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Revision 1.119 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 15 23:39:01 2009 UTC (10 years, 4 months ago) by parrello
Branch: MAIN
CVS Tags: HEAD, mgrast_dev_02212011, mgrast_dev_02222011, mgrast_dev_03252011, mgrast_dev_03312011, mgrast_dev_04012011, mgrast_dev_04052011, mgrast_dev_04082011, mgrast_dev_04132011, mgrast_dev_05262011, mgrast_dev_06072011, mgrast_dev_08022011, mgrast_dev_08112011, mgrast_dev_10262011, mgrast_dev_12152011, mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_4, mgrast_release_3_1_0, mgrast_release_3_1_1, mgrast_release_3_1_2, mgrast_version_3_2, myrast_33, myrast_rel40, rast_rel_2009_0925, rast_rel_2010_0118, rast_rel_2010_0526, rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119, rast_rel_2011_0928, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.118: +35 -0 lines
Diff to previous 1.118
Added "families_containing_peg".

Revision 1.118 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 28 17:59:37 2009 UTC (10 years, 5 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_07_09
Changes since 1.117: +86 -9 lines
Diff to previous 1.117
Changed the constructor to allow better interoperability with the other ERDB databases.

Revision 1.117 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 15 23:56:44 2009 UTC (10 years, 8 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_03_26, rast_rel_2009_05_18
Changes since 1.116: +65 -0 lines
Diff to previous 1.116
Added support for get_representative_genome and is_exchangable_subsystem.

Revision 1.116 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 2 22:26:56 2009 UTC (10 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.115: +69 -16 lines
Diff to previous 1.115
Fixed some subsystem and organism queries to make them faster.

Revision 1.115 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 5 06:38:30 2009 UTC (10 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.114: +19 -10 lines
Diff to previous 1.114
Updated subsystems_for_peg_complete to match new functionality.

Revision 1.114 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 19 20:36:43 2009 UTC (10 years, 10 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_02_05
Changes since 1.113: +117 -9 lines
Diff to previous 1.113
Fixed a bug in names_of_compound. Implemented find_role_in_org. Fixed some comments.

Revision 1.113 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 13 21:50:33 2008 UTC (11 years ago) by dejongh
Branch: MAIN
CVS Tags: rast_rel_2008_11_24, rast_rel_2008_12_18
Changes since 1.112: +10 -4 lines
Diff to previous 1.112
fix scenario_directory to work for All

Revision 1.112 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 12 18:25:30 2008 UTC (11 years ago) by dejongh
Branch: MAIN
Changes since 1.111: +8 -14 lines
Diff to previous 1.111
switch to scenario_directory

Revision 1.111 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 18 09:55:50 2008 UTC (11 years, 1 month ago) by parrello
Branch: MAIN
CVS Tags: mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2
Changes since 1.110: +29 -9 lines
Diff to previous 1.110
Fixed subsystems_for_pegs. Changed to fail more gracefully if the attribute database is unavailable.

Revision 1.110 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 15 11:52:22 2008 UTC (11 years, 1 month ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_10_29
Changes since 1.109: +10 -2 lines
Diff to previous 1.109
Changed to fail gracefully if an invalid subsystem ID is passed in to get_subsystem.

Revision 1.109 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 9 18:01:03 2008 UTC (11 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.108: +18 -5 lines
Diff to previous 1.108
Added "genome" parameter to seqs_with_role.

Revision 1.108 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Sep 20 14:26:14 2008 UTC (11 years, 2 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, mgrast_rel_2008_0923, mgrast_rel_2008_0924, rast_2008_0924, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_rel_2008_10_09, rast_release_2008_09_29
Changes since 1.107: +20 -12 lines
Diff to previous 1.107
Fixed search to be able to find an organism by name.

Revision 1.107 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 16 18:21:34 2008 UTC (11 years, 2 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_rel_2008_0917, mgrast_rel_2008_0919
Changes since 1.106: +31 -48 lines
Diff to previous 1.106
Added auxiliary role support.

Revision 1.106 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 7 03:11:45 2008 UTC (11 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.105: +59 -12 lines
Diff to previous 1.105
Fixed usable_subsystem to treat nonexistent  subsystems as unusable.

Revision 1.105 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 3 20:32:24 2008 UTC (11 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.104: +53 -15 lines
Diff to previous 1.104
Added subsystem_version and some clearinghouse methods. Fixed to fail gracefully when the attribute server is down.

