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Revision 1.837 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 24 19:13:48 2011 UTC (9 years ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_03252011, myrast_33
Changes since 1.836: +77 -2 lines
Diff to previous 1.836 , to selected 1.732
Missing-broker fixes.
add routine to reutrn subsystem estimate data.

Revision 1.836 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 18 15:38:08 2011 UTC (9 years ago) by olson
Branch: MAIN
Changes since 1.835: +7 -3 lines
Diff to previous 1.835 , to selected 1.732
really fix set-curator. fix flush_cache too.

Revision 1.835 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 18 15:05:05 2011 UTC (9 years ago) by olson
Branch: MAIN
Changes since 1.834: +181 -7 lines
Diff to previous 1.834 , to selected 1.732
Add broker communication for annotation updates
Fix reset_subsystem_curator to reindex the SS after changing curator.

Revision 1.834 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 1 20:27:04 2011 UTC (9 years, 1 month ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_02212011, mgrast_dev_02222011, mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2
Changes since 1.833: +12 -0 lines
Diff to previous 1.833 , to selected 1.732
add DESTROY methods to the cache objects so that shutdown doesn't trigger a cache load.

Revision 1.833 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 31 23:06:26 2011 UTC (9 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.832: +1 -1 lines
Diff to previous 1.832 , to selected 1.732
fix typo

Revision 1.832 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 31 22:57:52 2011 UTC (9 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.831: +17 -0 lines
Diff to previous 1.831 , to selected 1.732
Speedups; also update memcache in assign_function()

Revision 1.831 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 31 22:40:59 2011 UTC (9 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.830: +50 -22 lines
Diff to previous 1.830 , to selected 1.732
Speedups.

Revision 1.830 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 31 15:59:53 2011 UTC (9 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.829: +2 -2 lines
Diff to previous 1.829 , to selected 1.732
fix ss indexing

Revision 1.829 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 31 15:44:47 2011 UTC (9 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.828: +39 -0 lines
Diff to previous 1.828 , to selected 1.732
Subsystem speedup fixes.

Revision 1.828 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 30 17:43:50 2011 UTC (9 years, 2 months ago) by redwards
Branch: MAIN
Changes since 1.827: +3 -9 lines
Diff to previous 1.827 , to selected 1.732
correcting old attribute code -- lucky someone cares!

Revision 1.827 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 27 22:40:20 2011 UTC (9 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.826: +109 -3 lines
Diff to previous 1.826 , to selected 1.732
SS data speedups

Revision 1.826 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 21 20:32:39 2011 UTC (9 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.825: +26 -0 lines
Diff to previous 1.825 , to selected 1.732
add atomic regulon support

Revision 1.825 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 21 20:31:04 2011 UTC (9 years, 2 months ago) by redwards
Branch: MAIN
Changes since 1.824: +7 -2 lines
Diff to previous 1.824 , to selected 1.732
supporting delete_matching_attributes in old code (it was already there) and a minor modification to unify null vs undef in attributes

Revision 1.824 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 12 04:48:31 2011 UTC (9 years, 2 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2011_0119
Changes since 1.823: +4 -2 lines
Diff to previous 1.823 , to selected 1.732
Hack to prevent GC=1 from blowing up.

Revision 1.823 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 10 02:11:15 2011 UTC (9 years, 2 months ago) by redwards
Branch: MAIN
Changes since 1.822: +3 -2 lines
Diff to previous 1.822 , to selected 1.732
Fixing a broken mark_undeleted problem

Revision 1.822 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 10 02:09:45 2011 UTC (9 years, 2 months ago) by redwards
Branch: MAIN
Changes since 1.821: +8 -1 lines
Diff to previous 1.821 , to selected 1.732
Updating the genome/genus species information to include the rdb

Revision 1.821 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 23 18:03:19 2010 UTC (9 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.820: +211 -36 lines
Diff to previous 1.820 , to selected 1.732
Caching / FCGI speedup modifications.

Revision 1.820 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 11 17:18:44 2010 UTC (9 years, 4 months ago) by disz
Branch: MAIN
CVS Tags: rast_rel_2010_1206
Changes since 1.819: +2 -2 lines
Diff to previous 1.819 , to selected 1.732
FIGFAM 6 digit problem

Revision 1.819 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 24 15:25:35 2010 UTC (9 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.818: +1 -0 lines
Diff to previous 1.818 , to selected 1.732
add missing use

Revision 1.818 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 22 16:47:28 2010 UTC (9 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.817: +39 -0 lines
Diff to previous 1.817 , to selected 1.732
If we don't have sims for an org, see if we have RAST-generated sims file. If so
use FIGV::retrieve_sims to fill them in.

Revision 1.817 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 17 23:58:38 2010 UTC (9 years, 6 months ago) by redwards
Branch: MAIN
CVS Tags: rast_rel_2010_0928
Changes since 1.816: +2 -1 lines
Diff to previous 1.816 , to selected 1.732
correcting join attributes for non-pegs

Revision 1.816 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 15 19:23:19 2010 UTC (9 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.815: +5 -1 lines
Diff to previous 1.815 , to selected 1.732
don't do annotation/assigned_functions renaming when installing from PSEED to SEED.

Revision 1.815 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 12 20:04:39 2010 UTC (9 years, 8 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0827
Changes since 1.814: +27 -1 lines
Diff to previous 1.814 , to selected 1.732
add pegs_to_usable_subsystems()

Revision 1.814 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 3 19:42:21 2010 UTC (9 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.813: +114 -21 lines
Diff to previous 1.813 , to selected 1.732
Paranoia fixes for assign_function.

Revision 1.813 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 27 20:45:51 2010 UTC (9 years, 11 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2010_0526
Changes since 1.812: +2 -0 lines
Diff to previous 1.812 , to selected 1.732
turn off recognition of locks

Revision 1.812 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 23 20:24:13 2010 UTC (9 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.811: +121 -7 lines
Diff to previous 1.811 , to selected 1.732
memcached support

Revision 1.811 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 2 15:10:07 2010 UTC (10 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.810: +7 -3 lines
Diff to previous 1.810 , to selected 1.732
fixes to active subsystem

Revision 1.810 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 16 20:12:30 2010 UTC (10 years, 2 months ago) by redwards
Branch: MAIN
CVS Tags: rast_rel_2010_0118
Changes since 1.809: +1 -0 lines
Diff to previous 1.809 , to selected 1.732
adding load_dlits to load_all

Revision 1.809 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 16 20:12:00 2010 UTC (10 years, 2 months ago) by redwards
Branch: MAIN
Changes since 1.808: +17 -1 lines
Diff to previous 1.808 , to selected 1.732
adding by_all_aliases, and fixing featre aliases

Revision 1.808 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 7 10:37:32 2009 UTC (10 years, 3 months ago) by paczian
Branch: MAIN
Changes since 1.807: +2 -2 lines
Diff to previous 1.807 , to selected 1.732
added quotemeta for title variable in add_title and update_title

Revision 1.807 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 6 23:47:22 2009 UTC (10 years, 4 months ago) by dejongh
Branch: MAIN
Changes since 1.806: +1 -1 lines
Diff to previous 1.806 , to selected 1.732
Fix comment

Revision 1.806 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 6 23:44:59 2009 UTC (10 years, 4 months ago) by redwards
Branch: MAIN
Changes since 1.805: +4 -3 lines
Diff to previous 1.805 , to selected 1.732
1. Removing md5 ids from raw sims. 2. fixing a distinct SQL query that very occassionaly reported duplicate entries

Revision 1.805 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 23 18:51:49 2009 UTC (10 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.804: +33 -0 lines
Diff to previous 1.804 , to selected 1.732
add FIG::assess_completeness

Revision 1.804 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 23 20:29:30 2009 UTC (10 years, 6 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2009_0925
Changes since 1.803: +22 -6 lines
Diff to previous 1.803 , to selected 1.732
Add rewrite-loop breaking to the role rewrite process.

Revision 1.803 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 22 15:01:59 2009 UTC (10 years, 6 months ago) by redwards
Branch: MAIN
Changes since 1.802: +1 -1 lines
Diff to previous 1.802 , to selected 1.732
minor change to ignore blank lines while parsing transaction records

Revision 1.802 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 27 20:48:41 2009 UTC (10 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.801: +47 -0 lines
Diff to previous 1.801 , to selected 1.732
Support for Seedviewer Subsystems.pm speedups.

Revision 1.801 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 26 20:24:23 2009 UTC (10 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.800: +22 -8 lines
Diff to previous 1.800 , to selected 1.732
Optimize subsystems_for_peg for the case where we don't want non-active variants.

Revision 1.800 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 25 20:57:42 2009 UTC (10 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.799: +1 -1 lines
Diff to previous 1.799 , to selected 1.732
Fix missing quotes in query

Revision 1.799 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 19 21:43:33 2009 UTC (10 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.798: +21 -1 lines
Diff to previous 1.798 , to selected 1.732
Make wikipedia_link in the SEED case use the local SEED wikipedia cache.

Revision 1.798 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 19 17:03:55 2009 UTC (10 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.797: +0 -1 lines
Diff to previous 1.797 , to selected 1.732
*** empty log message ***

Revision 1.797 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 11 20:28:01 2009 UTC (10 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.796: +19 -0 lines
Diff to previous 1.796 , to selected 1.732
add co-occurs stuff

Revision 1.796 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 11 18:51:39 2009 UTC (10 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.795: +28 -0 lines
Diff to previous 1.795 , to selected 1.732
Added "sapling" method for accessing a Sapling database from the FIG object.

Revision 1.795 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 10 16:43:54 2009 UTC (10 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.794: +1 -1 lines
Diff to previous 1.794 , to selected 1.732
minor documentation fix

Revision 1.794 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 7 09:19:05 2009 UTC (10 years, 7 months ago) by paczian
Branch: MAIN
Changes since 1.793: +57 -20 lines
Diff to previous 1.793 , to selected 1.732
fixed protein_subsystem_to_roles

Revision 1.793 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 15 21:22:11 2009 UTC (10 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.792: +18 -0 lines
Diff to previous 1.792 , to selected 1.732
Adding a replace method to tell if one genome replaced an older version

Revision 1.792 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 10 01:25:56 2009 UTC (10 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.791: +2 -1 lines
Diff to previous 1.791 , to selected 1.732
fix bad calls to possibly_truncated

Revision 1.791 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 6 20:15:24 2009 UTC (10 years, 8 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2009_07_09
Changes since 1.790: +7 -7 lines
Diff to previous 1.790 , to selected 1.732
Make function_of() use sql parameters

Sorted returns from keep a sort on the id1.

Revision 1.790 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 3 15:42:10 2009 UTC (10 years, 8 months ago) by dejongh
Branch: MAIN
Changes since 1.789: +21 -10 lines
Diff to previous 1.789 , to selected 1.732
return hope_reactions with scenario information

Revision 1.789 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 2 23:07:44 2009 UTC (10 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.788: +16 -22 lines
Diff to previous 1.788 , to selected 1.732
Fixed attribute server documentation.

Revision 1.788 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 25 20:04:22 2009 UTC (10 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.787: +4 -2 lines
Diff to previous 1.787 , to selected 1.732
put in ext_bin

Revision 1.787 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 21 23:15:57 2009 UTC (10 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.786: +6 -2 lines
Diff to previous 1.786 , to selected 1.732
return distinct values on pros_for_role

Revision 1.786 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 16 20:27:25 2009 UTC (10 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.785: +37 -11 lines
Diff to previous 1.785 , to selected 1.732
change active_subsystems to use opendir/open instead of a backtick grep.

Revision 1.785 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 26 18:03:10 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.784: +5 -2 lines
Diff to previous 1.784 , to selected 1.732
fixes to blastit

Revision 1.784 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 21 18:53:27 2009 UTC (10 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.783: +13 -2 lines
Diff to previous 1.783 , to selected 1.732
make is_aux_role_in_subsystem use the database instead of instantiating Subsystem objs

Revision 1.783 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 21 18:50:42 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.782: +4 -4 lines
Diff to previous 1.782 , to selected 1.732
add variant to returned data on get_genome_subsystem_data

Revision 1.782 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 21 15:03:47 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.781: +8 -4 lines
Diff to previous 1.781 , to selected 1.732
clean up warnings

Revision 1.781 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 21 14:32:26 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.780: +8 -3 lines
Diff to previous 1.780 , to selected 1.732
suppress variant check in accessing subsystem data, if desired

Revision 1.780 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 21 13:53:12 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2009_05_18
Changes since 1.779: +3 -3 lines
Diff to previous 1.779 , to selected 1.732
fix operator in SQL

Revision 1.779 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 21 13:44:59 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.778: +1 -1 lines
Diff to previous 1.778 , to selected 1.732
fix operator in SQL

Revision 1.778 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 21 13:41:17 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.777: +1 -1 lines
Diff to previous 1.777 , to selected 1.732
fix operator in SQL

Revision 1.777 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 19 21:12:01 2009 UTC (10 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.776: +0 -2 lines
Diff to previous 1.776 , to selected 1.732
fix typo bug

Revision 1.776 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 19 20:51:33 2009 UTC (10 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.775: +74 -22 lines
Diff to previous 1.775 , to selected 1.732
On genome installation, rename any roles that were changed in the role rename log.
Don't perform subsystem salvage.

Revision 1.775 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 19 02:38:56 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.774: +2 -2 lines
Diff to previous 1.774 , to selected 1.732
fix blast to add ln2

Revision 1.774 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 17 13:58:19 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.773: +3 -1 lines
Diff to previous 1.773 , to selected 1.732
remove warning

Revision 1.773 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 17 13:42:25 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.772: +15 -6 lines
Diff to previous 1.772 , to selected 1.732
add blastx and get rid of warnings

Revision 1.772 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 11 18:35:38 2009 UTC (10 years, 10 months ago) by disz
Branch: MAIN
Changes since 1.771: +20 -0 lines
Diff to previous 1.771 , to selected 1.732
Added all_subsystems_with_roles

Revision 1.771 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 9 16:34:30 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.770: +2 -3 lines
Diff to previous 1.770 , to selected 1.732
minor fix

Revision 1.770 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 9 16:25:33 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.769: +14 -0 lines
Diff to previous 1.769 , to selected 1.732
add variant_code

Revision 1.769 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 9 15:30:01 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.768: +4 -4 lines
Diff to previous 1.768 , to selected 1.732
fix nonumeric comparisons

Revision 1.768 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 9 15:22:57 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.767: +1 -1 lines
Diff to previous 1.767 , to selected 1.732
make comparison of -1 nonnumeric compare

Revision 1.767 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 4 20:59:55 2009 UTC (10 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.766: +1 -1 lines
Diff to previous 1.766 , to selected 1.732
Fixed initialization error in fid_from_clearinghouse().

Revision 1.766 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 4 20:49:31 2009 UTC (10 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.765: +1 -1 lines
Diff to previous 1.765 , to selected 1.732
Fixed unitialized variable warning in add_annotation().

Revision 1.765 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 4 20:32:08 2009 UTC (10 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.764: +1 -1 lines
Diff to previous 1.764 , to selected 1.732
Fix bug in location_overlap().

Revision 1.764 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 4 19:49:37 2009 UTC (10 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.763: +32 -0 lines
Diff to previous 1.763 , to selected 1.732
add function FIG::location_overlap( loc1, loc2 )

Revision 1.763 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 3 04:38:19 2009 UTC (10 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.762: +5 -3 lines
Diff to previous 1.762 , to selected 1.732
Base $fig->is_plasmid() on TAXONOMY, not PLASMID file. (The PLASMID file is now obsolete.)

Revision 1.762 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 27 17:17:51 2009 UTC (10 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.761: +1 -1 lines
Diff to previous 1.761 , to selected 1.732
fix dumb mistake

Revision 1.761 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 27 17:11:29 2009 UTC (10 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.760: +15 -10 lines
Diff to previous 1.760 , to selected 1.732
Fixes for prots_with_md5/pegs_with_md5 to use the peg.synonyms where possible.

Revision 1.760 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 27 08:23:43 2009 UTC (10 years, 11 months ago) by paczian
Branch: MAIN
Changes since 1.759: +40 -1 lines
Diff to previous 1.759 , to selected 1.732
modified pegs_with_md5 to return only fig ids matching an md5 hash
added prots_with_md5 to return all ids matching an md5 hash

Revision 1.759 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 2 01:09:46 2009 UTC (11 years ago) by parrello
Branch: MAIN
Changes since 1.758: +26 -0 lines
Diff to previous 1.758 , to selected 1.732
Added a method to clear the subsystem cache.

Revision 1.758 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 1 18:46:41 2009 UTC (11 years ago) by gdpusch
Branch: MAIN
Changes since 1.757: +15 -0 lines
Diff to previous 1.757 , to selected 1.732
Added "is_plasmid()" function.

Revision 1.757 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 25 16:17:32 2009 UTC (11 years ago) by paczian
Branch: MAIN
CVS Tags: rast_rel_2009_03_26
Changes since 1.756: +4 -1 lines
Diff to previous 1.756 , to selected 1.732
added searching of alias column to search database function

Revision 1.756 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 24 18:35:15 2009 UTC (11 years ago) by overbeek
Branch: MAIN
Changes since 1.755: +1 -1 lines
Diff to previous 1.755 , to selected 1.732
minor correction in documentation

Revision 1.755 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 15 23:55:42 2009 UTC (11 years ago) by parrello
Branch: MAIN
Changes since 1.754: +1 -1 lines
Diff to previous 1.754 , to selected 1.732
Fixed the compiler warnings caused by use recursion.

Revision 1.754 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 9 18:30:16 2009 UTC (11 years ago) by disz
Branch: MAIN
Changes since 1.753: +18 -18 lines
Diff to previous 1.753 , to selected 1.732
Updated get_representative_genome

Revision 1.753 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 9 17:34:48 2009 UTC (11 years ago) by disz
Branch: MAIN
Changes since 1.752: +43 -0 lines
Diff to previous 1.752 , to selected 1.732
Added get_representative_genome

Revision 1.752 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 23 21:13:39 2009 UTC (11 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.751: +3 -3 lines
Diff to previous 1.751 , to selected 1.732
Fixed several methods so that they work for rna and other non-peg features.

Revision 1.751 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 9 17:47:16 2009 UTC (11 years, 1 month ago) by gdpusch
Branch: MAIN
Changes since 1.750: +104 -83 lines
Diff to previous 1.750 , to selected 1.732
Restored lost fix of TAXONOMY whitespace and "Candidatus" bugs

Revision 1.750 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 5 16:32:57 2009 UTC (11 years, 1 month ago) by paczian
Branch: MAIN
Changes since 1.749: +35 -3 lines
Diff to previous 1.749 , to selected 1.732
added function subsystems_for_pegs_complete
commented out warning for 'no taxonomy found' since it is triggered for every private organism

Revision 1.749 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 4 17:46:02 2009 UTC (11 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.748: +8 -0 lines
Diff to previous 1.748 , to selected 1.732
fix is_cluster_based_subsystem

Revision 1.748 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 2 12:50:20 2009 UTC (11 years, 1 month ago) by bartels
Branch: MAIN
CVS Tags: rast_rel_2009_02_05
Changes since 1.747: +116 -247 lines
Diff to previous 1.747 , to selected 1.732
bugfix

Revision 1.747 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 30 12:42:15 2009 UTC (11 years, 2 months ago) by paczian
Branch: MAIN
Changes since 1.746: +31 -0 lines
Diff to previous 1.746 , to selected 1.732
added function subsystems_for_pegs_complete

Revision 1.746 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 26 21:09:30 2009 UTC (11 years, 2 months ago) by gdpusch
Branch: MAIN
Changes since 1.745: +120 -98 lines
Diff to previous 1.745 , to selected 1.732
Fixed (hopefully) a TAXONOMY-sorting bug, and remaining instances of "Candidatus."

