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Revision 1.96 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 2 20:02:45 2010 UTC (9 years ago) by gdpusch
Branch: MAIN
CVS Tags: mgrast_dev_02212011, mgrast_dev_02222011, mgrast_dev_03252011, mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2, myrast_33, rast_rel_2010_1206, rast_rel_2011_0119
Changes since 1.95: +44 -30 lines
Diff to previous 1.95
Modified to gracefully handle Organism directories with no or empty Subsystems/ subdirectories.

Revision 1.95 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 22 20:31:40 2010 UTC (9 years ago) by gdpusch
Branch: MAIN
Changes since 1.94: +382 -549 lines
Diff to previous 1.94
Added support for auxilliary files written by RAST.

Revision 1.94 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 9 01:08:42 2010 UTC (9 years, 4 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2010_0827, rast_rel_2010_0928
Changes since 1.93: +26 -9 lines
Diff to previous 1.93
Fixed crashing of 'add_feature()' when no feature of that type yet exists.

Revision 1.93 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 29 19:17:42 2010 UTC (9 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.92: +26 -1 lines
Diff to previous 1.92
Add FIGV and FIGM function_of_bulk

Revision 1.92 - (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
CVS Tags: rast_rel_2009_0925, rast_rel_2010_0118, rast_rel_2010_0526
Changes since 1.91: +72 -0 lines
Diff to previous 1.91
Support for Seedviewer Subsystems.pm speedups.

Revision 1.91 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 26 20:23:42 2009 UTC (10 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.90: +2 -0 lines
Diff to previous 1.90
load needed indexes

Revision 1.90 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 27 19:01:43 2009 UTC (10 years, 6 months ago) by paczian
Branch: MAIN
CVS Tags: rast_rel_2009_07_09
Changes since 1.89: +5 -4 lines
Diff to previous 1.89
fixed eol the right way in load_deleted_features_hash

Revision 1.89 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 27 17:00:35 2009 UTC (10 years, 6 months ago) by paczian
Branch: MAIN
Changes since 1.88: +43 -3 lines
Diff to previous 1.88
added FIGfam support for RAST orgs
fixed deleted_fids hash

Revision 1.88 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 15 14:43:36 2009 UTC (10 years, 7 months ago) by dejongh
Branch: MAIN
CVS Tags: rast_rel_2009_05_18
Changes since 1.87: +5 -13 lines
Diff to previous 1.87
Force reloading of subsystem info when functional annotations change

Revision 1.87 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 7 10:15:13 2009 UTC (10 years, 7 months ago) by paczian
Branch: MAIN
Changes since 1.86: +14 -10 lines
Diff to previous 1.86
fixed call to seqs_with_role to match FIG.pm invocation

Revision 1.86 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 20 14:55:43 2009 UTC (10 years, 7 months ago) by paczian
Branch: MAIN
Changes since 1.85: +10 -0 lines
Diff to previous 1.85
added method genome_info

Revision 1.85 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 8 12:38:53 2009 UTC (10 years, 8 months ago) by dejongh
Branch: MAIN
Changes since 1.84: +57 -76 lines
Diff to previous 1.84
force reload of cached functions and roles after changing annotations, and ensure that old assigned functions are deleted before the new ones are written.  Always rewrite the bindings file in update_bindings_and_variant

Revision 1.84 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 1 18:50:57 2009 UTC (10 years, 8 months ago) by gdpusch
Branch: MAIN
Changes since 1.83: +3 -2 lines
Diff to previous 1.83
Modified "all_features()" so that it returns all features if the "type" argument is undef or null.

Revision 1.83 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 26 09:16:38 2009 UTC (10 years, 8 months ago) by dejongh
Branch: MAIN
CVS Tags: rast_rel_2009_03_26
Changes since 1.82: +12 -1 lines
Diff to previous 1.82
Fix invocation of seqs_with_role; add check for FIGV genome to pegs_to_subsystem

Revision 1.82 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 24 19:33:51 2009 UTC (10 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.81: +2 -1 lines
Diff to previous 1.81
minor test for valid call

Revision 1.81 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 12 16:06:04 2009 UTC (10 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.80: +1 -1 lines
Diff to previous 1.80
translation of unix time to a time string in feature_annotations was not working properly
and was destructive to the cached values as well. fixed.

