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Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 8 20:28:44 2013 UTC (6 years, 3 months ago) by parrello
Branch: MAIN
CVS Tags: HEAD, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.49: +4 -2 lines
Diff to previous 1.49
Updates for new incremental load.

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 26 02:10:46 2013 UTC (6 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.48: +2 -2 lines
Diff to previous 1.48
Support for initial version of the incremental load.

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 6 19:21:18 2011 UTC (7 years, 10 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_10262011, mgrast_dev_12152011, mgrast_release_3_1_2, mgrast_version_3_2
Changes since 1.47: +5 -3 lines
Diff to previous 1.47
Fixed load directory setting.

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 6 19:05:55 2011 UTC (7 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.46: +1 -3 lines
Diff to previous 1.46
Updates for new model loading procedure.

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 21 21:05:15 2011 UTC (7 years, 11 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2011_0928
Changes since 1.45: +66 -0 lines
Diff to previous 1.45
Changes to support complexes.

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 9 15:06:45 2011 UTC (7 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.44: +4 -0 lines
Diff to previous 1.44
Changed so an explicit DBD specification forces that DBD to override the internal one.

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 21 19:14:01 2011 UTC (8 years, 1 month ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_08022011, mgrast_dev_08112011, mgrast_release_3_1_1
Changes since 1.43: +4 -0 lines
Diff to previous 1.43
Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config optional
in places it isn't currently.

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 30 15:41:21 2011 UTC (8 years, 3 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_06072011, mgrast_release_3_1_0
Changes since 1.42: +1 -1 lines
Diff to previous 1.42
*** empty log message ***

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 30 15:35:09 2011 UTC (8 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.41: +2 -0 lines
Diff to previous 1.41
*** empty log message ***

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 30 15:21:21 2011 UTC (8 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.40: +16 -5 lines
Diff to previous 1.40
Fixed to save the section list in a file.

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 23 20:19:24 2011 UTC (8 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.39: +1 -16 lines
Diff to previous 1.39
loader fixes

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 20 13:04:23 2011 UTC (8 years, 6 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_03252011, mgrast_dev_03312011, mgrast_dev_04012011, mgrast_dev_04052011, mgrast_dev_04082011, mgrast_dev_04132011, mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_4, myrast_33
Changes since 1.38: +18 -2 lines
Diff to previous 1.38
More load fixes.

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 11 15:04:03 2011 UTC (8 years, 7 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2011_0119
Changes since 1.37: +3 -1 lines
Diff to previous 1.37
Updates for single-genome loader.

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 3 18:08:10 2011 UTC (8 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.36: +4 -6 lines
Diff to previous 1.36
Another attempt to fix the duplicate-subsystem problem.

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 25 15:57:45 2010 UTC (8 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.35: +7 -1 lines
Diff to previous 1.35
Fixes for duplicate-subsystem problem.

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 14 19:48:38 2010 UTC (8 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.34: +48 -2 lines
Diff to previous 1.34
Support for SQLite database load.

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 5 16:51:17 2010 UTC (8 years, 9 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2010_1206
Changes since 1.33: +1 -1 lines
Diff to previous 1.33
More loader updates.

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 18 20:05:33 2010 UTC (9 years, 2 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2010_0827, rast_rel_2010_0928
Changes since 1.32: +1 -1 lines
Diff to previous 1.32
New loader fixes.

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 24 13:44:57 2010 UTC (9 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.31: +1 -1 lines
Diff to previous 1.31
Updates for expression data and ACH loading.

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 14 13:29:15 2010 UTC (9 years, 5 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2010_0526
Changes since 1.30: +4 -0 lines
Diff to previous 1.30
Fixed to handle a zero start location better.

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 17 18:28:41 2010 UTC (9 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.29: +28 -3 lines
Diff to previous 1.29
Added genome filtering support to id processing.

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 1 20:14:28 2010 UTC (9 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.28: +1 -1 lines
Diff to previous 1.28
Sapling model updates.

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 24 16:45:02 2009 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2010_0118
Changes since 1.27: +39 -0 lines
Diff to previous 1.27
Added a utility for parsing protein sequence IDs.

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 16 01:45:19 2009 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.26: +77 -1 lines
Diff to previous 1.26
Sapling v08 changes.

