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Revision 1.155 - (view) (download) (annotate) - [select for diffs]
Sat Nov 23 21:22:50 2013 UTC (5 years, 11 months ago) by golsen
Branch: MAIN
CVS Tags: HEAD, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.154: +161 -62 lines
Diff to previous 1.154
Major modifications to the blast interface.
Use BlastInterface::blast() throughout.
Add support for more program options.
Add assigned functions to the matching sequences.

Revision 1.154 - (view) (download) (annotate) - [select for diffs]
Thu Nov 7 21:39:27 2013 UTC (6 years ago) by golsen
Branch: MAIN
Changes since 1.153: +1 -2 lines
Diff to previous 1.153
Minor style change.

Revision 1.153 - (view) (download) (annotate) - [select for diffs]
Mon Oct 14 22:00:09 2013 UTC (6 years ago) by golsen
Branch: MAIN
Changes since 1.152: +85 -22 lines
Diff to previous 1.152
Updated to use new genome selector code.

Revision 1.152 - (view) (download) (annotate) - [select for diffs]
Wed Jun 19 20:17:37 2013 UTC (6 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.151: +0 -1 lines
Diff to previous 1.151
Remove debuging statement.

Revision 1.151 - (view) (download) (annotate) - [select for diffs]
Wed Jun 19 20:09:51 2013 UTC (6 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.150: +37 -13 lines
Diff to previous 1.150
Add support for "text search" for an md5.

Revision 1.150 - (view) (download) (annotate) - [select for diffs]
Mon Apr 1 14:47:01 2013 UTC (6 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.149: +22 -29 lines
Diff to previous 1.149
Changes to the display of search results, and the default number of
features returned.

Revision 1.149 - (view) (download) (annotate) - [select for diffs]
Mon Jan 21 06:43:50 2013 UTC (6 years, 9 months ago) by golsen
Branch: MAIN
Changes since 1.148: +6 -6 lines
Diff to previous 1.148
Fix an annoying issue in use statements.

Revision 1.148 - (view) (download) (annotate) - [select for diffs]
Mon Jan 7 21:42:22 2013 UTC (6 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.147: +70 -74 lines
Diff to previous 1.147
Update the complete genome blast.

Revision 1.147 - (view) (download) (annotate) - [select for diffs]
Mon Jan 7 00:57:40 2013 UTC (6 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.146: +5 -60 lines
Diff to previous 1.146
Delete old (commented out) code.
Get rid of some unused subroutine args.

Revision 1.146 - (view) (download) (annotate) - [select for diffs]
Tue Dec 18 22:41:19 2012 UTC (6 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.145: +763 -693 lines
Diff to previous 1.145
Add the new graphics for RNAs.

Revision 1.145 - (view) (download) (annotate) - [select for diffs]
Thu Nov 29 19:23:32 2012 UTC (6 years, 11 months ago) by golsen
Branch: MAIN
Changes since 1.144: +8 -10 lines
Diff to previous 1.144
Changes in link urls to work around problems with $cgi->url(-relative=>1).

Revision 1.144 - (view) (download) (annotate) - [select for diffs]
Wed Aug 22 23:11:19 2012 UTC (7 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.143: +11 -2 lines
Diff to previous 1.143
Allow md5s as a query to identical SEED proteins.

Revision 1.143 - (view) (download) (annotate) - [select for diffs]
Sun Aug 19 20:32:49 2012 UTC (7 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.142: +15 -14 lines
Diff to previous 1.142
Set the target parameter on forms.

Revision 1.142 - (view) (download) (annotate) - [select for diffs]
Sun Aug 28 02:35:05 2011 UTC (8 years, 2 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_10262011, mgrast_dev_12152011, mgrast_release_3_1_2, mgrast_version_3_2, rast_rel_2011_0928
Changes since 1.141: +1 -1 lines
Diff to previous 1.141
fix dumb bug

Revision 1.141 - (view) (download) (annotate) - [select for diffs]
Sun Aug 14 23:03:04 2011 UTC (8 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.140: +150 -48 lines
Diff to previous 1.140
Add identical sequence search function to "Searching DNA or Protein Sequences".

Revision 1.140 - (view) (download) (annotate) - [select for diffs]
Wed Jun 22 21:11:37 2011 UTC (8 years, 4 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_08022011, mgrast_dev_08112011, mgrast_release_3_1_1, myrast_rel40
Changes since 1.139: +7 -13 lines
Diff to previous 1.139
Update to use the new Sphinx support in SeedSearch and sphinx_index_genome

Revision 1.139 - (view) (download) (annotate) - [select for diffs]
Thu Jan 27 22:36:58 2011 UTC (8 years, 9 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_02212011, mgrast_dev_02222011, mgrast_dev_03252011, mgrast_dev_03312011, mgrast_dev_04012011, mgrast_dev_04052011, mgrast_dev_04082011, mgrast_dev_04132011, mgrast_dev_05262011, mgrast_dev_06072011, mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_4, mgrast_release_3_1_0, myrast_33
Changes since 1.138: +6 -4 lines
Diff to previous 1.138
different flavor of sphinx fix

Revision 1.138 - (view) (download) (annotate) - [select for diffs]
Sun Jan 2 19:19:26 2011 UTC (8 years, 10 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2011_0119
Changes since 1.137: +2 -0 lines
Diff to previous 1.137
Disable use strict 'subs' for one line of Sphinx code that looks like a
bareword if Sphix::Search did not load.