Revision 1.80 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 9 14:42:27 2009 UTC (10 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.79: +1 -1 lines
Diff to previous 1.79
define some primitives that Bruce will fill in

Revision 1.79 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 5 16:21:59 2009 UTC (10 years, 10 months ago) by paczian
Branch: MAIN
Changes since 1.78: +1 -1 lines
Diff to previous 1.78
added peg in return value of subsystems_for_peg_complete

Revision 1.78 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 21 22:42:18 2009 UTC (10 years, 10 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2009_02_05
Changes since 1.77: +66 -69 lines
Diff to previous 1.77
Cache contig info.

Revision 1.77 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 20 11:12:53 2009 UTC (10 years, 10 months ago) by paczian
Branch: MAIN
Changes since 1.76: +42 -0 lines
Diff to previous 1.76
added the function "coupled_to_batch"

Revision 1.76 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 4 14:04:17 2008 UTC (11 years ago) by paczian
Branch: MAIN
CVS Tags: rast_rel_2008_12_18
Changes since 1.75: +21 -0 lines
Diff to previous 1.75
added subsystems_for_peg_complete
added protein_subsystem_to_roles

Revision 1.75 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 20 15:50:19 2008 UTC (11 years ago) by paczian
Branch: MAIN
CVS Tags: rast_rel_2008_11_24
Changes since 1.74: +1 -0 lines
Diff to previous 1.74
find_role_in_org will no longer return deleted fids

Revision 1.74 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 18 22:31:49 2008 UTC (11 years ago) by olson
Branch: MAIN
Changes since 1.73: +162 -154 lines
Diff to previous 1.73
Fix add_feature support.

Revision 1.73 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 13 21:50:15 2008 UTC (11 years, 1 month ago) by dejongh
Branch: MAIN
Changes since 1.72: +3 -2 lines
Diff to previous 1.72
fix scenario_directory to work for All

Revision 1.72 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 12 18:24:47 2008 UTC (11 years, 1 month ago) by dejongh
Branch: MAIN
Changes since 1.71: +8 -10 lines
Diff to previous 1.71
switch to scenario_directory

Revision 1.71 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 11 13:41:27 2008 UTC (11 years, 1 month ago) by paczian
Branch: MAIN
Changes since 1.70: +213 -10 lines
Diff to previous 1.70
updated for use with FIGM

Revision 1.70 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 6 11:05:12 2008 UTC (11 years, 1 month ago) by paczian
Branch: MAIN
CVS Tags: mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2
Changes since 1.69: +4 -2 lines
Diff to previous 1.69
added support for FIGM

Revision 1.69 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 10 19:27:34 2008 UTC (11 years, 2 months ago) by dsouza
Branch: MAIN
CVS Tags: rast_rel_2008_10_29
Changes since 1.68: +10 -6 lines
Diff to previous 1.68
peg hash from btree has contig and peg ids as keys -- filter them out in pegs_of. Same for rnas_of

Revision 1.68 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 2 21:48:41 2008 UTC (11 years, 2 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_10_09
Changes since 1.67: +35 -0 lines
Diff to previous 1.67
FIGM/FIGV changes for sims between RAST orgs.

Revision 1.67 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 1 17:08:35 2008 UTC (11 years, 2 months ago) by paczian
Branch: MAIN
Changes since 1.66: +26 -0 lines
Diff to previous 1.66
implemented get_corresponding_ids

Revision 1.66 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 1 00:22:44 2008 UTC (11 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.65: +3 -7 lines
Diff to previous 1.65
fix to sims in FIGV.pm

Revision 1.65 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 30 23:58:20 2008 UTC (11 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.64: +99 -35 lines
Diff to previous 1.64
add checks using is_deleted_feature to functions in FIGV.pm

Revision 1.64 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 30 00:18:02 2008 UTC (11 years, 2 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2008_09_30
Changes since 1.63: +92 -8 lines
Diff to previous 1.63
support is_deleted_fid and delete_feature in FIGV.pm

