since 1.206: +5 -3 lines
Diff to previous 1.206
Edit Role Reactions instead of Hope Reactions

Revision 1.206 - (view) (download) (annotate) - [select for diffs]
Tue May 15 21:13:53 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.205: +450 -16 lines
Diff to previous 1.205
Hope College  modifications.

Revision 1.205 - (view) (download) (annotate) - [select for diffs]
Tue May 1 20:15:14 2007 UTC (12 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.204: +2 -2 lines
Diff to previous 1.204
fix problem of users being set to master:

Revision 1.204 - (view) (download) (annotate) - [select for diffs]
Tue Mar 20 20:17:52 2007 UTC (12 years, 7 months ago) by hwang
Branch: MAIN
Changes since 1.203: +4 -1 lines
Diff to previous 1.203
Added a link to display_subsys.cgi. display_subsys.cgi has the precomputed literature links

Revision 1.203 - (view) (download) (annotate) - [select for diffs]
Fri Feb 16 16:48:51 2007 UTC (12 years, 8 months ago) by paarmann
Branch: MAIN
Changes since 1.202: +7 -1 lines
Diff to previous 1.202
added support for new diagrams

Revision 1.202 - (view) (download) (annotate) - [select for diffs]
Fri Feb 9 16:44:59 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.201: +1 -1 lines
Diff to previous 1.201
fix small bug in expanding alignments in subsys.cgi

Revision 1.201 - (view) (download) (annotate) - [select for diffs]
Fri Feb 9 15:37:48 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.200: +1 -1 lines
Diff to previous 1.200
fix small bug in expanding alignments in subsys.cgi

Revision 1.200 - (view) (download) (annotate) - [select for diffs]
Fri Feb 9 15:24:41 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.199: +5 -5 lines
Diff to previous 1.199
fix small bug in expanding alignments in subsys.cgi

Revision 1.199 - (view) (download) (annotate) - [select for diffs]
Fri Feb 9 03:50:05 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.198: +11 -1 lines
Diff to previous 1.198
make connections tighter in forming alignments

Revision 1.198 - (view) (download) (annotate) - [select for diffs]
Wed Feb 7 00:28:34 2007 UTC (12 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.197: +1 -0 lines
Diff to previous 1.197
adding Ross help on making trees

Revision 1.197 - (view) (download) (annotate) - [select for diffs]
Mon Feb 5 23:34:46 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.196: +12 -2 lines
Diff to previous 1.196
fixes to checking subsystems

Revision 1.196 - (view) (download) (annotate) - [select for diffs]
Wed Jan 24 05:44:21 2007 UTC (12 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.195: +1 -0 lines
Diff to previous 1.195
adding button for cyanos or plants

Revision 1.195 - (view) (download) (annotate) - [select for diffs]
Fri Jan 19 17:12:10 2007 UTC (12 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.194: +7 -4 lines
Diff to previous 1.194
add URI escaping

Revision 1.194 - (view) (download) (annotate) - [select for diffs]
Tue Jan 9 21:38:22 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.193: +11 -1 lines
Diff to previous 1.193
fixes to checking in check_subsys.cgi and subsys.cgi

Revision 1.193 - (view) (download) (annotate) - [select for diffs]
Tue Jan 9 21:18:14 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.192: +1 -1 lines
Diff to previous 1.192
handle parens in file names in subsys.cgi check_subsys.cgi

Revision 1.192 - (view) (download) (annotate) - [select for diffs]
Tue Jan 9 02:21:03 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.191: +7 -0 lines
Diff to previous 1.191
add subsystem checking summaries

Revision 1.191 - (view) (download) (annotate) - [select for diffs]
Tue Jan 2 04:03:20 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.190: +1 -1 lines
Diff to previous 1.190
more fixes on counting left-out PEGs

Revision 1.190 - (view) (download) (annotate) - [select for diffs]
Tue Jan 2 03:47:47 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.189: +13 -1 lines
Diff to previous 1.189
fix bug in counting pegs left out of subsystems

Revision 1.189 - (view) (download) (annotate) - [select for diffs]
Mon Jan 1 21:45:20 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.188: +4 -13 lines
Diff to previous 1.188
minor alterations to subsystem checking

Revision 1.188 - (view) (download) (annotate) - [select for diffs]
Mon Jan 1 03:34:34 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.187: +11 -7 lines
Diff to previous 1.187
fix in ordering output for checks

Revision 1.187 - (view) (download) (annotate) - [select for diffs]
Mon Jan 1 01:18:02 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.186: +19 -4 lines
Diff to previous 1.186
fixes to checking subsystems

Revision 1.186 - (view) (download) (annotate) - [select for diffs]
Sun Dec 31 23:51:58 2006 UTC (12 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.185: +122 -40 lines
Diff to previous 1.185
Some changes in how organism names and domains are looked.  Some changes
in how peg attribut keys are compiled, filtered, sorted, etc.  Some timing
code, which is turned off.  Some code clean up.

Revision 1.185 - (view) (download) (annotate) - [select for diffs]
Sun Dec 31 23:30:44 2006 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.184: +43 -19 lines
Diff to previous 1.184
initial rewrite of subsystem checking stuff

Revision 1.184 - (view) (download) (annotate) - [select for diffs]
Fri Dec 29 19:18:37 2006 UTC (12 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.183: +112 -22 lines
Diff to previous 1.183
Extensive modifications to Picker for adding genomes.

Primary goal was adding phylogenetic seletion to the picker list.
This required clean up of some exising code, including the way domain
labels are added to the organism names (needed to make Environmental
different from Eukaryota).  Environmental is 'M' for Metagenomic.

Made alphabetic and phylogenetic list display order case insensitive.

Also led to changes in compute_genome_counts to handle plasmids and
remove the root node from taxonomies where it is present.

Revision 1.183 - (view) (download) (annotate) - [select for diffs]
Wed Dec 20 16:43:05 2006 UTC (12 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.182: +41 -42 lines
Diff to previous 1.182
Make Phylogeny the default subsystem spreadsheet sort order.

