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Revision 1.125 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 29 23:29:26 2010 UTC (8 years, 11 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2010_1206
Changes since 1.124: +113 -1 lines
Diff to previous 1.124
New compare-regions support.

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Tue Nov 16 19:24:13 2010 UTC (8 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.123: +232 -2 lines
Diff to previous 1.123
New methods for alignment data.

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Fri Nov 5 16:50:31 2010 UTC (9 years ago) by parrello
Branch: MAIN
Changes since 1.122: +44 -41 lines
Diff to previous 1.122
Update to fail more gracefully in gene_correspondence_map.

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Wed Nov 3 16:01:20 2010 UTC (9 years ago) by parrello
Branch: MAIN
Changes since 1.121: +114 -0 lines
Diff to previous 1.121
Added support for intergenic region queries.

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Sun Oct 31 18:25:04 2010 UTC (9 years ago) by parrello
Branch: MAIN
Changes since 1.120: +63 -0 lines
Diff to previous 1.120
fid_experiments

Revision 1.120 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 28 15:25:53 2010 UTC (9 years ago) by parrello
Branch: MAIN
Changes since 1.119: +2 -1 lines
Diff to previous 1.119
Added genome name capability to genome_data method.

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Thu Oct 21 14:38:47 2010 UTC (9 years ago) by parrello
Branch: MAIN
Changes since 1.118: +21 -17 lines
Diff to previous 1.118
Fixed fid_possibly_truncated to work on nonexistent fids.

Revision 1.118 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 21 13:03:17 2010 UTC (9 years ago) by parrello
Branch: MAIN
Changes since 1.117: +26 -2 lines
Diff to previous 1.117
Enhanced "subsystems_for_role", removed reverse-arrow check for correspondence files.

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Tue Oct 19 17:20:10 2010 UTC (9 years ago) by parrello
Branch: MAIN
Changes since 1.116: +81 -6 lines
Diff to previous 1.116
Added new subsystems_for_roles method. Sped up figfam_fids_batch.

Revision 1.116 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 14 17:28:49 2010 UTC (9 years, 1 month ago) by parrello
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Changes since 1.115: +163 -1 lines
Diff to previous 1.115
Expression vector support methods.

Revision 1.115 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 11 16:21:42 2010 UTC (9 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.114: +158 -0 lines
Diff to previous 1.114
Added publications and genome-experiments methods.

Revision 1.114 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 14 17:19:02 2010 UTC (9 years, 2 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2010_0928
Changes since 1.113: +59 -0 lines
Diff to previous 1.113
Added a service for batch FIGfam retrieval.

Revision 1.113 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 14 12:01:33 2010 UTC (9 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.112: +2 -2 lines
Diff to previous 1.112
Another change to related_figfams.

Revision 1.112 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 13 21:17:59 2010 UTC (9 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.111: +2 -2 lines
Diff to previous 1.111
Fix to related_figfams output.

Revision 1.111 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 13 19:38:25 2010 UTC (9 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.110: +20 -4 lines
Diff to previous 1.110
Changed related_figfams to use precomputed relationship.

Revision 1.110 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 5 17:50:33 2010 UTC (9 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.109: +1 -1 lines
Diff to previous 1.109
Fixed a bad search pattern in locs_to_dna.

Revision 1.109 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 23 18:23:25 2010 UTC (9 years, 2 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2010_0827
Changes since 1.108: +12 -0 lines
Diff to previous 1.108
Fixed gene_correspondence to give better error messages.

Revision 1.108 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 23 17:24:25 2010 UTC (9 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.107: +13 -3 lines
Diff to previous 1.107
Various POD fixes.

Revision 1.107 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 11 20:34:44 2010 UTC (9 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.106: +128 -128 lines
Diff to previous 1.106
Fixed POD errors.

Revision 1.106 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 10 18:45:58 2010 UTC (9 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.105: +1 -1 lines
Diff to previous 1.105
Fixed a POD error.

