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Revision 1.147 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 22 21:18:41 2010 UTC (9 years, 8 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2010_0526, rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119
Changes since 1.146: +1 -1 lines
Diff to previous 1.146
minor fix

Revision 1.146 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 11 16:51:52 2010 UTC (9 years, 8 months ago) by paczian
Branch: MAIN
Changes since 1.145: +1 -1 lines
Diff to previous 1.145
added check for undef of cell in get_roles_for_genome

Revision 1.145 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 15 21:22:38 2009 UTC (10 years, 4 months ago) by redwards
Branch: MAIN
CVS Tags: rast_rel_2009_0925, rast_rel_2010_0118
Changes since 1.144: +2 -2 lines
Diff to previous 1.144
moving error messages from STDOUT to STDERR

Revision 1.144 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 19 20:45:38 2009 UTC (10 years, 10 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_02_05, rast_rel_2009_03_26, rast_rel_2009_05_18, rast_rel_2009_07_09
Changes since 1.143: +14 -0 lines
Diff to previous 1.143
Added a new method-- all_functions-- that allows SproutSubsys to retrieve role information more efficiently.

Revision 1.143 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 11 18:22:59 2008 UTC (10 years, 11 months ago) by dejongh
Branch: MAIN
CVS Tags: rast_rel_2008_12_18
Changes since 1.142: +0 -18 lines
Diff to previous 1.142
removed copy_hope_info

Revision 1.142 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 13 21:53:42 2008 UTC (11 years ago) by dejongh
Branch: MAIN
CVS Tags: rast_rel_2008_11_24
Changes since 1.141: +0 -50 lines
Diff to previous 1.141
Move get_hope_reactions_for_genome to model.pm

Revision 1.141 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 11 13:41:27 2008 UTC (11 years ago) by paczian
Branch: MAIN
Changes since 1.140: +6 -2 lines
Diff to previous 1.140
updated for use with FIGM

Revision 1.140 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 3 18:18:59 2008 UTC (11 years ago) by dejongh
Branch: MAIN
CVS Tags: mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2
Changes since 1.139: +32 -13 lines
Diff to previous 1.139
Changes to get_hope_reactions for a genome even if it isn't active in a subsystem, by looking at which Functional Roles are present in its annotation

Revision 1.139 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 15 11:52:55 2008 UTC (11 years, 1 month ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_10_29
Changes since 1.138: +2 -4 lines
Diff to previous 1.138
Fixed a bad URL.

Revision 1.138 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 13 20:26:02 2008 UTC (11 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.137: +40 -0 lines
Diff to previous 1.137
Add support for subsystem_metadata table. Updates via Subsystem::db_sync.

Revision 1.137 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 25 15:36:03 2008 UTC (11 years, 1 month ago) by bartels
Branch: MAIN
CVS Tags: rast_rel_2008_09_29, rast_rel_2008_09_30, rast_rel_2008_10_09, rast_release_2008_09_29
Changes since 1.136: +41 -0 lines
Diff to previous 1.136
inserted code to save rules and definitions for check variants

Revision 1.136 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Sep 6 20:34:52 2008 UTC (11 years, 2 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, mgrast_rel_2008_0917, mgrast_rel_2008_0919, mgrast_rel_2008_0923, mgrast_rel_2008_0924, rast_2008_0924
Changes since 1.135: +65 -0 lines
Diff to previous 1.135
Add support for $fig->change_funcrole()

Revision 1.135 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 28 15:28:05 2008 UTC (11 years, 3 months ago) by bartels
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806, rast_rel_2008_08_07
Changes since 1.134: +3 -2 lines
Diff to previous 1.134
*** empty log message ***

Revision 1.134 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 15 17:23:38 2008 UTC (11 years, 4 months ago) by bartels
Branch: MAIN
Changes since 1.133: +2 -3 lines
Diff to previous 1.133
*** empty log message ***

Revision 1.133 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 10 22:11:47 2008 UTC (11 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2008_07_21
Changes since 1.132: +4 -2 lines
Diff to previous 1.132
minor fixes due to changes to what a genome is

Revision 1.132 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 10 18:46:38 2008 UTC (11 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.131: +61 -2 lines
Diff to previous 1.131
Generalize rows of subsystems to be Genome:Loc