Revision 1.182 - (view) (download) (annotate) - [select for diffs]
Mon Dec 18 02:24:07 2006 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.181: +5 -7 lines
Diff to previous 1.181
fix preservation of subsets with deleted/added roles

Revision 1.181 - (view) (download) (annotate) - [select for diffs]
Thu Dec 14 17:05:51 2006 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.180: +1 -1 lines
Diff to previous 1.180
sort orgs for locking in subsys.cgi

Revision 1.180 - (view) (download) (annotate) - [select for diffs]
Sun Dec 10 02:36:59 2006 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.179: +69 -1 lines
Diff to previous 1.179
implement lock/unlock

Revision 1.179 - (view) (download) (annotate) - [select for diffs]
Mon Oct 30 23:29:38 2006 UTC (13 years ago) by redwards
Branch: MAIN
Changes since 1.178: +4 -0 lines
Diff to previous 1.178
fixing clustering so that clusters are only colored if they occupy > 1 role

Revision 1.178 - (view) (download) (annotate) - [select for diffs]
Fri Oct 13 19:33:54 2006 UTC (13 years, 1 month ago) by mkubal
Branch: MAIN
Changes since 1.177: +9 -10 lines
Diff to previous 1.177
coloring ma data on diagram

Revision 1.177 - (view) (download) (annotate) - [select for diffs]
Wed Oct 11 18:19:06 2006 UTC (13 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.176: +2 -1 lines
Diff to previous 1.176
Adding tools to handle essentiality data for Sveta

Revision 1.176 - (view) (download) (annotate) - [select for diffs]
Wed Aug 30 18:39:19 2006 UTC (13 years, 2 months ago) by redwards
Branch: MAIN
Changes since 1.175: +16 -19 lines
Diff to previous 1.175
Adding allow automatic update buttons

Revision 1.175 - (view) (download) (annotate) - [select for diffs]
Sat Aug 19 22:29:15 2006 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.174: +1 -0 lines
Diff to previous 1.174
add potentially_missed_assignments

Revision 1.174 - (view) (download) (annotate) - [select for diffs]
Thu Jul 27 16:00:04 2006 UTC (13 years, 3 months ago) by mkubal
Branch: MAIN
Changes since 1.173: +1 -0 lines
Diff to previous 1.173
sveta's request

Revision 1.173 - (view) (download) (annotate) - [select for diffs]
Thu Jul 27 15:32:23 2006 UTC (13 years, 3 months ago) by mkubal
Branch: MAIN
Changes since 1.172: +14 -4 lines
Diff to previous 1.172
sveta's request

Revision 1.172 - (view) (download) (annotate) - [select for diffs]
Mon Jul 24 19:13:00 2006 UTC (13 years, 3 months ago) by mkubal
Branch: MAIN
Changes since 1.171: +26 -22 lines
Diff to previous 1.171
latest with coloring diagrams'

Revision 1.171 - (view) (download) (annotate) - [select for diffs]
Sun Jul 23 05:17:14 2006 UTC (13 years, 3 months ago) by mkubal
Branch: MAIN
Changes since 1.170: +13 -7 lines
Diff to previous 1.170
latest

Revision 1.170 - (view) (download) (annotate) - [select for diffs]
Sat Jul 22 16:53:59 2006 UTC (13 years, 3 months ago) by mkubal
Branch: MAIN
Changes since 1.169: +4 -2 lines
Diff to previous 1.169
shade diagrams with multiple colors

Revision 1.169 - (view) (download) (annotate) - [select for diffs]
Sat Jul 22 15:43:27 2006 UTC (13 years, 3 months ago) by mkubal
Branch: MAIN
Changes since 1.168: +120 -27 lines
Diff to previous 1.168
shade diagrams with multiple colors

Revision 1.168 - (view) (download) (annotate) - [select for diffs]
Fri Jul 21 14:18:17 2006 UTC (13 years, 3 months ago) by mkubal
Branch: MAIN
Changes since 1.167: +35 -12 lines
Diff to previous 1.167
box more than one value on diagrams

Revision 1.167 - (view) (download) (annotate) - [select for diffs]
Tue Jul 18 16:52:36 2006 UTC (13 years, 3 months ago) by mkubal
Branch: MAIN
Changes since 1.166: +5 -5 lines
Diff to previous 1.166
color diagram improvements

Revision 1.166 - (view) (download) (annotate) - [select for diffs]
Tue Jul 18 16:09:30 2006 UTC (13 years, 3 months ago) by mkubal
Branch: MAIN
Changes since 1.165: +21 -6 lines
Diff to previous 1.165
color diagram improvements

Revision 1.165 - (view) (download) (annotate) - [select for diffs]
Mon Jul 17 19:50:08 2006 UTC (13 years, 3 months ago) by mkubal
Branch: MAIN
Changes since 1.164: +186 -55 lines
Diff to previous 1.164
added coloring diagrams by attribute value

Revision 1.164 - (view) (download) (annotate) - [select for diffs]
Sat Jul 1 21:15:26 2006 UTC (13 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.163: +3 -2 lines
Diff to previous 1.163
RAE: Adding BRC flags

Revision 1.163 - (view) (download) (annotate) - [select for diffs]
Mon Jun 19 21:19:22 2006 UTC (13 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.162: +8 -11 lines
Diff to previous 1.162
RAE: Simplifying making excel tables

Revision 1.162 - (view) (download) (annotate) - [select for diffs]
Mon Jun 5 19:42:57 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.161: +3 -3 lines
Diff to previous 1.161
RAE: case insensitive sorting of subsystem list

Revision 1.161 - (view) (download) (annotate) - [select for diffs]
Thu May 25 05:01:52 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.160: +3 -2 lines
Diff to previous 1.160
RAE: Correcting notes wrapping

Revision 1.160 - (view) (download) (annotate) - [select for diffs]
Wed May 17 16:07:55 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.159: +8 -1 lines
Diff to previous 1.159
RAE: Fixing sort by pattern

Revision 1.159 - (view) (download) (annotate) - [select for diffs]
Wed May 10 15:47:57 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.158: +1 -1 lines
Diff to previous 1.158
RAE: adding new excel functions

Revision 1.158 - (view) (download) (annotate) - [select for diffs]
Mon May 8 02:01:36 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.157: +26 -4 lines
Diff to previous 1.157
RAE: Adding a new display limit button

Revision 1.157 - (view) (download) (annotate) - [select for diffs]
Sun May 7 14:18:43 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.156: +18 -2 lines
Diff to previous 1.156
add last modified date on subsys editing

Revision 1.156 - (view) (download) (annotate) - [select for diffs]
Thu Apr 27 16:24:19 2006 UTC (13 years, 6 months ago) by mkubal
Branch: MAIN
Changes since 1.155: +118 -1 lines
Diff to previous 1.155
painting attributes on diagrams

