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Revision 1.130 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 23 13:28:14 2009 UTC (10 years, 8 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_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_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
Changes since 1.129: +61 -1 lines
Diff to previous 1.129
added links to set_prot_links

Revision 1.129 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 3 20:30:22 2008 UTC (11 years, 3 months ago) by parrello
Branch: MAIN
CVS Tags: 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, 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_release_2008_09_29
Changes since 1.128: +2 -2 lines
Diff to previous 1.128
Fixed URL references.

Revision 1.128 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 17 19:33:19 2008 UTC (11 years, 4 months ago) by dsouza
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806, rast_rel_2008_08_07
Changes since 1.127: +26 -13 lines
Diff to previous 1.127
Changed URL for SwissProt, TREMBL and UniProt links.

Revision 1.127 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 16 22:12:00 2008 UTC (11 years, 4 months ago) by dsouza
Branch: MAIN
Changes since 1.126: +13 -0 lines
Diff to previous 1.126
Added subroutine to create links to pubmed for dlits and ilits.

Revision 1.126 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 5 19:50:12 2008 UTC (11 years, 6 months ago) by arodri7
Branch: MAIN
CVS Tags: rast_rel_2008_07_21
Changes since 1.125: +40 -1 lines
Diff to previous 1.125
added alias links

Revision 1.125 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 25 16:29:08 2008 UTC (11 years, 6 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2008_06_16, rast_rel_2008_06_18
Changes since 1.124: +1 -1 lines
Diff to previous 1.124
fixes to get_dlits.cgi

Revision 1.124 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 14 09:06:09 2008 UTC (11 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.123: +2 -2 lines
Diff to previous 1.123
Changed the HTML escaping to the slightly more secure Tracer::Clean method.

Revision 1.123 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 29 05:43:12 2008 UTC (11 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.122: +138 -117 lines
Diff to previous 1.122
Changed so that in NMPDR mode the generated links point into the Seed Viewer.

Revision 1.122 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 2 21:23:07 2008 UTC (11 years, 8 months ago) by paczian
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.121: +1 -1 lines
Diff to previous 1.121
fixed broken cmr link

Revision 1.121 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 13 20:10:57 2008 UTC (11 years, 9 months ago) by paczian
Branch: MAIN
Changes since 1.120: +13 -0 lines
Diff to previous 1.120
added new keys to alias_url method

Revision 1.120 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 11 21:23:31 2008 UTC (11 years, 9 months ago) by paczian
Branch: MAIN
Changes since 1.119: +90 -0 lines
Diff to previous 1.119
added method alias_url

Revision 1.119 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 6 13:59:34 2007 UTC (12 years ago) by parrello
Branch: MAIN
Changes since 1.118: +72 -72 lines
Diff to previous 1.118
Changed POD format for better compatability with Wiki.

Revision 1.118 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 2 17:22:06 2007 UTC (12 years, 1 month ago) by dejongh
Branch: MAIN
Changes since 1.117: +2 -2 lines
Diff to previous 1.117
Make pop up windows resizable

Revision 1.117 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 23 03:36:39 2007 UTC (12 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.116: +1 -1 lines
Diff to previous 1.116
fix bug

Revision 1.116 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 23 03:23:27 2007 UTC (12 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.115: +9 -2 lines
Diff to previous 1.115
Add support for new peg.synonyms entries.

Revision 1.115 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 24 12:13:15 2007 UTC (12 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.114: +7 -3 lines
Diff to previous 1.114
Added the ability to specify a focus genome for a subsystem link.

Revision 1.114 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 15 21:12:18 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.113: +32 -1 lines
Diff to previous 1.113
Hope college modifications.

Revision 1.113 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 10 19:23:26 2007 UTC (12 years, 7 months ago) by mkubal
Branch: MAIN
Changes since 1.112: +1 -1 lines
Diff to previous 1.112
modified fid_link to make sRNA fid linked in search results table

Revision 1.112 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 1 12:49:13 2007 UTC (12 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.111: +18 -0 lines
Diff to previous 1.111
add img link

Revision 1.111 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 22 19:57:19 2007 UTC (12 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.110: +35 -26 lines
Diff to previous 1.110
Added trace messages.