Revision 1.137 - (view) (download) (annotate) - [select for diffs]
Thu Dec 23 18:03:19 2010 UTC (8 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.136: +403 -340 lines
Diff to previous 1.136
Caching / FCGI speedup modifications.

Revision 1.136 - (view) (download) (annotate) - [select for diffs]
Mon Jun 7 20:54:49 2010 UTC (9 years, 5 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206
Changes since 1.135: +15 -10 lines
Diff to previous 1.135
sphinx fixes

Revision 1.135 - (view) (download) (annotate) - [select for diffs]
Thu Apr 15 17:13:28 2010 UTC (9 years, 7 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0526
Changes since 1.134: +34 -6 lines
Diff to previous 1.134
Add paging in sphinx search

Revision 1.134 - (view) (download) (annotate) - [select for diffs]
Thu Apr 15 16:40:22 2010 UTC (9 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.133: +56 -1 lines
Diff to previous 1.133
Add sphinx search support.

Revision 1.133 - (view) (download) (annotate) - [select for diffs]
Wed Aug 26 00:05:15 2009 UTC (10 years, 2 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2009_0925, rast_rel_2010_0118
Changes since 1.132: +8 -2 lines
Diff to previous 1.132
Make the "use new subsytem editor" message go away when it is useless.

Revision 1.132 - (view) (download) (annotate) - [select for diffs]
Fri Sep 26 14:48:24 2008 UTC (11 years, 1 month ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, rast_rel_2008_10_09, rast_rel_2008_10_29, rast_rel_2008_11_24, rast_rel_2008_12_18, rast_rel_2009_02_05, rast_rel_2009_03_26, rast_rel_2009_05_18, rast_rel_2009_07_09
Changes since 1.131: +8 -2 lines
Diff to previous 1.131
set links to seed_viewer for anno3

Revision 1.131 - (view) (download) (annotate) - [select for diffs]
Thu Sep 4 13:07:26 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, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_release_2008_09_29
Changes since 1.130: +18 -13 lines
Diff to previous 1.130
included redirect rule for anno3_mode to point fig-id searches to seedviewer.cgi instead of protein.cgi

Revision 1.130 - (view) (download) (annotate) - [select for diffs]
Tue Apr 29 08:09:05 2008 UTC (11 years, 6 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806, rast_rel_2008_06_16, rast_rel_2008_06_18, rast_rel_2008_07_21, rast_rel_2008_08_07
Changes since 1.129: +0 -1 lines
Diff to previous 1.129
Added Etracing support.

Revision 1.129 - (view) (download) (annotate) - [select for diffs]
Wed Mar 19 12:47:40 2008 UTC (11 years, 7 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.128: +2 -1 lines
Diff to previous 1.128
fixes to support comparing genomes under RAST

Revision 1.128 - (view) (download) (annotate) - [select for diffs]
Fri Mar 7 11:22:29 2008 UTC (11 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.127: +10 -0 lines
Diff to previous 1.127
add links to clust_ss.cgi to index.cgi

Revision 1.127 - (view) (download) (annotate) - [select for diffs]
Fri Nov 30 22:50:40 2007 UTC (11 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.126: +2 -0 lines
Diff to previous 1.126
add a link to daniela's new editor

Revision 1.126 - (view) (download) (annotate) - [select for diffs]
Tue Oct 30 19:14:11 2007 UTC (12 years ago) by golsen
Branch: MAIN
Changes since 1.125: +43 -2 lines
Diff to previous 1.125
Add filtering of deleted fids to the display of blast similarities.

Revision 1.125 - (view) (download) (annotate) - [select for diffs]
Fri Oct 12 15:20:58 2007 UTC (12 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.124: +20 -3 lines
Diff to previous 1.124
handle comments in function translation

Revision 1.124 - (view) (download) (annotate) - [select for diffs]
Fri Aug 10 03:16:31 2007 UTC (12 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.123: +5 -5 lines
Diff to previous 1.123
more fixes resulting from change to korgs organism list.

Revision 1.123 - (view) (download) (annotate) - [select for diffs]
Wed Aug 8 20:45:55 2007 UTC (12 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.122: +34 -16 lines
Diff to previous 1.122
Fix per-org search problem by using separated values and value->label map in the CGI scrolling list
of organism names. This shoudl get propagated to the other scrolling lists of orgs.

Revision 1.122 - (view) (download) (annotate) - [select for diffs]
Wed Jun 20 20:48:11 2007 UTC (12 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.121: +2 -0 lines
Diff to previous 1.121
fix protein page redirects for CGI.pm in perl 5.8.8.

