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Revision 1.813 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 27 20:45:51 2010 UTC (9 years, 7 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2010_0526
Changes since 1.812: +2 -0 lines
Diff to previous 1.812
turn off recognition of locks

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Fri Apr 23 20:24:13 2010 UTC (9 years, 7 months ago) by olson
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Changes since 1.811: +121 -7 lines
Diff to previous 1.811
memcached support

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Tue Feb 2 15:10:07 2010 UTC (9 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.810: +7 -3 lines
Diff to previous 1.810
fixes to active subsystem

Revision 1.810 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 16 20:12:30 2010 UTC (9 years, 10 months ago) by redwards
Branch: MAIN
CVS Tags: rast_rel_2010_0118
Changes since 1.809: +1 -0 lines
Diff to previous 1.809
adding load_dlits to load_all

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Sat Jan 16 20:12:00 2010 UTC (9 years, 10 months ago) by redwards
Branch: MAIN
Changes since 1.808: +17 -1 lines
Diff to previous 1.808
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 ago) by paczian
Branch: MAIN
Changes since 1.807: +2 -2 lines
Diff to previous 1.807
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, 1 month ago) by dejongh
Branch: MAIN
Changes since 1.806: +1 -1 lines
Diff to previous 1.806
Fix comment

Revision 1.806 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 6 23:44:59 2009 UTC (10 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.805: +4 -3 lines
Diff to previous 1.805
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, 1 month ago) by olson
Branch: MAIN
Changes since 1.804: +33 -0 lines
Diff to previous 1.804
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, 2 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2009_0925
Changes since 1.803: +22 -6 lines
Diff to previous 1.803
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, 2 months ago) by redwards
Branch: MAIN
Changes since 1.802: +1 -1 lines
Diff to previous 1.802
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, 3 months ago) by olson
Branch: MAIN
Changes since 1.801: +47 -0 lines
Diff to previous 1.801
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, 3 months ago) by olson
Branch: MAIN
Changes since 1.800: +22 -8 lines
Diff to previous 1.800
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, 3 months ago) by olson
Branch: MAIN
Changes since 1.799: +1 -1 lines
Diff to previous 1.799
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, 3 months ago) by olson
Branch: MAIN
Changes since 1.798: +21 -1 lines
Diff to previous 1.798
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, 3 months ago) by parrello
Branch: MAIN
Changes since 1.797: +0 -1 lines
Diff to previous 1.797
*** empty log message ***

Revision 1.797 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 11 20:28:01 2009 UTC (10 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.796: +19 -0 lines
Diff to previous 1.796
add co-occurs stuff

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Tue Aug 11 18:51:39 2009 UTC (10 years, 4 months ago) by parrello
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Changes since 1.795: +28 -0 lines
Diff to previous 1.795
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, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.794: +1 -1 lines
Diff to previous 1.794
minor documentation fix

Revision 1.794 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 7 09:19:05 2009 UTC (10 years, 4 months ago) by paczian
Branch: MAIN
Changes since 1.793: +57 -20 lines
Diff to previous 1.793
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, 4 months ago) by redwards
Branch: MAIN
Changes since 1.792: +18 -0 lines
Diff to previous 1.792
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, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.791: +2 -1 lines
Diff to previous 1.791
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, 5 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
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, 5 months ago) by dejongh
Branch: MAIN
Changes since 1.789: +21 -10 lines
Diff to previous 1.789
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, 5 months ago) by parrello
Branch: MAIN
Changes since 1.788: +16 -22 lines
Diff to previous 1.788
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, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.787: +4 -2 lines
Diff to previous 1.787
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, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.786: +6 -2 lines
Diff to previous 1.786
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, 5 months ago) by olson
Branch: MAIN
Changes since 1.785: +37 -11 lines
Diff to previous 1.785
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, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.784: +5 -2 lines
Diff to previous 1.784
fixes to blastit

Revision 1.784 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 21 18:53:27 2009 UTC (10 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.783: +13 -2 lines
Diff to previous 1.783
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, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.782: +4 -4 lines
Diff to previous 1.782
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, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.781: +8 -4 lines
Diff to previous 1.781
clean up warnings

Revision 1.781 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 21 14:32:26 2009 UTC (10 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.780: +8 -3 lines
Diff to previous 1.780
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, 6 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
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, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.778: +1 -1 lines
Diff to previous 1.778
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, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.777: +1 -1 lines
Diff to previous 1.777
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, 6 months ago) by olson
Branch: MAIN
Changes since 1.776: +0 -2 lines
Diff to previous 1.776
fix typo bug

Revision 1.776 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 19 20:51:33 2009 UTC (10 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.775: +74 -22 lines
Diff to previous 1.775
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, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.774: +2 -2 lines
Diff to previous 1.774
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, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.773: +3 -1 lines
Diff to previous 1.773
remove warning

Revision 1.773 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 17 13:42:25 2009 UTC (10 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.772: +15 -6 lines
Diff to previous 1.772
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, 7 months ago) by disz
Branch: MAIN
Changes since 1.771: +20 -0 lines
Diff to previous 1.771
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, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.770: +2 -3 lines
Diff to previous 1.770
minor fix

Revision 1.770 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 9 16:25:33 2009 UTC (10 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.769: +14 -0 lines
Diff to previous 1.769
add variant_code

Revision 1.769 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 9 15:30:01 2009 UTC (10 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.768: +4 -4 lines
Diff to previous 1.768
fix nonumeric comparisons

Revision 1.768 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 9 15:22:57 2009 UTC (10 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.767: +1 -1 lines
Diff to previous 1.767
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, 7 months ago) by golsen
Branch: MAIN
Changes since 1.766: +1 -1 lines
Diff to previous 1.766
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, 7 months ago) by golsen
Branch: MAIN
Changes since 1.765: +1 -1 lines
Diff to previous 1.765
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, 7 months ago) by golsen
Branch: MAIN
Changes since 1.764: +1 -1 lines
Diff to previous 1.764
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, 7 months ago) by golsen
Branch: MAIN
Changes since 1.763: +32 -0 lines
Diff to previous 1.763
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, 7 months ago) by gdpusch
Branch: MAIN
Changes since 1.762: +5 -3 lines
Diff to previous 1.762
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, 7 months ago) by olson
Branch: MAIN
Changes since 1.761: +1 -1 lines
Diff to previous 1.761
fix dumb mistake

Revision 1.761 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 27 17:11:29 2009 UTC (10 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.760: +15 -10 lines
Diff to previous 1.760
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, 7 months ago) by paczian
Branch: MAIN
Changes since 1.759: +40 -1 lines
Diff to previous 1.759
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 (10 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.758: +26 -0 lines
Diff to previous 1.758
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 (10 years, 8 months ago) by gdpusch
Branch: MAIN
Changes since 1.757: +15 -0 lines
Diff to previous 1.757
Added "is_plasmid()" function.

Revision 1.757 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 25 16:17:32 2009 UTC (10 years, 8 months ago) by paczian
Branch: MAIN
CVS Tags: rast_rel_2009_03_26
Changes since 1.756: +4 -1 lines
Diff to previous 1.756
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 (10 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.755: +1 -1 lines
Diff to previous 1.755
minor correction in documentation

Revision 1.755 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 15 23:55:42 2009 UTC (10 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.754: +1 -1 lines
Diff to previous 1.754
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 (10 years, 9 months ago) by disz
Branch: MAIN
Changes since 1.753: +18 -18 lines
Diff to previous 1.753
Updated get_representative_genome

Revision 1.753 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 9 17:34:48 2009 UTC (10 years, 9 months ago) by disz
Branch: MAIN
Changes since 1.752: +43 -0 lines
Diff to previous 1.752
Added get_representative_genome

Revision 1.752 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 23 21:13:39 2009 UTC (10 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.751: +3 -3 lines
Diff to previous 1.751
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 (10 years, 10 months ago) by gdpusch
Branch: MAIN
Changes since 1.750: +104 -83 lines
Diff to previous 1.750
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 (10 years, 10 months ago) by paczian
Branch: MAIN
Changes since 1.749: +35 -3 lines
Diff to previous 1.749
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 (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.748: +8 -0 lines
Diff to previous 1.748
fix is_cluster_based_subsystem

Revision 1.748 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 2 12:50:20 2009 UTC (10 years, 10 months ago) by bartels
Branch: MAIN
CVS Tags: rast_rel_2009_02_05
Changes since 1.747: +116 -247 lines
Diff to previous 1.747
bugfix

Revision 1.747 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 30 12:42:15 2009 UTC (10 years, 10 months ago) by paczian
Branch: MAIN
Changes since 1.746: +31 -0 lines
Diff to previous 1.746
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 (10 years, 10 months ago) by gdpusch
Branch: MAIN
Changes since 1.745: +120 -98 lines
Diff to previous 1.745
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 (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.744: +17 -4 lines
Diff to previous 1.744
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 (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.743: +2 -2 lines
Diff to previous 1.743
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 (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.742: +7 -0 lines
Diff to previous 1.742
add is_cluster_based_subsystem

Revision 1.742 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 19 20:29:43 2009 UTC (10 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.741: +5 -4 lines
Diff to previous 1.741
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 (10 years, 11 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
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 ago) by gdpusch
Branch: MAIN
Changes since 1.739: +3 -0 lines
Diff to previous 1.739
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 ago) by gdpusch
Branch: MAIN
Changes since 1.738: +4 -0 lines
Diff to previous 1.738
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 ago) by bartels
Branch: MAIN
CVS Tags: rast_rel_2008_11_24
Changes since 1.737: +22 -0 lines
Diff to previous 1.737
*** empty log message ***

Revision 1.737 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 17 19:36:28 2008 UTC (11 years ago) by dejongh
Branch: MAIN
Changes since 1.736: +85 -0 lines
Diff to previous 1.736
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 ago) by dejongh
Branch: MAIN
Changes since 1.735: +9 -7 lines
Diff to previous 1.735
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 ago) by dejongh
Branch: MAIN
Changes since 1.734: +7 -14 lines
Diff to previous 1.734
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 ago) by bartels
Branch: MAIN
Changes since 1.733: +24 -1 lines
Diff to previous 1.733
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, 1 month 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) - [select for diffs]
Thu Oct 23 16:20:48 2008 UTC (11 years, 1 month 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, 1 month ago) by parrello
Branch: MAIN
Changes since 1.730: +2 -3 lines
Diff to previous 1.730
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, 1 month ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_10_29
Changes since 1.729: +43 -20 lines
Diff to previous 1.729
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, 1 month ago) by olson
Branch: MAIN
Changes since 1.728: +8 -1 lines
Diff to previous 1.728
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, 1 month ago) by paczian
Branch: MAIN
Changes since 1.727: +5 -2 lines
Diff to previous 1.727
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, 1 month ago) by parrello
Branch: MAIN
Changes since 1.726: +2 -1 lines
Diff to previous 1.726
Fixed a comment.

Revision 1.726 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 13 20:26:02 2008 UTC (11 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.725: +28 -13 lines
Diff to previous 1.725
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, 2 months ago) by parrello
Branch: MAIN
Changes since 1.724: +44 -0 lines
Diff to previous 1.724
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, 2 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
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, 3 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
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, 3 months ago) by olson
Branch: MAIN
Changes since 1.721: +1 -1 lines
Diff to previous 1.721
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, 3 months ago) by gdpusch
Branch: MAIN
Changes since 1.720: +11 -2 lines
Diff to previous 1.720
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, 3 months ago) by gdpusch
Branch: MAIN
Changes since 1.719: +41 -12 lines
Diff to previous 1.719
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, 3 months ago) by bartels
Branch: MAIN
Changes since 1.718: +7 -1 lines
Diff to previous 1.718
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, 3 months ago) by olson
Branch: MAIN
Changes since 1.717: +109 -1 lines
Diff to previous 1.717
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, 3 months ago) by bartels
Branch: MAIN
Changes since 1.716: +34 -6 lines
Diff to previous 1.716
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, 3 months ago) by parrello
Branch: MAIN
Changes since 1.715: +9 -4 lines
Diff to previous 1.715
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, 3 months ago) by golsen
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806
Changes since 1.714: +25 -22 lines
Diff to previous 1.714
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, 3 months ago) by olson
Branch: MAIN
Changes since 1.713: +1 -1 lines
Diff to previous 1.713
fix clearinghouse urls.

Revision 1.713 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 12 06:35:42 2008 UTC (11 years, 4 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
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, 4 months ago) by parrello
Branch: MAIN
Changes since 1.711: +31 -261 lines
Diff to previous 1.711
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, 4 months ago) by bartels
Branch: MAIN
Changes since 1.710: +37 -1 lines
Diff to previous 1.710
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, 4 months ago) by dsouza
Branch: MAIN
Changes since 1.709: +74 -0 lines
Diff to previous 1.709
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, 4 months ago) by golsen
Branch: MAIN
Changes since 1.708: +262 -15 lines
Diff to previous 1.708
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, 5 months ago) by olson
Branch: MAIN
Changes since 1.707: +26 -1 lines
Diff to previous 1.707
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, 5 months ago) by golsen
Branch: MAIN
Changes since 1.706: +45 -35 lines
Diff to previous 1.706
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, 5 months ago) by golsen
Branch: MAIN
Changes since 1.705: +1 -0 lines
Diff to previous 1.705
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, 5 months ago) by golsen
Branch: MAIN
Changes since 1.704: +18 -2 lines
Diff to previous 1.704
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, 5 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
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, 5 months ago) by bartels
Branch: MAIN
Changes since 1.702: +17 -1 lines
Diff to previous 1.702
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, 5 months ago) by disz
Branch: MAIN
Changes since 1.701: +4 -2 lines
Diff to previous 1.701
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, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.700: +101 -0 lines
Diff to previous 1.700
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, 5 months ago) by disz
Branch: MAIN
Changes since 1.699: +55 -44 lines
Diff to previous 1.699
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, 5 months ago) by disz
Branch: MAIN
Changes since 1.698: +11 -6 lines
Diff to previous 1.698
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, 5 months ago) by golsen
Branch: MAIN
Changes since 1.697: +86 -0 lines
Diff to previous 1.697
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, 5 months ago) by disz
Branch: MAIN
Changes since 1.696: +6 -9 lines
Diff to previous 1.696
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, 5 months ago) by disz
Branch: MAIN
Changes since 1.695: +259 -1 lines
Diff to previous 1.695
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, 6 months ago) by olson
Branch: MAIN
Changes since 1.694: +37 -2 lines
Diff to previous 1.694
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, 6 months ago) by olson
Branch: MAIN
Changes since 1.693: +1 -2 lines
Diff to previous 1.693
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, 6 months ago) by olson
Branch: MAIN
Changes since 1.692: +34 -0 lines
Diff to previous 1.692
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, 6 months ago) by olson
Branch: MAIN
Changes since 1.691: +37 -1 lines
Diff to previous 1.691
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, 6 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
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, 6 months ago) by golsen
Branch: MAIN
Changes since 1.689: +4 -3 lines
Diff to previous 1.689
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, 6 months ago) by gdpusch
Branch: MAIN
Changes since 1.688: +1 -2 lines
Diff to previous 1.688
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, 6 months ago) by olson
Branch: MAIN
Changes since 1.687: +10 -14 lines
Diff to previous 1.687
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, 7 months ago) by olson
Branch: MAIN
Changes since 1.686: +6 -0 lines
Diff to previous 1.686
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, 7 months ago) by paczian
Branch: MAIN
Changes since 1.685: +44 -0 lines
Diff to previous 1.685
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, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.684: +1 -0 lines
Diff to previous 1.684
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, 7 months ago) by parrello
Branch: MAIN
Changes since 1.683: +1 -1 lines
Diff to previous 1.683
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, 7 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
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, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.681: +1 -1 lines
Diff to previous 1.681
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, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.680: +3 -1 lines
Diff to previous 1.680
updates to FIGfam quality control

Revision 1.680 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 26 14:49:38 2008 UTC (11 years, 8 months ago) by wilke
Branch: MAIN
Changes since 1.679: +24 -9 lines
Diff to previous 1.679
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 (11 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.678: +6 -2 lines
Diff to previous 1.678
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 (11 years, 8 months ago) by mkubal
Branch: MAIN
Changes since 1.677: +28 -29 lines
Diff to previous 1.677
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 (11 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.676: +38 -7 lines
Diff to previous 1.676
changes to dsims

