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Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 18 15:56:56 2008 UTC (11 years, 9 months ago) by arodri7
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, rast_2008_0924, 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_release_2008_09_29
Changes since 1.45: +6 -0 lines
Diff to previous 1.45
Figfams update

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 12 20:20:42 2008 UTC (11 years, 10 months ago) by arodri7
Branch: MAIN
CVS Tags: rast_rel_2008_06_16, rast_rel_2008_06_18
Changes since 1.44: +1 -1 lines
Diff to previous 1.44
error check on PDB.connections file for older figfam release

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 8 19:31:39 2008 UTC (11 years, 11 months ago) by arodri7
Branch: MAIN
Changes since 1.43: +16 -2 lines
Diff to previous 1.43
updated and corrected place_in_figfam

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 1 02:40:50 2008 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.42: +35 -1 lines
Diff to previous 1.42
add connections between FIGfams and structures

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 17 20:45:23 2008 UTC (11 years, 11 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.41: +6 -10 lines
Diff to previous 1.41
Introduce get_figfam_data().

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 12 11:34:03 2008 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.40: +13 -13 lines
Diff to previous 1.40
fixes to figfam function resetting

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 11 14:15:15 2008 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.39: +4 -1 lines
Diff to previous 1.39
changes to FIGfams

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 11 12:00:34 2008 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.38: +28 -2 lines
Diff to previous 1.38
updates to FIGfam quality control

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 5 20:25:33 2008 UTC (12 years, 2 months ago) by arodri7
Branch: MAIN
Changes since 1.37: +20 -1 lines
Diff to previous 1.37
changes to FigFams.pm

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 31 15:32:16 2008 UTC (12 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.36: +8 -0 lines
Diff to previous 1.36
If the REPORT_FIGFAM_DETAILS envar is set, print to stderr the directory figfams taken from.

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 30 19:20:32 2008 UTC (12 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.35: +17 -5 lines
Diff to previous 1.35
fixes to FIGfam support

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 20 21:36:29 2008 UTC (12 years, 2 months ago) by gdpusch
Branch: MAIN
Changes since 1.34: +11 -7 lines
Diff to previous 1.34
Modified to "grandfather in" "FIG_Config.pm"s that do not contain a "$FigfamsData" variable, and to geive more explcit debug information if the tie creating "roles.db" failes. -- /gdp

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 16 16:34:23 2008 UTC (12 years, 2 months ago) by arodri7
Branch: MAIN
Changes since 1.33: +3 -5 lines
Diff to previous 1.33
modified the bulk routine for getting the figfam id of a peg id

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 15 20:58:20 2008 UTC (12 years, 2 months ago) by arodri7
Branch: MAIN
Changes since 1.32: +126 -2 lines
Diff to previous 1.32
added subroutine families_containing_peg_bulk which gets the figfam association given a set of pegs

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 16 14:22:52 2007 UTC (12 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.31: +0 -16 lines
Diff to previous 1.31
cleanup in FigFams.pm

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 16 14:19:38 2007 UTC (12 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.30: +24 -101 lines
Diff to previous 1.30
major fixes to FigFams.pm, FigFam.pm, FFs.pm and FF.pm

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 15 14:30:50 2007 UTC (12 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.29: +246 -394 lines
Diff to previous 1.29
redone FIGfam stuff

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 24 14:25:28 2007 UTC (12 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.28: +49 -1 lines
Diff to previous 1.28
add families_imlementing_role to FigFams.pm

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 13 15:10:06 2007 UTC (12 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.27: +7 -1 lines
Diff to previous 1.27
fixes to fc_figfams

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 4 00:58:56 2007 UTC (12 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.26: +83 -6 lines
Diff to previous 1.26
check figfams fixes

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 16 14:54:22 2007 UTC (12 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.25: +1 -1 lines
Diff to previous 1.25
code to check figfams on a cluster

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Sep 15 22:33:31 2007 UTC (12 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.24: +6 -17 lines
Diff to previous 1.24
FIGfams are now broadened to include PEGs with mismatching functions

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 1 16:22:17 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.23: +6 -3 lines
Diff to previous 1.23
minor fixes to FigFams to support FIGO

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 28 14:02:05 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.22: +53 -3 lines
Diff to previous 1.22
fixes to rebuilding figfams

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 17 12:42:10 2007 UTC (12 years, 10 months ago) by gdpusch
Branch: MAIN
Changes since 1.21: +3 -2 lines
Diff to previous 1.21
Added debugging statements. -- /gdp

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 14 14:19:16 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.20: +3 -0 lines
Diff to previous 1.20
update FigFam.pm

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 28 14:47:53 2007 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.19: +5 -1 lines
Diff to previous 1.19
add best_tree_using_proml_on_cluster

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 1 15:24:56 2007 UTC (13 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.18: +12 -5 lines
Diff to previous 1.18
fix for readonly data

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 17 20:57:18 2007 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.17: +1 -1 lines
Diff to previous 1.17
remove extraneous parameter on all_families

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 25 17:14:15 2006 UTC (13 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.16: +13 -0 lines
Diff to previous 1.16
changes to support updating FIGfam functions

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 21 18:20:53 2006 UTC (13 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.15: +10 -0 lines
Diff to previous 1.15
add initial version of FIGO.pm - OO services

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 17 21:17:42 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.14: +2 -0 lines
Diff to previous 1.14
fix bad tacking on of aliases in make_genome_dir_for_close

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 16 01:31:33 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.13: +10 -0 lines
Diff to previous 1.13
handle invalid family id gracefully in FikgFam.pm

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 12 18:01:57 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.12: +1 -1 lines
Diff to previous 1.12
Fixed missing declaration. -- /gdp

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 12 11:44:24 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.11: +4 -2 lines
Diff to previous 1.11
a slight modication to make the code more readable

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 29 14:59:53 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.10: +2 -0 lines
Diff to previous 1.10
fixes to find_genes_in_families

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 16 14:10:00 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.9: +2 -2 lines
Diff to previous 1.9
rebuild_repdb when reloading

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 31 17:11:20 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +15 -1 lines
Diff to previous 1.8
fixes to FigFams.pm

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 7 04:03:10 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +14 -0 lines
Diff to previous 1.7
add new_versions_of_features

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 3 15:55:21 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +1 -1 lines
Diff to previous 1.6
fixes to Assignments.pm

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 3 13:18:22 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +145 -9 lines
Diff to previous 1.5
 update genome parameters in default assignments

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 19 13:23:02 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.4: +30 -9 lines
Diff to previous 1.4
fix find_neighbors to allow for new family IDs

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 12 13:10:38 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +40 -1 lines
Diff to previous 1.3
fixes to making assignments based on consistency

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 3 19:28:52 2006 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.2: +20 -0 lines
Diff to previous 1.2
updates to ARPP/STAG

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 1 18:24:23 2006 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.1: +27 -2 lines
Diff to previous 1.1
fixes and errors to STAG

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Mar 25 23:12:56 2006 UTC (14 years ago) by overbeek
Branch: MAIN
add very buggy start of NewGenome.pm and FigFam stuff

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