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Revision 1.436 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 5 01:08:16 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.435: +47 -0 lines
Diff to previous 1.435
RAE: Swtiched to using SQL Count for the number of contigs

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Fri Feb 3 18:42:27 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.434: +3 -1 lines
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$/ fixes

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Tue Jan 31 04:09:13 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.433: +32 -51 lines
Diff to previous 1.433
fix of clustering

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Mon Jan 30 19:36:04 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.432: +6 -2 lines
Diff to previous 1.432
use is_genome checks for subsystems?

Revision 1.432 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 29 19:48:31 2006 UTC (13 years, 10 months ago) by efrank
Branch: MAIN
Changes since 1.431: +10 -6 lines
Diff to previous 1.431
fixes for controlled vocab from NCI demo.  fixes to accomodate RAE's
changes in key_info.  commit independent of other pkgs.

Revision 1.431 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 28 04:23:47 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.430: +29 -1 lines
Diff to previous 1.430
RAE: Updating POM -- pieces of metabolism

Revision 1.430 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 25 18:57:05 2006 UTC (13 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.429: +29 -9 lines
Diff to previous 1.429
Add more sim compute stuff.

Revision 1.429 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 23 19:20:54 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.428: +131 -4 lines
Diff to previous 1.428
changes to support dynamic sims and updates

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Wed Jan 18 17:41:13 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.427: +34 -0 lines
Diff to previous 1.427
RAE: Adding NMPDR checkbox to subsys.cgi

Revision 1.427 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 18 17:14:07 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.426: +36 -2 lines
Diff to previous 1.426
RAE: Adding NMPDR checkbox to subsys.cgi

Revision 1.426 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 16 00:22:42 2006 UTC (13 years, 10 months ago) by efrank
Branch: MAIN
Changes since 1.425: +49 -7 lines
Diff to previous 1.425
=head3 by_raw_alias

usage: $peg = $fig->by_raw_alias($alias)

Returns all FIG ids having the given alias.  Unlike by_alias, we do not attempt any
kind of normalization.  I'm not sure this function is needed, but by_alias searches
only in ext_alias table whereas here I'm searching in the features table.  ext_alias
does not have all external aliases which is keeping my code from working.  In partic\
ular,
it lacks EnsemblGene.  It would be nice to combine these two functions.  -Ed

=cut

=head3 get_cv_attributes

A simple wrapper around get_attriubtes to return only those attributes
that have meta_data indicating that the key is a controlled vocabulary.

See get_attributes for description of arguments and return types.

=cut

Revision 1.425 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 15 19:11:31 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.424: +2 -2 lines
Diff to previous 1.424
correction to is_deleted_fid

Revision 1.424 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 15 15:11:46 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.423: +2 -0 lines
Diff to previous 1.423
is_deleted_fid should return 0, if the argument is not a fid

Revision 1.423 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 14 23:55:45 2006 UTC (13 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.422: +1 -1 lines
Diff to previous 1.422
Fine tuning of the add a feature software.  (Still more to come in dealing
with previously deleted features)

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Fri Jan 13 22:15:35 2006 UTC (13 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.421: +26 -16 lines
Diff to previous 1.421
Minor changes to assign_function:
   Convert user of form master:xxx to master (clearly the intent)
   Clean-up and clarify flow

Revision 1.421 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 13 20:22:39 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.420: +200 -70 lines
Diff to previous 1.420
fixes to deleted_features, replace_features_with, etc

Revision 1.420 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 13 06:54:49 2006 UTC (13 years, 10 months ago) by parrello
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Changes since 1.419: +8 -9 lines
Diff to previous 1.419
Converted the relative-to-absolute path code to use a system-independent PERL utility.

Revision 1.419 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 12 23:48:15 2006 UTC (13 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.418: +101 -52 lines
Diff to previous 1.418
Greatly enhanced error checking and reporting for add_feature.
Make sure feature does not already exist (return existing fid if
this is the case).

Revision 1.418 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 12 04:14:24 2006 UTC (13 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.417: +50 -20 lines
Diff to previous 1.417
Running version of adding a feature with a fid from the clearinghouse.

Revision 1.417 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 11 22:58:57 2006 UTC (13 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.416: +30 -0 lines
Diff to previous 1.416
add_Feature additions

Revision 1.416 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 10 16:45:24 2006 UTC (13 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.415: +10 -1 lines
Diff to previous 1.415
fix to verify_dir

Revision 1.415 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 5 01:16:45 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.414: +7 -10 lines
Diff to previous 1.414
RAE: Correcting what is meant by non-zero variant code

Revision 1.414 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 3 18:32:04 2006 UTC (13 years, 11 months ago) by efrank
Branch: MAIN
Changes since 1.413: +48 -0 lines
Diff to previous 1.413
add subsystems_having_organisms

Revision 1.413 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 2 23:58:49 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.412: +1 -1 lines
Diff to previous 1.412
RAE: Adding statistics to protein families

Revision 1.412 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 30 11:52:40 2005 UTC (13 years, 11 months ago) by heiko
Branch: MAIN
Changes since 1.411: +83 -0 lines
Diff to previous 1.411
added best_bbh_candidates_additional function

Revision 1.411 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 24 21:03:57 2005 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.410: +4 -4 lines
Diff to previous 1.410
serious problem in setting max_expand in FIG::sims

Revision 1.410 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 21 23:51:50 2005 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.409: +60 -2 lines
Diff to previous 1.409
RAE: Adding statistics to protein families

Revision 1.409 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 20 17:59:08 2005 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.408: +39 -1 lines
Diff to previous 1.408
add abstract functional coupling

Revision 1.408 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 10 23:05:58 2005 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.407: +26 -0 lines
Diff to previous 1.407
RAE: extending protein families

Revision 1.407 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 10 18:08:17 2005 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.406: +20 -20 lines
Diff to previous 1.406
RAE: Changed attribute key to tag throughout

Revision 1.406 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 8 18:07:54 2005 UTC (13 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.405: +13 -0 lines
Diff to previous 1.405
Added a method that can be used to determine whether the data is being taken from SEED or NMPDR.

Revision 1.405 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 6 06:57:17 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.404: +28 -0 lines
Diff to previous 1.404
Updating protein families

Revision 1.404 - (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 1.403: +17 -0 lines
Diff to previous 1.403
Added license words.

Revision 1.403 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 2 20:13:44 2005 UTC (14 years ago) by olson
Branch: MAIN
Changes since 1.402: +16 -1 lines
Diff to previous 1.402
Don't save absolute paths in file_table in database; rather, strip them on file2N and restore on N2file.

Revision 1.402 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 1 22:28:13 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.401: +7 -1 lines
Diff to previous 1.401
Making attributes work for Ed

Revision 1.401 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 28 02:01:18 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.400: +1 -1 lines
Diff to previous 1.400
minor fix in reconizing aliases

Revision 1.400 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Nov 27 22:17:15 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.399: +2 -2 lines
Diff to previous 1.399
correcting tag names

Revision 1.399 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 24 02:12:41 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.398: +88 -33 lines
Diff to previous 1.398
updating subsys.cgi so that it works with attributes again. Quickly, this time

Revision 1.398 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 24 01:00:45 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.397: +33 -5 lines
Diff to previous 1.397
correcting and extending get_distinct_keys

Revision 1.397 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 23 23:24:11 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.396: +11 -3 lines
Diff to previous 1.396
correcting return when no data supplied

Revision 1.396 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 23 23:05:25 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.395: +16 -8 lines
Diff to previous 1.395
removing error messages from attributes

Revision 1.395 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 23 20:34:59 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.394: +287 -310 lines
Diff to previous 1.394
major changes to attributes and protein families. There are changes to several modules to deal with new attributes database, and simultaneous updates to protein families

Revision 1.394 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 23 17:49:12 2005 UTC (14 years ago) by parrello
Branch: MAIN
Changes since 1.393: +609 -3 lines
Diff to previous 1.393
Added access methods for the UserData object.
Fixed some documentation.

Revision 1.393 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 22 14:57:50 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.392: +5 -4 lines
Diff to previous 1.392
fixes to characterization of hypos

Revision 1.392 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 10 20:16:07 2005 UTC (14 years ago) by efrank
Branch: MAIN
CVS Tags: caBIG-00-00-00
Changes since 1.391: +1 -1 lines
Diff to previous 1.391
move cv files from Global to Global/CV

Revision 1.391 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 10 19:56:33 2005 UTC (14 years ago) by efrank
Branch: MAIN
Changes since 1.390: +32 -0 lines
Diff to previous 1.390
add search_cv_file as an encapsulation.
   cv, search_term -> ( (cv, term_id,term), ... )

I also have changes in index searching that I'm trying _not_ to commit.
If you see wierdness, i messed up the commit so yell at me.

Revision 1.390 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 2 21:39:25 2005 UTC (14 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.389: +126 -36 lines
Diff to previous 1.389
Fixed some documentation.
Rewrote some ENV tests to avoid compiler warnings.
Removed redundant variable declarations to avoid compiler warnings.
Added a new method to test whether a role ID is an EC number.