Revision 1.63 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 29 10:16:21 2008 UTC (11 years, 2 months ago) by paczian
Branch: MAIN
CVS Tags: rast_rel_2008_09_29, rast_release_2008_09_29
Changes since 1.62: +33 -18 lines
Diff to previous 1.62
getting the subsystem bindings from bindings file again, since annotators can now recalculate subsystems for RAST organisms

Revision 1.62 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 18 14:01:45 2008 UTC (11 years, 2 months ago) by paczian
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, mgrast_rel_2008_0917, mgrast_rel_2008_0919, mgrast_rel_2008_0923, mgrast_rel_2008_0924, rast_2008_0924
Changes since 1.61: +144 -1 lines
Diff to previous 1.61
RAST genomes now always compute the pegs for subsystems on the fly (ignoring their subsystem bindings)

Revision 1.61 - (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
Changes since 1.60: +35 -12 lines
Diff to previous 1.60
fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic reconstructions

Revision 1.60 - (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 1.59: +22 -15 lines
Diff to previous 1.59
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 1.59 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 23 16:19:02 2008 UTC (11 years, 3 months ago) by gdpusch
Branch: MAIN
Changes since 1.58: +45 -21 lines
Diff to previous 1.58
Streamlined FIG vs SPROUT handling and handling of "virtual" genomes, minor improvements to error-handling, including conditioning of stray debugging statements on $ENV{FIG_DEBUG}. -- /gdp

Revision 1.58 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 5 18:13:54 2008 UTC (11 years, 4 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_08_07
Changes since 1.57: +21 -3 lines
Diff to previous 1.57
Add some comments, fix perf bug whhere FIG->sims called on an empty list.

Revision 1.57 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 22 15:23:59 2008 UTC (11 years, 4 months ago) by paczian
Branch: MAIN
Changes since 1.56: +5 -3 lines
Diff to previous 1.56
changed retrieval of function in method all_features_detailed_fast to always be in scalar context

Revision 1.56 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 26 21:11:11 2008 UTC (11 years, 5 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_07_21
Changes since 1.55: +192 -16 lines
Diff to previous 1.55
Add annotation support to FIGV. Add FIGM.

Revision 1.55 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 24 16:25:54 2008 UTC (11 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.54: +368 -78 lines
Diff to previous 1.54
Add indexed access to data in Feature directories.

Revision 1.54 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 29 23:00:34 2008 UTC (11 years, 6 months ago) by redwards
Branch: MAIN
CVS Tags: rast_rel_2008_06_16, rast_rel_2008_06_18
Changes since 1.53: +66 -0 lines
Diff to previous 1.53
adding two find functions

Revision 1.53 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 6 16:50:14 2008 UTC (11 years, 7 months ago) by gdpusch
Branch: MAIN
Changes since 1.52: +15 -12 lines
Diff to previous 1.52
Improved the readability of FIGV::get_genome_subsystem_count(). -- /gdp

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 13 22:28:19 2008 UTC (11 years, 9 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.51: +27 -0 lines
Diff to previous 1.51
Add figv version of get_genome_subsystem_count().

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 9 20:34:14 2008 UTC (11 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.50: +8 -1 lines
Diff to previous 1.50
add array return for feature_location

Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 20 21:29:55 2008 UTC (11 years, 10 months ago) by gdpusch
Branch: MAIN
Changes since 1.49: +3 -2 lines
Diff to previous 1.49
Minor cosmetic change. -- /gdp

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 6 13:59:34 2007 UTC (12 years ago) by parrello
Branch: MAIN
Changes since 1.48: +57 -57 lines
Diff to previous 1.48
Changed POD format for better compatability with Wiki.

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 30 21:39:07 2007 UTC (12 years ago) by gdpusch
Branch: MAIN
Changes since 1.47: +8 -0 lines
Diff to previous 1.47
Added support to call &FIG::pick_gene_boundaries() and &FIG::call_start(). -- /gdp

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 22 16:24:10 2007 UTC (12 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.46: +2 -2 lines
Diff to previous 1.46
don't emit the harmless can't-tie-contig warnings.

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 20 19:44:10 2007 UTC (12 years, 1 month ago) by olson
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Changes since 1.45: +1 -1 lines
Diff to previous 1.45
bug fix

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 11 18:59:14 2007 UTC (12 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.44: +59 -0 lines
Diff to previous 1.44
add implementation of in_pch_pin_with that uses the local indexed PCHs.