Revision 1.104 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 6 14:00:57 2008 UTC (11 years, 3 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806, rast_rel_2008_08_07
Changes since 1.103: +221 -163 lines
Diff to previous 1.103
Added support for to_structured_english.

Revision 1.103 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 29 05:48:12 2008 UTC (11 years, 6 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_06_16, rast_rel_2008_06_18, rast_rel_2008_07_21
Changes since 1.102: +351 -40 lines
Diff to previous 1.102
Added some new FIG methods: next-feature, prev-feature, subsystem-version, and auxiliary-role.

Revision 1.102 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 23 15:48:57 2008 UTC (11 years, 8 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.101: +298 -0 lines
Diff to previous 1.101
Implemented feature_aliases_bulk, feature_aliasesI_in_tbl, coupled_to_batch, pegs_of, taxonomy_list, model_directory, organism_directory, and get_corresponding_ids.

Revision 1.101 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 5 02:09:34 2008 UTC (11 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.100: +22 -2 lines
Diff to previous 1.100
Fixed a compiler warnings. Added support for the SEED database host being different from the Sprout database host.

Revision 1.100 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 8 21:14:59 2008 UTC (11 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.99: +12 -3 lines
Diff to previous 1.99
Changed to allow undef for the parameters in genome_of and is_genome. FIG.pm allows this, and chromosomal_clusters.cgi depends on it.

Revision 1.99 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 13 02:05:17 2007 UTC (11 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.98: +34 -0 lines
Diff to previous 1.98
Added a missing pch method.

Revision 1.98 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 6 13:55:57 2007 UTC (11 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.97: +522 -141 lines
Diff to previous 1.97
Changed POD format for better compatability with Wiki. Added support for "genome_list", "contig_lengths", "get_genome_subsystem_count", "get_peg_keys", "all_subsystem_classifications", "subsystems_for"pegs", "run", "run_gathering_output", "is_locked_fid", and a partridge in a pear tree.

Revision 1.97 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 11 23:17:42 2007 UTC (12 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.96: +2 -1 lines
Diff to previous 1.96
Fixed a bug related to aliases.

Revision 1.96 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 22 18:51:03 2007 UTC (12 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.95: +121 -1 lines
Diff to previous 1.95
Fixed a comment. Added support for new methods required by the SEED viewer.

Revision 1.95 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 16 19:39:47 2007 UTC (12 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.94: +8 -8 lines
Diff to previous 1.94
Converted to use the new structuring of aliases.

Revision 1.94 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 2 22:31:15 2007 UTC (12 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.93: +20 -26 lines
Diff to previous 1.93
*** empty log message ***

Revision 1.93 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 7 22:13:48 2007 UTC (12 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.92: +4 -2 lines
Diff to previous 1.92
Fixed a major bug in attribute support.

Revision 1.92 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 7 21:17:37 2007 UTC (12 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.91: +20 -23 lines
Diff to previous 1.91
Fixed attribute handling.

Revision 1.91 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 11 13:06:36 2007 UTC (12 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.90: +1 -1 lines
Diff to previous 1.90
Fixed invalid DAS location reference.

Revision 1.90 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 10 03:48:23 2007 UTC (12 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.89: +582 -29 lines
Diff to previous 1.89
Added methods for Seed Viewer support.

Revision 1.89 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 22 22:08:11 2007 UTC (12 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.88: +2 -1 lines
Diff to previous 1.88
*** empty log message ***

Revision 1.88 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 15 05:05:57 2006 UTC (13 years ago) by parrello
Branch: MAIN
Changes since 1.87: +1 -1 lines
Diff to previous 1.87
Converted to use the configured splitter sequence for separating subsystem classes.

Revision 1.87 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 3 16:59:37 2006 UTC (13 years ago) by parrello
Branch: MAIN
Changes since 1.86: +7 -9 lines
Diff to previous 1.86
Removed obsolete SimBlocks reference. Added a CustomAttributes reference.

Revision 1.86 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 21 07:02:26 2006 UTC (13 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.85: +1 -1 lines
Diff to previous 1.85
Fixed the subsystem classification code to use colon instead of space as a delimiter between levels.

Revision 1.85 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 17 11:36:37 2006 UTC (13 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.84: +2 -4 lines
Diff to previous 1.84
Changed translation check to return TRUE for any real feature. Previously, it returned FALSE for features without protein translations, causing the protein page to fail.