Revision 1.121 - (view) (download) (annotate) - [select for diffs]
Tue Jun 12 21:32:30 2007 UTC (12 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.120: +0 -8 lines
Diff to previous 1.120
fix error in index.cgi

Revision 1.120 - (view) (download) (annotate) - [select for diffs]
Sat Jun 9 12:23:32 2007 UTC (12 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.119: +53 -0 lines
Diff to previous 1.119
add ability to filter aux roles on peg_to_subsystems

Revision 1.119 - (view) (download) (annotate) - [select for diffs]
Mon Apr 9 15:12:11 2007 UTC (12 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.118: +2 -1 lines
Diff to previous 1.118
fixes to Gary's comparison of genomes

Revision 1.118 - (view) (download) (annotate) - [select for diffs]
Sun Apr 8 23:21:03 2007 UTC (12 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.117: +1 -1 lines
Diff to previous 1.117
enhancements to Gary's genome comparison tool

Revision 1.117 - (view) (download) (annotate) - [select for diffs]
Sun Apr 8 21:36:16 2007 UTC (12 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.116: +22 -0 lines
Diff to previous 1.116
add Gary's compare genome stuff

Revision 1.116 - (view) (download) (annotate) - [select for diffs]
Mon Mar 12 01:13:24 2007 UTC (12 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.115: +19 -0 lines
Diff to previous 1.115
basic ability to compare metabolic reconstructions

Revision 1.115 - (view) (download) (annotate) - [select for diffs]
Mon Jan 22 20:11:25 2007 UTC (12 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.114: +10 -43 lines
Diff to previous 1.114
Adapted to new search display format for attribute-related searches.
Added tracing.

Revision 1.114 - (view) (download) (annotate) - [select for diffs]
Wed Jan 3 15:46:25 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.113: +6 -0 lines
Diff to previous 1.113
add ability to work on FIGfams

Revision 1.113 - (view) (download) (annotate) - [select for diffs]
Thu Dec 28 03:30:32 2006 UTC (12 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.112: +48 -31 lines
Diff to previous 1.112
Add support for plasmids to the genome picker.

Revision 1.112 - (view) (download) (annotate) - [select for diffs]
Fri Oct 27 00:47:48 2006 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.111: +12 -0 lines
Diff to previous 1.111
add find_ss_genes.cgi

Revision 1.111 - (view) (download) (annotate) - [select for diffs]
Wed Jul 19 21:59:16 2006 UTC (13 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.110: +1 -1 lines
Diff to previous 1.110
RAE: Getting rid of this is the new code

Revision 1.110 - (view) (download) (annotate) - [select for diffs]
Fri Jun 30 15:20:43 2006 UTC (13 years, 4 months ago) by mkubal
Branch: MAIN
Changes since 1.109: +0 -32 lines
Diff to previous 1.109
download_search_clearresults

Revision 1.109 - (view) (download) (annotate) - [select for diffs]
Fri Jun 30 15:10:18 2006 UTC (13 years, 4 months ago) by mkubal
Branch: MAIN
Changes since 1.108: +49 -3 lines
Diff to previous 1.108
download_search_clearresults

Revision 1.108 - (view) (download) (annotate) - [select for diffs]
Tue Jun 6 17:34:37 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.107: +1 -1 lines
Diff to previous 1.107
RAE: correcting the lack of sort on genomes list in index.cgi. Sorry!

Revision 1.107 - (view) (download) (annotate) - [select for diffs]
Tue Jun 6 02:25:37 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.106: +17 -2 lines
Diff to previous 1.106
RAE: adding more to heatmap, and removing the contigs for environmental samples

Revision 1.106 - (view) (download) (annotate) - [select for diffs]
Sat May 20 01:33:49 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.105: +1 -1 lines
Diff to previous 1.105
RAE: Sorting index.cgi search results by genus/species

Revision 1.105 - (view) (download) (annotate) - [select for diffs]
Fri May 5 17:52:36 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.104: +4 -1 lines
Diff to previous 1.104
hook in display of log entries

Revision 1.104 - (view) (download) (annotate) - [select for diffs]
Thu Mar 2 20:56:15 2006 UTC (13 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.103: +1 -1 lines
Diff to previous 1.103
Disable "propose_new_peg.cgi" link for blastn.

Revision 1.103 - (view) (download) (annotate) - [select for diffs]
Thu Mar 2 20:53:06 2006 UTC (13 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.102: +48 -27 lines
Diff to previous 1.102
Fixed calculation of region displayed in blastn and tblastn so that query
location is included.

Minor clean-up of "blast all complete genomes" in preparation for alignment
and tree options (not just extract sequences).

Revision 1.102 - (view) (download) (annotate) - [select for diffs]
Wed Feb 22 19:54:17 2006 UTC (13 years, 8 months ago) by paczian
Branch: MAIN
Changes since 1.101: +12 -5 lines
Diff to previous 1.101
*** empty log message ***

Revision 1.101 - (view) (download) (annotate) - [select for diffs]
Sun Feb 5 01:08:16 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.100: +1 -1 lines
Diff to previous 1.100
RAE: Swtiched to using SQL Count for the number of contigs

Revision 1.100 - (view) (download) (annotate) - [select for diffs]
Thu Jan 19 18:23:55 2006 UTC (13 years, 9 months ago) by golsen
Branch: MAIN
Changes since 1.99: +4 -2 lines
Diff to previous 1.99
Move "UniProt WebService Search" slightly to aviod increasing the page
width.

Revision 1.99 - (view) (download) (annotate) - [select for diffs]
Tue Jan 17 18:59:58 2006 UTC (13 years, 9 months ago) by mkubal
Branch: MAIN
Changes since 1.98: +2 -1 lines
Diff to previous 1.98
link to UniProt WebService

Revision 1.98 - (view) (download) (annotate) - [select for diffs]
Sun Jan 15 01:43:06 2006 UTC (13 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.97: +8 -7 lines
Diff to previous 1.97
Don't let e-value wrap in blastp of all complete genomes output table.

