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Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 5 19:45:28 2009 UTC (10 years ago) by olson
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_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 1.23: +6 -5 lines
Diff to previous 1.23
Switch to FFs and FF instead of FigFams and FigFam

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 7 22:29:05 2009 UTC (10 years, 4 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2009_07_09, rast_rel_2009_0925
Changes since 1.22: +5 -3 lines
Diff to previous 1.22
Major rewrite to prevent already-found PEGs from being re-called by every stage of RAST.

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 13 14:54:27 2008 UTC (11 years, 9 months ago) by gdpusch
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, mgrast_rel_2008_0806, mgrast_rel_2008_0917, mgrast_rel_2008_0919, mgrast_rel_2008_0923, mgrast_rel_2008_0924, mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, rast_2008_0924, rast_rel_2008_04_23, rast_rel_2008_06_16, rast_rel_2008_06_18, rast_rel_2008_07_21, rast_rel_2008_08_07, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_rel_2008_10_09, rast_rel_2008_10_29, rast_rel_2008_11_24, rast_rel_2008_12_18, rast_rel_2009_02_05, rast_rel_2009_03_26, rast_rel_2009_05_18, rast_release_2008_09_29
Changes since 1.21: +36 -16 lines
Diff to previous 1.21
Final clean-up. -- /gdp

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 31 15:31:39 2008 UTC (11 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.20: +1 -2 lines
Diff to previous 1.20
Put reporting of family directory used in the FigFams constructor, only printed if REPORT_FIGFAM_DETAILS
is specified in the environment.

Make the FIG_Config defaulting work properly for the figfams directory.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 30 22:50:37 2008 UTC (11 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.19: +1 -0 lines
Diff to previous 1.19
Log the pathname to the figfams directory used for the analysis.

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 30 19:29:31 2008 UTC (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.18: +2 -1 lines
Diff to previous 1.18
allow loose matching in rapid_propagation

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 17 12:36:47 2007 UTC (12 years, 6 months ago) by gdpusch
Branch: MAIN
Changes since 1.17: +48 -57 lines
Diff to previous 1.17
Added debugging statements. -- /gdp

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 28 22:52:00 2007 UTC (12 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.16: +7 -1 lines
Diff to previous 1.16
fix for readonly data

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 14 17:35:44 2006 UTC (13 years ago) by olson
Branch: MAIN
Changes since 1.15: +9 -1 lines
Diff to previous 1.15
Changes for rapid propagation on the cluster.

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 14 21:47:20 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.14: +1 -1 lines
Diff to previous 1.14
package up the steps in rapid propoagation

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 12 07:43:30 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.13: +2 -2 lines
Diff to previous 1.13
Fix duplicated declaration and typo. -- /gdp

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 5 00:28:58 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.12: +17 -21 lines
Diff to previous 1.12
fixes to rapid prop technology and added diffsF.cgi

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 4 18:58:35 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.11: +0 -1 lines
Diff to previous 1.11
Removed reddundant invocation of $orf->call_start(). -- /gdp

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 1 22:17:18 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.10: +3 -3 lines
Diff to previous 1.10
Fixed to read in closest genome before it is used, rather than after. -- /gdp

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 18 21:12:21 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.9: +1 -0 lines
Diff to previous 1.9
spiff up the lock/unlock stuff

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 18 06:02:34 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.8: +1 -2 lines
Diff to previous 1.8
Fixed bug for handling alternate "fam_data" dir. -- /gdp

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Sep 2 12:37:00 2006 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +1 -1 lines
Diff to previous 1.7
fix minor error in find_genes_based_on_neighbors

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 25 17:40:55 2006 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +55 -12 lines
Diff to previous 1.6
Rewrote interface to match SOP specification. -- /gdp

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 11 11:00:29 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +18 -3 lines
Diff to previous 1.5
Added checks and diagnostic msgs. -- /gdp

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 29 22:10:36 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.4: +2 -0 lines
Diff to previous 1.4
make all assignments master assignments

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 29 18:07:44 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +23 -10 lines
Diff to previous 1.3
set up find_neighbors to handle existing genomes

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 12 13:10:38 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.2: +18 -7 lines
Diff to previous 1.2
fixes to making assignments based on consistency

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 3 19:28:52 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.1: +35 -17 lines
Diff to previous 1.1
updates to ARPP/STAG

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 1 18:24:23 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
fixes and errors to STAG

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