Revision 1.105 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 30 20:45:22 2010 UTC (9 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.104: +12 -9 lines
Diff to previous 1.104
Enhancement to allow FIG IDs as locations in locs_to_dna

Revision 1.104 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 30 19:52:08 2010 UTC (9 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.103: +2 -0 lines
Diff to previous 1.103
POD fix

Revision 1.103 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 30 19:04:13 2010 UTC (9 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.102: +171 -0 lines
Diff to previous 1.102
find_closest_genes support

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Thu Jul 29 17:35:51 2010 UTC (9 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.101: +138 -0 lines
Diff to previous 1.101
Added support for using SAS_SERVER environment variable to configure the appropriate server.

Revision 1.101 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 28 18:10:57 2010 UTC (9 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.100: +5 -7 lines
Diff to previous 1.100
Faster figfam profiles.

Revision 1.100 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 28 16:25:53 2010 UTC (9 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.99: +114 -9 lines
Diff to previous 1.99
Server script support.

Revision 1.99 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 21 18:55:49 2010 UTC (9 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.98: +62 -0 lines
Diff to previous 1.98
Added support for the signature genes script.

Revision 1.98 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 20 21:10:32 2010 UTC (9 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.97: +180 -0 lines
Diff to previous 1.97
Added stuff to support new command-line scripts.

Revision 1.97 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 8 20:15:39 2010 UTC (9 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.96: +122 -23 lines
Diff to previous 1.96
Updates for new expression-data method.

Revision 1.96 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 29 20:56:44 2010 UTC (9 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.95: +60 -0 lines
Diff to previous 1.95
Added method to find FIGfams in a genome.

Revision 1.95 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 22 20:13:56 2010 UTC (9 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.94: +2 -0 lines
Diff to previous 1.94
*** empty log message ***

Revision 1.94 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 22 20:09:43 2010 UTC (9 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.93: +4 -0 lines
Diff to previous 1.93
Documentation fix.

Revision 1.93 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 22 20:02:37 2010 UTC (9 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.92: +70 -0 lines
Diff to previous 1.92
Added subsystem_genomes method.

Revision 1.92 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 22 19:15:13 2010 UTC (9 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.91: +7 -2 lines
Diff to previous 1.91
Documentation fixes.

Revision 1.91 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 22 17:41:09 2010 UTC (9 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.90: +4 -0 lines
Diff to previous 1.90
*** empty log message ***

Revision 1.90 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 22 17:33:10 2010 UTC (9 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.89: +310 -0 lines
Diff to previous 1.89
Added expression data methods.

Revision 1.89 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 18 20:04:49 2010 UTC (9 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.88: +36 -4 lines
Diff to previous 1.88
Added abbreviation option to subsystem_roles return.
Fixed -limit=none option on query method.

Revision 1.88 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 14 14:36:03 2010 UTC (9 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.87: +21 -4 lines
Diff to previous 1.87
Updates for auxiliary role filtering.

Revision 1.87 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 29 20:33:43 2010 UTC (9 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.86: +11 -6 lines
Diff to previous 1.86
Updated per Gordon's email.

Revision 1.86 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 28 14:03:22 2010 UTC (9 years, 6 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2010_0526
Changes since 1.85: +53 -0 lines
Diff to previous 1.85
Added "all_proteins" method.

Revision 1.85 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 13 21:16:46 2010 UTC (9 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.84: +59 -3 lines
Diff to previous 1.84
Added genome_domain method.

Revision 1.84 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 13 20:05:49 2010 UTC (9 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.83: +82 -0 lines
Diff to previous 1.83
Updated for computing previously-mapped genomes.

Revision 1.83 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 12 01:05:35 2010 UTC (9 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.82: +2 -0 lines
Diff to previous 1.82
Fixed a POD error.

Revision 1.82 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 2 16:29:22 2010 UTC (9 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.81: +180 -0 lines
Diff to previous 1.81
Added new "fid_correspondences" and "ids_to_lengths" methods.

Revision 1.81 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 25 16:10:54 2010 UTC (9 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.80: +2 -1 lines
Diff to previous 1.80
BBH update

Revision 1.80 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 19 14:46:06 2010 UTC (9 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.79: +8 -8 lines
Diff to previous 1.79
More detailed error tracking...