Revision 1.745 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 25 17:34:13 2009 UTC (11 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.744: +17 -4 lines
Diff to previous 1.744 , to selected 1.732
make ex_assertions.cgi ignore inactive variants

Revision 1.744 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 23 13:09:31 2009 UTC (11 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.743: +2 -2 lines
Diff to previous 1.743 , to selected 1.732
put ext_bin on invocations of formatdb and blastall

Revision 1.743 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 20 20:19:23 2009 UTC (11 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.742: +7 -0 lines
Diff to previous 1.742 , to selected 1.732
add is_cluster_based_subsystem

Revision 1.742 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 19 20:29:43 2009 UTC (11 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.741: +5 -4 lines
Diff to previous 1.741 , to selected 1.732
Fixed subsystems_for_peg so it works for non-pegs.

Revision 1.741 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 15 20:59:52 2008 UTC (11 years, 3 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_12_18
Changes since 1.740: +65 -3 lines
Diff to previous 1.740 , to selected 1.732
LRU cache used for get_subsystem().

Add clearinghouse_ping()

Revision 1.740 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 26 19:28:37 2008 UTC (11 years, 4 months ago) by gdpusch
Branch: MAIN
Changes since 1.739: +3 -0 lines
Diff to previous 1.739 , to selected 1.732
Strip any leading whitespace off the TAXONOMY string.

Revision 1.739 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 26 19:24:38 2008 UTC (11 years, 4 months ago) by gdpusch
Branch: MAIN
Changes since 1.738: +4 -0 lines
Diff to previous 1.738 , to selected 1.732
Automatically strip "Candidatus" off genus/species.

Revision 1.738 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 19 17:57:53 2008 UTC (11 years, 4 months ago) by bartels
Branch: MAIN
CVS Tags: rast_rel_2008_11_24
Changes since 1.737: +22 -0 lines
Diff to previous 1.737 , to selected 1.732
*** empty log message ***

Revision 1.737 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 17 19:36:28 2008 UTC (11 years, 4 months ago) by dejongh
Branch: MAIN
Changes since 1.736: +85 -0 lines
Diff to previous 1.736 , to selected 1.732
Added get_scenario_info to speed up reading scenario info for a list of subsystems

Revision 1.736 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 13 21:49:33 2008 UTC (11 years, 4 months ago) by dejongh
Branch: MAIN
Changes since 1.735: +9 -7 lines
Diff to previous 1.735 , to selected 1.732
fix scenario_directory to work for All

Revision 1.735 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 12 18:22:42 2008 UTC (11 years, 4 months ago) by dejongh
Branch: MAIN
Changes since 1.734: +7 -14 lines
Diff to previous 1.734 , to selected 1.732
switch to scenario_directory

Revision 1.734 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 12 16:03:53 2008 UTC (11 years, 4 months ago) by bartels
Branch: MAIN
Changes since 1.733: +24 -1 lines
Diff to previous 1.733 , to selected 1.732
added a function for getting dlits

Revision 1.733 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 25 13:37:47 2008 UTC (11 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2
Changes since 1.732: +34 -0 lines
Diff to previous 1.732
add routine to get close pegs in the same subsystem

Revision 1.732 - (view) (download) (as text) (annotate) - [selected]
Thu Oct 23 16:20:48 2008 UTC (11 years, 5 months ago) by paczian
Branch: MAIN
Changes since 1.731: +4 -0 lines
Diff to previous 1.731
fixed the case where function_of_bulk would break if there were no ids passed

Revision 1.731 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 18 10:18:41 2008 UTC (11 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.730: +2 -3 lines
Diff to previous 1.730 , to selected 1.732
Set to use old attributes if the attrHost variable is empty.

Revision 1.730 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 16 20:04:16 2008 UTC (11 years, 5 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_10_29
Changes since 1.729: +43 -20 lines
Diff to previous 1.729 , to selected 1.732
Add FIG.pm caching of all-subsystem data, and use that for subsystem-classification calls made after a
call to all_subsystem_classifications.

Revision 1.729 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 16 17:39:05 2008 UTC (11 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.728: +8 -1 lines
Diff to previous 1.728 , to selected 1.732
Heh. return inside eval returns from the eval, not the enclosing sub.

Revision 1.728 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 15 13:01:26 2008 UTC (11 years, 5 months ago) by paczian
Branch: MAIN
Changes since 1.727: +5 -2 lines
Diff to previous 1.727 , to selected 1.732
updated function 'search_database'
now excepts limit for protein searches
protein searches also return organism name and domain

Revision 1.727 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 15 11:51:21 2008 UTC (11 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.726: +2 -1 lines
Diff to previous 1.726 , to selected 1.732
Fixed a comment.

Revision 1.726 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 13 20:26:02 2008 UTC (11 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.725: +28 -13 lines
Diff to previous 1.725 , to selected 1.732
Add support for subsystem_metadata table. Updates via Subsystem::db_sync.

Revision 1.725 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 9 18:08:32 2008 UTC (11 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.724: +44 -0 lines
Diff to previous 1.724 , to selected 1.732
Added a new method for getting subsystem data of a genome's features. This is used by the Sprout loader.

Revision 1.724 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 22 12:42:31 2008 UTC (11 years, 6 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, mgrast_rel_2008_0923, mgrast_rel_2008_0924, rast_2008_0924, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_rel_2008_10_09, rast_release_2008_09_29
Changes since 1.723: +1 -1 lines
Diff to previous 1.723 , to selected 1.732
get rid of warning and update conditionally_assign

Revision 1.723 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 12 01:47:15 2008 UTC (11 years, 6 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_rel_2008_0917, mgrast_rel_2008_0919
Changes since 1.722: +11 -1 lines
Diff to previous 1.722 , to selected 1.732
fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic reconstructions

Revision 1.722 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 11 22:01:23 2008 UTC (11 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.721: +1 -1 lines
Diff to previous 1.721 , to selected 1.732
Remove load_attributes from load script, add load_id_correspondence.

Revision 1.721 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 11 14:57:59 2008 UTC (11 years, 6 months ago) by gdpusch
Branch: MAIN
Changes since 1.720: +11 -2 lines
Diff to previous 1.720 , to selected 1.732
Fixed typo in &possibly_truncated_stop(), and added POD for the mods to &possibly_truncated(). -- /gdp

Revision 1.720 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 11 14:46:03 2008 UTC (11 years, 6 months ago) by gdpusch
Branch: MAIN
Changes since 1.719: +41 -12 lines
Diff to previous 1.719 , to selected 1.732
Modified &possibly_truncated() to return whether STOP or START is truncated; added &possibly_truncated_stop(), and &possibly_truncated_start(). -- /gdp

Revision 1.719 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 10 09:55:54 2008 UTC (11 years, 6 months ago) by bartels
Branch: MAIN
Changes since 1.718: +7 -1 lines
Diff to previous 1.718 , to selected 1.732
changed function change_funcrole so that it keeps the comments

Revision 1.718 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Sep 6 20:34:52 2008 UTC (11 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.717: +109 -1 lines
Diff to previous 1.717 , to selected 1.732
Add support for $fig->change_funcrole()

Revision 1.717 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 5 10:40:29 2008 UTC (11 years, 6 months ago) by bartels
Branch: MAIN
Changes since 1.716: +34 -6 lines
Diff to previous 1.716 , to selected 1.732
changed publish_subsystem_to_clearinghouse so that it can be used by a webpage

Revision 1.716 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 3 20:27:26 2008 UTC (11 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.715: +9 -4 lines
Diff to previous 1.715 , to selected 1.732
Fixed to recover from an inability to reach the attribute server.

Revision 1.715 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 23 23:39:22 2008 UTC (11 years, 7 months ago) by golsen
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806
Changes since 1.714: +25 -22 lines
Diff to previous 1.714 , to selected 1.732
Move writing of assignment annotation from a case-by-case basis (and it
was missing in several key places) to the FIG::assign_function.

Modify the code in each of the calling locations to not make duplicate
annotations.

At the same time, remove (most) of the instances of making different
calls to assign_function depending on the user name.  assign_function
treats everyone as master (but writes an annotation with the real user
name).

Revision 1.714 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 15 20:01:18 2008 UTC (11 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.713: +1 -1 lines
Diff to previous 1.713 , to selected 1.732
fix clearinghouse urls.

Revision 1.713 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 12 06:35:42 2008 UTC (11 years, 7 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_08_07
Changes since 1.712: +21 -25 lines
Diff to previous 1.712 , to selected 1.732
Fixed for sprout compatability.

Revision 1.712 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 6 14:03:51 2008 UTC (11 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.711: +31 -261 lines
Diff to previous 1.711 , to selected 1.732
Moved to_structured_english to FIGRules.

Revision 1.711 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 28 15:27:11 2008 UTC (11 years, 8 months ago) by bartels
Branch: MAIN
Changes since 1.710: +37 -1 lines
Diff to previous 1.710 , to selected 1.732
added functions is_experimental_subsystem and is_private_subsystem

Revision 1.710 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 17 18:44:30 2008 UTC (11 years, 8 months ago) by dsouza
Branch: MAIN
Changes since 1.709: +74 -0 lines
Diff to previous 1.709 , to selected 1.732
Added uniprot_aliases. Most organisms do not have uniprot ids in their tbl
files, and so the regular alias routines are missing them. The new routine
gets the uiprot ids from other sources.

Revision 1.709 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 13 23:10:59 2008 UTC (11 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.708: +262 -15 lines
Diff to previous 1.708 , to selected 1.732
Many code clean-ups in the dlits routines, and associated literature.

Add support for indexing the translations in Global/nr.

Revision 1.708 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jul 12 22:51:27 2008 UTC (11 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.707: +26 -1 lines
Diff to previous 1.707 , to selected 1.732
Remove warning from dispaly_id_and_seq

Add mechanism in get_trnaslation to pull xxx id translations directly from NR.

Revision 1.707 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 10 19:35:33 2008 UTC (11 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.706: +45 -35 lines
Diff to previous 1.706 , to selected 1.732
A bug fix in an SQL statement in get_dlits (I still don't fully understand
the nature, but it left a query 'SELECT DISTINCT hash_role.role ...' hung).
Add code for an index of the dlits table by pubmed id.

Revision 1.706 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 9 15:59:57 2008 UTC (11 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.705: +1 -0 lines
Diff to previous 1.705 , to selected 1.732
Minor changes including:
   Display literature curator in literature curation table
   Do not display master: on literature curator
   Do not record msster: on literature curator
   Filter for real features before picking representative peg with md5

Revision 1.705 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 8 21:26:12 2008 UTC (11 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.704: +18 -2 lines
Diff to previous 1.704 , to selected 1.732
Add update of curator on propagation of 'G' status code.
Add logging of delete and insert events (but not that due to propagation
of 'G' status codes).

Revision 1.704 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 8 01:39:58 2008 UTC (11 years, 8 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2008_07_21
Changes since 1.703: +61 -42 lines
Diff to previous 1.703 , to selected 1.732
Improving navigation in the dlits scripts, and improving behavior in
the FIG.pm support for it.

Revision 1.703 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 7 21:19:48 2008 UTC (11 years, 8 months ago) by bartels
Branch: MAIN
Changes since 1.702: +17 -1 lines
Diff to previous 1.702 , to selected 1.732
added a function to read the curation log

Revision 1.702 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 30 20:45:01 2008 UTC (11 years, 9 months ago) by disz
Branch: MAIN
Changes since 1.701: +4 -2 lines
Diff to previous 1.701 , to selected 1.732
Changed text for ilit, dlit

Revision 1.701 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jun 28 05:58:33 2008 UTC (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.700: +101 -0 lines
Diff to previous 1.700 , to selected 1.732
code relating to dlit/ilit maintenance

Revision 1.700 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 26 19:27:00 2008 UTC (11 years, 9 months ago) by disz
Branch: MAIN
Changes since 1.699: +55 -44 lines
Diff to previous 1.699 , to selected 1.732
Fixed up ILIT text

Revision 1.699 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 24 15:15:07 2008 UTC (11 years, 9 months ago) by disz
Branch: MAIN
Changes since 1.698: +11 -6 lines
Diff to previous 1.698 , to selected 1.732
Added escape arg to structured english

Revision 1.698 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jun 21 23:23:38 2008 UTC (11 years, 9 months ago) by golsen
Branch: MAIN
Changes since 1.697: +86 -0 lines
Diff to previous 1.697 , to selected 1.732
Support for MD5 indexing of SEED translations.

Revision 1.697 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 20 20:35:19 2008 UTC (11 years, 9 months ago) by disz
Branch: MAIN
Changes since 1.696: +6 -9 lines
Diff to previous 1.696 , to selected 1.732
Removed  test code accidentally left in

Revision 1.696 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 20 20:27:49 2008 UTC (11 years, 9 months ago) by disz
Branch: MAIN
Changes since 1.695: +259 -1 lines
Diff to previous 1.695 , to selected 1.732
Added Structured English to Seed Viewer pages

Revision 1.695 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 12 17:16:35 2008 UTC (11 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.694: +37 -2 lines
Diff to previous 1.694 , to selected 1.732
Add lookup_subsystem_by_id

Revision 1.694 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 12 16:58:10 2008 UTC (11 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.693: +1 -2 lines
Diff to previous 1.693 , to selected 1.732
remove the debugging url

Revision 1.693 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 12 16:54:50 2008 UTC (11 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.692: +34 -0 lines
Diff to previous 1.692 , to selected 1.732
Add clearinghouse_register_subsystem_id

Revision 1.692 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 11 21:10:23 2008 UTC (11 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.691: +37 -1 lines
Diff to previous 1.691 , to selected 1.732
add metagenome register taxon method
in salvage, always add a * to the variant even if all roles were fulfilled.

Revision 1.691 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 28 17:46:03 2008 UTC (11 years, 10 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_06_16, rast_rel_2008_06_18
Changes since 1.690: +6 -5 lines
Diff to previous 1.690 , to selected 1.732
Changed display_id_and_seq to work in Sprout. Changed boundaries_of to be more tolerant of spaces in the location string.

Revision 1.690 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 24 23:09:40 2008 UTC (11 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.689: +4 -3 lines
Diff to previous 1.689 , to selected 1.732
Fix the code for adding links to a fid page so that the code to write
the new link to a file works (all old links were put in DBMS, but not
written to the disk), and add HTML escaping to the use-supplied link
name.

Revision 1.689 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 23 08:43:55 2008 UTC (11 years, 10 months ago) by gdpusch
Branch: MAIN
Changes since 1.688: +1 -2 lines
Diff to previous 1.688 , to selected 1.732
Fixed syntax error in definition of %named_hash. -- /gdp

Revision 1.688 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 20 19:06:04 2008 UTC (11 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.687: +10 -14 lines
Diff to previous 1.687 , to selected 1.732
fix up add_feature

Revision 1.687 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 9 19:24:12 2008 UTC (11 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.686: +6 -0 lines
Diff to previous 1.686 , to selected 1.732
don't die in perorm_subsystem_salvage() if a ss is missing.

Revision 1.686 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 1 15:52:34 2008 UTC (11 years, 11 months ago) by paczian
Branch: MAIN
Changes since 1.685: +44 -0 lines
Diff to previous 1.685 , to selected 1.732
added function subsystems_for_peg_complete which returns subsystem, role, variant, is_auxiliary tuples for all subsystems of a peg

Revision 1.685 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 30 12:51:17 2008 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.684: +1 -0 lines
Diff to previous 1.684 , to selected 1.732
minor fixes to lengths on blast

Revision 1.684 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 29 04:51:43 2008 UTC (11 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.683: +1 -1 lines
Diff to previous 1.683 , to selected 1.732
Changed a warning to a cluck to give us better information about how invalid locations get into the data.

Revision 1.683 - (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 1.682: +59 -1 lines
Diff to previous 1.682 , to selected 1.732
Introduce get_figfam_data().

Revision 1.682 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 16 00:55:53 2008 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.681: +1 -1 lines
Diff to previous 1.681 , to selected 1.732
fixes to the ACH_resolution stuff

Revision 1.681 - (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 1.680: +3 -1 lines
Diff to previous 1.680 , to selected 1.732
updates to FIGfam quality control

Revision 1.680 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 26 14:49:38 2008 UTC (12 years ago) by wilke
Branch: MAIN
Changes since 1.679: +24 -9 lines
Diff to previous 1.679 , to selected 1.732
updated get_organism_info_from_ncbi, using Gary Olsens function decode_html_chars to extract the correct string from the xml

Revision 1.679 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 20 16:56:12 2008 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.678: +6 -2 lines
Diff to previous 1.678 , to selected 1.732
allow suppression of cluster-based subsystems

Revision 1.678 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 20 14:54:19 2008 UTC (12 years ago) by mkubal
Branch: MAIN
Changes since 1.677: +28 -29 lines
Diff to previous 1.677 , to selected 1.732
fixed feature_aliases_bulk to not break on deleted ids

Revision 1.677 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 17 13:46:26 2008 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.676: +38 -7 lines
Diff to previous 1.676 , to selected 1.732
changes to dsims

Revision 1.676 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 13 19:22:39 2008 UTC (12 years ago) by paarmann
Branch: MAIN
Changes since 1.675: +21 -0 lines
Diff to previous 1.675 , to selected 1.732
added get_all_assertions which queries all annotations from the aclh for a set of pegs

Revision 1.675 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 12 21:18:14 2008 UTC (12 years ago) by olson
Branch: MAIN
Changes since 1.674: +6 -4 lines
Diff to previous 1.674 , to selected 1.732
Fix query for get_id_correspondence.

Revision 1.674 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 12 21:05:29 2008 UTC (12 years ago) by olson
Branch: MAIN
Changes since 1.673: +2 -2 lines
Diff to previous 1.673 , to selected 1.732
updates to the load_id_correspondence loader and searching code.

Revision 1.673 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 12 16:15:02 2008 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.672: +24 -0 lines
Diff to previous 1.672 , to selected 1.732
add get_assertions to access clearinghouse expert assertions

Revision 1.672 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 6 17:05:22 2008 UTC (12 years ago) by bartels
Branch: MAIN
Changes since 1.671: +31 -1 lines
Diff to previous 1.671 , to selected 1.732
added a method for getting the number of NEW diagrams

Revision 1.671 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 5 17:07:50 2008 UTC (12 years ago) by olson
Branch: MAIN
Changes since 1.670: +55 -0 lines
Diff to previous 1.670 , to selected 1.732
Finish load_id_correspondence; add get_corresponding_ids();

Revision 1.670 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 5 02:19:11 2008 UTC (12 years ago) by wilke
Branch: MAIN
Changes since 1.669: +53 -0 lines
Diff to previous 1.669 , to selected 1.732
added two functions
get_taxonomy_id_of and set_taxonomy_for

Revision 1.669 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 4 20:55:07 2008 UTC (12 years ago) by paczian
Branch: MAIN
Changes since 1.668: +2 -2 lines
Diff to previous 1.668 , to selected 1.732
added taxonomy to genome_info

Revision 1.668 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 4 00:11:58 2008 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.667: +1 -1 lines
Diff to previous 1.667 , to selected 1.732
fix stripping comments in roles_of_function

Revision 1.667 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 29 21:52:19 2008 UTC (12 years, 1 month ago) by paczian
Branch: MAIN
Changes since 1.666: +10 -7 lines
Diff to previous 1.666 , to selected 1.732
reverted to 1.665, readded corrected change from 1.666

Revision 1.666 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 29 21:12:45 2008 UTC (12 years, 1 month ago) by paczian
Branch: MAIN
Changes since 1.665: +31 -9 lines
Diff to previous 1.665 , to selected 1.732
 added method genome_info

Revision 1.665 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 28 19:12:37 2008 UTC (12 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.664: +5 -2 lines
Diff to previous 1.664 , to selected 1.732
make the parse test in boundaries_of also check for beginning & end > 0.

Revision 1.664 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 28 17:59:01 2008 UTC (12 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.663: +12 -11 lines
Diff to previous 1.663 , to selected 1.732
Fix boundaries_of bug leading ot incorrect parse failures where $end == 0.

