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Revision 1.128 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 30 19:53:01 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
CVS Tags: HEAD, mgrast_dev_03252011, mgrast_dev_03312011, mgrast_dev_04012011, mgrast_dev_04052011, mgrast_dev_04082011, mgrast_dev_04132011, 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, rast_rel_2009_07_09, rast_rel_2009_0925, rast_rel_2010_0118, rast_rel_2010_0526, rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119, rast_rel_2011_0928, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.127: +3 -3 lines
Diff to previous 1.127 , to selected 1.23
Fixed documentation for more compatibility with non-NMPDR environment.

Revision 1.127 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 4 18:49:49 2009 UTC (10 years, 4 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_05_18
Changes since 1.126: +19 -24 lines
Diff to previous 1.126 , to selected 1.23
Updated to use Bob's protocol for load options.

Revision 1.126 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 2 01:47:00 2009 UTC (10 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.125: +37 -7 lines
Diff to previous 1.125 , to selected 1.23
Made some changes to use memory more efficiently while loading.

Revision 1.125 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 16 00:24:23 2009 UTC (10 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.124: +40 -27 lines
Diff to previous 1.124 , to selected 1.23
Converted to new hint system.

Revision 1.124 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 4 00:09:43 2009 UTC (10 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.123: +17 -11 lines
Diff to previous 1.123 , to selected 1.23
Changed text on genome menu typamatic bar.

Revision 1.123 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 23 13:44:51 2009 UTC (10 years, 7 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_02_05, rast_rel_2009_03_26
Changes since 1.122: +2 -1 lines
Diff to previous 1.122 , to selected 1.23
Fixed a bug in InsertObject. Added support for demand-driven flow control.

Revision 1.122 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 19 21:46:21 2009 UTC (10 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.121: +228 -120 lines
Diff to previous 1.121 , to selected 1.23
ERDB 2.0 support

Revision 1.121 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 15 11:46:22 2008 UTC (10 years, 11 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, rast_rel_2008_10_29, rast_rel_2008_11_24, rast_rel_2008_12_18
Changes since 1.120: +3 -3 lines
Diff to previous 1.120 , to selected 1.23
Fixed a bug in the Genome menu buttons.

Revision 1.120 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 2 16:32:42 2008 UTC (10 years, 11 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_10_09
Changes since 1.119: +34 -12 lines
Diff to previous 1.119 , to selected 1.23
General load technology fixes.

Revision 1.119 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 30 15:23:55 2008 UTC (10 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.118: +170 -25 lines
Diff to previous 1.118 , to selected 1.23
New loader technology.

Revision 1.118 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Sep 20 14:32:34 2008 UTC (11 years 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_release_2008_09_29
Changes since 1.117: +15 -21 lines
Diff to previous 1.117 , to selected 1.23
Changed subsystem-data access method to use more efficient queries.

Revision 1.117 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 16 18:57:59 2008 UTC (11 years ago) by parrello
Branch: MAIN
CVS Tags: mgrast_rel_2008_0917, mgrast_rel_2008_0919
Changes since 1.116: +26 -52 lines
Diff to previous 1.116 , to selected 1.23
Added trace messages.

Revision 1.116 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 9 21:02:10 2008 UTC (11 years ago) by parrello
Branch: MAIN
Changes since 1.115: +5 -10 lines
Diff to previous 1.115 , to selected 1.23
Changes for v24 database.

Revision 1.115 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 7 03:13:32 2008 UTC (11 years ago) by parrello
Branch: MAIN
Changes since 1.114: +3 -1 lines
Diff to previous 1.114 , to selected 1.23
Fixed to not return nonexistent subsystems when listing the subsystems of a peg.

Revision 1.114 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 3 20:59:57 2008 UTC (11 years ago) by parrello
Branch: MAIN
Changes since 1.113: +49 -90 lines
Diff to previous 1.113 , to selected 1.23
Fixed some bugs. Added hint support.

Revision 1.113 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 12 06:01:49 2008 UTC (11 years, 1 month ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_08_07
Changes since 1.112: +14 -1 lines
Diff to previous 1.112 , to selected 1.23
Updated to be more aggressive in the GenomeOf function.

