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Revision 1.157 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 23 14:59:16 2014 UTC (4 years, 10 months ago) by overbeek
Branch: MAIN
CVS Tags: HEAD
Changes since 1.156: +8 -0 lines
Diff to previous 1.156
add change_funcrole

Revision 1.156 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 12 22:49:50 2011 UTC (8 years, 4 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_08022011, mgrast_dev_08112011, mgrast_dev_10262011, mgrast_dev_12152011, mgrast_release_3_1_1, mgrast_release_3_1_2, mgrast_version_3_2, rast_rel_2011_0928, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.155: +2 -3 lines
Diff to previous 1.155
Added model seed call to role-changer.

Revision 1.155 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 21 20:36:46 2011 UTC (8 years, 10 months ago) by redwards
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, myrast_rel40
Changes since 1.154: +8 -0 lines
Diff to previous 1.154
adding a method to list all phages

Revision 1.154 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 21 02:13:14 2010 UTC (9 years, 5 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119
Changes since 1.153: +2 -3 lines
Diff to previous 1.153
support for new figfams interface

Revision 1.153 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 30 14:41:36 2010 UTC (9 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.152: +7 -0 lines
Diff to previous 1.152
note that add_features cannot be used to add pegs

Revision 1.152 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 11 20:27:34 2009 UTC (10 years, 3 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2009_0925, rast_rel_2010_0118, rast_rel_2010_0526
Changes since 1.151: +6 -0 lines
Diff to previous 1.151
add coupled_to_batch

Revision 1.151 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 8 20:24:02 2009 UTC (10 years, 4 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2009_07_09
Changes since 1.150: +19 -0 lines
Diff to previous 1.150
add subsystem_classification & all_subsystem_classifications support

Revision 1.150 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 21 22:28:32 2009 UTC (10 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.149: +10 -4 lines
Diff to previous 1.149
bad pattern on a few commands

Revision 1.149 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 11 02:58:49 2009 UTC (10 years, 6 months ago) by redwards
Branch: MAIN
CVS Tags: rast_rel_2009_05_18
Changes since 1.148: +11 -8 lines
Diff to previous 1.148
fixing function_to_subsystems

Revision 1.148 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 9 16:25:57 2009 UTC (10 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.147: +10 -0 lines
Diff to previous 1.147
add variant_code

Revision 1.147 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 7 16:41:10 2009 UTC (10 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.146: +8 -0 lines
Diff to previous 1.146
add co_occurring_FIGfams

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Wed May 6 20:43:04 2009 UTC (10 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.145: +15 -0 lines
Diff to previous 1.145
add call to co-occurrence functions

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Mon Apr 27 19:10:37 2009 UTC (10 years, 6 months ago) by arodri7
Branch: MAIN
Changes since 1.144: +16 -0 lines
Diff to previous 1.144
added change_func_role to fig.pl

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Fri Apr 3 01:01:42 2009 UTC (10 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.143: +1 -1 lines
Diff to previous 1.143
add find_poss_errs and fix documentation in fig.pl

Revision 1.143 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Mar 14 10:55:17 2009 UTC (10 years, 8 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2009_03_26
Changes since 1.142: +10 -1 lines
Diff to previous 1.142
added co_occurrence routines

Revision 1.142 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 13 18:20:37 2009 UTC (10 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.141: +13 -6 lines
Diff to previous 1.141
handle non-existing pairset properly

Revision 1.141 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 11 02:03:12 2009 UTC (10 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.140: +10 -2 lines
Diff to previous 1.140
version going to Bruce

Revision 1.140 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 10 23:57:54 2009 UTC (10 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.139: +1 -1 lines
Diff to previous 1.139
minor fixes

Revision 1.139 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 9 18:33:20 2009 UTC (10 years, 8 months ago) by disz
Branch: MAIN
Changes since 1.138: +2 -2 lines
Diff to previous 1.138
updated get_representative_genome

Revision 1.138 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 9 18:30:42 2009 UTC (10 years, 8 months ago) by disz
Branch: MAIN
Changes since 1.137: +7 -0 lines
Diff to previous 1.137
added get_representative_genome

Revision 1.137 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 8 18:39:28 2009 UTC (10 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.136: +50 -5 lines
Diff to previous 1.136
added calls to co_occurrence routines to fig.pl