Revision 1.663 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 21 16:39:57 2008 UTC (12 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.662: +2 -2 lines
Diff to previous 1.662 , to selected 1.732
add delete_subsystem and rename_subsystem to FIG.pm

Revision 1.662 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 21 16:36:23 2008 UTC (12 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.661: +2 -2 lines
Diff to previous 1.661 , to selected 1.732
add routines to delete and rename subsusyems to FIG.pm

Revision 1.661 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 21 16:33:13 2008 UTC (12 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.660: +24 -0 lines
Diff to previous 1.660 , to selected 1.732
add routines to delete and rename subsusyems to FIG.pm

Revision 1.660 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 18 21:01:30 2008 UTC (12 years, 1 month ago) by paczian
Branch: MAIN
Changes since 1.659: +31 -3 lines
Diff to previous 1.659 , to selected 1.732
added method taxonomy_list for bulk retrieval of organism taxonomies

Revision 1.659 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 17 19:29:37 2008 UTC (12 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.658: +3 -3 lines
Diff to previous 1.658 , to selected 1.732
screen out bad genomes from genome list in FIG.pm

Revision 1.658 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 13 18:11:00 2008 UTC (12 years, 1 month ago) by gdpusch
Branch: MAIN
Changes since 1.657: +8 -4 lines
Diff to previous 1.657 , to selected 1.732
Appended the strand to the results returned by &boundaries_of(), -- /gdp

Revision 1.657 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 12 03:49:45 2008 UTC (12 years, 1 month ago) by gdpusch
Branch: MAIN
Changes since 1.656: +1 -2 lines
Diff to previous 1.656 , to selected 1.732
Removed a redundant "my %hits;" from "&dsims()", and added a "defined()" around a "$_ = <PARTITION>" that perl was kvetching about. -- /gdp

Revision 1.656 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 11 20:51:37 2008 UTC (12 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.655: +1 -0 lines
Diff to previous 1.655 , to selected 1.732
close a file left open in dsims

Revision 1.655 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 11 16:53:43 2008 UTC (12 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.654: +41 -28 lines
Diff to previous 1.654 , to selected 1.732
minor fixes to dsims

Revision 1.654 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 7 21:52:29 2008 UTC (12 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.653: +7 -5 lines
Diff to previous 1.653 , to selected 1.732
fixes to dsims in FIG.pl

Revision 1.653 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 7 21:43:35 2008 UTC (12 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.652: +2 -0 lines
Diff to previous 1.652 , to selected 1.732
make dsims handle min_nbsc properly

Revision 1.652 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 7 21:35:39 2008 UTC (12 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.651: +43 -36 lines
Diff to previous 1.651 , to selected 1.732
implemented new version of dsims based on partitions

Revision 1.651 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 5 01:09:49 2008 UTC (12 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.650: +2 -2 lines
Diff to previous 1.650 , to selected 1.732
Fixed some headings.

Revision 1.650 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 29 08:00:20 2008 UTC (12 years, 2 months ago) by gdpusch
Branch: MAIN
Changes since 1.649: +1 -0 lines
Diff to previous 1.649 , to selected 1.732
Fixed &FIG::flatten_dumper() to support OOP calling syntax. -- /gdp

Revision 1.649 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 25 21:13:50 2008 UTC (12 years, 2 months ago) by gdpusch
Branch: MAIN
Changes since 1.648: +4 -3 lines
Diff to previous 1.648 , to selected 1.732
Added search-interval constraint to &pick_gene_boundaries(). -- /gdp

Revision 1.648 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 20 21:33:42 2008 UTC (12 years, 2 months ago) by gdpusch
Branch: MAIN
Changes since 1.647: +16 -35 lines
Diff to previous 1.647 , to selected 1.732
Revised &pick_gene_boundaries() to use new code in "Location.pm". -- /gdp

Revision 1.647 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 2 01:42:50 2008 UTC (12 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.646: +521 -1 lines
Diff to previous 1.646 , to selected 1.732
Add next_feature and previous_feature functions, and some more general
functions for handling complex location descriptions: filtered_location
and boundaries_of_2.

Revision 1.646 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 6 15:44:05 2007 UTC (12 years, 3 months ago) by wilke
Branch: MAIN
Changes since 1.645: +82 -0 lines
Diff to previous 1.645 , to selected 1.732
get_organism_info_from_ncbi
For a given taxonomy ID returns a hash containing scientific name , genetic code , synonyms and lineage

Revision 1.645 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 6 13:47:40 2007 UTC (12 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.644: +347 -346 lines
Diff to previous 1.644 , to selected 1.732
Changed POD format for better compatability with Wiki.

Revision 1.644 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 3 20:05:26 2007 UTC (12 years, 3 months ago) by gdpusch
Branch: MAIN
Changes since 1.643: +52 -0 lines
Diff to previous 1.643 , to selected 1.732
Added sort function &by_locus(). -- /gdp

Revision 1.643 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 3 02:49:29 2007 UTC (12 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.642: +1 -1 lines
Diff to previous 1.642 , to selected 1.732
minor modifications

Revision 1.642 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 1 22:17:03 2007 UTC (12 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.641: +172 -0 lines
Diff to previous 1.641 , to selected 1.732
add possible_frameshift to FIG.pm (and, hence, FIGV.pm)

Revision 1.641 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 30 21:47:50 2007 UTC (12 years, 4 months ago) by gdpusch
Branch: MAIN
Changes since 1.640: +12 -5 lines
Diff to previous 1.640 , to selected 1.732
Added support for FIGV calls of &FIG::pick_gene_boundaries() and &FIG::call_start(). -- /gdp

Revision 1.640 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 14 20:33:09 2007 UTC (12 years, 4 months ago) by paczian
Branch: MAIN
Changes since 1.639: +47 -0 lines
Diff to previous 1.639 , to selected 1.732
updated perldoc for method wikipedia link
added method organism_directory

Revision 1.639 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 8 21:33:09 2007 UTC (12 years, 4 months ago) by bartels
Branch: MAIN
Changes since 1.638: +20 -0 lines
Diff to previous 1.638 , to selected 1.732
I added a method 'feature_aliases_in_tbl', which gives back only the aliases
in the tbl file and not external aliases.

Revision 1.638 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 1 22:10:11 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.637: +4 -0 lines
Diff to previous 1.637 , to selected 1.732
Fix no-results return from in_pch_pin_with_and_evidence.

Revision 1.637 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 1 16:33:29 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.636: +7 -1 lines
Diff to previous 1.636 , to selected 1.732
some fixes for RAST genome installation.

Revision 1.636 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 31 23:18:01 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.635: +14 -0 lines
Diff to previous 1.635 , to selected 1.732
If a genome is not marked COMPLETE, but it is marked NMPDR, mark it complete anyway. This until
Bruce makes the changes that always import NMPDR orgs even if not complete.

Revision 1.635 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 30 18:19:31 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.634: +19 -2 lines
Diff to previous 1.634 , to selected 1.732
fix get_genome_assignment_data & get_genome_stats to account for deleted genomes and pegs

Revision 1.634 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 18 21:09:48 2007 UTC (12 years, 5 months ago) by wilke
Branch: MAIN
Changes since 1.633: +43 -8 lines
Diff to previous 1.633 , to selected 1.732
added function md5sum_to_contig_genome

Revision 1.633 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 15 19:14:36 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.632: +34 -0 lines
Diff to previous 1.632 , to selected 1.732
Add sub interpret_error_code.

Revision 1.632 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 13 13:13:45 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.631: +2 -2 lines
Diff to previous 1.631 , to selected 1.732
fix coupled_to_batch in non-server ccase

Revision 1.631 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 11 18:59:00 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.630: +47 -1 lines
Diff to previous 1.630 , to selected 1.732
add batch coupling_and_evidence calls

Revision 1.630 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 9 21:16:35 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.629: +26 -2 lines
Diff to previous 1.629 , to selected 1.732
Add subsystem-at-a-time coupling lookup in get_ev_codes that goes iwth the new coupled_to_batch interface.

Revision 1.629 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 9 18:57:27 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.628: +137 -1 lines
Diff to previous 1.628 , to selected 1.732
Register new genomes' features with the clearinghouse in add_genome.

Allow missing peg stop truncations as reported by verify_genome_directory to not abort an add genome, if they are the only error reported.

Revision 1.628 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 5 18:33:12 2007 UTC (12 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.627: +4 -3 lines
Diff to previous 1.627 , to selected 1.732
add check_variants.cgi, a program to automatically validate variant codes

Revision 1.627 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 4 19:48:40 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.626: +50 -5 lines
Diff to previous 1.626 , to selected 1.732
add in_pch_pin_with and in_pch_pin_with_and_evidence

Revision 1.626 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 1 15:33:11 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.625: +19 -0 lines
Diff to previous 1.625 , to selected 1.732
Add support for $fig->sims([list of ids]) in the non-sim-server case.

Revision 1.625 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 26 03:32:54 2007 UTC (12 years, 6 months ago) by gdpusch
Branch: MAIN
Changes since 1.624: +1 -1 lines
Diff to previous 1.624 , to selected 1.732
Minor fix to POD of &taxonomy_of(). -- /gdp

Revision 1.624 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 24 20:53:51 2007 UTC (12 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.623: +10 -0 lines
Diff to previous 1.623 , to selected 1.732
add a routine in FIG.pm giving who set the function of a peg

Revision 1.623 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 20 17:36:10 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.622: +1 -1 lines
Diff to previous 1.622 , to selected 1.732
fix vc * bug

Revision 1.622 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 19 21:54:46 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.621: +6 -0 lines
Diff to previous 1.621 , to selected 1.732
add index_annotations to add_genome_body

Revision 1.621 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 19 21:08:12 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.620: +109 -0 lines
Diff to previous 1.620 , to selected 1.732
add perform_subsystem_salvage and its invocation in add_genome_body.

Revision 1.620 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 17 19:52:10 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.619: +1 -1 lines
Diff to previous 1.619 , to selected 1.732
fix typoe

Revision 1.619 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 17 19:17:15 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.618: +1 -1 lines
Diff to previous 1.618 , to selected 1.732
Fix a corner case in all_features_detailed_fast that made a contig with exactly two pegs show nothing at all in the context view.

Revision 1.618 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 17 17:35:19 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.617: +5 -5 lines
Diff to previous 1.617 , to selected 1.732
minor fix to rast install code

Revision 1.617 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 17 17:32:13 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.616: +46 -17 lines
Diff to previous 1.616 , to selected 1.732
Mods for RAST org installation

Revision 1.616 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 11 23:17:15 2007 UTC (12 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.615: +2 -2 lines
Diff to previous 1.615 , to selected 1.732
Removed some "my"s to prevent compiler warnings.

Revision 1.615 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 6 21:25:34 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.614: +57 -14 lines
Diff to previous 1.614 , to selected 1.732
add_genome mods for rast import

Revision 1.614 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 5 21:17:04 2007 UTC (12 years, 6 months ago) by mkubal
Branch: MAIN
Changes since 1.613: +2 -2 lines
Diff to previous 1.613 , to selected 1.732
changed model_directory to default to Data/Organisms

Revision 1.613 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 5 20:59:52 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.612: +26 -5 lines
Diff to previous 1.612 , to selected 1.732
add support for asserting presence of genomes (for use in the RAST import environment).

Revision 1.612 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 28 18:46:40 2007 UTC (12 years, 7 months ago) by paczian
Branch: MAIN
Changes since 1.611: +2 -2 lines
Diff to previous 1.611 , to selected 1.732
commented out warn statements in all_subsystems

Revision 1.611 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 27 18:27:33 2007 UTC (12 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.610: +6 -3 lines
Diff to previous 1.610 , to selected 1.732
add strip comments argument on function_of

Revision 1.610 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 15 21:28:27 2007 UTC (12 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.609: +3 -1 lines
Diff to previous 1.609 , to selected 1.732
Make NMPDR-generated GFF files validate cleanly.

Revision 1.609 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 14 21:34:06 2007 UTC (12 years, 7 months ago) by arodri7
Branch: MAIN
Changes since 1.608: +61 -0 lines
Diff to previous 1.608 , to selected 1.732
made additions to FIG.pm - added batch method to get subsystem data

Revision 1.608 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 22 18:38:05 2007 UTC (12 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.607: +23 -1 lines
Diff to previous 1.607 , to selected 1.732
Added some POD documentation.

Revision 1.607 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 20 19:27:56 2007 UTC (12 years, 8 months ago) by paczian
Branch: MAIN
Changes since 1.606: +1 -1 lines
Diff to previous 1.606 , to selected 1.732
removed addition of subsystems in all_features_detailed_fast, as it introduced an unforeseen error

Revision 1.606 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 16 19:15:36 2007 UTC (12 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.605: +104 -70 lines
Diff to previous 1.605 , to selected 1.732
Moved coupling code to FIGRules. Added support for the Subsystem List Editor.

Revision 1.605 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 16 16:34:29 2007 UTC (12 years, 8 months ago) by paczian
Branch: MAIN
Changes since 1.604: +1 -1 lines
Diff to previous 1.604 , to selected 1.732
added subsystem information to function all_features_detailed_fast

Revision 1.604 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 9 19:23:32 2007 UTC (12 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.603: +1 -1 lines
Diff to previous 1.603 , to selected 1.732
fix bug in undeleting features

Revision 1.603 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 28 22:04:24 2007 UTC (12 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.602: +147 -0 lines
Diff to previous 1.602 , to selected 1.732
add get_basic_statistics() and get_peg_statistics(); both use caching.

Revision 1.602 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 27 21:48:54 2007 UTC (12 years, 9 months ago) by gdpusch
Branch: MAIN
Changes since 1.601: +11 -11 lines
Diff to previous 1.601 , to selected 1.732
Fixed duplicate declaration of $cache_dir in &get_cache_directory(). -- /gdp

Revision 1.601 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 25 21:33:18 2007 UTC (12 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.600: +118 -0 lines
Diff to previous 1.600 , to selected 1.732
add caching support for $fig->all_usable_subsystems() - new routine.

Revision 1.600 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 25 19:41:45 2007 UTC (12 years, 9 months ago) by gdpusch
Branch: MAIN
Changes since 1.599: +18 -3 lines
Diff to previous 1.599 , to selected 1.732
Added boolean test "&is_viral()". -- /gdp

Revision 1.599 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 12 20:46:57 2007 UTC (12 years, 9 months ago) by paczian
Branch: MAIN
Changes since 1.598: +9 -0 lines
Diff to previous 1.598 , to selected 1.732
introduced a method called 'genome_list' which returns a list of all complete genomes, every entry composed of genome_id, genome_name, maindomain

Revision 1.598 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jun 9 12:23:32 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.597: +25 -5 lines
Diff to previous 1.597 , to selected 1.732
add ability to filter aux roles on peg_to_subsystems

Revision 1.597 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 7 16:21:54 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.596: +1 -1 lines
Diff to previous 1.596 , to selected 1.732
fix to auto_assign

Revision 1.596 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 30 15:41:42 2007 UTC (12 years, 10 months ago) by paczian
Branch: MAIN
Changes since 1.595: +6 -6 lines
Diff to previous 1.595 , to selected 1.732
changed scenario_directory to model_directory

Revision 1.595 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 29 19:16:26 2007 UTC (12 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.594: +10 -2 lines
Diff to previous 1.594 , to selected 1.732
Changes for using $fig->scenario_directory() instead of constructed paths.

Revision 1.594 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 25 16:46:44 2007 UTC (12 years, 10 months ago) by paczian
Branch: MAIN
Changes since 1.593: +25 -0 lines
Diff to previous 1.593 , to selected 1.732
added the function scenario_directory, which returns the scenario directory

Revision 1.593 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 23 22:01:06 2007 UTC (12 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.592: +171 -0 lines
Diff to previous 1.592 , to selected 1.732
Add $fig->compute_genome_similarity and supporting routines.

Revision 1.592 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 23 21:17:58 2007 UTC (12 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.591: +0 -1 lines
Diff to previous 1.591 , to selected 1.732
Not using URI now.

Revision 1.591 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 23 20:51:08 2007 UTC (12 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.590: +80 -0 lines
Diff to previous 1.590 , to selected 1.732
FIG.pm support for installing subsystme dir

Revision 1.590 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 23 19:13:59 2007 UTC (12 years, 10 months ago) by paczian
Branch: MAIN
Changes since 1.589: +5 -1 lines
Diff to previous 1.589 , to selected 1.732
added the option of getting all non -1 variant subsystems in subsystems_for_genome

Revision 1.589 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 15 21:12:18 2007 UTC (12 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.588: +118 -6 lines
Diff to previous 1.588 , to selected 1.732
Hope college modifications.

Revision 1.588 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 14 16:13:25 2007 UTC (12 years, 10 months ago) by paczian
Branch: MAIN
Changes since 1.587: +39 -0 lines
Diff to previous 1.587 , to selected 1.732
added the function get_genome_subsystem_count

Revision 1.587 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 11 05:49:48 2007 UTC (12 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.586: +30 -0 lines
Diff to previous 1.586 , to selected 1.732
Added a method to download attribute keys and their definitions.

Revision 1.586 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 7 00:43:26 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.585: +1 -1 lines
Diff to previous 1.585 , to selected 1.732
add computation of alignments to building FIGFAMS

Revision 1.585 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 28 16:03:25 2007 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.584: +1 -1 lines
Diff to previous 1.584 , to selected 1.732
Added initial support for alternate genetic codes. -- /gdp

Revision 1.584 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 28 15:52:30 2007 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.583: +7 -1 lines
Diff to previous 1.583 , to selected 1.732
Added initial support for alternate genetic codes. -- /gdp

Revision 1.583 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 28 15:50:12 2007 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.582: +12 -0 lines
Diff to previous 1.582 , to selected 1.732
Added initial support for alternate genetic codes. -- /gdp

Revision 1.582 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 27 22:12:28 2007 UTC (12 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.581: +65 -0 lines
Diff to previous 1.581 , to selected 1.732
Added support for the new QueryAttributes feature.

Revision 1.581 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 27 16:53:43 2007 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.580: +18 -0 lines
Diff to previous 1.580 , to selected 1.732
add recast_ids

Revision 1.580 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 10 03:30:01 2007 UTC (12 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.579: +100 -39 lines
Diff to previous 1.579 , to selected 1.732
Moved the guts of wikipedia_link to FIGRules so that SFXlate can use it.
Added POD documentation to some more methods.

Revision 1.579 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 16 04:33:22 2007 UTC (13 years ago) by redwards
Branch: MAIN
Changes since 1.578: +1 -1 lines
Diff to previous 1.578 , to selected 1.732
updating db_xref

Revision 1.578 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 15 15:31:03 2007 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.577: +2 -1 lines
Diff to previous 1.577 , to selected 1.732
problem using subsystem that does not exist

Revision 1.577 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 12 20:51:23 2007 UTC (13 years ago) by olson
Branch: MAIN
Changes since 1.576: +78 -46 lines
Diff to previous 1.576 , to selected 1.732
caching fix for taxonomy_of, support non-pegs in translate_pegs

Revision 1.576 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 7 01:47:05 2007 UTC (13 years ago) by redwards
Branch: MAIN
Changes since 1.575: +47 -0 lines
Diff to previous 1.575 , to selected 1.732
changes to gff3 file to be in line with BRC requirements

Revision 1.575 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 26 21:30:18 2007 UTC (13 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.574: +19 -0 lines
Diff to previous 1.574 , to selected 1.732
add function_of_quick that uses a cached prepared statement

Revision 1.574 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 26 20:47:01 2007 UTC (13 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.573: +18 -0 lines
Diff to previous 1.573 , to selected 1.732
add caching to build_tree_of_all

Revision 1.573 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 15 22:40:40 2007 UTC (13 years, 1 month ago) by paarmann
Branch: MAIN
Changes since 1.572: +35 -0 lines
Diff to previous 1.572 , to selected 1.732
moved the method rewrite_db_xrefs here, because it's used in more than one place now

Revision 1.572 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 11 22:37:11 2007 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.571: +49 -0 lines
Diff to previous 1.571 , to selected 1.732
add PHOB.pm to support some phylogeny stuff

Revision 1.571 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 9 23:05:17 2007 UTC (13 years, 1 month ago) by paarmann
Branch: MAIN
Changes since 1.570: +1 -0 lines
Diff to previous 1.570 , to selected 1.732
added quoting to catalyzes

Revision 1.570 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 9 22:51:33 2007 UTC (13 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.569: +63 -8 lines
Diff to previous 1.569 , to selected 1.732
Added a user name to the custom attributes constructor and fixed some comments.