Revision 1.155 - (view) (download) (annotate) - [select for diffs]
Thu Apr 13 01:41:06 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.154: +2 -2 lines
Diff to previous 1.154
pass cgi to seqs_to_align in subsys.cgi

Revision 1.154 - (view) (download) (annotate) - [select for diffs]
Wed Apr 12 14:44:26 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.153: +14 -4 lines
Diff to previous 1.153
handle master: in subsys.cgi

Revision 1.153 - (view) (download) (annotate) - [select for diffs]
Thu Apr 6 23:28:13 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.152: +9 -3 lines
Diff to previous 1.152
do not show -1 variant sequences in subsys.cgi, unless requested

Revision 1.152 - (view) (download) (annotate) - [select for diffs]
Mon Apr 3 18:48:15 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.151: +2 -0 lines
Diff to previous 1.151
RAE: Adding functional coupling paper to list of projects

Revision 1.151 - (view) (download) (annotate) - [select for diffs]
Thu Mar 23 22:35:01 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.150: +1 -3 lines
Diff to previous 1.150
RAE: Debugging a weird ss error on yersinia that I cant replicate elsewhere

Revision 1.150 - (view) (download) (annotate) - [select for diffs]
Thu Mar 23 22:27:14 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.149: +0 -1 lines
Diff to previous 1.149
RAE: Debugging a weird ss error on yersinia that I cant replicate elsewhere

Revision 1.149 - (view) (download) (annotate) - [select for diffs]
Thu Mar 23 22:13:52 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.148: +2 -1 lines
Diff to previous 1.148
RAE: Debugging a weird ss error on yersinia that I cant replicate elsewhere

Revision 1.148 - (view) (download) (annotate) - [select for diffs]
Mon Mar 20 02:01:08 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.147: +14 -2 lines
Diff to previous 1.147
RAE: Adding a link into set variants from subsys.cgi and back

Revision 1.147 - (view) (download) (annotate) - [select for diffs]
Sun Mar 19 21:30:56 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.146: +37 -12 lines
Diff to previous 1.146
RAE: Initial release of setting.cgi and format changes on subsys.cgi

Revision 1.146 - (view) (download) (annotate) - [select for diffs]
Fri Mar 10 23:30:51 2006 UTC (13 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.145: +1 -1 lines
Diff to previous 1.145
RAE: inactivating the cat /tmp/ssa_parms line

Revision 1.145 - (view) (download) (annotate) - [select for diffs]
Fri Mar 10 17:04:08 2006 UTC (13 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.144: +30 -27 lines
Diff to previous 1.144
fixes to processing subsets of columns in subsys.cgi

Revision 1.144 - (view) (download) (annotate) - [select for diffs]
Sat Feb 11 13:13:49 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.143: +1 -34 lines
Diff to previous 1.143
fix subsys.cgi to use compute_clusters in FIG.pm

Revision 1.143 - (view) (download) (annotate) - [select for diffs]
Wed Jan 25 16:44:56 2006 UTC (13 years, 9 months ago) by olson
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.142: +2 -1 lines
Diff to previous 1.142
add explicit path setting

Revision 1.142 - (view) (download) (annotate) - [select for diffs]
Sun Jan 22 18:48:00 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.141: +1 -1 lines
Diff to previous 1.141
RAE: Minor bug fix

Revision 1.141 - (view) (download) (annotate) - [select for diffs]
Wed Jan 18 17:47:45 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.140: +1 -1 lines
Diff to previous 1.140
RAE: Removing a diagnostic report

Revision 1.140 - (view) (download) (annotate) - [select for diffs]
Wed Jan 18 17:41:13 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.139: +23 -2 lines
Diff to previous 1.139
RAE: Adding NMPDR checkbox to subsys.cgi

Revision 1.139 - (view) (download) (annotate) - [select for diffs]
Wed Jan 18 17:14:07 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.138: +105 -76 lines
Diff to previous 1.138
RAE: Adding NMPDR checkbox to subsys.cgi

Revision 1.138 - (view) (download) (annotate) - [select for diffs]
Fri Jan 13 06:22:12 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.137: +3 -3 lines
Diff to previous 1.137
RAE: Correcting labels for Sveta

Revision 1.137 - (view) (download) (annotate) - [select for diffs]
Tue Jan 10 20:43:18 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.136: +1 -1 lines
Diff to previous 1.136
RAE: OOps. didnt test this properly

Revision 1.136 - (view) (download) (annotate) - [select for diffs]
Tue Jan 10 20:35:46 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.135: +47 -1 lines
Diff to previous 1.135
RAE: Adding buttons for groups of organisms

Revision 1.135 - (view) (download) (annotate) - [select for diffs]
Sun Jan 8 21:34:55 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.134: +13 -1 lines
Diff to previous 1.134
RAE: using style rather than tables to display multiple pegs. Much better for rendering

Revision 1.134 - (view) (download) (annotate) - [select for diffs]
Thu Jan 5 01:15:50 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.133: +4 -1 lines
Diff to previous 1.133
Adding Svetas selected genomes

Revision 1.133 - (view) (download) (annotate) - [select for diffs]
Mon Jan 2 19:12:18 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.132: +4 -4 lines
Diff to previous 1.132
fix to extend alignment in subsys.cgi

Revision 1.132 - (view) (download) (annotate) - [select for diffs]
Fri Dec 30 23:20:24 2005 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.131: +1 -1 lines
Diff to previous 1.131
simple fix to subsys.cgi for expanding alignments

Revision 1.131 - (view) (download) (annotate) - [select for diffs]
Fri Dec 30 23:05:17 2005 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.130: +1 -1 lines
Diff to previous 1.130
fix bug in realigning in subsys.cgi

Revision 1.130 - (view) (download) (annotate) - [select for diffs]
Mon Dec 5 19:12:12 2005 UTC (13 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.129: +17 -0 lines
Diff to previous 1.129
add license words

Revision 1.129 - (view) (download) (annotate) - [select for diffs]
Thu Nov 24 02:12:41 2005 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.128: +5 -7 lines
Diff to previous 1.128
updating subsys.cgi so that it works with attributes again. Quickly, this time

Revision 1.128 - (view) (download) (annotate) - [select for diffs]
Wed Nov 23 17:50:13 2005 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.127: +7 -29 lines
Diff to previous 1.127
correcting bug on links on old page

Revision 1.127 - (view) (download) (annotate) - [select for diffs]
Wed Nov 2 21:44:23 2005 UTC (14 years ago) by parrello
Branch: MAIN
CVS Tags: caBIG-00-00-00
Changes since 1.126: +1787 -1787 lines
Diff to previous 1.126
Converted tabs to spaces.