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Sat Mar 7 00:11:31 2009 UTC (10 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.135: +42 -0 lines
Diff to previous 1.135
add functional coupling calls to fig.pl

Revision 1.135 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 4 17:46:36 2009 UTC (10 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.134: +6 -0 lines
Diff to previous 1.134
add is_cluster_based_subsystem to fig.pl

Revision 1.134 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 29 20:24:13 2009 UTC (10 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2009_02_05
Changes since 1.133: +75 -0 lines
Diff to previous 1.133
additions to support partitioning of sims

Revision 1.133 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 23 23:39:22 2008 UTC (11 years, 2 months ago) by golsen
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, mgrast_rel_2008_0806, mgrast_rel_2008_0917, mgrast_rel_2008_0919, mgrast_rel_2008_0923, mgrast_rel_2008_0924, mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, rast_2008_0924, rast_rel_2008_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_release_2008_09_29
Changes since 1.132: +10 -43 lines
Diff to previous 1.132
Move writing of assignment annotation from a case-by-case basis (and it
was missing in several key places) to the FIG::assign_function.

Modify the code in each of the calling locations to not make duplicate
annotations.

At the same time, remove (most) of the instances of making different
calls to assign_function depending on the user name.  assign_function
treats everyone as master (but writes an annotation with the real user
name).

Revision 1.132 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jun 28 05:58:33 2008 UTC (11 years, 4 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2008_07_21, rast_rel_2008_08_07
Changes since 1.131: +134 -3 lines
Diff to previous 1.131
code relating to dlit/ilit maintenance

Revision 1.131 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 11 14:15:16 2008 UTC (11 years, 7 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2008_04_23, rast_rel_2008_06_16, rast_rel_2008_06_18
Changes since 1.130: +1 -1 lines
Diff to previous 1.130
changes to FIGfams

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Wed Mar 5 17:29:23 2008 UTC (11 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.129: +9 -0 lines
Diff to previous 1.129
add get_corresponding_ids

Revision 1.129 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 19 20:34:57 2007 UTC (12 years ago) by olson
Branch: MAIN
Changes since 1.128: +7 -7 lines
Diff to previous 1.128
Changes to make the passing of a sims cutoff of 0 work properly (using defined($maxP) instead  of $maxP
as a test to see if maxP was set).

Revision 1.128 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 23 14:44:36 2007 UTC (12 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.127: +1 -1 lines
Diff to previous 1.127
minor typo in fig.pl

Revision 1.127 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 13 15:10:06 2007 UTC (12 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.126: +2 -1 lines
Diff to previous 1.126
fixes to fc_figfams

Revision 1.126 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 24 20:53:51 2007 UTC (12 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.125: +14 -0 lines
Diff to previous 1.125
add a routine in FIG.pm giving who set the function of a peg

Revision 1.125 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 28 14:02:05 2007 UTC (12 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.124: +15 -0 lines
Diff to previous 1.124
fixes to rebuilding figfams

Revision 1.124 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 26 16:43:12 2007 UTC (12 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.123: +29 -1 lines
Diff to previous 1.123
minor fixes to supporting deletion of features

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Mon Jun 25 19:43:17 2007 UTC (12 years, 4 months ago) by gdpusch
Branch: MAIN
Changes since 1.122: +7 -5 lines
Diff to previous 1.122
Added "v" (viral) filter to "genomes" coommand. -- /gdp

Revision 1.122 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 15 18:52:08 2007 UTC (12 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.121: +24 -0 lines
Diff to previous 1.121
set up fig command to handle adding features from a file

Revision 1.121 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 28 14:47:53 2007 UTC (12 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.120: +1 -0 lines
Diff to previous 1.120
add best_tree_using_proml_on_cluster

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Fri Apr 27 16:53:44 2007 UTC (12 years, 6 months ago) by overbeek
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Changes since 1.119: +7 -0 lines
Diff to previous 1.119
add recast_ids

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Thu Feb 8 18:34:32 2007 UTC (12 years, 9 months ago) by overbeek
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Changes since 1.118: +10 -4 lines
Diff to previous 1.118
Added &get_dna_seq($fid). -- /gdp

Revision 1.118 - (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 1.117: +5 -0 lines
Diff to previous 1.117
add comments to functions

Revision 1.117 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 13 23:36:00 2006 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.116: +12 -14 lines
Diff to previous 1.116
fixes to add_feature, delete_feature, and replace_feature_with

Revision 1.116 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 1 23:22:45 2006 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.115: +6 -0 lines
Diff to previous 1.115
add GO attribute genertation

Revision 1.115 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 30 23:04:16 2006 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.114: +16 -0 lines
Diff to previous 1.114
put in the fr2go stuff

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Wed Nov 29 20:59:44 2006 UTC (12 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.113: +8 -0 lines
Diff to previous 1.113
Add FIGV support for peg/subsystem indexing.