Revision 1.131 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 17 13:53:58 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 1.130: +3 -2 lines
Diff to previous 1.130
minor fix to Subsystems.pm

Revision 1.130 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 16 15:23:18 2008 UTC (11 years, 6 months ago) by bartels
Branch: MAIN
Changes since 1.129: +10 -4 lines
Diff to previous 1.129
fixed a bug that broke the hundred by a hundred attributes in the old
interface

Revision 1.129 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 1 21:40:53 2008 UTC (11 years, 6 months ago) by bartels
Branch: MAIN
Changes since 1.128: +1 -1 lines
Diff to previous 1.128
*** empty log message ***

Revision 1.128 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 30 16:01:28 2008 UTC (11 years, 6 months ago) by bartels
Branch: MAIN
Changes since 1.127: +10 -10 lines
Diff to previous 1.127
now fixed it correctly...

Revision 1.127 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 30 15:35:57 2008 UTC (11 years, 6 months ago) by bartels
Branch: MAIN
Changes since 1.126: +9 -9 lines
Diff to previous 1.126
fixed something...

Revision 1.126 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 28 16:32:27 2008 UTC (11 years, 6 months ago) by bartels
Branch: MAIN
Changes since 1.125: +63 -1 lines
Diff to previous 1.125
added stuff for empty cells

Revision 1.125 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 28 16:38:25 2008 UTC (11 years, 7 months ago) by bartels
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.124: +114 -0 lines
Diff to previous 1.124
added a function for changing just the string of a functional role

Revision 1.124 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 20 19:28:37 2008 UTC (11 years, 8 months ago) by bartels
Branch: MAIN
Changes since 1.123: +40 -6 lines
Diff to previous 1.123
added support for variant descriptions

Revision 1.123 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 19 22:54:44 2008 UTC (11 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.122: +1 -1 lines
Diff to previous 1.122
get rid of debugging Dumper in Subsystem.pm

Revision 1.122 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 19 18:36:34 2008 UTC (11 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.121: +16 -0 lines
Diff to previous 1.121
validate genome id is of the proper form  before writing its row to spreadsheet.

Revision 1.121 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 11 19:13:06 2008 UTC (11 years, 9 months ago) by bartels
Branch: MAIN
Changes since 1.120: +7 -2 lines
Diff to previous 1.120
*** empty log message ***

Revision 1.120 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 9 21:08:22 2007 UTC (11 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.119: +1 -1 lines
Diff to previous 1.119
Fixed bad spelling in a call to FIGRules.

Revision 1.119 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 6 13:59:34 2007 UTC (11 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.118: +76 -103 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 19:12:58 2007 UTC (12 years ago) by dejongh
Branch: MAIN
Changes since 1.117: +13 -11 lines
Diff to previous 1.117
Hope College updates

Revision 1.117 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 9 21:16:35 2007 UTC (12 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.116: +19 -0 lines
Diff to previous 1.116
Add subsystem-at-a-time coupling lookup in get_ev_codes that goes iwth the new coupled_to_batch interface.

Revision 1.116 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 30 23:32:33 2007 UTC (12 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.115: +2 -0 lines
Diff to previous 1.115
fixes to Subsystem.pm

Revision 1.115 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 30 23:08:43 2007 UTC (12 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.114: +21 -2 lines
Diff to previous 1.114
minor modifications to get subsystems statistics

Revision 1.114 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 21 14:16:06 2007 UTC (12 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.113: +7 -4 lines
Diff to previous 1.113
Make coupling coloring work when the pch server is in use.

Revision 1.113 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 18 16:48:07 2007 UTC (12 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.112: +1 -0 lines
Diff to previous 1.112
added missing "use"

Revision 1.112 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 8 21:55:29 2007 UTC (12 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.111: +12 -2 lines
Diff to previous 1.111
Fix diagram update bug on isntall of existing subystem.

Revision 1.111 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 24 17:31:16 2007 UTC (12 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.110: +2 -1 lines
Diff to previous 1.110
Commented out a debug print.

Revision 1.110 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 18 18:08:43 2007 UTC (12 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.109: +122 -2 lines
Diff to previous 1.109
add support for description and literature in the notes section.

Revision 1.109 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 14 19:46:50 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.108: +3 -3 lines
Diff to previous 1.108
change GetFile back to file_read - it is not an error for the files not to exist.