Revision 1.112 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 28 17:39:38 2008 UTC (11 years, 3 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806, rast_rel_2008_06_16, rast_rel_2008_06_18, rast_rel_2008_07_21
Changes since 1.111: +1 -1 lines
Diff to previous 1.111 , to selected 1.23
Fixed a bug in the genome menu.

Revision 1.111 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 7 23:11:51 2008 UTC (11 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.110: +71 -5 lines
Diff to previous 1.110 , to selected 1.23
Changed so that keywords are stemmed before being used for text searching.

Revision 1.110 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 29 20:54:51 2008 UTC (11 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.109: +20 -13 lines
Diff to previous 1.109 , to selected 1.23
Changed genome control code generation slightly to be a little simpler.

Revision 1.109 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 23 16:32:05 2008 UTC (11 years, 5 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.108: +183 -53 lines
Diff to previous 1.108 , to selected 1.23
Reworked code for generating a genome menu.

Revision 1.108 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 14 19:13:33 2008 UTC (11 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.107: +104 -39 lines
Diff to previous 1.107 , to selected 1.23
Cleaned up the group-handling stuff.

Revision 1.107 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 7 00:06:16 2008 UTC (11 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.106: +2 -2 lines
Diff to previous 1.106 , to selected 1.23
Changed RealCoreGenomes so that it will work with the config file capabilities currently in NmpdrSetup.

Revision 1.106 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 6 23:21:02 2008 UTC (11 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.105: +28 -0 lines
Diff to previous 1.105 , to selected 1.23
Added a method to return the true core NMPDR genomes.

Revision 1.105 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 30 22:14:02 2008 UTC (11 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.104: +5 -2 lines
Diff to previous 1.104 , to selected 1.23
Added ability to specify an alternate host for Sprout.

Revision 1.104 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 23 00:56:31 2008 UTC (11 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.103: +2 -2 lines
Diff to previous 1.103 , to selected 1.23
Added support for concurrent and low-priority loading.

Revision 1.103 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 7 18:30:14 2007 UTC (11 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.102: +17 -28 lines
Diff to previous 1.102 , to selected 1.23
Fixed group file management to remove the old, awful concept of the sort-of group.

Revision 1.102 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 6 14:56:23 2007 UTC (11 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.101: +263 -178 lines
Diff to previous 1.101 , to selected 1.23
Changed POD format for better compatability with Wiki. Improved handling of the group file used during the load.

Revision 1.101 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 20 23:29:24 2007 UTC (12 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.100: +1 -1 lines
Diff to previous 1.100 , to selected 1.23
Fixed a bad comment.

Revision 1.100 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 16 19:59:50 2007 UTC (12 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.99: +164 -247 lines
Diff to previous 1.99 , to selected 1.23
Updated to use a more PPO-friendly database structure.

Revision 1.99 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 27 22:21:46 2007 UTC (12 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.98: +85 -96 lines
Diff to previous 1.98 , to selected 1.23
Converted to use the new attribute system for most properties.

Revision 1.98 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 10 06:13:33 2007 UTC (12 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.97: +73 -3 lines
Diff to previous 1.97 , to selected 1.23
Converted from DBObject to ERDBObject. Added a SimMatrix command that corresponds to BBHMatrix.

Revision 1.97 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 4 13:09:10 2007 UTC (12 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.96: +1 -0 lines
Diff to previous 1.96 , to selected 1.23
Fixed a bug in "AddProperty".

Revision 1.96 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 6 03:37:26 2006 UTC (12 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.95: +53 -0 lines
Diff to previous 1.95 , to selected 1.23
Added support for batch BBH queries.

Revision 1.95 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 29 20:31:32 2006 UTC (12 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.94: +2 -2 lines
Diff to previous 1.94 , to selected 1.23
Changed to use new format for delete methods.

Revision 1.94 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 3 00:42:25 2006 UTC (12 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.93: +9 -2 lines
Diff to previous 1.93 , to selected 1.23
Fixed BBH code to filter out non-Sprout genomes.