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Wed Nov 29 15:19:19 2006 UTC (12 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.112: +10 -0 lines
Diff to previous 1.112
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 1.112 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 15 18:36:53 2006 UTC (13 years, 2 months ago) by overbeek
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Changes since 1.111: +22 -0 lines
Diff to previous 1.111
introduce locks on features to block assignments

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Fri Jul 14 22:22:29 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.110: +1 -1 lines
Diff to previous 1.110
Fixed obsolete form of boundaries_of.

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Tue Jun 13 23:32:15 2006 UTC (13 years, 5 months ago) by overbeek
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Changes since 1.109: +5 -0 lines
Diff to previous 1.109
RAE: moving PIRSF to links

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Fri May 19 13:48:16 2006 UTC (13 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.108: +1 -1 lines
Diff to previous 1.108
bugfix.

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Fri May 19 13:44:05 2006 UTC (13 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.107: +10 -2 lines
Diff to previous 1.107
Some changes to add_genome logic.

(Only log after genome add completes; turn some formerly fatal errors into nonfatal
with warnings so that we don't end up with a partially-added genome).

Revision 1.107 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 18 12:27:21 2006 UTC (13 years, 6 months ago) by overbeek
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Changes since 1.106: +8 -0 lines
Diff to previous 1.106
add normalizded bit scores to BBHs

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Sun May 7 12:25:12 2006 UTC (13 years, 6 months ago) by overbeek
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Changes since 1.105: +4 -3 lines
Diff to previous 1.105
minor changes to logging correspondences

Revision 1.105 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 7 04:04:40 2006 UTC (13 years, 6 months ago) by overbeek
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Changes since 1.104: +8 -0 lines
Diff to previous 1.104
add ability to log arbitrary correspondences

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Fri May 5 14:38:00 2006 UTC (13 years, 6 months ago) by overbeek
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Changes since 1.103: +91 -32 lines
Diff to previous 1.103
added new logging

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Thu May 4 20:05:54 2006 UTC (13 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.102: +20 -10 lines
Diff to previous 1.102
Turn off sim server support unless enabled in FIG_Config,for now.

add dont_mark_complete to fig add_genome.

Revision 1.102 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 28 18:09:19 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.101: +24 -0 lines
Diff to previous 1.101
must have a role index on subsystem_index, added is_NMPDR_genome, etc.

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Tue Feb 14 15:07:08 2006 UTC (13 years, 9 months ago) by overbeek
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Changes since 1.100: +20 -1 lines
Diff to previous 1.100
add logging on update operations

Revision 1.100 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 5 01:08:16 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.99: +16 -0 lines
Diff to previous 1.99
RAE: Swtiched to using SQL Count for the number of contigs

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Wed Jan 25 04:12:20 2006 UTC (13 years, 9 months ago) by overbeek
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Changes since 1.98: +1 -1 lines
Diff to previous 1.98
RAE: Updating proteinfamilies

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Mon Jan 23 19:20:54 2006 UTC (13 years, 9 months ago) by overbeek
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Changes since 1.97: +28 -0 lines
Diff to previous 1.97
changes to support dynamic sims and updates

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Fri Jan 13 20:22:40 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.96: +25 -0 lines
Diff to previous 1.96
fixes to deleted_features, replace_features_with, etc

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Thu Jan 5 01:17:24 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.95: +10 -3 lines
Diff to previous 1.95
RAE: Adding subsystem_genomes and correct genomes_for_subsystems

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Tue Jan 3 18:31:43 2006 UTC (13 years, 10 months ago) by efrank
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Changes since 1.94: +7 -0 lines
Diff to previous 1.94
add subsystems_having_organism

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Sat Dec 24 21:03:57 2005 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.93: +0 -1 lines
Diff to previous 1.93
serious problem in setting max_expand in FIG::sims

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Wed Dec 21 23:51:50 2005 UTC (13 years, 11 months ago) by overbeek
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Changes since 1.92: +18 -0 lines
Diff to previous 1.92
RAE: Adding statistics to protein families

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Tue Dec 20 17:59:09 2005 UTC (13 years, 11 months ago) by overbeek
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Changes since 1.91: +7 -0 lines
Diff to previous 1.91
add abstract functional coupling

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Mon Dec 5 18:56:37 2005 UTC (13 years, 11 months ago) by olson
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Changes since 1.90: +17 -0 lines
Diff to previous 1.90
Add license words.