Revision 1.108 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 11 17:37:59 2007 UTC (12 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.107: +35 -28 lines
Diff to previous 1.107
Factored out some FIG references to make it easier to move the code to Sprout. Fixed a messy problem in the handling of diagrams when the user is coming from "display_subsys.cgi" instead of the other thing whose name I can't remember right now.

Revision 1.107 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 22 18:16:37 2007 UTC (12 years, 6 months ago) by dejongh
Branch: MAIN
Changes since 1.106: +10 -5 lines
Diff to previous 1.106
get_hope_reactions_for_genome now returns a hash of reactions to pegs

Revision 1.106 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 18 16:57:19 2007 UTC (12 years, 6 months ago) by dejongh
Branch: MAIN
Changes since 1.105: +26 -0 lines
Diff to previous 1.105
Added get_hope_reactions_for_genome

Revision 1.105 - (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 1.104: +476 -1 lines
Diff to previous 1.104
Hope college modifications.

Revision 1.104 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 10 03:50:30 2007 UTC (12 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.103: +21 -2 lines
Diff to previous 1.103
Added some POD documentation.

Revision 1.103 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 5 21:31:06 2007 UTC (12 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.102: +1 -1 lines
Diff to previous 1.102
do bulk lookup of attributes correctly

Revision 1.102 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 5 21:03:50 2007 UTC (12 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.101: +11 -2 lines
Diff to previous 1.101
do bulk lookup of attributes

Revision 1.101 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 4 21:31:55 2007 UTC (12 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.100: +3 -3 lines
Diff to previous 1.100
add comma and colon to banned characters

Revision 1.100 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 4 21:22:52 2007 UTC (12 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.99: +22 -0 lines
Diff to previous 1.99
make role abbreviations space-free and unique on write to spreadsheet

Revision 1.99 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 12 13:39:05 2007 UTC (12 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.98: +6 -3 lines
Diff to previous 1.98
fixes to allow non-peg features in subsystems

Revision 1.98 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 16 22:28:01 2007 UTC (12 years, 9 months ago) by paarmann
Branch: MAIN
Changes since 1.97: +2 -0 lines
Diff to previous 1.97
create_new_diagram now returns the id of the created diagram

Revision 1.97 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 16 16:46:22 2007 UTC (12 years, 9 months ago) by paarmann
Branch: MAIN
Changes since 1.96: +25 -0 lines
Diff to previous 1.96
added support for new diagrams

Revision 1.96 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 26 21:33:03 2007 UTC (12 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.95: +51 -0 lines
Diff to previous 1.95
add get_roles_for_genome and get_abbr_for_role

Revision 1.95 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 19 17:01:06 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.94: +1 -0 lines
Diff to previous 1.94
make sure things work, even if the table aux_roles does not exist

Revision 1.94 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 18 03:08:57 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.93: +34 -3 lines
Diff to previous 1.93
add comments to functions

Revision 1.93 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 13 19:11:05 2006 UTC (12 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.92: +2 -2 lines
Diff to previous 1.92
remove debug prints

Revision 1.92 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 29 15:19:19 2006 UTC (12 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.91: +29 -0 lines
Diff to previous 1.91
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 1.91 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 22 05:07:46 2006 UTC (13 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.90: +38 -0 lines
Diff to previous 1.90
Added a method to get the roles of a peg in the subsystem.

Revision 1.90 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 17 18:44:03 2006 UTC (13 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.89: +9 -1 lines
Diff to previous 1.89
Updated diagram URL computer to specify SPROUT=1 if called from Sprout pages.

Revision 1.89 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 26 21:10:13 2006 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.88: +0 -1 lines
Diff to previous 1.88
add add_to_subsystems

Revision 1.88 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 1 21:06:19 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.87: +1 -1 lines
Diff to previous 1.87
RAE: removing extra new line

Revision 1.87 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 12 12:05:55 2006 UTC (13 years, 6 months ago) by heiko
Branch: MAIN
Changes since 1.86: +24 -4 lines
Diff to previous 1.86
added a strict param to the function functional_role_instances that only selects pegs that are still in sync with the role

Revision 1.86 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Apr 2 16:57:10 2006 UTC (13 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.85: +1 -1 lines
Diff to previous 1.85
Changed a warning to a trace message.