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 11 18:30:52 2007 UTC (12 years, 2 months ago) by olson
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Changes since 1.43: +62 -13 lines
Diff to previous 1.43
add new get_attributes

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 18 15:53:18 2007 UTC (12 years, 2 months ago) by olson
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Changes since 1.42: +1 -1 lines
Diff to previous 1.42
fix typo

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 16 21:51:21 2007 UTC (12 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.41: +8 -0 lines
Diff to previous 1.41
add code to search for mobile elements

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 7 15:53:40 2007 UTC (12 years, 3 months ago) by olson
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Changes since 1.40: +1 -1 lines
Diff to previous 1.40
fix bug in the absence of a contigs index

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 15 19:34:04 2007 UTC (12 years, 4 months ago) by olson
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Changes since 1.39: +1 -0 lines
Diff to previous 1.39
Missing chomp in contig_lengths.

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 24 17:01:14 2007 UTC (12 years, 4 months ago) by olson
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Changes since 1.38: +3 -3 lines
Diff to previous 1.38
fix checks for existence of contig indexes

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 23 20:41:51 2007 UTC (12 years, 4 months ago) by formsma
Branch: MAIN
Changes since 1.37: +6 -2 lines
Diff to previous 1.37
Modfied model_directory subroutine with additional condition that so that it utlizes $self->{_genome} if avalible and $organism isn't defined - Kevin

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 17 20:27:31 2007 UTC (12 years, 4 months ago) by olson
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Changes since 1.36: +44 -22 lines
Diff to previous 1.36
Use contig btrees where possible. GREATLY accelerates access.

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 17 19:04:56 2007 UTC (12 years, 4 months ago) by olson
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Changes since 1.35: +51 -12 lines
Diff to previous 1.35
accelerated contigs processing via btree index

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Fri Jul 6 21:55:20 2007 UTC (12 years, 5 months ago) by olson
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Changes since 1.34: +43 -0 lines
Diff to previous 1.34
add taxa_to_seed_ids()

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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 1.33: +160 -1 lines
Diff to previous 1.33
add get_basic_statistics() and get_peg_statistics(); both use caching.

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 26 20:29:33 2007 UTC (12 years, 5 months ago) by olson
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Changes since 1.32: +3 -0 lines
Diff to previous 1.32
add some missing chomps in contig processing code

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Wed Jun 13 20:40:48 2007 UTC (12 years, 6 months ago) by paarmann
Branch: MAIN
Changes since 1.31: +1 -1 lines
Diff to previous 1.31
*** empty log message ***

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 12 18:16:15 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.30: +94 -1 lines
Diff to previous 1.30
get_genome_assignment_data: use assigned_functions for function lookup if proposed_functions is missing
Add search_database

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Tue Jun 5 19:47:42 2007 UTC (12 years, 6 months ago) by olson
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Changes since 1.29: +15 -0 lines
Diff to previous 1.29
If no local coupling data computed, just return, do not fail.

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 30 15:41:42 2007 UTC (12 years, 6 months ago) by paczian
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Changes since 1.28: +5 -5 lines
Diff to previous 1.28
changed scenario_directory to model_directory

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 29 19:24:42 2007 UTC (12 years, 6 months ago) by olson
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Changes since 1.27: +1 -1 lines
Diff to previous 1.27
fix typo

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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 1.26: +273 -46 lines
Diff to previous 1.26
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 1.25: +31 -1 lines
Diff to previous 1.25
added the function scenario_directory, which returns the scenario directory

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 13 23:38:37 2007 UTC (12 years, 8 months ago) by olson
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Changes since 1.24: +5 -1 lines
Diff to previous 1.24
bugfix

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Tue Apr 10 03:48:49 2007 UTC (12 years, 8 months ago) by parrello
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Changes since 1.23: +7 -7 lines
Diff to previous 1.23
Fixed some compiler warnings.

