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Revision 1.22 - (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 1.21: +4 -3 lines
Diff to previous 1.21
Switch to FFs and FF instead of FigFams and FigFam

Revision 1.21 - (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 1.20: +2 -2 lines
Diff to previous 1.20
Major rewrite to prevent already-found PEGs from being re-called by every stage of RAST.

Revision 1.20 - (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 1.19: +43 -17 lines
Diff to previous 1.19
Final clean-up. -- /gdp

Revision 1.19 - (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 1.18: +1 -3 lines
Diff to previous 1.18
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 1.18 - (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 1.17: +2 -0 lines
Diff to previous 1.17
Log the pathname to the figfams directory used for the analysis.

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 17 12:38:28 2007 UTC (12 years, 6 months ago) by gdpusch
Branch: MAIN
Changes since 1.16: +17 -23 lines
Diff to previous 1.16
Minor cosmetic changes. -- /gdp

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 27 19:14:35 2007 UTC (12 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.15: +13 -3 lines
Diff to previous 1.15
fixes to rapid propagation

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]
Sat Oct 14 20:48:51 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.13: +0 -6 lines
Diff to previous 1.13
do not promote genes that fail to match a FIGfam

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 14 04:35:38 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.12: +1 -1 lines
Diff to previous 1.12
Minor cosmetic change to debugging output. -- /gdp

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 12 17:58:08 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.11: +5 -1 lines
Diff to previous 1.11
Added optional debugging info. -- /gdp

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 12 10:35:22 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.10: +1 -1 lines
Diff to previous 1.10
Added check to make sure $sims is defined before re-calling STARTs. -- /gdp

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 12 07:45:24 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.9: +6 -2 lines
Diff to previous 1.9
Fixed failure to re-call STARTs and duplicate declarations. -- /gdp

Revision 1.9 - (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 1.8: +15 -21 lines
Diff to previous 1.8
fixes to rapid prop technology and added diffsF.cgi

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 4 18:59:47 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.7: +16 -1 lines
Diff to previous 1.7
Added copyleft notice. -- /gdp

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 18 21:19:56 2006 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +1 -1 lines
Diff to previous 1.6
Script defaults to SEED copy of FigfamsData. -- /gdp

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 18 21:12:21 2006 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +34 -8 lines
Diff to previous 1.5
spiff up the lock/unlock stuff

Revision 1.5 - (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 1.4: +8 -3 lines
Diff to previous 1.4
fix minor error in find_genes_based_on_neighbors

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 29 14:59:53 2006 UTC (13 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +4 -9 lines
Diff to previous 1.3
fixes to find_genes_in_families

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 30 02:50:58 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.2: +32 -10 lines
Diff to previous 1.2
fixs to rapid propagation

Revision 1.2 - (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 1.1: +22 -34 lines
Diff to previous 1.1
fixes to making assignments based on consistency

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 1 18:26:58 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
add initial terrible version of find_genes_in_families.pl

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