Revision 1.85 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 23 22:27:14 2006 UTC (13 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.84: +2 -2 lines
Diff to previous 1.84
RAE: Debugging a weird ss error on yersinia that I cant replicate elsewhere

Revision 1.84 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 21 17:06:47 2006 UTC (13 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.83: +11 -2 lines
Diff to previous 1.83
more empty-SS fixes

Revision 1.83 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 21 16:59:12 2006 UTC (13 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.82: +2 -2 lines
Diff to previous 1.82
Some null-ref checks.

Revision 1.82 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 31 04:11:08 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.81: +1 -2 lines
Diff to previous 1.81
fix of clustering

Revision 1.81 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 31 04:09:13 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.80: +2 -1 lines
Diff to previous 1.80
fix of clustering

Revision 1.80 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 30 19:36:04 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.79: +1 -1 lines
Diff to previous 1.79
use is_genome checks for subsystems?

Revision 1.79 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 5 02:30:25 2006 UTC (13 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.78: +2 -2 lines
Diff to previous 1.78
remove variant debug messages.

Revision 1.78 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 30 11:52:01 2005 UTC (13 years, 10 months ago) by heiko
Branch: MAIN
Changes since 1.77: +36 -0 lines
Diff to previous 1.77
added functional_role_instances function

Revision 1.77 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 8 19:50:50 2005 UTC (13 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.76: +20 -9 lines
Diff to previous 1.76
Added trace messages.

Revision 1.76 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 5 19:06:30 2005 UTC (13 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.75: +17 -0 lines
Diff to previous 1.75
Added license words.

Revision 1.75 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 28 22:39:45 2005 UTC (13 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.74: +218 -31 lines
Diff to previous 1.74
Split "get_diagrams" into subroutines so that tasks performed by both the FIG and Sprout functions use common code.

Revision 1.74 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 12 21:03:16 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-00-00-00
Changes since 1.73: +4 -2 lines
Diff to previous 1.73
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 1.73 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 12 02:45:35 2005 UTC (14 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.72: +271 -92 lines
Diff to previous 1.72
Upgraded the documentation.

Revision 1.72 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 3 20:00:13 2005 UTC (14 years, 1 month ago) by redwards
Branch: MAIN
CVS Tags: caBIG-dataload-0
Changes since 1.71: +2 -0 lines
Diff to previous 1.71
removing leading/trailing spaces

Revision 1.71 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 15 19:04:46 2005 UTC (14 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.70: +1 -1 lines
Diff to previous 1.70
Remove debug print.

Revision 1.70 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 15 18:47:58 2005 UTC (14 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.69: +267 -61 lines
Diff to previous 1.69
Careful cleanup of subsystem indexing. Patched a bunch of spots where needed updates didn't happen.

Add variant code to subsystem index.

Revision 1.69 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 15 14:33:49 2005 UTC (14 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.68: +696 -696 lines
Diff to previous 1.68
Converted tabs to spaces.

Revision 1.68 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 10 16:25:28 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.67: +5 -5 lines
Diff to previous 1.67
Add a force_backups option to write_subsystem.

Revision 1.67 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 10 12:03:36 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.66: +51 -7 lines
Diff to previous 1.66
More logging and sanity checks on diagram code.

Revision 1.66 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 9 18:08:41 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.65: +22 -1 lines
Diff to previous 1.65
Use system and an array to do the rm -r so we don't get bashed by ()s.

Revision 1.65 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 8 21:54:39 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.64: +111 -26 lines
Diff to previous 1.64
More diagram changes.

Add new simple start page.

Revision 1.64 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 8 20:05:08 2005 UTC (14 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.63: +3 -3 lines
Diff to previous 1.63
Fixed module attributes that were causing massive compile warnings.

Revision 1.63 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 4 13:27:40 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.62: +1 -1 lines
Diff to previous 1.62
fix bad bug in db_synch for subsystems

Revision 1.62 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 3 21:16:29 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.61: +36 -5 lines
Diff to previous 1.61
Support gif/png/jpeg file type detection on diagram upload.
Support the multiple file types on packaging for clearinghouse.

Revision 1.61 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 3 17:40:42 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.60: +140 -18 lines
Diff to previous 1.60
Add support for creating and parsing diagram data as part of subsystem clearinghouse packages.