Revision 1.569 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 8 18:35:56 2007 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.568: +91 -1 lines
Diff to previous 1.568 , to selected 1.732
Added &get_dna_seq($fid). -- /gdp

Revision 1.568 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 6 16:24:39 2007 UTC (13 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.567: +1 -1 lines
Diff to previous 1.567 , to selected 1.732
Changed call signature for the Custom Attributes constructor to pass in a user name.

Revision 1.567 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 5 23:05:21 2007 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.566: +1 -1 lines
Diff to previous 1.566 , to selected 1.732
strip trailing spaces off roles

Revision 1.566 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 5 03:12:11 2007 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.565: +0 -1 lines
Diff to previous 1.565 , to selected 1.732
initial, undebugged version of edit_feature.cgi

Revision 1.565 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 3 03:13:46 2007 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.564: +1 -1 lines
Diff to previous 1.564 , to selected 1.732
beef up error messages from the clearinghouse mon add_feature failure

Revision 1.564 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 3 02:50:49 2007 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.563: +43 -17 lines
Diff to previous 1.563 , to selected 1.732
fixes to add_features and display of non-peg features

Revision 1.563 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 30 00:26:33 2007 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.562: +3 -0 lines
Diff to previous 1.562 , to selected 1.732
Added tracing for attributes.

Revision 1.562 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 25 02:37:37 2007 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.561: +0 -42 lines
Diff to previous 1.561 , to selected 1.732
Removed support for full-text attribute search.

Revision 1.561 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 24 10:23:10 2007 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.560: +188 -33 lines
Diff to previous 1.560 , to selected 1.732
Fixed a bug in the erase_attribute_entirely method.

Revision 1.560 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 22 20:03:42 2007 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.559: +237 -51 lines
Diff to previous 1.559 , to selected 1.732
Added a find_attributes method for word-searching the attribute data base and converted search_index to use Glimpse for attribute searches.

Revision 1.559 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 19 17:42:43 2007 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.558: +1 -1 lines
Diff to previous 1.558 , to selected 1.732
fix on assignments with user of master

Revision 1.558 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 18 03:08:56 2007 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.557: +8 -1 lines
Diff to previous 1.557 , to selected 1.732
add comments to functions

Revision 1.557 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 12 21:24:27 2007 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.556: +4 -4 lines
Diff to previous 1.556 , to selected 1.732
add support for # as a comment initiator in gene functions

Revision 1.556 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 10 17:51:37 2007 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.555: +1 -1 lines
Diff to previous 1.555 , to selected 1.732
make assignments without user fail

Revision 1.555 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 31 22:45:33 2006 UTC (13 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.554: +6 -4 lines
Diff to previous 1.554 , to selected 1.732
Change the key used in caching peg keys in get_peg_keys so that it
extends naturally to any feature type:  _attribute_keys->{ type }

Revision 1.554 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 31 22:23:57 2006 UTC (13 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.553: +28 -14 lines
Diff to previous 1.553 , to selected 1.732
Add caching for get_peg_keys().  This speeds scripts that use it more than
once (e.g., subsys.cgi).

Revision 1.553 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 23 03:55:37 2006 UTC (13 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.552: +2 -0 lines
Diff to previous 1.552 , to selected 1.732
lock/unlock should annotate only on real change

Revision 1.552 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 23 03:43:49 2006 UTC (13 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.551: +0 -1 lines
Diff to previous 1.551 , to selected 1.732
add lock_subsys.cgi

Revision 1.551 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 13 23:36:00 2006 UTC (13 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.550: +58 -28 lines
Diff to previous 1.550 , to selected 1.732
fixes to add_feature, delete_feature, and replace_feature_with

Revision 1.550 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 10 20:30:01 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.549: +44 -29 lines
Diff to previous 1.549 , to selected 1.732
Enhanced "get_attributes" so that you can specify a list of object IDs.

Revision 1.549 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 1 23:22:45 2006 UTC (13 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.548: +17 -1 lines
Diff to previous 1.548 , to selected 1.732
add GO attribute genertation

Revision 1.548 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 30 23:04:16 2006 UTC (13 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.547: +15 -15 lines
Diff to previous 1.547 , to selected 1.732
put in the fr2go stuff

Revision 1.547 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 29 21:20:31 2006 UTC (13 years, 4 months ago) by hwang
Branch: MAIN
Changes since 1.546: +19 -0 lines
Diff to previous 1.546 , to selected 1.732
added subroutine fr_to_go.
Give the routine a peg, and it returns the GO values

Revision 1.546 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 29 20:45:06 2006 UTC (13 years, 4 months ago) by mkubal
Branch: MAIN
Changes since 1.545: +13 -0 lines
Diff to previous 1.545 , to selected 1.732
new go_number_to_term method

Revision 1.545 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 28 17:00:05 2006 UTC (13 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.544: +1 -1 lines
Diff to previous 1.544 , to selected 1.732
remove warning from boundaries_of and add genes_in_region to FIGV

Revision 1.544 - (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 1.543: +0 -1 lines
Diff to previous 1.543 , to selected 1.732
add initial version of FIGO.pm - OO services

Revision 1.543 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 16 22:08:46 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.542: +118 -88 lines
Diff to previous 1.542 , to selected 1.732
Added support for more attribute methods.

Revision 1.542 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 16 19:57:30 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.541: +4 -1 lines
Diff to previous 1.541 , to selected 1.732
Added an override available from the FIG_Config.pm so that the attribute migration can work properly.

Revision 1.541 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 15 11:51:19 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.540: +51 -47 lines
Diff to previous 1.540 , to selected 1.732
Added support for the EraseAttribute method.

Revision 1.540 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 13 22:28:28 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.539: +2 -1 lines
Diff to previous 1.539 , to selected 1.732
Made CustomAttributes a conditional import.

Revision 1.539 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 10 21:59:15 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.538: +4 -1 lines
Diff to previous 1.538 , to selected 1.732
Converted to new attribute system.

Revision 1.538 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 9 21:14:29 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.537: +147 -128 lines
Diff to previous 1.537 , to selected 1.732
Converted to use the new attribute system if it is available (which it isn't on most machines.

Revision 1.537 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 8 23:12:49 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.536: +4 -29 lines
Diff to previous 1.536 , to selected 1.732
Removed redundant copy of essentiality_data. Fixed an extraneous "my". Added some tracing.

Revision 1.536 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 7 19:56:44 2006 UTC (13 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.535: +0 -1 lines
Diff to previous 1.535 , to selected 1.732
Fix leftover <<<<< from a cvs update conflict marker.

Revision 1.535 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 7 16:21:11 2006 UTC (13 years, 4 months ago) by paczian
Branch: MAIN
Changes since 1.534: +35 -5 lines
Diff to previous 1.534 , to selected 1.732
exchanged DISTINCTROW for equivalent DISTINCT which is supported by Postgress

Revision 1.534 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Nov 5 03:51:58 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.533: +1 -29 lines
Diff to previous 1.533 , to selected 1.732
Removed a multiply-defined method. Fixed an extraneous "my".

Revision 1.533 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 2 17:12:19 2006 UTC (13 years, 5 months ago) by paczian
Branch: MAIN
Changes since 1.532: +305 -1 lines
Diff to previous 1.532 , to selected 1.732
added methods for feature retrieval, neccessary for the genome browser

Revision 1.532 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 14 17:29:32 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.531: +84 -0 lines
Diff to previous 1.531 , to selected 1.732
Added "virulent" and "essential" methods.

Revision 1.531 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 11 18:19:06 2006 UTC (13 years, 5 months ago) by redwards
Branch: MAIN
Changes since 1.530: +25 -0 lines
Diff to previous 1.530 , to selected 1.732
Adding tools to handle essentiality data for Sveta

Revision 1.530 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 10 18:37:14 2006 UTC (13 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.529: +1 -1 lines
Diff to previous 1.529 , to selected 1.732
readonly fixes; seed-run-job update to run from input file

Revision 1.529 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 4 18:53:32 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.528: +32 -0 lines
Diff to previous 1.528 , to selected 1.732
Added routine to "flatten" Data::Dumper format. -- /gdp

Revision 1.528 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 4 18:00:12 2006 UTC (13 years, 5 months ago) by paczian
Branch: MAIN
Changes since 1.527: +9 -1 lines
Diff to previous 1.527 , to selected 1.732
added multiple value query capability to essentiality_data()

Revision 1.527 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 2 18:09:07 2006 UTC (13 years, 6 months ago) by paczian
Branch: MAIN
Changes since 1.526: +28 -0 lines
Diff to previous 1.526 , to selected 1.732
added essentiality_data retrieval method

Revision 1.526 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 2 02:56:39 2006 UTC (13 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.525: +0 -63 lines
Diff to previous 1.525 , to selected 1.732
Removed the config-based tracing.

Revision 1.525 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 27 13:39:16 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.524: +1 -1 lines
Diff to previous 1.524 , to selected 1.732
allow spaces in abbr for roles in subsystems - fix pattern

Revision 1.524 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 25 18:49:25 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.523: +1 -1 lines
Diff to previous 1.523 , to selected 1.732
Fixed typo in "pseudogene" rule of &hypo(). -- /gdp

Revision 1.523 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 18 21:12:21 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.522: +3 -0 lines
Diff to previous 1.522 , to selected 1.732
spiff up the lock/unlock stuff

Revision 1.522 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 18 02:19:34 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.521: +1 -1 lines
Diff to previous 1.521 , to selected 1.732
promote remaining orfs in rapid_propagation

Revision 1.521 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 15 19:05:22 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.520: +4 -0 lines
Diff to previous 1.520 , to selected 1.732
added a little error checking to lock/unlock fids

Revision 1.520 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 15 18:36:53 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.519: +82 -1 lines
Diff to previous 1.519 , to selected 1.732
introduce locks on features to block assignments

Revision 1.519 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 14 21:09:14 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.518: +1 -1 lines
Diff to previous 1.518 , to selected 1.732
Use DAS configs from FIG/var instead of in Data so no chance of being wiped out by mirror.

Revision 1.518 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 14 14:11:51 2006 UTC (13 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.517: +115 -133 lines
Diff to previous 1.517 , to selected 1.732
Converted to provide BBH server support for Sprout.

Revision 1.517 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 6 13:59:26 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.516: +1 -0 lines
Diff to previous 1.516 , to selected 1.732
remove debugging in all_bbhs

Revision 1.516 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 4 20:08:52 2006 UTC (13 years, 6 months ago) by redwards
Branch: MAIN
Changes since 1.515: +23 -5 lines
Diff to previous 1.515 , to selected 1.732
adding a new method for environmental genomes

Revision 1.515 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 31 19:49:47 2006 UTC (13 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.514: +32 -0 lines
Diff to previous 1.514 , to selected 1.732
add bbh server support

Revision 1.514 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 31 18:06:42 2006 UTC (13 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.513: +95 -0 lines
Diff to previous 1.513 , to selected 1.732
network coupling server support

Revision 1.513 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 30 18:39:19 2006 UTC (13 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.512: +14 -1 lines
Diff to previous 1.512 , to selected 1.732
Adding allow automatic update buttons

Revision 1.512 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 26 21:10:12 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.511: +5 -0 lines
Diff to previous 1.511 , to selected 1.732
add add_to_subsystems

Revision 1.511 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 25 04:19:45 2006 UTC (13 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.510: +1 -0 lines
Diff to previous 1.510 , to selected 1.732
ignoring evidence codes in the transaction logs

Revision 1.510 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 24 22:28:16 2006 UTC (13 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.509: +1 -1 lines
Diff to previous 1.509 , to selected 1.732
killing error messages

Revision 1.509 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 23 20:53:50 2006 UTC (13 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.508: +2 -1 lines
Diff to previous 1.508 , to selected 1.732
restoring the ev_code_cron to almost right

Revision 1.508 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 22 22:15:26 2006 UTC (13 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.507: +1 -1 lines
Diff to previous 1.507 , to selected 1.732
hopefully fixing the evidence code bug

Revision 1.507 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 18 17:03:49 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.506: +4 -0 lines
Diff to previous 1.506 , to selected 1.732
RAE: Adding docs to attributes

Revision 1.506 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 10 07:28:01 2006 UTC (13 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.505: +141 -8 lines
Diff to previous 1.505 , to selected 1.732
Added methods to support the genome statistics page.
Updated some documentation.

Revision 1.505 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 8 22:19:37 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.504: +1 -2 lines
Diff to previous 1.504 , to selected 1.732
RAE: updating IFC/DFC

Revision 1.504 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 30 01:43:56 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.503: +54 -11 lines
Diff to previous 1.503 , to selected 1.732
Fixed some comments.

Revision 1.503 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 25 22:07:01 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.502: +1 -1 lines
Diff to previous 1.502 , to selected 1.732
Fixed another bad return from coupling_and_evidence.

Revision 1.502 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 25 22:02:09 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.501: +1 -1 lines
Diff to previous 1.501 , to selected 1.732
Fixed bad return from coupling_and_evidence.

Revision 1.501 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 25 20:39:11 2006 UTC (13 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.500: +5 -0 lines
Diff to previous 1.500 , to selected 1.732
Added SameFuncWhy. TD

Revision 1.500 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jul 22 20:22:05 2006 UTC (13 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.499: +10 -0 lines
Diff to previous 1.499 , to selected 1.732
minor reformatting

Revision 1.499 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 20 19:22:53 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.498: +5 -1 lines
Diff to previous 1.498 , to selected 1.732
Fixed the documentation for bbhs.

Revision 1.498 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 20 18:24:07 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.497: +13 -2 lines
Diff to previous 1.497 , to selected 1.732
Updated documentation.

Revision 1.497 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 14 18:42:17 2006 UTC (13 years, 8 months ago) by mkubal
Branch: MAIN
Changes since 1.496: +1 -1 lines
Diff to previous 1.496 , to selected 1.732
changed format of search results for attributes again

Revision 1.496 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 14 18:12:30 2006 UTC (13 years, 8 months ago) by mkubal
Branch: MAIN
Changes since 1.495: +6 -1 lines
Diff to previous 1.495 , to selected 1.732
changed format of search results for attributes

Revision 1.495 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 13 06:50:08 2006 UTC (13 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.494: +25 -4 lines
Diff to previous 1.494 , to selected 1.732
Enhanced "all_features" to match the SFXlate signature.

Revision 1.494 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jul 1 21:16:52 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.493: +20 -0 lines
Diff to previous 1.493 , to selected 1.732
RAE: Adding BRC info

Revision 1.493 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 30 20:59:06 2006 UTC (13 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.492: +15 -12 lines
Diff to previous 1.492 , to selected 1.732
Fixed read_all_annotations to return an empty list if no annotations file exists.

Revision 1.492 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 27 01:32:36 2006 UTC (13 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.491: +27 -3 lines
Diff to previous 1.491 , to selected 1.732
Documented "uniprot_aliases_bulk".

Revision 1.491 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 27 00:58:24 2006 UTC (13 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.490: +25 -0 lines
Diff to previous 1.490 , to selected 1.732
Added documentation for "function_of_bulk".

Revision 1.490 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 27 00:42:01 2006 UTC (13 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.489: +20 -0 lines
Diff to previous 1.489 , to selected 1.732
Added documentation for the "is_genome" method.

Revision 1.489 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 25 07:38:35 2006 UTC (13 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.488: +2 -1 lines
Diff to previous 1.488 , to selected 1.732
Fixed the deprecated-boundary-method warning message.

Revision 1.488 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 25 03:27:51 2006 UTC (13 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.487: +15 -11 lines
Diff to previous 1.487 , to selected 1.732
Changed boundaries_of from a static to an instance method.

Revision 1.487 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 25 01:12:13 2006 UTC (13 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.486: +1 -1 lines
Diff to previous 1.486 , to selected 1.732
*** empty log message ***

Revision 1.486 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 25 00:13:19 2006 UTC (13 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.485: +6 -130 lines
Diff to previous 1.485 , to selected 1.732
Moved the network sims method to FIGRules.

Revision 1.485 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 18 06:48:42 2006 UTC (13 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.484: +821 -821 lines
Diff to previous 1.484 , to selected 1.732
Fixed two compile warnings, cleaned out some tabs.

Revision 1.484 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 16 13:20:22 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.483: +103 -0 lines
Diff to previous 1.483 , to selected 1.732
just add comments to ToCall.pm

Revision 1.483 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 13 23:32:15 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.482: +39 -6 lines
Diff to previous 1.482 , to selected 1.732
RAE: moving PIRSF to links

Revision 1.482 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 13 03:10:03 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.481: +8 -8 lines
Diff to previous 1.481 , to selected 1.732
Drat, I thought I'd already turned off the sim debug logging.

Revision 1.481 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 29 22:10:36 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.480: +1 -1 lines
Diff to previous 1.480 , to selected 1.732
make all assignments master assignments

Revision 1.480 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 23 19:08:27 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.479: +34 -12 lines
Diff to previous 1.479 , to selected 1.732
Robustify netowrk sims code; change the timeout on the LWP::UserAgent, retry 10 times on failure.

Revision 1.479 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 19 13:57:59 2006 UTC (13 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.478: +2 -2 lines
Diff to previous 1.478 , to selected 1.732
bugfix.

Revision 1.478 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 19 13:44:05 2006 UTC (13 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.477: +97 -33 lines
Diff to previous 1.477 , to selected 1.732
Some changes to add_genome logic.

(Only log after genome add completes; turn some formerly fatal errors into nonfatal
with warnings so that we don't end up with a partially-added genome).

Revision 1.477 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 19 07:25:50 2006 UTC (13 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.476: +100 -0 lines
Diff to previous 1.476 , to selected 1.732
Added a method to read annotations directly from the flat files.

Revision 1.476 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 18 12:27:21 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.475: +5 -2 lines
Diff to previous 1.475 , to selected 1.732
add normalizded bit scores to BBHs

Revision 1.475 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 18 01:05:29 2006 UTC (13 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.474: +1 -1 lines
Diff to previous 1.474 , to selected 1.732
Fixed a bad call to the Upstream function.

Revision 1.474 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 17 01:10:16 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.473: +6 -0 lines
Diff to previous 1.473 , to selected 1.732
RAE: correcting error in transaction log

Revision 1.473 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 17 00:58:54 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.472: +1 -1 lines
Diff to previous 1.472 , to selected 1.732
RAE: correcting error in transaction log

Revision 1.472 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 12 15:07:23 2006 UTC (13 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.471: +31 -9 lines
Diff to previous 1.471 , to selected 1.732
fix simserver bug

Revision 1.471 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 7 12:32:46 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.470: +3 -3 lines
Diff to previous 1.470 , to selected 1.732
use Logs, not LOGS for GenomeLog

Revision 1.470 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 7 12:25:12 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.469: +2 -2 lines
Diff to previous 1.469 , to selected 1.732
minor changes to logging correspondences

Revision 1.469 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 7 04:04:40 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.468: +7 -0 lines
Diff to previous 1.468 , to selected 1.732
add ability to log arbitrary correspondences

Revision 1.468 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 6 19:25:14 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.467: +7 -0 lines
Diff to previous 1.467 , to selected 1.732
add ability to show maps in log

Revision 1.467 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 5 16:43:09 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.466: +1 -1 lines
Diff to previous 1.466 , to selected 1.732
crude version of show_log.cgi

Revision 1.466 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 5 14:38:00 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.465: +146 -36 lines
Diff to previous 1.465 , to selected 1.732
added new logging

Revision 1.465 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 4 20:05:54 2006 UTC (13 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.464: +28 -9 lines
Diff to previous 1.464 , to selected 1.732
Turn off sim server support unless enabled in FIG_Config,for now.

add dont_mark_complete to fig add_genome.