Revision 1.389 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 28 16:05:02 2005 UTC (14 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.388: +1 -1 lines
Diff to previous 1.388
Strip  xxx identifiers from feature_aliases output.

Revision 1.388 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 28 16:03:12 2005 UTC (14 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.387: +62 -0 lines
Diff to previous 1.387
Add run_gathering_output() for safe backtick-like  functionality.

Revision 1.387 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 27 16:20:34 2005 UTC (14 years, 1 month ago) by efrank
Branch: MAIN
Changes since 1.386: +16 -1 lines
Diff to previous 1.386
make add_cv_term give error status if passed empty strings.
make search_index_by_attribute be case insensitive.

How do you do this on just one line?  Right now I used 2 lines (a bunch of times)
     $user =~ s/^\s*//g;
     $user =~ s/\s*$//g;

Revision 1.386 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 26 22:12:03 2005 UTC (14 years, 1 month ago) by efrank
Branch: MAIN
Changes since 1.385: +37 -4 lines
Diff to previous 1.385
key_info:  modify to return  nothing if the passed key has no associated
	   data (rather than returning empty hash).

search_index:  modify to call search_index_by_attributes so that attributes are
	   included in the search without building glimpse indexes

search_index_by_attribues:   supports search_index.

Also, in search_index, turned off old attribute search.

Revision 1.385 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 26 19:33:11 2005 UTC (14 years, 1 month ago) by efrank
Branch: MAIN
Changes since 1.384: +7 -3 lines
Diff to previous 1.384
key_info() was returning and empty hash to say it had nothing that matches
a key.  this was making downstream code very confusing.  so now i return
nothing if there's no match for the key.

Revision 1.384 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 26 16:38:12 2005 UTC (14 years, 1 month ago) by efrank
Branch: MAIN
Changes since 1.383: +76 -0 lines
Diff to previous 1.383
add new sub, add_cv_term($user, $peg, $vocab, $id, $term);

=head3 add_cv_term

Add a controlled vocabulary term to a peg.  Pass in the peg, the vocab
name, the termId, and the term (see next paragraph).  returns error string
if problem, else returns nothing.

   my $status = $fig->add_cv_term( "master:EdF",
   				   "fig|9606.3.peg.26823", "MyVocab", "1234", "A thing of wonder.");
				      if ($status) {print "error adding cv term: $status\n";}

				      Controlled vocabulary is read-only text associated with a peg.  Each
				      is a triple, namely (vocab name, termId, term text).  The termId is an
				      id that is used in the particulary vocabulary and the term text is the
				      actual term.  For example, the GO has the term "U12-type nuclear mRNA
				      branch site recognition" with termId GO:0000371.  Thus, the triplet is
				      (GO, GO:0000371, "U12-type nuclear mRNA branch site recognition").
				      Don't be confused by the GO: in GO:0000371.  We don't add the GO:.
				      That's just what GO decided to do.

				      termIds can not have ';' in them.

				      This routine encapsulates our present implementation via attributes.

				      =cut

Revision 1.383 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 25 14:50:23 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.382: +45 -10 lines
Diff to previous 1.382
protein families again

Revision 1.382 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 24 21:50:35 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.381: +40 -0 lines
Diff to previous 1.381
Assorted relative-path fixes.

remove length check in indexing function assignments.

Revision 1.381 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 24 19:36:38 2005 UTC (14 years, 1 month ago) by mkubal
Branch: MAIN
Changes since 1.380: +10 -4 lines
Diff to previous 1.380
fixed key_info

Revision 1.380 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 22 17:43:49 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.379: +41 -14 lines
Diff to previous 1.379
changing the format of attribute_keys

Revision 1.379 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 20 10:22:04 2005 UTC (14 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.378: +171 -57 lines
Diff to previous 1.378
Added new documentation.
Fixed attributes to prevent return of duplicate items.

Revision 1.378 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 13 20:13:48 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.377: +12 -2 lines
Diff to previous 1.377
Workaround for peg.synonyms file that has multiple entries.

Revision 1.377 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 12 21:03:16 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.376: +14 -2 lines
Diff to previous 1.376
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 1.376 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 12 02:28:16 2005 UTC (14 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.375: +137 -1 lines
Diff to previous 1.375
Added the "compute_clusters" method for use by UnvSubsys.
Added a "FIG" method for compatability with SFXlate.
Added more documentation.

Revision 1.375 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 11 20:38:38 2005 UTC (14 years, 1 month ago) by efrank
Branch: MAIN
Changes since 1.374: +24 -0 lines
Diff to previous 1.374
add find_by_attribute.  this takes a single string argument.  it returns
triples, (featureId, key, value) of all attributes in which the search string
is a substring of either key or value.  the search is via the attribute table,
not via the glimpse indexes so tha searches immediately after edits of
attributes work.

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Sat Oct 8 14:14:47 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.373: +1 -1 lines
Diff to previous 1.373
minor fix to not include xxx entries in expanded sims

Revision 1.373 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 6 22:44:02 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.372: +17 -2 lines
Diff to previous 1.372
adding more functions with external ids

Revision 1.372 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 6 21:22:48 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.371: +47 -0 lines
Diff to previous 1.371
loading external ids and external protein families

Revision 1.371 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 6 02:22:41 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.370: +0 -2 lines
Diff to previous 1.370
remove debug

Revision 1.370 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 5 20:34:02 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-dataload-0
Changes since 1.369: +71 -8 lines
Diff to previous 1.369
fixes to update_uniq_id_data

Revision 1.369 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 18 14:27:13 2005 UTC (14 years, 2 months ago) by overbeek
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Changes since 1.368: +4 -1 lines
Diff to previous 1.368
fix display_subsys.cgi

Revision 1.368 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 14 20:04:19 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.367: +6 -2 lines
Diff to previous 1.367
Correcting display of classifications

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Sun Sep 11 17:02:40 2005 UTC (14 years, 2 months ago) by overbeek
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Changes since 1.366: +19 -0 lines
Diff to previous 1.366
fixes to display of reactions

Revision 1.366 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 11 16:34:41 2005 UTC (14 years, 2 months ago) by overbeek
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Changes since 1.365: +20 -0 lines
Diff to previous 1.365
add functiontion to FIG.pm to get active subsystems for a genome

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Sat Sep 10 07:39:18 2005 UTC (14 years, 2 months ago) by parrello
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Changes since 1.364: +1816 -1816 lines
Diff to previous 1.364
Converted tabs to spaces to fix indenting.

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Fri Sep 9 13:28:58 2005 UTC (14 years, 2 months ago) by overbeek
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Changes since 1.363: +23 -5 lines
Diff to previous 1.363
upgrade sigs.cgi to run under Sprout

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Thu Sep 8 16:12:22 2005 UTC (14 years, 2 months ago) by overbeek
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Changes since 1.362: +3 -2 lines
Diff to previous 1.362
Added `formatdb` invocation to &add_genome(). Changed "VERBOSE" flag name to "FIG_VERBOSE". -- /gdp

Revision 1.362 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 6 19:58:53 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.361: +2 -1 lines
Diff to previous 1.361
make annotation requests by master return all non-assignment annotations.

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Tue Sep 6 18:52:35 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.360: +117 -27 lines
Diff to previous 1.360
Make annotations_made_fast return new Annotation objects instead of arrays of data.

Add the Annotation object.

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Fri Sep 2 22:23:33 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.359: +2 -5 lines
Diff to previous 1.359
Remove the debugging file setting in add_annotations_batch.

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Fri Sep 2 22:21:57 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.358: +129 -0 lines
Diff to previous 1.358
Add $fig->add_annotations_batch() that does filehandle conservation and uses COPY TABLE instead
of INSERT to add annotations to the database. Now used by 'fig add_annotations' so that
large annotation file installs don't take overnight.

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Thu Sep 1 20:52:51 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.357: +12 -3 lines
Diff to previous 1.357
Force is_deleted_fid to set the value of $/ that it wants, since use of that method
within a loop with $/ set to something else breaks is_deleted_fid. Darn global input
record separator.

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Thu Sep 1 19:23:49 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.356: +95 -14 lines
Diff to previous 1.356
Add FIG::by_genome_id for sorting genome ID lists.

Add $fig->extract_assignments_from_annoatations to transform the output of annotations_made_fast
to a list of the current assignments (per the annotations data).

Revision 1.356 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 1 18:14:53 2005 UTC (14 years, 3 months ago) by olson
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Changes since 1.355: +96 -9 lines
Diff to previous 1.355
make package_annotations use $fig->annotations_made_fast.

Add date parsing to FIG.pm ($fig->parse_date) using Date::Parse if available.

Revision 1.355 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 1 09:30:07 2005 UTC (14 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.354: +191 -64 lines
Diff to previous 1.354
Tweaked tracing, added more documentation, fixed so that the annotations will work properly in environments where the number of characters in a file is different from the number of bytes.