Revision 1.126 - (view) (download) (annotate) - [select for diffs]
Tue Oct 25 02:01:47 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.125: +3 -2 lines
Diff to previous 1.125
removing attributes look ups

Revision 1.125 - (view) (download) (annotate) - [select for diffs]
Mon Oct 24 21:48:58 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.124: +1 -1 lines
Diff to previous 1.124
Fix a relative link bug.

Revision 1.124 - (view) (download) (annotate) - [select for diffs]
Mon Oct 24 02:39:45 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.123: +3 -3 lines
Diff to previous 1.123
fix test for valid subsystem

Revision 1.123 - (view) (download) (annotate) - [select for diffs]
Sun Oct 23 04:27:37 2005 UTC (14 years ago) by golsen
Branch: MAIN
Changes since 1.122: +14 -13 lines
Diff to previous 1.122
Convert display order selection to pop-up menu (save space) and give it
a label (who knows when that was lost).

Revision 1.122 - (view) (download) (annotate) - [select for diffs]
Mon Oct 3 20:10:12 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.121: +2 -2 lines
Diff to previous 1.121
adding a couple of new lines here and there

Revision 1.121 - (view) (download) (annotate) - [select for diffs]
Mon Oct 3 20:05:34 2005 UTC (14 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.120: +86 -54 lines
Diff to previous 1.120
Initial release of cookies code, including myseed

Revision 1.120 - (view) (download) (annotate) - [select for diffs]
Thu Sep 15 18:47:59 2005 UTC (14 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.119: +1 -0 lines
Diff to previous 1.119
Careful cleanup of subsystem indexing. Patched a bunch of spots where needed updates didn't happen.

Add variant code to subsystem index.

Revision 1.119 - (view) (download) (annotate) - [select for diffs]
Wed Sep 14 22:16:25 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.118: +10 -12 lines
Diff to previous 1.118
Correcting display of classifications

Revision 1.118 - (view) (download) (annotate) - [select for diffs]
Wed Sep 14 20:04:19 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.117: +0 -1 lines
Diff to previous 1.117
Correcting display of classifications

Revision 1.117 - (view) (download) (annotate) - [select for diffs]
Wed Sep 14 19:20:28 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.116: +17 -11 lines
Diff to previous 1.116
removing popup menus

Revision 1.116 - (view) (download) (annotate) - [select for diffs]
Sun Sep 11 16:34:41 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.115: +1 -1 lines
Diff to previous 1.115
add functiontion to FIG.pm to get active subsystems for a genome

Revision 1.115 - (view) (download) (annotate) - [select for diffs]
Tue Sep 6 21:14:10 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.114: +27 -8 lines
Diff to previous 1.114
Set defaults for non-curator better.

Revision 1.114 - (view) (download) (annotate) - [select for diffs]
Mon Aug 22 05:43:02 2005 UTC (14 years, 2 months ago) by redwards
Branch: MAIN
Changes since 1.113: +26 -4 lines
Diff to previous 1.113
Adding menus to subsys.cgi

Revision 1.113 - (view) (download) (annotate) - [select for diffs]
Fri Aug 19 15:47:54 2005 UTC (14 years, 2 months ago) by redwards
Branch: MAIN
Changes since 1.112: +14 -0 lines
Diff to previous 1.112
adding rss feeds for subsystem updates

Revision 1.112 - (view) (download) (annotate) - [select for diffs]
Thu Aug 18 19:11:29 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.111: +25 -11 lines
Diff to previous 1.111
checking in the new interface since no one complains hugely!

Revision 1.111 - (view) (download) (annotate) - [select for diffs]
Wed Aug 10 12:03:36 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.110: +11 -2 lines
Diff to previous 1.110
More logging and sanity checks on diagram code.

Revision 1.110 - (view) (download) (annotate) - [select for diffs]
Tue Aug 9 19:04:39 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.109: +1 -1 lines
Diff to previous 1.109
Commit first version of coloring code.

Revision 1.109 - (view) (download) (annotate) - [select for diffs]
Mon Aug 8 21:54:39 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.108: +107 -3 lines
Diff to previous 1.108
More diagram changes.

Add new simple start page.

Revision 1.108 - (view) (download) (annotate) - [select for diffs]
Sat Aug 6 15:30:29 2005 UTC (14 years, 3 months ago) by redwards
Branch: MAIN
Changes since 1.107: +116 -12 lines
Diff to previous 1.107
New interface for subsys.cgi, but it is commented out at the moment

Revision 1.107 - (view) (download) (annotate) - [select for diffs]
Thu Aug 4 22:25:12 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.106: +3 -3 lines
Diff to previous 1.106
fixing help links

Revision 1.106 - (view) (download) (annotate) - [select for diffs]
Thu Aug 4 19:53:23 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.105: +3 -3 lines
Diff to previous 1.105
fixiing subsys.cgi color by ga

Revision 1.105 - (view) (download) (annotate) - [select for diffs]
Wed Aug 3 21:16:40 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.104: +1 -7 lines
Diff to previous 1.104
turn on diagram support.

Revision 1.104 - (view) (download) (annotate) - [select for diffs]
Wed Aug 3 17:44:53 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.103: +121 -1 lines
Diff to previous 1.103
And the display code, protected with an enable_diagrams CGI parameter.

Revision 1.103 - (view) (download) (annotate) - [select for diffs]
Sat Jul 30 20:25:38 2005 UTC (14 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.102: +4 -30 lines
Diff to previous 1.102
Change code to use mouseover function in FIGjs.pm

Revision 1.102 - (view) (download) (annotate) - [select for diffs]
Sat Jul 30 18:05:42 2005 UTC (14 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.101: +30 -3 lines
Diff to previous 1.101
Add quotation mark escaping to roles (and all other fields) in pop-up
Tool tips attached to abbreviations.

This really needs to be looked at in other scripts that use tool tips.
Single quotes need to get a backslash.  Double quotes need HTML char code.

