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Revision 1.71 - (view) (download) (annotate) - [select for diffs]
Sun Jun 19 02:28:31 2005 UTC (14 years, 9 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, 10 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, 11 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 (15 years 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 (15 years 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 (15 years 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 (15 years 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 (15 years 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 (15 years 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 (15 years, 1 month 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 (15 years, 1 month 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 (15 years, 1 month 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 (15 years, 1 month 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 (15 years, 2 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 (15 years, 2 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 (15 years, 2 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 (15 years, 2 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 (15 years, 4 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 (15 years, 4 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, 5 months 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, 5 months 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, 5 months 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, 5 months 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, 6 months 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, 6 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, 7 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, 7 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, 8 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, 9 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, 9 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, 9 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, 9 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, 9 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, 9 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, 9 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, 9 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, 10 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, 10 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, 11 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, 11 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, 11 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, 11 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, 11 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 (16 years 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 (16 years 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 (16 years 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 (16 years 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 (16 years 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 (16 years 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 (16 years 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 (16 years 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 (16 years, 1 month 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 (16 years, 1 month 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 (16 years, 1 month 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 (16 years, 1 month 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 (16 years, 1 month 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 (16 years, 1 month 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 (16 years, 2 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 (16 years, 2 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 (16 years, 3 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 (16 years, 3 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 (16 years, 3 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 (16 years, 3 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 (16 years, 3 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 (16 years, 3 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 (16 years, 3 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 (16 years, 3 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 (16 years, 3 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 (16 years, 3 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 (16 years, 4 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 - (view) (download) (annotate) - [select for diffs]
Mon Dec 1 16:57:09 2003 UTC (16 years, 4 months ago) by efrank
Branch: MAIN
Branch point for: initial
Initial revision

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