Revision 1.97 - (view) (download) (annotate) - [select for diffs]
Wed Jan 4 19:32:00 2006 UTC (13 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.96: +98 -69 lines
Diff to previous 1.96
Add a page for proposing a new PEG.  This is not complete, and the 'create'
button is currently functionless, but it is worth some feedback as to the
direction it is headed.

The page is linked from the graphical display of tblastn output in index.cgi
(click on the "Q" object in the figure) (intentionally obscure for now).

Add a new blast output parsing perl package.  This can read from a file,
a pipe or a text array of lines (D=STDIN).  It can collect all output
(possibly memory intensive), or it can deliver quanta of output by being
called repeatedly with the same HANDLE or ARRAY (which can be made very
memory light).  It maintains separate state information for each input,
so multiple open streams works (silly me).  [Note that this is for full
text output, not the tabular output.  The alignments are also returned.
If you don't want them, slice-up the output with map{}.  You also get
useful information such as query and subject definitions (not just ids),
and their lengths.  There are huge quantities of description in the file.
It should work with all recent versions of blastall, and all -p options,
with the possible exception of tblastx, but it might work on that too.]
This package is intended to replace, and extend, all of the functionality
previously achieved by piping output through the rationalize_blast script.
Because it no longer requires the script, the shell invocation is no
longer required.  And this works with pipes opened with '-|', so ....
It is currently used in index.cgi and propose_new_peg.cgi.

Revision 1.96 - (view) (download) (annotate) - [select for diffs]
Thu Dec 29 21:28:53 2005 UTC (13 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.95: +21 -13 lines
Diff to previous 1.95
Add genome to description lines with "Extract Matched Sequences".

Revision 1.95 - (view) (download) (annotate) - [select for diffs]
Wed Dec 28 21:22:48 2005 UTC (13 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.94: +31 -27 lines
Diff to previous 1.94
Slight clean-up of text search interface.

Revision 1.94 - (view) (download) (annotate) - [select for diffs]
Wed Dec 7 21:07:24 2005 UTC (13 years, 11 months ago) by golsen
Branch: MAIN
Changes since 1.93: +1 -1 lines
Diff to previous 1.93
Very minor text change on blastn and tblastn display.  Slight clarification.

Revision 1.93 - (view) (download) (annotate) - [select for diffs]
Mon Dec 5 19:12:12 2005 UTC (13 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.92: +17 -0 lines
Diff to previous 1.92
add license words

Revision 1.92 - (view) (download) (annotate) - [select for diffs]
Fri Nov 18 22:46:32 2005 UTC (13 years, 11 months ago) by efrank
Branch: MAIN
Changes since 1.91: +140 -0 lines
Diff to previous 1.91
extend search capability.  added dropdown that lets you select "Directly"
"Via GO" or "Via Hugo."   "Directly" corresponds to the search we've always
done.  The "Via X" causes the search to search for terms in vocabulary
X and return those terms via a substring search.  The returned, (full) terms
can then be used to launch a normal PEG search.  so, if you know say "kinase"
but not the full GO term, you can use this to find it then find the pegs
having that.

tested and proved it does not blow up if the cv files are not installed.

Revision 1.91 - (view) (download) (annotate) - [select for diffs]
Tue Nov 15 01:45:25 2005 UTC (14 years ago) by golsen
Branch: MAIN
Changes since 1.90: +36 -19 lines
Diff to previous 1.90
Fixed bug in fid-based query sequence for "blastp against complete
genomes".  A protein query is now supplied.  Made numerous small
changes in the behaviour.

One score per database sequence.
Sort by bit-score.
Turn on low-complexity filtering.
Limit output to 1000 sequences.
Put blank spaces into alias list so that it can wrap.
Use the "execute_blast" routine to exec blast as a child without shell.
Some general code clean-up.

Revision 1.90 - (view) (download) (annotate) - [select for diffs]
Thu Nov 3 22:07:59 2005 UTC (14 years ago) by olson
Branch: MAIN
CVS Tags: caBIG-00-00-00
Changes since 1.89: +1 -1 lines
Diff to previous 1.89
fixes.

Revision 1.89 - (view) (download) (annotate) - [select for diffs]
Thu Nov 3 22:04:53 2005 UTC (14 years ago) by olson
Branch: MAIN
Changes since 1.88: +12 -41 lines
Diff to previous 1.88
New index.cgi using FIG_CGI

Revision 1.88 - (view) (download) (annotate) - [select for diffs]
Mon Oct 24 21:42:53 2005 UTC (14 years ago) by golsen
Branch: MAIN
Changes since 1.87: +36 -15 lines
Diff to previous 1.87
Use exec to prevent shell interpretation of blast options (security
hole).

Revision 1.87 - (view) (download) (annotate) - [select for diffs]
Mon Oct 24 14:41:30 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.86: +2 -4 lines
Diff to previous 1.86
removing cookies

Revision 1.86 - (view) (download) (annotate) - [select for diffs]
Sun Oct 23 23:11:53 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.85: +22 -0 lines
Diff to previous 1.85
put back in Gary Olsens code to graphically display a tblastn hit

Revision 1.85 - (view) (download) (annotate) - [select for diffs]
Tue Oct 18 20:11:45 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.84: +4 -4 lines
Diff to previous 1.84
remove debug.