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Tue Aug 30 18:04:55 2005 UTC (14 years, 3 months ago) by overbeek
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Changes since 1.353: +1 -1 lines
Diff to previous 1.353
Fixed &possibly_truncated() so that it does not blow up on non-PEG features. -- /gdp

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Tue Aug 30 07:27:59 2005 UTC (14 years, 3 months ago) by overbeek
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Changes since 1.352: +20 -2 lines
Diff to previous 1.352
Invoked `assess_completeness` from &add_genomes(). -- /gdp

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Mon Aug 22 05:43:02 2005 UTC (14 years, 3 months ago) by redwards
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Changes since 1.351: +5 -3 lines
Diff to previous 1.351
Adding menus to subsys.cgi

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Sat Aug 20 12:32:29 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.350: +2 -1 lines
Diff to previous 1.350
fixes to calling starts

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Sat Aug 20 02:37:22 2005 UTC (14 years, 3 months ago) by overbeek
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Changes since 1.349: +5 -3 lines
Diff to previous 1.349
fixes to call_starts

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Fri Aug 19 19:52:19 2005 UTC (14 years, 3 months ago) by redwards
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Changes since 1.348: +10 -6 lines
Diff to previous 1.348
Adding more details to organisms.cgi and correcting get_key_values

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Wed Aug 17 03:15:01 2005 UTC (14 years, 3 months ago) by overbeek
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Changes since 1.347: +2 -0 lines
Diff to previous 1.347
removing blank lines from attribute_keys

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Tue Aug 16 19:41:12 2005 UTC (14 years, 3 months ago) by overbeek
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Changes since 1.346: +2 -1 lines
Diff to previous 1.346
NMPDR updates

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Mon Aug 15 21:41:29 2005 UTC (14 years, 3 months ago) by parrello
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Changes since 1.345: +3 -1 lines
Diff to previous 1.345
*** empty log message ***

Revision 1.345 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 15 21:34:53 2005 UTC (14 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.344: +12 -10 lines
Diff to previous 1.344
Fixed change_attribute to work properly if the attribute value has quotes in it.

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Mon Aug 15 21:16:19 2005 UTC (14 years, 3 months ago) by parrello
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Changes since 1.343: +1 -1 lines
Diff to previous 1.343
Fixed "add_attributes" to work correctly when quotes are present in attribute values.

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Mon Aug 15 20:25:02 2005 UTC (14 years, 3 months ago) by overbeek
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Changes since 1.342: +6 -2 lines
Diff to previous 1.342
Modified &to_aliases to make "TYPE" argument optional instead of mandatory. -- /gdp

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Tue Aug 9 00:56:02 2005 UTC (14 years, 4 months ago) by parrello
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Changes since 1.341: +1 -1 lines
Diff to previous 1.341
Changed "add_feature" to save the return from the INSERT into the feature table so that it can be viewed during debugging.

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Mon Aug 8 21:54:39 2005 UTC (14 years, 4 months ago) by olson
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Changes since 1.340: +2 -1 lines
Diff to previous 1.340
More diagram changes.

Add new simple start page.

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Mon Aug 8 20:04:33 2005 UTC (14 years, 4 months ago) by parrello
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Changes since 1.339: +63 -34 lines
Diff to previous 1.339
Updated "add_feature" to allow the caller to specify the feature ID.

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Mon Aug 8 18:43:08 2005 UTC (14 years, 4 months ago) by overbeek
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Changes since 1.338: +41 -0 lines
Diff to previous 1.338
adding fig versus kegg

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Sun Aug 7 22:06:58 2005 UTC (14 years, 4 months ago) by overbeek
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Changes since 1.337: +2 -1 lines
Diff to previous 1.337
fix to multi-functional roles

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Sat Aug 6 15:30:29 2005 UTC (14 years, 4 months ago) by redwards
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Changes since 1.336: +30 -3 lines
Diff to previous 1.336
New interface for subsys.cgi, but it is commented out at the moment

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Sat Aug 6 14:58:56 2005 UTC (14 years, 4 months ago) by overbeek
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Changes since 1.335: +64 -5 lines
Diff to previous 1.335
fixes to bugs in calling starts

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Fri Aug 5 13:14:26 2005 UTC (14 years, 4 months ago) by overbeek
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Changes since 1.334: +7 -3 lines
Diff to previous 1.334
adding options to add_genome

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Thu Aug 4 18:28:36 2005 UTC (14 years, 4 months ago) by olson
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Changes since 1.333: +8 -3 lines
Diff to previous 1.333
Make enqueue_similarities ignore a $fig argument if invoked as a method call.

Add a $time_made argument to add_annotation.

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Thu Aug 4 01:27:25 2005 UTC (14 years, 4 months ago) by overbeek
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Changes since 1.332: +5 -1 lines
Diff to previous 1.332
Modified &possibly_truncated() to accept either FID or location. -- /gdp

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Thu Aug 4 01:20:59 2005 UTC (14 years, 4 months ago) by overbeek
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Changes since 1.331: +20 -12 lines
Diff to previous 1.331
Modified &possibly_truncated() to accept either FID or location. -- /gdp

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Wed Aug 3 23:00:37 2005 UTC (14 years, 4 months ago) by overbeek
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Changes since 1.330: +10 -3 lines
Diff to previous 1.330
Adding a force to the add_genomes

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Wed Aug 3 21:16:29 2005 UTC (14 years, 4 months ago) by olson
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Changes since 1.329: +24 -13 lines
Diff to previous 1.329
Support gif/png/jpeg file type detection on diagram upload.
Support the multiple file types on packaging for clearinghouse.

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Wed Aug 3 17:40:42 2005 UTC (14 years, 4 months ago) by olson
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Changes since 1.328: +47 -1 lines
Diff to previous 1.328
Add support for creating and parsing diagram data as part of subsystem clearinghouse packages.

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Mon Aug 1 22:23:15 2005 UTC (14 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.327: +42 -42 lines
Diff to previous 1.327
Changed attributes to capital-case in order to prevent the avalanche of compile-time warnings.

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Mon Aug 1 18:52:58 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.326: +7 -8 lines
Diff to previous 1.326
update stuff relating to protein families

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Sun Jul 31 17:08:02 2005 UTC (14 years, 4 months ago) by overbeek
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Changes since 1.325: +21 -16 lines
Diff to previous 1.325
Cosmetic changes to make clear that &display_id_and_seq() and &display_seq() take sequence-pointers, not sequences. -- /gdp

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Sun Jul 31 01:09:59 2005 UTC (14 years, 4 months ago) by overbeek
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Changes since 1.324: +30 -9 lines
Diff to previous 1.324
 fixes to pick_gene_boundaries

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Fri Jul 29 22:27:46 2005 UTC (14 years, 4 months ago) by olson
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Changes since 1.323: +40 -0 lines
Diff to previous 1.323
Publish/install changes for reactions.

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Fri Jul 29 18:13:11 2005 UTC (14 years, 4 months ago) by olson
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Changes since 1.322: +27 -2 lines
Diff to previous 1.322
Support "fig load_all N" and "fig load_all list"

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Thu Jul 28 18:03:24 2005 UTC (14 years, 4 months ago) by overbeek
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Changes since 1.321: +72 -0 lines
Diff to previous 1.321
commit code to expand regions of similarity to PEGs and to recall starts

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Wed Jul 27 19:41:56 2005 UTC (14 years, 4 months ago) by parrello
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Changes since 1.320: +1 -3 lines
Diff to previous 1.320
Fixed some POD comments.

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Tue Jul 26 20:06:03 2005 UTC (14 years, 4 months ago) by parrello
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Changes since 1.319: +380 -111 lines
Diff to previous 1.319
Added "upstream_of" method to compute upstream sequences.
Cleaned up some documentation.

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Tue Jul 26 04:53:36 2005 UTC (14 years, 4 months ago) by mkubal
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Changes since 1.318: +1 -1 lines
Diff to previous 1.318
7-26-05

Revision 1.318 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jul 23 19:47:36 2005 UTC (14 years, 4 months ago) by overbeek
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Changes since 1.317: +3 -1 lines
Diff to previous 1.317
altering location in FIG.pm

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Tue Jul 19 16:29:35 2005 UTC (14 years, 4 months ago) by overbeek
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Changes since 1.316: +4 -4 lines
Diff to previous 1.316
standardize returned DNA to lower case, as per GJO's request. -- /gdp

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Tue Jul 19 16:14:21 2005 UTC (14 years, 4 months ago) by redwards
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Changes since 1.315: +2 -1 lines
Diff to previous 1.315
More final touches for Attributes code

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Tue Jul 19 05:26:12 2005 UTC (14 years, 4 months ago) by redwards
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Changes since 1.314: +2 -2 lines
Diff to previous 1.314
minor chagnes to attributes

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Tue Jul 19 04:54:21 2005 UTC (14 years, 4 months ago) by redwards
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Changes since 1.313: +36 -9 lines
Diff to previous 1.313
Updating attributes code in seed

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Mon Jul 18 03:12:11 2005 UTC (14 years, 4 months ago) by redwards
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Changes since 1.312: +54 -9 lines
Diff to previous 1.312
Updating attributes code

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Sun Jul 17 19:04:27 2005 UTC (14 years, 4 months ago) by redwards
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Changes since 1.311: +63 -29 lines
Diff to previous 1.311
Making attributes interface work

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Wed Jul 13 01:49:54 2005 UTC (14 years, 4 months ago) by redwards
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Changes since 1.310: +22 -37 lines
Diff to previous 1.310
minor changes to subsys_vectors to allow complete genomes

