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Revision 1.120 - (view) (download) (annotate) - [select for diffs]
Wed Jan 9 23:35:36 2013 UTC (6 years, 10 months ago) by golsen
Branch: MAIN
CVS Tags: HEAD, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.119: +233 -238 lines
Diff to previous 1.119
Attempt to fix problems with global variables and many structural issues.
Deal with some error conditions not previously handled.

Revision 1.119 - (view) (download) (annotate) - [select for diffs]
Sun Jan 6 20:53:02 2013 UTC (6 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.118: +19 -8 lines
Diff to previous 1.118
Handle missing dbms tables in pin look-up.

Revision 1.118 - (view) (download) (annotate) - [select for diffs]
Fri Aug 17 22:24:43 2012 UTC (7 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.117: +2 -1 lines
Diff to previous 1.117
Add missing "use FIGjs;"

Revision 1.117 - (view) (download) (annotate) - [select for diffs]
Thu Aug 7 16:37:48 2008 UTC (11 years, 3 months ago) by arodri7
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_rel_2008_0625, mgrast_rel_2008_0917, mgrast_rel_2008_0919, mgrast_rel_2008_0923, mgrast_rel_2008_0924, mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_4, mgrast_release_3_1_0, mgrast_release_3_1_1, mgrast_release_3_1_2, mgrast_version_3_2, myrast_33, myrast_rel40, rast_2008_0924, rast_rel_2008_08_07, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_rel_2008_10_09, rast_rel_2008_10_29, rast_rel_2008_11_24, rast_rel_2008_12_18, rast_rel_2009_02_05, rast_rel_2009_03_26, rast_rel_2009_05_18, rast_rel_2009_07_09, rast_rel_2009_0925, rast_rel_2010_0118, rast_rel_2010_0526, rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119, rast_rel_2011_0928, rast_release_2008_09_29
Changes since 1.116: +2 -2 lines
Diff to previous 1.116
changed checkbox name for figfams

Revision 1.116 - (view) (download) (annotate) - [select for diffs]
Mon Jul 21 18:41:13 2008 UTC (11 years, 3 months ago) by dsouza
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806
Changes since 1.115: +47 -8 lines
Diff to previous 1.115
Added checkbox and button for figfams when they may need to be merged

Revision 1.115 - (view) (download) (annotate) - [select for diffs]
Thu Jul 17 19:36:48 2008 UTC (11 years, 4 months ago) by dsouza
Branch: MAIN
Changes since 1.114: +34 -3 lines
Diff to previous 1.114
Changed accessing and display of uniprot aliases.

Revision 1.114 - (view) (download) (annotate) - [select for diffs]
Wed Jul 16 22:09:57 2008 UTC (11 years, 4 months ago) by dsouza
Branch: MAIN
Changes since 1.113: +1 -1 lines
Diff to previous 1.113
Added pubmed links for dlits and ilits.

Revision 1.113 - (view) (download) (annotate) - [select for diffs]
Tue Apr 29 08:01:10 2008 UTC (11 years, 6 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_06_16, rast_rel_2008_06_18, rast_rel_2008_07_21
Changes since 1.112: +0 -1 lines
Diff to previous 1.112
Added tracing support.

Revision 1.112 - (view) (download) (annotate) - [select for diffs]
Mon Mar 10 17:57:13 2008 UTC (11 years, 8 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.111: +10 -12 lines
Diff to previous 1.111
fixes to generating cluster based subsystems

Revision 1.111 - (view) (download) (annotate) - [select for diffs]
Sat Mar 1 15:36:53 2008 UTC (11 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.110: +2 -2 lines
Diff to previous 1.110
change ::data/FigfamsData to ::FigfamsData

Revision 1.110 - (view) (download) (annotate) - [select for diffs]
Wed Feb 20 12:18:11 2008 UTC (11 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.109: +6 -13 lines
Diff to previous 1.109
fixes to cbss

Revision 1.109 - (view) (download) (annotate) - [select for diffs]
Tue Feb 19 03:14:28 2008 UTC (11 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.108: +6 -0 lines
Diff to previous 1.108
minor fix

Revision 1.108 - (view) (download) (annotate) - [select for diffs]
Mon Feb 18 22:54:10 2008 UTC (11 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.107: +1 -1 lines
Diff to previous 1.107
minor fix