Revision 1.84 - (view) (download) (annotate) - [select for diffs]
Thu Oct 13 21:52:56 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.83: +1 -1 lines
Diff to previous 1.83
add an anchor to the "exporting assignments" section.

Revision 1.83 - (view) (download) (annotate) - [select for diffs]
Thu Oct 13 20:14:26 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.82: +27 -0 lines
Diff to previous 1.82
Display the file FIGdisk/config/motd, if it exists, on the SEED front apge.

Revision 1.82 - (view) (download) (annotate) - [select for diffs]
Wed Oct 12 21:03:16 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.81: +1 -1 lines
Diff to previous 1.81
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 1.81 - (view) (download) (annotate) - [select for diffs]
Sat Oct 8 14:14:47 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.80: +6 -0 lines
Diff to previous 1.80
minor fix to not include xxx entries in expanded sims

Revision 1.80 - (view) (download) (annotate) - [select for diffs]
Mon Oct 3 20:05:34 2005 UTC (14 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.79: +5 -2 lines
Diff to previous 1.79
Initial release of cookies code, including myseed

Revision 1.79 - (view) (download) (annotate) - [select for diffs]
Fri Sep 16 04:24:43 2005 UTC (14 years, 1 month ago) by mkubal
Branch: MAIN
Changes since 1.78: +3 -3 lines
Diff to previous 1.78
search can now find find phage and pi

Revision 1.78 - (view) (download) (annotate) - [select for diffs]
Tue Aug 16 20:30:26 2005 UTC (14 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.77: +15 -3 lines
Diff to previous 1.77
Added some trace messages. Fixed a compatability problem with the use of the back-tick operator.

Revision 1.77 - (view) (download) (annotate) - [select for diffs]
Wed Aug 10 17:13:45 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.76: +3 -1 lines
Diff to previous 1.76
fixes to displaying reactions and status of models

Revision 1.76 - (view) (download) (annotate) - [select for diffs]
Thu Aug 4 22:25:12 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.75: +1 -1 lines
Diff to previous 1.75
fixing help links

Revision 1.75 - (view) (download) (annotate) - [select for diffs]
Tue Jul 26 20:22:47 2005 UTC (14 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.74: +531 -553 lines
Diff to previous 1.74
Fixed indenting.

Revision 1.74 - (view) (download) (annotate) - [select for diffs]
Tue Jul 26 17:37:47 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.73: +4 -1 lines
Diff to previous 1.73
handle bad maps

Revision 1.73 - (view) (download) (annotate) - [select for diffs]
Fri Jul 15 04:48:56 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.72: +10 -6 lines
Diff to previous 1.72
fix translate functions

Revision 1.70.2.2 - (view) (download) (annotate) - [select for diffs]
Tue Jul 12 15:39:01 2005 UTC (14 years, 4 months ago) by olson
Branch: Branch-bobdev_news
CVS Tags: merge-bodev_news-3
Changes since 1.70.2.1: +1 -0 lines
Diff to previous 1.70.2.1 , to branch point 1.70 , to next main 1.155
Merged changes from trunk.

Revision 1.72 - (view) (download) (annotate) - [select for diffs]
Sun Jul 10 18:17:42 2005 UTC (14 years, 4 months ago) by golsen
Branch: MAIN
CVS Tags: merge-trunktag-bodev_news-3
Changes since 1.71: +1 -0 lines
Diff to previous 1.71
Add project description to genome statistics report.
Format PEG statistics as a table (easier to read).
Add title to "Statistics Page" when no genome is selected.
Some minor code clean up.

Revision 1.70.2.1 - (view) (download) (annotate) - [select for diffs]
Mon Jun 27 15:26:45 2005 UTC (14 years, 4 months ago) by olson
Branch: Branch-bobdev_news
CVS Tags: merge-bobdev_news-1, merge-bobdev_news-2
Changes since 1.70: +1 -1 lines
Diff to previous 1.70
Merged from trunk.

Revision 1.71 - (view) (download) (annotate) - [select for diffs]
Sun Jun 19 02:28:31 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-1, merge-trunktag-bobdev_news-2
Changes since 1.70: +1 -1 lines
Diff to previous 1.70
escape | in some search patterns

Revision 1.70 - (view) (download) (annotate) - [select for diffs]
Tue May 17 16:04:08 2005 UTC (14 years, 5 months ago) by olson
Branch: MAIN
CVS Tags: Root-bobdev_news
Branch point for: Branch-bobdev_news
Changes since 1.69: +2 -1 lines
Diff to previous 1.69
Bundle of misc bob changes, including sim computation code and search-for-substring.

Revision 1.69 - (view) (download) (annotate) - [select for diffs]
Fri Apr 15 18:13:18 2005 UTC (14 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.68: +8 -7 lines
Diff to previous 1.68
New subsystems code is now the official code.

Revision 1.68 - (view) (download) (annotate) - [select for diffs]
Thu Apr 7 04:54:02 2005 UTC (14 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.67: +4 -2 lines
Diff to previous 1.67
Add a "view simiarities" option to the text search report page.  Provide
the user with a form to define similarities options, and with links to
the protein similarities page for each of the selected proteins.