Revision 1.93 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 22 05:15:56 2006 UTC (12 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.92: +50 -57 lines
Diff to previous 1.92 , to selected 1.23
Changed to use the primary functional assignment of a feature whenever possible.

Revision 1.92 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 16 07:41:50 2006 UTC (12 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.91: +3 -2 lines
Diff to previous 1.91 , to selected 1.23
Fixed the protein translation so that it is no longer case-sensitive.

Revision 1.91 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 14 18:12:48 2006 UTC (12 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.90: +44 -0 lines
Diff to previous 1.90 , to selected 1.23
Changed the subsystem classification implementation so that we can reconstruct the correct hierarchy.

Revision 1.90 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 29 15:10:05 2006 UTC (12 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.89: +106 -57 lines
Diff to previous 1.89 , to selected 1.23
Added support for specifying all genomes or feature types more simply in GET-style URLs, Converted property name control to a drop-down. Added a string search to the genome menu. Enhanced the FidSearch to let the user specify multiple genomes. Fixed a whole bunch of bugs.

Revision 1.89 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 27 16:55:38 2006 UTC (12 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.88: +1 -1 lines
Diff to previous 1.88 , to selected 1.23
First round for the search overhaul.

Revision 1.88 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 27 12:34:46 2006 UTC (12 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.87: +40 -4 lines
Diff to previous 1.87 , to selected 1.23
Added a relationship between features and subsystems.

Revision 1.87 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 26 13:46:03 2006 UTC (12 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.86: +0 -91 lines
Diff to previous 1.86 , to selected 1.23
Initial code for the new search.

Revision 1.86 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 24 17:14:16 2006 UTC (12 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.85: +95 -4 lines
Diff to previous 1.85 , to selected 1.23
Moved NMPDR group into the Genome record. This insures that all of the information required to generate a popup menu of genomes is available without access to secondary tables.

Revision 1.85 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 19 00:14:04 2006 UTC (13 years ago) by parrello
Branch: MAIN
Changes since 1.84: +73 -6 lines
Diff to previous 1.84 , to selected 1.23
Integrated group file processing. Added the ability to generate a fast genome menu, and to specify a preselected genome.

Revision 1.84 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 14 14:11:09 2006 UTC (13 years ago) by parrello
Branch: MAIN
Changes since 1.83: +9 -22 lines
Diff to previous 1.83 , to selected 1.23
Converted to use the BBH server.

Revision 1.83 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 6 19:30:22 2006 UTC (13 years ago) by parrello
Branch: MAIN
Changes since 1.82: +61 -0 lines
Diff to previous 1.82 , to selected 1.23
Added support for the group data file.

Revision 1.82 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Sep 2 07:00:54 2006 UTC (13 years ago) by parrello
Branch: MAIN
Changes since 1.81: +42 -0 lines
Diff to previous 1.81 , to selected 1.23
Moved in the method for fixing group hashes from GenomeStats.

Revision 1.81 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 24 17:32:09 2006 UTC (13 years ago) by parrello
Branch: MAIN
Changes since 1.80: +1 -1 lines
Diff to previous 1.80 , to selected 1.23
Changed the substitution logic in the annotation methods to prevent an execution warning.

Revision 1.80 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 10 07:34:37 2006 UTC (13 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.79: +61 -1 lines
Diff to previous 1.79 , to selected 1.23
Added new methods to support genome statistics functions.

Revision 1.79 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 31 20:07:06 2006 UTC (13 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.78: +3 -2 lines
Diff to previous 1.78 , to selected 1.23
Add support for a Sprout database on a different machine.

Revision 1.78 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 26 14:47:03 2006 UTC (13 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.77: +4 -1 lines
Diff to previous 1.77 , to selected 1.23
Added the ability to specify a DBD directory in FIG_Config.

Revision 1.77 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 23 16:44:10 2006 UTC (13 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.76: +3 -0 lines
Diff to previous 1.76 , to selected 1.23
Added tracing.

Revision 1.76 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 25 18:03:29 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.75: +1 -1 lines
Diff to previous 1.75 , to selected 1.23
*** empty log message ***

Revision 1.75 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 25 18:02:35 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.74: +64 -0 lines
Diff to previous 1.74 , to selected 1.23
Created a method to perform the boundaries_of function.