Revision 1.676 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 13 19:22:39 2008 UTC (11 years, 9 months ago) by paarmann
Branch: MAIN
Changes since 1.675: +21 -0 lines
Diff to previous 1.675
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 (11 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.674: +6 -4 lines
Diff to previous 1.674
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 (11 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.673: +2 -2 lines
Diff to previous 1.673
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 (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.672: +24 -0 lines
Diff to previous 1.672
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 (11 years, 9 months ago) by bartels
Branch: MAIN
Changes since 1.671: +31 -1 lines
Diff to previous 1.671
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 (11 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.670: +55 -0 lines
Diff to previous 1.670
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 (11 years, 9 months ago) by wilke
Branch: MAIN
Changes since 1.669: +53 -0 lines
Diff to previous 1.669
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 (11 years, 9 months ago) by paczian
Branch: MAIN
Changes since 1.668: +2 -2 lines
Diff to previous 1.668
added taxonomy to genome_info

Revision 1.668 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 4 00:11:58 2008 UTC (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.667: +1 -1 lines
Diff to previous 1.667
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 (11 years, 9 months ago) by paczian
Branch: MAIN
Changes since 1.666: +10 -7 lines
Diff to previous 1.666
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 (11 years, 9 months ago) by paczian
Branch: MAIN
Changes since 1.665: +31 -9 lines
Diff to previous 1.665
 added method genome_info

Revision 1.665 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 28 19:12:37 2008 UTC (11 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.664: +5 -2 lines
Diff to previous 1.664
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 (11 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.663: +12 -11 lines
Diff to previous 1.663
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 (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.662: +2 -2 lines
Diff to previous 1.662
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 (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.661: +2 -2 lines
Diff to previous 1.661
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 (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.660: +24 -0 lines
Diff to previous 1.660
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 (11 years, 9 months ago) by paczian
Branch: MAIN
Changes since 1.659: +31 -3 lines
Diff to previous 1.659
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 (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.658: +3 -3 lines
Diff to previous 1.658
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 (11 years, 9 months ago) by gdpusch
Branch: MAIN
Changes since 1.657: +8 -4 lines
Diff to previous 1.657
Appended the strand to the results returned by &boundaries_of(), -- /gdp

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Tue Feb 12 03:49:45 2008 UTC (11 years, 10 months ago) by gdpusch
Branch: MAIN
Changes since 1.656: +1 -2 lines
Diff to previous 1.656
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 (11 years, 10 months ago) by overbeek
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Changes since 1.655: +1 -0 lines
Diff to previous 1.655
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 (11 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.654: +41 -28 lines
Diff to previous 1.654
minor fixes to dsims

Revision 1.654 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 7 21:52:29 2008 UTC (11 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.653: +7 -5 lines
Diff to previous 1.653
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 (11 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.652: +2 -0 lines
Diff to previous 1.652
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 (11 years, 10 months ago) by overbeek
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Changes since 1.651: +43 -36 lines
Diff to previous 1.651
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 (11 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.650: +2 -2 lines
Diff to previous 1.650
Fixed some headings.

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Tue Jan 29 08:00:20 2008 UTC (11 years, 10 months ago) by gdpusch
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Changes since 1.649: +1 -0 lines
Diff to previous 1.649
Fixed &FIG::flatten_dumper() to support OOP calling syntax. -- /gdp

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Fri Jan 25 21:13:50 2008 UTC (11 years, 10 months ago) by gdpusch
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Changes since 1.648: +4 -3 lines
Diff to previous 1.648
Added search-interval constraint to &pick_gene_boundaries(). -- /gdp

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Sun Jan 20 21:33:42 2008 UTC (11 years, 10 months ago) by gdpusch
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Changes since 1.647: +16 -35 lines
Diff to previous 1.647
Revised &pick_gene_boundaries() to use new code in "Location.pm". -- /gdp

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Wed Jan 2 01:42:50 2008 UTC (11 years, 11 months ago) by golsen
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Changes since 1.646: +521 -1 lines
Diff to previous 1.646
Add next_feature and previous_feature functions, and some more general
functions for handling complex location descriptions: filtered_location
and boundaries_of_2.

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Thu Dec 6 15:44:05 2007 UTC (12 years ago) by wilke
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Changes since 1.645: +82 -0 lines
Diff to previous 1.645
get_organism_info_from_ncbi
For a given taxonomy ID returns a hash containing scientific name , genetic code , synonyms and lineage

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Thu Dec 6 13:47:40 2007 UTC (12 years ago) by parrello
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Changes since 1.644: +347 -346 lines
Diff to previous 1.644
Changed POD format for better compatability with Wiki.

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Mon Dec 3 20:05:26 2007 UTC (12 years ago) by gdpusch
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Changes since 1.643: +52 -0 lines
Diff to previous 1.643
Added sort function &by_locus(). -- /gdp

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Mon Dec 3 02:49:29 2007 UTC (12 years ago) by overbeek
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Changes since 1.642: +1 -1 lines
Diff to previous 1.642
minor modifications

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Sat Dec 1 22:17:03 2007 UTC (12 years ago) by overbeek
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Changes since 1.641: +172 -0 lines
Diff to previous 1.641
add possible_frameshift to FIG.pm (and, hence, FIGV.pm)

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Fri Nov 30 21:47:50 2007 UTC (12 years ago) by gdpusch
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Changes since 1.640: +12 -5 lines
Diff to previous 1.640
Added support for FIGV calls of &FIG::pick_gene_boundaries() and &FIG::call_start(). -- /gdp

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Wed Nov 14 20:33:09 2007 UTC (12 years ago) by paczian
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Changes since 1.639: +47 -0 lines
Diff to previous 1.639
updated perldoc for method wikipedia link
added method organism_directory

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Thu Nov 8 21:33:09 2007 UTC (12 years, 1 month ago) by bartels
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Changes since 1.638: +20 -0 lines
Diff to previous 1.638
I added a method 'feature_aliases_in_tbl', which gives back only the aliases
in the tbl file and not external aliases.

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Thu Nov 1 22:10:11 2007 UTC (12 years, 1 month ago) by olson
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Changes since 1.637: +4 -0 lines
Diff to previous 1.637
Fix no-results return from in_pch_pin_with_and_evidence.

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Thu Nov 1 16:33:29 2007 UTC (12 years, 1 month ago) by olson
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Changes since 1.636: +7 -1 lines
Diff to previous 1.636
some fixes for RAST genome installation.

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Wed Oct 31 23:18:01 2007 UTC (12 years, 1 month ago) by olson
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Changes since 1.635: +14 -0 lines
Diff to previous 1.635
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.

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Tue Oct 30 18:19:31 2007 UTC (12 years, 1 month ago) by olson
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Changes since 1.634: +19 -2 lines
Diff to previous 1.634
fix get_genome_assignment_data & get_genome_stats to account for deleted genomes and pegs

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Thu Oct 18 21:09:48 2007 UTC (12 years, 1 month ago) by wilke
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Changes since 1.633: +43 -8 lines
Diff to previous 1.633
added function md5sum_to_contig_genome

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Mon Oct 15 19:14:36 2007 UTC (12 years, 1 month ago) by olson
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Changes since 1.632: +34 -0 lines
Diff to previous 1.632
Add sub interpret_error_code.

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Sat Oct 13 13:13:45 2007 UTC (12 years, 2 months ago) by olson
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Changes since 1.631: +2 -2 lines
Diff to previous 1.631
fix coupled_to_batch in non-server ccase

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Thu Oct 11 18:59:00 2007 UTC (12 years, 2 months ago) by olson
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Changes since 1.630: +47 -1 lines
Diff to previous 1.630
add batch coupling_and_evidence calls

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Tue Oct 9 21:16:35 2007 UTC (12 years, 2 months ago) by olson
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Changes since 1.629: +26 -2 lines
Diff to previous 1.629
Add subsystem-at-a-time coupling lookup in get_ev_codes that goes iwth the new coupled_to_batch interface.

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Tue Oct 9 18:57:27 2007 UTC (12 years, 2 months ago) by olson
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Changes since 1.628: +137 -1 lines
Diff to previous 1.628
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.

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Fri Oct 5 18:33:12 2007 UTC (12 years, 2 months ago) by overbeek
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Changes since 1.627: +4 -3 lines
Diff to previous 1.627
add check_variants.cgi, a program to automatically validate variant codes

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Thu Oct 4 19:48:40 2007 UTC (12 years, 2 months ago) by olson
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Changes since 1.626: +50 -5 lines
Diff to previous 1.626
add in_pch_pin_with and in_pch_pin_with_and_evidence

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Mon Oct 1 15:33:11 2007 UTC (12 years, 2 months ago) by olson
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Changes since 1.625: +19 -0 lines
Diff to previous 1.625
Add support for $fig->sims([list of ids]) in the non-sim-server case.

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Wed Sep 26 03:32:54 2007 UTC (12 years, 2 months ago) by gdpusch
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Changes since 1.624: +1 -1 lines
Diff to previous 1.624
Minor fix to POD of &taxonomy_of(). -- /gdp

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Mon Sep 24 20:53:51 2007 UTC (12 years, 2 months ago) by overbeek
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Changes since 1.623: +10 -0 lines
Diff to previous 1.623
add a routine in FIG.pm giving who set the function of a peg

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Thu Sep 20 17:36:10 2007 UTC (12 years, 2 months ago) by olson
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Changes since 1.622: +1 -1 lines
Diff to previous 1.622
fix vc * bug

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Wed Sep 19 21:54:46 2007 UTC (12 years, 2 months ago) by olson
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Changes since 1.621: +6 -0 lines
Diff to previous 1.621
add index_annotations to add_genome_body

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Wed Sep 19 21:08:12 2007 UTC (12 years, 2 months ago) by olson
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Changes since 1.620: +109 -0 lines
Diff to previous 1.620
add perform_subsystem_salvage and its invocation in add_genome_body.

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Mon Sep 17 19:52:10 2007 UTC (12 years, 2 months ago) by olson
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Changes since 1.619: +1 -1 lines
Diff to previous 1.619
fix typoe

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Mon Sep 17 19:17:15 2007 UTC (12 years, 2 months ago) by olson
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Changes since 1.618: +1 -1 lines
Diff to previous 1.618
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.

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Mon Sep 17 17:35:19 2007 UTC (12 years, 2 months ago) by olson
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Changes since 1.617: +5 -5 lines
Diff to previous 1.617
minor fix to rast install code

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Mon Sep 17 17:32:13 2007 UTC (12 years, 2 months ago) by olson
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Changes since 1.616: +46 -17 lines
Diff to previous 1.616
Mods for RAST org installation

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Tue Sep 11 23:17:15 2007 UTC (12 years, 3 months ago) by parrello
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Changes since 1.615: +2 -2 lines
Diff to previous 1.615
Removed some "my"s to prevent compiler warnings.

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Thu Sep 6 21:25:34 2007 UTC (12 years, 3 months ago) by olson
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Changes since 1.614: +57 -14 lines
Diff to previous 1.614
add_genome mods for rast import

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Wed Sep 5 21:17:04 2007 UTC (12 years, 3 months ago) by mkubal
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Changes since 1.613: +2 -2 lines
Diff to previous 1.613
changed model_directory to default to Data/Organisms

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Wed Sep 5 20:59:52 2007 UTC (12 years, 3 months ago) by olson
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Changes since 1.612: +26 -5 lines
Diff to previous 1.612
add support for asserting presence of genomes (for use in the RAST import environment).

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Tue Aug 28 18:46:40 2007 UTC (12 years, 3 months ago) by paczian
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Changes since 1.611: +2 -2 lines
Diff to previous 1.611
commented out warn statements in all_subsystems

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Mon Aug 27 18:27:33 2007 UTC (12 years, 3 months ago) by overbeek
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Changes since 1.610: +6 -3 lines
Diff to previous 1.610
add strip comments argument on function_of

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Wed Aug 15 21:28:27 2007 UTC (12 years, 3 months ago) by olson
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Changes since 1.609: +3 -1 lines
Diff to previous 1.609
Make NMPDR-generated GFF files validate cleanly.

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Tue Aug 14 21:34:06 2007 UTC (12 years, 3 months ago) by arodri7
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Changes since 1.608: +61 -0 lines
Diff to previous 1.608
made additions to FIG.pm - added batch method to get subsystem data

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Sun Jul 22 18:38:05 2007 UTC (12 years, 4 months ago) by parrello
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Changes since 1.607: +23 -1 lines
Diff to previous 1.607
Added some POD documentation.

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Fri Jul 20 19:27:56 2007 UTC (12 years, 4 months ago) by paczian
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Changes since 1.606: +1 -1 lines
Diff to previous 1.606
removed addition of subsystems in all_features_detailed_fast, as it introduced an unforeseen error

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Mon Jul 16 19:15:36 2007 UTC (12 years, 4 months ago) by parrello
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Changes since 1.605: +104 -70 lines
Diff to previous 1.605
Moved coupling code to FIGRules. Added support for the Subsystem List Editor.

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Mon Jul 16 16:34:29 2007 UTC (12 years, 4 months ago) by paczian
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Changes since 1.604: +1 -1 lines
Diff to previous 1.604
added subsystem information to function all_features_detailed_fast

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Mon Jul 9 19:23:32 2007 UTC (12 years, 5 months ago) by overbeek
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Changes since 1.603: +1 -1 lines
Diff to previous 1.603
fix bug in undeleting features

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Thu Jun 28 22:04:24 2007 UTC (12 years, 5 months ago) by olson
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Changes since 1.602: +147 -0 lines
Diff to previous 1.602
add get_basic_statistics() and get_peg_statistics(); both use caching.

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Wed Jun 27 21:48:54 2007 UTC (12 years, 5 months ago) by gdpusch
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Changes since 1.601: +11 -11 lines
Diff to previous 1.601
Fixed duplicate declaration of $cache_dir in &get_cache_directory(). -- /gdp

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Mon Jun 25 21:33:18 2007 UTC (12 years, 5 months ago) by olson
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Changes since 1.600: +118 -0 lines
Diff to previous 1.600
add caching support for $fig->all_usable_subsystems() - new routine.

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Mon Jun 25 19:41:45 2007 UTC (12 years, 5 months ago) by gdpusch
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Changes since 1.599: +18 -3 lines
Diff to previous 1.599
Added boolean test "&is_viral()". -- /gdp

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Tue Jun 12 20:46:57 2007 UTC (12 years, 6 months ago) by paczian
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Changes since 1.598: +9 -0 lines
Diff to previous 1.598
introduced a method called 'genome_list' which returns a list of all complete genomes, every entry composed of genome_id, genome_name, maindomain

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Sat Jun 9 12:23:32 2007 UTC (12 years, 6 months ago) by overbeek
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Changes since 1.597: +25 -5 lines
Diff to previous 1.597
add ability to filter aux roles on peg_to_subsystems

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Thu Jun 7 16:21:54 2007 UTC (12 years, 6 months ago) by overbeek
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Changes since 1.596: +1 -1 lines
Diff to previous 1.596
fix to auto_assign

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Wed May 30 15:41:42 2007 UTC (12 years, 6 months ago) by paczian
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Changes since 1.595: +6 -6 lines
Diff to previous 1.595
changed scenario_directory to model_directory

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Tue May 29 19:16:26 2007 UTC (12 years, 6 months ago) by olson
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Changes since 1.594: +10 -2 lines
Diff to previous 1.594
Changes for using $fig->scenario_directory() instead of constructed paths.

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Fri May 25 16:46:44 2007 UTC (12 years, 6 months ago) by paczian
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Changes since 1.593: +25 -0 lines
Diff to previous 1.593
added the function scenario_directory, which returns the scenario directory

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Wed May 23 22:01:06 2007 UTC (12 years, 6 months ago) by olson
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Changes since 1.592: +171 -0 lines
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Add $fig->compute_genome_similarity and supporting routines.

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Wed May 23 21:17:58 2007 UTC (12 years, 6 months ago) by olson
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Changes since 1.591: +0 -1 lines
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Not using URI now.

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Wed May 23 20:51:08 2007 UTC (12 years, 6 months ago) by olson
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Changes since 1.590: +80 -0 lines
Diff to previous 1.590
FIG.pm support for installing subsystme dir

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Wed May 23 19:13:59 2007 UTC (12 years, 6 months ago) by paczian
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Changes since 1.589: +5 -1 lines
Diff to previous 1.589
added the option of getting all non -1 variant subsystems in subsystems_for_genome

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Tue May 15 21:12:18 2007 UTC (12 years, 6 months ago) by olson
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Changes since 1.588: +118 -6 lines
Diff to previous 1.588
Hope college modifications.