Revision 1.110 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 5 23:06:47 2006 UTC (13 years ago) by paczian
Branch: MAIN
Changes since 1.109: +1 -1 lines
Diff to previous 1.109
corrected evidence_codes_explain

Revision 1.109 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 29 15:19:19 2006 UTC (13 years ago) by olson
Branch: MAIN
Changes since 1.108: +3 -2 lines
Diff to previous 1.108
Rollup commit of 48hr changes.

Added add_virtual_genome to Subsystem.pm to support UnvSubsys doing
the right thing when handed a FIGV.

Added propagation of 48hr_job thru the various link generation scripts in order for protein.cgi/display_subsys.cgi
to properly show virtual genomes.

Revision 1.108 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Nov 19 15:11:40 2006 UTC (13 years ago) by paczian
Branch: MAIN
Changes since 1.107: +24 -0 lines
Diff to previous 1.107
added 'evidence_codes_explain' method

Revision 1.107 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Nov 5 03:50:10 2006 UTC (13 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.106: +1 -1 lines
Diff to previous 1.106
Fixed a major blunder by yours truly that I hope no one noticed.

Revision 1.106 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 3 16:58:50 2006 UTC (13 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.105: +48 -14 lines
Diff to previous 1.105
Upgraded "sub_link" to work in NMPDR.

Revision 1.105 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 17 12:32:12 2006 UTC (13 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.104: +5 -2 lines
Diff to previous 1.104
Added tracing.

Revision 1.104 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 29 17:08:21 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.103: +0 -3 lines
Diff to previous 1.103
Removed some writes to STDERR that were clogging the log.

Revision 1.103 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 29 14:58:09 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.102: +4 -4 lines
Diff to previous 1.102
Fixed some code that was causing warnings.

Revision 1.102 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 28 22:59:05 2006 UTC (13 years, 2 months ago) by redwards
Branch: MAIN
Changes since 1.101: +23 -5 lines
Diff to previous 1.101
fixing broken links on map pages that refered fig ids to KEGG

Revision 1.101 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 25 19:34:14 2006 UTC (13 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.100: +16 -12 lines
Diff to previous 1.100
complete use-strict-ification fixes

Revision 1.100 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 24 15:22:58 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.99: +35 -24 lines
Diff to previous 1.99
Fixed some compile errors.

Revision 1.99 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 19 21:19:14 2006 UTC (13 years, 2 months ago) by mkubal
Branch: MAIN
Changes since 1.98: +3 -3 lines
Diff to previous 1.98
handle hope rxs

Revision 1.98 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 24 22:58:34 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.97: +3 -3 lines
Diff to previous 1.97
Changed fid_link so that it goes to the Protein page for Sprout.

Revision 1.97 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 25 19:32:19 2006 UTC (13 years, 4 months ago) by paczian
Branch: MAIN
Changes since 1.96: +26 -26 lines
Diff to previous 1.96
added target=_blank and quoting to all hrefs

Revision 1.96 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 19 15:41:47 2006 UTC (13 years, 4 months ago) by paczian
Branch: MAIN
Changes since 1.95: +20 -0 lines
Diff to previous 1.95
added function trembl_link
added support for trembl to set_prot_links

Revision 1.95 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 27 22:40:49 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.94: +2 -1 lines
Diff to previous 1.94
updates to Toby's new interface

Revision 1.94 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 6 03:14:43 2006 UTC (13 years, 6 months ago) by hwang
Branch: MAIN
Changes since 1.93: +1 -14 lines
Diff to previous 1.93
removed type=internal if clause. protein.cgi is recognizing internal and pointing to internal scripts instead. D

Revision 1.93 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 5 00:40:56 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.92: +5 -5 lines
Diff to previous 1.92
fix setting links to other BRCs

Revision 1.92 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 1 16:08:18 2006 UTC (13 years, 6 months ago) by hwang
Branch: MAIN
Changes since 1.91: +15 -1 lines
Diff to previous 1.91
Added a clause that if the type is internal for LinksToTools, then an internal script will be used.