Revision 1.79 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 18 23:06:47 2010 UTC (9 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.78: +1 -0 lines
Diff to previous 1.78
Fixed a bug in the corresponding-genes code.

Revision 1.78 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 16 20:24:05 2010 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.77: +7 -4 lines
Diff to previous 1.77
Added option to include reverse correspondences in correspondence map output.

Revision 1.77 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 16 19:50:43 2010 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.76: +49 -31 lines
Diff to previous 1.76
Made gene correspondence submission more robust.

Revision 1.76 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 14 13:26:32 2010 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.75: +179 -107 lines
Diff to previous 1.75
Updates for new gene correspondence system.

Revision 1.75 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 9 18:46:15 2010 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.74: +3 -0 lines
Diff to previous 1.74
Added "contig_sequences" to methods call.

Revision 1.74 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 7 01:41:18 2010 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.73: +82 -24 lines
Diff to previous 1.73
Made some documentation changes, added "contig_sequences".

Revision 1.73 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 25 20:40:04 2010 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.72: +1 -0 lines
Diff to previous 1.72
*** empty log message ***

Revision 1.72 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 25 20:30:10 2010 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.71: +184 -20 lines
Diff to previous 1.71
Added enhanced support for gene correspondence maps.

Revision 1.71 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 19 18:50:38 2010 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.70: +96 -0 lines
Diff to previous 1.70
Added another fid-mapping method.

Revision 1.70 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 18 15:27:03 2010 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.69: +84 -2 lines
Diff to previous 1.69
Fixed a POD error.

Revision 1.69 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 17 19:30:46 2010 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.68: +30 -4 lines
Diff to previous 1.68
Added genome filtering to more methods.

Revision 1.68 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 17 18:28:24 2010 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.67: +9 -2 lines
Diff to previous 1.67
Added genome filtering to "ids_to_functions".

Revision 1.67 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 17 16:29:16 2010 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.66: +87 -0 lines
Diff to previous 1.66
Added new "genome_ids" function.

Revision 1.66 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 9 18:49:26 2010 UTC (9 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.65: +33 -25 lines
Diff to previous 1.65
Faster version of all_figfams when role search is used.

Revision 1.65 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 3 19:16:03 2010 UTC (9 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.64: +65 -127 lines
Diff to previous 1.64
Changed occ_of_role to use new functional role index.

Revision 1.64 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 29 23:23:57 2010 UTC (9 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.63: +4 -5 lines
Diff to previous 1.63
Changed "all_features" to return an empty list when a genome has no results.

Revision 1.63 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 29 16:09:21 2010 UTC (9 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.62: +16 -13 lines
Diff to previous 1.62
Fixed ids_to_subsystems to work the way the description says.

Revision 1.62 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 19 17:44:59 2010 UTC (9 years, 9 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2010_0118
Changes since 1.61: +83 -0 lines
Diff to previous 1.61
Added ids_to_annotations method.

Revision 1.61 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 5 17:25:20 2010 UTC (9 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.60: +2 -0 lines
Diff to previous 1.60
Fixed a POD error.

Revision 1.60 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 24 16:45:44 2009 UTC (9 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.59: +9 -8 lines
Diff to previous 1.59
Converted to allow prefixed protein IDs.

Revision 1.59 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 23 03:23:03 2009 UTC (9 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.58: +77 -10 lines
Diff to previous 1.58
Added new capabilities to "equiv_sequence_ids".

Revision 1.58 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 19 00:32:36 2009 UTC (9 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.57: +1 -0 lines
Diff to previous 1.57
*** empty log message ***

Revision 1.57 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 19 00:03:55 2009 UTC (9 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.56: +232 -73 lines
Diff to previous 1.56
Added existence-checking methods.

Revision 1.56 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 17 20:47:58 2009 UTC (9 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.55: +59 -0 lines
Diff to previous 1.55
Added subsystem_roles.

Revision 1.55 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 16 22:21:18 2009 UTC (9 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.54: +1 -12 lines
Diff to previous 1.54
Cleaned up equiv_ids_for_sequences.