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Mon May 14 16:13:25 2007 UTC (12 years, 7 months ago) by paczian
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Changes since 1.587: +39 -0 lines
Diff to previous 1.587
added the function get_genome_subsystem_count

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Fri May 11 05:49:48 2007 UTC (12 years, 7 months ago) by parrello
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Changes since 1.586: +30 -0 lines
Diff to previous 1.586
Added a method to download attribute keys and their definitions.

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Mon May 7 00:43:26 2007 UTC (12 years, 7 months ago) by overbeek
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Changes since 1.585: +1 -1 lines
Diff to previous 1.585
add computation of alignments to building FIGFAMS

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Sat Apr 28 16:03:25 2007 UTC (12 years, 7 months ago) by overbeek
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Changes since 1.584: +1 -1 lines
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Added initial support for alternate genetic codes. -- /gdp

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Sat Apr 28 15:52:30 2007 UTC (12 years, 7 months ago) by overbeek
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Changes since 1.583: +7 -1 lines
Diff to previous 1.583
Added initial support for alternate genetic codes. -- /gdp

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Sat Apr 28 15:50:12 2007 UTC (12 years, 7 months ago) by overbeek
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Changes since 1.582: +12 -0 lines
Diff to previous 1.582
Added initial support for alternate genetic codes. -- /gdp

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Fri Apr 27 22:12:28 2007 UTC (12 years, 7 months ago) by parrello
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Changes since 1.581: +65 -0 lines
Diff to previous 1.581
Added support for the new QueryAttributes feature.

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Fri Apr 27 16:53:43 2007 UTC (12 years, 7 months ago) by overbeek
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Changes since 1.580: +18 -0 lines
Diff to previous 1.580
add recast_ids

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Tue Apr 10 03:30:01 2007 UTC (12 years, 8 months ago) by parrello
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Changes since 1.579: +100 -39 lines
Diff to previous 1.579
Moved the guts of wikipedia_link to FIGRules so that SFXlate can use it.
Added POD documentation to some more methods.

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Fri Mar 16 04:33:22 2007 UTC (12 years, 8 months ago) by redwards
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Changes since 1.578: +1 -1 lines
Diff to previous 1.578
updating db_xref

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Thu Mar 15 15:31:03 2007 UTC (12 years, 8 months ago) by overbeek
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Changes since 1.577: +2 -1 lines
Diff to previous 1.577
problem using subsystem that does not exist

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Mon Mar 12 20:51:23 2007 UTC (12 years, 9 months ago) by olson
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Changes since 1.576: +78 -46 lines
Diff to previous 1.576
caching fix for taxonomy_of, support non-pegs in translate_pegs

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Wed Mar 7 01:47:05 2007 UTC (12 years, 9 months ago) by redwards
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Changes since 1.575: +47 -0 lines
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changes to gff3 file to be in line with BRC requirements

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Mon Feb 26 21:30:18 2007 UTC (12 years, 9 months ago) by olson
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Changes since 1.574: +19 -0 lines
Diff to previous 1.574
add function_of_quick that uses a cached prepared statement

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Mon Feb 26 20:47:01 2007 UTC (12 years, 9 months ago) by olson
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Changes since 1.573: +18 -0 lines
Diff to previous 1.573
add caching to build_tree_of_all

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Thu Feb 15 22:40:40 2007 UTC (12 years, 9 months ago) by paarmann
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Changes since 1.572: +35 -0 lines
Diff to previous 1.572
moved the method rewrite_db_xrefs here, because it's used in more than one place now

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Sun Feb 11 22:37:11 2007 UTC (12 years, 10 months ago) by overbeek
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Changes since 1.571: +49 -0 lines
Diff to previous 1.571
add PHOB.pm to support some phylogeny stuff

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Fri Feb 9 23:05:17 2007 UTC (12 years, 10 months ago) by paarmann
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Changes since 1.570: +1 -0 lines
Diff to previous 1.570
added quoting to catalyzes

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Fri Feb 9 22:51:33 2007 UTC (12 years, 10 months ago) by parrello
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Changes since 1.569: +63 -8 lines
Diff to previous 1.569
Added a user name to the custom attributes constructor and fixed some comments.

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Thu Feb 8 18:35:56 2007 UTC (12 years, 10 months ago) by overbeek
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Changes since 1.568: +91 -1 lines
Diff to previous 1.568
Added &get_dna_seq($fid). -- /gdp

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Tue Feb 6 16:24:39 2007 UTC (12 years, 10 months ago) by parrello
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Changes since 1.567: +1 -1 lines
Diff to previous 1.567
Changed call signature for the Custom Attributes constructor to pass in a user name.

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Mon Feb 5 23:05:21 2007 UTC (12 years, 10 months ago) by overbeek
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Changes since 1.566: +1 -1 lines
Diff to previous 1.566
strip trailing spaces off roles

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Mon Feb 5 03:12:11 2007 UTC (12 years, 10 months ago) by overbeek
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Changes since 1.565: +0 -1 lines
Diff to previous 1.565
initial, undebugged version of edit_feature.cgi

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Sat Feb 3 03:13:46 2007 UTC (12 years, 10 months ago) by overbeek
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Changes since 1.564: +1 -1 lines
Diff to previous 1.564
beef up error messages from the clearinghouse mon add_feature failure

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Sat Feb 3 02:50:49 2007 UTC (12 years, 10 months ago) by overbeek
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Changes since 1.563: +43 -17 lines
Diff to previous 1.563
fixes to add_features and display of non-peg features

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Tue Jan 30 00:26:33 2007 UTC (12 years, 10 months ago) by parrello
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Changes since 1.562: +3 -0 lines
Diff to previous 1.562
Added tracing for attributes.

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Thu Jan 25 02:37:37 2007 UTC (12 years, 10 months ago) by parrello
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Changes since 1.561: +0 -42 lines
Diff to previous 1.561
Removed support for full-text attribute search.

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Wed Jan 24 10:23:10 2007 UTC (12 years, 10 months ago) by parrello
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Changes since 1.560: +188 -33 lines
Diff to previous 1.560
Fixed a bug in the erase_attribute_entirely method.

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Mon Jan 22 20:03:42 2007 UTC (12 years, 10 months ago) by parrello
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Changes since 1.559: +237 -51 lines
Diff to previous 1.559
Added a find_attributes method for word-searching the attribute data base and converted search_index to use Glimpse for attribute searches.

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Fri Jan 19 17:42:43 2007 UTC (12 years, 10 months ago) by overbeek
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Changes since 1.558: +1 -1 lines
Diff to previous 1.558
fix on assignments with user of master

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Thu Jan 18 03:08:56 2007 UTC (12 years, 10 months ago) by overbeek
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Changes since 1.557: +8 -1 lines
Diff to previous 1.557
add comments to functions

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Fri Jan 12 21:24:27 2007 UTC (12 years, 11 months ago) by overbeek
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Changes since 1.556: +4 -4 lines
Diff to previous 1.556
add support for # as a comment initiator in gene functions

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Wed Jan 10 17:51:37 2007 UTC (12 years, 11 months ago) by overbeek
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Changes since 1.555: +1 -1 lines
Diff to previous 1.555
make assignments without user fail

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Sun Dec 31 22:45:33 2006 UTC (12 years, 11 months ago) by golsen
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Changes since 1.554: +6 -4 lines
Diff to previous 1.554
Change the key used in caching peg keys in get_peg_keys so that it
extends naturally to any feature type:  _attribute_keys->{ type }

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Sun Dec 31 22:23:57 2006 UTC (12 years, 11 months ago) by golsen
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Changes since 1.553: +28 -14 lines
Diff to previous 1.553
Add caching for get_peg_keys().  This speeds scripts that use it more than
once (e.g., subsys.cgi).

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Sat Dec 23 03:55:37 2006 UTC (12 years, 11 months ago) by overbeek
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Changes since 1.552: +2 -0 lines
Diff to previous 1.552
lock/unlock should annotate only on real change

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Sat Dec 23 03:43:49 2006 UTC (12 years, 11 months ago) by overbeek
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Changes since 1.551: +0 -1 lines
Diff to previous 1.551
add lock_subsys.cgi

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Wed Dec 13 23:36:00 2006 UTC (12 years, 11 months ago) by overbeek
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Changes since 1.550: +58 -28 lines
Diff to previous 1.550
fixes to add_feature, delete_feature, and replace_feature_with

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Sun Dec 10 20:30:01 2006 UTC (13 years ago) by parrello
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Changes since 1.549: +44 -29 lines
Diff to previous 1.549
Enhanced "get_attributes" so that you can specify a list of object IDs.

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Fri Dec 1 23:22:45 2006 UTC (13 years ago) by overbeek
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Changes since 1.548: +17 -1 lines
Diff to previous 1.548
add GO attribute genertation

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Thu Nov 30 23:04:16 2006 UTC (13 years ago) by overbeek
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Changes since 1.547: +15 -15 lines
Diff to previous 1.547
put in the fr2go stuff

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Wed Nov 29 21:20:31 2006 UTC (13 years ago) by hwang
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Changes since 1.546: +19 -0 lines
Diff to previous 1.546
added subroutine fr_to_go.
Give the routine a peg, and it returns the GO values

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Wed Nov 29 20:45:06 2006 UTC (13 years ago) by mkubal
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Changes since 1.545: +13 -0 lines
Diff to previous 1.545
new go_number_to_term method

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Tue Nov 28 17:00:05 2006 UTC (13 years ago) by overbeek
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Changes since 1.544: +1 -1 lines
Diff to previous 1.544
remove warning from boundaries_of and add genes_in_region to FIGV

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Tue Nov 21 18:20:53 2006 UTC (13 years ago) by overbeek
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Changes since 1.543: +0 -1 lines
Diff to previous 1.543
add initial version of FIGO.pm - OO services

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Thu Nov 16 22:08:46 2006 UTC (13 years ago) by parrello
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Changes since 1.542: +118 -88 lines
Diff to previous 1.542
Added support for more attribute methods.

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Thu Nov 16 19:57:30 2006 UTC (13 years ago) by parrello
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Changes since 1.541: +4 -1 lines
Diff to previous 1.541
Added an override available from the FIG_Config.pm so that the attribute migration can work properly.

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Wed Nov 15 11:51:19 2006 UTC (13 years ago) by parrello
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Changes since 1.540: +51 -47 lines
Diff to previous 1.540
Added support for the EraseAttribute method.

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Mon Nov 13 22:28:28 2006 UTC (13 years ago) by parrello
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Changes since 1.539: +2 -1 lines
Diff to previous 1.539
Made CustomAttributes a conditional import.

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Fri Nov 10 21:59:15 2006 UTC (13 years, 1 month ago) by parrello
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Changes since 1.538: +4 -1 lines
Diff to previous 1.538
Converted to new attribute system.

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Thu Nov 9 21:14:29 2006 UTC (13 years, 1 month ago) by parrello
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Changes since 1.537: +147 -128 lines
Diff to previous 1.537
Converted to use the new attribute system if it is available (which it isn't on most machines.

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Wed Nov 8 23:12:49 2006 UTC (13 years, 1 month ago) by parrello
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Changes since 1.536: +4 -29 lines
Diff to previous 1.536
Removed redundant copy of essentiality_data. Fixed an extraneous "my". Added some tracing.

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Tue Nov 7 19:56:44 2006 UTC (13 years, 1 month ago) by olson
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Changes since 1.535: +0 -1 lines
Diff to previous 1.535
Fix leftover <<<<< from a cvs update conflict marker.

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Tue Nov 7 16:21:11 2006 UTC (13 years, 1 month ago) by paczian
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Changes since 1.534: +35 -5 lines
Diff to previous 1.534
exchanged DISTINCTROW for equivalent DISTINCT which is supported by Postgress

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Sun Nov 5 03:51:58 2006 UTC (13 years, 1 month ago) by parrello
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Changes since 1.533: +1 -29 lines
Diff to previous 1.533
Removed a multiply-defined method. Fixed an extraneous "my".

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Thu Nov 2 17:12:19 2006 UTC (13 years, 1 month ago) by paczian
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Changes since 1.532: +305 -1 lines
Diff to previous 1.532
added methods for feature retrieval, neccessary for the genome browser

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Sat Oct 14 17:29:32 2006 UTC (13 years, 1 month ago) by parrello
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Changes since 1.531: +84 -0 lines
Diff to previous 1.531
Added "virulent" and "essential" methods.

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Wed Oct 11 18:19:06 2006 UTC (13 years, 2 months ago) by redwards
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Changes since 1.530: +25 -0 lines
Diff to previous 1.530
Adding tools to handle essentiality data for Sveta

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Tue Oct 10 18:37:14 2006 UTC (13 years, 2 months ago) by olson
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Changes since 1.529: +1 -1 lines
Diff to previous 1.529
readonly fixes; seed-run-job update to run from input file

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Wed Oct 4 18:53:32 2006 UTC (13 years, 2 months ago) by overbeek
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Changes since 1.528: +32 -0 lines
Diff to previous 1.528
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, 2 months ago) by paczian
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Changes since 1.527: +9 -1 lines
Diff to previous 1.527
added multiple value query capability to essentiality_data()

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Mon Oct 2 18:09:07 2006 UTC (13 years, 2 months ago) by paczian
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Changes since 1.526: +28 -0 lines
Diff to previous 1.526
added essentiality_data retrieval method

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Mon Oct 2 02:56:39 2006 UTC (13 years, 2 months ago) by parrello
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Changes since 1.525: +0 -63 lines
Diff to previous 1.525
Removed the config-based tracing.

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Wed Sep 27 13:39:16 2006 UTC (13 years, 2 months ago) by overbeek
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Changes since 1.524: +1 -1 lines
Diff to previous 1.524
allow spaces in abbr for roles in subsystems - fix pattern

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Mon Sep 25 18:49:25 2006 UTC (13 years, 2 months ago) by overbeek
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Changes since 1.523: +1 -1 lines
Diff to previous 1.523
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, 2 months ago) by overbeek
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Changes since 1.522: +3 -0 lines
Diff to previous 1.522
spiff up the lock/unlock stuff

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Mon Sep 18 02:19:34 2006 UTC (13 years, 2 months ago) by overbeek
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Changes since 1.521: +1 -1 lines
Diff to previous 1.521
promote remaining orfs in rapid_propagation

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Fri Sep 15 19:05:22 2006 UTC (13 years, 2 months ago) by overbeek
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Changes since 1.520: +4 -0 lines
Diff to previous 1.520
added a little error checking to lock/unlock fids

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Fri Sep 15 18:36:53 2006 UTC (13 years, 2 months ago) by overbeek
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Changes since 1.519: +82 -1 lines
Diff to previous 1.519
introduce locks on features to block assignments

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Thu Sep 14 21:09:14 2006 UTC (13 years, 2 months ago) by overbeek
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Changes since 1.518: +1 -1 lines
Diff to previous 1.518
Use DAS configs from FIG/var instead of in Data so no chance of being wiped out by mirror.

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Thu Sep 14 14:11:51 2006 UTC (13 years, 2 months ago) by parrello
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Changes since 1.517: +115 -133 lines
Diff to previous 1.517
Converted to provide BBH server support for Sprout.

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Wed Sep 6 13:59:26 2006 UTC (13 years, 3 months ago) by overbeek
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Changes since 1.516: +1 -0 lines
Diff to previous 1.516
remove debugging in all_bbhs

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Mon Sep 4 20:08:52 2006 UTC (13 years, 3 months ago) by redwards
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Changes since 1.515: +23 -5 lines
Diff to previous 1.515
adding a new method for environmental genomes

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Thu Aug 31 19:49:47 2006 UTC (13 years, 3 months ago) by olson
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Changes since 1.514: +32 -0 lines
Diff to previous 1.514
add bbh server support

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Thu Aug 31 18:06:42 2006 UTC (13 years, 3 months ago) by olson
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Changes since 1.513: +95 -0 lines
Diff to previous 1.513
network coupling server support

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Wed Aug 30 18:39:19 2006 UTC (13 years, 3 months ago) by redwards
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Changes since 1.512: +14 -1 lines
Diff to previous 1.512
Adding allow automatic update buttons

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Sat Aug 26 21:10:12 2006 UTC (13 years, 3 months ago) by overbeek
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Changes since 1.511: +5 -0 lines
Diff to previous 1.511
add add_to_subsystems

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Fri Aug 25 04:19:45 2006 UTC (13 years, 3 months ago) by redwards
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Changes since 1.510: +1 -0 lines
Diff to previous 1.510
ignoring evidence codes in the transaction logs

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Thu Aug 24 22:28:16 2006 UTC (13 years, 3 months ago) by redwards
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Changes since 1.509: +1 -1 lines
Diff to previous 1.509
killing error messages

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Wed Aug 23 20:53:50 2006 UTC (13 years, 3 months ago) by redwards
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Changes since 1.508: +2 -1 lines
Diff to previous 1.508
restoring the ev_code_cron to almost right

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Tue Aug 22 22:15:26 2006 UTC (13 years, 3 months ago) by redwards
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Changes since 1.507: +1 -1 lines
Diff to previous 1.507
hopefully fixing the evidence code bug

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Fri Aug 18 17:03:49 2006 UTC (13 years, 3 months ago) by overbeek
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Changes since 1.506: +4 -0 lines
Diff to previous 1.506
RAE: Adding docs to attributes

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Thu Aug 10 07:28:01 2006 UTC (13 years, 4 months ago) by parrello
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Changes since 1.505: +141 -8 lines
Diff to previous 1.505
Added methods to support the genome statistics page.
Updated some documentation.

