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Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 15 21:48:19 2010 UTC (9 years, 1 month ago) by olson
Branch: MAIN
CVS Tags: 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, myrast_33, myrast_rel40, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119, rast_rel_2011_0928
Changes since 1.48: +13 -2 lines
Diff to previous 1.48
Clean up errors.

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 16 20:21:50 2010 UTC (9 years, 4 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0827
Changes since 1.47: +88 -757 lines
Diff to previous 1.47
Major update to figfams code. Remove old FigFam/FigFams modules that were tied to the
original decision procedure; update FF/FFs to use the Kmer-based stuff. Add new berkeley
db table processing routines to SeedUtils.

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 26 10:34:51 2010 UTC (9 years, 9 months ago) by bartels
Branch: MAIN
CVS Tags: rast_rel_2010_0526
Changes since 1.46: +11 -0 lines
Diff to previous 1.46
added a function

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 9 09:12:10 2009 UTC (10 years, 4 months ago) by paczian
Branch: MAIN
CVS Tags: rast_rel_2009_07_09, rast_rel_2009_0925, rast_rel_2010_0118
Changes since 1.45: +12 -2 lines
Diff to previous 1.45
fixed rast figfam display

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jun 20 21:35:07 2009 UTC (10 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.44: +7 -1 lines
Diff to previous 1.44
fixes to support Kmer analysis

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jun 20 05:44:42 2009 UTC (10 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.43: +1 -0 lines
Diff to previous 1.43
strip comments on roles

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 3 20:18:24 2009 UTC (10 years, 5 months ago) by gdpusch
Branch: MAIN
Changes since 1.42: +5 -2 lines
Diff to previous 1.42
Added confession if new() cannot fetch a new FF.pm object

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 3 02:27:08 2009 UTC (10 years, 5 months ago) by arodri7
Branch: MAIN
Changes since 1.41: +5 -3 lines
Diff to previous 1.41
fixed check for figfam object

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 28 19:51:58 2009 UTC (10 years, 5 months ago) by arodri7
Branch: MAIN
Changes since 1.40: +1 -1 lines
Diff to previous 1.40
fixed a RDONLY bug message, took quotes out

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 27 19:29:08 2009 UTC (10 years, 5 months ago) by arodri7
Branch: MAIN
Changes since 1.39: +170 -2 lines
Diff to previous 1.39
updated tie

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 27 17:00:35 2009 UTC (10 years, 5 months ago) by paczian
Branch: MAIN
Changes since 1.38: +15 -5 lines
Diff to previous 1.38
added FIGfam support for RAST orgs
fixed deleted_fids hash

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 13 17:32:52 2009 UTC (10 years, 6 months ago) by arodri7
Branch: MAIN
CVS Tags: rast_rel_2009_05_18
Changes since 1.37: +2 -169 lines
Diff to previous 1.37
updated non-essential functions

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 14 16:43:17 2009 UTC (10 years, 7 months ago) by arodri7
Branch: MAIN
Changes since 1.36: +55 -6 lines
Diff to previous 1.36
updates for release 9 FIGfams

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 2 01:07:40 2009 UTC (10 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.35: +8 -2 lines
Diff to previous 1.35
Changed to allow the caller to pass in a FIG object. Added a destructor to clean a circular reference.

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 31 20:33:33 2009 UTC (10 years, 7 months ago) by arodri7
Branch: MAIN
Changes since 1.34: +35 -86 lines
Diff to previous 1.34
added subsystems based figfams function

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 4 20:57:20 2009 UTC (10 years, 8 months ago) by arodri7
Branch: MAIN
CVS Tags: rast_rel_2009_03_26
Changes since 1.33: +2 -0 lines
Diff to previous 1.33
update to decision procedures

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 4 20:49:18 2009 UTC (10 years, 8 months ago) by arodri7
Branch: MAIN
Changes since 1.32: +6 -3 lines
Diff to previous 1.32
update to decision procedures

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 6 16:33:07 2009 UTC (10 years, 9 months ago) by arodri7
Branch: MAIN
Changes since 1.31: +5 -6 lines
Diff to previous 1.31
added place_in_family_bulk documentation

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 6 16:08:04 2009 UTC (10 years, 9 months ago) by arodri7
Branch: MAIN
Changes since 1.30: +52 -9 lines
Diff to previous 1.30
added place_in_family_bulk documentation

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 2 17:03:14 2009 UTC (10 years, 9 months ago) by arodri7
Branch: MAIN
CVS Tags: rast_rel_2009_02_05
Changes since 1.29: +6 -1 lines
Diff to previous 1.29
corrected function related to figfam webpage: division error

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 25 17:41:04 2009 UTC (10 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.28: +0 -1 lines
Diff to previous 1.28
revert change

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 25 17:34:13 2009 UTC (10 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.27: +1 -0 lines
Diff to previous 1.27
make ex_assertions.cgi ignore inactive variants

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 19 20:26:23 2009 UTC (10 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.26: +4 -5 lines
Diff to previous 1.26
Added the path to a blastall call so that it works in NMPDR.