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Wed Dec 16 19:09:13 2009 UTC (9 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.53: +2 -2 lines
Diff to previous 1.53
minor changes in documentation

Revision 1.53 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 16 18:48:43 2009 UTC (9 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.52: +2 -2 lines
Diff to previous 1.52
Moved a call to increase likelihood of a useful error message.

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 16 01:44:35 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.51: +101 -8 lines
Diff to previous 1.51
New method for finding the ID of the protein sequence.

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 14 22:22:28 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.50: +43 -15 lines
Diff to previous 1.50
Minor fixes for Monday.

Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 14 20:20:03 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.49: +67 -6 lines
Diff to previous 1.49
*** empty log message ***

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 11 19:07:18 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.48: +87 -13 lines
Diff to previous 1.48
Fixed some POD comments, added "ids_to_assertions", renamed "equiv" methods.

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 11 17:15:40 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.47: +1 -1 lines
Diff to previous 1.47
Fixed a POD error.

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 11 02:04:22 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.46: +140 -10 lines
Diff to previous 1.46
Finished updating return documentation.

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 10 23:20:19 2009 UTC (9 years, 11 months ago) by parrello
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Changes since 1.45: +95 -29 lines
Diff to previous 1.45
Added precise feature to equiv_sequence_ids.

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Thu Dec 10 22:38:54 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.44: +1 -1 lines
Diff to previous 1.44
*** empty log message ***

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 10 22:30:22 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.43: +124 -8 lines
Diff to previous 1.43
New return documentation, through line 2700.

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 10 19:25:07 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.42: +2 -0 lines
Diff to previous 1.42
Fixed a pod error.

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 10 19:12:52 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.41: +284 -277 lines
Diff to previous 1.41
Finished conversion.

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 10 16:40:12 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.40: +164 -157 lines
Diff to previous 1.40
*** empty log message ***

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 10 15:13:28 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.39: +162 -155 lines
Diff to previous 1.39
Converted through related_clusters.

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Wed Dec 9 21:06:30 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.38: +224 -167 lines
Diff to previous 1.38
Converted up through "pegs_implementing_roles".

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Wed Dec 9 19:29:43 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.37: +2615 -2454 lines
Diff to previous 1.37
Conversion through "make_runs".

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 8 20:57:41 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.36: +256 -190 lines
Diff to previous 1.36
Fixed equiv_sequence_ids to handle prefixed and non-prefixed formats on input and to put prefixed formats on output.

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 8 19:33:18 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.35: +442 -449 lines
Diff to previous 1.35
Added equiv_sequence_ids

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Tue Dec 8 14:49:59 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.34: +2806 -1570 lines
Diff to previous 1.34
Provisional version after movement and reorganization.

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 6 18:21:07 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.33: +25 -40 lines
Diff to previous 1.33
Added new subsystem methods.

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Sat Dec 5 01:14:54 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.32: +6 -5 lines
Diff to previous 1.32
Added genetic code to return from "genome_metrics".

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Fri Dec 4 20:12:14 2009 UTC (9 years, 11 months ago) by disz
Branch: MAIN
Changes since 1.31: +8 -2 lines
Diff to previous 1.31
changed doc to say XXserver->new() insetad of XX->new

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 4 18:48:10 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.30: +21 -0 lines
Diff to previous 1.30
Added an exclusion filter to ids_to_subsystems.

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Thu Dec 3 15:34:16 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.29: +176 -0 lines
Diff to previous 1.29
Added server to search for roles and/or functions in a genome.

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Wed Nov 25 22:36:53 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.28: +1 -1 lines
Diff to previous 1.28
Fixed representative_genomes to skip genomes not in main database.

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Wed Nov 25 20:37:39 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.27: +586 -390 lines
Diff to previous 1.27
Added four more methods.

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Tue Nov 24 20:28:21 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.26: +54 -0 lines
Diff to previous 1.26
Added genome_contigs.

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Tue Nov 24 19:23:36 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.25: +317 -20 lines
Diff to previous 1.25
New methods for Sapling server.