Revision 1.74 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 25 07:34:46 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.73: +39 -0 lines
Diff to previous 1.73 , to selected 1.23
Added support for mapped synonym IDs.

Revision 1.73 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 25 02:44:43 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.72: +4 -3 lines
Diff to previous 1.72 , to selected 1.23
*** empty log message ***

Revision 1.72 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 25 02:37:04 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.71: +1 -1 lines
Diff to previous 1.71 , to selected 1.23
Fixed a bug in CouplingEvidence.

Revision 1.71 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 25 00:07:22 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.70: +66 -37 lines
Diff to previous 1.70 , to selected 1.23
Added a method to request similarities from the network.

Revision 1.70 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 23 19:08:58 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.69: +1 -0 lines
Diff to previous 1.69 , to selected 1.23
Added tracing.

Revision 1.69 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 23 01:34:42 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.68: +5 -4 lines
Diff to previous 1.68 , to selected 1.23
Fixed GeneMenu method to include the strain in the genome list.

Revision 1.68 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 18 08:51:59 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.67: +1 -1 lines
Diff to previous 1.67 , to selected 1.23
Fixed a POD error.

Revision 1.67 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 18 07:39:54 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.66: +1 -1 lines
Diff to previous 1.66 , to selected 1.23
*** empty log message ***

Revision 1.66 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 18 07:33:53 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.65: +1 -1 lines
Diff to previous 1.65 , to selected 1.23
*** empty log message ***

Revision 1.65 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 18 07:20:33 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.64: +1 -1 lines
Diff to previous 1.64 , to selected 1.23
*** empty log message ***

Revision 1.64 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 18 07:09:55 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.63: +1 -1 lines
Diff to previous 1.63 , to selected 1.23
*** empty log message ***

Revision 1.63 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 18 07:03:00 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.62: +1 -1 lines
Diff to previous 1.62 , to selected 1.23
*** empty log message ***

Revision 1.62 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 18 05:38:12 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.61: +122 -0 lines
Diff to previous 1.61 , to selected 1.23
Added new methods used by the GenomeStats script.

Revision 1.61 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 14 20:15:48 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.60: +1 -1 lines
Diff to previous 1.60 , to selected 1.23
*** empty log message ***

Revision 1.60 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 14 19:47:19 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.59: +4 -4 lines
Diff to previous 1.59 , to selected 1.23
Fixed a bug in the computation of coupled features.

Revision 1.59 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 7 01:53:03 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.58: +89 -0 lines
Diff to previous 1.58 , to selected 1.23
Added methods to get a count of Contigs for a genome and to create an HTML menu of genomes.

Revision 1.58 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 6 05:07:15 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.57: +65 -346 lines
Diff to previous 1.57 , to selected 1.23
Added new methods to support the ShowCounts script. Converted to inherit ERDB methods.

Revision 1.57 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 13 03:10:15 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.56: +5 -2 lines
Diff to previous 1.56 , to selected 1.23
Added the ability to specify the database socket when creating a Sprout object.

Revision 1.56 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 19 03:34:15 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.55: +9 -6 lines
Diff to previous 1.55 , to selected 1.23
Added support for the new "hash-string" key type that creates a key from a digest of symbolic information.

Revision 1.55 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 3 18:33:58 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.54: +7 -2 lines
Diff to previous 1.54 , to selected 1.23
Updated the documentation.

Revision 1.54 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 16 04:10:07 2006 UTC (13 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.53: +1 -1 lines
Diff to previous 1.53 , to selected 1.23
Fixed to expect the DBD files in the $FIG_Config::fig directory.

Revision 1.53 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 28 08:59:17 2006 UTC (13 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.52: +36 -0 lines
Diff to previous 1.52 , to selected 1.23
Added a method for deleting genomes.

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 12 21:48:57 2005 UTC (13 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.51: +9 -1 lines
Diff to previous 1.51 , to selected 1.23
Added code taken from the FIG "function_of" that cleans excess data out of functional assignments.