Revision 1.101 - (view) (download) (annotate) - [select for diffs]
Sat Jul 30 13:11:13 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.100: +1 -11 lines
Diff to previous 1.100
put reactions in a separate window

Revision 1.100 - (view) (download) (annotate) - [select for diffs]
Sat Jul 30 13:02:32 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.99: +2 -2 lines
Diff to previous 1.99
fixes to reactions in subsystems

Revision 1.99 - (view) (download) (annotate) - [select for diffs]
Sat Jul 30 12:09:22 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.98: +12 -10 lines
Diff to previous 1.98
always allow reactions for curator

Revision 1.98 - (view) (download) (annotate) - [select for diffs]
Fri Jul 29 20:02:20 2005 UTC (14 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.97: +17 -10 lines
Diff to previous 1.97
Add a tooltip pop-up to the role abbreviations in the table, giving the
role or roles associated with the column.

Revision 1.97 - (view) (download) (annotate) - [select for diffs]
Fri Jul 29 19:31:21 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.96: +54 -26 lines
Diff to previous 1.96
add reactions to subsystems

Revision 1.96 - (view) (download) (annotate) - [select for diffs]
Thu Jul 28 20:50:05 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.95: +38 -9 lines
Diff to previous 1.95
show reactions in subsystems, if they are there

Revision 1.95 - (view) (download) (annotate) - [select for diffs]
Tue Jul 26 04:54:27 2005 UTC (14 years, 3 months ago) by mkubal
Branch: MAIN
Changes since 1.94: +1 -1 lines
Diff to previous 1.94
7-26-05

Revision 1.94 - (view) (download) (annotate) - [select for diffs]
Wed Jul 20 02:05:10 2005 UTC (14 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.93: +33 -24 lines
Diff to previous 1.93
A little further work on the user interface to select roles (this time
for sequences and alignments).

Revision 1.93 - (view) (download) (annotate) - [select for diffs]
Sat Jul 16 00:41:58 2005 UTC (14 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.92: +2 -2 lines
Diff to previous 1.92
Minor layout change for clarification of options.

Revision 1.92 - (view) (download) (annotate) - [select for diffs]
Fri Jul 15 20:14:16 2005 UTC (14 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.91: +1 -1 lines
Diff to previous 1.91
Alphabetize the genome list in subsys.cgi

Revision 1.91 - (view) (download) (annotate) - [select for diffs]
Thu Jul 14 22:20:36 2005 UTC (14 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.90: +64 -29 lines
Diff to previous 1.90
Make some of the parameter entry boxes on the subsystem page into menus
with all of the valid options.

Revision 1.90 - (view) (download) (annotate) - [select for diffs]
Thu Jul 14 07:06:30 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
Changes since 1.89: +3 -3 lines
Diff to previous 1.89
hide -1 variants by default in ss

Revision 1.78.2.3 - (view) (download) (annotate) - [select for diffs]
Tue Jul 12 15:39:01 2005 UTC (14 years, 4 months ago) by olson
Branch: Branch-bobdev_news
CVS Tags: merge-bodev_news-3
Changes since 1.78.2.2: +190 -92 lines
Diff to previous 1.78.2.2 , to branch point 1.78 , to next main 1.218
Merged changes from trunk.

Revision 1.89 - (view) (download) (annotate) - [select for diffs]
Sun Jul 10 02:01:44 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
CVS Tags: merge-trunktag-bodev_news-3
Changes since 1.88: +29 -3 lines
Diff to previous 1.88
added a move field to subsys.cgi

Revision 1.88 - (view) (download) (annotate) - [select for diffs]
Sat Jul 9 21:46:15 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
Changes since 1.87: +58 -39 lines
Diff to previous 1.87
added index subsystems to subsys.cgi

Revision 1.87 - (view) (download) (annotate) - [select for diffs]
Fri Jul 8 21:24:18 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
Changes since 1.86: +1 -1 lines
Diff to previous 1.86
fixing subsys quotes

Revision 1.86 - (view) (download) (annotate) - [select for diffs]
Fri Jul 8 19:17:08 2005 UTC (14 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.85: +12 -5 lines
Diff to previous 1.85
Minor change in "superscript" display in cells.  Should not be a completely
nonredundant list, and actually sorted by number.

Revision 1.85 - (view) (download) (annotate) - [select for diffs]
Fri Jul 8 17:03:52 2005 UTC (14 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.84: +83 -46 lines
Diff to previous 1.84
Modify the subsystems display code so that PEGs within subsystem cells can
be individually colored, when necessary.  Looks complicated, but it is just
placing a small, one-row table into the cell (only when multiple colors are
present).

Introduced some minor code simplification, notably in deciding if an
organism row is to be displayed.

Revision 1.84 - (view) (download) (annotate) - [select for diffs]
Thu Jul 7 16:31:12 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
Changes since 1.83: +12 -3 lines
Diff to previous 1.83
adding labels to subsystem page

Revision 1.83 - (view) (download) (annotate) - [select for diffs]
Fri Jul 1 02:09:16 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
Changes since 1.82: +1 -1 lines
Diff to previous 1.82
Changed proteinfamilies.cgi

Revision 1.78.2.2 - (view) (download) (annotate) - [select for diffs]
Wed Jun 29 16:11:00 2005 UTC (14 years, 4 months ago) by olson
Branch: Branch-bobdev_news
CVS Tags: merge-bobdev_news-2
Changes since 1.78.2.1: +20 -6 lines
Diff to previous 1.78.2.1 , to branch point 1.78
Merge from trunk.

Revision 1.82 - (view) (download) (annotate) - [select for diffs]
Tue Jun 28 17:25:04 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-2
Changes since 1.81: +5 -3 lines
Diff to previous 1.81
commiting FIG.pm::clean_spaces to remove leading, trailing, and extra spaces. Please use it

Revision 1.81 - (view) (download) (annotate) - [select for diffs]
Tue Jun 28 16:29:41 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
Changes since 1.80: +15 -3 lines
Diff to previous 1.80
sorting in subsys.cgi

Revision 1.78.2.1 - (view) (download) (annotate) - [select for diffs]
Mon Jun 27 15:26:45 2005 UTC (14 years, 4 months ago) by olson
Branch: Branch-bobdev_news
CVS Tags: merge-bobdev_news-1
Changes since 1.78: +30 -2 lines
Diff to previous 1.78
Merged from trunk.