Revision 1.84 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 14 18:03:15 2006 UTC (13 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.83: +8 -3 lines
Diff to previous 1.83
Converted the subsystem classification implementation to expect an ordered, space-delimited list.

Revision 1.83 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 27 16:56:36 2006 UTC (13 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.82: +1 -1 lines
Diff to previous 1.82
Removed redundant sort for pegs_to_subsystems.

Revision 1.82 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 19 17:32:25 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.81: +41 -1 lines
Diff to previous 1.81
Added "usable_subsystem" method.

Revision 1.81 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 12 08:40:58 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.80: +6 -11 lines
Diff to previous 1.80
Fixed subsystem classification method to return a list reference instead of a string.

Revision 1.80 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 10 07:29:22 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.79: +220 -1 lines
Diff to previous 1.79
Added new methods to support the genome statistics page.

Revision 1.79 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 3 03:13:31 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.78: +4 -4 lines
Diff to previous 1.78
Fixed the family functions to use the new table.

Revision 1.78 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 30 01:44:36 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.77: +179 -104 lines
Diff to previous 1.77
Added support for protein families.

Revision 1.77 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 26 14:48:12 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.76: +4 -1 lines
Diff to previous 1.76
Added the ability to specify a DBD directory in FIG_Config.

Revision 1.76 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 20 19:23:23 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.75: +2 -1 lines
Diff to previous 1.75
Enhanced bbhs to default the cutoff level.

Revision 1.75 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 20 18:24:28 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.74: +26 -0 lines
Diff to previous 1.74
Added "contigs_of".

Revision 1.74 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 13 06:50:37 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.73: +16 -3 lines
Diff to previous 1.73
Enhanced "all_features" to match FIG signature.

Revision 1.73 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 9 21:33:59 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.72: +1 -1 lines
Diff to previous 1.72
Changed to allow specification of a different DBMS for Sprout.

Revision 1.72 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 27 01:32:59 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.71: +53 -0 lines
Diff to previous 1.71
Added support for "uniprot_aliases_bulk".

Revision 1.71 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 27 00:58:46 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.70: +50 -0 lines
Diff to previous 1.70
Added support for "function_of_bulk".

Revision 1.70 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 27 00:42:40 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.69: +29 -0 lines
Diff to previous 1.69
Added support for the "is_genome" method.

Revision 1.69 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 26 19:25:30 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.68: +38 -0 lines
Diff to previous 1.68
Added "subsystem_classification" method.

Revision 1.68 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 25 18:01:41 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.67: +1 -3 lines
Diff to previous 1.67
Fixed boundaries_of to call a Sprout method instead of the FIG method.

Revision 1.67 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 25 07:35:51 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.66: +7 -7 lines
Diff to previous 1.66
Converted map_to_ids so it actually works.

Revision 1.66 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 25 00:52:31 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.65: +35 -15 lines
Diff to previous 1.65
Added tracing.

Revision 1.65 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jun 24 15:59:14 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.64: +3 -2 lines
Diff to previous 1.64
Added more tracing. Fixed a duplicated variable name.

Revision 1.64 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jun 24 15:55:14 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.63: +2 -2 lines
Diff to previous 1.63
Replaced an EACH loop with a FOR loop in the BBH method.

Revision 1.63 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 6 06:54:19 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.62: +1 -3 lines
Diff to previous 1.62
Fixed "get_db" to return the correct object for a Sprout request.

Revision 1.62 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 6 05:00:04 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.61: +3 -16 lines
Diff to previous 1.61
Changed "genome_counts" to use the new GenomeCounts method instead of a direct GetAll.

Revision 1.61 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 13 03:09:04 2006 UTC (13 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.60: +6 -5 lines
Diff to previous 1.60
Modified so that FIG and Sprout use different connection parameters.

Revision 1.60 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 13 19:17:33 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.59: +47 -0 lines
Diff to previous 1.59
Added the "genome_counts" method.

Revision 1.59 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 16 04:08:51 2006 UTC (13 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.58: +3 -16 lines
Diff to previous 1.58
Fixed to expect the DBD files in the $FIG_Config::fig directory.

Revision 1.58 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 15 08:44:36 2006 UTC (13 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.57: +0 -1 lines
Diff to previous 1.57
*** empty log message ***

Revision 1.57 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 28 08:52:26 2006 UTC (13 years, 9 months ago) by parrello
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.56: +38 -0 lines
Diff to previous 1.56
Added a "delete_genomes" command.