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Thu Dec 1 22:28:13 2005 UTC (13 years, 11 months ago) by overbeek
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Changes since 1.89: +2 -1 lines
Diff to previous 1.89
Making attributes work for Ed

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Wed Nov 23 20:34:59 2005 UTC (13 years, 11 months ago) by overbeek
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Changes since 1.88: +16 -1 lines
Diff to previous 1.88
major changes to attributes and protein families. There are changes to several modules to deal with new attributes database, and simultaneous updates to protein families

Revision 1.88 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 11 20:40:57 2005 UTC (14 years, 1 month ago) by efrank
Branch: MAIN
CVS Tags: caBIG-00-00-00
Changes since 1.87: +12 -0 lines
Diff to previous 1.87


add find_by_attribute. this takes a single string arg and returns triples,
(featureId, key, value) of all attributes in which the search tstring
is a substring of either key or value. the search is via the attribute
table, not via the glimpse indesces so that searches immediately after edits
of attribs still work.

not sure i've got th parse of the args right (for strings that are multiple words)

Revision 1.87 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 11 00:25:33 2005 UTC (14 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.86: +2 -2 lines
Diff to previous 1.86
adding maximum expansion to sims

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Mon Oct 10 20:09:56 2005 UTC (14 years, 1 month ago) by overbeek
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Changes since 1.85: +4 -3 lines
Diff to previous 1.85
add_attributes bug fix

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Thu Oct 6 22:44:02 2005 UTC (14 years, 1 month ago) by overbeek
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Changes since 1.84: +3 -3 lines
Diff to previous 1.84
adding more functions with external ids

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Thu Oct 6 21:22:48 2005 UTC (14 years, 1 month ago) by overbeek
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Changes since 1.83: +14 -0 lines
Diff to previous 1.83
loading external ids and external protein families

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Tue Oct 4 02:29:29 2005 UTC (14 years, 1 month ago) by redwards
Branch: MAIN
CVS Tags: caBIG-dataload-0
Changes since 1.82: +8 -0 lines
Diff to previous 1.82
adding differentiate protein families

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Mon Oct 3 20:02:53 2005 UTC (14 years, 1 month ago) by redwards
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Changes since 1.81: +7 -0 lines
Diff to previous 1.81
adding command line method to add a single attribute

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Fri Sep 30 16:00:19 2005 UTC (14 years, 1 month ago) by overbeek
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Changes since 1.80: +8 -0 lines
Diff to previous 1.80
Add "init_local_sim_computation" method to create a sim computation askfor pool.

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Sun Sep 4 15:13:20 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.79: +5 -0 lines
Diff to previous 1.79
add ability to get epoch date from fig.pl

Revision 1.79 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 2 22:21:57 2005 UTC (14 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.78: +6 -19 lines
Diff to previous 1.78
Add $fig->add_annotations_batch() that does filehandle conservation and uses COPY TABLE instead
of INSERT to add annotations to the database. Now used by 'fig add_annotations' so that
large annotation file installs don't take overnight.

Revision 1.78 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 2 16:27:14 2005 UTC (14 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.77: +10 -3 lines
Diff to previous 1.77
Allow the user  to specify a time to convert with epoch_to_readable

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Fri Aug 19 19:52:19 2005 UTC (14 years, 3 months ago) by redwards
Branch: MAIN
Changes since 1.76: +13 -0 lines
Diff to previous 1.76
Adding more details to organisms.cgi and correcting get_key_values

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Wed Aug 17 02:52:18 2005 UTC (14 years, 3 months ago) by redwards
Branch: MAIN
Changes since 1.75: +7 -0 lines
Diff to previous 1.75
adding erase attribute

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Tue Aug 16 19:41:59 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.74: +28 -0 lines
Diff to previous 1.74
NMPDR updates.