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Tue Jul 12 22:10:07 2005 UTC (14 years, 4 months ago) by redwards
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Changes since 1.309: +14 -0 lines
Diff to previous 1.309
minor changes to subsys_vectors.cgi

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Tue Jul 12 14:34:14 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
CVS Tags: merge-trunktag-bodev_news-3
Changes since 1.308: +91 -40 lines
Diff to previous 1.308
Changing attributes and modifying protein.cgi with show/hides

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Tue Jul 12 00:34:32 2005 UTC (14 years, 4 months ago) by overbeek
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Changes since 1.307: +16 -16 lines
Diff to previous 1.307
updates to build protein families

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Sun Jul 10 04:59:11 2005 UTC (14 years, 4 months ago) by redwards
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Changes since 1.306: +8 -1 lines
Diff to previous 1.306
making index_subsystems work

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Sat Jul 9 21:46:15 2005 UTC (14 years, 4 months ago) by redwards
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Changes since 1.305: +17 -0 lines
Diff to previous 1.305
added index subsystems to subsys.cgi

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Fri Jul 1 02:09:16 2005 UTC (14 years, 5 months ago) by redwards
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Changes since 1.304: +46 -26 lines
Diff to previous 1.304
Changed proteinfamilies.cgi

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Wed Jun 29 15:06:12 2005 UTC (14 years, 5 months ago) by olson
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CVS Tags: merge-trunktag-bobdev_news-2
Changes since 1.303: +2 -2 lines
Diff to previous 1.303
Tweak tracing.

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Wed Jun 29 00:28:01 2005 UTC (14 years, 5 months ago) by redwards
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Changes since 1.302: +88 -5 lines
Diff to previous 1.302
Initial release of proteinfamilies.cgi into the wild

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Tue Jun 28 17:25:04 2005 UTC (14 years, 5 months ago) by redwards
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Changes since 1.301: +20 -0 lines
Diff to previous 1.301
commiting FIG.pm::clean_spaces to remove leading, trailing, and extra spaces. Please use it

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Fri Jun 24 21:39:14 2005 UTC (14 years, 5 months ago) by parrello
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-1
Changes since 1.300: +16 -17 lines
Diff to previous 1.300
Fixed the environment-variable tracing so that it does not override previous tracing options if they were set.

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Thu Jun 23 21:24:48 2005 UTC (14 years, 5 months ago) by overbeek
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Changes since 1.299: +5 -0 lines
Diff to previous 1.299
finally

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Thu Jun 23 19:35:07 2005 UTC (14 years, 5 months ago) by olson
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Changes since 1.298: +33 -2 lines
Diff to previous 1.298
Add some more gene  name mapping stuff.

Add Tracer environment variable for affecting tracing.

Fix typo in invocation of load_coupling.

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Wed Jun 22 21:00:24 2005 UTC (14 years, 5 months ago) by parrello
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Changes since 1.297: +514 -531 lines
Diff to previous 1.297
Replaced tabs with spaces to make indenting device-independent.
Moved "Open" and "OpenDir" to the Tracer.pm module.
Added more POD documentation.

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Mon Jun 20 21:58:56 2005 UTC (14 years, 5 months ago) by olson
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Changes since 1.296: +63 -0 lines
Diff to previous 1.296
Add genome/peg id mapping routines. (For functional coupling support).

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Mon Jun 20 17:08:32 2005 UTC (14 years, 5 months ago) by overbeek
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Changes since 1.295: +1 -1 lines
Diff to previous 1.295
add new protein family routines

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Mon Jun 20 17:04:45 2005 UTC (14 years, 5 months ago) by overbeek
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Changes since 1.294: +72 -11 lines
Diff to previous 1.294
add new protein family routines

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Mon Jun 20 04:03:44 2005 UTC (14 years, 5 months ago) by overbeek
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Changes since 1.293: +6 -1 lines
Diff to previous 1.293
disable old protein families

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Mon Jun 13 16:43:48 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: Root-bobdev_news
Branch point for: Branch-bobdev_news
Changes since 1.292: +20 -33 lines
Diff to previous 1.292
Ross change commit after cleanup

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Mon Jun 13 09:32:09 2005 UTC (14 years, 5 months ago) by parrello
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Changes since 1.291: +160 -2 lines
Diff to previous 1.291
Added Open and OpenDir methods for streamlining file and directory operations.

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Fri Jun 10 16:08:52 2005 UTC (14 years, 5 months ago) by overbeek
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Changes since 1.290: +7 -7 lines
Diff to previous 1.290
fixes to cached pin displays

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Fri Jun 10 15:36:37 2005 UTC (14 years, 5 months ago) by redwards
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Changes since 1.289: +7 -9 lines
Diff to previous 1.289
adding correspondence.cgi

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Thu Jun 9 20:03:15 2005 UTC (14 years, 5 months ago) by overbeek
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Changes since 1.288: +95 -1 lines
Diff to previous 1.288
re-add couipling routines

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Thu Jun 9 18:39:05 2005 UTC (14 years, 5 months ago) by parrello
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Changes since 1.287: +39 -28 lines
Diff to previous 1.287
*** empty log message ***

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Thu Jun 9 05:36:30 2005 UTC (14 years, 5 months ago) by parrello
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Changes since 1.286: +2333 -1628 lines
Diff to previous 1.286
*** empty log message ***

Revision 1.286 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 8 23:05:21 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.285: +7 -30 lines
Diff to previous 1.285
major change to BBHs (use precomputed)

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Tue Jun 7 16:41:23 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.284: +2 -1 lines
Diff to previous 1.284
Fixed typo in &hypo(), and added new rule. -- /gdp

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Wed Jun 1 01:18:50 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.283: +91 -12 lines
Diff to previous 1.283
install precomputed functional coupling data

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Sun May 29 13:33:56 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.282: +24 -0 lines
Diff to previous 1.282
add test for existence of relation that works only under Postgres

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Wed May 25 18:58:27 2005 UTC (14 years, 6 months ago) by redwards
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Changes since 1.281: +39 -0 lines
Diff to previous 1.281
added subsystems_roles method to FIG.pm

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Wed May 25 16:07:23 2005 UTC (14 years, 6 months ago) by olson
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Changes since 1.280: +92 -0 lines
Diff to previous 1.280
Code for similarity request export.

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Fri May 20 11:23:07 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.279: +1 -1 lines
Diff to previous 1.279
fix bug in search_indexes

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Tue May 17 16:04:08 2005 UTC (14 years, 6 months ago) by olson
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Changes since 1.278: +307 -19 lines
Diff to previous 1.278
Bundle of misc bob changes, including sim computation code and search-for-substring.

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Tue May 10 12:03:39 2005 UTC (14 years, 6 months ago) by overbeek
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Changes since 1.277: +4 -1 lines
Diff to previous 1.277
fixes to using trees under subsystems

Revision 1.277 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 5 17:43:03 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.276: +5 -3 lines
Diff to previous 1.276
fix indexing search code

Revision 1.276 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 3 21:03:38 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.275: +1 -1 lines
Diff to previous 1.275
add css generation modules

Revision 1.275 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 29 16:43:29 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.274: +1 -0 lines
Diff to previous 1.274
add assign_to_close_strains

Revision 1.274 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 18 18:29:31 2005 UTC (14 years, 7 months ago) by mkubal
Branch: MAIN
Changes since 1.273: +2 -3 lines
Diff to previous 1.273
revised on Monday

Revision 1.273 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 18 06:26:04 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.272: +1 -1 lines
Diff to previous 1.272
minor fix to select tag/values

Revision 1.272 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 18 06:19:40 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.271: +3 -1 lines
Diff to previous 1.271
minor fix to select tag/values

Revision 1.271 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Apr 17 16:30:19 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.270: +2 -0 lines
Diff to previous 1.270
handle missing annotations file gracefully

Revision 1.270 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 15 23:23:13 2005 UTC (14 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.269: +7 -27 lines
Diff to previous 1.269
Fix bunged index search

Revision 1.269 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 14 18:52:19 2005 UTC (14 years, 7 months ago) by mkubal
Branch: MAIN
Changes since 1.268: +2 -1 lines
Diff to previous 1.268
search_index now returns attributes

Revision 1.268 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 13 15:37:30 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.267: +30 -21 lines
Diff to previous 1.267
changed genome stats to show attributes

Revision 1.267 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Apr 10 03:32:30 2005 UTC (14 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.266: +1 -1 lines
Diff to previous 1.266
Re-enable "duplicates" in sims.  Multiple regions of matching is common
in eukaryotic sequences, and only seeing one is disorienting.

Revision 1.266 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 8 20:22:23 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.265: +10 -15 lines
Diff to previous 1.265
changed tag/value pairs completely. Ooops!

Revision 1.265 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 7 19:16:10 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.264: +30 -15 lines
Diff to previous 1.264
many changes to key/value pairs to make them work

Revision 1.264 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Apr 3 19:43:41 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.263: +5 -2 lines
Diff to previous 1.263
changing pir corresepondence

Revision 1.263 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Apr 3 19:11:11 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.262: +97 -8 lines
Diff to previous 1.262
Added a script to load pir superfamilies in the background. This will download all the data and install it. Changed pir.cgi to background this job as it takes a while.