Revision 1.107 - (view) (download) (annotate) - [select for diffs]
Mon Feb 18 22:47:16 2008 UTC (11 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.106: +1 -1 lines
Diff to previous 1.106
minor fix

Revision 1.106 - (view) (download) (annotate) - [select for diffs]
Mon Feb 18 20:06:31 2008 UTC (11 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.105: +34 -12 lines
Diff to previous 1.105
new suport for cluster-based subsystems

Revision 1.105 - (view) (download) (annotate) - [select for diffs]
Mon Feb 18 16:20:58 2008 UTC (11 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.104: +1 -1 lines
Diff to previous 1.104
changes to subsystem generation from clusters

Revision 1.104 - (view) (download) (annotate) - [select for diffs]
Sun Feb 17 14:02:33 2008 UTC (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.103: +1 -1 lines
Diff to previous 1.103
minor corrections to chromosomal_clusters.cgi to handle cluster-based subsystems

Revision 1.103 - (view) (download) (annotate) - [select for diffs]
Sun Feb 17 13:23:18 2008 UTC (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.102: +2 -1 lines
Diff to previous 1.102
minor corrections to chromosomal_clusters.cgi to handle cluster-based subsystems

Revision 1.102 - (view) (download) (annotate) - [select for diffs]
Sun Feb 17 03:32:29 2008 UTC (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.101: +3 -1 lines
Diff to previous 1.101
minor corrections to chromosomal_clusters.cgi to handle cluster-based subsystems

Revision 1.101 - (view) (download) (annotate) - [select for diffs]
Sun Feb 17 03:23:52 2008 UTC (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.100: +9 -1 lines
Diff to previous 1.100
minor corrections to chromosomal_clusters.cgi to handle cluster-based subsystems

Revision 1.100 - (view) (download) (annotate) - [select for diffs]
Sat Feb 16 21:07:59 2008 UTC (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.99: +95 -3 lines
Diff to previous 1.99
add the ability to trigger cluster based subsystems from chromosomal_clusters.cgi

Revision 1.99 - (view) (download) (annotate) - [select for diffs]
Tue Sep 25 21:23:28 2007 UTC (12 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.98: +1 -1 lines
Diff to previous 1.98
$fig->resolve_id => &resolve_id($fig

Revision 1.98 - (view) (download) (annotate) - [select for diffs]
Wed May 16 05:15:28 2007 UTC (12 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.97: +8 -2 lines
Diff to previous 1.97
Fixed a bug in the evidence code commentary stuff.

Revision 1.97 - (view) (download) (annotate) - [select for diffs]
Fri May 11 06:09:36 2007 UTC (12 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.96: +726 -709 lines
Diff to previous 1.96
Changed to get all the attributes in a single batch.

Revision 1.96 - (view) (download) (annotate) - [select for diffs]
Thu May 10 15:32:27 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.95: +1 -1 lines
Diff to previous 1.95
fix resolve_id call

Revision 1.95 - (view) (download) (annotate) - [select for diffs]
Tue Apr 10 15:08:47 2007 UTC (12 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.94: +6 -1 lines
Diff to previous 1.94
use $FIG_Config::pin_server_url

Revision 1.94 - (view) (download) (annotate) - [select for diffs]
Tue Apr 10 03:55:33 2007 UTC (12 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.93: +52 -27 lines
Diff to previous 1.93
Fixed to work correctly in Sprout when the pin server is not available.

Revision 1.93 - (view) (download) (annotate) - [select for diffs]
Wed Mar 14 16:36:25 2007 UTC (12 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.92: +5 -0 lines
Diff to previous 1.92
add config option for pins server

Revision 1.92 - (view) (download) (annotate) - [select for diffs]
Mon Dec 25 18:32:36 2006 UTC (12 years, 10 months ago) by redwards
Branch: MAIN
Changes since 1.91: +4 -1 lines
Diff to previous 1.91
Adding java buttons

Revision 1.91 - (view) (download) (annotate) - [select for diffs]
Wed Sep 13 19:01:33 2006 UTC (13 years, 2 months ago) by paczian
Branch: MAIN
Changes since 1.90: +3 -2 lines
Diff to previous 1.90
fixed the display of the evidence codes to the old version

Revision 1.90 - (view) (download) (annotate) - [select for diffs]
Tue Sep 5 16:58:59 2006 UTC (13 years, 2 months ago) by paczian
Branch: MAIN
Changes since 1.89: +12 -1 lines
Diff to previous 1.89
updated evidence_codes to comply to the new way to store evidence codes in the attributes

Revision 1.89 - (view) (download) (annotate) - [select for diffs]
Thu Aug 10 07:31:38 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.88: +1 -1 lines
Diff to previous 1.88
Fixed a bug in the way SPROUT mode was detected.