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Tue Apr 3 12:24:31 2007 UTC (12 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.22: +30 -2 lines
Diff to previous 1.22
fixed to comp_MR.cgi and FIGV.pm

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 23 20:52:59 2007 UTC (12 years, 8 months ago) by olson
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Changes since 1.21: +5 -0 lines
Diff to previous 1.21
fix peg_to_roles_in_subsystems

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Wed Mar 14 20:49:33 2007 UTC (12 years, 9 months ago) by olson
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Changes since 1.20: +1 -0 lines
Diff to previous 1.20
load_pseq - chomp away

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Mon Mar 12 21:57:11 2007 UTC (12 years, 9 months ago) by paarmann
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Changes since 1.19: +7 -0 lines
Diff to previous 1.19
added method organism_directory

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Fri Feb 9 22:45:44 2007 UTC (12 years, 10 months ago) by overbeek
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Changes since 1.18: +12 -0 lines
Diff to previous 1.18
implement peg_to_subsystems in FIGV.pm

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 15 21:44:02 2007 UTC (12 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.17: +1 -1 lines
Diff to previous 1.17
fix nasty sims bug

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 13 16:36:36 2006 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.16: +5 -0 lines
Diff to previous 1.16
add support for FIGV in sigs.cgi

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 13 05:51:32 2006 UTC (13 years ago) by olson
Branch: MAIN
Changes since 1.15: +64 -0 lines
Diff to previous 1.15
add bbhs

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 5 22:43:07 2006 UTC (13 years ago) by paczian
Branch: MAIN
Changes since 1.14: +3 -3 lines
Diff to previous 1.14
fixed a bug in dna_seq

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 30 20:43:10 2006 UTC (13 years ago) by olson
Branch: MAIN
Changes since 1.13: +40 -0 lines
Diff to previous 1.13
Add FIGV::active_subsystems

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 30 20:18:22 2006 UTC (13 years ago) by olson
Branch: MAIN
Changes since 1.12: +87 -1 lines
Diff to previous 1.12
create and index expanded sims in the postproc; use them in FIGV::sims.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 30 17:58:38 2006 UTC (13 years ago) by paczian
Branch: MAIN
Changes since 1.11: +1 -1 lines
Diff to previous 1.11
corrected a typo in line 1023: @$4 -> $4

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 29 23:28:12 2006 UTC (13 years ago) by olson
Branch: MAIN
Changes since 1.10: +17 -9 lines
Diff to previous 1.10
Fix all_features_detailed_fast

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 29 21:52:27 2006 UTC (13 years ago) by olson
Branch: MAIN
Changes since 1.9: +180 -3 lines
Diff to previous 1.9
Mods to support seed2genbank with FIGV.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 29 20:59:44 2006 UTC (13 years ago) by olson
Branch: MAIN
Changes since 1.8: +64 -36 lines
Diff to previous 1.8
Add FIGV support for peg/subsystem indexing.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 29 15:19:19 2006 UTC (13 years ago) by olson
Branch: MAIN
Changes since 1.7: +48 -1 lines
Diff to previous 1.7
Rollup commit of 48hr changes.

Added add_virtual_genome to Subsystem.pm to support UnvSubsys doing
the right thing when handed a FIGV.

Added propagation of 48hr_job thru the various link generation scripts in order for protein.cgi/display_subsys.cgi
to properly show virtual genomes.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 29 09:18:26 2006 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.6: +350 -0 lines
Diff to previous 1.6
more complete version of FIGV.pm

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 28 23:16:55 2006 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.5: +83 -0 lines
Diff to previous 1.5
add taxonomy stuff to FIGV.pm

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 28 22:21:58 2006 UTC (13 years ago) by olson
Branch: MAIN
Changes since 1.4: +20 -2 lines
Diff to previous 1.4
remove debug, add stub get_subsystems

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 28 21:22:05 2006 UTC (13 years ago) by olson
Branch: MAIN
Changes since 1.3: +101 -0 lines
Diff to previous 1.3
mods to make protein.cgi work

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 28 17:09:22 2006 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.2: +1 -1 lines
Diff to previous 1.2
initialize evidence and ann in rp directory

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 28 17:00:05 2006 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.1: +49 -0 lines
Diff to previous 1.1
remove warning from boundaries_of and add genes_in_region to FIGV

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 27 18:32:56 2006 UTC (13 years ago) by overbeek
Branch: MAIN
initial version of FIGV.pm to demonstrate concept

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