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Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 11 17:42:31 2010 UTC (9 years, 3 months ago) by disz
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_1206, rast_rel_2011_0119, rast_rel_2011_0928, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.38: +1 -1 lines
Diff to previous 1.38
FigFam 6 digit problem

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 17 17:16:25 2010 UTC (10 years, 1 month ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2010_0118, rast_rel_2010_0526, rast_rel_2010_0827, rast_rel_2010_0928
Changes since 1.37: +2 -2 lines
Diff to previous 1.37
Fixed problem finding Universals.

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 17 16:55:19 2010 UTC (10 years, 1 month ago) by gdpusch
Branch: MAIN
Changes since 1.36: +2 -1 lines
Diff to previous 1.36
Fixed problem finding Universals.

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 17 00:48:59 2010 UTC (10 years, 1 month ago) by gdpusch
Branch: MAIN
Changes since 1.35: +1 -0 lines
Diff to previous 1.35
Fixed problem finding Universals.

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 5 19:45:28 2009 UTC (10 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.34: +2 -2 lines
Diff to previous 1.34
Switch to FFs and FF instead of FigFams and FigFam

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 8 20:28:12 2009 UTC (10 years, 7 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2009_07_09, rast_rel_2009_0925
Changes since 1.33: +1 -1 lines
Diff to previous 1.33
fix usage message

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 7 22:29:05 2009 UTC (10 years, 7 months ago) by gdpusch
Branch: MAIN
Changes since 1.32: +24 -11 lines
Diff to previous 1.32
Major rewrite to prevent already-found PEGs from being re-called by every stage of RAST.

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 15 23:24:10 2009 UTC (10 years, 9 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2009_05_18
Changes since 1.31: +14 -2 lines
Diff to previous 1.31
Added some bulletproofing against the case that no ORFs have yet been called, and some debugging lines.

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 24 13:22:57 2008 UTC (11 years, 3 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2008_12_18, rast_rel_2009_02_05, rast_rel_2009_03_26
Changes since 1.30: +50 -14 lines
Diff to previous 1.30
Increased set of "Universal" functional roles to 44, and moved definitions to the __DATA__ block.

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Apr 20 13:00:15 2008 UTC (11 years, 10 months ago) by overbeek
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_release_2008_09_29
Changes since 1.29: +1 -1 lines
Diff to previous 1.29
return empty list of failure to open FIFfam

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 17 20:48:15 2008 UTC (11 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.28: +2 -1 lines
Diff to previous 1.28
Introduct &FIG::get_figfams_data()

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 18 22:24:44 2008 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.27: +24 -9 lines
Diff to previous 1.27
Fixed attempt to open the "called_by" file in protected disk when "old" selected. -- /gdp

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Mar 1 15:52:45 2008 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.26: +1 -1 lines
Diff to previous 1.26
changes from ::data/FigfamsData to ::FigfamsData

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 13 23:02:03 2008 UTC (12 years ago) by gdpusch
Branch: MAIN
Changes since 1.25: +24 -6 lines
Diff to previous 1.25
Added comments and divide-by-zero protection. -- /gdp

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 13 14:54:27 2008 UTC (12 years ago) by gdpusch
Branch: MAIN
Changes since 1.24: +66 -32 lines
Diff to previous 1.24
Final clean-up. -- /gdp

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 30 19:29:31 2008 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.23: +2 -1 lines
Diff to previous 1.23
allow loose matching in rapid_propagation

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 7 22:19:15 2007 UTC (12 years, 2 months ago) by gdpusch
Branch: MAIN
Changes since 1.22: +3 -1 lines
Diff to previous 1.22
Reconciled the normalization used by both "find_neighbors" scripts. -- /gdp

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 17 12:39:19 2007 UTC (12 years, 9 months ago) by gdpusch
Branch: MAIN
Changes since 1.21: +62 -56 lines
Diff to previous 1.21
Added debugging statements. -- /gdp

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 23 19:15:40 2007 UTC (12 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.20: +1 -1 lines
Diff to previous 1.20
compute_pchs_from_sims.pl

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 5 20:51:41 2007 UTC (12 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.19: +6 -1 lines
Diff to previous 1.19
fix r/o bug

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 14 17:35:44 2006 UTC (13 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.18: +9 -1 lines
Diff to previous 1.18
Changes for rapid propagation on the cluster.

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 14 23:59:26 2006 UTC (13 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.17: +2 -2 lines
Diff to previous 1.17
minor fixes to rapid propagation

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 14 21:47:20 2006 UTC (13 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.16: +1 -1 lines
Diff to previous 1.16
package up the steps in rapid propoagation

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 12 07:46:44 2006 UTC (13 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.15: +4 -4 lines
Diff to previous 1.15
Fix duplicated declarations. -- /gdp

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 5 00:28:58 2006 UTC (13 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.14: +21 -31 lines
Diff to previous 1.14
fixes to rapid prop technology and added diffsF.cgi

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 1 13:13:02 2006 UTC (13 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.13: +0 -4 lines
Diff to previous 1.13
remove unused reference to FigFams.pm

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 18 06:04:00 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.12: +1 -1 lines
Diff to previous 1.12
Fixed bug for handling alternate "fam_data" dir. -- /gdp

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 1 11:30:30 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.11: +1 -1 lines
Diff to previous 1.11
Fixed syntax error in ARGV-parsing regexp. -- /gdp

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 1 11:21:19 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.10: +1 -1 lines
Diff to previous 1.10
Fixed syntax error in ARGV-parsing regexp. -- /gdp

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 25 17:41:43 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.9: +56 -12 lines
Diff to previous 1.9
Rewrote interface to match SOP specification. -- /gdp

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 29 18:07:44 2006 UTC (13 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +21 -10 lines
Diff to previous 1.8
set up find_neighbors to handle existing genomes

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 24 23:21:33 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +1 -0 lines
Diff to previous 1.7
Fixed bad invocation of call_start(). -- /gdp

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 7 04:03:10 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +1 -0 lines
Diff to previous 1.6
add new_versions_of_features

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 19 13:23:02 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +33 -13 lines
Diff to previous 1.5
fix find_neighbors to allow for new family IDs

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 12 13:10:38 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.4: +1 -1 lines
Diff to previous 1.4
fixes to making assignments based on consistency

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 3 19:28:52 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +9 -5 lines
Diff to previous 1.3
updates to ARPP/STAG

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 1 18:24:23 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.2: +55 -43 lines
Diff to previous 1.2
fixes and errors to STAG

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 31 19:37:40 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.1: +48 -18 lines
Diff to previous 1.1
next version of the STAG code

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Mar 25 23:12:56 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
add very buggy start of NewGenome.pm and FigFam stuff

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