Revision 1.88 - (view) (download) (annotate) - [select for diffs]
Tue Aug 8 21:30:27 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.87: +1 -1 lines
Diff to previous 1.87
Fixed a glitch in the handling of the SPROUT= parameter.

Revision 1.87 - (view) (download) (annotate) - [select for diffs]
Sat Aug 5 03:12:15 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.86: +25 -21 lines
Diff to previous 1.86
Modified so that Sprout pages stay Sprout-like.

Revision 1.86 - (view) (download) (annotate) - [select for diffs]
Mon Jul 31 16:44:53 2006 UTC (13 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.85: +6 -1 lines
Diff to previous 1.85
Turn off pin cache.

Revision 1.85 - (view) (download) (annotate) - [select for diffs]
Fri Jul 28 02:07:28 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.84: +73 -73 lines
Diff to previous 1.84
Changed to use the new PageBuilder call signature.

Revision 1.84 - (view) (download) (annotate) - [select for diffs]
Thu Jul 20 20:13:23 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.83: +7 -2 lines
Diff to previous 1.83
Added external template support.

Revision 1.83 - (view) (download) (annotate) - [select for diffs]
Wed Jun 28 21:50:48 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.82: +10 -10 lines
Diff to previous 1.82
Removed trace messages.

Revision 1.82 - (view) (download) (annotate) - [select for diffs]
Wed Jun 28 17:14:03 2006 UTC (13 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.81: +21 -1 lines
Diff to previous 1.81
RAE: adding ss names popup

Revision 1.81 - (view) (download) (annotate) - [select for diffs]
Wed Jun 28 06:05:47 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.80: +1 -1 lines
Diff to previous 1.80
Added the missing $cgi parm to a call to "add_commentary_form".

Revision 1.80 - (view) (download) (annotate) - [select for diffs]
Tue Jun 27 22:40:49 2006 UTC (13 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.79: +38 -2 lines
Diff to previous 1.79
updates to Toby's new interface

Revision 1.79 - (view) (download) (annotate) - [select for diffs]
Tue Jun 27 00:32:24 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.78: +69 -62 lines
Diff to previous 1.78
Another try at getting Sprout pins to work.

Revision 1.78 - (view) (download) (annotate) - [select for diffs]
Mon Jun 26 23:51:01 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.77: +27 -28 lines
Diff to previous 1.77
Changed to skip only the DB cache code if not in SEED mode.

Revision 1.77 - (view) (download) (annotate) - [select for diffs]
Sun Jun 25 23:37:02 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.76: +0 -1 lines
Diff to previous 1.76
Removed extra tick call.

Revision 1.76 - (view) (download) (annotate) - [select for diffs]
Sun Jun 25 23:29:00 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.75: +1 -0 lines
Diff to previous 1.75
Added some more messages.

Revision 1.75 - (view) (download) (annotate) - [select for diffs]
Sun Jun 25 03:27:17 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.74: +2 -3 lines
Diff to previous 1.74
Changed boundaries_of from a static to an instance method.

Revision 1.74 - (view) (download) (annotate) - [select for diffs]
Sun Jun 25 03:10:22 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.73: +1 -1 lines
Diff to previous 1.73
Lots of tracing until I find what's wrong...

Revision 1.73 - (view) (download) (annotate) - [select for diffs]
Sun Jun 25 03:02:24 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.72: +1 -1 lines
Diff to previous 1.72
more tracing...

Revision 1.72 - (view) (download) (annotate) - [select for diffs]
Sun Jun 25 02:35:12 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.71: +1 -1 lines
Diff to previous 1.71
Commented out a trace line.