Revision 1.262 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 2 11:56:12 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.261: +2 -0 lines
Diff to previous 1.261
add update_subsys_conflicts to fig.pl

Revision 1.261 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 31 18:05:28 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.260: +3 -0 lines
Diff to previous 1.260
fix to asses_completeness

Revision 1.260 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 30 19:58:20 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.259: +27 -0 lines
Diff to previous 1.259
Add genome_with_md5sum.

Warn on FigGFF errors only if you're bob.

Revision 1.259 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 30 15:53:37 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.258: +4 -4 lines
Diff to previous 1.258
changing attributes returned back to variables

Revision 1.258 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 29 20:41:17 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.257: +7 -5 lines
Diff to previous 1.257
minor changes to rae.cgi

Revision 1.257 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 29 19:29:39 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.256: +3 -2 lines
Diff to previous 1.256
add make_pu from ids and seqs

Revision 1.256 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 29 18:42:26 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.255: +7 -0 lines
Diff to previous 1.255
broaden set of acceptable aliases as dbxrefs

Revision 1.255 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 23 18:54:39 2005 UTC (14 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.254: +1 -1 lines
Diff to previous 1.254
Removed constraint that sims request had to be by a fig ID.  Ross seems to
have solved the orginal problem that names that could not be mapped
returned a representitive ID with undefined length, which crashed sims().
Now failure to map a name returns an empty list, and sims graceful returns
an empty list of similarities.

Revision 1.254 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 21 22:01:22 2005 UTC (14 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.253: +0 -1 lines
Diff to previous 1.253
A few similarities tweeks.  Move the submit button on the default protein
page (to shorten the line slightly).  Remove a debug statement that was
writing to the error log.

Revision 1.253 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 21 21:39:32 2005 UTC (14 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.252: +7 -4 lines
Diff to previous 1.252
Add options to Similarities to override Max expand when asking for FIG IDs.
It gets annoying to have to constantly increase the value, and it is not
predictable how many sims will need to be expanded to get any desired
number of FIG IDs.

Revision 1.252 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 21 18:33:49 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.251: +1 -1 lines
Diff to previous 1.251
fix to best_bbh_candidates and added fill_subsys

Revision 1.251 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 20 22:26:16 2005 UTC (14 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.250: +36 -2 lines
Diff to previous 1.250
When sorting similarities by percent identity or bit score per position,
include a penalty for very sort sequences, so that they do not randomly
appear much higher in the similaries list than they should.  The current
treatment for this is roughly a two standard deviation penalty.

The original behavior is still available as non-star versions.
The "help" information has been updated (and other aspects clarified
as well).

Revision 1.250 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Mar 19 01:27:13 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.249: +4 -0 lines
Diff to previous 1.249
update hypo

Revision 1.249 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 16 17:56:22 2005 UTC (14 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.248: +2 -2 lines
Diff to previous 1.248
Fix end condition test on expand_raw_sims to promptly return.

Revision 1.248 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 16 15:17:45 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.247: +1 -0 lines
Diff to previous 1.247
remove ddd: in front of some organisms (mostly uniprot)

Revision 1.247 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 16 15:11:56 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.246: +2 -1 lines
Diff to previous 1.246
change spaces to _s in subsystem names

Revision 1.246 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 16 00:18:09 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.245: +1 -1 lines
Diff to previous 1.245
make the gff stuff work again.

Revision 1.245 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 15 23:56:53 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.244: +76 -1 lines
Diff to previous 1.244
Put the FigGFF code in a require for now.

Add fast anno lookup.

Revision 1.244 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 14 19:17:37 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.243: +13 -0 lines
Diff to previous 1.243
Add general-purpose GFF writing stuff.

Revision 1.243 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 14 02:04:44 2005 UTC (14 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.242: +3 -3 lines
Diff to previous 1.242
Minor fix in expand_raw_sims so that it stops when it should

Revision 1.242 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 13 00:55:21 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.241: +59 -17 lines
Diff to previous 1.241
Initial commit of organisms.cgi which allows separate entry pages for different groups of organisms

Revision 1.241 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 11 22:03:13 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.240: +10 -2 lines
Diff to previous 1.240
fix for mapped_prot_ids

Revision 1.240 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 11 04:11:30 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.239: +4 -5 lines
Diff to previous 1.239
Making tag/value pairs work

Revision 1.239 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 11 03:04:32 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.238: +12 -5 lines
Diff to previous 1.238
Making tag/value pairs work

Revision 1.238 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 11 01:04:32 2005 UTC (14 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.237: +247 -122 lines
Diff to previous 1.237
Many new options for similarities

Revision 1.237 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 8 21:14:53 2005 UTC (14 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.236: +19 -1 lines
Diff to previous 1.236
Add contig_md5sum.

Revision 1.236 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 8 21:06:04 2005 UTC (14 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.235: +30 -0 lines
Diff to previous 1.235
Add support for computing MD5 checksums for contigs and genomes.

The checksum of a genome is defined as the checksum of its signature file. The signature
file consists of tab-separated lines, one for each contig, ordered by the contig id.
Each line contains the contig ID, the length of the contig in nucleotides, and the
MD5 checksum of the nucleotide data, with uppercase letters forced to lower case.

The signature file is written by index_contigs to
The genome's md5 checksum is written by index_contigs to <genomedir>/MD5SUM.

The md5.c code here is extracted from the Perl Digest::MD5 module. We use the perl
configuration to build it so that it will work correctly on 64-bit architectures.

Revision 1.235 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 6 15:10:02 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.234: +1 -0 lines
Diff to previous 1.234
disconnect get_attributes until I can talk to Rob

Revision 1.234 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Mar 5 04:29:59 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.233: +10 -2 lines
Diff to previous 1.233
added highlight by peg attribute to subsystem

Revision 1.233 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 4 23:16:42 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.232: +23 -17 lines
Diff to previous 1.232
tweaks to coloring ss by oa

Revision 1.232 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 4 22:37:06 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.231: +128 -13 lines
Diff to previous 1.231
Added color by organism attributes to subsystems page

Revision 1.231 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 4 18:29:21 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.230: +3 -0 lines
Diff to previous 1.230
Added attribute editing to the protein.cgi page

Revision 1.230 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 4 06:22:10 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.229: +204 -18 lines
Diff to previous 1.229
Big updates to FIG.pm for the addition of methods to properly handle attributes. Also modified genome_statistics to take advantage of these new methods. load_attributes will load genomes and other attributes but doesn't not yet use the new methods (but should), and Attributes.html is some docs.

Revision 1.229 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 27 01:39:55 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.228: +51 -3 lines
Diff to previous 1.228
major changes in notion of function and load_attributes

Revision 1.228 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 26 19:49:59 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.227: +4 -0 lines
Diff to previous 1.227
filters for data mining

Revision 1.227 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 26 11:01:13 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.226: +20 -3 lines
Diff to previous 1.226
add reset_curator.cgi

Revision 1.226 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 16 18:59:20 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.225: +3 -1 lines
Diff to previous 1.225
highlight subsystems with no genomes attached

Revision 1.225 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 18:41:04 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.224: +1 -1 lines
Diff to previous 1.224
Fix subsystem_classification in FIG.pm

Revision 1.224 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 18:18:14 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.223: +8 -17 lines
Diff to previous 1.223
Moved the subsystem_classification getting/setting into subsys.pm where it belongs, and so I ammended FIG.pm. Also added the boxes on the subsystem page so you can see the classifications.

Revision 1.223 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 17:20:43 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.222: +6 -5 lines
Diff to previous 1.222
minor change to FIG::subsystem_classification

Revision 1.222 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 06:49:27 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.221: +3 -3 lines
Diff to previous 1.221
Initial addition of subsys_summary.cgi and minor modification of FIG.pm

Revision 1.221 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 05:38:43 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.220: +6 -3 lines
Diff to previous 1.220
changes to subsystem_classification

Revision 1.220 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 04:51:47 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.219: +9 -14 lines
Diff to previous 1.219
fix routine for locating candidates for a role in a genome

Revision 1.219 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 04:08:00 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.218: +35 -0 lines
Diff to previous 1.218
Minor changes to pir.cgi and added subsystem_classification to FIG.pm

Revision 1.218 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 04:01:01 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.217: +20 -72 lines
Diff to previous 1.217
many fixes to extending subsystems

Revision 1.217 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 03:50:04 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.216: +26 -0 lines
Diff to previous 1.216
Add some pod to FIG.pm

Revision 1.216 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 03:00:57 2005 UTC (14 years, 9 months ago) by mkubal
Branch: MAIN
Changes since 1.215: +19 -15 lines
Diff to previous 1.215
update

Revision 1.215 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 11 06:34:05 2005 UTC (14 years, 9 months ago) by mkubal
Branch: MAIN
Changes since 1.214: +85 -3 lines
Diff to previous 1.214
added all_for_genome, etc

Revision 1.214 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 10 13:33:37 2005 UTC (14 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.213: +26 -0 lines
Diff to previous 1.213
Add subsystems_for_genome.