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 22 07:08:18 2008 UTC (10 years, 10 months ago) by arodri7
Branch: MAIN
Changes since 1.25: +184 -5 lines
Diff to previous 1.25
made changes to steps in decision procedures to make it faster

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 4 15:36:34 2008 UTC (11 years, 2 months ago) by arodri7
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, 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_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_release_2008_09_29
Changes since 1.24: +3 -3 lines
Diff to previous 1.24
corrected errors for merge_figfams

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 29 14:25:39 2008 UTC (11 years, 3 months ago) by arodri7
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806, rast_rel_2008_08_07
Changes since 1.23: +4 -4 lines
Diff to previous 1.23
added merge figfams functions

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 29 14:20:14 2008 UTC (11 years, 3 months ago) by arodri7
Branch: MAIN
Changes since 1.22: +41 -4 lines
Diff to previous 1.22
added merge figfams functions

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 18 15:53:34 2008 UTC (11 years, 3 months ago) by paczian
Branch: MAIN
Changes since 1.21: +1 -1 lines
Diff to previous 1.21
corrected type in line 550 ($mergerFF -> $mergeFF)

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 18 15:16:40 2008 UTC (11 years, 3 months ago) by arodri7
Branch: MAIN
Changes since 1.20: +47 -1 lines
Diff to previous 1.20
added merge capabilities

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 18 20:26:37 2008 UTC (11 years, 4 months ago) by arodri7
Branch: MAIN
CVS Tags: rast_rel_2008_07_21
Changes since 1.19: +4 -4 lines
Diff to previous 1.19
update FIGfams

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 18 15:56:42 2008 UTC (11 years, 4 months ago) by arodri7
Branch: MAIN
Changes since 1.18: +161 -0 lines
Diff to previous 1.18
Figfams update

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 25 01:34:07 2008 UTC (11 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2008_06_16, rast_rel_2008_06_18
Changes since 1.17: +1 -1 lines
Diff to previous 1.17
update to get_dlit.cgi

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 8 19:31:28 2008 UTC (11 years, 6 months ago) by arodri7
Branch: MAIN
Changes since 1.16: +21 -0 lines
Diff to previous 1.16
updated and corrected place_in_figfam

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 1 02:54:12 2008 UTC (11 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.15: +1 -1 lines
Diff to previous 1.15
allow filtered connections to PDB from FIGfams

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 1 02:40:50 2008 UTC (11 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.14: +22 -0 lines
Diff to previous 1.14
add connections between FIGfams and structures

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 17 21:00:10 2008 UTC (11 years, 6 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.13: +20 -11 lines
Diff to previous 1.13
RAST installation tweaks.

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Apr 13 00:20:59 2008 UTC (11 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.12: +4 -2 lines
Diff to previous 1.12
fixes to FIGfam stuff

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 12 17:35:43 2008 UTC (11 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.11: +3 -3 lines
Diff to previous 1.11
we cannot use /tmp anymore, alas

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 11 12:00:34 2008 UTC (11 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.10: +12 -1 lines
Diff to previous 1.10
updates to FIGfam quality control

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 20 20:20:30 2008 UTC (11 years, 7 months ago) by arodri7
Branch: MAIN
Changes since 1.9: +13 -5 lines
Diff to previous 1.9
in place_in_figfam at the blastall command I took out the head -n 20 which asks for the top 20 blast results, but we need to look at all results because the right result might be lower than the top 20 lines

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 22 00:32:31 2008 UTC (11 years, 8 months ago) by gdpusch
Branch: MAIN
Changes since 1.8: +5 -3 lines
Diff to previous 1.8
Fixed collision between filehandle FF and package FF. -- /gdp

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 21 16:39:57 2008 UTC (11 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +0 -2 lines
Diff to previous 1.7
add delete_subsystem and rename_subsystem to FIG.pm

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 18 19:28:38 2008 UTC (11 years, 8 months ago) by arodri7
Branch: MAIN
Changes since 1.6: +54 -49 lines
Diff to previous 1.6
functions for bulk figfam function added - sub family_functions

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 18 13:53:11 2008 UTC (11 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +6 -0 lines
Diff to previous 1.5
support family_containing_peg in FFs.pm

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 8 16:09:22 2008 UTC (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.4: +48 -33 lines
Diff to previous 1.4
minor fix to place_in_family

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 16 14:19:38 2007 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +50 -8 lines
Diff to previous 1.3
major fixes to FigFams.pm, FigFam.pm, FFs.pm and FF.pm

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 15 14:52:24 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.2: +6 -0 lines
Diff to previous 1.2
make tolerant to missing FIGfam data

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 15 14:30:50 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.1: +72 -14 lines
Diff to previous 1.1
redone FIGfam stuff

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 26 14:27:36 2007 UTC (12 years ago) by overbeek
Branch: MAIN
initial undebugged versions of FF.pm and FFs.pm

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