Revision 1.464 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 2 16:09:44 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.463: +565 -3 lines
Diff to previous 1.463 , to selected 1.732
attempt to commit figfam stuff

Revision 1.463 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 28 19:33:38 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.462: +1 -1 lines
Diff to previous 1.462 , to selected 1.732
to avoid getting clobbered

Revision 1.462 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 28 18:09:18 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.461: +35 -0 lines
Diff to previous 1.461 , to selected 1.732
must have a role index on subsystem_index, added is_NMPDR_genome, etc.

Revision 1.461 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 28 14:36:14 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.460: +1 -1 lines
Diff to previous 1.460 , to selected 1.732
fixes to usable_subsystem

Revision 1.460 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 19 03:40:36 2006 UTC (13 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.459: +2 -77 lines
Diff to previous 1.459 , to selected 1.732
Moved upstream region code into FIGRules so it can be used by Sprout.

Revision 1.459 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 13 02:44:28 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.458: +1 -1 lines
Diff to previous 1.458 , to selected 1.732
pull master: off curator

Revision 1.458 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 13 01:33:23 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.457: +1 -1 lines
Diff to previous 1.457 , to selected 1.732
leave master: on subsystem_curator

Revision 1.457 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 12 21:09:52 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.456: +3 -3 lines
Diff to previous 1.456 , to selected 1.732
fix bug in perl, I think: watch out for make

Revision 1.456 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 12 20:36:45 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.455: +1 -1 lines
Diff to previous 1.455 , to selected 1.732
usable_sub => usable_subsystem

Revision 1.455 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 12 20:25:50 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.454: +8 -0 lines
Diff to previous 1.454 , to selected 1.732
minor changes to eliminate master:

Revision 1.454 - (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 1.453: +19 -1 lines
Diff to previous 1.453 , to selected 1.732
fixes to making assignments based on consistency

Revision 1.453 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 29 20:41:33 2006 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.452: +37 -3 lines
Diff to previous 1.452 , to selected 1.732
Add support for readonly database instance, and for FileLocking module.

Revision 1.452 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 29 19:40:35 2006 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.451: +4 -3 lines
Diff to previous 1.451 , to selected 1.732
Fixed some compiler warnings.

Revision 1.451 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 26 13:23:30 2006 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.450: +3 -3 lines
Diff to previous 1.450 , to selected 1.732
Fixed some lines that were generating compiler warnings.

Revision 1.450 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 23 04:51:54 2006 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.449: +26 -0 lines
Diff to previous 1.449 , to selected 1.732
RAE: Yummy attributes

Revision 1.449 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 22 16:31:15 2006 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.448: +17 -2 lines
Diff to previous 1.448 , to selected 1.732
RAE: making 0 and -1 work

Revision 1.448 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 21 15:53:30 2006 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.447: +146 -2 lines
Diff to previous 1.447 , to selected 1.732
fixes to split_and_trim

Revision 1.447 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 19 21:30:55 2006 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.446: +13 -3 lines
Diff to previous 1.446 , to selected 1.732
RAE: Initial release of setting.cgi and format changes on subsys.cgi

Revision 1.446 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 24 19:42:18 2006 UTC (14 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.445: +156 -0 lines
Diff to previous 1.445 , to selected 1.732
Added helper methodsa for the Markups object.

Revision 1.445 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 18 23:46:03 2006 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.444: +2 -2 lines
Diff to previous 1.444 , to selected 1.732
Fixed incorrect POD for &subsystems_for_genome(). -- /gdp

Revision 1.444 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 17 00:25:59 2006 UTC (14 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.443: +11 -7 lines
Diff to previous 1.443 , to selected 1.732
Fixed to create user-data directories when they don't exist.

Revision 1.443 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 16 13:11:36 2006 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.442: +13 -1 lines
Diff to previous 1.442 , to selected 1.732
handle deleted fids in mapped_prot_ids

Revision 1.442 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 15 22:12:26 2006 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.441: +131 -0 lines
Diff to previous 1.441 , to selected 1.732
minor fixes to assignment for close strains

Revision 1.441 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 15 08:43:43 2006 UTC (14 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.440: +2 -2 lines
Diff to previous 1.440 , to selected 1.732
Fixed a bug in the user-data handler

Revision 1.440 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 14 15:07:07 2006 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.439: +43 -1 lines
Diff to previous 1.439 , to selected 1.732
add logging on update operations

Revision 1.439 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 11 15:17:13 2006 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.438: +22 -1 lines
Diff to previous 1.438 , to selected 1.732
Corrected typo in variable name that wasaborting compilation. -- /gdp

Revision 1.438 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 9 20:42:51 2006 UTC (14 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.437: +93 -1 lines
Diff to previous 1.437 , to selected 1.732
Fix Rob's bug.

Revision 1.437 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 9 19:34:26 2006 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.436: +19 -1 lines
Diff to previous 1.436 , to selected 1.732
RAE: Updating organisms.cgi for more genomes in cyanoseed

Revision 1.436 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 5 01:08:16 2006 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.435: +47 -0 lines
Diff to previous 1.435 , to selected 1.732
RAE: Swtiched to using SQL Count for the number of contigs

Revision 1.435 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 3 18:42:27 2006 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.434: +3 -1 lines
Diff to previous 1.434 , to selected 1.732
$/ fixes

Revision 1.434 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 31 04:09:13 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.433: +32 -51 lines
Diff to previous 1.433 , to selected 1.732
fix of clustering

Revision 1.433 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 30 19:36:04 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.432: +6 -2 lines
Diff to previous 1.432 , to selected 1.732
use is_genome checks for subsystems?

Revision 1.432 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 29 19:48:31 2006 UTC (14 years, 2 months ago) by efrank
Branch: MAIN
Changes since 1.431: +10 -6 lines
Diff to previous 1.431 , to selected 1.732
fixes for controlled vocab from NCI demo.  fixes to accomodate RAE's
changes in key_info.  commit independent of other pkgs.

Revision 1.431 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 28 04:23:47 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.430: +29 -1 lines
Diff to previous 1.430 , to selected 1.732
RAE: Updating POM -- pieces of metabolism

Revision 1.430 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 25 18:57:05 2006 UTC (14 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.429: +29 -9 lines
Diff to previous 1.429 , to selected 1.732
Add more sim compute stuff.

Revision 1.429 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 23 19:20:54 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.428: +131 -4 lines
Diff to previous 1.428 , to selected 1.732
changes to support dynamic sims and updates

Revision 1.428 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 18 17:41:13 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.427: +34 -0 lines
Diff to previous 1.427 , to selected 1.732
RAE: Adding NMPDR checkbox to subsys.cgi

Revision 1.427 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 18 17:14:07 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.426: +36 -2 lines
Diff to previous 1.426 , to selected 1.732
RAE: Adding NMPDR checkbox to subsys.cgi

Revision 1.426 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 16 00:22:42 2006 UTC (14 years, 2 months ago) by efrank
Branch: MAIN
Changes since 1.425: +49 -7 lines
Diff to previous 1.425 , to selected 1.732
=head3 by_raw_alias

usage: $peg = $fig->by_raw_alias($alias)

Returns all FIG ids having the given alias.  Unlike by_alias, we do not attempt any
kind of normalization.  I'm not sure this function is needed, but by_alias searches
only in ext_alias table whereas here I'm searching in the features table.  ext_alias
does not have all external aliases which is keeping my code from working.  In partic\
ular,
it lacks EnsemblGene.  It would be nice to combine these two functions.  -Ed

=cut

=head3 get_cv_attributes

A simple wrapper around get_attriubtes to return only those attributes
that have meta_data indicating that the key is a controlled vocabulary.

See get_attributes for description of arguments and return types.

=cut

Revision 1.425 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 15 19:11:31 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.424: +2 -2 lines
Diff to previous 1.424 , to selected 1.732
correction to is_deleted_fid

Revision 1.424 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 15 15:11:46 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.423: +2 -0 lines
Diff to previous 1.423 , to selected 1.732
is_deleted_fid should return 0, if the argument is not a fid

Revision 1.423 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 14 23:55:45 2006 UTC (14 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.422: +1 -1 lines
Diff to previous 1.422 , to selected 1.732
Fine tuning of the add a feature software.  (Still more to come in dealing
with previously deleted features)

Revision 1.422 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 13 22:15:35 2006 UTC (14 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.421: +26 -16 lines
Diff to previous 1.421 , to selected 1.732
Minor changes to assign_function:
   Convert user of form master:xxx to master (clearly the intent)
   Clean-up and clarify flow

Revision 1.421 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 13 20:22:39 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.420: +200 -70 lines
Diff to previous 1.420 , to selected 1.732
fixes to deleted_features, replace_features_with, etc

Revision 1.420 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 13 06:54:49 2006 UTC (14 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.419: +8 -9 lines
Diff to previous 1.419 , to selected 1.732
Converted the relative-to-absolute path code to use a system-independent PERL utility.

Revision 1.419 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 12 23:48:15 2006 UTC (14 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.418: +101 -52 lines
Diff to previous 1.418 , to selected 1.732
Greatly enhanced error checking and reporting for add_feature.
Make sure feature does not already exist (return existing fid if
this is the case).

Revision 1.418 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 12 04:14:24 2006 UTC (14 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.417: +50 -20 lines
Diff to previous 1.417 , to selected 1.732
Running version of adding a feature with a fid from the clearinghouse.

Revision 1.417 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 11 22:58:57 2006 UTC (14 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.416: +30 -0 lines
Diff to previous 1.416 , to selected 1.732
add_Feature additions

Revision 1.416 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 10 16:45:24 2006 UTC (14 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.415: +10 -1 lines
Diff to previous 1.415 , to selected 1.732
fix to verify_dir

Revision 1.415 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 5 01:16:45 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.414: +7 -10 lines
Diff to previous 1.414 , to selected 1.732
RAE: Correcting what is meant by non-zero variant code

Revision 1.414 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 3 18:32:04 2006 UTC (14 years, 2 months ago) by efrank
Branch: MAIN
Changes since 1.413: +48 -0 lines
Diff to previous 1.413 , to selected 1.732
add subsystems_having_organisms

Revision 1.413 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 2 23:58:49 2006 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.412: +1 -1 lines
Diff to previous 1.412 , to selected 1.732
RAE: Adding statistics to protein families

Revision 1.412 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 30 11:52:40 2005 UTC (14 years, 3 months ago) by heiko
Branch: MAIN
Changes since 1.411: +83 -0 lines
Diff to previous 1.411 , to selected 1.732
added best_bbh_candidates_additional function

Revision 1.411 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 24 21:03:57 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.410: +4 -4 lines
Diff to previous 1.410 , to selected 1.732
serious problem in setting max_expand in FIG::sims

Revision 1.410 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 21 23:51:50 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.409: +60 -2 lines
Diff to previous 1.409 , to selected 1.732
RAE: Adding statistics to protein families

Revision 1.409 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 20 17:59:08 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.408: +39 -1 lines
Diff to previous 1.408 , to selected 1.732
add abstract functional coupling

Revision 1.408 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 10 23:05:58 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.407: +26 -0 lines
Diff to previous 1.407 , to selected 1.732
RAE: extending protein families

Revision 1.407 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 10 18:08:17 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.406: +20 -20 lines
Diff to previous 1.406 , to selected 1.732
RAE: Changed attribute key to tag throughout

Revision 1.406 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 8 18:07:54 2005 UTC (14 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.405: +13 -0 lines
Diff to previous 1.405 , to selected 1.732
Added a method that can be used to determine whether the data is being taken from SEED or NMPDR.

Revision 1.405 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 6 06:57:17 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.404: +28 -0 lines
Diff to previous 1.404 , to selected 1.732
Updating protein families

Revision 1.404 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 5 19:06:30 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.403: +17 -0 lines
Diff to previous 1.403 , to selected 1.732
Added license words.

Revision 1.403 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 2 20:13:44 2005 UTC (14 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.402: +16 -1 lines
Diff to previous 1.402 , to selected 1.732
Don't save absolute paths in file_table in database; rather, strip them on file2N and restore on N2file.

Revision 1.402 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 1 22:28:13 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.401: +7 -1 lines
Diff to previous 1.401 , to selected 1.732
Making attributes work for Ed

Revision 1.401 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 28 02:01:18 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.400: +1 -1 lines
Diff to previous 1.400 , to selected 1.732
minor fix in reconizing aliases

Revision 1.400 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Nov 27 22:17:15 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.399: +2 -2 lines
Diff to previous 1.399 , to selected 1.732
correcting tag names

Revision 1.399 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 24 02:12:41 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.398: +88 -33 lines
Diff to previous 1.398 , to selected 1.732
updating subsys.cgi so that it works with attributes again. Quickly, this time

Revision 1.398 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 24 01:00:45 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.397: +33 -5 lines
Diff to previous 1.397 , to selected 1.732
correcting and extending get_distinct_keys

Revision 1.397 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 23 23:24:11 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.396: +11 -3 lines
Diff to previous 1.396 , to selected 1.732
correcting return when no data supplied

Revision 1.396 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 23 23:05:25 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.395: +16 -8 lines
Diff to previous 1.395 , to selected 1.732
removing error messages from attributes

Revision 1.395 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 23 20:34:59 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.394: +287 -310 lines
Diff to previous 1.394 , to selected 1.732
major changes to attributes and protein families. There are changes to several modules to deal with new attributes database, and simultaneous updates to protein families

Revision 1.394 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 23 17:49:12 2005 UTC (14 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.393: +609 -3 lines
Diff to previous 1.393 , to selected 1.732
Added access methods for the UserData object.
Fixed some documentation.

Revision 1.393 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 22 14:57:50 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.392: +5 -4 lines
Diff to previous 1.392 , to selected 1.732
fixes to characterization of hypos

Revision 1.392 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 10 20:16:07 2005 UTC (14 years, 4 months ago) by efrank
Branch: MAIN
CVS Tags: caBIG-00-00-00
Changes since 1.391: +1 -1 lines
Diff to previous 1.391 , to selected 1.732
move cv files from Global to Global/CV

Revision 1.391 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 10 19:56:33 2005 UTC (14 years, 4 months ago) by efrank
Branch: MAIN
Changes since 1.390: +32 -0 lines
Diff to previous 1.390 , to selected 1.732
add search_cv_file as an encapsulation.
   cv, search_term -> ( (cv, term_id,term), ... )

I also have changes in index searching that I'm trying _not_ to commit.
If you see wierdness, i messed up the commit so yell at me.

Revision 1.390 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 2 21:39:25 2005 UTC (14 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.389: +126 -36 lines
Diff to previous 1.389 , to selected 1.732
Fixed some documentation.
Rewrote some ENV tests to avoid compiler warnings.
Removed redundant variable declarations to avoid compiler warnings.
Added a new method to test whether a role ID is an EC number.

Revision 1.389 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 28 16:05:02 2005 UTC (14 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.388: +1 -1 lines
Diff to previous 1.388 , to selected 1.732
Strip  xxx identifiers from feature_aliases output.

Revision 1.388 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 28 16:03:12 2005 UTC (14 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.387: +62 -0 lines
Diff to previous 1.387 , to selected 1.732
Add run_gathering_output() for safe backtick-like  functionality.

Revision 1.387 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 27 16:20:34 2005 UTC (14 years, 5 months ago) by efrank
Branch: MAIN
Changes since 1.386: +16 -1 lines
Diff to previous 1.386 , to selected 1.732
make add_cv_term give error status if passed empty strings.
make search_index_by_attribute be case insensitive.

How do you do this on just one line?  Right now I used 2 lines (a bunch of times)
     $user =~ s/^\s*//g;
     $user =~ s/\s*$//g;

Revision 1.386 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 26 22:12:03 2005 UTC (14 years, 5 months ago) by efrank
Branch: MAIN
Changes since 1.385: +37 -4 lines
Diff to previous 1.385 , to selected 1.732
key_info:  modify to return  nothing if the passed key has no associated
	   data (rather than returning empty hash).

search_index:  modify to call search_index_by_attributes so that attributes are
	   included in the search without building glimpse indexes

search_index_by_attribues:   supports search_index.

Also, in search_index, turned off old attribute search.

Revision 1.385 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 26 19:33:11 2005 UTC (14 years, 5 months ago) by efrank
Branch: MAIN
Changes since 1.384: +7 -3 lines
Diff to previous 1.384 , to selected 1.732
key_info() was returning and empty hash to say it had nothing that matches
a key.  this was making downstream code very confusing.  so now i return
nothing if there's no match for the key.

Revision 1.384 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 26 16:38:12 2005 UTC (14 years, 5 months ago) by efrank
Branch: MAIN
Changes since 1.383: +76 -0 lines
Diff to previous 1.383 , to selected 1.732
add new sub, add_cv_term($user, $peg, $vocab, $id, $term);

=head3 add_cv_term

Add a controlled vocabulary term to a peg.  Pass in the peg, the vocab
name, the termId, and the term (see next paragraph).  returns error string
if problem, else returns nothing.

   my $status = $fig->add_cv_term( "master:EdF",
   				   "fig|9606.3.peg.26823", "MyVocab", "1234", "A thing of wonder.");
				      if ($status) {print "error adding cv term: $status\n";}

				      Controlled vocabulary is read-only text associated with a peg.  Each
				      is a triple, namely (vocab name, termId, term text).  The termId is an
				      id that is used in the particulary vocabulary and the term text is the
				      actual term.  For example, the GO has the term "U12-type nuclear mRNA
				      branch site recognition" with termId GO:0000371.  Thus, the triplet is
				      (GO, GO:0000371, "U12-type nuclear mRNA branch site recognition").
				      Don't be confused by the GO: in GO:0000371.  We don't add the GO:.
				      That's just what GO decided to do.

				      termIds can not have ';' in them.

				      This routine encapsulates our present implementation via attributes.

				      =cut

Revision 1.383 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 25 14:50:23 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.382: +45 -10 lines
Diff to previous 1.382 , to selected 1.732
protein families again

Revision 1.382 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 24 21:50:35 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.381: +40 -0 lines
Diff to previous 1.381 , to selected 1.732
Assorted relative-path fixes.

remove length check in indexing function assignments.

Revision 1.381 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 24 19:36:38 2005 UTC (14 years, 5 months ago) by mkubal
Branch: MAIN
Changes since 1.380: +10 -4 lines
Diff to previous 1.380 , to selected 1.732
fixed key_info

Revision 1.380 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 22 17:43:49 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.379: +41 -14 lines
Diff to previous 1.379 , to selected 1.732
changing the format of attribute_keys

Revision 1.379 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 20 10:22:04 2005 UTC (14 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.378: +171 -57 lines
Diff to previous 1.378 , to selected 1.732
Added new documentation.
Fixed attributes to prevent return of duplicate items.

Revision 1.378 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 13 20:13:48 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.377: +12 -2 lines
Diff to previous 1.377 , to selected 1.732
Workaround for peg.synonyms file that has multiple entries.

Revision 1.377 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 12 21:03:16 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.376: +14 -2 lines
Diff to previous 1.376 , to selected 1.732
Broad minor fixes to make the SEED use relative paths throughout.

(The motivation this is to fully enable hiding the actual location of a running SEED system behind a web proxy so that things like NMPDR protein page references can be made stable across multiple releases).

This involved things like the following:

Changing $cgi->url() to $cgi->url(-relative => 1)
Changing $cgi->self_url() to $cgi->url(-relative => 1, -query => 1, -path_info => 1)

Changing the definition of FIG::cgi_url() to return "." (this may break something, but I haven't found it yet).