Revision 1.213 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 7 00:27:34 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.212: +76 -14 lines
Diff to previous 1.212
no message

Revision 1.212 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 5 04:12:35 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.211: +1 -1 lines
Diff to previous 1.211
head -1 should be head -n 1

Revision 1.211 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 31 14:01:07 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.210: +2 -1 lines
Diff to previous 1.210
add pegs_in_subsystems

Revision 1.210 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 27 00:31:21 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.209: +133 -68 lines
Diff to previous 1.209
no message

Revision 1.209 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 26 18:37:58 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.208: +8 -10 lines
Diff to previous 1.208
fix bugs introduced into by_alias function

Revision 1.208 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 23 00:38:22 2005 UTC (14 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.207: +3 -2 lines
Diff to previous 1.207
Time stamp individual load steps

Revision 1.207 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 18 21:06:41 2005 UTC (14 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.206: +1 -1 lines
Diff to previous 1.206
fix dumb typo.

Revision 1.206 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 18 21:02:45 2005 UTC (14 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.205: +15 -0 lines
Diff to previous 1.205
Add peg_in_gendb and genome_in_gendb

Revision 1.205 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 18 20:55:32 2005 UTC (14 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.204: +6 -0 lines
Diff to previous 1.204
add get_system_name() call.

Revision 1.204 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 16 16:05:20 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.203: +16 -2 lines
Diff to previous 1.203
fix to scoring fc

Revision 1.203 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 13 17:32:51 2005 UTC (14 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.202: +1 -1 lines
Diff to previous 1.202
More fixes for Sprout integration.

Revision 1.202 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 12 21:22:08 2005 UTC (14 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.201: +2 -1 lines
Diff to previous 1.201
sprout debugging

Revision 1.201 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 12 20:18:56 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.200: +13 -12 lines
Diff to previous 1.200
no message

Revision 1.200 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 12 20:08:30 2005 UTC (14 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.199: +297 -301 lines
Diff to previous 1.199
no message

Revision 1.199 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 11 18:59:39 2005 UTC (14 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.198: +1 -1 lines
Diff to previous 1.198
I ran into a bug today where I was using by_alias to look up aliases
for the peg-mapping code, and one of the aliases was DR6', with a
single-quote. Because the code in by_alias doesn't quote its argument,
the SQL failed with a syntax error.

The perl DBI library has a mechanism designed to solve this
problem. If you use ? in a sql string where you want to substitute an
argument from code, DBI will do the appropriate quoting for you. I've
made this accessible via the SQL method in the DBrtns module, so the
by_alias code now looks like this:

    if (($relational_db_response = $rdbH->SQL("SELECT id FROM ext_alias WHERE ( alias = ? )", undef, $alias))

and works properly in the face of $alias having a single-quote in
it. I believe this mechanism is also more efficient. Note the second
argument of SQL is a verbose flag, which means that any bound
variables (to replace ?s in the query) have to start at the third
argument.

I've also made a change in the SQL method such that the query is done
inside an eval{} block, and if it fails, the error is reraised using
confess so that it is possible to see the full backtrace so you can
find in the source where the bad query was.

Revision 1.198 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 9 17:15:12 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.197: +1 -1 lines
Diff to previous 1.197
fix disambiguating maps

Revision 1.197 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 8 18:22:00 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.196: +1 -1 lines
Diff to previous 1.196
add check to assign_function

Revision 1.196 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 7 18:55:21 2005 UTC (14 years, 11 months ago) by olson
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Changes since 1.195: +2 -2 lines
Diff to previous 1.195
add option to not create a release info file to get_release_info()

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Wed Jan 5 16:19:44 2005 UTC (14 years, 11 months ago) by olson
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Changes since 1.194: +78 -4 lines
Diff to previous 1.194
p2p changes.

Revision 1.194 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 3 02:23:12 2005 UTC (14 years, 11 months ago) by overbeek
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Changes since 1.193: +0 -1 lines
Diff to previous 1.193
fix stupid error in cleaning up aliases

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Mon Jan 3 02:21:08 2005 UTC (14 years, 11 months ago) by overbeek
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Changes since 1.192: +4 -27 lines
Diff to previous 1.192
automatically generate aliases from mapped IDs

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Wed Dec 29 17:59:36 2004 UTC (14 years, 11 months ago) by overbeek
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Changes since 1.191: +1 -1 lines
Diff to previous 1.191
minor fix to FIG.pm and addition of generate_kegg_map_ec_tables

Revision 1.191 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 16 22:57:43 2004 UTC (14 years, 11 months ago) by overbeek
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Changes since 1.190: +2 -1 lines
Diff to previous 1.190
fixes to assigned_function

Revision 1.190 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 15 02:04:34 2004 UTC (14 years, 11 months ago) by overbeek
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Changes since 1.189: +9 -5 lines
Diff to previous 1.189
allow set of seeks to cores for bbhs

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Mon Dec 13 19:24:15 2004 UTC (14 years, 11 months ago) by redwards
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Changes since 1.188: +4 -4 lines
Diff to previous 1.188
Minor changes to FIG.pm POD

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Fri Dec 10 07:04:39 2004 UTC (14 years, 11 months ago) by redwards
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Changes since 1.187: +18 -0 lines
Diff to previous 1.187
Changes to subsys.cgi that warn if a subsystem doesn't exist

Revision 1.187 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 8 21:28:10 2004 UTC (14 years, 11 months ago) by overbeek
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Changes since 1.186: +9 -2 lines
Diff to previous 1.186
raw time for annotations

Revision 1.186 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 6 18:25:18 2004 UTC (15 years ago) by olson
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Changes since 1.185: +1 -1 lines
Diff to previous 1.185
fix a comment

Revision 1.185 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 5 16:35:15 2004 UTC (15 years ago) by overbeek
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Changes since 1.184: +2 -2 lines
Diff to previous 1.184
add checking for subsystems

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Fri Dec 3 18:55:20 2004 UTC (15 years ago) by olson
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Changes since 1.183: +39 -2 lines
Diff to previous 1.183
Add subsystem_roles() method.
Add status callback to translate_pegs.
Remove setting of sticky bit in verify_dir.

Revision 1.183 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 10 22:10:22 2004 UTC (15 years ago) by olson
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Changes since 1.182: +46 -0 lines
Diff to previous 1.182
add higher-level construct support

Revision 1.182 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 5 14:57:59 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.181: +0 -1 lines
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untested changes to extract_genomes - copy-all-but in Global

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Thu Nov 4 18:27:29 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.180: +4 -1 lines
Diff to previous 1.180
allow external IDs on subsystem displays

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Wed Nov 3 17:46:17 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.179: +7 -0 lines
Diff to previous 1.179
add is_complete function to FIG.pm

Revision 1.179 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 2 14:45:31 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.178: +81 -1 lines
Diff to previous 1.178
fix bug in subsys.cgi and add Literature to Global

Revision 1.178 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 25 20:59:34 2004 UTC (15 years, 1 month ago) by redwards
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Changes since 1.177: +8 -0 lines
Diff to previous 1.177
Adding  some pod

Revision 1.177 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 23 21:41:38 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.176: +1 -1 lines
Diff to previous 1.176
stupid error in FIG.pm

Revision 1.176 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 23 19:58:28 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.175: +2 -2 lines
Diff to previous 1.175
fix bound in find_role_in_org

Revision 1.175 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 22 19:30:37 2004 UTC (15 years, 1 month ago) by heiko
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Changes since 1.174: +23 -0 lines
Diff to previous 1.174
added function
all_features_detailed
will return fig_id, location, type as array

Revision 1.174 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 22 16:55:42 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.173: +7 -7 lines
Diff to previous 1.173
fill_in_cell for Heiko

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Sun Oct 17 16:40:13 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.172: +9 -7 lines
Diff to previous 1.172
added homologs_in_clusters.cgi

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Sun Oct 17 00:05:17 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.171: +4 -0 lines
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fix to by_alias

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Sun Oct 17 00:02:34 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.170: +21 -6 lines
Diff to previous 1.170
fixes to UniProt IDs on chromosomal_clusters.cgi

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Sat Oct 16 20:42:28 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.169: +22 -2 lines
Diff to previous 1.169
fixes to generalize chromosomal_clusters.cgi for UniProt

Revision 1.169 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 15 17:04:09 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.168: +97 -48 lines
Diff to previous 1.168
peg links generalized to fid links

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Fri Oct 15 00:38:11 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.167: +15 -4 lines
Diff to previous 1.167
fixes to subsystem code

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Mon Oct 11 23:55:40 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.166: +1 -0 lines
Diff to previous 1.166
remove extra EOLs on changed locations

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Mon Oct 11 21:38:58 2004 UTC (15 years, 1 month ago) by overbeek
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Changes since 1.165: +7 -2 lines
Diff to previous 1.165
fixes to change_location_of_feature

Revision 1.165 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 11 18:46:45 2004 UTC (15 years, 1 month ago) by olson
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Changes since 1.164: +10 -44 lines
Diff to previous 1.164
More fixes for sprout support.