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Mon Aug 8 21:08:56 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.73: +7 -14 lines
Diff to previous 1.73
minor mod to make ss by homol better on memory

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Mon Aug 8 19:42:47 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.72: +26 -0 lines
Diff to previous 1.72
find protein families for proteins in a genome

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Sat Aug 6 00:32:22 2005 UTC (14 years, 3 months ago) by redwards
Branch: MAIN
Changes since 1.71: +5 -1 lines
Diff to previous 1.71
adding help to the commmand line

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Fri Aug 5 16:22:53 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.70: +13 -3 lines
Diff to previous 1.70
subsystems by homology really by homology

Revision 1.70 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 5 16:07:26 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.69: +1 -1 lines
Diff to previous 1.69
correcting spelling

Revision 1.69 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 5 16:03:33 2005 UTC (14 years, 3 months ago) by overbeek
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Changes since 1.68: +16 -0 lines
Diff to previous 1.68
find pegs in subsys by homoology

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Fri Aug 5 13:14:26 2005 UTC (14 years, 3 months ago) by overbeek
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Changes since 1.67: +28 -11 lines
Diff to previous 1.67
adding options to add_genome

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Wed Aug 3 23:00:37 2005 UTC (14 years, 3 months ago) by overbeek
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Changes since 1.66: +3 -2 lines
Diff to previous 1.66
Adding a force to the add_genomes

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Mon Aug 1 18:52:58 2005 UTC (14 years, 3 months ago) by overbeek
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Changes since 1.65: +22 -1 lines
Diff to previous 1.65
update stuff relating to protein families

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Fri Jul 29 18:14:21 2005 UTC (14 years, 3 months ago) by olson
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Changes since 1.64: +2 -2 lines
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Support "fig load_all N" and "fig load_all list"

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Fri Jul 22 16:17:06 2005 UTC (14 years, 4 months ago) by redwards
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Changes since 1.63: +14 -0 lines
Diff to previous 1.63
adding get_keys to fig.pl

Revision 1.61.2.2 - (view) (download) (as text) (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 1.61.2.1: +7 -7 lines
Diff to previous 1.61.2.1 , to branch point 1.61 , to next main 1.157
Merged changes from trunk.

Revision 1.63 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 12 00:34:32 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
CVS Tags: merge-trunktag-bodev_news-3
Changes since 1.62: +7 -7 lines
Diff to previous 1.62
updates to build protein families

Revision 1.61.2.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 27 15:26:44 2005 UTC (14 years, 4 months ago) by olson
Branch: Branch-bobdev_news
CVS Tags: merge-bobdev_news-1, merge-bobdev_news-2
Changes since 1.61: +19 -3 lines
Diff to previous 1.61
Merged from trunk.

Revision 1.62 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 20 17:04:45 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-1, merge-trunktag-bobdev_news-2
Changes since 1.61: +19 -3 lines
Diff to previous 1.61
add new protein family routines

Revision 1.61 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 13 16:43:57 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: Root-bobdev_news
Branch point for: Branch-bobdev_news
Changes since 1.60: +14 -1 lines
Diff to previous 1.60
Ross change commit after cleanup

Revision 1.60 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 9 05:51:06 2005 UTC (14 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.59: +1 -1 lines
Diff to previous 1.59
*** empty log message ***

Revision 1.59 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 1 01:18:50 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.58: +15 -0 lines
Diff to previous 1.58
install precomputed functional coupling data

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Thu May 12 20:38:37 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.57: +11 -0 lines
Diff to previous 1.57
add tool to generate gene blocks for variation analysis

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Thu Apr 21 14:08:50 2005 UTC (14 years, 7 months ago) by overbeek
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Changes since 1.56: +1 -1 lines
Diff to previous 1.56
Fixed typo in default pscore for sims command. -- /gdp

Revision 1.56 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 13 00:03:52 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.55: +9 -0 lines
Diff to previous 1.55
fixed load_attributes. Hopefully

Revision 1.55 - (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
CVS Tags: efrank-preMakefileToStandardMk
Changes since 1.54: +1 -5 lines
Diff to previous 1.54
many changes to key/value pairs to make them work

Revision 1.54 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 7 02:18:04 2005 UTC (14 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.53: +1 -1 lines
Diff to previous 1.53
Fix to search_index so that it can take multiple word query.

