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Revision 1.63 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 29 10:16:21 2008 UTC (11 years, 6 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 , to selected 1.32
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, 6 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 , to selected 1.32
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, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.60: +35 -12 lines
Diff to previous 1.60 , to selected 1.32
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, 7 months ago) by golsen
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806
Changes since 1.59: +22 -15 lines
Diff to previous 1.59 , to selected 1.32
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, 7 months ago) by gdpusch
Branch: MAIN
Changes since 1.58: +45 -21 lines
Diff to previous 1.58 , to selected 1.32
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, 7 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 , to selected 1.32
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, 8 months ago) by paczian
Branch: MAIN
Changes since 1.56: +5 -3 lines
Diff to previous 1.56 , to selected 1.32
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, 9 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 , to selected 1.32
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, 9 months ago) by olson
Branch: MAIN
Changes since 1.54: +368 -78 lines
Diff to previous 1.54 , to selected 1.32
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, 10 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 , to selected 1.32
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, 10 months ago) by gdpusch
Branch: MAIN
Changes since 1.52: +15 -12 lines
Diff to previous 1.52 , to selected 1.32
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 (12 years ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.51: +27 -0 lines
Diff to previous 1.51 , to selected 1.32
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 (12 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.50: +8 -1 lines
Diff to previous 1.50 , to selected 1.32
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 (12 years, 2 months ago) by gdpusch
Branch: MAIN
Changes since 1.49: +3 -2 lines
Diff to previous 1.49 , to selected 1.32
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, 3 months ago) by parrello
Branch: MAIN
Changes since 1.48: +57 -57 lines
Diff to previous 1.48 , to selected 1.32
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, 4 months ago) by gdpusch
Branch: MAIN
Changes since 1.47: +8 -0 lines
Diff to previous 1.47 , to selected 1.32
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, 5 months ago) by olson
Branch: MAIN
Changes since 1.46: +2 -2 lines
Diff to previous 1.46 , to selected 1.32
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, 5 months ago) by olson
Branch: MAIN
Changes since 1.45: +1 -1 lines
Diff to previous 1.45 , to selected 1.32
bug fix

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 11 18:59:14 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.44: +59 -0 lines
Diff to previous 1.44 , to selected 1.32
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, 5 months ago) by olson
Branch: MAIN
Changes since 1.43: +62 -13 lines
Diff to previous 1.43 , to selected 1.32
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, 6 months ago) by olson
Branch: MAIN
Changes since 1.42: +1 -1 lines
Diff to previous 1.42 , to selected 1.32
fix typo

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 16 21:51:21 2007 UTC (12 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.41: +8 -0 lines
Diff to previous 1.41 , to selected 1.32
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, 6 months ago) by olson
Branch: MAIN
Changes since 1.40: +1 -1 lines
Diff to previous 1.40 , to selected 1.32
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, 7 months ago) by olson
Branch: MAIN
Changes since 1.39: +1 -0 lines
Diff to previous 1.39 , to selected 1.32
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, 8 months ago) by olson
Branch: MAIN
Changes since 1.38: +3 -3 lines
Diff to previous 1.38 , to selected 1.32
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, 8 months ago) by formsma
Branch: MAIN
Changes since 1.37: +6 -2 lines
Diff to previous 1.37 , to selected 1.32
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, 8 months ago) by olson
Branch: MAIN
Changes since 1.36: +44 -22 lines
Diff to previous 1.36 , to selected 1.32
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, 8 months ago) by olson
Branch: MAIN
Changes since 1.35: +51 -12 lines
Diff to previous 1.35 , to selected 1.32
accelerated contigs processing via btree index

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 6 21:55:20 2007 UTC (12 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.34: +43 -0 lines
Diff to previous 1.34 , to selected 1.32
add taxa_to_seed_ids()

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 28 22:04:24 2007 UTC (12 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.33: +160 -1 lines
Diff to previous 1.33 , to selected 1.32
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, 9 months ago) by olson
Branch: MAIN
Changes since 1.32: +3 -0 lines
Diff to previous 1.32
add some missing chomps in contig processing code

Revision 1.32 - (view) (download) (as text) (annotate) - [selected]
Wed Jun 13 20:40:48 2007 UTC (12 years, 9 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, 9 months ago) by olson
Branch: MAIN
Changes since 1.30: +94 -1 lines
Diff to previous 1.30 , to selected 1.32
get_genome_assignment_data: use assigned_functions for function lookup if proposed_functions is missing
Add search_database