Revision 1.67 - (view) (download) (annotate) - [select for diffs]
Thu Apr 7 02:57:19 2005 UTC (14 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.66: +6 -27 lines
Diff to previous 1.66
Clean-up to remove superfluous code, variables and parameters from the
text search report code, now that RAE has done it with JavaScript (much
nicer that way).

Revision 1.66 - (view) (download) (annotate) - [select for diffs]
Wed Apr 6 22:40:40 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.65: +1 -0 lines
Diff to previous 1.65
adding help functions all over the place

Revision 1.65 - (view) (download) (annotate) - [select for diffs]
Sun Mar 27 22:20:39 2005 UTC (14 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.64: +249 -1 lines
Diff to previous 1.64
Add graphics to blastn and tblastn hits on contigs.  Hot link the proteins
to the protein pages.  Color-code proteins by their translation frame, so
the relative frames of tblastn matches and existing protein features is
easily seen.

Revision 1.64 - (view) (download) (annotate) - [select for diffs]
Wed Mar 16 17:52:34 2005 UTC (14 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.63: +9 -9 lines
Diff to previous 1.63
Cosmetic interface changes on entry page

Revision 1.63 - (view) (download) (annotate) - [select for diffs]
Sun Mar 13 21:32:38 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.62: +36 -11 lines
Diff to previous 1.62
Allow searching groups of organisms and add search to organisms.cgi

Revision 1.62 - (view) (download) (annotate) - [select for diffs]
Wed Mar 9 18:08:44 2005 UTC (14 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.61: +6 -2 lines
Diff to previous 1.61
Enable hot links from proteins and external protein identifiers on Assignment export page

Revision 1.61 - (view) (download) (annotate) - [select for diffs]
Sun Mar 6 15:10:02 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.60: +2 -2 lines
Diff to previous 1.60
disconnect get_attributes until I can talk to Rob

Revision 1.60 - (view) (download) (annotate) - [select for diffs]
Tue Feb 15 05:17:31 2005 UTC (14 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.59: +8 -10 lines
Diff to previous 1.59
Add some more formating nicities.

Revision 1.59 - (view) (download) (annotate) - [select for diffs]
Tue Feb 15 05:01:23 2005 UTC (14 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.58: +54 -26 lines
Diff to previous 1.58
Make organism-specific text search an option, not default.  Remove filtering of roles (which I think was incorrect).  Add some formating nicities.

Revision 1.58 - (view) (download) (annotate) - [select for diffs]
Fri Jan 28 18:16:57 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.57: +1 -1 lines
Diff to previous 1.57
Added a reset button to index.cgi so you can escape from a bug where you have selected an organism
and then can't deselect that.

Revision 1.57 - (view) (download) (annotate) - [select for diffs]
Wed Jan 26 23:46:20 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.56: +10 -0 lines
Diff to previous 1.56
fix bug in removing genomes from a subsystem

Revision 1.56 - (view) (download) (annotate) - [select for diffs]
Wed Jan 26 19:58:00 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.55: +16 -7 lines
Diff to previous 1.55
allow multiple translations

Revision 1.55 - (view) (download) (annotate) - [select for diffs]
Sun Jan 23 15:43:49 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.54: +12 -8 lines
Diff to previous 1.54
fixes to index.cgi

Revision 1.54 - (view) (download) (annotate) - [select for diffs]
Wed Dec 8 16:56:24 2004 UTC (14 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.53: +24 -1 lines
Diff to previous 1.53
add informative errors about the server not being running.

Revision 1.53 - (view) (download) (annotate) - [select for diffs]
Wed Nov 24 18:27:06 2004 UTC (14 years, 11 months ago) by redwards
Branch: MAIN
Changes since 1.52: +25 -0 lines
Diff to previous 1.52
Modified index.cgi so that if an organism is selected the text search will only return results from
that organism, as per Matt's request. If no organism is selected this will still return all the results

Revision 1.52 - (view) (download) (annotate) - [select for diffs]
Thu Nov 4 18:27:29 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.51: +11 -3 lines
Diff to previous 1.51
allow external IDs on subsystem displays

Revision 1.51 - (view) (download) (annotate) - [select for diffs]
Thu Nov 4 16:13:35 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.50: +65 -1 lines
Diff to previous 1.50
add ability to find subsystems for OlgaZ

Revision 1.50 - (view) (download) (annotate) - [select for diffs]
Sun Oct 24 02:45:41 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.49: +16 -4 lines
Diff to previous 1.49
minor additions to genome statistics

Revision 1.49 - (view) (download) (annotate) - [select for diffs]
Sat Oct 23 19:51:41 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.48: +27 -3 lines
Diff to previous 1.48
introduce genome statistics

Revision 1.48 - (view) (download) (annotate) - [select for diffs]
Fri Oct 8 22:04:48 2004 UTC (15 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.47: +2 -2 lines
Diff to previous 1.47
Added number of contigs to menu

Revision 1.47 - (view) (download) (annotate) - [select for diffs]
Sat Sep 11 00:45:40 2004 UTC (15 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.46: +80 -20 lines
Diff to previous 1.46
Add domain and completeness controls to organism selection list.