Revision 1.164 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 8 22:04:48 2004 UTC (15 years, 1 month ago) by redwards
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Changes since 1.163: +1 -1 lines
Diff to previous 1.163
Added number of contigs to menu

Revision 1.163 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 5 22:06:28 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.162: +55 -0 lines
Diff to previous 1.162
more DAS fixes

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Mon Oct 4 15:56:10 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.161: +29 -0 lines
Diff to previous 1.161
Changes for DAS integration

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Fri Oct 1 19:48:37 2004 UTC (15 years, 2 months ago) by overbeek
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Changes since 1.160: +5 -5 lines
Diff to previous 1.160
minor fixes to exporting sets

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Fri Sep 24 20:27:22 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.159: +20 -1 lines
Diff to previous 1.159
doc fix

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Fri Sep 24 18:58:42 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.158: +7 -4 lines
Diff to previous 1.158
Possible fix for beg_of and contig_of
More p2p stuff

Revision 1.158 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 24 18:34:32 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.157: +165 -1 lines
Diff to previous 1.157
Some contig manipulation stuff, more p2p stuff.

Revision 1.157 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 23 20:04:04 2004 UTC (15 years, 2 months ago) by redwards
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Changes since 1.156: +16 -2 lines
Diff to previous 1.156
$fig->adjacent_genes was not returning adjacent genes

Revision 1.156 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 22 19:32:29 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.155: +0 -2 lines
Diff to previous 1.155
remove print

Revision 1.155 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 22 19:29:51 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.154: +134 -1 lines
Diff to previous 1.154
Mods for P2P update stuff.

Revision 1.154 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 20 21:16:02 2004 UTC (15 years, 2 months ago) by overbeek
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Changes since 1.153: +6 -3 lines
Diff to previous 1.153
subsystem_genomes should return just genomes with an operational variant

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Thu Sep 16 15:15:57 2004 UTC (15 years, 2 months ago) by olson
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Changes since 1.152: +4 -4 lines
Diff to previous 1.152
remove inappropriate setting of g+s bit

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Thu Sep 16 04:35:03 2004 UTC (15 years, 2 months ago) by overbeek
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Changes since 1.151: +4 -4 lines
Diff to previous 1.151
Fixed errors in POD documentation. -- /gdp

Revision 1.151 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 13 02:12:20 2004 UTC (15 years, 2 months ago) by overbeek
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Changes since 1.150: +19 -0 lines
Diff to previous 1.150
add attributes as key-value pairs attached to fids

Revision 1.150 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Sep 11 00:46:49 2004 UTC (15 years, 2 months ago) by golsen
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Changes since 1.149: +9 -3 lines
Diff to previous 1.149
Add domain-based selection to genomes function.  Used to generate domain-specfic genome lists.

Revision 1.149 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 9 00:00:09 2004 UTC (15 years, 2 months ago) by overbeek
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Changes since 1.148: +0 -1 lines
Diff to previous 1.148
minor fixes

Revision 1.148 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 7 02:54:16 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.147: +17 -2 lines
Diff to previous 1.147
add new subsystem interface

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Fri Aug 27 21:55:57 2004 UTC (15 years, 3 months ago) by mkubal
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Changes since 1.146: +81 -2 lines
Diff to previous 1.146
added adjacent_genes() and supporting methods

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Fri Aug 27 18:32:07 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.145: +14 -0 lines
Diff to previous 1.145
set current user

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Tue Aug 24 22:12:17 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.144: +6 -4 lines
Diff to previous 1.144
minor changes to indexing translations

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Mon Aug 23 18:58:54 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.143: +1 -1 lines
Diff to previous 1.143
sort sims into the correct order

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Mon Aug 23 18:51:34 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.142: +3 -3 lines
Diff to previous 1.142
fix evil bug in index searches

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Mon Aug 23 18:35:51 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.141: +17 -2 lines
Diff to previous 1.141
sort sims by bit score

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Mon Aug 23 03:34:32 2004 UTC (15 years, 3 months ago) by golsen
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Changes since 1.140: +200 -2 lines
Diff to previous 1.140
Fix a typo in annotations_made and start adding infrastructure to fix genes_in_region issues

Revision 1.140 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 22 21:36:42 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.139: +1 -0 lines
Diff to previous 1.139
have function_of append to end of lines

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Fri Aug 20 17:37:58 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.138: +70 -89 lines
Diff to previous 1.138
update feature alterations

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Fri Aug 20 00:42:54 2004 UTC (15 years, 3 months ago) by golsen
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Changes since 1.137: +8 -8 lines
Diff to previous 1.137
Fixed major error in org_of

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Thu Aug 19 23:45:58 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.136: +31 -0 lines
Diff to previous 1.136
handle changes to feature locations

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Wed Aug 18 15:46:51 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.135: +179 -22 lines
Diff to previous 1.135
add abilities to add, delete and update features

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Mon Aug 16 22:10:55 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.134: +160 -60 lines
Diff to previous 1.134
straighten out FIG.pm

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Fri Aug 13 14:04:20 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.133: +126 -0 lines
Diff to previous 1.133
interface for Bielefeld in FIG.pm

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Thu Aug 12 11:39:44 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.132: +1 -1 lines
Diff to previous 1.132
fix errors relating to read_annotations

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Mon Aug 9 13:36:18 2004 UTC (15 years, 3 months ago) by overbeek
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Changes since 1.131: +2 -2 lines
Diff to previous 1.131
major fix in read_annotations in FIG.pm

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Sat Aug 7 18:48:39 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.130: +1 -1 lines
Diff to previous 1.130
fixes to aliases_of

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Mon Aug 2 20:02:29 2004 UTC (15 years, 4 months ago) by golsen
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Changes since 1.129: +81 -0 lines
Diff to previous 1.129
Colorize organisms by domain in similarities list.  Changes protein.cgi and FIG.pm

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Sun Aug 1 11:50:25 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.128: +1 -2 lines
Diff to previous 1.128
fix order on genes returned in a region

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Sun Jul 25 21:48:15 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.127: +3 -1 lines
Diff to previous 1.127
sort links

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Sun Jul 18 22:58:36 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.126: +41 -6 lines
Diff to previous 1.126
handle bug that lost notes for subsystems

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Fri Jul 16 21:58:03 2004 UTC (15 years, 4 months ago) by gdpusch
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Changes since 1.125: +19 -5 lines
Diff to previous 1.125
Added out-of-bounds checks to &extract_seq(), plus debugging information for loci whose sequences could not be extracted.

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Fri Jul 16 20:41:26 2004 UTC (15 years, 4 months ago) by overbeek
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Changes since 1.124: +4 -0 lines
Diff to previous 1.124
updates to ssa2.cgi and warnings when assignments fail

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Mon Jul 12 21:14:53 2004 UTC (15 years, 4 months ago) by olson
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Changes since 1.123: +6 -0 lines
Diff to previous 1.123
Add "umask 0" to fig.pm to ensure all new files are world writable.

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Thu Jul 1 21:17:53 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.122: +282 -45 lines
Diff to previous 1.122
More sim/askfor/pool stuff.

Make fig load_all show progress.

Fix run_in_background to do the right thing with an open db handle.

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Mon Jun 28 20:11:14 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.121: +42 -2 lines
Diff to previous 1.121
Add assignments_made_for_protein
expand some code for readability.

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Sun Jun 27 22:49:49 2004 UTC (15 years, 5 months ago) by overbeek
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Changes since 1.120: +9 -1 lines
Diff to previous 1.120
handle names of subsystems just a bit better

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Wed Jun 23 21:33:43 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.119: +58 -10 lines
Diff to previous 1.119
Add assignments_made_full, which returns the date and id of person who made the assignment.
assignments_made now just maps the result of assignments_made.

Add some comments.

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Wed Jun 16 16:52:10 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.118: +1 -0 lines
Diff to previous 1.118
Modifications to fix & finish up the automated subsystem extension.

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Wed Jun 16 14:25:36 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.117: +1 -0 lines
Diff to previous 1.117
New map support.

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Wed Jun 16 14:04:40 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.116: +98 -0 lines
Diff to previous 1.116
add background job support.

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Mon Jun 14 22:04:24 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.115: +96 -0 lines
Diff to previous 1.115
Add background job support

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Thu Jun 10 14:00:36 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.114: +5 -5 lines
Diff to previous 1.114
Add scalar decl to is_bacterial and friends.

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Thu Jun 10 13:39:55 2004 UTC (15 years, 5 months ago) by olson
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Changes since 1.113: +30 -0 lines
Diff to previous 1.113
add more funcs for tutorials

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Tue Jun 8 20:26:23 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.112: +159 -4 lines
Diff to previous 1.112
add some scalar annotations; add find_role_in_org

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Tue Jun 8 17:19:43 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.111: +16 -2 lines
Diff to previous 1.111
Guard the rquire of figrpc in case we don't have the necessary modules installed for it.

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Tue Jun 8 15:02:14 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.110: +70 -14 lines
Diff to previous 1.110
Add capability for :scalar :list :remote annotations to FIG interface. This works with
modules that are declared as subclasses of FIGAttributes.