Revision 1.60 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 1 22:22:13 2005 UTC (14 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.59: +81 -81 lines
Diff to previous 1.59
Changed attributes to capital-case in order to prevent the avalanche of compile-time warnings.

Revision 1.59 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jul 30 13:02:31 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.58: +10 -3 lines
Diff to previous 1.58
fixes to reactions in subsystems

Revision 1.58 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 29 19:31:21 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.57: +54 -1 lines
Diff to previous 1.57
add reactions to subsystems

Revision 1.57 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 29 18:13:45 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.56: +9 -2 lines
Diff to previous 1.56
Make index_subsystems use file load instead of inserts.

Revision 1.56 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 21 18:38:58 2005 UTC (14 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.55: +3 -0 lines
Diff to previous 1.55
Convert space to _ in constructor.

Revision 1.55 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 12 21:08:09 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
Changes since 1.54: +6 -2 lines
Diff to previous 1.54
improved subsys_vectors.cgi

Revision 1.54 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 8 23:05:21 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: Root-bobdev_news, merge-bobdev_news-1, merge-bobdev_news-2, merge-bodev_news-3, merge-trunktag-bobdev_news-1, merge-trunktag-bobdev_news-2, merge-trunktag-bodev_news-3
Branch point for: Branch-bobdev_news
Changes since 1.53: +1 -0 lines
Diff to previous 1.53
major change to BBHs (use precomputed)

Revision 1.53 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 10 12:03:39 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.52: +3 -1 lines
Diff to previous 1.52
fixes to using trees under subsystems

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 25 19:59:11 2005 UTC (14 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.51: +48 -1 lines
Diff to previous 1.51
add get_sorted_rows.

Fix get_subsetC to not fail on empty subsets.

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 8 20:22:23 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.50: +1 -1 lines
Diff to previous 1.50
changed tag/value pairs completely. Ooops!

Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 7 19:16:10 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.49: +8 -4 lines
Diff to previous 1.49
many changes to key/value pairs to make them work

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 5 18:24:34 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.48: +4 -0 lines
Diff to previous 1.48
strip leading/trailing spaces on subsystem aabr and names

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Mar 12 20:30:38 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.47: +24 -0 lines
Diff to previous 1.47
Changed Subsystems to allow selection of active_subsetR (rows) based on tag/value pairs

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 26 11:01:13 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.46: +14 -6 lines
Diff to previous 1.46
add reset_curator.cgi

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 24 22:02:39 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.45: +4 -2 lines
Diff to previous 1.45
add set_variants.cgi and fixes to Subsystems.pm

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 14 18:22:14 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.44: +1 -0 lines
Diff to previous 1.44
initialize classification data when creating subsystem

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 18:18:14 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.43: +31 -0 lines
Diff to previous 1.43
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 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 26 23:46:20 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.42: +9 -0 lines
Diff to previous 1.42
fix bug in removing genomes from a subsystem

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 30 17:06:13 2004 UTC (14 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.41: +36 -1 lines
Diff to previous 1.41
Add support for sending a list of genomes to billogix extension code.

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 12 03:48:02 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.40: +6 -0 lines
Diff to previous 1.40
fix bug in -save parm for align_with_clustal

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 25 20:32:35 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.39: +4 -2 lines
Diff to previous 1.39
add document on exchange of annotations and assignments

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 16 20:42:28 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.38: +5 -2 lines
Diff to previous 1.38
fixes to generalize chromosomal_clusters.cgi for UniProt

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 12 11:56:23 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.37: +7 -3 lines
Diff to previous 1.37
updates to subsys.cgi

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 10 17:13:55 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.36: +62 -17 lines
Diff to previous 1.36
many fixes to subsystems code

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 6 21:37:02 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.35: +5 -2 lines
Diff to previous 1.35
fix bug in copying a subsystem

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 28 20:39:39 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.34: +18 -10 lines
Diff to previous 1.34
fix subset and sorting problems in subsys.cgi

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 23 19:58:28 2004 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.33: +7 -0 lines
Diff to previous 1.33
subsys.cgi was not letting the user delete genomes or set variants

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 17 00:56:04 2004 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.32: +8 -2 lines
Diff to previous 1.32
fixes to subsys.cgi

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 9 00:00:09 2004 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.31: +1 -1 lines
Diff to previous 1.31
minor fixes

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 7 02:54:16 2004 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.30: +71 -11 lines
Diff to previous 1.30
add new subsystem interface

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 1 18:39:23 2004 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.29: +30 -0 lines
Diff to previous 1.29
Add set/get active subsets.