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 5 19:47:42 2007 UTC (12 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.29: +15 -0 lines
Diff to previous 1.29 , to selected 1.32
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, 10 months ago) by paczian
Branch: MAIN
Changes since 1.28: +5 -5 lines
Diff to previous 1.28 , to selected 1.32
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, 10 months ago) by olson
Branch: MAIN
Changes since 1.27: +1 -1 lines
Diff to previous 1.27 , to selected 1.32
fix typo

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 29 19:16:26 2007 UTC (12 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.26: +273 -46 lines
Diff to previous 1.26 , to selected 1.32
Changes for using $fig->scenario_directory() instead of constructed paths.

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 25 16:46:44 2007 UTC (12 years, 10 months ago) by paczian
Branch: MAIN
Changes since 1.25: +31 -1 lines
Diff to previous 1.25 , to selected 1.32
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, 11 months ago) by olson
Branch: MAIN
Changes since 1.24: +5 -1 lines
Diff to previous 1.24 , to selected 1.32
bugfix

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 10 03:48:49 2007 UTC (12 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.23: +7 -7 lines
Diff to previous 1.23 , to selected 1.32
Fixed some compiler warnings.

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 3 12:24:31 2007 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.22: +30 -2 lines
Diff to previous 1.22 , to selected 1.32
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 (13 years ago) by olson
Branch: MAIN
Changes since 1.21: +5 -0 lines
Diff to previous 1.21 , to selected 1.32
fix peg_to_roles_in_subsystems

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 14 20:49:33 2007 UTC (13 years ago) by olson
Branch: MAIN
Changes since 1.20: +1 -0 lines
Diff to previous 1.20 , to selected 1.32
load_pseq - chomp away

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 12 21:57:11 2007 UTC (13 years ago) by paarmann
Branch: MAIN
Changes since 1.19: +7 -0 lines
Diff to previous 1.19 , to selected 1.32
added method organism_directory

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 9 22:45:44 2007 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.18: +12 -0 lines
Diff to previous 1.18 , to selected 1.32
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 (13 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.17: +1 -1 lines
Diff to previous 1.17 , to selected 1.32
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, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.16: +5 -0 lines
Diff to previous 1.16 , to selected 1.32
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, 3 months ago) by olson
Branch: MAIN
Changes since 1.15: +64 -0 lines
Diff to previous 1.15 , to selected 1.32
add bbhs

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 5 22:43:07 2006 UTC (13 years, 3 months ago) by paczian
Branch: MAIN
Changes since 1.14: +3 -3 lines
Diff to previous 1.14 , to selected 1.32
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, 4 months ago) by olson
Branch: MAIN
Changes since 1.13: +40 -0 lines
Diff to previous 1.13 , to selected 1.32
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, 4 months ago) by olson
Branch: MAIN
Changes since 1.12: +87 -1 lines
Diff to previous 1.12 , to selected 1.32
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, 4 months ago) by paczian
Branch: MAIN
Changes since 1.11: +1 -1 lines
Diff to previous 1.11 , to selected 1.32
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, 4 months ago) by olson
Branch: MAIN
Changes since 1.10: +17 -9 lines
Diff to previous 1.10 , to selected 1.32
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, 4 months ago) by olson
Branch: MAIN
Changes since 1.9: +180 -3 lines
Diff to previous 1.9 , to selected 1.32
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, 4 months ago) by olson
Branch: MAIN
Changes since 1.8: +64 -36 lines
Diff to previous 1.8 , to selected 1.32
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, 4 months ago) by olson
Branch: MAIN
Changes since 1.7: +48 -1 lines
Diff to previous 1.7 , to selected 1.32
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, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +350 -0 lines
Diff to previous 1.6 , to selected 1.32
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, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +83 -0 lines
Diff to previous 1.5 , to selected 1.32
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, 4 months ago) by olson
Branch: MAIN
Changes since 1.4: +20 -2 lines
Diff to previous 1.4 , to selected 1.32
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, 4 months ago) by olson
Branch: MAIN
Changes since 1.3: +101 -0 lines
Diff to previous 1.3 , to selected 1.32
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, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.2: +1 -1 lines
Diff to previous 1.2 , to selected 1.32
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, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.1: +49 -0 lines
Diff to previous 1.1 , to selected 1.32
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, 4 months ago) by overbeek
Branch: MAIN
Diff to selected 1.32
initial version of FIGV.pm to demonstrate concept

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