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Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 23 16:05:38 2008 UTC (11 years, 3 months ago) by gdpusch
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_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, 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_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_rel_2009_02_05, rast_rel_2009_03_26, rast_rel_2009_05_18, rast_rel_2009_07_09, rast_rel_2009_0925, 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, rast_release_2008_09_29
Changes since 1.33: +15 -19 lines
Diff to previous 1.33
Streamlined FIGV handling, and conditioning of stray debugging statements on $ENV{FIG_DEBUG}. -- /gdp

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 6 16:45:37 2008 UTC (11 years, 7 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2008_06_16, rast_rel_2008_06_18, rast_rel_2008_07_21, rast_rel_2008_08_07
Changes since 1.32: +100 -71 lines
Diff to previous 1.32
Added support for non-installed genome directories. -- /gdp

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 6 13:59:34 2007 UTC (12 years ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.31: +106 -106 lines
Diff to previous 1.31
Changed POD format for better compatability with Wiki.

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 1 22:17:03 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.30: +2 -165 lines
Diff to previous 1.30
add possible_frameshift to FIG.pm (and, hence, FIGV.pm)

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 30 21:35:51 2007 UTC (12 years ago) by gdpusch
Branch: MAIN
Changes since 1.29: +43 -30 lines
Diff to previous 1.29
Fixed POD. -- /gdp

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 21 20:41:05 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.28: +1 -1 lines
Diff to previous 1.28
add code to fix frameshifts in a genome

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 13 15:10:06 2007 UTC (12 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.27: +10 -5 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, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.26: +32 -11 lines
Diff to previous 1.26
check figfams fixes

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 26 04:03:48 2007 UTC (12 years, 2 months ago) by gdpusch
Branch: MAIN
Changes since 1.25: +42 -6 lines
Diff to previous 1.25
Added &GenomeO::taxonomy_of() method; Fixed POD documentation. -- /gdp

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 26 03:40:10 2007 UTC (12 years, 2 months ago) by gdpusch
Branch: MAIN
Changes since 1.24: +17 -1 lines
Diff to previous 1.24
Added &GenomeO::taxonomy_of() method. -- /gdp

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 25 08:47:33 2007 UTC (12 years, 2 months ago) by gdpusch
Branch: MAIN
Changes since 1.23: +258 -27 lines
Diff to previous 1.23
Added POD documentation. -- /gdp

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 7 00:43:26 2007 UTC (12 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.22: +42 -35 lines
Diff to previous 1.22
add computation of alignments to building FIGFAMS

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 12 18:35:28 2007 UTC (12 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.21: +47 -18 lines
Diff to previous 1.21
Added some comments to &possible_frameshipd(). -- /gdp

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 27 17:57:49 2007 UTC (12 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.20: +10 -3 lines
Diff to previous 1.20
Rolled back modifictions to Sims access; added "$figO->function_of($id)" method.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 25 14:21:41 2007 UTC (12 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.19: +13 -2 lines
Diff to previous 1.19
tighten length constraints for figfam matching

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 19 19:49:25 2007 UTC (12 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.18: +1 -1 lines
Diff to previous 1.18
fix FIGO coupling_evidence

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 13 02:38:06 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.17: +1 -3 lines
Diff to previous 1.17
fix members function in FIGO

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 13 02:05:51 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.16: +26 -0 lines
Diff to previous 1.16
minor addition to FIGO.pm - get a figfam object

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 11 00:21:50 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.15: +117 -2 lines
Diff to previous 1.15
add the writeup on the notion of subsystem

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 4 18:49:52 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.14: +3 -3 lines
Diff to previous 1.14
fixes to possible frameshifts computations

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 4 18:35:59 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.13: +9 -3 lines
Diff to previous 1.13
update possible_frameshifts

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 28 21:55:44 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.12: +331 -19 lines
Diff to previous 1.12
remove debugging line from representative_sequences.pm

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 27 08:31:50 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.11: +23 -2 lines
Diff to previous 1.11
Added methods, and fixed various bugs.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 26 22:21:38 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.10: +5 -5 lines
Diff to previous 1.10
minor fixes to FIGO.pm

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 26 22:03:12 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.9: +9 -1 lines
Diff to previous 1.9
fixes to FIGO.pm

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 26 21:06:58 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +183 -63 lines
Diff to previous 1.8
More POD documentation

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 22 14:28:32 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +4 -7 lines
Diff to previous 1.7
fixes to error conditions in FIGO.pm

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 22 14:05:27 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +5 -4 lines
Diff to previous 1.6
fixes to error conditions in FIGO.pm

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 22 13:43:18 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +9 -7 lines
Diff to previous 1.5
update to BBHs in FIGO.pm

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 22 03:54:53 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.4: +11 -2 lines
Diff to previous 1.4
exhancements to FIGO.pm

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 22 03:01:29 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +1185 -8 lines
Diff to previous 1.3
Added POD documentation. -- /gdp

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 17 17:14:11 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.2: +102 -0 lines
Diff to previous 1.2
add possible_frameshift logic to FIGO.pm

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 23 16:15:30 2006 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.1: +65 -0 lines
Diff to previous 1.1
updates to FIGO.pm to add BBHs and sims

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 21 18:20:53 2006 UTC (13 years ago) by overbeek
Branch: MAIN
add initial version of FIGO.pm - OO services

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