Revision 1.56 - (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 1.55: +7 -0 lines
Diff to previous 1.55
add abstract functional coupling

Revision 1.55 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 8 18:13:02 2005 UTC (13 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.54: +25 -14 lines
Diff to previous 1.54
Added a method that can be used to determine whether the data is being taken from SEED or NMPDR.
Changed the "FIG" method to work like the same method in FIG.pm.

Revision 1.54 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 7 19:38:22 2005 UTC (13 years, 11 months ago) by golsen
Branch: MAIN
Changes since 1.53: +1 -1 lines
Diff to previous 1.53
Don't mean to be pedantic, but I figured that I might as well add newlines
at the end of text files that lack one.  Identified with a script:

/bin/sh -O extglob -c 'for f in */*.@(c|css|html|js|pl|pm|py|TXT); do perl -e '"'"'while(<>) {$s = ! /\n$/} exit $s'"'"' $f || echo $f; done'

fixed with a script:

/bin/sh
for file in _list_; do echo "" >> $file; done

Revision 1.53 - (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 1.52: +17 -0 lines
Diff to previous 1.52
Added license words.

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Nov 12 05:19:44 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.51: +1 -1 lines
Diff to previous 1.51
*** empty log message ***

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Nov 12 05:04:26 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.50: +9 -6 lines
Diff to previous 1.50
Hopefully the last of the compound names fixes.

Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Nov 12 04:34:22 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.49: +5 -6 lines
Diff to previous 1.49
Reversed previous fix.

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Nov 12 04:26:27 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.48: +6 -5 lines
Diff to previous 1.48
Fixed "names_of_compound" to avoid a PostGres error.

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 11 20:03:16 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.47: +6 -2 lines
Diff to previous 1.47
Added trace messages for the EC problem in Sprout.

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 9 19:34:33 2005 UTC (14 years ago) by parrello
Branch: MAIN
CVS Tags: caBIG-00-00-00
Changes since 1.46: +2 -2 lines
Diff to previous 1.46
Fixed a case error in the specification of the EC field.

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 2 22:07:38 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.45: +240 -64 lines
Diff to previous 1.45
Changed "cas_to_cid" to return an empty string if more than one compound has the same CAS ID. (This matches FIG functionality.)
Fixed spelling of "stiochiometry".
Implemented "catalyzes", "ec_to_maps", "displayable_reaction", "all_maps", "role_to_maps", "map_to_ecs", and "map_name".

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 20 11:55:20 2005 UTC (14 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.44: +5 -2 lines
Diff to previous 1.44
Fixed function_of per discussion with Ross.

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 20 10:22:48 2005 UTC (14 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.43: +128 -12 lines
Diff to previous 1.43
Added the first wave of KEGG-method analogs.
Changed "function_of" to behave more like the FIG method.

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 18 06:41:55 2005 UTC (14 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.42: +204 -22 lines
Diff to previous 1.42
Fixed error in subsystems_for_peg that caused duplicate entries in the result list.

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 13 15:27:54 2005 UTC (14 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.41: +11 -5 lines
Diff to previous 1.41
Modified the "new_sprout_only" method to allow specification of the "noDBOpen" option. This allows it to be used in "LoadSproutTables".

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 12 21:54:29 2005 UTC (14 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.40: +16 -3 lines
Diff to previous 1.40
conditionally import sprout code so that plain seed works properly

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 12 02:34:46 2005 UTC (14 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.39: +123 -29 lines
Diff to previous 1.39
Added "compute_clusters" and "get_subsystem" methods for SFXlate so that it can be used in "UnvSubsys" as a FIG object replacement.
Fixed "coupling_and_evidence" to remove the bogus reflexive coupling. This helps it to function like the corresponding FIG method.
Added the "raw flag" to the feature_annotations method.
Fixed up some comments.

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 5 20:34:02 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-dataload-0
Changes since 1.38: +3 -1 lines
Diff to previous 1.38
fixes to update_uniq_id_data

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 9 20:57:38 2005 UTC (14 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.37: +2 -1 lines
Diff to previous 1.37
Fixed a bug in the coupling_evidence loop.

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 9 14:48:33 2005 UTC (14 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.36: +41 -16 lines
Diff to previous 1.36
Added an implementation of "all_features"

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 6 21:12:37 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.35: +17 -2 lines
Diff to previous 1.35
NMPDR seed fixes

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 1 09:33:46 2005 UTC (14 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.34: +7 -4 lines
Diff to previous 1.34
Fixed a bug in the handling of subsystem roles. Fixed another bug in the handling of location strings.