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 8 18:02:52 2005 UTC (13 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.50: +2 -1 lines
Diff to previous 1.50 , to selected 1.23
Fixed a bug in the IsComplete method.

Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 21 03:29:35 2005 UTC (13 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.49: +1 -1 lines
Diff to previous 1.49 , to selected 1.23
Another fix to the icky function_of mess.

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 20 18:03:43 2005 UTC (13 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.48: +1 -0 lines
Diff to previous 1.48 , to selected 1.23
Added more tracing.

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 20 12:33:00 2005 UTC (13 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.47: +33 -24 lines
Diff to previous 1.47 , to selected 1.23
Another attempt to get functional assignment into line.

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 20 12:02:43 2005 UTC (13 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.46: +6 -5 lines
Diff to previous 1.46 , to selected 1.23
Changed "AllFunctionsOf" to get user data from the MadeAnnotation relationship.

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 20 11:52:36 2005 UTC (13 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.45: +3 -7 lines
Diff to previous 1.45 , to selected 1.23
Changed AllFunctionsOf to map users to roles instead of roles to users. This allows more than one user to make the same assignment without losing it.

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 20 10:20:27 2005 UTC (13 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.44: +69 -1 lines
Diff to previous 1.44 , to selected 1.23
Added a new function to produce the output expected by "functions_of" in a list context.
Fixed documentation errors.

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 20 09:32:18 2005 UTC (13 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.43: +1 -1 lines
Diff to previous 1.43 , to selected 1.23
Fixed an error in the comments.

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 18 18:36:26 2005 UTC (13 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.42: +2 -2 lines
Diff to previous 1.42 , to selected 1.23
Fixed error in the parsing of functional assignments.

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 18 06:58:09 2005 UTC (13 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.41: +8 -3 lines
Diff to previous 1.41 , to selected 1.23
Okay, this time I've REALLY fixed the duplicate-role problem in SubsystemsOf

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 18 02:24:23 2005 UTC (13 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.40: +9 -4 lines
Diff to previous 1.40 , to selected 1.23
Fixed a bug in the FeatureLocation method's segment recombination code for the "-" strand.

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 12 03:12:24 2005 UTC (13 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.39: +69 -12 lines
Diff to previous 1.39 , to selected 1.23
Fixed a bug in location parsing.
Added support for the UnvSubsys feature clustering.
Added support for the "raw flag" on feature_annotations.
Changed the timestamp conversion for compatability
Fixed BBH methods to allow multiple target hits.

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 14 14:04:13 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.38: +1 -1 lines
Diff to previous 1.38 , to selected 1.23
*** empty log message ***

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 14 14:02:44 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.37: +6 -6 lines
Diff to previous 1.37 , to selected 1.23
*** empty log message ***

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 14 13:55:54 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.36: +1 -1 lines
Diff to previous 1.36 , to selected 1.23
*** empty log message ***

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 14 13:52:34 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.35: +2 -2 lines
Diff to previous 1.35 , to selected 1.23
*** empty log message ***

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 14 13:47:26 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.34: +3 -3 lines
Diff to previous 1.34 , to selected 1.23
*** empty log message ***

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 14 13:43:31 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.33: +1 -1 lines
Diff to previous 1.33 , to selected 1.23
*** empty log message ***

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 14 13:26:27 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.32: +1 -1 lines
Diff to previous 1.32 , to selected 1.23
*** empty log message ***

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 14 13:24:14 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.31: +2 -0 lines
Diff to previous 1.31 , to selected 1.23
*** empty log message ***

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 14 13:14:12 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.30: +1 -1 lines
Diff to previous 1.30 , to selected 1.23
*** empty log message ***

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 14 13:13:25 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.29: +1 -0 lines
Diff to previous 1.29 , to selected 1.23
*** empty log message ***

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 14 13:06:53 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.28: +5 -2 lines
Diff to previous 1.28 , to selected 1.23
*** empty log message ***

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 14 13:01:40 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.27: +1 -1 lines
Diff to previous 1.27 , to selected 1.23
*** empty log message ***

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 14 12:56:13 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.26: +1 -2 lines
Diff to previous 1.26 , to selected 1.23
Attempted to fix the DNA sequence methods.