Revision 1.46 - (view) (download) (annotate) - [select for diffs]
Tue Sep 7 02:54:16 2004 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.45: +8 -6 lines
Diff to previous 1.45
add new subsystem interface

Revision 1.45 - (view) (download) (annotate) - [select for diffs]
Fri Aug 20 22:19:55 2004 UTC (15 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.44: +41 -28 lines
Diff to previous 1.44
Clean-up of blast interface in preparation for adding functionality to tblastn output

Revision 1.44 - (view) (download) (annotate) - [select for diffs]
Tue Jul 27 21:41:05 2004 UTC (15 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.43: +1 -1 lines
Diff to previous 1.43
testing that my cvs works now

Revision 1.43 - (view) (download) (annotate) - [select for diffs]
Wed Jun 30 17:59:52 2004 UTC (15 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.42: +1 -1 lines
Diff to previous 1.42
change label on map section

Revision 1.42 - (view) (download) (annotate) - [select for diffs]
Mon Jun 28 20:22:42 2004 UTC (15 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.41: +16 -16 lines
Diff to previous 1.41
Move the subsystem block out of the middle of the other form

Revision 1.41 - (view) (download) (annotate) - [select for diffs]
Mon Jun 28 19:36:33 2004 UTC (15 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.40: +42 -37 lines
Diff to previous 1.40
more cleanup

Revision 1.40 - (view) (download) (annotate) - [select for diffs]
Mon Jun 28 19:14:22 2004 UTC (15 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.39: +0 -19 lines
Diff to previous 1.39
New page header

Revision 1.39 - (view) (download) (annotate) - [select for diffs]
Wed Jun 23 15:41:33 2004 UTC (15 years, 4 months ago) by disz
Branch: MAIN
Changes since 1.38: +7 -7 lines
Diff to previous 1.38
local map fixes, removed extra subsystem logon lines

Revision 1.38 - (view) (download) (annotate) - [select for diffs]
Wed Jun 16 14:25:36 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.37: +11 -2 lines
Diff to previous 1.37
New map support.

Revision 1.37 - (view) (download) (annotate) - [select for diffs]
Wed Jun 16 14:06:17 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.36: +4 -1 lines
Diff to previous 1.36
add link to control panel

Revision 1.36 - (view) (download) (annotate) - [select for diffs]
Mon Jun 14 22:09:40 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.35: +11 -3 lines
Diff to previous 1.35
add cvs release date to header

Revision 1.35 - (view) (download) (annotate) - [select for diffs]
Thu Jun 3 00:17:29 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.34: +2 -3 lines
Diff to previous 1.34
fix invocation of protein.cgi from index.cgi

Revision 1.34 - (view) (download) (annotate) - [select for diffs]
Tue May 11 16:17:06 2004 UTC (15 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.33: +1 -2 lines
Diff to previous 1.33
Remove the old p2p link.

Revision 1.33 - (view) (download) (annotate) - [select for diffs]
Sat May 8 07:56:45 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.32: +3 -1 lines
Diff to previous 1.32
minor fixes

Revision 1.32 - (view) (download) (annotate) - [select for diffs]
Wed May 5 16:40:35 2004 UTC (15 years, 6 months ago) by disz
Branch: MAIN
Changes since 1.31: +1 -2 lines
Diff to previous 1.31
Single p2 link again

Revision 1.31 - (view) (download) (annotate) - [select for diffs]
Mon May 3 17:04:11 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.30: +34 -0 lines
Diff to previous 1.30
fixes to links in HTML.pm, code to sync systems after an update, and fixes to index.cgi and protein.cgi

Revision 1.30 - (view) (download) (annotate) - [select for diffs]
Fri Apr 23 21:49:03 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.29: +117 -6 lines
Diff to previous 1.29
fixes to index.cgi to blast against all complete

Revision 1.29 - (view) (download) (annotate) - [select for diffs]
Sun Apr 11 20:22:18 2004 UTC (15 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.28: +10 -3 lines
Diff to previous 1.28
Minor format changes in Searching DNA or Protein Sequences; primarily a test that my code is upto date

Revision 1.28 - (view) (download) (annotate) - [select for diffs]
Thu Apr 8 16:38:05 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.27: +51 -4 lines
Diff to previous 1.27
support translation generation of new assignments

Revision 1.27 - (view) (download) (annotate) - [select for diffs]
Fri Apr 2 18:02:20 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.26: +7 -1 lines
Diff to previous 1.26
add a new version of the spreadsheet software

Revision 1.26 - (view) (download) (annotate) - [select for diffs]
Thu Apr 1 18:36:23 2004 UTC (15 years, 7 months ago) by disz
Branch: MAIN
Changes since 1.25: +4 -2 lines
Diff to previous 1.25
Added subsystems to p2p

Revision 1.25 - (view) (download) (annotate) - [select for diffs]
Fri Mar 26 21:54:11 2004 UTC (15 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.24: +1 -1 lines
Diff to previous 1.24
Fix baseurl stuff some more.

Revision 1.24 - (view) (download) (annotate) - [select for diffs]
Fri Mar 26 21:42:55 2004 UTC (15 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.23: +2 -1 lines
Diff to previous 1.23
add hostname to the banner

Revision 1.23 - (view) (download) (annotate) - [select for diffs]
Sun Mar 21 02:20:55 2004 UTC (15 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.22: +18 -8 lines
Diff to previous 1.22
Add HTML structuring tags in HTML.pm; Add titles to some pages in index.cgi and protein.cgi; Pretty-up the HTML produced for tables (add newlines and indents)

Revision 1.22 - (view) (download) (annotate) - [select for diffs]
Fri Mar 19 22:48:15 2004 UTC (15 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.21: +4 -4 lines
Diff to previous 1.21
More cleanly localize checkbox control for show_indexed_objects.