Revision 1.71 - (view) (download) (annotate) - [select for diffs]
Sun Jun 25 01:53:07 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.70: +1 -1 lines
Diff to previous 1.70
Added some ticking.

Revision 1.70 - (view) (download) (annotate) - [select for diffs]
Fri Jun 23 23:49:07 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.69: +4 -1 lines
Diff to previous 1.69
Fixed so it will not try to find precomputed pins if this is Sprout.

Revision 1.69 - (view) (download) (annotate) - [select for diffs]
Thu Jun 22 21:09:48 2006 UTC (13 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.68: +6 -1 lines
Diff to previous 1.68
re-apply some bug fixes made after I forked this file

Revision 1.68 - (view) (download) (annotate) - [select for diffs]
Thu Jun 22 19:50:18 2006 UTC (13 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.67: +25 -9 lines
Diff to previous 1.67
more tweaks

Revision 1.67 - (view) (download) (annotate) - [select for diffs]
Thu Jun 22 19:32:00 2006 UTC (13 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.66: +499 -180 lines
Diff to previous 1.66
Install new chromosmal_clusters that uses the server-cached data.

Revision 1.66 - (view) (download) (annotate) - [select for diffs]
Tue Jun 13 19:05:28 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.65: +2 -0 lines
Diff to previous 1.65
RAE: Adding check/uncheck all buttons

Revision 1.65 - (view) (download) (annotate) - [select for diffs]
Wed Mar 22 21:58:19 2006 UTC (13 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.64: +1 -15 lines
Diff to previous 1.64
bad code that slipped in somehow.

Revision 1.64 - (view) (download) (annotate) - [select for diffs]
Tue Mar 21 15:53:30 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.63: +15 -2 lines
Diff to previous 1.63
fixes to split_and_trim

Revision 1.63 - (view) (download) (annotate) - [select for diffs]
Thu Mar 16 02:25:51 2006 UTC (13 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.62: +1 -1 lines
Diff to previous 1.62
fixes on commentary due to change in GG format

Revision 1.62 - (view) (download) (annotate) - [select for diffs]
Fri Mar 3 23:09:29 2006 UTC (13 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.61: +2 -1 lines
Diff to previous 1.61
Minor change in information displayed on contig abbreviation mouse-over.

Revision 1.61 - (view) (download) (annotate) - [select for diffs]
Fri Mar 3 22:36:37 2006 UTC (13 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.60: +3 -1 lines
Diff to previous 1.60
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 1.60 - (view) (download) (annotate) - [select for diffs]
Fri Mar 3 20:14:56 2006 UTC (13 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.59: +9 -1 lines
Diff to previous 1.59
Fix for bug 322

Revision 1.59 - (view) (download) (annotate) - [select for diffs]
Thu Dec 29 01:06:00 2005 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.58: +12 -1 lines
Diff to previous 1.58
RAE:Adding boxes to paste ids in if nothing is provided

Revision 1.58 - (view) (download) (annotate) - [select for diffs]
Mon Dec 5 19:12:11 2005 UTC (13 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.57: +17 -0 lines
Diff to previous 1.57
add license words

Revision 1.57 - (view) (download) (annotate) - [select for diffs]
Thu Nov 3 22:20:23 2005 UTC (14 years ago) by olson
Branch: MAIN
CVS Tags: caBIG-00-00-00
Changes since 1.56: +1 -1 lines
Diff to previous 1.56
make it use the cache. wups.

Revision 1.56 - (view) (download) (annotate) - [select for diffs]
Fri Oct 28 11:43:46 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.55: +7 -3 lines
Diff to previous 1.55
fix of fix in chromosomal_clusters.cgi

Revision 1.55 - (view) (download) (annotate) - [select for diffs]
Fri Oct 28 01:21:51 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.54: +2 -2 lines
Diff to previous 1.54
bug in chromosomal clusters

Revision 1.54 - (view) (download) (annotate) - [select for diffs]
Wed Oct 12 21:03:16 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.53: +5 -2 lines
Diff to previous 1.53
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 1.53 - (view) (download) (annotate) - [select for diffs]
Wed Oct 12 16:13:00 2005 UTC (14 years, 1 month ago) by disz
Branch: MAIN
Changes since 1.52: +5 -5 lines
Diff to previous 1.52
Removed attributes from mouseover popup

