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Revision 1.54 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 26 20:25:20 2009 UTC (10 years, 3 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, rast_rel_2009_0925, rast_rel_2010_0118, rast_rel_2010_0526, rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119
Changes since 1.53: +21 -13 lines
Diff to previous 1.53
Optimize to_structured_english.

Revision 1.53 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 21 18:56:28 2009 UTC (10 years, 6 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_07_09
Changes since 1.52: +8 -7 lines
Diff to previous 1.52
Fixed run-time warning in GetHopeReactions.

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 13 07:39:59 2009 UTC (10 years, 8 months ago) by paczian
Branch: MAIN
CVS Tags: rast_rel_2009_05_18
Changes since 1.51: +1 -1 lines
Diff to previous 1.51
removed STDERR for wikipedia

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 5 19:56:13 2009 UTC (10 years, 9 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_03_26
Changes since 1.50: +46 -0 lines
Diff to previous 1.50
Added a new method to clean up FASTA sequences.

Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 19 20:27:54 2009 UTC (10 years, 10 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_02_05
Changes since 1.49: +130 -13 lines
Diff to previous 1.49
Moved in the crude-distance subroutine so it can be shared. Fixed an error in the BBH API and documentation.

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 9 12:29:53 2009 UTC (10 years, 11 months ago) by paczian
Branch: MAIN
Changes since 1.48: +12 -5 lines
Diff to previous 1.48
enhanced ec number detection in function assignment

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 3 09:16:46 2008 UTC (11 years, 1 month ago) by paczian
Branch: MAIN
CVS Tags: mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, rast_rel_2008_11_24, rast_rel_2008_12_18
Changes since 1.47: +112 -5 lines
Diff to previous 1.47
moved encoded_annotation_to_natural_english to this module to be self contained

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Nov 1 17:15:38 2008 UTC (11 years, 1 month ago) by golsen
Branch: MAIN
Changes since 1.46: +1 -1 lines
Diff to previous 1.46
Change a 'use' to a 'require' so that the failure is graceful.

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 31 16:22:24 2008 UTC (11 years, 1 month ago) by paczian
Branch: MAIN
Changes since 1.45: +7 -4 lines
Diff to previous 1.45
formulated encoded_annotation_to_natural_english call so it does not break when SeedViewer is not checked out

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 31 11:08:31 2008 UTC (11 years, 1 month ago) by paczian
Branch: MAIN
Changes since 1.44: +4 -2 lines
Diff to previous 1.44
upgraded add_func_assertion to parse encoded protein functions

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 20 20:41:47 2008 UTC (11 years, 1 month ago) by disz
Branch: MAIN
Changes since 1.43: +3 -1 lines
Diff to previous 1.43
Fixed test of Variant code in structured english

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 18 10:14:31 2008 UTC (11 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.42: +5 -5 lines
Diff to previous 1.42
Fixed a pattern for matching FIG IDs.

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 9 18:02:03 2008 UTC (11 years, 2 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_10_29
Changes since 1.41: +2 -1 lines
Diff to previous 1.41
Fixed bad subsystem call.

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 16 20:10:05 2008 UTC (11 years, 2 months ago) by disz
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_rel_2008_10_09, rast_release_2008_09_29
Changes since 1.40: +20 -15 lines
Diff to previous 1.40
New wording in structured english

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 7 03:11:45 2008 UTC (11 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.39: +7 -7 lines
Diff to previous 1.39
Fixed usable_subsystem to treat nonexistent  subsystems as unusable.

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 5 01:42:40 2008 UTC (11 years, 3 months ago) by disz
Branch: MAIN
Changes since 1.38: +17 -3 lines
Diff to previous 1.38
Check for variant code of 0, -1 in to_structured english

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 3 20:28:44 2008 UTC (11 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.37: +73 -0 lines
Diff to previous 1.37
Added the search code for the wiki ID box.

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 2 18:41:41 2008 UTC (11 years, 3 months ago) by disz
Branch: MAIN
Changes since 1.36: +1 -1 lines
Diff to previous 1.36
Fixed Structured English to include items that aren't in subsystems

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 12 06:35:42 2008 UTC (11 years, 4 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806, rast_rel_2008_08_07
Changes since 1.35: +43 -2 lines
Diff to previous 1.35
Fixed for sprout compatability.

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 6 21:45:05 2008 UTC (11 years, 4 months ago) by paczian
Branch: MAIN
Changes since 1.34: +4 -4 lines
Diff to previous 1.34
commented out print STDERR lines

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 6 14:03:51 2008 UTC (11 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.33: +306 -0 lines
Diff to previous 1.33
Moved to_structured_english to FIGRules.

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 16 19:27:12 2008 UTC (11 years, 7 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_06_16, rast_rel_2008_06_18, rast_rel_2008_07_21
Changes since 1.32: +11 -3 lines
Diff to previous 1.32
Added load information to the robot trace.

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 16 08:30:21 2008 UTC (11 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.31: +26 -0 lines
Diff to previous 1.31
Added a method for logging robot activity.

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 14 20:42:30 2008 UTC (11 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.30: +2 -2 lines
Diff to previous 1.30
Fixed spelling error in msnbot name. Made google test tring shorter so that it catches more bots.