Revision 1.53 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 2 11:56:12 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.52: +6 -0 lines
Diff to previous 1.52
add update_subsys_conflicts to fig.pl

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 9 20:15:42 2005 UTC (14 years, 9 months ago) by overbeek
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Changes since 1.51: +5 -0 lines
Diff to previous 1.51
put UniProt ids in trees of columns

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 24 19:18:38 2005 UTC (14 years, 9 months ago) by overbeek
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Changes since 1.50: +12 -0 lines
Diff to previous 1.50
correct concept of user assign in make_annotations_for_sprout

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Sun Dec 5 14:01:53 2004 UTC (14 years, 11 months ago) by overbeek
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Changes since 1.49: +1 -1 lines
Diff to previous 1.49
fix to help for seqs_with_role

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 3 17:46:17 2004 UTC (15 years ago) by overbeek
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Changes since 1.48: +6 -0 lines
Diff to previous 1.48
add is_complete function to FIG.pm

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 2 14:45:31 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.47: +15 -0 lines
Diff to previous 1.47
fix bug in subsys.cgi and add Literature to Global

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Sun Oct 17 00:02:34 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.46: +1 -1 lines
Diff to previous 1.46
fixes to UniProt IDs on chromosomal_clusters.cgi

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Fri Oct 15 17:04:09 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.45: +16 -11 lines
Diff to previous 1.45
peg links generalized to fid links

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 1 19:48:37 2004 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.44: +0 -1 lines
Diff to previous 1.44
minor fixes to exporting sets

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 22 17:25:38 2004 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.43: +2 -2 lines
Diff to previous 1.43
restructured code for presenting chromosomal clusters

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 13 02:12:21 2004 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.42: +14 -0 lines
Diff to previous 1.42
add attributes as key-value pairs attached to fids

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Wed Aug 18 18:46:19 2004 UTC (15 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.41: +33 -0 lines
Diff to previous 1.41
commit untested implementation of feature maintenance

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 2 17:18:55 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.40: +2 -2 lines
Diff to previous 1.40
alter length constraint on BBHs

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 1 19:07:45 2004 UTC (15 years, 5 months ago) by mkubal
Branch: MAIN
Changes since 1.39: +16 -4 lines
Diff to previous 1.39
correct fig.pl to be able to use FIGrpc

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 19 14:15:57 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.38: +11 -0 lines
Diff to previous 1.38
add all_contigs

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 19 13:17:39 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.37: +19 -1 lines
Diff to previous 1.37
fixes on memory leak and genome version

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 27 21:31:30 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.36: +11 -4 lines
Diff to previous 1.36
add the old pull_orfs

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 27 15:41:28 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.35: +11 -0 lines
Diff to previous 1.35
basic query tools

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 24 15:02:08 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.34: +13 -0 lines
Diff to previous 1.34
tools for McCune to build expert automated assignments

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 23 21:49:03 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.33: +2 -2 lines
Diff to previous 1.33
fixes to index.cgi to blast against all complete

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 23 16:59:41 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.32: +15 -0 lines
Diff to previous 1.32
fixes to best_bbh_candidates

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Thu Apr 1 14:54:57 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.31: +13 -0 lines
Diff to previous 1.31
fixes to candidates for a role

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Mon Mar 29 23:11:55 2004 UTC (15 years, 7 months ago) by mkubal
Branch: MAIN
Changes since 1.30: +146 -150 lines
Diff to previous 1.30
added routines to fig.pl

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Thu Mar 25 18:40:21 2004 UTC (15 years, 7 months ago) by mkubal
Branch: MAIN
Changes since 1.29: +55 -254 lines
Diff to previous 1.29
functions added to help menu by MK 03/25/04

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Tue Mar 23 20:42:11 2004 UTC (15 years, 8 months ago) by mkubal
Branch: MAIN
Changes since 1.28: +517 -20 lines
Diff to previous 1.28
fig.pl updated with marked subroutines from FIG.pm by Mike Kubal 3/23/04

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Tue Mar 23 01:04:35 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.27: +1 -1 lines
Diff to previous 1.27
fix exporting chromosomal clusters

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Fri Mar 19 18:45:37 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.26: +2 -0 lines
Diff to previous 1.26
fixes to coupling and protein.cgi