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Tue Aug 8 22:19:37 2006 UTC (13 years, 4 months ago) by overbeek
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Changes since 1.504: +1 -2 lines
Diff to previous 1.504
RAE: updating IFC/DFC

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Sun Jul 30 01:43:56 2006 UTC (13 years, 4 months ago) by parrello
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Changes since 1.503: +54 -11 lines
Diff to previous 1.503
Fixed some comments.

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Tue Jul 25 22:07:01 2006 UTC (13 years, 4 months ago) by parrello
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Changes since 1.502: +1 -1 lines
Diff to previous 1.502
Fixed another bad return from coupling_and_evidence.

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Tue Jul 25 22:02:09 2006 UTC (13 years, 4 months ago) by parrello
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Changes since 1.501: +1 -1 lines
Diff to previous 1.501
Fixed bad return from coupling_and_evidence.

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Tue Jul 25 20:39:11 2006 UTC (13 years, 4 months ago) by overbeek
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Changes since 1.500: +5 -0 lines
Diff to previous 1.500
Added SameFuncWhy. TD

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Sat Jul 22 20:22:05 2006 UTC (13 years, 4 months ago) by overbeek
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Changes since 1.499: +10 -0 lines
Diff to previous 1.499
minor reformatting

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Thu Jul 20 19:22:53 2006 UTC (13 years, 4 months ago) by parrello
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Changes since 1.498: +5 -1 lines
Diff to previous 1.498
Fixed the documentation for bbhs.

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Thu Jul 20 18:24:07 2006 UTC (13 years, 4 months ago) by parrello
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Changes since 1.497: +13 -2 lines
Diff to previous 1.497
Updated documentation.

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Fri Jul 14 18:42:17 2006 UTC (13 years, 4 months ago) by mkubal
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Changes since 1.496: +1 -1 lines
Diff to previous 1.496
changed format of search results for attributes again

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Fri Jul 14 18:12:30 2006 UTC (13 years, 4 months ago) by mkubal
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Changes since 1.495: +6 -1 lines
Diff to previous 1.495
changed format of search results for attributes

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Thu Jul 13 06:50:08 2006 UTC (13 years, 5 months ago) by parrello
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Changes since 1.494: +25 -4 lines
Diff to previous 1.494
Enhanced "all_features" to match the SFXlate signature.

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Sat Jul 1 21:16:52 2006 UTC (13 years, 5 months ago) by overbeek
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Changes since 1.493: +20 -0 lines
Diff to previous 1.493
RAE: Adding BRC info

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Fri Jun 30 20:59:06 2006 UTC (13 years, 5 months ago) by parrello
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Changes since 1.492: +15 -12 lines
Diff to previous 1.492
Fixed read_all_annotations to return an empty list if no annotations file exists.

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Tue Jun 27 01:32:36 2006 UTC (13 years, 5 months ago) by parrello
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Changes since 1.491: +27 -3 lines
Diff to previous 1.491
Documented "uniprot_aliases_bulk".

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Tue Jun 27 00:58:24 2006 UTC (13 years, 5 months ago) by parrello
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Changes since 1.490: +25 -0 lines
Diff to previous 1.490
Added documentation for "function_of_bulk".

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Tue Jun 27 00:42:01 2006 UTC (13 years, 5 months ago) by parrello
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Changes since 1.489: +20 -0 lines
Diff to previous 1.489
Added documentation for the "is_genome" method.

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Sun Jun 25 07:38:35 2006 UTC (13 years, 5 months ago) by parrello
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Changes since 1.488: +2 -1 lines
Diff to previous 1.488
Fixed the deprecated-boundary-method warning message.

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Sun Jun 25 03:27:51 2006 UTC (13 years, 5 months ago) by parrello
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Changes since 1.487: +15 -11 lines
Diff to previous 1.487
Changed boundaries_of from a static to an instance method.

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Sun Jun 25 01:12:13 2006 UTC (13 years, 5 months ago) by parrello
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Changes since 1.486: +1 -1 lines
Diff to previous 1.486
*** empty log message ***

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Sun Jun 25 00:13:19 2006 UTC (13 years, 5 months ago) by parrello
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Changes since 1.485: +6 -130 lines
Diff to previous 1.485
Moved the network sims method to FIGRules.

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Sun Jun 18 06:48:42 2006 UTC (13 years, 5 months ago) by parrello
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Changes since 1.484: +821 -821 lines
Diff to previous 1.484
Fixed two compile warnings, cleaned out some tabs.

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Fri Jun 16 13:20:22 2006 UTC (13 years, 5 months ago) by overbeek
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Changes since 1.483: +103 -0 lines
Diff to previous 1.483
just add comments to ToCall.pm

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Tue Jun 13 23:32:15 2006 UTC (13 years, 6 months ago) by overbeek
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Changes since 1.482: +39 -6 lines
Diff to previous 1.482
RAE: moving PIRSF to links

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Tue Jun 13 03:10:03 2006 UTC (13 years, 6 months ago) by overbeek
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Changes since 1.481: +8 -8 lines
Diff to previous 1.481
Drat, I thought I'd already turned off the sim debug logging.

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Mon May 29 22:10:36 2006 UTC (13 years, 6 months ago) by overbeek
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Changes since 1.480: +1 -1 lines
Diff to previous 1.480
make all assignments master assignments

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Tue May 23 19:08:27 2006 UTC (13 years, 6 months ago) by overbeek
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Changes since 1.479: +34 -12 lines
Diff to previous 1.479
Robustify netowrk sims code; change the timeout on the LWP::UserAgent, retry 10 times on failure.

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Fri May 19 13:57:59 2006 UTC (13 years, 6 months ago) by olson
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Changes since 1.478: +2 -2 lines
Diff to previous 1.478
bugfix.

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Fri May 19 13:44:05 2006 UTC (13 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.477: +97 -33 lines
Diff to previous 1.477
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).

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Fri May 19 07:25:50 2006 UTC (13 years, 6 months ago) by parrello
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Changes since 1.476: +100 -0 lines
Diff to previous 1.476
Added a method to read annotations directly from the flat files.

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Thu May 18 12:27:21 2006 UTC (13 years, 6 months ago) by overbeek
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Changes since 1.475: +5 -2 lines
Diff to previous 1.475
add normalizded bit scores to BBHs

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Thu May 18 01:05:29 2006 UTC (13 years, 6 months ago) by parrello
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Changes since 1.474: +1 -1 lines
Diff to previous 1.474
Fixed a bad call to the Upstream function.

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Wed May 17 01:10:16 2006 UTC (13 years, 6 months ago) by overbeek
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Changes since 1.473: +6 -0 lines
Diff to previous 1.473
RAE: correcting error in transaction log

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Wed May 17 00:58:54 2006 UTC (13 years, 6 months ago) by overbeek
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Changes since 1.472: +1 -1 lines
Diff to previous 1.472
RAE: correcting error in transaction log

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Fri May 12 15:07:23 2006 UTC (13 years, 7 months ago) by olson
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Changes since 1.471: +31 -9 lines
Diff to previous 1.471
fix simserver bug

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Sun May 7 12:32:46 2006 UTC (13 years, 7 months ago) by overbeek
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Changes since 1.470: +3 -3 lines
Diff to previous 1.470
use Logs, not LOGS for GenomeLog

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Sun May 7 12:25:12 2006 UTC (13 years, 7 months ago) by overbeek
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Changes since 1.469: +2 -2 lines
Diff to previous 1.469
minor changes to logging correspondences

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Sun May 7 04:04:40 2006 UTC (13 years, 7 months ago) by overbeek
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Changes since 1.468: +7 -0 lines
Diff to previous 1.468
add ability to log arbitrary correspondences

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Sat May 6 19:25:14 2006 UTC (13 years, 7 months ago) by overbeek
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Changes since 1.467: +7 -0 lines
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add ability to show maps in log

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Fri May 5 16:43:09 2006 UTC (13 years, 7 months ago) by overbeek
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Changes since 1.466: +1 -1 lines
Diff to previous 1.466
crude version of show_log.cgi

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Fri May 5 14:38:00 2006 UTC (13 years, 7 months ago) by overbeek
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Changes since 1.465: +146 -36 lines
Diff to previous 1.465
added new logging

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Thu May 4 20:05:54 2006 UTC (13 years, 7 months ago) by olson
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Changes since 1.464: +28 -9 lines
Diff to previous 1.464
Turn off sim server support unless enabled in FIG_Config,for now.

add dont_mark_complete to fig add_genome.

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Tue May 2 16:09:44 2006 UTC (13 years, 7 months ago) by overbeek
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Changes since 1.463: +565 -3 lines
Diff to previous 1.463
attempt to commit figfam stuff

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Fri Apr 28 19:33:38 2006 UTC (13 years, 7 months ago) by overbeek
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Changes since 1.462: +1 -1 lines
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to avoid getting clobbered

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Fri Apr 28 18:09:18 2006 UTC (13 years, 7 months ago) by overbeek
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Changes since 1.461: +35 -0 lines
Diff to previous 1.461
must have a role index on subsystem_index, added is_NMPDR_genome, etc.

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Fri Apr 28 14:36:14 2006 UTC (13 years, 7 months ago) by overbeek
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Changes since 1.460: +1 -1 lines
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fixes to usable_subsystem

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Wed Apr 19 03:40:36 2006 UTC (13 years, 7 months ago) by parrello
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Changes since 1.459: +2 -77 lines
Diff to previous 1.459
Moved upstream region code into FIGRules so it can be used by Sprout.

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Thu Apr 13 02:44:28 2006 UTC (13 years, 8 months ago) by overbeek
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Changes since 1.458: +1 -1 lines
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pull master: off curator

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Thu Apr 13 01:33:23 2006 UTC (13 years, 8 months ago) by overbeek
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Changes since 1.457: +1 -1 lines
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leave master: on subsystem_curator

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Wed Apr 12 21:09:52 2006 UTC (13 years, 8 months ago) by overbeek
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Changes since 1.456: +3 -3 lines
Diff to previous 1.456
fix bug in perl, I think: watch out for make

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Wed Apr 12 20:36:45 2006 UTC (13 years, 8 months ago) by overbeek
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Changes since 1.455: +1 -1 lines
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usable_sub => usable_subsystem

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Wed Apr 12 20:25:50 2006 UTC (13 years, 8 months ago) by overbeek
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Changes since 1.454: +8 -0 lines
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minor changes to eliminate master:

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Wed Apr 12 13:10:38 2006 UTC (13 years, 8 months ago) by overbeek
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Changes since 1.453: +19 -1 lines
Diff to previous 1.453
fixes to making assignments based on consistency

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Wed Mar 29 20:41:33 2006 UTC (13 years, 8 months ago) by overbeek
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Changes since 1.452: +37 -3 lines
Diff to previous 1.452
Add support for readonly database instance, and for FileLocking module.

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Wed Mar 29 19:40:35 2006 UTC (13 years, 8 months ago) by parrello
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Changes since 1.451: +4 -3 lines
Diff to previous 1.451
Fixed some compiler warnings.

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Sun Mar 26 13:23:30 2006 UTC (13 years, 8 months ago) by parrello
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Changes since 1.450: +3 -3 lines
Diff to previous 1.450
Fixed some lines that were generating compiler warnings.

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Thu Mar 23 04:51:54 2006 UTC (13 years, 8 months ago) by overbeek
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Changes since 1.449: +26 -0 lines
Diff to previous 1.449
RAE: Yummy attributes

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Wed Mar 22 16:31:15 2006 UTC (13 years, 8 months ago) by overbeek
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Changes since 1.448: +17 -2 lines
Diff to previous 1.448
RAE: making 0 and -1 work

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Tue Mar 21 15:53:30 2006 UTC (13 years, 8 months ago) by overbeek
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Changes since 1.447: +146 -2 lines
Diff to previous 1.447
fixes to split_and_trim

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Sun Mar 19 21:30:55 2006 UTC (13 years, 8 months ago) by overbeek
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Changes since 1.446: +13 -3 lines
Diff to previous 1.446
RAE: Initial release of setting.cgi and format changes on subsys.cgi

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Fri Feb 24 19:42:18 2006 UTC (13 years, 9 months ago) by parrello
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Changes since 1.445: +156 -0 lines
Diff to previous 1.445
Added helper methodsa for the Markups object.

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Sat Feb 18 23:46:03 2006 UTC (13 years, 9 months ago) by overbeek
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Changes since 1.444: +2 -2 lines
Diff to previous 1.444
Fixed incorrect POD for &subsystems_for_genome(). -- /gdp

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Fri Feb 17 00:25:59 2006 UTC (13 years, 9 months ago) by parrello
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Changes since 1.443: +11 -7 lines
Diff to previous 1.443
Fixed to create user-data directories when they don't exist.

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Thu Feb 16 13:11:36 2006 UTC (13 years, 9 months ago) by overbeek
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Changes since 1.442: +13 -1 lines
Diff to previous 1.442
handle deleted fids in mapped_prot_ids

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Wed Feb 15 22:12:26 2006 UTC (13 years, 9 months ago) by overbeek
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Changes since 1.441: +131 -0 lines
Diff to previous 1.441
minor fixes to assignment for close strains

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Wed Feb 15 08:43:43 2006 UTC (13 years, 9 months ago) by parrello
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Changes since 1.440: +2 -2 lines
Diff to previous 1.440
Fixed a bug in the user-data handler

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Tue Feb 14 15:07:07 2006 UTC (13 years, 9 months ago) by overbeek
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Changes since 1.439: +43 -1 lines
Diff to previous 1.439
add logging on update operations

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Sat Feb 11 15:17:13 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.438: +22 -1 lines
Diff to previous 1.438
Corrected typo in variable name that wasaborting compilation. -- /gdp

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Thu Feb 9 20:42:51 2006 UTC (13 years, 10 months ago) by olson
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Changes since 1.437: +93 -1 lines
Diff to previous 1.437
Fix Rob's bug.

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Thu Feb 9 19:34:26 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.436: +19 -1 lines
Diff to previous 1.436
RAE: Updating organisms.cgi for more genomes in cyanoseed

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Sun Feb 5 01:08:16 2006 UTC (13 years, 10 months 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
RAE: Swtiched to using SQL Count for the number of contigs

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Fri Feb 3 18:42:27 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.434: +3 -1 lines
Diff to previous 1.434
$/ fixes

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Tue Jan 31 04:09:13 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.433: +32 -51 lines
Diff to previous 1.433
fix of clustering

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Mon Jan 30 19:36:04 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.432: +6 -2 lines
Diff to previous 1.432
use is_genome checks for subsystems?

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Sun Jan 29 19:48:31 2006 UTC (13 years, 10 months ago) by efrank
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Changes since 1.431: +10 -6 lines
Diff to previous 1.431
fixes for controlled vocab from NCI demo.  fixes to accomodate RAE's
changes in key_info.  commit independent of other pkgs.

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Sat Jan 28 04:23:47 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.430: +29 -1 lines
Diff to previous 1.430
RAE: Updating POM -- pieces of metabolism

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Wed Jan 25 18:57:05 2006 UTC (13 years, 10 months ago) by olson
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Changes since 1.429: +29 -9 lines
Diff to previous 1.429
Add more sim compute stuff.