Revision 1.376 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 12 02:28:16 2005 UTC (14 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.375: +137 -1 lines
Diff to previous 1.375 , to selected 1.732
Added the "compute_clusters" method for use by UnvSubsys.
Added a "FIG" method for compatability with SFXlate.
Added more documentation.

Revision 1.375 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 11 20:38:38 2005 UTC (14 years, 5 months ago) by efrank
Branch: MAIN
Changes since 1.374: +24 -0 lines
Diff to previous 1.374 , to selected 1.732
add find_by_attribute.  this takes a single string argument.  it returns
triples, (featureId, key, value) of all attributes in which the search string
is a substring of either key or value.  the search is via the attribute table,
not via the glimpse indexes so tha searches immediately after edits of
attributes work.

Revision 1.374 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 8 14:14:47 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.373: +1 -1 lines
Diff to previous 1.373 , to selected 1.732
minor fix to not include xxx entries in expanded sims

Revision 1.373 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 6 22:44:02 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.372: +17 -2 lines
Diff to previous 1.372 , to selected 1.732
adding more functions with external ids

Revision 1.372 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 6 21:22:48 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.371: +47 -0 lines
Diff to previous 1.371 , to selected 1.732
loading external ids and external protein families

Revision 1.371 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 6 02:22:41 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.370: +0 -2 lines
Diff to previous 1.370 , to selected 1.732
remove debug

Revision 1.370 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 5 20:34:02 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-dataload-0
Changes since 1.369: +71 -8 lines
Diff to previous 1.369 , to selected 1.732
fixes to update_uniq_id_data

Revision 1.369 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 18 14:27:13 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.368: +4 -1 lines
Diff to previous 1.368 , to selected 1.732
fix display_subsys.cgi

Revision 1.368 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 14 20:04:19 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.367: +6 -2 lines
Diff to previous 1.367 , to selected 1.732
Correcting display of classifications

Revision 1.367 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 11 17:02:40 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.366: +19 -0 lines
Diff to previous 1.366 , to selected 1.732
fixes to display of reactions

Revision 1.366 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 11 16:34:41 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.365: +20 -0 lines
Diff to previous 1.365 , to selected 1.732
add functiontion to FIG.pm to get active subsystems for a genome

Revision 1.365 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Sep 10 07:39:18 2005 UTC (14 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.364: +1816 -1816 lines
Diff to previous 1.364 , to selected 1.732
Converted tabs to spaces to fix indenting.

Revision 1.364 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 9 13:28:58 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.363: +23 -5 lines
Diff to previous 1.363 , to selected 1.732
upgrade sigs.cgi to run under Sprout

Revision 1.363 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 8 16:12:22 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.362: +3 -2 lines
Diff to previous 1.362 , to selected 1.732
Added `formatdb` invocation to &add_genome(). Changed "VERBOSE" flag name to "FIG_VERBOSE". -- /gdp

Revision 1.362 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 6 19:58:53 2005 UTC (14 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.361: +2 -1 lines
Diff to previous 1.361 , to selected 1.732
make annotation requests by master return all non-assignment annotations.

Revision 1.361 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 6 18:52:35 2005 UTC (14 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.360: +117 -27 lines
Diff to previous 1.360 , to selected 1.732
Make annotations_made_fast return new Annotation objects instead of arrays of data.

Add the Annotation object.

Revision 1.360 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 2 22:23:33 2005 UTC (14 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.359: +2 -5 lines
Diff to previous 1.359 , to selected 1.732
Remove the debugging file setting in add_annotations_batch.

Revision 1.359 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 2 22:21:57 2005 UTC (14 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.358: +129 -0 lines
Diff to previous 1.358 , to selected 1.732
Add $fig->add_annotations_batch() that does filehandle conservation and uses COPY TABLE instead
of INSERT to add annotations to the database. Now used by 'fig add_annotations' so that
large annotation file installs don't take overnight.

Revision 1.358 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 1 20:52:51 2005 UTC (14 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.357: +12 -3 lines
Diff to previous 1.357 , to selected 1.732
Force is_deleted_fid to set the value of $/ that it wants, since use of that method
within a loop with $/ set to something else breaks is_deleted_fid. Darn global input
record separator.

Revision 1.357 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 1 19:23:49 2005 UTC (14 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.356: +95 -14 lines
Diff to previous 1.356 , to selected 1.732
Add FIG::by_genome_id for sorting genome ID lists.

Add $fig->extract_assignments_from_annoatations to transform the output of annotations_made_fast
to a list of the current assignments (per the annotations data).

Revision 1.356 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 1 18:14:53 2005 UTC (14 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.355: +96 -9 lines
Diff to previous 1.355 , to selected 1.732
make package_annotations use $fig->annotations_made_fast.

Add date parsing to FIG.pm ($fig->parse_date) using Date::Parse if available.

Revision 1.355 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 1 09:30:07 2005 UTC (14 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.354: +191 -64 lines
Diff to previous 1.354 , to selected 1.732
Tweaked tracing, added more documentation, fixed so that the annotations will work properly in environments where the number of characters in a file is different from the number of bytes.

Revision 1.354 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 30 18:04:55 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.353: +1 -1 lines
Diff to previous 1.353 , to selected 1.732
Fixed &possibly_truncated() so that it does not blow up on non-PEG features. -- /gdp

Revision 1.353 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 30 07:27:59 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.352: +20 -2 lines
Diff to previous 1.352 , to selected 1.732
Invoked `assess_completeness` from &add_genomes(). -- /gdp

Revision 1.352 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 22 05:43:02 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.351: +5 -3 lines
Diff to previous 1.351 , to selected 1.732
Adding menus to subsys.cgi

Revision 1.351 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 20 12:32:29 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.350: +2 -1 lines
Diff to previous 1.350 , to selected 1.732
fixes to calling starts

Revision 1.350 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 20 02:37:22 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.349: +5 -3 lines
Diff to previous 1.349 , to selected 1.732
fixes to call_starts

Revision 1.349 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 19 19:52:19 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.348: +10 -6 lines
Diff to previous 1.348 , to selected 1.732
Adding more details to organisms.cgi and correcting get_key_values

Revision 1.348 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 17 03:15:01 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.347: +2 -0 lines
Diff to previous 1.347 , to selected 1.732
removing blank lines from attribute_keys

Revision 1.347 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 16 19:41:12 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.346: +2 -1 lines
Diff to previous 1.346 , to selected 1.732
NMPDR updates

Revision 1.346 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 15 21:41:29 2005 UTC (14 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.345: +3 -1 lines
Diff to previous 1.345 , to selected 1.732
*** empty log message ***

Revision 1.345 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 15 21:34:53 2005 UTC (14 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.344: +12 -10 lines
Diff to previous 1.344 , to selected 1.732
Fixed change_attribute to work properly if the attribute value has quotes in it.

Revision 1.344 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 15 21:16:19 2005 UTC (14 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.343: +1 -1 lines
Diff to previous 1.343 , to selected 1.732
Fixed "add_attributes" to work correctly when quotes are present in attribute values.

Revision 1.343 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 15 20:25:02 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.342: +6 -2 lines
Diff to previous 1.342 , to selected 1.732
Modified &to_aliases to make "TYPE" argument optional instead of mandatory. -- /gdp

Revision 1.342 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 9 00:56:02 2005 UTC (14 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.341: +1 -1 lines
Diff to previous 1.341 , to selected 1.732
Changed "add_feature" to save the return from the INSERT into the feature table so that it can be viewed during debugging.

Revision 1.341 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 8 21:54:39 2005 UTC (14 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.340: +2 -1 lines
Diff to previous 1.340 , to selected 1.732
More diagram changes.

Add new simple start page.

Revision 1.340 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 8 20:04:33 2005 UTC (14 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.339: +63 -34 lines
Diff to previous 1.339 , to selected 1.732
Updated "add_feature" to allow the caller to specify the feature ID.

Revision 1.339 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 8 18:43:08 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.338: +41 -0 lines
Diff to previous 1.338 , to selected 1.732
adding fig versus kegg

Revision 1.338 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 7 22:06:58 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.337: +2 -1 lines
Diff to previous 1.337 , to selected 1.732
fix to multi-functional roles

Revision 1.337 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 6 15:30:29 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.336: +30 -3 lines
Diff to previous 1.336 , to selected 1.732
New interface for subsys.cgi, but it is commented out at the moment

Revision 1.336 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 6 14:58:56 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.335: +64 -5 lines
Diff to previous 1.335 , to selected 1.732
fixes to bugs in calling starts

Revision 1.335 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 5 13:14:26 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.334: +7 -3 lines
Diff to previous 1.334 , to selected 1.732
adding options to add_genome

Revision 1.334 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 4 18:28:36 2005 UTC (14 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.333: +8 -3 lines
Diff to previous 1.333 , to selected 1.732
Make enqueue_similarities ignore a $fig argument if invoked as a method call.

Add a $time_made argument to add_annotation.

Revision 1.333 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 4 01:27:25 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.332: +5 -1 lines
Diff to previous 1.332 , to selected 1.732
Modified &possibly_truncated() to accept either FID or location. -- /gdp

Revision 1.332 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 4 01:20:59 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.331: +20 -12 lines
Diff to previous 1.331 , to selected 1.732
Modified &possibly_truncated() to accept either FID or location. -- /gdp

Revision 1.331 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 3 23:00:37 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.330: +10 -3 lines
Diff to previous 1.330 , to selected 1.732
Adding a force to the add_genomes

Revision 1.330 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 3 21:16:29 2005 UTC (14 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.329: +24 -13 lines
Diff to previous 1.329 , to selected 1.732
Support gif/png/jpeg file type detection on diagram upload.
Support the multiple file types on packaging for clearinghouse.

Revision 1.329 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 3 17:40:42 2005 UTC (14 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.328: +47 -1 lines
Diff to previous 1.328 , to selected 1.732
Add support for creating and parsing diagram data as part of subsystem clearinghouse packages.

Revision 1.328 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 1 22:23:15 2005 UTC (14 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.327: +42 -42 lines
Diff to previous 1.327 , to selected 1.732
Changed attributes to capital-case in order to prevent the avalanche of compile-time warnings.

Revision 1.327 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 1 18:52:58 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.326: +7 -8 lines
Diff to previous 1.326 , to selected 1.732
update stuff relating to protein families

Revision 1.326 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 31 17:08:02 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.325: +21 -16 lines
Diff to previous 1.325 , to selected 1.732
Cosmetic changes to make clear that &display_id_and_seq() and &display_seq() take sequence-pointers, not sequences. -- /gdp

Revision 1.325 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 31 01:09:59 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.324: +30 -9 lines
Diff to previous 1.324 , to selected 1.732
 fixes to pick_gene_boundaries

Revision 1.324 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 29 22:27:46 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.323: +40 -0 lines
Diff to previous 1.323 , to selected 1.732
Publish/install changes for reactions.

Revision 1.323 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 29 18:13:11 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.322: +27 -2 lines
Diff to previous 1.322 , to selected 1.732
Support "fig load_all N" and "fig load_all list"

Revision 1.322 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 28 18:03:24 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.321: +72 -0 lines
Diff to previous 1.321 , to selected 1.732
commit code to expand regions of similarity to PEGs and to recall starts

Revision 1.321 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 27 19:41:56 2005 UTC (14 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.320: +1 -3 lines
Diff to previous 1.320 , to selected 1.732
Fixed some POD comments.

Revision 1.320 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 26 20:06:03 2005 UTC (14 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.319: +380 -111 lines
Diff to previous 1.319 , to selected 1.732
Added "upstream_of" method to compute upstream sequences.
Cleaned up some documentation.

Revision 1.319 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 26 04:53:36 2005 UTC (14 years, 8 months ago) by mkubal
Branch: MAIN
Changes since 1.318: +1 -1 lines
Diff to previous 1.318 , to selected 1.732
7-26-05

Revision 1.318 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jul 23 19:47:36 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.317: +3 -1 lines
Diff to previous 1.317 , to selected 1.732
altering location in FIG.pm

Revision 1.317 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 19 16:29:35 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.316: +4 -4 lines
Diff to previous 1.316 , to selected 1.732
standardize returned DNA to lower case, as per GJO's request. -- /gdp

Revision 1.316 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 19 16:14:21 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.315: +2 -1 lines
Diff to previous 1.315 , to selected 1.732
More final touches for Attributes code

Revision 1.315 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 19 05:26:12 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.314: +2 -2 lines
Diff to previous 1.314 , to selected 1.732
minor chagnes to attributes

Revision 1.314 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 19 04:54:21 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.313: +36 -9 lines
Diff to previous 1.313 , to selected 1.732
Updating attributes code in seed

Revision 1.313 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 18 03:12:11 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.312: +54 -9 lines
Diff to previous 1.312 , to selected 1.732
Updating attributes code

Revision 1.312 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 17 19:04:27 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.311: +63 -29 lines
Diff to previous 1.311 , to selected 1.732
Making attributes interface work

Revision 1.311 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 13 01:49:54 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.310: +22 -37 lines
Diff to previous 1.310 , to selected 1.732
minor changes to subsys_vectors to allow complete genomes

Revision 1.310 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 12 22:10:07 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.309: +14 -0 lines
Diff to previous 1.309 , to selected 1.732
minor changes to subsys_vectors.cgi

Revision 1.309 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 12 14:34:14 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
CVS Tags: merge-trunktag-bodev_news-3
Changes since 1.308: +91 -40 lines
Diff to previous 1.308 , to selected 1.732
Changing attributes and modifying protein.cgi with show/hides

Revision 1.308 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 12 00:34:32 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.307: +16 -16 lines
Diff to previous 1.307 , to selected 1.732
updates to build protein families

Revision 1.307 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 10 04:59:11 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.306: +8 -1 lines
Diff to previous 1.306 , to selected 1.732
making index_subsystems work

Revision 1.306 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jul 9 21:46:15 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.305: +17 -0 lines
Diff to previous 1.305 , to selected 1.732
added index subsystems to subsys.cgi

Revision 1.305 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 1 02:09:16 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.304: +46 -26 lines
Diff to previous 1.304 , to selected 1.732
Changed proteinfamilies.cgi

Revision 1.304 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 29 15:06:12 2005 UTC (14 years, 9 months ago) by olson
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-2
Changes since 1.303: +2 -2 lines
Diff to previous 1.303 , to selected 1.732
Tweak tracing.

Revision 1.303 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 29 00:28:01 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.302: +88 -5 lines
Diff to previous 1.302 , to selected 1.732
Initial release of proteinfamilies.cgi into the wild

Revision 1.302 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 28 17:25:04 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.301: +20 -0 lines
Diff to previous 1.301 , to selected 1.732
commiting FIG.pm::clean_spaces to remove leading, trailing, and extra spaces. Please use it

Revision 1.301 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 24 21:39:14 2005 UTC (14 years, 9 months ago) by parrello
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-1
Changes since 1.300: +16 -17 lines
Diff to previous 1.300 , to selected 1.732
Fixed the environment-variable tracing so that it does not override previous tracing options if they were set.

Revision 1.300 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 23 21:24:48 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.299: +5 -0 lines
Diff to previous 1.299 , to selected 1.732
finally

Revision 1.299 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 23 19:35:07 2005 UTC (14 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.298: +33 -2 lines
Diff to previous 1.298 , to selected 1.732
Add some more gene  name mapping stuff.

Add Tracer environment variable for affecting tracing.

Fix typo in invocation of load_coupling.

Revision 1.298 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 22 21:00:24 2005 UTC (14 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.297: +514 -531 lines
Diff to previous 1.297 , to selected 1.732
Replaced tabs with spaces to make indenting device-independent.
Moved "Open" and "OpenDir" to the Tracer.pm module.
Added more POD documentation.

Revision 1.297 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 20 21:58:56 2005 UTC (14 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.296: +63 -0 lines
Diff to previous 1.296 , to selected 1.732
Add genome/peg id mapping routines. (For functional coupling support).

Revision 1.296 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 20 17:08:32 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.295: +1 -1 lines
Diff to previous 1.295 , to selected 1.732
add new protein family routines

Revision 1.295 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 20 17:04:45 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.294: +72 -11 lines
Diff to previous 1.294 , to selected 1.732
add new protein family routines

Revision 1.294 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 20 04:03:44 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.293: +6 -1 lines
Diff to previous 1.293 , to selected 1.732
disable old protein families

Revision 1.293 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 13 16:43:48 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: Root-bobdev_news
Branch point for: Branch-bobdev_news
Changes since 1.292: +20 -33 lines
Diff to previous 1.292 , to selected 1.732
Ross change commit after cleanup

Revision 1.292 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 13 09:32:09 2005 UTC (14 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.291: +160 -2 lines
Diff to previous 1.291 , to selected 1.732
Added Open and OpenDir methods for streamlining file and directory operations.

Revision 1.291 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 10 16:08:52 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.290: +7 -7 lines
Diff to previous 1.290 , to selected 1.732
fixes to cached pin displays

Revision 1.290 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 10 15:36:37 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.289: +7 -9 lines
Diff to previous 1.289 , to selected 1.732
adding correspondence.cgi

Revision 1.289 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 9 20:03:15 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.288: +95 -1 lines
Diff to previous 1.288 , to selected 1.732
re-add couipling routines

Revision 1.288 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 9 18:39:05 2005 UTC (14 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.287: +39 -28 lines
Diff to previous 1.287 , to selected 1.732
*** empty log message ***

Revision 1.287 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 9 05:36:30 2005 UTC (14 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.286: +2333 -1628 lines
Diff to previous 1.286 , to selected 1.732
*** empty log message ***

Revision 1.286 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 8 23:05:21 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.285: +7 -30 lines
Diff to previous 1.285 , to selected 1.732
major change to BBHs (use precomputed)

Revision 1.285 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 7 16:41:23 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.284: +2 -1 lines
Diff to previous 1.284 , to selected 1.732
Fixed typo in &hypo(), and added new rule. -- /gdp

Revision 1.284 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 1 01:18:50 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.283: +91 -12 lines
Diff to previous 1.283 , to selected 1.732
install precomputed functional coupling data

Revision 1.283 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 29 13:33:56 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.282: +24 -0 lines
Diff to previous 1.282 , to selected 1.732
add test for existence of relation that works only under Postgres

Revision 1.282 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 25 18:58:27 2005 UTC (14 years, 10 months ago) by redwards
Branch: MAIN
Changes since 1.281: +39 -0 lines
Diff to previous 1.281 , to selected 1.732
added subsystems_roles method to FIG.pm

Revision 1.281 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 25 16:07:23 2005 UTC (14 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.280: +92 -0 lines
Diff to previous 1.280 , to selected 1.732
Code for similarity request export.

Revision 1.280 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 20 11:23:07 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.279: +1 -1 lines
Diff to previous 1.279 , to selected 1.732
fix bug in search_indexes

Revision 1.279 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 17 16:04:08 2005 UTC (14 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.278: +307 -19 lines
Diff to previous 1.278 , to selected 1.732
Bundle of misc bob changes, including sim computation code and search-for-substring.