Revision 1.91 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 17 17:50:38 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.90: +2 -1 lines
Diff to previous 1.90
RAE: Correcting uniprot links

Revision 1.90 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 6 22:04:12 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.89: +18 -0 lines
Diff to previous 1.89
RAE: Adding writing excel tables to raelib, html, and initial trial in select.cgi

Revision 1.89 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 5 18:42:12 2006 UTC (13 years, 8 months ago) by efrank
Branch: MAIN
CVS Tags: caBIG-05Apr06-00
Changes since 1.88: +27 -8 lines
Diff to previous 1.88
fix for caBIG.

1. fix link to Ensembl
2. turn off link it IPI
3. add link to HUGO (HGNC)

Apparently, links in Ensembl and IPI changed recently.

Revision 1.88 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 3 18:42:27 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-13Feb06-00
Changes since 1.87: +2 -0 lines
Diff to previous 1.87
$/ fixes

Revision 1.87 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 2 00:12:31 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.86: +4 -3 lines
Diff to previous 1.86
RAE: Correcting missing options in HTML.pm and preventing show version in check_int_anno.cgi

Revision 1.86 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 1 23:51:38 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.85: +1 -1 lines
Diff to previous 1.85
RAE: Adding quotes around fid_link

Revision 1.85 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 28 04:23:48 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.84: +3 -3 lines
Diff to previous 1.84
RAE: Updating POM -- pieces of metabolism

Revision 1.84 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 25 02:22:48 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.83: +1 -1 lines
Diff to previous 1.83
RAE: update to TIGR links

Revision 1.83 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 25 02:20:42 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.82: +2 -2 lines
Diff to previous 1.82
RAE: update to TIGR links

Revision 1.82 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 25 01:45:33 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.81: +3 -3 lines
Diff to previous 1.81
RAE: update to TIGR links

Revision 1.81 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 24 23:51:22 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.80: +7 -2 lines
Diff to previous 1.80
RAE: update to TIGR links

Revision 1.80 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 24 23:09:39 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.79: +107 -1 lines
Diff to previous 1.79
RAE: Adding new routines to link into the BRCs

Revision 1.79 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 5 18:45:51 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.78: +5 -5 lines
Diff to previous 1.78
RAE: Correcting relative URL links to css and js files

Revision 1.78 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 28 04:03:24 2005 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.77: +10 -9 lines
Diff to previous 1.77
another minor change to abstract functional coupling

Revision 1.77 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 28 04:00:26 2005 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.76: +10 -2 lines
Diff to previous 1.76
show only one FC per peg

Revision 1.76 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 28 03:28:05 2005 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.75: +11 -0 lines
Diff to previous 1.75
reorder table of abstract functional couplings

Revision 1.75 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 23 18:13:45 2005 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.74: +8 -2 lines
Diff to previous 1.74
clean up help for abstract functional coupling

Revision 1.74 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 20 17:59:09 2005 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.73: +13 -0 lines
Diff to previous 1.73
add abstract functional coupling

Revision 1.73 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 15 22:03:26 2005 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.72: +2 -1 lines
Diff to previous 1.72
RAE: adding class to tables

Revision 1.72 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 5 19:06:30 2005 UTC (14 years ago) by olson
Branch: MAIN
Changes since 1.71: +17 -0 lines
Diff to previous 1.71
Added license words.

Revision 1.71 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 2 21:58:00 2005 UTC (14 years, 1 month ago) by parrello
Branch: MAIN
CVS Tags: caBIG-00-00-00
Changes since 1.70: +3 -3 lines
Diff to previous 1.70
Fixed a bug in "show_page". The "last" directive had been coded as "$last".