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Mon Jan 23 19:20:54 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.428: +131 -4 lines
Diff to previous 1.428
changes to support dynamic sims and updates

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Wed Jan 18 17:41:13 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.427: +34 -0 lines
Diff to previous 1.427
RAE: Adding NMPDR checkbox to subsys.cgi

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Wed Jan 18 17:14:07 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.426: +36 -2 lines
Diff to previous 1.426
RAE: Adding NMPDR checkbox to subsys.cgi

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Mon Jan 16 00:22:42 2006 UTC (13 years, 10 months ago) by efrank
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Changes since 1.425: +49 -7 lines
Diff to previous 1.425
=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 (13 years, 10 months ago) by overbeek
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Changes since 1.424: +2 -2 lines
Diff to previous 1.424
correction to is_deleted_fid

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Sun Jan 15 15:11:46 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.423: +2 -0 lines
Diff to previous 1.423
is_deleted_fid should return 0, if the argument is not a fid

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Sat Jan 14 23:55:45 2006 UTC (13 years, 10 months ago) by golsen
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Changes since 1.422: +1 -1 lines
Diff to previous 1.422
Fine tuning of the add a feature software.  (Still more to come in dealing
with previously deleted features)

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Fri Jan 13 22:15:35 2006 UTC (13 years, 10 months ago) by golsen
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Changes since 1.421: +26 -16 lines
Diff to previous 1.421
Minor changes to assign_function:
   Convert user of form master:xxx to master (clearly the intent)
   Clean-up and clarify flow

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Fri Jan 13 20:22:39 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.420: +200 -70 lines
Diff to previous 1.420
fixes to deleted_features, replace_features_with, etc

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Fri Jan 13 06:54:49 2006 UTC (13 years, 10 months ago) by parrello
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Changes since 1.419: +8 -9 lines
Diff to previous 1.419
Converted the relative-to-absolute path code to use a system-independent PERL utility.

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Thu Jan 12 23:48:15 2006 UTC (13 years, 11 months ago) by golsen
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Changes since 1.418: +101 -52 lines
Diff to previous 1.418
Greatly enhanced error checking and reporting for add_feature.
Make sure feature does not already exist (return existing fid if
this is the case).

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Thu Jan 12 04:14:24 2006 UTC (13 years, 11 months ago) by golsen
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Changes since 1.417: +50 -20 lines
Diff to previous 1.417
Running version of adding a feature with a fid from the clearinghouse.

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Wed Jan 11 22:58:57 2006 UTC (13 years, 11 months ago) by olson
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Changes since 1.416: +30 -0 lines
Diff to previous 1.416
add_Feature additions

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Tue Jan 10 16:45:24 2006 UTC (13 years, 11 months ago) by olson
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Changes since 1.415: +10 -1 lines
Diff to previous 1.415
fix to verify_dir

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Thu Jan 5 01:16:45 2006 UTC (13 years, 11 months ago) by overbeek
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Changes since 1.414: +7 -10 lines
Diff to previous 1.414
RAE: Correcting what is meant by non-zero variant code

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Tue Jan 3 18:32:04 2006 UTC (13 years, 11 months ago) by efrank
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Changes since 1.413: +48 -0 lines
Diff to previous 1.413
add subsystems_having_organisms

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Mon Jan 2 23:58:49 2006 UTC (13 years, 11 months ago) by overbeek
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Changes since 1.412: +1 -1 lines
Diff to previous 1.412
RAE: Adding statistics to protein families

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Fri Dec 30 11:52:40 2005 UTC (13 years, 11 months ago) by heiko
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Changes since 1.411: +83 -0 lines
Diff to previous 1.411
added best_bbh_candidates_additional function

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Sat Dec 24 21:03:57 2005 UTC (13 years, 11 months ago) by overbeek
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Changes since 1.410: +4 -4 lines
Diff to previous 1.410
serious problem in setting max_expand in FIG::sims

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Wed Dec 21 23:51:50 2005 UTC (13 years, 11 months ago) by overbeek
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Changes since 1.409: +60 -2 lines
Diff to previous 1.409
RAE: Adding statistics to protein families

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Tue Dec 20 17:59:08 2005 UTC (13 years, 11 months ago) by overbeek
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Changes since 1.408: +39 -1 lines
Diff to previous 1.408
add abstract functional coupling

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Sat Dec 10 23:05:58 2005 UTC (14 years ago) by overbeek
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Changes since 1.407: +26 -0 lines
Diff to previous 1.407
RAE: extending protein families

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Sat Dec 10 18:08:17 2005 UTC (14 years ago) by overbeek
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Changes since 1.406: +20 -20 lines
Diff to previous 1.406
RAE: Changed attribute key to tag throughout

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Thu Dec 8 18:07:54 2005 UTC (14 years ago) by parrello
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Changes since 1.405: +13 -0 lines
Diff to previous 1.405
Added a method that can be used to determine whether the data is being taken from SEED or NMPDR.

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Tue Dec 6 06:57:17 2005 UTC (14 years ago) by overbeek
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Changes since 1.404: +28 -0 lines
Diff to previous 1.404
Updating protein families

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Mon Dec 5 19:06:30 2005 UTC (14 years ago) by olson
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Changes since 1.403: +17 -0 lines
Diff to previous 1.403
Added license words.

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Fri Dec 2 20:13:44 2005 UTC (14 years ago) by olson
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Changes since 1.402: +16 -1 lines
Diff to previous 1.402
Don't save absolute paths in file_table in database; rather, strip them on file2N and restore on N2file.

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Thu Dec 1 22:28:13 2005 UTC (14 years ago) by overbeek
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Changes since 1.401: +7 -1 lines
Diff to previous 1.401
Making attributes work for Ed

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Mon Nov 28 02:01:18 2005 UTC (14 years ago) by overbeek
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Changes since 1.400: +1 -1 lines
Diff to previous 1.400
minor fix in reconizing aliases

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Sun Nov 27 22:17:15 2005 UTC (14 years ago) by overbeek
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Changes since 1.399: +2 -2 lines
Diff to previous 1.399
correcting tag names

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Thu Nov 24 02:12:41 2005 UTC (14 years ago) by overbeek
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Changes since 1.398: +88 -33 lines
Diff to previous 1.398
updating subsys.cgi so that it works with attributes again. Quickly, this time

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Thu Nov 24 01:00:45 2005 UTC (14 years ago) by overbeek
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Changes since 1.397: +33 -5 lines
Diff to previous 1.397
correcting and extending get_distinct_keys

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Wed Nov 23 23:24:11 2005 UTC (14 years ago) by overbeek
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Changes since 1.396: +11 -3 lines
Diff to previous 1.396
correcting return when no data supplied

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Wed Nov 23 23:05:25 2005 UTC (14 years ago) by overbeek
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Changes since 1.395: +16 -8 lines
Diff to previous 1.395
removing error messages from attributes

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Wed Nov 23 20:34:59 2005 UTC (14 years ago) by overbeek
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Changes since 1.394: +287 -310 lines
Diff to previous 1.394
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

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Wed Nov 23 17:49:12 2005 UTC (14 years ago) by parrello
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Changes since 1.393: +609 -3 lines
Diff to previous 1.393
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 ago) by overbeek
Branch: MAIN
Changes since 1.392: +5 -4 lines
Diff to previous 1.392
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, 1 month ago) by efrank
Branch: MAIN
CVS Tags: caBIG-00-00-00
Changes since 1.391: +1 -1 lines
Diff to previous 1.391
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, 1 month ago) by efrank
Branch: MAIN
Changes since 1.390: +32 -0 lines
Diff to previous 1.390
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, 1 month ago) by parrello
Branch: MAIN
Changes since 1.389: +126 -36 lines
Diff to previous 1.389
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, 1 month ago) by olson
Branch: MAIN
Changes since 1.388: +1 -1 lines
Diff to previous 1.388
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, 1 month ago) by olson
Branch: MAIN
Changes since 1.387: +62 -0 lines
Diff to previous 1.387
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, 1 month ago) by efrank
Branch: MAIN
Changes since 1.386: +16 -1 lines
Diff to previous 1.386
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, 1 month ago) by efrank
Branch: MAIN
Changes since 1.385: +37 -4 lines
Diff to previous 1.385
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, 1 month ago) by efrank
Branch: MAIN
Changes since 1.384: +7 -3 lines
Diff to previous 1.384
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, 1 month ago) by efrank
Branch: MAIN
Changes since 1.383: +76 -0 lines
Diff to previous 1.383
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, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.382: +45 -10 lines
Diff to previous 1.382
protein families again

Revision 1.382 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 24 21:50:35 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.381: +40 -0 lines
Diff to previous 1.381
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, 1 month ago) by mkubal
Branch: MAIN
Changes since 1.380: +10 -4 lines
Diff to previous 1.380
fixed key_info

Revision 1.380 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 22 17:43:49 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.379: +41 -14 lines
Diff to previous 1.379
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, 1 month ago) by parrello
Branch: MAIN
Changes since 1.378: +171 -57 lines
Diff to previous 1.378
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, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.377: +12 -2 lines
Diff to previous 1.377
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, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.376: +14 -2 lines
Diff to previous 1.376
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, 2 months ago) by parrello
Branch: MAIN
Changes since 1.375: +137 -1 lines
Diff to previous 1.375
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, 2 months ago) by efrank
Branch: MAIN
Changes since 1.374: +24 -0 lines
Diff to previous 1.374
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, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.373: +1 -1 lines
Diff to previous 1.373
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, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.372: +17 -2 lines
Diff to previous 1.372
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, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.371: +47 -0 lines
Diff to previous 1.371
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, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.370: +0 -2 lines
Diff to previous 1.370
remove debug

Revision 1.370 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 5 20:34:02 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-dataload-0
Changes since 1.369: +71 -8 lines
Diff to previous 1.369
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, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.368: +4 -1 lines
Diff to previous 1.368
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, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.367: +6 -2 lines
Diff to previous 1.367
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, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.366: +19 -0 lines
Diff to previous 1.366
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, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.365: +20 -0 lines
Diff to previous 1.365
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, 3 months ago) by parrello
Branch: MAIN
Changes since 1.364: +1816 -1816 lines
Diff to previous 1.364
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, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.363: +23 -5 lines
Diff to previous 1.363
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, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.362: +3 -2 lines
Diff to previous 1.362
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, 3 months ago) by olson
Branch: MAIN
Changes since 1.361: +2 -1 lines
Diff to previous 1.361
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, 3 months ago) by olson
Branch: MAIN
Changes since 1.360: +117 -27 lines
Diff to previous 1.360
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, 3 months ago) by olson
Branch: MAIN
Changes since 1.359: +2 -5 lines
Diff to previous 1.359
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, 3 months ago) by olson
Branch: MAIN
Changes since 1.358: +129 -0 lines
Diff to previous 1.358
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, 3 months ago) by olson
Branch: MAIN
Changes since 1.357: +12 -3 lines
Diff to previous 1.357
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, 3 months ago) by olson
Branch: MAIN
Changes since 1.356: +95 -14 lines
Diff to previous 1.356
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, 3 months ago) by olson
Branch: MAIN
Changes since 1.355: +96 -9 lines
Diff to previous 1.355
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, 3 months ago) by parrello
Branch: MAIN
Changes since 1.354: +191 -64 lines
Diff to previous 1.354
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, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.353: +1 -1 lines
Diff to previous 1.353
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, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.352: +20 -2 lines
Diff to previous 1.352
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, 3 months ago) by redwards
Branch: MAIN
Changes since 1.351: +5 -3 lines
Diff to previous 1.351
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, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.350: +2 -1 lines
Diff to previous 1.350
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, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.349: +5 -3 lines
Diff to previous 1.349
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, 3 months ago) by redwards
Branch: MAIN
Changes since 1.348: +10 -6 lines
Diff to previous 1.348
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, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.347: +2 -0 lines
Diff to previous 1.347
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, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.346: +2 -1 lines
Diff to previous 1.346
NMPDR updates

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

Revision 1.345 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 15 21:34:53 2005 UTC (14 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.344: +12 -10 lines
Diff to previous 1.344
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, 3 months ago) by parrello
Branch: MAIN
Changes since 1.343: +1 -1 lines
Diff to previous 1.343
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, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.342: +6 -2 lines
Diff to previous 1.342
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, 4 months ago) by parrello
Branch: MAIN
Changes since 1.341: +1 -1 lines
Diff to previous 1.341
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, 4 months ago) by olson
Branch: MAIN
Changes since 1.340: +2 -1 lines
Diff to previous 1.340
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, 4 months ago) by parrello
Branch: MAIN
Changes since 1.339: +63 -34 lines
Diff to previous 1.339
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, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.338: +41 -0 lines
Diff to previous 1.338
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, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.337: +2 -1 lines
Diff to previous 1.337
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, 4 months ago) by redwards
Branch: MAIN
Changes since 1.336: +30 -3 lines
Diff to previous 1.336
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, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.335: +64 -5 lines
Diff to previous 1.335
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, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.334: +7 -3 lines
Diff to previous 1.334
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, 4 months ago) by olson
Branch: MAIN
Changes since 1.333: +8 -3 lines
Diff to previous 1.333
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, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.332: +5 -1 lines
Diff to previous 1.332
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, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.331: +20 -12 lines
Diff to previous 1.331
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, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.330: +10 -3 lines
Diff to previous 1.330
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, 4 months ago) by olson
Branch: MAIN
Changes since 1.329: +24 -13 lines
Diff to previous 1.329
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, 4 months ago) by olson
Branch: MAIN
Changes since 1.328: +47 -1 lines
Diff to previous 1.328
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, 4 months ago) by parrello
Branch: MAIN
Changes since 1.327: +42 -42 lines
Diff to previous 1.327
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, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.326: +7 -8 lines
Diff to previous 1.326
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, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.325: +21 -16 lines
Diff to previous 1.325
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, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.324: +30 -9 lines
Diff to previous 1.324
 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, 4 months ago) by olson
Branch: MAIN
Changes since 1.323: +40 -0 lines
Diff to previous 1.323
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, 4 months ago) by olson
Branch: MAIN
Changes since 1.322: +27 -2 lines
Diff to previous 1.322
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, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.321: +72 -0 lines
Diff to previous 1.321
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, 4 months ago) by parrello
Branch: MAIN
Changes since 1.320: +1 -3 lines
Diff to previous 1.320
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, 4 months ago) by parrello
Branch: MAIN
Changes since 1.319: +380 -111 lines
Diff to previous 1.319
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, 4 months ago) by mkubal
Branch: MAIN
Changes since 1.318: +1 -1 lines
Diff to previous 1.318
7-26-05

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Sat Jul 23 19:47:36 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.317: +3 -1 lines
Diff to previous 1.317
altering location in FIG.pm

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Tue Jul 19 16:29:35 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.316: +4 -4 lines
Diff to previous 1.316
standardize returned DNA to lower case, as per GJO's request. -- /gdp

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Tue Jul 19 16:14:21 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
Changes since 1.315: +2 -1 lines
Diff to previous 1.315
More final touches for Attributes code

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Tue Jul 19 05:26:12 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
Changes since 1.314: +2 -2 lines
Diff to previous 1.314
minor chagnes to attributes

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Tue Jul 19 04:54:21 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
Changes since 1.313: +36 -9 lines
Diff to previous 1.313
Updating attributes code in seed

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Mon Jul 18 03:12:11 2005 UTC (14 years, 4 months ago) by redwards
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Changes since 1.312: +54 -9 lines
Diff to previous 1.312
Updating attributes code

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Sun Jul 17 19:04:27 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
Changes since 1.311: +63 -29 lines
Diff to previous 1.311
Making attributes interface work

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Wed Jul 13 01:49:54 2005 UTC (14 years, 5 months ago) by redwards
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Changes since 1.310: +22 -37 lines
Diff to previous 1.310
minor changes to subsys_vectors to allow complete genomes

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Tue Jul 12 22:10:07 2005 UTC (14 years, 5 months ago) by redwards
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Changes since 1.309: +14 -0 lines
Diff to previous 1.309
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, 5 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
Changing attributes and modifying protein.cgi with show/hides

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Tue Jul 12 00:34:32 2005 UTC (14 years, 5 months ago) by overbeek
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Changes since 1.307: +16 -16 lines
Diff to previous 1.307
updates to build protein families

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Sun Jul 10 04:59:11 2005 UTC (14 years, 5 months ago) by redwards
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Changes since 1.306: +8 -1 lines
Diff to previous 1.306
making index_subsystems work

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Sat Jul 9 21:46:15 2005 UTC (14 years, 5 months ago) by redwards
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Changes since 1.305: +17 -0 lines
Diff to previous 1.305
added index subsystems to subsys.cgi

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Fri Jul 1 02:09:16 2005 UTC (14 years, 5 months ago) by redwards
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Changes since 1.304: +46 -26 lines
Diff to previous 1.304
Changed proteinfamilies.cgi

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Wed Jun 29 15:06:12 2005 UTC (14 years, 5 months ago) by olson
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CVS Tags: merge-trunktag-bobdev_news-2
Changes since 1.303: +2 -2 lines
Diff to previous 1.303
Tweak tracing.