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Thu Mar 18 21:38:57 2004 UTC (15 years, 8 months ago) by gdpusch
Branch: MAIN
Changes since 1.25: +8 -2 lines
Diff to previous 1.25
Added "verify_dir()" function. -- /mike

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Wed Mar 17 20:18:22 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.24: +36 -8 lines
Diff to previous 1.24
for Gordon and Mike

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Wed Mar 17 18:17:34 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.23: +18 -0 lines
Diff to previous 1.23
basic export of subsystems stuff

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Tue Mar 9 03:55:40 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.22: +9 -1 lines
Diff to previous 1.22
add load_distances

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Wed Mar 3 14:56:43 2004 UTC (15 years, 8 months ago) by overbeek
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add merged annotations

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Wed Mar 3 12:49:23 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.20: +13 -0 lines
Diff to previous 1.20
fixes from DOE meeting

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Thu Feb 5 14:05:53 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.19: +4 -3 lines
Diff to previous 1.19
handle complete genomes in fig

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Thu Feb 5 03:29:26 2004 UTC (15 years, 9 months ago) by overbeek
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Changes since 1.18: +1 -1 lines
Diff to previous 1.18
allow complete option on genomes

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Fri Jan 16 14:59:48 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.17: +12 -4 lines
Diff to previous 1.17
add ability to process assignment sets

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Fri Jan 9 19:05:45 2004 UTC (15 years, 10 months ago) by overbeek
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Changes since 1.16: +9 -3 lines
Diff to previous 1.16
stuff

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 9 04:28:42 2004 UTC (15 years, 10 months ago) by overbeek
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Changes since 1.15: +1 -1 lines
Diff to previous 1.15
fix auto_assign

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Thu Jan 8 20:43:47 2004 UTC (15 years, 10 months ago) by overbeek
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Changes since 1.14: +2 -2 lines
Diff to previous 1.14
fix spelling

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Tue Jan 6 23:08:26 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.13: +4 -4 lines
Diff to previous 1.13
fix in extract_genomes

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Tue Jan 6 18:14:48 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.12: +21 -0 lines
Diff to previous 1.12
fix stick behavior for checked sims

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Tue Jan 6 13:19:18 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.11: +3 -3 lines
Diff to previous 1.11
make args consistent for auto assignment

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Tue Jan 6 11:52:31 2004 UTC (15 years, 10 months ago) by overbeek
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Changes since 1.10: +24 -44 lines
Diff to previous 1.10
translate auto_assignments

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Mon Dec 29 02:22:37 2003 UTC (15 years, 10 months ago) by overbeek
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Changes since 1.9: +6 -0 lines
Diff to previous 1.9
numerous performance issues

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 28 17:11:29 2003 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +6 -0 lines
Diff to previous 1.8
cleanup issues relating to large numbers of partial genomes

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Sat Dec 20 21:08:43 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +20 -1 lines
Diff to previous 1.7
fixed issues relating to addition/deletion of genomes

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Sat Dec 20 15:19:21 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +5 -0 lines
Diff to previous 1.6
for incremental additions to the DB, delete old versions of things

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Fri Dec 19 20:09:34 2003 UTC (15 years, 11 months ago) by overbeek
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Changes since 1.5: +0 -6 lines
Diff to previous 1.5
get rid of set_urls, since it will not work anymore

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Fri Dec 5 15:33:56 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
CVS Tags: delong-01, delong-02
Changes since 1.4: +1 -1 lines
Diff to previous 1.4
fix auto_assignG in fig

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Thu Dec 4 21:35:45 2003 UTC (15 years, 11 months ago) by overbeek
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Changes since 1.3: +9 -1 lines
Diff to previous 1.3
add trans to function_of

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Wed Dec 3 21:24:31 2003 UTC (15 years, 11 months ago) by overbeek
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Changes since 1.2: +38 -2 lines
Diff to previous 1.2
*** empty log message ***

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Wed Dec 3 19:39:29 2003 UTC (15 years, 11 months ago) by efrank
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Changes since 1.1: +32 -0 lines
Diff to previous 1.1

fixed a bunch of changes

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 1 20:46:40 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
CVS Tags: V00-00-00, V00-00-01

Makefile:
	get it to work with the release tools

All the rest:
	had to rename foo to foo.pl so that makefiles could recognize
	perl source from, say, Makefiles and READMEs

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