Revision 1.80 - (view) (download) (annotate) - [select for diffs]
Mon Jun 20 22:02:11 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-1
Changes since 1.79: +3 -2 lines
Diff to previous 1.79
no check on subsystem, if you are not owner

Revision 1.79 - (view) (download) (annotate) - [select for diffs]
Fri Jun 17 19:38:31 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.78: +28 -1 lines
Diff to previous 1.78
subsys.cgi now does an initial check_subsys.cgi

Revision 1.78 - (view) (download) (annotate) - [select for diffs]
Thu Jun 9 16:58:01 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: Root-bobdev_news
Branch point for: Branch-bobdev_news
Changes since 1.77: +17 -1 lines
Diff to previous 1.77
fix formatting of seqs in subsys.cgi

Revision 1.77 - (view) (download) (annotate) - [select for diffs]
Thu Jun 9 16:33:41 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.76: +60 -10 lines
Diff to previous 1.76
fixes to alignments in subsys.cgi

Revision 1.76 - (view) (download) (annotate) - [select for diffs]
Tue May 10 12:03:39 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.75: +166 -104 lines
Diff to previous 1.75
fixes to using trees under subsystems

Revision 1.75 - (view) (download) (annotate) - [select for diffs]
Thu Apr 28 21:11:11 2005 UTC (14 years, 6 months ago) by golsen
Branch: MAIN
Changes since 1.74: +8 -4 lines
Diff to previous 1.74
Add uri_escape to subsystem names used in links.

Revision 1.74 - (view) (download) (annotate) - [select for diffs]
Tue Apr 26 14:28:41 2005 UTC (14 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.73: +8 -4 lines
Diff to previous 1.73
URI-escape ssa names in links so that subsystems with + in their names can be viewed.

Revision 1.73 - (view) (download) (annotate) - [select for diffs]
Sat Apr 16 22:01:39 2005 UTC (14 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.72: +10 -14 lines
Diff to previous 1.72
Format changed on subsys options form

Revision 1.72 - (view) (download) (annotate) - [select for diffs]
Tue Apr 12 18:18:25 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.71: +3 -3 lines
Diff to previous 1.71
minor fix to subsys.cgi

Revision 1.71 - (view) (download) (annotate) - [select for diffs]
Tue Apr 12 15:34:25 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.70: +3 -1 lines
Diff to previous 1.70
fix to show_missing with matches

Revision 1.70 - (view) (download) (annotate) - [select for diffs]
Mon Apr 11 12:16:45 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.69: +2 -2 lines
Diff to previous 1.69
comment out debugging messages in subsys.cgi

Revision 1.69 - (view) (download) (annotate) - [select for diffs]
Mon Apr 11 06:42:19 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.68: +2 -2 lines
Diff to previous 1.68
minor change to subsys.cgi to debug Svetas problem

Revision 1.68 - (view) (download) (annotate) - [select for diffs]
Mon Apr 11 06:39:13 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.67: +2 -2 lines
Diff to previous 1.67
minor change to subsys.cgi to debug Svetas problem

Revision 1.67 - (view) (download) (annotate) - [select for diffs]
Fri Apr 8 20:22:23 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.66: +2 -2 lines
Diff to previous 1.66
changed tag/value pairs completely. Ooops!

Revision 1.66 - (view) (download) (annotate) - [select for diffs]
Thu Apr 7 19:16:10 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.65: +12 -5 lines
Diff to previous 1.65
many changes to key/value pairs to make them work

Revision 1.65 - (view) (download) (annotate) - [select for diffs]
Thu Apr 7 04:27:01 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.64: +4 -1 lines
Diff to previous 1.64
Removed change ownership from the FIG help pages

Revision 1.64 - (view) (download) (annotate) - [select for diffs]
Wed Apr 6 22:40:40 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.63: +11 -5 lines
Diff to previous 1.63
adding help functions all over the place

Revision 1.63 - (view) (download) (annotate) - [select for diffs]
Wed Apr 6 15:32:09 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.62: +4 -0 lines
Diff to previous 1.62
hide -1 variants in subsys.cgi

Revision 1.62 - (view) (download) (annotate) - [select for diffs]
Wed Apr 6 01:01:22 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.61: +4 -1 lines
Diff to previous 1.61
added change annotation by function to check subsys.cgi

Revision 1.61 - (view) (download) (annotate) - [select for diffs]
Mon Mar 21 20:00:07 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.60: +1 -0 lines
Diff to previous 1.60
Every page deserves a title, even subsystem pages

Revision 1.60 - (view) (download) (annotate) - [select for diffs]
Sat Mar 19 15:00:12 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.59: +1 -1 lines
Diff to previous 1.59
make show_clusters a sticky attribute

Revision 1.59 - (view) (download) (annotate) - [select for diffs]
Sat Mar 12 20:30:39 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.58: +18 -2 lines
Diff to previous 1.58
Changed Subsystems to allow selection of active_subsetR (rows) based on tag/value pairs

Revision 1.58 - (view) (download) (annotate) - [select for diffs]
Fri Mar 11 04:11:30 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.57: +13 -4 lines
Diff to previous 1.57
Making tag/value pairs work

Revision 1.57 - (view) (download) (annotate) - [select for diffs]
Thu Mar 10 23:13:37 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.56: +2 -2 lines
Diff to previous 1.56
fix bad subsystem name

Revision 1.56 - (view) (download) (annotate) - [select for diffs]
Thu Mar 10 20:39:00 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.55: +6 -1 lines
Diff to previous 1.55
fix by_variant and by_pattern sort codes in subsys.cgi

Revision 1.55 - (view) (download) (annotate) - [select for diffs]
Sun Mar 6 15:10:02 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.54: +2 -2 lines
Diff to previous 1.54
disconnect get_attributes until I can talk to Rob

Revision 1.54 - (view) (download) (annotate) - [select for diffs]
Sat Mar 5 04:29:59 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.53: +11 -5 lines
Diff to previous 1.53
added highlight by peg attribute to subsystem

Revision 1.53 - (view) (download) (annotate) - [select for diffs]
Fri Mar 4 23:16:43 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.52: +1 -2 lines
Diff to previous 1.52
tweaks to coloring ss by oa

Revision 1.52 - (view) (download) (annotate) - [select for diffs]
Fri Mar 4 22:37:06 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.51: +89 -30 lines
Diff to previous 1.51
Added color by organism attributes to subsystems page