Revision 1.52 - (view) (download) (annotate) - [select for diffs]
Sat Oct 1 20:32:19 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.51: +9 -1 lines
Diff to previous 1.51
support alignment of DNA via fid_checked.cgi

Revision 1.51 - (view) (download) (annotate) - [select for diffs]
Wed Sep 21 20:34:55 2005 UTC (14 years, 1 month ago) by disz
Branch: MAIN
Changes since 1.50: +1 -1 lines
Diff to previous 1.50
Added attributes to tooltip

Revision 1.50 - (view) (download) (annotate) - [select for diffs]
Wed Sep 21 20:32:32 2005 UTC (14 years, 1 month ago) by disz
Branch: MAIN
Changes since 1.49: +8 -1 lines
Diff to previous 1.49
Added Features to tooltip popup

Revision 1.49 - (view) (download) (annotate) - [select for diffs]
Wed Sep 21 18:42:50 2005 UTC (14 years, 1 month ago) by disz
Branch: MAIN
Changes since 1.48: +5 -3 lines
Diff to previous 1.48
Added Organism name to tooltip popup

Revision 1.48 - (view) (download) (annotate) - [select for diffs]
Sat Aug 13 20:44:05 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.47: +23 -5 lines
Diff to previous 1.47
add evidence codes to commentaries

Revision 1.47 - (view) (download) (annotate) - [select for diffs]
Fri Jul 22 12:54:35 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.46: +1 -1 lines
Diff to previous 1.46
minor fixes

Revision 1.41.2.3 - (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 1.41.2.2: +7 -6 lines
Diff to previous 1.41.2.2 , to branch point 1.41 , to next main 1.120
Merged changes from trunk.

Revision 1.46 - (view) (download) (annotate) - [select for diffs]
Sat Jul 2 19:41:22 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
CVS Tags: merge-trunktag-bodev_news-3
Changes since 1.45: +7 -6 lines
Diff to previous 1.45
fix bad bug in chromosomal_clusters.cgi - missed pinned_regions

Revision 1.41.2.2 - (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 1.41.2.1: +64 -8 lines
Diff to previous 1.41.2.1 , to branch point 1.41
Merge from trunk.

Revision 1.45 - (view) (download) (annotate) - [select for diffs]
Mon Jun 27 21:47:44 2005 UTC (14 years, 4 months ago) by olson
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-2
Changes since 1.44: +34 -43 lines
Diff to previous 1.44
Finish SPROUT support.

Revision 1.44 - (view) (download) (annotate) - [select for diffs]
Mon Jun 27 20:38:02 2005 UTC (14 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.43: +70 -5 lines
Diff to previous 1.43
Add SPROUT support.

Revision 1.41.2.1 - (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 1.41: +18 -13 lines
Diff to previous 1.41
Merged from trunk.

Revision 1.43 - (view) (download) (annotate) - [select for diffs]
Thu Jun 23 21:30:27 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-1
Changes since 1.42: +1 -1 lines
Diff to previous 1.42
fix bad sims call in chromosomal_clusters.cgi

Revision 1.42 - (view) (download) (annotate) - [select for diffs]
Thu Jun 23 21:24:49 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.41: +17 -12 lines
Diff to previous 1.41
finally

Revision 1.41 - (view) (download) (annotate) - [select for diffs]
Mon Jun 13 19:44:32 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: Root-bobdev_news
Branch point for: Branch-bobdev_news
Changes since 1.40: +2 -152 lines
Diff to previous 1.40
interface routines hack

Revision 1.40 - (view) (download) (annotate) - [select for diffs]
Mon Jun 13 16:44:04 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.39: +221 -53 lines
Diff to previous 1.39
Ross change commit after cleanup

Revision 1.39 - (view) (download) (annotate) - [select for diffs]
Fri Jun 10 16:08:52 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.38: +1 -1 lines
Diff to previous 1.38
fixes to cached pin displays

Revision 1.38 - (view) (download) (annotate) - [select for diffs]
Fri Jun 10 13:00:08 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.37: +6 -7 lines
Diff to previous 1.37
fixes to chromosomal_clusters.cgi