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 29 18:36:05 2004 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.28: +17 -2 lines
Diff to previous 1.28
add roles_with_abbrevations

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 27 17:57:17 2004 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.27: +1 -1 lines
Diff to previous 1.27
darn typos

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Fri Aug 27 17:55:45 2004 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.26: +1 -1 lines
Diff to previous 1.26
Fix typo.

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Fri Aug 27 15:36:29 2004 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.25: +110 -0 lines
Diff to previous 1.25
Added get/set_notes, set_pegs_in_cell, functionality for importing notes
from copied subsystem.

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 26 21:26:52 2004 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.24: +974 -41 lines
Diff to previous 1.24
Massive changes to suppor new subsystem editor.

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 16 22:10:55 2004 UTC (15 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.23: +0 -2 lines
Diff to previous 1.23
straighten out FIG.pm

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 3 19:13:25 2004 UTC (15 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.22: +131 -54 lines
Diff to previous 1.22
Add chunked execution of subsystem extension.

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 20 18:20:14 2004 UTC (15 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.21: +12 -0 lines
Diff to previous 1.21
changes to delete subsystem_index entries when a subsystem is deleted

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Thu Jun 24 19:28:23 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.20: +8 -8 lines
Diff to previous 1.20
scalar decls

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Thu Jun 24 19:14:57 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.19: +7 -0 lines
Diff to previous 1.19
add call to get role from abbreviation

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 24 18:41:39 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.18: +39 -1 lines
Diff to previous 1.18
Check for existence of rows file after prolog run finishes

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Wed Jun 23 21:32:24 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.17: +3 -0 lines
Diff to previous 1.17
ELimiate spaces from subsystem name used in jobid, should help in
assignment stuff.

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 18 14:48:55 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.16: +35 -0 lines
Diff to previous 1.16
Changes for new clearing house display.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 17 18:31:45 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.15: +4 -3 lines
Diff to previous 1.15
subsystem extension filename tweaks

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 16 17:33:53 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.14: +1 -1 lines
Diff to previous 1.14
Fix dumb typo.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 16 16:52:10 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.13: +78 -2 lines
Diff to previous 1.13
Modifications to fix & finish up the automated subsystem extension.

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 16 14:05:42 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.12: +46 -1 lines
Diff to previous 1.12
Add support to allow only one subsystem extension to run for a given subsystem.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 14 22:04:35 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.11: +129 -1 lines
Diff to previous 1.11
Add subsystem extension support

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 10 13:40:07 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.10: +1 -1 lines
Diff to previous 1.10
remove missing subsystem warning for now

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 8 15:02:15 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.9: +4 -1 lines
Diff to previous 1.9
Add capability for :scalar :list :remote annotations to FIG interface. This works with
modules that are declared as subclasses of FIGAttributes.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 7 19:58:21 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.8: +0 -2 lines
Diff to previous 1.8
mods for removing empty seqs from export

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 4 16:26:13 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.7: +2 -2 lines
Diff to previous 1.7
fix filename used for area table

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 4 16:21:10 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.6: +132 -2 lines
Diff to previous 1.6
Add diagram api

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 1 20:30:14 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.5: +3 -1 lines
Diff to previous 1.5
Use DBI's prepare/execute to insert stuff, to get around quoting problems.

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 1 20:22:03 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.4: +65 -1 lines
Diff to previous 1.4
add db_sync, initialization of data structrues on load

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 27 19:27:53 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.3: +8 -1 lines
Diff to previous 1.3
add get_role_abbr, fix loading of abbrevs

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 26 22:34:24 2004 UTC (15 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.2: +21 -0 lines
Diff to previous 1.2
add more accessors

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 25 16:19:23 2004 UTC (15 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.1: +158 -42 lines
Diff to previous 1.1
more docs, more accessors

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 24 21:55:18 2004 UTC (15 years, 6 months ago) by olson
Branch: MAIN
Beginning of sim queueing stuff.
First implementation of Subsystem object, with FIG::peg_in_subsystem_cell
implemented in terms of it.

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