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 17 01:40:51 2005 UTC (14 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.33: +28 -0 lines
Diff to previous 1.33
Added "subsystem_curator" function that calls through to the FIG object.

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 16 19:41:12 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.32: +21 -5 lines
Diff to previous 1.32
NMPDR updates

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 26 20:11:39 2005 UTC (14 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.31: +1 -0 lines
Diff to previous 1.31
Added a trace message for tracking annotation problems.

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 22 12:54:34 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.30: +18 -0 lines
Diff to previous 1.30
minor fixes

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 29 15:02:50 2005 UTC (14 years, 4 months ago) by olson
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-2, merge-trunktag-bodev_news-3
Changes since 1.29: +4 -3 lines
Diff to previous 1.29
Fix SproutDBD not found problem.

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 29 14:48:26 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.28: +1 -1 lines
Diff to previous 1.28
fix bug in SFXlate.pm

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 28 21:25:35 2005 UTC (14 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.27: +47 -7 lines
Diff to previous 1.27
Fixed the hunting order for the Sprout XML files.
Updated POD comments.

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 27 20:00:55 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.26: +23 -13 lines
Diff to previous 1.26
after Sprout runs

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 24 21:41:28 2005 UTC (14 years, 5 months ago) by parrello
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-1
Changes since 1.25: +3 -3 lines
Diff to previous 1.25
Changed peg_to_subsystems to use the new Sprout SubsystemList method. This removes the need for it to access Role information.

Revision 1.25 - (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
Changes since 1.24: +14 -15 lines
Diff to previous 1.24
finally

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 22 21:03:00 2005 UTC (14 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.23: +935 -143 lines
Diff to previous 1.23
Replaced tabs with spaces to make indenting device-independent.
Added POD documentation.
Finished implementing the methods required by InterfaceRoutines.pm

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 5 03:18:28 2005 UTC (14 years, 6 months ago) by parrello
Branch: MAIN
CVS Tags: Root-bobdev_news
Branch point for: Branch-bobdev_news
Changes since 1.22: +49 -2 lines
Diff to previous 1.22
*** empty log message ***

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 4 03:08:12 2005 UTC (14 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.21: +14 -2 lines
Diff to previous 1.21
*** empty log message ***

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 7 18:59:57 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.20: +2 -2 lines
Diff to previous 1.20
use sproutdbd from the FIG dir instead of the data dir

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 27 00:31:21 2005 UTC (14 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.19: +35 -3 lines
Diff to previous 1.19
no message

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 26 17:42:35 2005 UTC (14 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.18: +241 -37 lines
Diff to previous 1.18
no message

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 25 21:19:08 2005 UTC (14 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.17: +4 -4 lines
Diff to previous 1.17
fix bug

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 25 21:02:23 2005 UTC (14 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.16: +1 -1 lines
Diff to previous 1.16
change gb feature link name

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 25 21:01:22 2005 UTC (14 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.15: +76 -1 lines
Diff to previous 1.15
add get_gb_feature_link

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 25 02:19:27 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.14: +33 -1 lines
Diff to previous 1.14
no message

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 25 01:36:41 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.13: +1 -1 lines
Diff to previous 1.13
no message

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 25 01:01:21 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.12: +120 -52 lines
Diff to previous 1.12
no message

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 24 17:39:24 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.11: +2 -2 lines
Diff to previous 1.11
no message

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 24 17:31:19 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.10: +1 -1 lines
Diff to previous 1.10
no message

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 24 07:05:56 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.9: +934 -148 lines
Diff to previous 1.9
no message

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 20 16:52:22 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.8: +1 -1 lines
Diff to previous 1.8
no message

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 19 18:47:00 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.7: +13 -3 lines
Diff to previous 1.7
no message

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 18 20:55:32 2005 UTC (14 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.6: +6 -1 lines
Diff to previous 1.6
add get_system_name() call.

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 18 08:10:46 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.5: +11 -10 lines
Diff to previous 1.5
no message

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 13 23:53:58 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.4: +6 -6 lines
Diff to previous 1.4
no message

Revision 1.4 - (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 1.3: +4 -4 lines
Diff to previous 1.3
More fixes for Sprout integration.

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 13 15:47:40 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.2: +34 -5 lines
Diff to previous 1.2
no message

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 12 21:22:08 2005 UTC (14 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.1: +10 -2 lines
Diff to previous 1.1
sprout debugging

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 12 20:09:17 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
no message

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