Revision 1.51 - (view) (download) (annotate) - [select for diffs]
Sat Feb 26 11:01:13 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.50: +9 -24 lines
Diff to previous 1.50
add reset_curator.cgi

Revision 1.50 - (view) (download) (annotate) - [select for diffs]
Fri Feb 25 22:55:20 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.49: +1 -1 lines
Diff to previous 1.49
make list of existing subsystems sorted case insensitively

Revision 1.49 - (view) (download) (annotate) - [select for diffs]
Thu Feb 24 22:02:39 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.48: +4 -0 lines
Diff to previous 1.48
add set_variants.cgi and fixes to Subsystems.pm

Revision 1.48 - (view) (download) (annotate) - [select for diffs]
Mon Feb 21 21:59:27 2005 UTC (14 years, 8 months ago) by mkubal
Branch: MAIN
Changes since 1.47: +36 -14 lines
Diff to previous 1.47
improved

Revision 1.47 - (view) (download) (annotate) - [select for diffs]
Fri Feb 18 18:05:06 2005 UTC (14 years, 8 months ago) by mkubal
Branch: MAIN
Changes since 1.46: +30 -2 lines
Diff to previous 1.46
display genomes by variant

Revision 1.46 - (view) (download) (annotate) - [select for diffs]
Wed Feb 16 18:59:21 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.45: +11 -3 lines
Diff to previous 1.45
highlight subsystems with no genomes attached

Revision 1.45 - (view) (download) (annotate) - [select for diffs]
Tue Feb 15 21:40:29 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.44: +2 -2 lines
Diff to previous 1.44
Use

            my $q = "SELECT subsystem, role FROM subsystem_index WHERE role = ?";
            if (my $relational_db_response = $rdbH->SQL($q, 0, $role))

to do the select, so that DBI can quote the ' that shows up in some role names.

Revision 1.44 - (view) (download) (annotate) - [select for diffs]
Mon Feb 14 21:49:25 2005 UTC (14 years, 9 months ago) by golsen
Branch: MAIN
Changes since 1.43: +30 -4 lines
Diff to previous 1.43
Allow user to see incomplete genomes of addition to a subsystem

Revision 1.43 - (view) (download) (annotate) - [select for diffs]
Mon Feb 14 00:57:27 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.42: +9 -2 lines
Diff to previous 1.42
minor fixes to alignments

Revision 1.42 - (view) (download) (annotate) - [select for diffs]
Sat Feb 12 18:34:46 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.41: +1 -1 lines
Diff to previous 1.41
Minor changes to subsys.cgi dealing with classifications.

Revision 1.41 - (view) (download) (annotate) - [select for diffs]
Sat Feb 12 18:18:14 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.40: +18 -0 lines
Diff to previous 1.40
Moved the subsystem_classification getting/setting into subsys.pm where it belongs, and so I ammended FIG.pm. Also added the boxes on the subsystem page so you can see the classifications.

Revision 1.40 - (view) (download) (annotate) - [select for diffs]
Fri Feb 11 20:33:51 2005 UTC (14 years, 9 months ago) by mkubal
Branch: MAIN
Changes since 1.39: +47 -21 lines
Diff to previous 1.39
faster mwm in ss

Revision 1.39 - (view) (download) (annotate) - [select for diffs]
Thu Feb 10 17:48:01 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.38: +1 -1 lines
Diff to previous 1.38
fix by_variant with external ids

Revision 1.38 - (view) (download) (annotate) - [select for diffs]
Wed Feb 9 20:15:43 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.37: +1 -1 lines
Diff to previous 1.37
put UniProt ids in trees of columns

Revision 1.37 - (view) (download) (annotate) - [select for diffs]
Sat Feb 5 16:05:29 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.36: +1 -1 lines
Diff to previous 1.36
have sort in load_features use FIG/Tmp for sort files

Revision 1.36 - (view) (download) (annotate) - [select for diffs]
Fri Feb 4 21:21:18 2005 UTC (14 years, 9 months ago) by mkubal
Branch: MAIN
Changes since 1.35: +157 -0 lines
Diff to previous 1.35
missing with matches in ss

Revision 1.35 - (view) (download) (annotate) - [select for diffs]
Wed Feb 2 01:07:44 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.34: +1 -0 lines
Diff to previous 1.34
Minor changes to ubsys.cgi  (mainly commenting) and raelib adding tagvalue

Revision 1.34 - (view) (download) (annotate) - [select for diffs]
Mon Jan 31 07:29:39 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.33: +1 -1 lines
Diff to previous 1.33
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 1.33 - (view) (download) (annotate) - [select for diffs]
Sun Jan 30 18:18:46 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.32: +11 -5 lines
Diff to previous 1.32
Enhancements to subsys.cgi coloring based on tag/value pairs

Revision 1.32 - (view) (download) (annotate) - [select for diffs]
Sun Jan 30 17:16:57 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.31: +99 -4 lines
Diff to previous 1.31
Changes to pir.cgi and subsys,cgi to allow linking between. Added a function in
subsys.cgi so that you can color the columns by tag/value pairs

Revision 1.31 - (view) (download) (annotate) - [select for diffs]
Sat Jan 29 06:38:31 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.30: +1 -1 lines
Diff to previous 1.30
Changed width in <pre> text for notes. Note that this should really be a style sheet item

Revision 1.30 - (view) (download) (annotate) - [select for diffs]
Mon Jan 24 02:59:52 2005 UTC (14 years, 9 months ago) by golsen
Branch: MAIN
Changes since 1.29: +1 -1 lines
Diff to previous 1.29
Bug fix on new version of organism adding

Revision 1.29 - (view) (download) (annotate) - [select for diffs]
Sun Jan 23 23:53:16 2005 UTC (14 years, 9 months ago) by golsen
Branch: MAIN
Changes since 1.28: +53 -14 lines
Diff to previous 1.28
More adding order options to Pick Organisms to Extend list

Revision 1.28 - (view) (download) (annotate) - [select for diffs]
Sun Jan 23 17:15:00 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.27: +2 -1 lines
Diff to previous 1.27
add author to display of subsystems

Revision 1.27 - (view) (download) (annotate) - [select for diffs]
Tue Jan 18 18:15:23 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.26: +12 -0 lines
Diff to previous 1.26
fix active subset code in subsys.cgi

Revision 1.26 - (view) (download) (annotate) - [select for diffs]
Wed Jan 5 20:24:14 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.25: +2 -1 lines
Diff to previous 1.25
minor fixes to subsys.cgi and tree_utilities.pm

Revision 1.25 - (view) (download) (annotate) - [select for diffs]
Fri Dec 10 07:04:39 2004 UTC (14 years, 11 months ago) by redwards
Branch: MAIN
Changes since 1.24: +18 -0 lines
Diff to previous 1.24
Changes to subsys.cgi that warn if a subsystem doesn't exist

Revision 1.24 - (view) (download) (annotate) - [select for diffs]
Thu Dec 9 18:26:36 2004 UTC (14 years, 11 months ago) by redwards
Branch: MAIN
Changes since 1.23: +1 -1 lines
Diff to previous 1.23
Very minor change to correct ignore_alt error I made yesterday.