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 5 21:40:39 2008 UTC (11 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.29: +68 -0 lines
Diff to previous 1.29
Added a robot mode test function.

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 23 15:53:43 2008 UTC (11 years, 8 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.28: +10 -10 lines
Diff to previous 1.28
Changed nmpdr_mode to allow use of a cookie for overriding a script's operating mode.

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 5 01:22:19 2008 UTC (11 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.27: +1 -1 lines
Diff to previous 1.27
Fixed coupling function to fail more softly.

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 6 13:49:52 2007 UTC (12 years ago) by parrello
Branch: MAIN
Changes since 1.26: +28 -28 lines
Diff to previous 1.26
Changed POD format for better compatability with Wiki.

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 29 17:46:08 2007 UTC (12 years ago) by parrello
Branch: MAIN
Changes since 1.25: +135 -3 lines
Diff to previous 1.25
Added nmpdr_mode function.

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 19 20:34:58 2007 UTC (12 years ago) by olson
Branch: MAIN
Changes since 1.24: +4 -4 lines
Diff to previous 1.24
Changes to make the passing of a sims cutoff of 0 work properly (using defined($maxP) instead  of $maxP
as a test to see if maxP was set).

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 20 16:01:30 2007 UTC (12 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.23: +3 -3 lines
Diff to previous 1.23
Change default server URLs.

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 17 19:52:10 2007 UTC (12 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.22: +15 -14 lines
Diff to previous 1.22
fix typoe

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 22 18:50:08 2007 UTC (12 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.21: +38 -0 lines
Diff to previous 1.21
Added a method to compute the correct end-of-line character for a user's web browser.

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 16 19:35:23 2007 UTC (12 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.20: +4 -0 lines
Diff to previous 1.20
Moved in coupling server code.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 7 19:31:45 2007 UTC (12 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.19: +132 -1 lines
Diff to previous 1.19
Added support for the coupling server.
Moved in temporary file-name methods from SearchHelper.

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 18 19:28:37 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.18: +3 -2 lines
Diff to previous 1.18
fix sim return for mutiple ids

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 27 22:12:52 2007 UTC (12 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.17: +100 -0 lines
Diff to previous 1.17
Added methods to encode and decode BLAST scores.

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 10 03:47:58 2007 UTC (12 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.16: +128 -25 lines
Diff to previous 1.16
Moved in the guts of wikipedia_link.
Changed the network sims method to be more compatible with Sprout.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 2 23:17:31 2007 UTC (12 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.15: +8 -0 lines
Diff to previous 1.15
move simserver url config into FIG_Config

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 6 03:32:37 2006 UTC (13 years ago) by parrello
Branch: MAIN
Changes since 1.14: +94 -2 lines
Diff to previous 1.14
Added a method to provide support for the BBH needs of the signature genes tool.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 2 02:57:13 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.13: +4 -0 lines
Diff to previous 1.13
Added more tracing.

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 26 13:36:19 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.12: +35 -0 lines
Diff to previous 1.12
Added a method to parse feature IDs.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 14 14:50:37 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.11: +17 -8 lines
Diff to previous 1.11
Added retry logic to the BBH service.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 14 14:24:32 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.10: +1 -1 lines
Diff to previous 1.10
Fixed a spelling error.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 14 14:18:13 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.9: +1 -1 lines
Diff to previous 1.9
Fixed error message.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 14 14:11:51 2006 UTC (13 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.8: +46 -0 lines
Diff to previous 1.8
Converted to provide BBH server support for Sprout.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 10 07:28:37 2006 UTC (13 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.7: +1 -1 lines
Diff to previous 1.7
Fixed a comment.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 17 20:27:24 2006 UTC (13 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.6: +2 -1 lines
Diff to previous 1.6
swing simserver over to anno-2.

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 25 00:55:24 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.5: +1 -0 lines
Diff to previous 1.5
*** empty log message ***

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 25 00:14:30 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.4: +215 -0 lines
Diff to previous 1.4
Added a method to request similarities from the network.

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 19 03:39:59 2006 UTC (13 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.3: +170 -24 lines
Diff to previous 1.3
Added a method to compute upstream regions.

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 7 19:38:22 2005 UTC (14 years ago) by golsen
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.2: +1 -1 lines
Diff to previous 1.2
Don't mean to be pedantic, but I figured that I might as well add newlines
at the end of text files that lack one.  Identified with a script:

/bin/sh -O extglob -c 'for f in */*.@(c|css|html|js|pl|pm|py|TXT); do perl -e '"'"'while(<>) {$s = ! /\n$/} exit $s'"'"' $f || echo $f; done'

fixed with a script:

/bin/sh
for file in _list_; do echo "" >> $file; done

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 5 19:06:30 2005 UTC (14 years ago) by olson
Branch: MAIN
Changes since 1.1: +17 -0 lines
Diff to previous 1.1
Added license words.

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 12 20:34:04 2005 UTC (14 years, 11 months ago) by olson
Branch: MAIN
CVS Tags: Root-bobdev_news, caBIG-00-00-00, caBIG-dataload-0, merge-bobdev_news-1, merge-bobdev_news-2, merge-bodev_news-3, merge-trunktag-bobdev_news-1, merge-trunktag-bobdev_news-2, merge-trunktag-bodev_news-3
Branch point for: Branch-bobdev_news
Move this here from Sprout.

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