Revision 1.37 - (view) (download) (annotate) - [select for diffs]
Thu Jun 9 21:36:02 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.36: +35 -2 lines
Diff to previous 1.36
set of the ability to access piined region caches via URLs

Revision 1.36 - (view) (download) (annotate) - [select for diffs]
Wed Jun 1 03:22:16 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.35: +1 -1 lines
Diff to previous 1.35
remove debugging output from chromosomal_clusters.cgi

Revision 1.35 - (view) (download) (annotate) - [select for diffs]
Wed Jun 1 02:59:52 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.34: +29 -4 lines
Diff to previous 1.34
fixes to chromosomal_clusters.cgi

Revision 1.34 - (view) (download) (annotate) - [select for diffs]
Wed May 25 03:35:53 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.33: +5 -4 lines
Diff to previous 1.33
fix to pin caching

Revision 1.33 - (view) (download) (annotate) - [select for diffs]
Sun May 15 12:42:38 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.32: +5 -3 lines
Diff to previous 1.32
fixes to caching in chromosomal_clusters.cgi

Revision 1.32 - (view) (download) (annotate) - [select for diffs]
Sun May 15 11:49:37 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.31: +9 -0 lines
Diff to previous 1.31
minor fixes in computing functional coupling

Revision 1.31 - (view) (download) (annotate) - [select for diffs]
Sun May 8 14:58:35 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.30: +76 -6 lines
Diff to previous 1.30
cache pinned region output

Revision 1.30 - (view) (download) (annotate) - [select for diffs]
Thu Mar 24 03:17:38 2005 UTC (14 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.29: +313 -203 lines
Diff to previous 1.29
Extensive code clean-up.  Some clean-up of colors (unmatched pegs are now
gray, as we had intended).  Added color coding of functions on the
commentary page.  Still need to add explanation page.

Revision 1.29 - (view) (download) (annotate) - [select for diffs]
Wed Jan 19 20:32:27 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.28: +16 -4 lines
Diff to previous 1.28
fixes to annotation via commentary

Revision 1.28 - (view) (download) (annotate) - [select for diffs]
Sun Jan 9 17:15:12 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.27: +3 -0 lines
Diff to previous 1.27
fix disambiguating maps

Revision 1.27 - (view) (download) (annotate) - [select for diffs]
Sat Jan 8 18:22:01 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.26: +1 -1 lines
Diff to previous 1.26
add check to assign_function

Revision 1.26 - (view) (download) (annotate) - [select for diffs]
Tue Nov 16 18:44:56 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.25: +1 -1 lines
Diff to previous 1.25
minor fixes

Revision 1.25 - (view) (download) (annotate) - [select for diffs]
Tue Nov 16 17:12:22 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.24: +1 -1 lines
Diff to previous 1.24
fix red eq color0 again

Revision 1.24 - (view) (download) (annotate) - [select for diffs]
Tue Nov 16 03:29:35 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.23: +3 -3 lines
Diff to previous 1.23
add assign_using_tree and fix overlays in pinned regions

Revision 1.23 - (view) (download) (annotate) - [select for diffs]
Fri Nov 12 02:43:45 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.22: +19 -7 lines
Diff to previous 1.22
made addition for PIR - null maps

Revision 1.22 - (view) (download) (annotate) - [select for diffs]
Thu Nov 11 04:25:47 2004 UTC (15 years ago) by olson
Branch: MAIN
Changes since 1.21: +27 -32 lines
Diff to previous 1.21
GenDB changes

Revision 1.21 - (view) (download) (annotate) - [select for diffs]
Tue Nov 2 18:27:10 2004 UTC (15 years ago) by redwards
Branch: MAIN
Changes since 1.20: +5 -2 lines
Diff to previous 1.20
Added Javascript buttons to bottom of chromosomal_clusters.cgi

Revision 1.20 - (view) (download) (annotate) - [select for diffs]
Tue Nov 2 18:15:16 2004 UTC (15 years ago) by redwards
Branch: MAIN
Changes since 1.19: +1 -1 lines
Diff to previous 1.19
Add align button to chromosomal_clusters.cgi per Andreis request

Revision 1.19 - (view) (download) (annotate) - [select for diffs]
Tue Nov 2 17:49:52 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.18: +1 -0 lines
Diff to previous 1.18
on save, get all of the maps (chromosomal_clusters.cgi)