Revision 1.278 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 10 12:03:39 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.277: +4 -1 lines
Diff to previous 1.277 , to selected 1.732
fixes to using trees under subsystems

Revision 1.277 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 5 17:43:03 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.276: +5 -3 lines
Diff to previous 1.276 , to selected 1.732
fix indexing search code

Revision 1.276 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 3 21:03:38 2005 UTC (14 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.275: +1 -1 lines
Diff to previous 1.275 , to selected 1.732
add css generation modules

Revision 1.275 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 29 16:43:29 2005 UTC (14 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.274: +1 -0 lines
Diff to previous 1.274 , to selected 1.732
add assign_to_close_strains

Revision 1.274 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 18 18:29:31 2005 UTC (14 years, 11 months ago) by mkubal
Branch: MAIN
Changes since 1.273: +2 -3 lines
Diff to previous 1.273 , to selected 1.732
revised on Monday

Revision 1.273 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 18 06:26:04 2005 UTC (14 years, 11 months ago) by redwards
Branch: MAIN
Changes since 1.272: +1 -1 lines
Diff to previous 1.272 , to selected 1.732
minor fix to select tag/values

Revision 1.272 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 18 06:19:40 2005 UTC (14 years, 11 months ago) by redwards
Branch: MAIN
Changes since 1.271: +3 -1 lines
Diff to previous 1.271 , to selected 1.732
minor fix to select tag/values

Revision 1.271 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Apr 17 16:30:19 2005 UTC (14 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.270: +2 -0 lines
Diff to previous 1.270 , to selected 1.732
handle missing annotations file gracefully

Revision 1.270 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 15 23:23:13 2005 UTC (14 years, 11 months ago) by golsen
Branch: MAIN
Changes since 1.269: +7 -27 lines
Diff to previous 1.269 , to selected 1.732
Fix bunged index search

Revision 1.269 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 14 18:52:19 2005 UTC (14 years, 11 months ago) by mkubal
Branch: MAIN
Changes since 1.268: +2 -1 lines
Diff to previous 1.268 , to selected 1.732
search_index now returns attributes

Revision 1.268 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 13 15:37:30 2005 UTC (14 years, 11 months ago) by redwards
Branch: MAIN
Changes since 1.267: +30 -21 lines
Diff to previous 1.267 , to selected 1.732
changed genome stats to show attributes

Revision 1.267 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Apr 10 03:32:30 2005 UTC (14 years, 11 months ago) by golsen
Branch: MAIN
Changes since 1.266: +1 -1 lines
Diff to previous 1.266 , to selected 1.732
Re-enable "duplicates" in sims.  Multiple regions of matching is common
in eukaryotic sequences, and only seeing one is disorienting.

Revision 1.266 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 8 20:22:23 2005 UTC (14 years, 11 months ago) by redwards
Branch: MAIN
Changes since 1.265: +10 -15 lines
Diff to previous 1.265 , to selected 1.732
changed tag/value pairs completely. Ooops!

Revision 1.265 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 7 19:16:10 2005 UTC (14 years, 11 months ago) by redwards
Branch: MAIN
Changes since 1.264: +30 -15 lines
Diff to previous 1.264 , to selected 1.732
many changes to key/value pairs to make them work

Revision 1.264 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Apr 3 19:43:41 2005 UTC (15 years ago) by redwards
Branch: MAIN
Changes since 1.263: +5 -2 lines
Diff to previous 1.263 , to selected 1.732
changing pir corresepondence

Revision 1.263 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Apr 3 19:11:11 2005 UTC (15 years ago) by redwards
Branch: MAIN
Changes since 1.262: +97 -8 lines
Diff to previous 1.262 , to selected 1.732
Added a script to load pir superfamilies in the background. This will download all the data and install it. Changed pir.cgi to background this job as it takes a while.

Revision 1.262 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 2 11:56:12 2005 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.261: +2 -0 lines
Diff to previous 1.261 , to selected 1.732
add update_subsys_conflicts to fig.pl

Revision 1.261 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 31 18:05:28 2005 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.260: +3 -0 lines
Diff to previous 1.260 , to selected 1.732
fix to asses_completeness

Revision 1.260 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 30 19:58:20 2005 UTC (15 years ago) by olson
Branch: MAIN
Changes since 1.259: +27 -0 lines
Diff to previous 1.259 , to selected 1.732
Add genome_with_md5sum.

Warn on FigGFF errors only if you're bob.

Revision 1.259 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 30 15:53:37 2005 UTC (15 years ago) by redwards
Branch: MAIN
Changes since 1.258: +4 -4 lines
Diff to previous 1.258 , to selected 1.732
changing attributes returned back to variables

Revision 1.258 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 29 20:41:17 2005 UTC (15 years ago) by redwards
Branch: MAIN
Changes since 1.257: +7 -5 lines
Diff to previous 1.257 , to selected 1.732
minor changes to rae.cgi

Revision 1.257 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 29 19:29:39 2005 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.256: +3 -2 lines
Diff to previous 1.256 , to selected 1.732
add make_pu from ids and seqs

Revision 1.256 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 29 18:42:26 2005 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.255: +7 -0 lines
Diff to previous 1.255 , to selected 1.732
broaden set of acceptable aliases as dbxrefs

Revision 1.255 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 23 18:54:39 2005 UTC (15 years ago) by golsen
Branch: MAIN
Changes since 1.254: +1 -1 lines
Diff to previous 1.254 , to selected 1.732
Removed constraint that sims request had to be by a fig ID.  Ross seems to
have solved the orginal problem that names that could not be mapped
returned a representitive ID with undefined length, which crashed sims().
Now failure to map a name returns an empty list, and sims graceful returns
an empty list of similarities.

Revision 1.254 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 21 22:01:22 2005 UTC (15 years ago) by golsen
Branch: MAIN
Changes since 1.253: +0 -1 lines
Diff to previous 1.253 , to selected 1.732
A few similarities tweeks.  Move the submit button on the default protein
page (to shorten the line slightly).  Remove a debug statement that was
writing to the error log.

Revision 1.253 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 21 21:39:32 2005 UTC (15 years ago) by golsen
Branch: MAIN
Changes since 1.252: +7 -4 lines
Diff to previous 1.252 , to selected 1.732
Add options to Similarities to override Max expand when asking for FIG IDs.
It gets annoying to have to constantly increase the value, and it is not
predictable how many sims will need to be expanded to get any desired
number of FIG IDs.

Revision 1.252 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 21 18:33:49 2005 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.251: +1 -1 lines
Diff to previous 1.251 , to selected 1.732
fix to best_bbh_candidates and added fill_subsys

Revision 1.251 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 20 22:26:16 2005 UTC (15 years ago) by golsen
Branch: MAIN
Changes since 1.250: +36 -2 lines
Diff to previous 1.250 , to selected 1.732
When sorting similarities by percent identity or bit score per position,
include a penalty for very sort sequences, so that they do not randomly
appear much higher in the similaries list than they should.  The current
treatment for this is roughly a two standard deviation penalty.

The original behavior is still available as non-star versions.
The "help" information has been updated (and other aspects clarified
as well).

Revision 1.250 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Mar 19 01:27:13 2005 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.249: +4 -0 lines
Diff to previous 1.249 , to selected 1.732
update hypo

Revision 1.249 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 16 17:56:22 2005 UTC (15 years ago) by golsen
Branch: MAIN
Changes since 1.248: +2 -2 lines
Diff to previous 1.248 , to selected 1.732
Fix end condition test on expand_raw_sims to promptly return.

Revision 1.248 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 16 15:17:45 2005 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.247: +1 -0 lines
Diff to previous 1.247 , to selected 1.732
remove ddd: in front of some organisms (mostly uniprot)

Revision 1.247 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 16 15:11:56 2005 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.246: +2 -1 lines
Diff to previous 1.246 , to selected 1.732
change spaces to _s in subsystem names

Revision 1.246 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 16 00:18:09 2005 UTC (15 years ago) by olson
Branch: MAIN
Changes since 1.245: +1 -1 lines
Diff to previous 1.245 , to selected 1.732
make the gff stuff work again.

Revision 1.245 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 15 23:56:53 2005 UTC (15 years ago) by olson
Branch: MAIN
Changes since 1.244: +76 -1 lines
Diff to previous 1.244 , to selected 1.732
Put the FigGFF code in a require for now.

Add fast anno lookup.

Revision 1.244 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 14 19:17:37 2005 UTC (15 years ago) by olson
Branch: MAIN
Changes since 1.243: +13 -0 lines
Diff to previous 1.243 , to selected 1.732
Add general-purpose GFF writing stuff.

Revision 1.243 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 14 02:04:44 2005 UTC (15 years ago) by golsen
Branch: MAIN
Changes since 1.242: +3 -3 lines
Diff to previous 1.242 , to selected 1.732
Minor fix in expand_raw_sims so that it stops when it should

Revision 1.242 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 13 00:55:21 2005 UTC (15 years ago) by redwards
Branch: MAIN
Changes since 1.241: +59 -17 lines
Diff to previous 1.241 , to selected 1.732
Initial commit of organisms.cgi which allows separate entry pages for different groups of organisms

Revision 1.241 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 11 22:03:13 2005 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.240: +10 -2 lines
Diff to previous 1.240 , to selected 1.732
fix for mapped_prot_ids

Revision 1.240 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 11 04:11:30 2005 UTC (15 years ago) by redwards
Branch: MAIN
Changes since 1.239: +4 -5 lines
Diff to previous 1.239 , to selected 1.732
Making tag/value pairs work

Revision 1.239 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 11 03:04:32 2005 UTC (15 years ago) by redwards
Branch: MAIN
Changes since 1.238: +12 -5 lines
Diff to previous 1.238 , to selected 1.732
Making tag/value pairs work

Revision 1.238 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 11 01:04:32 2005 UTC (15 years ago) by golsen
Branch: MAIN
Changes since 1.237: +247 -122 lines
Diff to previous 1.237 , to selected 1.732
Many new options for similarities

Revision 1.237 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 8 21:14:53 2005 UTC (15 years ago) by olson
Branch: MAIN
Changes since 1.236: +19 -1 lines
Diff to previous 1.236 , to selected 1.732
Add contig_md5sum.

Revision 1.236 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 8 21:06:04 2005 UTC (15 years ago) by olson
Branch: MAIN
Changes since 1.235: +30 -0 lines
Diff to previous 1.235 , to selected 1.732
Add support for computing MD5 checksums for contigs and genomes.

The checksum of a genome is defined as the checksum of its signature file. The signature
file consists of tab-separated lines, one for each contig, ordered by the contig id.
Each line contains the contig ID, the length of the contig in nucleotides, and the
MD5 checksum of the nucleotide data, with uppercase letters forced to lower case.

The signature file is written by index_contigs to
The genome's md5 checksum is written by index_contigs to <genomedir>/MD5SUM.

The md5.c code here is extracted from the Perl Digest::MD5 module. We use the perl
configuration to build it so that it will work correctly on 64-bit architectures.

Revision 1.235 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 6 15:10:02 2005 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.234: +1 -0 lines
Diff to previous 1.234 , to selected 1.732
disconnect get_attributes until I can talk to Rob

Revision 1.234 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Mar 5 04:29:59 2005 UTC (15 years ago) by redwards
Branch: MAIN
Changes since 1.233: +10 -2 lines
Diff to previous 1.233 , to selected 1.732
added highlight by peg attribute to subsystem

Revision 1.233 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 4 23:16:42 2005 UTC (15 years ago) by redwards
Branch: MAIN
Changes since 1.232: +23 -17 lines
Diff to previous 1.232 , to selected 1.732
tweaks to coloring ss by oa

Revision 1.232 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 4 22:37:06 2005 UTC (15 years ago) by redwards
Branch: MAIN
Changes since 1.231: +128 -13 lines
Diff to previous 1.231 , to selected 1.732
Added color by organism attributes to subsystems page

Revision 1.231 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 4 18:29:21 2005 UTC (15 years ago) by redwards
Branch: MAIN
Changes since 1.230: +3 -0 lines
Diff to previous 1.230 , to selected 1.732
Added attribute editing to the protein.cgi page

Revision 1.230 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 4 06:22:10 2005 UTC (15 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.229: +204 -18 lines
Diff to previous 1.229 , to selected 1.732
Big updates to FIG.pm for the addition of methods to properly handle attributes. Also modified genome_statistics to take advantage of these new methods. load_attributes will load genomes and other attributes but doesn't not yet use the new methods (but should), and Attributes.html is some docs.

Revision 1.229 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 27 01:39:55 2005 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.228: +51 -3 lines
Diff to previous 1.228 , to selected 1.732
major changes in notion of function and load_attributes

Revision 1.228 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 26 19:49:59 2005 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.227: +4 -0 lines
Diff to previous 1.227 , to selected 1.732
filters for data mining

Revision 1.227 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 26 11:01:13 2005 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.226: +20 -3 lines
Diff to previous 1.226 , to selected 1.732
add reset_curator.cgi

Revision 1.226 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 16 18:59:20 2005 UTC (15 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.225: +3 -1 lines
Diff to previous 1.225 , to selected 1.732
highlight subsystems with no genomes attached

Revision 1.225 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 18:41:04 2005 UTC (15 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.224: +1 -1 lines
Diff to previous 1.224 , to selected 1.732
Fix subsystem_classification in FIG.pm

Revision 1.224 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 18:18:14 2005 UTC (15 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.223: +8 -17 lines
Diff to previous 1.223 , to selected 1.732
Moved the subsystem_classification getting/setting into subsys.pm where it belongs, and so I ammended FIG.pm. Also added the boxes on the subsystem page so you can see the classifications.

Revision 1.223 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 17:20:43 2005 UTC (15 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.222: +6 -5 lines
Diff to previous 1.222 , to selected 1.732
minor change to FIG::subsystem_classification

Revision 1.222 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 06:49:27 2005 UTC (15 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.221: +3 -3 lines
Diff to previous 1.221 , to selected 1.732
Initial addition of subsys_summary.cgi and minor modification of FIG.pm

Revision 1.221 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 05:38:43 2005 UTC (15 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.220: +6 -3 lines
Diff to previous 1.220 , to selected 1.732
changes to subsystem_classification

Revision 1.220 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 04:51:47 2005 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.219: +9 -14 lines
Diff to previous 1.219 , to selected 1.732
fix routine for locating candidates for a role in a genome

Revision 1.219 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 04:08:00 2005 UTC (15 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.218: +35 -0 lines
Diff to previous 1.218 , to selected 1.732
Minor changes to pir.cgi and added subsystem_classification to FIG.pm

Revision 1.218 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 04:01:01 2005 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.217: +20 -72 lines
Diff to previous 1.217 , to selected 1.732
many fixes to extending subsystems

Revision 1.217 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 03:50:04 2005 UTC (15 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.216: +26 -0 lines
Diff to previous 1.216 , to selected 1.732
Add some pod to FIG.pm

Revision 1.216 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 03:00:57 2005 UTC (15 years, 1 month ago) by mkubal
Branch: MAIN
Changes since 1.215: +19 -15 lines
Diff to previous 1.215 , to selected 1.732
update

Revision 1.215 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 11 06:34:05 2005 UTC (15 years, 1 month ago) by mkubal
Branch: MAIN
Changes since 1.214: +85 -3 lines
Diff to previous 1.214 , to selected 1.732
added all_for_genome, etc

Revision 1.214 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 10 13:33:37 2005 UTC (15 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.213: +26 -0 lines
Diff to previous 1.213 , to selected 1.732
Add subsystems_for_genome.

Revision 1.213 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 7 00:27:34 2005 UTC (15 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.212: +76 -14 lines
Diff to previous 1.212 , to selected 1.732
no message

Revision 1.212 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 5 04:12:35 2005 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.211: +1 -1 lines
Diff to previous 1.211 , to selected 1.732
head -1 should be head -n 1

Revision 1.211 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 31 14:01:07 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.210: +2 -1 lines
Diff to previous 1.210 , to selected 1.732
add pegs_in_subsystems

Revision 1.210 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 27 00:31:21 2005 UTC (15 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.209: +133 -68 lines
Diff to previous 1.209 , to selected 1.732
no message

Revision 1.209 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 26 18:37:58 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.208: +8 -10 lines
Diff to previous 1.208 , to selected 1.732
fix bugs introduced into by_alias function

Revision 1.208 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 23 00:38:22 2005 UTC (15 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.207: +3 -2 lines
Diff to previous 1.207 , to selected 1.732
Time stamp individual load steps

Revision 1.207 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 18 21:06:41 2005 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.206: +1 -1 lines
Diff to previous 1.206 , to selected 1.732
fix dumb typo.

Revision 1.206 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 18 21:02:45 2005 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.205: +15 -0 lines
Diff to previous 1.205 , to selected 1.732
Add peg_in_gendb and genome_in_gendb

Revision 1.205 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 18 20:55:32 2005 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.204: +6 -0 lines
Diff to previous 1.204 , to selected 1.732
add get_system_name() call.

Revision 1.204 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 16 16:05:20 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.203: +16 -2 lines
Diff to previous 1.203 , to selected 1.732
fix to scoring fc

Revision 1.203 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 13 17:32:51 2005 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.202: +1 -1 lines
Diff to previous 1.202 , to selected 1.732
More fixes for Sprout integration.

Revision 1.202 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 12 21:22:08 2005 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.201: +2 -1 lines
Diff to previous 1.201 , to selected 1.732
sprout debugging

Revision 1.201 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 12 20:18:56 2005 UTC (15 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.200: +13 -12 lines
Diff to previous 1.200 , to selected 1.732
no message

Revision 1.200 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 12 20:08:30 2005 UTC (15 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.199: +297 -301 lines
Diff to previous 1.199 , to selected 1.732
no message

Revision 1.199 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 11 18:59:39 2005 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.198: +1 -1 lines
Diff to previous 1.198 , to selected 1.732
I ran into a bug today where I was using by_alias to look up aliases
for the peg-mapping code, and one of the aliases was DR6', with a
single-quote. Because the code in by_alias doesn't quote its argument,
the SQL failed with a syntax error.

The perl DBI library has a mechanism designed to solve this
problem. If you use ? in a sql string where you want to substitute an
argument from code, DBI will do the appropriate quoting for you. I've
made this accessible via the SQL method in the DBrtns module, so the
by_alias code now looks like this:

    if (($relational_db_response = $rdbH->SQL("SELECT id FROM ext_alias WHERE ( alias = ? )", undef, $alias))

and works properly in the face of $alias having a single-quote in
it. I believe this mechanism is also more efficient. Note the second
argument of SQL is a verbose flag, which means that any bound
variables (to replace ?s in the query) have to start at the third
argument.

I've also made a change in the SQL method such that the query is done
inside an eval{} block, and if it fails, the error is reraised using
confess so that it is possible to see the full backtrace so you can
find in the source where the bad query was.

Revision 1.198 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 9 17:15:12 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.197: +1 -1 lines
Diff to previous 1.197 , to selected 1.732
fix disambiguating maps

Revision 1.197 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 8 18:22:00 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.196: +1 -1 lines
Diff to previous 1.196 , to selected 1.732
add check to assign_function

Revision 1.196 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 7 18:55:21 2005 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.195: +2 -2 lines
Diff to previous 1.195 , to selected 1.732
add option to not create a release info file to get_release_info()

Revision 1.195 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 5 16:19:44 2005 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.194: +78 -4 lines
Diff to previous 1.194 , to selected 1.732
p2p changes.

Revision 1.194 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 3 02:23:12 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.193: +0 -1 lines
Diff to previous 1.193 , to selected 1.732
fix stupid error in cleaning up aliases

Revision 1.193 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 3 02:21:08 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.192: +4 -27 lines
Diff to previous 1.192 , to selected 1.732
automatically generate aliases from mapped IDs

Revision 1.192 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 29 17:59:36 2004 UTC (15 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.191: +1 -1 lines
Diff to previous 1.191 , to selected 1.732
minor fix to FIG.pm and addition of generate_kegg_map_ec_tables

Revision 1.191 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 16 22:57:43 2004 UTC (15 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.190: +2 -1 lines
Diff to previous 1.190 , to selected 1.732
fixes to assigned_function

Revision 1.190 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 15 02:04:34 2004 UTC (15 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.189: +9 -5 lines
Diff to previous 1.189 , to selected 1.732
allow set of seeks to cores for bbhs

Revision 1.189 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 13 19:24:15 2004 UTC (15 years, 3 months ago) by redwards
Branch: MAIN
Changes since 1.188: +4 -4 lines
Diff to previous 1.188 , to selected 1.732
Minor changes to FIG.pm POD

Revision 1.188 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 10 07:04:39 2004 UTC (15 years, 3 months ago) by redwards
Branch: MAIN
Changes since 1.187: +18 -0 lines
Diff to previous 1.187 , to selected 1.732
Changes to subsys.cgi that warn if a subsystem doesn't exist

Revision 1.187 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 8 21:28:10 2004 UTC (15 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.186: +9 -2 lines
Diff to previous 1.186 , to selected 1.732
raw time for annotations

Revision 1.186 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 6 18:25:18 2004 UTC (15 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.185: +1 -1 lines
Diff to previous 1.185 , to selected 1.732
fix a comment

Revision 1.185 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 5 16:35:15 2004 UTC (15 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.184: +2 -2 lines
Diff to previous 1.184 , to selected 1.732
add checking for subsystems

Revision 1.184 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 3 18:55:20 2004 UTC (15 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.183: +39 -2 lines
Diff to previous 1.183 , to selected 1.732
Add subsystem_roles() method.
Add status callback to translate_pegs.
Remove setting of sticky bit in verify_dir.

