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Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 11 16:43:53 2010 UTC (9 years, 1 month ago) by disz
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, mgrast_version_3_2, myrast_33, myrast_rel40, rast_rel_2010_1206, rast_rel_2011_0119, rast_rel_2011_0928
Changes since 1.34: +1 -1 lines
Diff to previous 1.34
FigFam 6 digit fix

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 16 20:21:50 2010 UTC (9 years, 5 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0827, rast_rel_2010_0928
Changes since 1.33: +5 -603 lines
Diff to previous 1.33
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 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 4 20:12:14 2009 UTC (10 years ago) by disz
Branch: MAIN
CVS Tags: rast_rel_2010_0118, rast_rel_2010_0526
Changes since 1.32: +16 -7 lines
Diff to previous 1.32
changed doc to say XXserver->new() insetad of XX->new

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 3 02:36:48 2009 UTC (10 years, 6 months ago) by arodri7
Branch: MAIN
CVS Tags: rast_rel_2009_07_09, rast_rel_2009_0925
Changes since 1.31: +3 -3 lines
Diff to previous 1.31
replaced backticks for reading files

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 14 16:41:52 2009 UTC (10 years, 7 months ago) by arodri7
Branch: MAIN
CVS Tags: rast_rel_2009_05_18
Changes since 1.30: +6 -5 lines
Diff to previous 1.30
updates for release 9 FIGfams

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 2 01:06:20 2009 UTC (10 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.29: +1 -1 lines
Diff to previous 1.29
Added a pragma to suppress spurious warnings.

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 13 14:46:54 2009 UTC (10 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2009_03_26
Changes since 1.28: +0 -1 lines
Diff to previous 1.28
remove duplicate line

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 4 21:33:22 2009 UTC (10 years, 9 months ago) by arodri7
Branch: MAIN
Changes since 1.27: +2 -0 lines
Diff to previous 1.27
changes to decision procedure

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 4 21:29:48 2009 UTC (10 years, 9 months ago) by arodri7
Branch: MAIN
Changes since 1.26: +12 -4 lines
Diff to previous 1.26
changes to decision procedure

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 4 21:15:35 2009 UTC (10 years, 9 months ago) by arodri7
Branch: MAIN
Changes since 1.25: +2 -1 lines
Diff to previous 1.25
changes to decision procedure

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 4 20:57:32 2009 UTC (10 years, 9 months ago) by arodri7
Branch: MAIN
Changes since 1.24: +2 -1 lines
Diff to previous 1.24
update to decision procedures

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 4 20:49:30 2009 UTC (10 years, 9 months ago) by arodri7
Branch: MAIN
Changes since 1.23: +1 -1 lines
Diff to previous 1.23
update to decision procedures

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 22 07:08:04 2008 UTC (10 years, 11 months ago) by arodri7
Branch: MAIN
CVS Tags: rast_rel_2009_02_05
Changes since 1.22: +23 -4 lines
Diff to previous 1.22
made changes to steps in decision procedures to make it faster

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 11 16:16:24 2008 UTC (11 years, 4 months ago) by olson
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_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_release_2008_09_29
Changes since 1.21: +4 -4 lines
Diff to previous 1.21
Fix bug where return of should_be_member is lost.

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 16 16:58:36 2008 UTC (11 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.20: +8 -3 lines
Diff to previous 1.20
handle abnormal eol in should_be_member

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 8 19:30:10 2008 UTC (11 years, 7 months ago) by arodri7
Branch: MAIN
CVS Tags: rast_rel_2008_06_16, rast_rel_2008_06_18, rast_rel_2008_07_21
Changes since 1.19: +0 -1 lines
Diff to previous 1.19
updated and corrected sub new

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 17 21:00:10 2008 UTC (11 years, 7 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.18: +2 -2 lines
Diff to previous 1.18
RAST installation tweaks.

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 12 17:35:43 2008 UTC (11 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.17: +4 -4 lines
Diff to previous 1.17
we cannot use /tmp anymore, alas

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 11 12:00:34 2008 UTC (11 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.16: +9 -6 lines
Diff to previous 1.16
updates to FIGfam quality control

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 31 18:19:06 2008 UTC (11 years, 8 months ago) by arodri7
Branch: MAIN
Changes since 1.15: +173 -71 lines
Diff to previous 1.15
made the ross_sims be default decision procedure and in the place_in_figfam script made it check all blast results

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 13 22:19:48 2008 UTC (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.14: +2 -2 lines
Diff to previous 1.14
minor fix to length 2 of sims

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 9 16:26:00 2008 UTC (11 years, 10 months ago) by gdpusch
Branch: MAIN
Changes since 1.13: +0 -1 lines
Diff to previous 1.13
Removed duplicate "my" declaration in same scope. --/gdp

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 30 19:20:32 2008 UTC (11 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.12: +70 -30 lines
Diff to previous 1.12
fixes to FIGfam support

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 26 01:22:57 2008 UTC (11 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.11: +29 -1 lines
Diff to previous 1.11
FIGfam update

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 5 15:35:52 2008 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.10: +37 -17 lines
Diff to previous 1.10
additions to FIGfam maintenance

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 8 22:41:08 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.9: +14 -4 lines
Diff to previous 1.9
fixes to returning similarities in should_be_member

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 6 13:45:05 2007 UTC (12 years ago) by parrello
Branch: MAIN
Changes since 1.8: +33 -33 lines
Diff to previous 1.8
Changed POD format for better compatability with Wiki.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Nov 18 15:09:30 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.7: +2 -2 lines
Diff to previous 1.7
fixes to find_poss_subsys_instances.cgi

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 16 14:19:38 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.6: +2 -2 lines
Diff to previous 1.6
major fixes to FigFams.pm, FigFam.pm, FFs.pm and FF.pm

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 15 21:06:50 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.5: +1 -1 lines
Diff to previous 1.5
fix to FF.pm

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 15 16:44:09 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.4: +5 -3 lines
Diff to previous 1.4
fix rep in FigFam.pm

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 15 16:29:40 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.3: +1 -1 lines
Diff to previous 1.3
change grep to fgrep in FF.pm

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 15 16:22:03 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.2: +1 -1 lines
Diff to previous 1.2
fixes to FigFam repdb

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: +59 -15 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, 1 month ago) by overbeek
Branch: MAIN
initial undebugged versions of FF.pm and FFs.pm

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