Revision 1.18 - (view) (download) (annotate) - [select for diffs]
Tue Nov 2 17:26:25 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.17: +3 -1 lines
Diff to previous 1.17
make color0 and red equivalent in chromosomal_clusters.cgi

Revision 1.17 - (view) (download) (annotate) - [select for diffs]
Sun Oct 31 00:56:03 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.16: +20 -6 lines
Diff to previous 1.16
add uni labels on maps

Revision 1.16 - (view) (download) (annotate) - [select for diffs]
Thu Oct 21 19:13:45 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.15: +41 -2 lines
Diff to previous 1.15
show correspondence when external functions are used

Revision 1.15 - (view) (download) (annotate) - [select for diffs]
Sun Oct 17 16:40:13 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.14: +2 -0 lines
Diff to previous 1.14
added homologs_in_clusters.cgi

Revision 1.14 - (view) (download) (annotate) - [select for diffs]
Sun Oct 17 00:02:34 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.13: +50 -4 lines
Diff to previous 1.13
fixes to UniProt IDs on chromosomal_clusters.cgi

Revision 1.13 - (view) (download) (annotate) - [select for diffs]
Fri Sep 24 19:35:58 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.12: +9 -9 lines
Diff to previous 1.12
fix bug in chromosomal_clusters causing lines not aligned on red

Revision 1.12 - (view) (download) (annotate) - [select for diffs]
Wed Sep 22 17:25:38 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.11: +497 -339 lines
Diff to previous 1.11
restructured code for presenting chromosomal clusters

Revision 1.11 - (view) (download) (annotate) - [select for diffs]
Mon Sep 20 13:35:25 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.10: +15 -1 lines
Diff to previous 1.10
add some comments to assignment1

Revision 1.10 - (view) (download) (annotate) - [select for diffs]
Sat Aug 14 13:15:49 2004 UTC (15 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.9: +1 -1 lines
Diff to previous 1.9
add commentary to displayed regions in protein.cgi

Revision 1.9 - (view) (download) (annotate) - [select for diffs]
Tue May 11 12:35:22 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +1 -0 lines
Diff to previous 1.8
default to selected on pick maps

Revision 1.8 - (view) (download) (annotate) - [select for diffs]
Fri Feb 20 14:34:56 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +1 -1 lines
Diff to previous 1.7
fix expansion parm bug

Revision 1.7 - (view) (download) (annotate) - [select for diffs]
Fri Feb 20 13:29:42 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +20 -20 lines
Diff to previous 1.6
fix commentary

Revision 1.6 - (view) (download) (annotate) - [select for diffs]
Mon Dec 29 02:22:37 2003 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +3 -3 lines
Diff to previous 1.5
numerous performance issues

Revision 1.5 - (view) (download) (annotate) - [select for diffs]
Tue Dec 16 16:59:42 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
Changes since 1.4: +0 -13 lines
Diff to previous 1.4
Removed stray tool_hdr content that got copied in here

Revision 1.4 - (view) (download) (annotate) - [select for diffs]
Thu Dec 4 15:26:45 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
CVS Tags: delong-01, delong-02
Changes since 1.3: +3 -0 lines
Diff to previous 1.3
add dropped lien

Revision 1.3 - (view) (download) (annotate) - [select for diffs]
Thu Dec 4 15:23:35 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
Changes since 1.2: +13 -0 lines
Diff to previous 1.2
Added chunk of code that was lost

Revision 1.2 - (view) (download) (annotate) - [select for diffs]
Wed Dec 3 21:24:31 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.1: +13 -20 lines
Diff to previous 1.1
*** empty log message ***

Revision 1.1.1.1 - (view) (download) (annotate) - [select for diffs] (vendor branch)
Mon Dec 1 16:57:09 2003 UTC (15 years, 11 months ago) by efrank
Branch: initial
CVS Tags: V00-00-00, V00-00-01, V00-00-02, init, preRossMerge-03Dec03
Changes since 1.1: +0 -0 lines
Diff to previous 1.1 , to next main 1.120

import


Revision 1.1 - (view) (download) (annotate) - [select for diffs]
Mon Dec 1 16:57:09 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
Branch point for: initial
Initial revision

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