Log of /FigKernelPackages/SFXlate.pm
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1.119 -
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Wed Jul 15 23:39:01 2009 UTC (10 years, 5 months ago) by
parrello
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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_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
Changes since
1.118: +35 -0 lines
Diff to
previous 1.118
Added "families_containing_peg".
Revision
1.105 -
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Wed Sep 3 20:32:24 2008 UTC (11 years, 3 months ago) by
parrello
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Changes since
1.104: +53 -15 lines
Diff to
previous 1.104
Added subsystem_version and some clearinghouse methods. Fixed to fail gracefully when the attribute server is down.
Revision
1.101 -
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Tue Feb 5 02:09:34 2008 UTC (11 years, 10 months ago) by
parrello
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Changes since
1.100: +22 -2 lines
Diff to
previous 1.100
Fixed a compiler warnings. Added support for the SEED database host being different from the Sprout database host.
Revision
1.100 -
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Tue Jan 8 21:14:59 2008 UTC (11 years, 11 months ago) by
parrello
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Changes since
1.99: +12 -3 lines
Diff to
previous 1.99
Changed to allow undef for the parameters in genome_of and is_genome. FIG.pm allows this, and chromosomal_clusters.cgi depends on it.
Revision
1.98 -
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Thu Dec 6 13:55:57 2007 UTC (12 years ago) by
parrello
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Changes since
1.97: +522 -141 lines
Diff to
previous 1.97
Changed POD format for better compatability with Wiki. Added support for "genome_list", "contig_lengths", "get_genome_subsystem_count", "get_peg_keys", "all_subsystem_classifications", "subsystems_for"pegs", "run", "run_gathering_output", "is_locked_fid", and a partridge in a pear tree.
Revision
1.85 -
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Tue Oct 17 11:36:37 2006 UTC (13 years, 2 months ago) by
parrello
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Changes since
1.84: +2 -4 lines
Diff to
previous 1.84
Changed translation check to return TRUE for any real feature. Previously, it returned FALSE for features without protein translations, causing the protein page to fail.
Revision
1.55 -
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Thu Dec 8 18:13:02 2005 UTC (14 years ago) by
parrello
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Changes since
1.54: +25 -14 lines
Diff to
previous 1.54
Added a method that can be used to determine whether the data is being taken from SEED or NMPDR.
Changed the "FIG" method to work like the same method in FIG.pm.
Revision
1.54 -
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Wed Dec 7 19:38:22 2005 UTC (14 years ago) by
golsen
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Changes since
1.53: +1 -1 lines
Diff to
previous 1.53
Don't mean to be pedantic, but I figured that I might as well add newlines
at the end of text files that lack one. Identified with a script:
/bin/sh -O extglob -c 'for f in */*.@(c|css|html|js|pl|pm|py|TXT); do perl -e '"'"'while(<>) {$s = ! /\n$/} exit $s'"'"' $f || echo $f; done'
fixed with a script:
/bin/sh
for file in _list_; do echo "" >> $file; done
Revision
1.46 -
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Wed Nov 2 22:07:38 2005 UTC (14 years, 1 month ago) by
parrello
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Changes since
1.45: +240 -64 lines
Diff to
previous 1.45
Changed "cas_to_cid" to return an empty string if more than one compound has the same CAS ID. (This matches FIG functionality.)
Fixed spelling of "stiochiometry".
Implemented "catalyzes", "ec_to_maps", "displayable_reaction", "all_maps", "role_to_maps", "map_to_ecs", and "map_name".
Revision
1.44 -
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Thu Oct 20 10:22:48 2005 UTC (14 years, 1 month ago) by
parrello
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Changes since
1.43: +128 -12 lines
Diff to
previous 1.43
Added the first wave of KEGG-method analogs.
Changed "function_of" to behave more like the FIG method.
Revision
1.42 -
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Thu Oct 13 15:27:54 2005 UTC (14 years, 2 months ago) by
parrello
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Changes since
1.41: +11 -5 lines
Diff to
previous 1.41
Modified the "new_sprout_only" method to allow specification of the "noDBOpen" option. This allows it to be used in "LoadSproutTables".
Revision
1.40 -
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Wed Oct 12 02:34:46 2005 UTC (14 years, 2 months ago) by
parrello
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Changes since
1.39: +123 -29 lines
Diff to
previous 1.39
Added "compute_clusters" and "get_subsystem" methods for SFXlate so that it can be used in "UnvSubsys" as a FIG object replacement.
Fixed "coupling_and_evidence" to remove the bogus reflexive coupling. This helps it to function like the corresponding FIG method.
Added the "raw flag" to the feature_annotations method.
Fixed up some comments.
Revision
1.35 -
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Thu Sep 1 09:33:46 2005 UTC (14 years, 3 months ago) by
parrello
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Changes since
1.34: +7 -4 lines
Diff to
previous 1.34
Fixed a bug in the handling of subsystem roles. Fixed another bug in the handling of location strings.
Revision
1.24 -
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Wed Jun 22 21:03:00 2005 UTC (14 years, 5 months ago) by
parrello
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Changes since
1.23: +935 -143 lines
Diff to
previous 1.23
Replaced tabs with spaces to make indenting device-independent.
Added POD documentation.
Finished implementing the methods required by InterfaceRoutines.pm
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