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Wed Jun 29 00:28:01 2005 UTC (14 years, 5 months ago) by redwards
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Changes since 1.302: +88 -5 lines
Diff to previous 1.302
Initial release of proteinfamilies.cgi into the wild

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Tue Jun 28 17:25:04 2005 UTC (14 years, 5 months ago) by redwards
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Changes since 1.301: +20 -0 lines
Diff to previous 1.301
commiting FIG.pm::clean_spaces to remove leading, trailing, and extra spaces. Please use it

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Fri Jun 24 21:39:14 2005 UTC (14 years, 5 months ago) by parrello
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CVS Tags: merge-trunktag-bobdev_news-1
Changes since 1.300: +16 -17 lines
Diff to previous 1.300
Fixed the environment-variable tracing so that it does not override previous tracing options if they were set.

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Thu Jun 23 21:24:48 2005 UTC (14 years, 5 months ago) by overbeek
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Changes since 1.299: +5 -0 lines
Diff to previous 1.299
finally

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Thu Jun 23 19:35:07 2005 UTC (14 years, 5 months ago) by olson
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Changes since 1.298: +33 -2 lines
Diff to previous 1.298
Add some more gene  name mapping stuff.

Add Tracer environment variable for affecting tracing.

Fix typo in invocation of load_coupling.

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Wed Jun 22 21:00:24 2005 UTC (14 years, 5 months ago) by parrello
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Changes since 1.297: +514 -531 lines
Diff to previous 1.297
Replaced tabs with spaces to make indenting device-independent.
Moved "Open" and "OpenDir" to the Tracer.pm module.
Added more POD documentation.

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Mon Jun 20 21:58:56 2005 UTC (14 years, 5 months ago) by olson
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Changes since 1.296: +63 -0 lines
Diff to previous 1.296
Add genome/peg id mapping routines. (For functional coupling support).

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Mon Jun 20 17:08:32 2005 UTC (14 years, 5 months ago) by overbeek
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Changes since 1.295: +1 -1 lines
Diff to previous 1.295
add new protein family routines

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Mon Jun 20 17:04:45 2005 UTC (14 years, 5 months ago) by overbeek
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Changes since 1.294: +72 -11 lines
Diff to previous 1.294
add new protein family routines

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Mon Jun 20 04:03:44 2005 UTC (14 years, 5 months ago) by overbeek
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Changes since 1.293: +6 -1 lines
Diff to previous 1.293
disable old protein families

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Mon Jun 13 16:43:48 2005 UTC (14 years, 6 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
Ross change commit after cleanup

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Mon Jun 13 09:32:09 2005 UTC (14 years, 6 months ago) by parrello
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Changes since 1.291: +160 -2 lines
Diff to previous 1.291
Added Open and OpenDir methods for streamlining file and directory operations.

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Fri Jun 10 16:08:52 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.290: +7 -7 lines
Diff to previous 1.290
fixes to cached pin displays

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Fri Jun 10 15:36:37 2005 UTC (14 years, 6 months ago) by redwards
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Changes since 1.289: +7 -9 lines
Diff to previous 1.289
adding correspondence.cgi

Revision 1.289 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 9 20:03:15 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.288: +95 -1 lines
Diff to previous 1.288
re-add couipling routines

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Thu Jun 9 18:39:05 2005 UTC (14 years, 6 months ago) by parrello
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Changes since 1.287: +39 -28 lines
Diff to previous 1.287
*** empty log message ***

Revision 1.287 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 9 05:36:30 2005 UTC (14 years, 6 months ago) by parrello
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Changes since 1.286: +2333 -1628 lines
Diff to previous 1.286
*** empty log message ***

Revision 1.286 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 8 23:05:21 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.285: +7 -30 lines
Diff to previous 1.285
major change to BBHs (use precomputed)

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Tue Jun 7 16:41:23 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.284: +2 -1 lines
Diff to previous 1.284
Fixed typo in &hypo(), and added new rule. -- /gdp

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Wed Jun 1 01:18:50 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.283: +91 -12 lines
Diff to previous 1.283
install precomputed functional coupling data

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Sun May 29 13:33:56 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.282: +24 -0 lines
Diff to previous 1.282
add test for existence of relation that works only under Postgres

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Wed May 25 18:58:27 2005 UTC (14 years, 6 months ago) by redwards
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Changes since 1.281: +39 -0 lines
Diff to previous 1.281
added subsystems_roles method to FIG.pm

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Wed May 25 16:07:23 2005 UTC (14 years, 6 months ago) by olson
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Changes since 1.280: +92 -0 lines
Diff to previous 1.280
Code for similarity request export.

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Fri May 20 11:23:07 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.279: +1 -1 lines
Diff to previous 1.279
fix bug in search_indexes

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Tue May 17 16:04:08 2005 UTC (14 years, 6 months ago) by olson
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Changes since 1.278: +307 -19 lines
Diff to previous 1.278
Bundle of misc bob changes, including sim computation code and search-for-substring.

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Tue May 10 12:03:39 2005 UTC (14 years, 7 months ago) by overbeek
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Changes since 1.277: +4 -1 lines
Diff to previous 1.277
fixes to using trees under subsystems

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Thu May 5 17:43:03 2005 UTC (14 years, 7 months ago) by overbeek
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Changes since 1.276: +5 -3 lines
Diff to previous 1.276
fix indexing search code

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Tue May 3 21:03:38 2005 UTC (14 years, 7 months ago) by overbeek
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Changes since 1.275: +1 -1 lines
Diff to previous 1.275
add css generation modules

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Fri Apr 29 16:43:29 2005 UTC (14 years, 7 months ago) by overbeek
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Changes since 1.274: +1 -0 lines
Diff to previous 1.274
add assign_to_close_strains

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Mon Apr 18 18:29:31 2005 UTC (14 years, 7 months ago) by mkubal
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Changes since 1.273: +2 -3 lines
Diff to previous 1.273
revised on Monday

Revision 1.273 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 18 06:26:04 2005 UTC (14 years, 7 months ago) by redwards
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Changes since 1.272: +1 -1 lines
Diff to previous 1.272
minor fix to select tag/values

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Mon Apr 18 06:19:40 2005 UTC (14 years, 7 months ago) by redwards
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Changes since 1.271: +3 -1 lines
Diff to previous 1.271
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, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.270: +2 -0 lines
Diff to previous 1.270
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, 7 months ago) by golsen
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Changes since 1.269: +7 -27 lines
Diff to previous 1.269
Fix bunged index search

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Thu Apr 14 18:52:19 2005 UTC (14 years, 7 months ago) by mkubal
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Changes since 1.268: +2 -1 lines
Diff to previous 1.268
search_index now returns attributes

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Wed Apr 13 15:37:30 2005 UTC (14 years, 8 months ago) by redwards
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Changes since 1.267: +30 -21 lines
Diff to previous 1.267
changed genome stats to show attributes

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Sun Apr 10 03:32:30 2005 UTC (14 years, 8 months ago) by golsen
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Changes since 1.266: +1 -1 lines
Diff to previous 1.266
Re-enable "duplicates" in sims.  Multiple regions of matching is common
in eukaryotic sequences, and only seeing one is disorienting.

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Fri Apr 8 20:22:23 2005 UTC (14 years, 8 months ago) by redwards
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Changes since 1.265: +10 -15 lines
Diff to previous 1.265
changed tag/value pairs completely. Ooops!

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Thu Apr 7 19:16:10 2005 UTC (14 years, 8 months ago) by redwards
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Changes since 1.264: +30 -15 lines
Diff to previous 1.264
many changes to key/value pairs to make them work

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Sun Apr 3 19:43:41 2005 UTC (14 years, 8 months ago) by redwards
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Changes since 1.263: +5 -2 lines
Diff to previous 1.263
changing pir corresepondence

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Sun Apr 3 19:11:11 2005 UTC (14 years, 8 months ago) by redwards
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Changes since 1.262: +97 -8 lines
Diff to previous 1.262
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.

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Sat Apr 2 11:56:12 2005 UTC (14 years, 8 months ago) by overbeek
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Changes since 1.261: +2 -0 lines
Diff to previous 1.261
add update_subsys_conflicts to fig.pl

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Thu Mar 31 18:05:28 2005 UTC (14 years, 8 months ago) by overbeek
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Changes since 1.260: +3 -0 lines
Diff to previous 1.260
fix to asses_completeness

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Wed Mar 30 19:58:20 2005 UTC (14 years, 8 months ago) by olson
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Changes since 1.259: +27 -0 lines
Diff to previous 1.259
Add genome_with_md5sum.

Warn on FigGFF errors only if you're bob.

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Wed Mar 30 15:53:37 2005 UTC (14 years, 8 months ago) by redwards
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Changes since 1.258: +4 -4 lines
Diff to previous 1.258
changing attributes returned back to variables

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Tue Mar 29 20:41:17 2005 UTC (14 years, 8 months ago) by redwards
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Changes since 1.257: +7 -5 lines
Diff to previous 1.257
minor changes to rae.cgi

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Tue Mar 29 19:29:39 2005 UTC (14 years, 8 months ago) by overbeek
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Changes since 1.256: +3 -2 lines
Diff to previous 1.256
add make_pu from ids and seqs

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Tue Mar 29 18:42:26 2005 UTC (14 years, 8 months ago) by overbeek
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Changes since 1.255: +7 -0 lines
Diff to previous 1.255
broaden set of acceptable aliases as dbxrefs

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Wed Mar 23 18:54:39 2005 UTC (14 years, 8 months ago) by golsen
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Changes since 1.254: +1 -1 lines
Diff to previous 1.254
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.

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Mon Mar 21 22:01:22 2005 UTC (14 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.253: +0 -1 lines
Diff to previous 1.253
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.

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Mon Mar 21 21:39:32 2005 UTC (14 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.252: +7 -4 lines
Diff to previous 1.252
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.

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Mon Mar 21 18:33:49 2005 UTC (14 years, 8 months ago) by overbeek
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Changes since 1.251: +1 -1 lines
Diff to previous 1.251
fix to best_bbh_candidates and added fill_subsys

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Sun Mar 20 22:26:16 2005 UTC (14 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.250: +36 -2 lines
Diff to previous 1.250
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).

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Sat Mar 19 01:27:13 2005 UTC (14 years, 8 months ago) by overbeek
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Changes since 1.249: +4 -0 lines
Diff to previous 1.249
update hypo

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Wed Mar 16 17:56:22 2005 UTC (14 years, 8 months ago) by golsen
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Changes since 1.248: +2 -2 lines
Diff to previous 1.248
Fix end condition test on expand_raw_sims to promptly return.

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Wed Mar 16 15:17:45 2005 UTC (14 years, 8 months ago) by overbeek
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Changes since 1.247: +1 -0 lines
Diff to previous 1.247
remove ddd: in front of some organisms (mostly uniprot)

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Wed Mar 16 15:11:56 2005 UTC (14 years, 8 months ago) by overbeek
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Changes since 1.246: +2 -1 lines
Diff to previous 1.246
change spaces to _s in subsystem names

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Wed Mar 16 00:18:09 2005 UTC (14 years, 8 months ago) by olson
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Changes since 1.245: +1 -1 lines
Diff to previous 1.245
make the gff stuff work again.

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Tue Mar 15 23:56:53 2005 UTC (14 years, 8 months ago) by olson
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Changes since 1.244: +76 -1 lines
Diff to previous 1.244
Put the FigGFF code in a require for now.

Add fast anno lookup.

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Mon Mar 14 19:17:37 2005 UTC (14 years, 9 months ago) by olson
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Changes since 1.243: +13 -0 lines
Diff to previous 1.243
Add general-purpose GFF writing stuff.

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Mon Mar 14 02:04:44 2005 UTC (14 years, 9 months ago) by golsen
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Changes since 1.242: +3 -3 lines
Diff to previous 1.242
Minor fix in expand_raw_sims so that it stops when it should

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Sun Mar 13 00:55:21 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.241: +59 -17 lines
Diff to previous 1.241
Initial commit of organisms.cgi which allows separate entry pages for different groups of organisms

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Fri Mar 11 22:03:13 2005 UTC (14 years, 9 months ago) by overbeek
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Changes since 1.240: +10 -2 lines
Diff to previous 1.240
fix for mapped_prot_ids

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Fri Mar 11 04:11:30 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.239: +4 -5 lines
Diff to previous 1.239
Making tag/value pairs work

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Fri Mar 11 03:04:32 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.238: +12 -5 lines
Diff to previous 1.238
Making tag/value pairs work

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Fri Mar 11 01:04:32 2005 UTC (14 years, 9 months ago) by golsen
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Changes since 1.237: +247 -122 lines
Diff to previous 1.237
Many new options for similarities

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Tue Mar 8 21:14:53 2005 UTC (14 years, 9 months ago) by olson
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Changes since 1.236: +19 -1 lines
Diff to previous 1.236
Add contig_md5sum.

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Tue Mar 8 21:06:04 2005 UTC (14 years, 9 months ago) by olson
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Changes since 1.235: +30 -0 lines
Diff to previous 1.235
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.

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Sun Mar 6 15:10:02 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.234: +1 -0 lines
Diff to previous 1.234
disconnect get_attributes until I can talk to Rob

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Sat Mar 5 04:29:59 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.233: +10 -2 lines
Diff to previous 1.233
added highlight by peg attribute to subsystem

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Fri Mar 4 23:16:42 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.232: +23 -17 lines
Diff to previous 1.232
tweaks to coloring ss by oa

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Fri Mar 4 22:37:06 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.231: +128 -13 lines
Diff to previous 1.231
Added color by organism attributes to subsystems page

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Fri Mar 4 18:29:21 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.230: +3 -0 lines
Diff to previous 1.230
Added attribute editing to the protein.cgi page

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Fri Mar 4 06:22:10 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.229: +204 -18 lines
Diff to previous 1.229
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 (14 years, 9 months ago) by overbeek
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Changes since 1.228: +51 -3 lines
Diff to previous 1.228
major changes in notion of function and load_attributes

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Sat Feb 26 19:49:59 2005 UTC (14 years, 9 months ago) by overbeek
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Changes since 1.227: +4 -0 lines
Diff to previous 1.227
filters for data mining

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Sat Feb 26 11:01:13 2005 UTC (14 years, 9 months ago) by overbeek
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Changes since 1.226: +20 -3 lines
Diff to previous 1.226
add reset_curator.cgi

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Wed Feb 16 18:59:20 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.225: +3 -1 lines
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highlight subsystems with no genomes attached

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Sat Feb 12 18:41:04 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.224: +1 -1 lines
Diff to previous 1.224
Fix subsystem_classification in FIG.pm

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Sat Feb 12 18:18:14 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.223: +8 -17 lines
Diff to previous 1.223
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.

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Sat Feb 12 17:20:43 2005 UTC (14 years, 9 months ago) by redwards
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Changes since 1.222: +6 -5 lines
Diff to previous 1.222
minor change to FIG::subsystem_classification

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Sat Feb 12 06:49:27 2005 UTC (14 years, 10 months ago) by redwards
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Changes since 1.221: +3 -3 lines
Diff to previous 1.221
Initial addition of subsys_summary.cgi and minor modification of FIG.pm

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Sat Feb 12 05:38:43 2005 UTC (14 years, 10 months ago) by redwards
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Changes since 1.220: +6 -3 lines
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changes to subsystem_classification

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Sat Feb 12 04:51:47 2005 UTC (14 years, 10 months ago) by overbeek
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Changes since 1.219: +9 -14 lines
Diff to previous 1.219
fix routine for locating candidates for a role in a genome

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Sat Feb 12 04:08:00 2005 UTC (14 years, 10 months ago) by redwards
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Changes since 1.218: +35 -0 lines
Diff to previous 1.218
Minor changes to pir.cgi and added subsystem_classification to FIG.pm

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Sat Feb 12 04:01:01 2005 UTC (14 years, 10 months ago) by overbeek
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Changes since 1.217: +20 -72 lines
Diff to previous 1.217
many fixes to extending subsystems

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Sat Feb 12 03:50:04 2005 UTC (14 years, 10 months ago) by redwards
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Changes since 1.216: +26 -0 lines
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Add some pod to FIG.pm

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Sat Feb 12 03:00:57 2005 UTC (14 years, 10 months ago) by mkubal
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Changes since 1.215: +19 -15 lines
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update

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Fri Feb 11 06:34:05 2005 UTC (14 years, 10 months ago) by mkubal
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Changes since 1.214: +85 -3 lines
Diff to previous 1.214
added all_for_genome, etc

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Thu Feb 10 13:33:37 2005 UTC (14 years, 10 months ago) by olson
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Changes since 1.213: +26 -0 lines
Diff to previous 1.213
Add subsystems_for_genome.