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Tue Nov 3 21:20:07 2009 UTC (10 years ago) by parrello
Branch: MAIN
Changes since 1.24: +44 -0 lines
Diff to previous 1.24
Error handling restructure.

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Thu Oct 29 18:26:59 2009 UTC (10 years ago) by parrello
Branch: MAIN
Changes since 1.23: +20 -8 lines
Diff to previous 1.23
Final server updates.

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Tue Oct 27 08:24:36 2009 UTC (10 years ago) by parrello
Branch: MAIN
Changes since 1.22: +10 -1 lines
Diff to previous 1.22
Added unusable-subsystem filter to ids_to_subsystems.

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Tue Oct 27 06:07:31 2009 UTC (10 years ago) by parrello
Branch: MAIN
Changes since 1.21: +27 -2 lines
Diff to previous 1.21
Added option to return location strings from genes_in_region.

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Mon Oct 26 15:13:16 2009 UTC (10 years ago) by parrello
Branch: MAIN
Changes since 1.20: +170 -4 lines
Diff to previous 1.20
Fixed an error in the documentation. Added "ids_to_data" method.

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Tue Oct 20 20:38:31 2009 UTC (10 years ago) by parrello
Branch: MAIN
Changes since 1.19: +92 -0 lines
Diff to previous 1.19
Added feature_assignments method.

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Sun Oct 11 22:09:58 2009 UTC (10 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.18: +3 -1 lines
Diff to previous 1.18
Fixed figfam_fids to but the FIGfam ID in FASTA output.

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Sun Oct 11 19:54:48 2009 UTC (10 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.17: +9 -3 lines
Diff to previous 1.17
Fixed FASTA output to include FIG ID when it is different from the input ID.

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 7 21:20:03 2009 UTC (10 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.16: +154 -6 lines
Diff to previous 1.16
Added new functions for Andrei's project.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 9 15:20:23 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_0925
Changes since 1.15: +53 -0 lines
Diff to previous 1.15
Added "genes_in_region" method.

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 8 17:01:18 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.14: +189 -0 lines
Diff to previous 1.14
Added a "get" method per Bob's suggestion.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 31 22:07:19 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.13: +9 -2 lines
Diff to previous 1.13
Added stripped return format for "ids_to_fasta".

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Mon Aug 31 02:32:10 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.12: +7 -2 lines
Diff to previous 1.12
Fixed "justFirst" option in make_runs.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 27 19:43:34 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.11: +4 -4 lines
Diff to previous 1.11
Fixed some documentation errors.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 19 17:04:38 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.10: +201 -196 lines
Diff to previous 1.10
Converted to use leading "-" in parameters.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 4 16:53:41 2009 UTC (10 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.9: +16 -11 lines
Diff to previous 1.9
Finished documentation and examples for Berkeley methods.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 3 21:31:42 2009 UTC (10 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.8: +327 -185 lines
Diff to previous 1.8
Updated to Sapling Server for Berkeley.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 22 18:32:59 2009 UTC (10 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.7: +26 -14 lines
Diff to previous 1.7
More make_runs stuff.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 22 17:02:05 2009 UTC (10 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.6: +269 -37 lines
Diff to previous 1.6
Updated for in_runs.

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Wed Jul 15 23:37:46 2009 UTC (10 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.5: +704 -5 lines
Diff to previous 1.5
Updates for operon pipeline.

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 30 20:11:54 2009 UTC (10 years, 4 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_07_09
Changes since 1.4: +276 -37 lines
Diff to previous 1.4
Additional functionality for sapling server.

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 18 01:29:19 2009 UTC (10 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.3: +285 -10 lines
Diff to previous 1.3
Finished up the Sapling server methods.

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 16 16:37:23 2009 UTC (10 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.2: +103 -161 lines
Diff to previous 1.2
New Sapling server support.

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 28 17:57:17 2009 UTC (10 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.1: +232 -10 lines
Diff to previous 1.1
New module to perform the internal functions of the sapling server.

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 12 19:35:30 2009 UTC (10 years, 6 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2009_05_18
initial version

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