Revision 1.183 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 10 22:10:22 2004 UTC (15 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.182: +46 -0 lines
Diff to previous 1.182 , to selected 1.732
add higher-level construct support

Revision 1.182 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 5 14:57:59 2004 UTC (15 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.181: +0 -1 lines
Diff to previous 1.181 , to selected 1.732
untested changes to extract_genomes - copy-all-but in Global

Revision 1.181 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 4 18:27:29 2004 UTC (15 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.180: +4 -1 lines
Diff to previous 1.180 , to selected 1.732
allow external IDs on subsystem displays

Revision 1.180 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 3 17:46:17 2004 UTC (15 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.179: +7 -0 lines
Diff to previous 1.179 , to selected 1.732
add is_complete function to FIG.pm

Revision 1.179 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 2 14:45:31 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.178: +81 -1 lines
Diff to previous 1.178 , to selected 1.732
fix bug in subsys.cgi and add Literature to Global

Revision 1.178 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 25 20:59:34 2004 UTC (15 years, 5 months ago) by redwards
Branch: MAIN
Changes since 1.177: +8 -0 lines
Diff to previous 1.177 , to selected 1.732
Adding  some pod

Revision 1.177 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 23 21:41:38 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.176: +1 -1 lines
Diff to previous 1.176 , to selected 1.732
stupid error in FIG.pm

Revision 1.176 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 23 19:58:28 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.175: +2 -2 lines
Diff to previous 1.175 , to selected 1.732
fix bound in find_role_in_org

Revision 1.175 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 22 19:30:37 2004 UTC (15 years, 5 months ago) by heiko
Branch: MAIN
Changes since 1.174: +23 -0 lines
Diff to previous 1.174 , to selected 1.732
added function
all_features_detailed
will return fig_id, location, type as array

Revision 1.174 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 22 16:55:42 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.173: +7 -7 lines
Diff to previous 1.173 , to selected 1.732
fill_in_cell for Heiko

Revision 1.173 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 17 16:40:13 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.172: +9 -7 lines
Diff to previous 1.172 , to selected 1.732
added homologs_in_clusters.cgi

Revision 1.172 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 17 00:05:17 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.171: +4 -0 lines
Diff to previous 1.171 , to selected 1.732
fix to by_alias

Revision 1.171 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 17 00:02:34 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.170: +21 -6 lines
Diff to previous 1.170 , to selected 1.732
fixes to UniProt IDs on chromosomal_clusters.cgi

Revision 1.170 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 16 20:42:28 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.169: +22 -2 lines
Diff to previous 1.169 , to selected 1.732
fixes to generalize chromosomal_clusters.cgi for UniProt

Revision 1.169 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 15 17:04:09 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.168: +97 -48 lines
Diff to previous 1.168 , to selected 1.732
peg links generalized to fid links

Revision 1.168 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 15 00:38:11 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.167: +15 -4 lines
Diff to previous 1.167 , to selected 1.732
fixes to subsystem code

Revision 1.167 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 11 23:55:40 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.166: +1 -0 lines
Diff to previous 1.166 , to selected 1.732
remove extra EOLs on changed locations

Revision 1.166 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 11 21:38:58 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.165: +7 -2 lines
Diff to previous 1.165 , to selected 1.732
fixes to change_location_of_feature

Revision 1.165 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 11 18:46:45 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.164: +10 -44 lines
Diff to previous 1.164 , to selected 1.732
More fixes for sprout support.

Revision 1.164 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 8 22:04:48 2004 UTC (15 years, 5 months ago) by redwards
Branch: MAIN
Changes since 1.163: +1 -1 lines
Diff to previous 1.163 , to selected 1.732
Added number of contigs to menu

Revision 1.163 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 5 22:06:28 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.162: +55 -0 lines
Diff to previous 1.162 , to selected 1.732
more DAS fixes

Revision 1.162 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 4 15:56:10 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.161: +29 -0 lines
Diff to previous 1.161 , to selected 1.732
Changes for DAS integration

Revision 1.161 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 1 19:48:37 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.160: +5 -5 lines
Diff to previous 1.160 , to selected 1.732
minor fixes to exporting sets

Revision 1.160 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 24 20:27:22 2004 UTC (15 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.159: +20 -1 lines
Diff to previous 1.159 , to selected 1.732
doc fix

Revision 1.159 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 24 18:58:42 2004 UTC (15 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.158: +7 -4 lines
Diff to previous 1.158 , to selected 1.732
Possible fix for beg_of and contig_of
More p2p stuff

Revision 1.158 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 24 18:34:32 2004 UTC (15 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.157: +165 -1 lines
Diff to previous 1.157 , to selected 1.732
Some contig manipulation stuff, more p2p stuff.

Revision 1.157 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 23 20:04:04 2004 UTC (15 years, 6 months ago) by redwards
Branch: MAIN
Changes since 1.156: +16 -2 lines
Diff to previous 1.156 , to selected 1.732
$fig->adjacent_genes was not returning adjacent genes

Revision 1.156 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 22 19:32:29 2004 UTC (15 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.155: +0 -2 lines
Diff to previous 1.155 , to selected 1.732
remove print

Revision 1.155 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 22 19:29:51 2004 UTC (15 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.154: +134 -1 lines
Diff to previous 1.154 , to selected 1.732
Mods for P2P update stuff.

Revision 1.154 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 20 21:16:02 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.153: +6 -3 lines
Diff to previous 1.153 , to selected 1.732
subsystem_genomes should return just genomes with an operational variant

Revision 1.153 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 16 15:15:57 2004 UTC (15 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.152: +4 -4 lines
Diff to previous 1.152 , to selected 1.732
remove inappropriate setting of g+s bit

Revision 1.152 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 16 04:35:03 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.151: +4 -4 lines
Diff to previous 1.151 , to selected 1.732
Fixed errors in POD documentation. -- /gdp

Revision 1.151 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 13 02:12:20 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.150: +19 -0 lines
Diff to previous 1.150 , to selected 1.732
add attributes as key-value pairs attached to fids

Revision 1.150 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Sep 11 00:46:49 2004 UTC (15 years, 6 months ago) by golsen
Branch: MAIN
Changes since 1.149: +9 -3 lines
Diff to previous 1.149 , to selected 1.732
Add domain-based selection to genomes function.  Used to generate domain-specfic genome lists.

Revision 1.149 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 9 00:00:09 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.148: +0 -1 lines
Diff to previous 1.148 , to selected 1.732
minor fixes

Revision 1.148 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 7 02:54:16 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.147: +17 -2 lines
Diff to previous 1.147 , to selected 1.732
add new subsystem interface

Revision 1.147 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 27 21:55:57 2004 UTC (15 years, 7 months ago) by mkubal
Branch: MAIN
Changes since 1.146: +81 -2 lines
Diff to previous 1.146 , to selected 1.732
added adjacent_genes() and supporting methods

Revision 1.146 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 27 18:32:07 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.145: +14 -0 lines
Diff to previous 1.145 , to selected 1.732
set current user

Revision 1.145 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 24 22:12:17 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.144: +6 -4 lines
Diff to previous 1.144 , to selected 1.732
minor changes to indexing translations

Revision 1.144 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 23 18:58:54 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.143: +1 -1 lines
Diff to previous 1.143 , to selected 1.732
sort sims into the correct order

Revision 1.143 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 23 18:51:34 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.142: +3 -3 lines
Diff to previous 1.142 , to selected 1.732
fix evil bug in index searches

Revision 1.142 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 23 18:35:51 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.141: +17 -2 lines
Diff to previous 1.141 , to selected 1.732
sort sims by bit score

Revision 1.141 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 23 03:34:32 2004 UTC (15 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.140: +200 -2 lines
Diff to previous 1.140 , to selected 1.732
Fix a typo in annotations_made and start adding infrastructure to fix genes_in_region issues

Revision 1.140 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 22 21:36:42 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.139: +1 -0 lines
Diff to previous 1.139 , to selected 1.732
have function_of append to end of lines

Revision 1.139 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 20 17:37:58 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.138: +70 -89 lines
Diff to previous 1.138 , to selected 1.732
update feature alterations

Revision 1.138 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 20 00:42:54 2004 UTC (15 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.137: +8 -8 lines
Diff to previous 1.137 , to selected 1.732
Fixed major error in org_of

Revision 1.137 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 19 23:45:58 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.136: +31 -0 lines
Diff to previous 1.136 , to selected 1.732
handle changes to feature locations

Revision 1.136 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 18 15:46:51 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.135: +179 -22 lines
Diff to previous 1.135 , to selected 1.732
add abilities to add, delete and update features

Revision 1.135 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 16 22:10:55 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.134: +160 -60 lines
Diff to previous 1.134 , to selected 1.732
straighten out FIG.pm

Revision 1.134 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 13 14:04:20 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.133: +126 -0 lines
Diff to previous 1.133 , to selected 1.732
interface for Bielefeld in FIG.pm

Revision 1.133 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 12 11:39:44 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.132: +1 -1 lines
Diff to previous 1.132 , to selected 1.732
fix errors relating to read_annotations

Revision 1.132 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 9 13:36:18 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.131: +2 -2 lines
Diff to previous 1.131 , to selected 1.732
major fix in read_annotations in FIG.pm

Revision 1.131 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 7 18:48:39 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.130: +1 -1 lines
Diff to previous 1.130 , to selected 1.732
fixes to aliases_of

Revision 1.130 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 2 20:02:29 2004 UTC (15 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.129: +81 -0 lines
Diff to previous 1.129 , to selected 1.732
Colorize organisms by domain in similarities list.  Changes protein.cgi and FIG.pm

Revision 1.129 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 1 11:50:25 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.128: +1 -2 lines
Diff to previous 1.128 , to selected 1.732
fix order on genes returned in a region

Revision 1.128 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 25 21:48:15 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.127: +3 -1 lines
Diff to previous 1.127 , to selected 1.732
sort links

Revision 1.127 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 18 22:58:36 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.126: +41 -6 lines
Diff to previous 1.126 , to selected 1.732
handle bug that lost notes for subsystems

Revision 1.126 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 16 21:58:03 2004 UTC (15 years, 8 months ago) by gdpusch
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Changes since 1.125: +19 -5 lines
Diff to previous 1.125 , to selected 1.732
Added out-of-bounds checks to &extract_seq(), plus debugging information for loci whose sequences could not be extracted.

Revision 1.125 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 16 20:41:26 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.124: +4 -0 lines
Diff to previous 1.124 , to selected 1.732
updates to ssa2.cgi and warnings when assignments fail

Revision 1.124 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 12 21:14:53 2004 UTC (15 years, 8 months ago) by olson
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Changes since 1.123: +6 -0 lines
Diff to previous 1.123 , to selected 1.732
Add "umask 0" to fig.pm to ensure all new files are world writable.

Revision 1.123 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 1 21:17:53 2004 UTC (15 years, 9 months ago) by olson
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Changes since 1.122: +282 -45 lines
Diff to previous 1.122 , to selected 1.732
More sim/askfor/pool stuff.

Make fig load_all show progress.

Fix run_in_background to do the right thing with an open db handle.

Revision 1.122 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 28 20:11:14 2004 UTC (15 years, 9 months ago) by olson
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Changes since 1.121: +42 -2 lines
Diff to previous 1.121 , to selected 1.732
Add assignments_made_for_protein
expand some code for readability.

Revision 1.121 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 27 22:49:49 2004 UTC (15 years, 9 months ago) by overbeek
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Changes since 1.120: +9 -1 lines
Diff to previous 1.120 , to selected 1.732
handle names of subsystems just a bit better

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Wed Jun 23 21:33:43 2004 UTC (15 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.119: +58 -10 lines
Diff to previous 1.119 , to selected 1.732
Add assignments_made_full, which returns the date and id of person who made the assignment.
assignments_made now just maps the result of assignments_made.

Add some comments.

Revision 1.119 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 16 16:52:10 2004 UTC (15 years, 9 months ago) by olson
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Changes since 1.118: +1 -0 lines
Diff to previous 1.118 , to selected 1.732
Modifications to fix & finish up the automated subsystem extension.

Revision 1.118 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 16 14:25:36 2004 UTC (15 years, 9 months ago) by olson
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Changes since 1.117: +1 -0 lines
Diff to previous 1.117 , to selected 1.732
New map support.

Revision 1.117 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 16 14:04:40 2004 UTC (15 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.116: +98 -0 lines
Diff to previous 1.116 , to selected 1.732
add background job support.

Revision 1.116 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 14 22:04:24 2004 UTC (15 years, 9 months ago) by olson
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Changes since 1.115: +96 -0 lines
Diff to previous 1.115 , to selected 1.732
Add background job support

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Thu Jun 10 14:00:36 2004 UTC (15 years, 9 months ago) by olson
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Changes since 1.114: +5 -5 lines
Diff to previous 1.114 , to selected 1.732
Add scalar decl to is_bacterial and friends.

Revision 1.114 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 10 13:39:55 2004 UTC (15 years, 9 months ago) by olson
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Changes since 1.113: +30 -0 lines
Diff to previous 1.113 , to selected 1.732
add more funcs for tutorials

Revision 1.113 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 8 20:26:23 2004 UTC (15 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.112: +159 -4 lines
Diff to previous 1.112 , to selected 1.732
add some scalar annotations; add find_role_in_org

Revision 1.112 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 8 17:19:43 2004 UTC (15 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.111: +16 -2 lines
Diff to previous 1.111 , to selected 1.732
Guard the rquire of figrpc in case we don't have the necessary modules installed for it.

Revision 1.111 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 8 15:02:14 2004 UTC (15 years, 9 months ago) by olson
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Changes since 1.110: +70 -14 lines
Diff to previous 1.110 , to selected 1.732
Add capability for :scalar :list :remote annotations to FIG interface. This works with
modules that are declared as subclasses of FIGAttributes.

Revision 1.110 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 3 20:58:04 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.109: +1 -1 lines
Diff to previous 1.109 , to selected 1.732
reorder load of databases just slightly

Revision 1.109 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 3 08:12:44 2004 UTC (15 years, 10 months ago) by gdpusch
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Changes since 1.108: +1 -1 lines
Diff to previous 1.108 , to selected 1.732
Fixed typo in pod-documentation

Revision 1.108 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 2 09:45:16 2004 UTC (15 years, 10 months ago) by gdpusch
Branch: MAIN
Changes since 1.107: +30 -29 lines
Diff to previous 1.107 , to selected 1.732
Added check for "defined" status of filehandle reads from <SSA>; removed various "masking" redefinitions of "my" variables.

Revision 1.107 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 2 09:23:35 2004 UTC (15 years, 10 months ago) by gdpusch
Branch: MAIN
Changes since 1.106: +46 -16 lines
Diff to previous 1.106 , to selected 1.732
Fixed typos in various $fig->genome_*() accessor functions.

Revision 1.106 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 1 20:45:39 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.105: +1 -1 lines
Diff to previous 1.105 , to selected 1.732
fix typo.

Revision 1.105 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 1 20:40:55 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.104: +2 -2 lines
Diff to previous 1.104 , to selected 1.732
Add $force_load argument to get_subsystem; results in the discarding
of the cached subsystem if there is one.

Revision 1.104 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 1 20:21:44 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.103: +20 -0 lines
Diff to previous 1.103 , to selected 1.732
add subsystems_for_peg

Revision 1.103 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 1 19:06:17 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.102: +3 -2 lines
Diff to previous 1.102 , to selected 1.732
fix the call to figrpc

Revision 1.102 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 1 19:02:37 2004 UTC (15 years, 10 months ago) by olson
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Changes since 1.101: +13 -0 lines
Diff to previous 1.101 , to selected 1.732
added redirect in FIG constructor to create a FIGrpc if the FIG_URL environment variable is set

Revision 1.101 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 1 00:45:38 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.100: +5 -2 lines
Diff to previous 1.100 , to selected 1.732
make bbhs sensitive to lengths of match - watch out for fused proteins

Revision 1.100 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 30 15:04:26 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.99: +21 -9 lines
Diff to previous 1.99 , to selected 1.732
precomputed BBHs

Revision 1.99 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 29 14:08:58 2004 UTC (15 years, 10 months ago) by overbeek
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Changes since 1.98: +1 -1 lines
Diff to previous 1.98 , to selected 1.732
untested changes to extract_genomes

Revision 1.98 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 28 19:27:00 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.97: +21 -5 lines
Diff to previous 1.97 , to selected 1.732
attempt to change FIG.pm to keep mac-1 up

Revision 1.97 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 27 18:22:11 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.96: +0 -1 lines
Diff to previous 1.96 , to selected 1.732
doh, had left a debug print in there

Revision 1.96 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 26 22:34:17 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.95: +19 -0 lines
Diff to previous 1.95 , to selected 1.732
add genome_and_peg_of

Revision 1.95 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 24 22:02:47 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.94: +10 -3 lines
Diff to previous 1.94 , to selected 1.732
Factor out the subsystem caching.

Revision 1.94 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 24 21:59:32 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.93: +8 -1 lines
Diff to previous 1.93 , to selected 1.732
cache subsystem objects, since they can be expensive to create.

Revision 1.93 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 24 21:55:18 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.92: +196 -34 lines
Diff to previous 1.92 , to selected 1.732
Beginning of sim queueing stuff.
First implementation of Subsystem object, with FIG::peg_in_subsystem_cell
implemented in terms of it.

Revision 1.92 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 24 21:14:16 2004 UTC (15 years, 10 months ago) by gdpusch
Branch: MAIN
Changes since 1.91: +60 -3 lines
Diff to previous 1.91 , to selected 1.732
Changed name of genome-size access method to \&genome_szdna($genome_id) to match the SQL keyword; added \&genome_pegs($genome) and \&genome_rnas($genome) to return number of PEGs and RNAs, resp.

Revision 1.91 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 24 21:03:39 2004 UTC (15 years, 10 months ago) by gdpusch
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Changes since 1.90: +28 -0 lines
Diff to previous 1.90 , to selected 1.732
Added access method \&genome_size($genome_id) to return the number of base-pairs in an organism\'s contig files.

Revision 1.90 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 24 19:32:36 2004 UTC (15 years, 10 months ago) by olson
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Changes since 1.89: +47 -0 lines
Diff to previous 1.89 , to selected 1.732
add file_head and file_read

Revision 1.89 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 22 11:43:00 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.88: +6 -0 lines
Diff to previous 1.88 , to selected 1.732
fix error in tutorial

Revision 1.88 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 21 18:05:55 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.87: +6 -2 lines
Diff to previous 1.87 , to selected 1.732
fixes to similarities

Revision 1.87 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 20 12:26:47 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.86: +14 -2 lines
Diff to previous 1.86 , to selected 1.732
make aliases include external aliases

Revision 1.86 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 19 15:54:10 2004 UTC (15 years, 10 months ago) by overbeek
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Changes since 1.85: +3 -0 lines
Diff to previous 1.85 , to selected 1.732
allow comma-separated contiguous regions in dna_seq argument list

Revision 1.85 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 19 14:15:57 2004 UTC (15 years, 10 months ago) by overbeek
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Changes since 1.84: +25 -0 lines
Diff to previous 1.84 , to selected 1.732
add all_contigs

Revision 1.84 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 19 13:17:39 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.83: +25 -9 lines
Diff to previous 1.83 , to selected 1.732
fixes on memory leak and genome version

Revision 1.83 - (view) (download) (as text) (