Revision 1.70 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 24 21:50:35 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.69: +6 -4 lines
Diff to previous 1.69
Assorted relative-path fixes.

remove length check in indexing function assignments.

Revision 1.69 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 14 20:24:27 2005 UTC (14 years, 1 month ago) by efrank
Branch: MAIN
Changes since 1.68: +199 -1 lines
Diff to previous 1.68
Extend set_prot_links:
    o refseq links now do NM as well as NP links (inclding XM etc)
    o Added new links:
           ensembl
	   EntrezGene
	   MIM
	   UniGene
	   IPI (International Protein Index)
	   WP  (wormbase)
	   FB  (fly base)
	   SGD  (yeast)

Added supporting foo_link() subroutines to support mods above to
set_prot_links.

Revision 1.68 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 14 14:00:40 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.67: +39 -2 lines
Diff to previous 1.67
fix links

Revision 1.67 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 12 21:53:22 2005 UTC (14 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.66: +27 -2 lines
Diff to previous 1.66
programmatically determine top dir.

Revision 1.66 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 12 21:03:16 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.65: +4 -8 lines
Diff to previous 1.65
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 1.65 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 11 17:14:48 2005 UTC (14 years, 2 months ago) by redwards
Branch: MAIN
Changes since 1.64: +9 -4 lines
Diff to previous 1.64
removing some stderr output

Revision 1.64 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 8 14:14:47 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.63: +9 -4 lines
Diff to previous 1.63
minor fix to not include xxx entries in expanded sims

Revision 1.63 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 4 02:30:28 2005 UTC (14 years, 2 months ago) by redwards
Branch: MAIN
CVS Tags: caBIG-dataload-0
Changes since 1.62: +7 -2 lines
Diff to previous 1.62
disabling adding cookies to the HTML

Revision 1.62 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 3 23:22:48 2005 UTC (14 years, 2 months ago) by redwards
Branch: MAIN
Changes since 1.61: +60 -1 lines
Diff to previous 1.61
adding cids and merges to proteinfamilies.cgi

Revision 1.61 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 3 20:05:34 2005 UTC (14 years, 2 months ago) by redwards
Branch: MAIN
Changes since 1.60: +12 -6 lines
Diff to previous 1.60
Initial release of cookies code, including myseed

Revision 1.60 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 16 20:00:12 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.59: +13 -16 lines
Diff to previous 1.59
fix fid_link

Revision 1.59 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 16 15:18:26 2005 UTC (14 years, 2 months ago) by mkubal
Branch: MAIN
Changes since 1.58: +2 -1 lines
Diff to previous 1.58
move } in fid_link to proper spot

Revision 1.58 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 16 15:09:32 2005 UTC (14 years, 2 months ago) by mkubal
Branch: MAIN
Changes since 1.57: +1 -1 lines
Diff to previous 1.57
removed extra return in fid_link

Revision 1.57 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 16 05:13:13 2005 UTC (14 years, 2 months ago) by mkubal
Branch: MAIN
Changes since 1.56: +35 -21 lines
Diff to previous 1.56
fid_link formats link for pi and pp to feature.cgi

Revision 1.56 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 12 14:53:13 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.55: +11 -1 lines
Diff to previous 1.55
display_subsys.cgi that works

Revision 1.55 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 19 15:47:54 2005 UTC (14 years, 3 months ago) by redwards
Branch: MAIN
Changes since 1.54: +148 -1 lines
Diff to previous 1.54
adding rss feeds for subsystem updates

Revision 1.54 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 18 19:16:03 2005 UTC (14 years, 3 months ago) by redwards
Branch: MAIN
Changes since 1.53: +1 -0 lines
Diff to previous 1.53
Keeping usernames in the header

Revision 1.53 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 14 00:51:59 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.52: +24 -0 lines
Diff to previous 1.52
fixes to consistent_sets

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 6 15:30:29 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
Changes since 1.51: +1 -1 lines
Diff to previous 1.51
New interface for subsys.cgi, but it is commented out at the moment

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 1 16:29:22 2005 UTC (14 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.50: +5 -4 lines
Diff to previous 1.50
Replace use of $FIG_Config::cgi_url with &FIG::cgi_url()

Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jul 30 13:11:13 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.49: +10 -0 lines
Diff to previous 1.49
put reactions in a separate window

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 26 20:09:20 2005 UTC (14 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.48: +273 -268 lines
Diff to previous 1.48
Fixed some indenting issues.