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 11 19:07:33 2009 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.25: +1 -1 lines
Diff to previous 1.25
Fixed DNA sequence computation.

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 30 17:39:10 2009 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.24: +11 -2 lines
Diff to previous 1.24
Added options to allow Sapling to run on my laptop.

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 30 11:44:21 2009 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.23: +1 -0 lines
Diff to previous 1.23
Added a trace message for server connections.

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 25 20:37:04 2009 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.22: +12 -2 lines
Diff to previous 1.22
Fixed an error in GetLocations.

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 29 18:31:48 2009 UTC (9 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.21: +8 -1 lines
Diff to previous 1.21
Fixes for ACH processing.

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 8 21:30:33 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_0925
Changes since 1.20: +13 -0 lines
Diff to previous 1.20
Changed to allow for storing the DBD metadata in the database. This is currently only activated for Sapling.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 31 22:07:53 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.19: +4 -3 lines
Diff to previous 1.19
Fixed offset error in "ComputeDNA".

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 30 22:12:57 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.18: +5 -1 lines
Diff to previous 1.18
Fixed a bug in FindGapRight.

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 27 19:54:22 2009 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.17: +62 -0 lines
Diff to previous 1.17
New stuff to update functional couplings on the fly.

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 19 17:09:03 2009 UTC (10 years ago) by parrello
Branch: MAIN
Changes since 1.16: +41 -0 lines
Diff to previous 1.16
Added a method to return a list of the genomes in a pair set.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 11 19:36:46 2009 UTC (10 years ago) by parrello
Branch: MAIN
Changes since 1.15: +52 -0 lines
Diff to previous 1.15
Added a method for finding the OTU of a genome.

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 4 16:53:18 2009 UTC (10 years ago) by parrello
Branch: MAIN
Changes since 1.14: +1 -1 lines
Diff to previous 1.14
Fix to alias method.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 3 21:32:54 2009 UTC (10 years ago) by parrello
Branch: MAIN
Changes since 1.13: +423 -21 lines
Diff to previous 1.13
Updates to Sapling for new Sapling server functions.

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 15 23:39:58 2009 UTC (10 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.12: +33 -1 lines
Diff to previous 1.12
Fixed general problems with loading to make the process more robust.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 1 21:35:03 2009 UTC (10 years, 1 month ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_07_09
Changes since 1.11: +70 -0 lines
Diff to previous 1.11
Fixed pegs_for_role to return an empty list if the role is not found.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 30 19:53:51 2009 UTC (10 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.10: +125 -23 lines
Diff to previous 1.10
Fixed error in subsystem Contains relationship.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 16 21:58:36 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.9: +16 -7 lines
Diff to previous 1.9
Fixed diagram URL. Updated to use new key scheme for faster subsystem queries.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 4 18:22:32 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.8: +105 -5 lines
Diff to previous 1.8
Added a GetSubsystem method.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 28 18:08:56 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.7: +156 -8 lines
Diff to previous 1.7
General fixes and improvements to the Sapling load process.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 4 18:49:49 2009 UTC (10 years, 3 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_05_18
Changes since 1.6: +3 -3 lines
Diff to previous 1.6
Updated to use Bob's protocol for load options.

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 21 21:22:10 2009 UTC (10 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.5: +1 -1 lines
Diff to previous 1.5
add $FIG_Config::saplingDB

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 4 00:08:55 2009 UTC (10 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.4: +5 -4 lines
Diff to previous 1.4
Changed defaults to work with new scheme.

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 2 22:29:03 2009 UTC (10 years, 5 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_03_26
Changes since 1.3: +76 -11 lines
Diff to previous 1.3
Added support for DNA sequence chunking.

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 5 07:16:16 2009 UTC (10 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.2: +2 -2 lines
Diff to previous 1.2
Changed the default mysql user name from "root" to "seed".
Added a FIG_Config parameter for specifying the database server.

Revision 1.2 - (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
Changes since 1.1: +1 -1 lines
Diff to previous 1.1
Fixed a bug in InsertObject. Added support for demand-driven flow control.

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 19 21:43:05 2009 UTC (10 years, 7 months ago) by parrello
Branch: MAIN
Sapling support.

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