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Mon Feb 7 00:27:34 2005 UTC (14 years, 10 months ago) by parrello
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Changes since 1.212: +76 -14 lines
Diff to previous 1.212
no message

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Sat Feb 5 04:12:35 2005 UTC (14 years, 10 months ago) by overbeek
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Changes since 1.211: +1 -1 lines
Diff to previous 1.211
head -1 should be head -n 1

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Mon Jan 31 14:01:07 2005 UTC (14 years, 10 months ago) by overbeek
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Changes since 1.210: +2 -1 lines
Diff to previous 1.210
add pegs_in_subsystems

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Thu Jan 27 00:31:21 2005 UTC (14 years, 10 months ago) by parrello
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Changes since 1.209: +133 -68 lines
Diff to previous 1.209
no message

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Wed Jan 26 18:37:58 2005 UTC (14 years, 10 months ago) by overbeek
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Changes since 1.208: +8 -10 lines
Diff to previous 1.208
fix bugs introduced into by_alias function

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Sun Jan 23 00:38:22 2005 UTC (14 years, 10 months ago) by golsen
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Changes since 1.207: +3 -2 lines
Diff to previous 1.207
Time stamp individual load steps

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Tue Jan 18 21:06:41 2005 UTC (14 years, 10 months ago) by olson
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Changes since 1.206: +1 -1 lines
Diff to previous 1.206
fix dumb typo.

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Tue Jan 18 21:02:45 2005 UTC (14 years, 10 months ago) by olson
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Changes since 1.205: +15 -0 lines
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Add peg_in_gendb and genome_in_gendb

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Tue Jan 18 20:55:32 2005 UTC (14 years, 10 months ago) by olson
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Changes since 1.204: +6 -0 lines
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add get_system_name() call.

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Sun Jan 16 16:05:20 2005 UTC (14 years, 10 months ago) by overbeek
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Changes since 1.203: +16 -2 lines
Diff to previous 1.203
fix to scoring fc

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Thu Jan 13 17:32:51 2005 UTC (14 years, 10 months ago) by olson
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Changes since 1.202: +1 -1 lines
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More fixes for Sprout integration.

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Wed Jan 12 21:22:08 2005 UTC (14 years, 11 months ago) by olson
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Changes since 1.201: +2 -1 lines
Diff to previous 1.201
sprout debugging

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Wed Jan 12 20:18:56 2005 UTC (14 years, 11 months ago) by parrello
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Changes since 1.200: +13 -12 lines
Diff to previous 1.200
no message

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Wed Jan 12 20:08:30 2005 UTC (14 years, 11 months ago) by parrello
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Changes since 1.199: +297 -301 lines
Diff to previous 1.199
no message

Revision 1.199 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 11 18:59:39 2005 UTC (14 years, 11 months ago) by olson
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Changes since 1.198: +1 -1 lines
Diff to previous 1.198
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.

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Sun Jan 9 17:15:12 2005 UTC (14 years, 11 months ago) by overbeek
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Changes since 1.197: +1 -1 lines
Diff to previous 1.197
fix disambiguating maps

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Sat Jan 8 18:22:00 2005 UTC (14 years, 11 months ago) by overbeek
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Changes since 1.196: +1 -1 lines
Diff to previous 1.196
add check to assign_function

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Fri Jan 7 18:55:21 2005 UTC (14 years, 11 months ago) by olson
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Changes since 1.195: +2 -2 lines
Diff to previous 1.195
add option to not create a release info file to get_release_info()

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Wed Jan 5 16:19:44 2005 UTC (14 years, 11 months ago) by olson
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Changes since 1.194: +78 -4 lines
Diff to previous 1.194
p2p changes.

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Mon Jan 3 02:23:12 2005 UTC (14 years, 11 months ago) by overbeek
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Changes since 1.193: +0 -1 lines
Diff to previous 1.193
fix stupid error in cleaning up aliases

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Mon Jan 3 02:21:08 2005 UTC (14 years, 11 months ago) by overbeek
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Changes since 1.192: +4 -27 lines
Diff to previous 1.192
automatically generate aliases from mapped IDs

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Wed Dec 29 17:59:36 2004 UTC (14 years, 11 months ago) by overbeek
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Changes since 1.191: +1 -1 lines
Diff to previous 1.191
minor fix to FIG.pm and addition of generate_kegg_map_ec_tables

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Thu Dec 16 22:57:43 2004 UTC (14 years, 11 months ago) by overbeek
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Changes since 1.190: +2 -1 lines
Diff to previous 1.190
fixes to assigned_function

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Wed Dec 15 02:04:34 2004 UTC (14 years, 11 months ago) by overbeek
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Changes since 1.189: +9 -5 lines
Diff to previous 1.189
allow set of seeks to cores for bbhs

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Mon Dec 13 19:24:15 2004 UTC (14 years, 11 months ago) by redwards
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Changes since 1.188: +4 -4 lines
Diff to previous 1.188
Minor changes to FIG.pm POD

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Fri Dec 10 07:04:39 2004 UTC (15 years ago) by redwards
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Changes since 1.187: +18 -0 lines
Diff to previous 1.187
Changes to subsys.cgi that warn if a subsystem doesn't exist

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Wed Dec 8 21:28:10 2004 UTC (15 years ago) by overbeek
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Changes since 1.186: +9 -2 lines
Diff to previous 1.186
raw time for annotations

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Mon Dec 6 18:25:18 2004 UTC (15 years ago) by olson
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Changes since 1.185: +1 -1 lines
Diff to previous 1.185
fix a comment

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Sun Dec 5 16:35:15 2004 UTC (15 years ago) by overbeek
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Changes since 1.184: +2 -2 lines
Diff to previous 1.184
add checking for subsystems

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Fri Dec 3 18:55:20 2004 UTC (15 years ago) by olson
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Changes since 1.183: +39 -2 lines
Diff to previous 1.183
Add subsystem_roles() method.
Add status callback to translate_pegs.
Remove setting of sticky bit in verify_dir.

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Wed Nov 10 22:10:22 2004 UTC (15 years, 1 month ago) by olson
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Changes since 1.182: +46 -0 lines
Diff to previous 1.182
add higher-level construct support

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Fri Nov 5 14:57:59 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.181: +0 -1 lines
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untested changes to extract_genomes - copy-all-but in Global

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Thu Nov 4 18:27:29 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.180: +4 -1 lines
Diff to previous 1.180
allow external IDs on subsystem displays

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Wed Nov 3 17:46:17 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.179: +7 -0 lines
Diff to previous 1.179
add is_complete function to FIG.pm

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Tue Nov 2 14:45:31 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.178: +81 -1 lines
Diff to previous 1.178
fix bug in subsys.cgi and add Literature to Global

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Mon Oct 25 20:59:34 2004 UTC (15 years, 1 month ago) by redwards
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Changes since 1.177: +8 -0 lines
Diff to previous 1.177
Adding  some pod

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Sat Oct 23 21:41:38 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.176: +1 -1 lines
Diff to previous 1.176
stupid error in FIG.pm

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Sat Oct 23 19:58:28 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.175: +2 -2 lines
Diff to previous 1.175
fix bound in find_role_in_org

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Fri Oct 22 19:30:37 2004 UTC (15 years, 1 month ago) by heiko
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Changes since 1.174: +23 -0 lines
Diff to previous 1.174
added function
all_features_detailed
will return fig_id, location, type as array

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Fri Oct 22 16:55:42 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.173: +7 -7 lines
Diff to previous 1.173
fill_in_cell for Heiko

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Sun Oct 17 16:40:13 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.172: +9 -7 lines
Diff to previous 1.172
added homologs_in_clusters.cgi

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Sun Oct 17 00:05:17 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.171: +4 -0 lines
Diff to previous 1.171
fix to by_alias

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Sun Oct 17 00:02:34 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.170: +21 -6 lines
Diff to previous 1.170
fixes to UniProt IDs on chromosomal_clusters.cgi

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Sat Oct 16 20:42:28 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.169: +22 -2 lines
Diff to previous 1.169
fixes to generalize chromosomal_clusters.cgi for UniProt

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Fri Oct 15 17:04:09 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.168: +97 -48 lines
Diff to previous 1.168
peg links generalized to fid links

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Fri Oct 15 00:38:11 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.167: +15 -4 lines
Diff to previous 1.167
fixes to subsystem code

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Mon Oct 11 23:55:40 2004 UTC (15 years, 2 months ago) by overbeek
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Changes since 1.166: +1 -0 lines
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remove extra EOLs on changed locations

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Mon Oct 11 21:38:58 2004 UTC (15 years, 2 months ago) by overbeek
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Changes since 1.165: +7 -2 lines
Diff to previous 1.165
fixes to change_location_of_feature

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Mon Oct 11 18:46:45 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.164: +10 -44 lines
Diff to previous 1.164
More fixes for sprout support.

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Fri Oct 8 22:04:48 2004 UTC (15 years, 2 months ago) by redwards
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Changes since 1.163: +1 -1 lines
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Added number of contigs to menu

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Tue Oct 5 22:06:28 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.162: +55 -0 lines
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more DAS fixes

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Mon Oct 4 15:56:10 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.161: +29 -0 lines
Diff to previous 1.161
Changes for DAS integration

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Fri Oct 1 19:48:37 2004 UTC (15 years, 2 months ago) by overbeek
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Changes since 1.160: +5 -5 lines
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minor fixes to exporting sets

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Fri Sep 24 20:27:22 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.159: +20 -1 lines
Diff to previous 1.159
doc fix

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Fri Sep 24 18:58:42 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.158: +7 -4 lines
Diff to previous 1.158
Possible fix for beg_of and contig_of
More p2p stuff

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Fri Sep 24 18:34:32 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.157: +165 -1 lines
Diff to previous 1.157
Some contig manipulation stuff, more p2p stuff.

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Thu Sep 23 20:04:04 2004 UTC (15 years, 2 months ago) by redwards
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Changes since 1.156: +16 -2 lines
Diff to previous 1.156
$fig->adjacent_genes was not returning adjacent genes

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Wed Sep 22 19:32:29 2004 UTC (15 years, 2 months ago) by olson
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remove print

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Wed Sep 22 19:29:51 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.154: +134 -1 lines
Diff to previous 1.154
Mods for P2P update stuff.

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Mon Sep 20 21:16:02 2004 UTC (15 years, 2 months ago) by overbeek
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Changes since 1.153: +6 -3 lines
Diff to previous 1.153
subsystem_genomes should return just genomes with an operational variant

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Thu Sep 16 15:15:57 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.152: +4 -4 lines
Diff to previous 1.152
remove inappropriate setting of g+s bit

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Thu Sep 16 04:35:03 2004 UTC (15 years, 2 months ago) by overbeek
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Changes since 1.151: +4 -4 lines
Diff to previous 1.151
Fixed errors in POD documentation. -- /gdp

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Mon Sep 13 02:12:20 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.150: +19 -0 lines
Diff to previous 1.150
add attributes as key-value pairs attached to fids

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Sat Sep 11 00:46:49 2004 UTC (15 years, 3 months ago) by golsen
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Changes since 1.149: +9 -3 lines
Diff to previous 1.149
Add domain-based selection to genomes function.  Used to generate domain-specfic genome lists.

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Thu Sep 9 00:00:09 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.148: +0 -1 lines
Diff to previous 1.148
minor fixes

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Tue Sep 7 02:54:16 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.147: +17 -2 lines
Diff to previous 1.147
add new subsystem interface

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Fri Aug 27 21:55:57 2004 UTC (15 years, 3 months ago) by mkubal
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Changes since 1.146: +81 -2 lines
Diff to previous 1.146
added adjacent_genes() and supporting methods

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Fri Aug 27 18:32:07 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.145: +14 -0 lines
Diff to previous 1.145
set current user

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Tue Aug 24 22:12:17 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.144: +6 -4 lines
Diff to previous 1.144
minor changes to indexing translations

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Mon Aug 23 18:58:54 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.143: +1 -1 lines
Diff to previous 1.143
sort sims into the correct order

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Mon Aug 23 18:51:34 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.142: +3 -3 lines
Diff to previous 1.142
fix evil bug in index searches

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Mon Aug 23 18:35:51 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.141: +17 -2 lines
Diff to previous 1.141
sort sims by bit score

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Mon Aug 23 03:34:32 2004 UTC (15 years, 3 months ago) by golsen
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Changes since 1.140: +200 -2 lines
Diff to previous 1.140
Fix a typo in annotations_made and start adding infrastructure to fix genes_in_region issues

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Sun Aug 22 21:36:42 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.139: +1 -0 lines
Diff to previous 1.139
have function_of append to end of lines

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Fri Aug 20 17:37:58 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.138: +70 -89 lines
Diff to previous 1.138
update feature alterations

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Fri Aug 20 00:42:54 2004 UTC (15 years, 3 months ago) by golsen
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Changes since 1.137: +8 -8 lines
Diff to previous 1.137
Fixed major error in org_of

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Thu Aug 19 23:45:58 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.136: +31 -0 lines
Diff to previous 1.136
handle changes to feature locations

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Wed Aug 18 15:46:51 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.135: +179 -22 lines
Diff to previous 1.135
add abilities to add, delete and update features

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Mon Aug 16 22:10:55 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.134: +160 -60 lines
Diff to previous 1.134
straighten out FIG.pm

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Fri Aug 13 14:04:20 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.133: +126 -0 lines
Diff to previous 1.133
interface for Bielefeld in FIG.pm

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Thu Aug 12 11:39:44 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.132: +1 -1 lines
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fix errors relating to read_annotations

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Mon Aug 9 13:36:18 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.131: +2 -2 lines
Diff to previous 1.131
major fix in read_annotations in FIG.pm

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Sat Aug 7 18:48:39 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.130: +1 -1 lines
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fixes to aliases_of

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Mon Aug 2 20:02:29 2004 UTC (15 years, 4 months ago) by golsen
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Changes since 1.129: +81 -0 lines
Diff to previous 1.129
Colorize organisms by domain in similarities list.  Changes protein.cgi and FIG.pm

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Sun Aug 1 11:50:25 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.128: +1 -2 lines
Diff to previous 1.128
fix order on genes returned in a region

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Sun Jul 25 21:48:15 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.127: +3 -1 lines
Diff to previous 1.127
sort links

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Sun Jul 18 22:58:36 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.126: +41 -6 lines
Diff to previous 1.126
handle bug that lost notes for subsystems

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Fri Jul 16 21:58:03 2004 UTC (15 years, 4 months ago) by gdpusch
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Changes since 1.125: +19 -5 lines
Diff to previous 1.125
Added out-of-bounds checks to &extract_seq(), plus debugging information for loci whose sequences could not be extracted.

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Fri Jul 16 20:41:26 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.124: +4 -0 lines
Diff to previous 1.124
updates to ssa2.cgi and warnings when assignments fail

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Mon Jul 12 21:14:53 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.123: +6 -0 lines
Diff to previous 1.123
Add "umask 0" to fig.pm to ensure all new files are world writable.

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Thu Jul 1 21:17:53 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.122: +282 -45 lines
Diff to previous 1.122
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.

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Mon Jun 28 20:11:14 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.121: +42 -2 lines
Diff to previous 1.121
Add assignments_made_for_protein
expand some code for readability.

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Sun Jun 27 22:49:49 2004 UTC (15 years, 5 months ago) by overbeek
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Changes since 1.120: +9 -1 lines
Diff to previous 1.120
handle names of subsystems just a bit better

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Wed Jun 23 21:33:43 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.119: +58 -10 lines
Diff to previous 1.119
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.

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Wed Jun 16 16:52:10 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.118: +1 -0 lines
Diff to previous 1.118
Modifications to fix & finish up the automated subsystem extension.

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Wed Jun 16 14:25:36 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.117: +1 -0 lines
Diff to previous 1.117
New map support.

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Wed Jun 16 14:04:40 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.116: +98 -0 lines
Diff to previous 1.116
add background job support.

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Mon Jun 14 22:04:24 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.115: +96 -0 lines
Diff to previous 1.115
Add background job support

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Thu Jun 10 14:00:36 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.114: +5 -5 lines
Diff to previous 1.114
Add scalar decl to is_bacterial and friends.