Revision 1.23 - (view) (download) (annotate) - [select for diffs]
Thu Dec 9 06:02:26 2004 UTC (14 years, 11 months ago) by redwards
Branch: MAIN
Changes since 1.22: +2 -2 lines
Diff to previous 1.22
Maintain the state of ignore alternatives

Revision 1.22 - (view) (download) (annotate) - [select for diffs]
Thu Dec 9 06:00:02 2004 UTC (14 years, 11 months ago) by redwards
Branch: MAIN
Changes since 1.21: +62 -0 lines
Diff to previous 1.21
Fixed bugs with "show PEGs in roles that do not match precisely".
Also, added a new function to allow reannotation of an entire column at once.

Revision 1.21 - (view) (download) (annotate) - [select for diffs]
Thu Dec 9 00:53:45 2004 UTC (14 years, 11 months ago) by redwards
Branch: MAIN
Changes since 1.20: +14 -2 lines
Diff to previous 1.20
Fix a bug in subsys.cgi that was messing up "show PEGs in roles that do not match precisely" around line 975

Revision 1.20 - (view) (download) (annotate) - [select for diffs]
Sun Dec 5 16:35:16 2004 UTC (14 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.19: +6 -2 lines
Diff to previous 1.19
add checking for subsystems

Revision 1.19 - (view) (download) (annotate) - [select for diffs]
Tue Nov 16 03:29:35 2004 UTC (14 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.18: +35 -3 lines
Diff to previous 1.18
add assign_using_tree and fix overlays in pinned regions

Revision 1.18 - (view) (download) (annotate) - [select for diffs]
Wed Nov 10 23:28:45 2004 UTC (15 years ago) by olson
Branch: MAIN
Changes since 1.17: +16 -0 lines
Diff to previous 1.17
suport for construct editor.

Revision 1.17 - (view) (download) (annotate) - [select for diffs]
Thu Nov 4 18:27:29 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.16: +37 -1 lines
Diff to previous 1.16
allow external IDs on subsystem displays

Revision 1.16 - (view) (download) (annotate) - [select for diffs]
Wed Nov 3 19:08:19 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.15: +1 -1 lines
Diff to previous 1.15
homologs drawn in on subsys.cgi alignments must be from complete genomes

Revision 1.15 - (view) (download) (annotate) - [select for diffs]
Tue Nov 2 14:45:31 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.14: +1 -1 lines
Diff to previous 1.14
fix bug in subsys.cgi and add Literature to Global

Revision 1.14 - (view) (download) (annotate) - [select for diffs]
Sat Oct 30 23:58:47 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.13: +74 -57 lines
Diff to previous 1.13
handle no user in subsys.cgi properly

Revision 1.13 - (view) (download) (annotate) - [select for diffs]
Wed Oct 27 16:15:28 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.12: +7 -1 lines
Diff to previous 1.12
minor fix to support deletion of genomes from a subsystem

Revision 1.12 - (view) (download) (annotate) - [select for diffs]
Tue Oct 12 13:55:56 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.11: +7 -9 lines
Diff to previous 1.11
fix to notes on subsys.cgi

Revision 1.11 - (view) (download) (annotate) - [select for diffs]
Tue Oct 12 11:56:23 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.10: +4 -21 lines
Diff to previous 1.10
updates to subsys.cgi

Revision 1.10 - (view) (download) (annotate) - [select for diffs]
Mon Oct 11 13:41:14 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.9: +13 -10 lines
Diff to previous 1.9
handle notes properly in subsys.cgi

Revision 1.9 - (view) (download) (annotate) - [select for diffs]
Sun Oct 10 17:13:55 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.8: +83 -73 lines
Diff to previous 1.8
many fixes to subsystems code

Revision 1.8 - (view) (download) (annotate) - [select for diffs]
Tue Sep 28 20:39:39 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.7: +37 -17 lines
Diff to previous 1.7
fix subset and sorting problems in subsys.cgi

Revision 1.7 - (view) (download) (annotate) - [select for diffs]
Thu Sep 23 19:58:28 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.6: +39 -1 lines
Diff to previous 1.6
subsys.cgi was not letting the user delete genomes or set variants

Revision 1.6 - (view) (download) (annotate) - [select for diffs]
Mon Sep 20 14:29:45 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.5: +11 -1 lines
Diff to previous 1.5
add column headers every 10th row in subsys.cgi

Revision 1.5 - (view) (download) (annotate) - [select for diffs]
Fri Sep 17 01:03:24 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.4: +15 -3 lines
Diff to previous 1.4
in subsys.cgi, when refilling, reset cells only if they change

Revision 1.4 - (view) (download) (annotate) - [select for diffs]
Fri Sep 17 00:56:04 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.3: +11 -11 lines
Diff to previous 1.3
fixes to subsys.cgi

Revision 1.3 - (view) (download) (annotate) - [select for diffs]
Sat Sep 11 13:23:47 2004 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.2: +93 -1 lines
Diff to previous 1.2
support checking assignments in subsystems

Revision 1.2 - (view) (download) (annotate) - [select for diffs]
Thu Sep 9 02:31:00 2004 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.1: +1 -1 lines
Diff to previous 1.1
minor fixes

Revision 1.1 - (view) (download) (annotate) - [select for diffs]
Tue Sep 7 02:54:16 2004 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
add new subsystem interface

This form allows you to request diffs between any two revisions of this file. For each of the two "sides" of the diff, select a symbolic revision name using the selection box, or choose 'Use Text Field' and enter a numeric revision.

  Diffs between and
  Type of Diff should be a

Sort log by:

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3