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 13 18:33:20 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.25: +1 -0 lines
Diff to previous 1.25 , to selected 1.23
Added some tracing.

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 11 17:29:52 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.24: +8 -1 lines
Diff to previous 1.24 , to selected 1.23
Updated to allow for situations where the sprout database does not exist yet.

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 11 17:08:59 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.23: +3 -3 lines
Diff to previous 1.23
Changed FASTA methods to normalize to lower case instead of upper case.

Revision 1.23 - (view) (download) (as text) (annotate) - [selected]
Fri Sep 9 21:15:47 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.22: +4 -1 lines
Diff to previous 1.22
Fixed a bug in the GetCoupling code that handles the ordering of evidence pairs.

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 9 21:10:46 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.21: +1 -0 lines
Diff to previous 1.21 , to selected 1.23
Added trace messages.

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 9 20:40:41 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.20: +2 -0 lines
Diff to previous 1.20 , to selected 1.23
Added trace messages for Coupling.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 24 19:31:20 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.19: +11 -6 lines
Diff to previous 1.19 , to selected 1.23
Fixed FeatureLocations to return a comma-delimited string rather than a space-delimited string.

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 14 23:32:08 2005 UTC (14 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.18: +97 -12 lines
Diff to previous 1.18 , to selected 1.23
Added direct Sprout loading facility.

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 28 21:34:15 2005 UTC (14 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.17: +96 -16 lines
Diff to previous 1.17 , to selected 1.23
Added methods to find and identify the Sprout load files.

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 27 20:00:55 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.16: +3 -3 lines
Diff to previous 1.16 , to selected 1.23
after Sprout runs

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 24 21:45:45 2005 UTC (14 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.15: +33 -1 lines
Diff to previous 1.15 , to selected 1.23
Added a new method that returns a list of Subsystem names without extracting Role information.

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 22 21:30:45 2005 UTC (14 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.14: +1168 -862 lines
Diff to previous 1.14 , to selected 1.23
Fixed the tabs.
Added some new methods required by SFXlate.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 9 19:06:55 2005 UTC (14 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.13: +11 -7 lines
Diff to previous 1.13 , to selected 1.23
*** empty log message ***

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 5 03:14:03 2005 UTC (14 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.12: +3 -16 lines
Diff to previous 1.12 , to selected 1.23
*** empty log message ***

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 4 03:24:43 2005 UTC (14 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.11: +10 -19 lines
Diff to previous 1.11 , to selected 1.23
*** empty log message ***

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 8 09:17:40 2005 UTC (14 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.10: +41 -25 lines
Diff to previous 1.10 , to selected 1.23
no message

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 25 18:41:45 2005 UTC (14 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.9: +113 -109 lines
Diff to previous 1.9 , to selected 1.23
no message

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 7 00:32:07 2005 UTC (14 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.8: +35 -15 lines
Diff to previous 1.8 , to selected 1.23
no message

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 27 00:30:20 2005 UTC (14 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.7: +46 -0 lines
Diff to previous 1.7 , to selected 1.23
no message

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 26 22:26:09 2005 UTC (14 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.6: +8 -1 lines
Diff to previous 1.6 , to selected 1.23
no message

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 26 17:41:53 2005 UTC (14 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.5: +0 -1 lines
Diff to previous 1.5 , to selected 1.23
no message

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 25 03:02:07 2005 UTC (14 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.4: +18 -7 lines
Diff to previous 1.4 , to selected 1.23
no message

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 25 01:36:09 2005 UTC (14 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.3: +1 -1 lines
Diff to previous 1.3 , to selected 1.23
no message

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 25 01:00:20 2005 UTC (14 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.2: +161 -76 lines
Diff to previous 1.2 , to selected 1.23
no message

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 23 22:31:29 2005 UTC (14 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.1: +1 -1 lines
Diff to previous 1.1 , to selected 1.23
no message

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 23 16:12:29 2005 UTC (14 years, 7 months ago) by parrello
Branch: MAIN
Diff to selected 1.23
no message

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