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Thu Jun 10 13:39:55 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.113: +30 -0 lines
Diff to previous 1.113
add more funcs for tutorials

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Tue Jun 8 20:26:23 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.112: +159 -4 lines
Diff to previous 1.112
add some scalar annotations; add find_role_in_org

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Tue Jun 8 17:19:43 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.111: +16 -2 lines
Diff to previous 1.111
Guard the rquire of figrpc in case we don't have the necessary modules installed for it.

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Tue Jun 8 15:02:14 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.110: +70 -14 lines
Diff to previous 1.110
Add capability for :scalar :list :remote annotations to FIG interface. This works with
modules that are declared as subclasses of FIGAttributes.

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Thu Jun 3 20:58:04 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.109: +1 -1 lines
Diff to previous 1.109
reorder load of databases just slightly

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Thu Jun 3 08:12:44 2004 UTC (15 years, 6 months ago) by gdpusch
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Changes since 1.108: +1 -1 lines
Diff to previous 1.108
Fixed typo in pod-documentation

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Wed Jun 2 09:45:16 2004 UTC (15 years, 6 months ago) by gdpusch
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Changes since 1.107: +30 -29 lines
Diff to previous 1.107
Added check for "defined" status of filehandle reads from <SSA>; removed various "masking" redefinitions of "my" variables.

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Wed Jun 2 09:23:35 2004 UTC (15 years, 6 months ago) by gdpusch
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Changes since 1.106: +46 -16 lines
Diff to previous 1.106
Fixed typos in various $fig->genome_*() accessor functions.

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Tue Jun 1 20:45:39 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.105: +1 -1 lines
Diff to previous 1.105
fix typo.

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Tue Jun 1 20:40:55 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.104: +2 -2 lines
Diff to previous 1.104
Add $force_load argument to get_subsystem; results in the discarding
of the cached subsystem if there is one.

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Tue Jun 1 20:21:44 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.103: +20 -0 lines
Diff to previous 1.103
add subsystems_for_peg

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Tue Jun 1 19:06:17 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.102: +3 -2 lines
Diff to previous 1.102
fix the call to figrpc

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Tue Jun 1 19:02:37 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.101: +13 -0 lines
Diff to previous 1.101
added redirect in FIG constructor to create a FIGrpc if the FIG_URL environment variable is set

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Tue Jun 1 00:45:38 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.100: +5 -2 lines
Diff to previous 1.100
make bbhs sensitive to lengths of match - watch out for fused proteins

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Sun May 30 15:04:26 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.99: +21 -9 lines
Diff to previous 1.99
precomputed BBHs

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Sat May 29 14:08:58 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.98: +1 -1 lines
Diff to previous 1.98
untested changes to extract_genomes

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Fri May 28 19:27:00 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.97: +21 -5 lines
Diff to previous 1.97
attempt to change FIG.pm to keep mac-1 up

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Thu May 27 18:22:11 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.96: +0 -1 lines
Diff to previous 1.96
doh, had left a debug print in there

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Wed May 26 22:34:17 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.95: +19 -0 lines
Diff to previous 1.95
add genome_and_peg_of

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Mon May 24 22:02:47 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.94: +10 -3 lines
Diff to previous 1.94
Factor out the subsystem caching.

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Mon May 24 21:59:32 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.93: +8 -1 lines
Diff to previous 1.93
cache subsystem objects, since they can be expensive to create.

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Mon May 24 21:55:18 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.92: +196 -34 lines
Diff to previous 1.92
Beginning of sim queueing stuff.
First implementation of Subsystem object, with FIG::peg_in_subsystem_cell
implemented in terms of it.

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Mon May 24 21:14:16 2004 UTC (15 years, 6 months ago) by gdpusch
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Changes since 1.91: +60 -3 lines
Diff to previous 1.91
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.

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Mon May 24 21:03:39 2004 UTC (15 years, 6 months ago) by gdpusch
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Changes since 1.90: +28 -0 lines
Diff to previous 1.90
Added access method \&genome_size($genome_id) to return the number of base-pairs in an organism\'s contig files.

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Mon May 24 19:32:36 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.89: +47 -0 lines
Diff to previous 1.89
add file_head and file_read

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Sat May 22 11:43:00 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.88: +6 -0 lines
Diff to previous 1.88
fix error in tutorial

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Fri May 21 18:05:55 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.87: +6 -2 lines
Diff to previous 1.87
fixes to similarities

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Thu May 20 12:26:47 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.86: +14 -2 lines
Diff to previous 1.86
make aliases include external aliases

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Wed May 19 15:54:10 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.85: +3 -0 lines
Diff to previous 1.85
allow comma-separated contiguous regions in dna_seq argument list

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Wed May 19 14:15:57 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.84: +25 -0 lines
Diff to previous 1.84
add all_contigs

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Wed May 19 13:17:39 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.83: +25 -9 lines
Diff to previous 1.83
fixes on memory leak and genome version

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Tue May 18 00:44:54 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.82: +1 -1 lines
Diff to previous 1.82
set max open files to 50

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Mon May 17 09:22:50 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.81: +91 -8 lines
Diff to previous 1.81
support addition of links to pegs

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Fri May 14 18:06:51 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.80: +41 -1 lines
Diff to previous 1.80
fixed up links

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Thu May 13 20:59:56 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.79: +1 -2 lines
Diff to previous 1.79
fix add_genome

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Tue May 4 16:27:23 2004 UTC (15 years, 7 months ago) by olson
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Changes since 1.78: +43 -3 lines
Diff to previous 1.78
more protection around the code that pokes at the clearing house, in case xmlrpc libs are missing

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Mon May 3 17:16:50 2004 UTC (15 years, 7 months ago) by olson
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Changes since 1.77: +11 -0 lines
Diff to previous 1.77
Add comment.

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Sat May 1 02:56:38 2004 UTC (15 years, 7 months ago) by olson
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Changes since 1.76: +3 -2 lines
Diff to previous 1.76
Comment out import of Clearinghouse until we get the env updated.

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Thu Apr 29 16:41:16 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.75: +9 -0 lines
Diff to previous 1.75
tools for query

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Wed Apr 28 21:59:32 2004 UTC (15 years, 7 months ago) by olson
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Changes since 1.74: +184 -0 lines
Diff to previous 1.74
Clearinghouse publishing stuff

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Wed Apr 28 04:34:52 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.73: +4 -1 lines
Diff to previous 1.73
fix to definition of bbh

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Tue Apr 27 15:41:28 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.72: +22 -0 lines
Diff to previous 1.72
basic query tools

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Sat Apr 24 23:27:05 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.71: +4 -3 lines
Diff to previous 1.71
make sure that external_calls produces one function for each peg

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Sat Apr 24 15:02:08 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.70: +34 -6 lines
Diff to previous 1.70
tools for McCune to build expert automated assignments

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Fri Apr 23 21:51:15 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.69: +1 -0 lines
Diff to previous 1.69
make load_all build blast dbs for fig proteins

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Fri Apr 23 21:49:02 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.68: +1 -1 lines
Diff to previous 1.68
fixes to index.cgi to blast against all complete

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Fri Apr 23 17:23:40 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.67: +2 -2 lines
Diff to previous 1.67
fixes to best_candidates

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Fri Apr 23 16:59:40 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.66: +9 -5 lines
Diff to previous 1.66
fixes to best_bbh_candidates

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Mon Apr 19 11:36:39 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.65: +4 -2 lines
Diff to previous 1.65
fix a bad bug in assignment permissions

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Fri Apr 9 15:26:05 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.64: +17 -3 lines
Diff to previous 1.64
pass back more detailed data for candidates for a role

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Fri Apr 9 14:55:36 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.63: +85 -0 lines
Diff to previous 1.63
more intelligent candidates for function

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Thu Apr 8 11:49:33 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.62: +11 -0 lines
Diff to previous 1.62
fixes in auto assignments

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Thu Apr 1 22:58:44 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.61: +8 -0 lines
Diff to previous 1.61
allow p2p to send me epoch dates, rather than readable dates

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Thu Apr 1 22:10:34 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.60: +1 -1 lines
Diff to previous 1.60
turn off warning messages for translation failures when translating PEG ids

Revision 1.60 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 1 22:07:31 2004 UTC (15 years, 8 months ago) by disz
Branch: MAIN
Changes since 1.59: +4 -4 lines
Diff to previous 1.59
More P2P fixes.
Add setgid to the mkdir/chmod's.

Revision 1.59 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 1 14:54:57 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.58: +66 -0 lines
Diff to previous 1.58
fixes to candidates for a role

Revision 1.58 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 31 19:20:24 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.57: +11 -1 lines
Diff to previous 1.57
p2p for updating release

Revision 1.57 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 31 18:39:15 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.56: +3 -3 lines
Diff to previous 1.56
p2p changes

Revision 1.56 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 31 16:32:22 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.55: +52 -0 lines
Diff to previous 1.55
attempt to fix package/install for p2p

Revision 1.55 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 31 11:14:47 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.54: +148 -0 lines
Diff to previous 1.54
move PEG translation into FIG.pm

Revision 1.54 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 29 23:13:14 2004 UTC (15 years, 8 months ago) by mkubal
Branch: MAIN
Changes since 1.53: +2 -2 lines
Diff to previous 1.53
removes ## markers in FIG.pm

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Mon Mar 29 23:12:40 2004 UTC (15 years, 8 months ago) by mkubal
Branch: MAIN
Changes since 1.52: +7 -104 lines
Diff to previous 1.52
removes ## markers in FIG.pm and fixed Blast.pm

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Fri Mar 26 21:38:38 2004 UTC (15 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.51: +18 -0 lines
Diff to previous 1.51
Make get_local_hostname check for a FIGdisk/config/hostname file and use
that as the local hostname if present.

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Fri Mar 26 13:01:46 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.50: +11 -2 lines
Diff to previous 1.50
better peg mapping when importing spreadsheets

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Thu Mar 25 17:10:50 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.49: +11 -0 lines
Diff to previous 1.49
includes errors

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Thu Mar 25 13:48:27 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.48: +3 -1 lines
Diff to previous 1.48
improvements on importing subsystems

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Wed Mar 24 00:05:40 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.47: +1 -1 lines
Diff to previous 1.47
export subsystems stuff

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Tue Mar 23 21:54:03 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.46: +7 -1 lines
Diff to previous 1.46
Broke a semicolon-chained set of commands in &delete_genomes() into separate &run() invocations, so that if any of them fail, the delete operation will abort. -- /gdp

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 22 02:33:57 2004 UTC (15 years, 8 months ago) by gdpusch
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Changes since 1.45: +1 -1 lines
Diff to previous 1.45
Fixed failure to declare two variables in routine &read_fasta_record(). -- /gdp

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Mon Mar 22 01:51:30 2004 UTC (15 years, 8 months ago) by gdpusch
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Changes since 1.44: +58 -1 lines
Diff to previous 1.44
Added routine &read_fasta_record(). -- /gdp

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Fri Mar 19 21:58:31 2004 UTC (15 years, 8 months ago) by golsen
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Changes since 1.43: +24 -13 lines
Diff to previous 1.43
Relative base address support and cgi_url() based on current http request

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Fri Mar 19 18:45:36 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.42: +39 -22 lines
Diff to previous 1.42
fixes to coupling and protein.cgi

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Thu Mar 18 16:02:32 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.41: +19 -0 lines
Diff to previous 1.41
add versions to spreadsheets

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Thu Mar 18 13:16:40 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.40: +1 -1 lines
Diff to previous 1.40
exchangable flags on spreadsheet

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Wed Mar 17 20:18:22 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.39: +105 -6 lines
Diff to previous 1.39
for Gordon and Mike

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 17 18:17:34 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.38: +107 -0 lines
Diff to previous 1.38
basic export of subsystems stuff

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 15 23:06:47 2004 UTC (15 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.37: +33 -0 lines
Diff to previous 1.37
Add get_seed_id()

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Mon Mar 15 04:37:50 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.36: +2 -4 lines
Diff to previous 1.36
new spreadsheet

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Sun Mar 14 03:46:16 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.35: +298 -188 lines
Diff to previous 1.35
fixes

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 9 23:19:23 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.34: +97 -0 lines
Diff to previous 1.34
fixed distances and spreadsheet

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Fri Mar 5 22:17:16 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.33: +25 -0 lines
Diff to previous 1.33
support gi and NP numbers for access to fig IDs

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 3 14:56:43 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.32: +48 -1 lines
Diff to previous 1.32
add merged annotations

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Wed Mar 3 12:49:23 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.31: +4 -2 lines
Diff to previous 1.31
fixes from DOE meeting

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Thu Feb 19 12:55:35 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.30: +1 -1 lines
Diff to previous 1.30
fix bug due to change in sims

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Tue Feb 17 22:23:36 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.29: +9 -5 lines
Diff to previous 1.29
preserve translation through similarities

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Sun Feb 15 17:12:54 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.28: +7 -4 lines
Diff to previous 1.28
added Gary Olsen changes

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Tue Feb 10 22:35:57 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.27: +19 -1 lines
Diff to previous 1.27
in get_local_hostname, ensure that we get a FQDN. If we don't, just bail and
use our IP address.

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Tue Feb 3 16:45:57 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.26: +9 -0 lines
Diff to previous 1.26
minor fixes

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Mon Jan 26 22:51:32 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.25: +12 -4 lines
Diff to previous 1.25
fixes

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Wed Jan 21 18:27:29 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.24: +1 -0 lines
Diff to previous 1.24
from the Penn trip

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Fri Jan 16 19:37:40 2004 UTC (15 years, 10 months ago) by overbeek
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Changes since 1.23: +2 -2 lines
Diff to previous 1.23
chop delimiter off annotations

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Wed Jan 14 20:20:32 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.22: +9 -99 lines
Diff to previous 1.22
synch up Ross

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Thu Jan 8 16:31:59 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.21: +8 -0 lines
Diff to previous 1.21
handle loops in translation

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Wed Jan 7 03:34:13 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.20: +9 -0 lines
Diff to previous 1.20
make Assignments files have readable names

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 6 23:08:26 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.19: +1 -1 lines
Diff to previous 1.19
fix in extract_genomes

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Tue Jan 6 18:14:48 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.18: +14 -4 lines
Diff to previous 1.18
fix stick behavior for checked sims

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 5 12:26:58 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.17: +2 -1 lines
Diff to previous 1.17
minor bugs

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 3 14:13:48 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.16: +41 -1 lines
Diff to previous 1.16
fix P2P to use get_assignments

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Sat Jan 3 06:03:43 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.15: +25 -20 lines
Diff to previous 1.15
changes to annotations to allow extraction of assignments

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 30 05:21:24 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.14: +2 -2 lines
Diff to previous 1.14
fix order of database loads

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 29 02:22:37 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.13: +17 -12 lines
Diff to previous 1.13
numerous performance issues

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 28 17:11:29 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.12: +55 -18 lines
Diff to previous 1.12
cleanup issues relating to large numbers of partial genomes

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 23 22:38:31 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.11: +1 -1 lines
Diff to previous 1.11
make plugging URLs more robust

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 23 22:29:51 2003 UTC (15 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.10: +5 -5 lines
Diff to previous 1.10
remove prints

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 23 22:28:10 2003 UTC (15 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.9: +207 -0 lines
Diff to previous 1.9
Add IP-determination logic.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 22 01:24:22 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +14 -5 lines
Diff to previous 1.8
add pins and clusters properly

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 21 01:20:59 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +0 -1 lines
Diff to previous 1.7
allow multiple sims files in update_sims

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 20 21:08:43 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +26 -3 lines
Diff to previous 1.6
fixed issues relating to addition/deletion of genomes

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 19 20:09:34 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +0 -18 lines
Diff to previous 1.5
get rid of set_urls, since it will not work anymore

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 5 14:31:23 2003 UTC (16 years ago) by overbeek
Branch: MAIN
CVS Tags: delong-01, delong-02
Changes since 1.4: +1 -1 lines
Diff to previous 1.4
fix permissions on added genome

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 4 21:49:02 2003 UTC (16 years ago) by overbeek
Branch: MAIN
Changes since 1.3: +6 -2 lines
Diff to previous 1.3
fix bug in function translation

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 3 21:24:31 2003 UTC (16 years ago) by overbeek
Branch: MAIN
Changes since 1.2: +4 -3 lines
Diff to previous 1.2
*** empty log message ***

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 3 19:39:29 2003 UTC (16 years ago) by efrank
Branch: MAIN
Changes since 1.1: +25 -5 lines
Diff to previous 1.1

fixed a bunch of changes

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 1 16:54:26 2003 UTC (16 years ago) by efrank
Branch: MAIN
Branch point for: initial
Initial revision

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