Revision 1.21 - (view) (download) (annotate) - [select for diffs]
Fri Mar 19 21:58:31 2004 UTC (15 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.20: +13 -13 lines
Diff to previous 1.20
Relative base address support and cgi_url() based on current http request

Revision 1.20 - (view) (download) (annotate) - [select for diffs]
Fri Mar 5 19:18:37 2004 UTC (15 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.19: +1 -1 lines
Diff to previous 1.19
CHange reference to p2p update script

Revision 1.19 - (view) (download) (annotate) - [select for diffs]
Mon Feb 23 17:28:24 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.18: +11 -0 lines
Diff to previous 1.18
fixes to ssa.cgi

Revision 1.18 - (view) (download) (annotate) - [select for diffs]
Thu Feb 19 14:37:02 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.17: +2 -1 lines
Diff to previous 1.17
fix urls to get them plugged correctly

Revision 1.17 - (view) (download) (annotate) - [select for diffs]
Sun Feb 15 17:12:54 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.16: +165 -54 lines
Diff to previous 1.16
added Gary Olsen changes

Revision 1.16 - (view) (download) (annotate) - [select for diffs]
Fri Feb 13 20:29:28 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.15: +1 -0 lines
Diff to previous 1.15
clip master: when saving assignments

Revision 1.15 - (view) (download) (annotate) - [select for diffs]
Tue Feb 10 18:44:58 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.14: +5 -2 lines
Diff to previous 1.14
try to fix importing assignments (the user)

Revision 1.14 - (view) (download) (annotate) - [select for diffs]
Fri Jan 16 14:59:48 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.13: +9 -1 lines
Diff to previous 1.13
add ability to process assignment sets

Revision 1.13 - (view) (download) (annotate) - [select for diffs]
Wed Jan 14 20:20:32 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.12: +17 -6 lines
Diff to previous 1.12
synch up Ross

Revision 1.12 - (view) (download) (annotate) - [select for diffs]
Wed Jan 7 03:34:13 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.11: +1 -1 lines
Diff to previous 1.11
make Assignments files have readable names

Revision 1.11 - (view) (download) (annotate) - [select for diffs]
Wed Jan 7 03:12:44 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.10: +15 -1 lines
Diff to previous 1.10
make p2p assignments get written to Assignments

Revision 1.10 - (view) (download) (annotate) - [select for diffs]
Tue Jan 6 18:14:48 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.9: +4 -1 lines
Diff to previous 1.9
fix stick behavior for checked sims

Revision 1.9 - (view) (download) (annotate) - [select for diffs]
Sat Jan 3 14:13:48 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +1 -38 lines
Diff to previous 1.8
fix P2P to use get_assignments

Revision 1.8 - (view) (download) (annotate) - [select for diffs]
Sat Jan 3 13:47:50 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +10 -2 lines
Diff to previous 1.7
added ma field to annotations to indicate master assignments

Revision 1.7 - (view) (download) (annotate) - [select for diffs]
Sat Jan 3 06:03:43 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +104 -1 lines
Diff to previous 1.6
changes to annotations to allow extraction of assignments

Revision 1.6 - (view) (download) (annotate) - [select for diffs]
Sun Dec 28 17:11:29 2003 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +4 -3 lines
Diff to previous 1.5
cleanup issues relating to large numbers of partial genomes

Revision 1.5 - (view) (download) (annotate) - [select for diffs]
Tue Dec 23 16:53:37 2003 UTC (15 years, 10 months ago) by efrank
Branch: MAIN
Changes since 1.4: +7 -1 lines
Diff to previous 1.4
P2P Stuff

Revision 1.4 - (view) (download) (annotate) - [select for diffs]
Wed Dec 17 16:27:11 2003 UTC (15 years, 10 months ago) by efrank
Branch: MAIN
Changes since 1.3: +1 -0 lines
Diff to previous 1.3
:P2P Stuff

Revision 1.3 - (view) (download) (annotate) - [select for diffs]
Tue Dec 16 16:59:42 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
Changes since 1.2: +0 -13 lines
Diff to previous 1.2
Removed stray tool_hdr content that got copied in here

Revision 1.2 - (view) (download) (annotate) - [select for diffs]
Wed Dec 3 21:24:31 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
CVS Tags: delong-01, delong-02
Changes since 1.1: +18 -1 lines
Diff to previous 1.1
*** empty log message ***

Revision 1.1.1.1 - (view) (download) (annotate) - [select for diffs] (vendor branch)
Mon Dec 1 16:57:09 2003 UTC (15 years, 11 months ago) by efrank
Branch: initial
CVS Tags: V00-00-00, V00-00-01, V00-00-02, init, preRossMerge-03Dec03
Changes since 1.1: +0 -0 lines
Diff to previous 1.1 , to next main 1.155

import


Revision 1.1 - (view) (download) (annotate) - [select for diffs]
Mon Dec 1 16:57:09 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
Branch point for: initial
Initial revision

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