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 22 21:39:19 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.47: +1 -1 lines
Diff to previous 1.47
adding js link to right place

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 22 20:42:30 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
Changes since 1.46: +78 -3 lines
Diff to previous 1.46
fixing access to /FIG

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 29 04:33:02 2005 UTC (14 years, 5 months ago) by redwards
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-2, merge-trunktag-bodev_news-3
Changes since 1.45: +9 -58 lines
Diff to previous 1.45
Changes to javascript to externalize everything into FIG.js and clean up the code

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 28 23:02:07 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.44: +1 -1 lines
Diff to previous 1.44
a bad bug in add_assertions_of_function

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 28 18:46:43 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.43: +18 -0 lines
Diff to previous 1.43
add tigr links

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 23 21:24:48 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-1
Changes since 1.42: +4 -2 lines
Diff to previous 1.42
finally

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 3 17:38:50 2005 UTC (14 years, 7 months ago) by olson
Branch: MAIN
CVS Tags: Root-bobdev_news
Branch point for: Branch-bobdev_news
Changes since 1.41: +26 -16 lines
Diff to previous 1.41
add %options to the compute_page_header routine

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 28 20:56:37 2005 UTC (14 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.40: +3 -2 lines
Diff to previous 1.40
Add uri_escape to subsystem link in sub_link().

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 24 03:15:06 2005 UTC (14 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.39: +23 -16 lines
Diff to previous 1.39
Just cosmetic changes while checking functionality.

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 20 00:08:39 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.38: +1 -1 lines
Diff to previous 1.38
changes to organisms.cgi to bring in my seed

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Mar 19 22:11:15 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.37: +18 -3 lines
Diff to previous 1.37
changes to organisms.cgi and css to make them work for IE and other browsers

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 15 22:29:27 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.36: +5 -2 lines
Diff to previous 1.36
Another correction to HTML.pm

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 15 21:01:14 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.35: +3 -0 lines
Diff to previous 1.35
corrected newline bug in HTML.pm

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 13 00:55:21 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.34: +16 -3 lines
Diff to previous 1.34
Initial commit of organisms.cgi which allows separate entry pages for different groups of organisms

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Mar 12 20:30:38 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.33: +36 -3 lines
Diff to previous 1.33
Changed Subsystems to allow selection of active_subsetR (rows) based on tag/value pairs

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 25 22:51:37 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.32: +3 -3 lines
Diff to previous 1.32
fix error on passing user to index.cgi -- header fix

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 19 00:22:57 2005 UTC (14 years, 9 months ago) by efrank
Branch: MAIN
Changes since 1.31: +1 -1 lines
Diff to previous 1.31
comment out an accidentally left in call to Dumper that was hurling
every line of HTML to error log.

doing the commit in case someone does a lwc update

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 18 19:31:12 2005 UTC (14 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.30: +32 -0 lines
Diff to previous 1.30
Add support for using HTML.pm from python.

Note we needed to add

    shift if UNIVERSAL::isa($_[0],__PACKAGE__);

to the functions in HTML.pm because they're used as methods when called from python.

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 16 18:59:21 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.29: +5 -3 lines
Diff to previous 1.29
highlight subsystems with no genomes attached

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 25 08:40:10 2005 UTC (14 years, 10 months ago) by redwards
Branch: MAIN
Changes since 1.28: +4 -2 lines
Diff to previous 1.28
Changes to protein.cgi to allow comments in FIGdisk/FIG/Data/Global/LinksToTools and nicer tables

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 13 17:32:51 2005 UTC (14 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.27: +2 -1 lines
Diff to previous 1.27
More fixes for Sprout integration.

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 21 20:20:52 2004 UTC (14 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.26: +8 -6 lines
Diff to previous 1.26
Add the ability to use stuff like "@colspan=2" in the headers in make_table.

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 17 21:32:57 2004 UTC (14 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.25: +5 -0 lines
Diff to previous 1.25
Add hook on compute_html_header for stuffing additional lines into the
blue header text.

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 6 18:26:05 2004 UTC (15 years ago) by olson
Branch: MAIN
Changes since 1.24: +23 -16 lines
Diff to previous 1.24
Factor out the page header stuff ffrom show_page into compute_html_header,
for the purpose of doing incremental-output pages.

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 17 14:40:19 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.23: +1 -1 lines
Diff to previous 1.23
fix URL in HTML.pm and add record.cgi

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 16 18:44:56 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.22: +1 -1 lines
Diff to previous 1.22
minor fixes

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 4 16:13:35 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.21: +16 -0 lines
Diff to previous 1.21
add ability to find subsystems for OlgaZ

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 30 14:33:50 2004 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.20: +12 -0 lines
Diff to previous 1.20
Add site-specific page trailer.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 23 21:46:44 2004 UTC (15 years, 3 months ago) by redwards
Branch: MAIN
Changes since 1.19: +71 -2 lines
Diff to previous 1.19
Added javascript buttons for check all/none
Added color for annotations that are not the same as the primary annotations

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 7 17:55:16 2004 UTC (15 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.18: +16 -0 lines
Diff to previous 1.18
set RefSeq links

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 4 12:30:40 2004 UTC (15 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.17: +3 -0 lines
Diff to previous 1.17
minor fixes to the headers

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 28 19:37:31 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.16: +3 -2 lines
Diff to previous 1.16
fixie to table stuff

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 28 19:16:47 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.15: +1 -0 lines
Diff to previous 1.15
need use POSIX

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 28 19:15:30 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.14: +33 -2 lines
Diff to previous 1.14
page header fixups

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jun 26 14:27:01 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.13: +17 -0 lines
Diff to previous 1.13
add support for UniProt links

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 8 21:32:56 2004 UTC (15 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.12: +4 -0 lines
Diff to previous 1.12
add comment

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 14 18:06:51 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.11: +17 -0 lines
Diff to previous 1.11
fixed up links

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 3 17:04:11 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.10: +48 -8 lines
Diff to previous 1.10
fixes to links in HTML.pm, code to sync systems after an update, and fixes to index.cgi and protein.cgi

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 3 18:30:57 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.9: +1 -1 lines
Diff to previous 1.9
fix links in ssa2.cgi

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 2 18:02:20 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +7 -10 lines
Diff to previous 1.8
add a new version of the spreadsheet software

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 26 21:54:11 2004 UTC (15 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.7: +1 -1 lines
Diff to previous 1.7
Fix baseurl stuff some more.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 26 21:39:08 2004 UTC (15 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.6: +11 -8 lines
Diff to previous 1.6
Mke base href absolute, not relative.

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 21 02:20:55 2004 UTC (15 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.5: +217 -49 lines
Diff to previous 1.5
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 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 19 21:58:31 2004 UTC (15 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.4: +17 -1 lines
Diff to previous 1.4
Relative base address support and cgi_url() based on current http request

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 19 20:26:58 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +2 -2 lines
Diff to previous 1.3
bug in HTML.pm

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 19 18:45:37 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.2: +16 -2 lines
Diff to previous 1.2
fixes to coupling and protein.cgi

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 23 16:35:17 2003 UTC (15 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.1: +22 -5 lines
Diff to previous 1.1
Determine the location of html.hdr by first trying Html/html.hdr, then
by looking explicitly in $FIG_Config::fig/CGI. This is needed for some reason
when running outof a user's public_html.

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

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