Revision 1.110 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 3 20:58:04 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.109: +1 -1 lines
Diff to previous 1.109
reorder load of databases just slightly

Revision 1.109 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 3 08:12:44 2004 UTC (15 years, 6 months ago) by gdpusch
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Changes since 1.108: +1 -1 lines
Diff to previous 1.108
Fixed typo in pod-documentation

Revision 1.108 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 2 09:45:16 2004 UTC (15 years, 6 months ago) by gdpusch
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Changes since 1.107: +30 -29 lines
Diff to previous 1.107
Added check for "defined" status of filehandle reads from <SSA>; removed various "masking" redefinitions of "my" variables.

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Wed Jun 2 09:23:35 2004 UTC (15 years, 6 months ago) by gdpusch
Branch: MAIN
Changes since 1.106: +46 -16 lines
Diff to previous 1.106
Fixed typos in various $fig->genome_*() accessor functions.

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Tue Jun 1 20:45:39 2004 UTC (15 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.105: +1 -1 lines
Diff to previous 1.105
fix typo.

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Tue Jun 1 20:40:55 2004 UTC (15 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.104: +2 -2 lines
Diff to previous 1.104
Add $force_load argument to get_subsystem; results in the discarding
of the cached subsystem if there is one.

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Tue Jun 1 20:21:44 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.103: +20 -0 lines
Diff to previous 1.103
add subsystems_for_peg

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Tue Jun 1 19:06:17 2004 UTC (15 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.102: +3 -2 lines
Diff to previous 1.102
fix the call to figrpc

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Tue Jun 1 19:02:37 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.101: +13 -0 lines
Diff to previous 1.101
added redirect in FIG constructor to create a FIGrpc if the FIG_URL environment variable is set

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Tue Jun 1 00:45:38 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.100: +5 -2 lines
Diff to previous 1.100
make bbhs sensitive to lengths of match - watch out for fused proteins

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Sun May 30 15:04:26 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.99: +21 -9 lines
Diff to previous 1.99
precomputed BBHs

Revision 1.99 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 29 14:08:58 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.98: +1 -1 lines
Diff to previous 1.98
untested changes to extract_genomes

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Fri May 28 19:27:00 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.97: +21 -5 lines
Diff to previous 1.97
attempt to change FIG.pm to keep mac-1 up

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Thu May 27 18:22:11 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.96: +0 -1 lines
Diff to previous 1.96
doh, had left a debug print in there

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Wed May 26 22:34:17 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.95: +19 -0 lines
Diff to previous 1.95
add genome_and_peg_of

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Mon May 24 22:02:47 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.94: +10 -3 lines
Diff to previous 1.94
Factor out the subsystem caching.

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Mon May 24 21:59:32 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.93: +8 -1 lines
Diff to previous 1.93
cache subsystem objects, since they can be expensive to create.

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Mon May 24 21:55:18 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.92: +196 -34 lines
Diff to previous 1.92
Beginning of sim queueing stuff.
First implementation of Subsystem object, with FIG::peg_in_subsystem_cell
implemented in terms of it.

Revision 1.92 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 24 21:14:16 2004 UTC (15 years, 6 months ago) by gdpusch
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Changes since 1.91: +60 -3 lines
Diff to previous 1.91
Changed name of genome-size access method to \&genome_szdna($genome_id) to match the SQL keyword; added \&genome_pegs($genome) and \&genome_rnas($genome) to return number of PEGs and RNAs, resp.

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Mon May 24 21:03:39 2004 UTC (15 years, 6 months ago) by gdpusch
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Changes since 1.90: +28 -0 lines
Diff to previous 1.90
Added access method \&genome_size($genome_id) to return the number of base-pairs in an organism\'s contig files.

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Mon May 24 19:32:36 2004 UTC (15 years, 6 months ago) by olson
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Changes since 1.89: +47 -0 lines
Diff to previous 1.89
add file_head and file_read

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Sat May 22 11:43:00 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.88: +6 -0 lines
Diff to previous 1.88
fix error in tutorial

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Fri May 21 18:05:55 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.87: +6 -2 lines
Diff to previous 1.87
fixes to similarities

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Thu May 20 12:26:47 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.86: +14 -2 lines
Diff to previous 1.86
make aliases include external aliases

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Wed May 19 15:54:10 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.85: +3 -0 lines
Diff to previous 1.85
allow comma-separated contiguous regions in dna_seq argument list

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Wed May 19 14:15:57 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.84: +25 -0 lines
Diff to previous 1.84
add all_contigs

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Wed May 19 13:17:39 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.83: +25 -9 lines
Diff to previous 1.83
fixes on memory leak and genome version

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Tue May 18 00:44:54 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.82: +1 -1 lines
Diff to previous 1.82
set max open files to 50

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Mon May 17 09:22:50 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.81: +91 -8 lines
Diff to previous 1.81
support addition of links to pegs

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Fri May 14 18:06:51 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.80: +41 -1 lines
Diff to previous 1.80
fixed up links

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Thu May 13 20:59:56 2004 UTC (15 years, 6 months ago) by overbeek
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Changes since 1.79: +1 -2 lines
Diff to previous 1.79
fix add_genome

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Tue May 4 16:27:23 2004 UTC (15 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.78: +43 -3 lines
Diff to previous 1.78
more protection around the code that pokes at the clearing house, in case xmlrpc libs are missing

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Mon May 3 17:16:50 2004 UTC (15 years, 7 months ago) by olson
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Changes since 1.77: +11 -0 lines
Diff to previous 1.77
Add comment.

Revision 1.77 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 1 02:56:38 2004 UTC (15 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.76: +3 -2 lines
Diff to previous 1.76
Comment out import of Clearinghouse until we get the env updated.

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Thu Apr 29 16:41:16 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.75: +9 -0 lines
Diff to previous 1.75
tools for query

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Wed Apr 28 21:59:32 2004 UTC (15 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.74: +184 -0 lines
Diff to previous 1.74
Clearinghouse publishing stuff

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Wed Apr 28 04:34:52 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.73: +4 -1 lines
Diff to previous 1.73
fix to definition of bbh

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Tue Apr 27 15:41:28 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.72: +22 -0 lines
Diff to previous 1.72
basic query tools

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Sat Apr 24 23:27:05 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.71: +4 -3 lines
Diff to previous 1.71
make sure that external_calls produces one function for each peg

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Sat Apr 24 15:02:08 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.70: +34 -6 lines
Diff to previous 1.70
tools for McCune to build expert automated assignments

Revision 1.70 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 23 21:51:15 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.69: +1 -0 lines
Diff to previous 1.69
make load_all build blast dbs for fig proteins

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Fri Apr 23 21:49:02 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.68: +1 -1 lines
Diff to previous 1.68
fixes to index.cgi to blast against all complete

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Fri Apr 23 17:23:40 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.67: +2 -2 lines
Diff to previous 1.67
fixes to best_candidates

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Fri Apr 23 16:59:40 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.66: +9 -5 lines
Diff to previous 1.66
fixes to best_bbh_candidates

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Mon Apr 19 11:36:39 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.65: +4 -2 lines
Diff to previous 1.65
fix a bad bug in assignment permissions

Revision 1.65 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 9 15:26:05 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.64: +17 -3 lines
Diff to previous 1.64
pass back more detailed data for candidates for a role

Revision 1.64 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 9 14:55:36 2004 UTC (15 years, 7 months ago) by overbeek
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Changes since 1.63: +85 -0 lines
Diff to previous 1.63
more intelligent candidates for function

Revision 1.63 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 8 11:49:33 2004 UTC (15 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.62: +11 -0 lines
Diff to previous 1.62
fixes in auto assignments

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Thu Apr 1 22:58:44 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.61: +8 -0 lines
Diff to previous 1.61
allow p2p to send me epoch dates, rather than readable dates

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Thu Apr 1 22:10:34 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.60: +1 -1 lines
Diff to previous 1.60
turn off warning messages for translation failures when translating PEG ids

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Thu Apr 1 22:07:31 2004 UTC (15 years, 8 months ago) by disz
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Changes since 1.59: +4 -4 lines
Diff to previous 1.59
More P2P fixes.
Add setgid to the mkdir/chmod's.

Revision 1.59 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 1 14:54:57 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.58: +66 -0 lines
Diff to previous 1.58
fixes to candidates for a role

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Wed Mar 31 19:20:24 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.57: +11 -1 lines
Diff to previous 1.57
p2p for updating release

Revision 1.57 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 31 18:39:15 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.56: +3 -3 lines
Diff to previous 1.56
p2p changes

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Wed Mar 31 16:32:22 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.55: +52 -0 lines
Diff to previous 1.55
attempt to fix package/install for p2p

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Wed Mar 31 11:14:47 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.54: +148 -0 lines
Diff to previous 1.54
move PEG translation into FIG.pm

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Mon Mar 29 23:13:14 2004 UTC (15 years, 8 months ago) by mkubal
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Changes since 1.53: +2 -2 lines
Diff to previous 1.53
removes ## markers in FIG.pm

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Mon Mar 29 23:12:40 2004 UTC (15 years, 8 months ago) by mkubal
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Changes since 1.52: +7 -104 lines
Diff to previous 1.52
removes ## markers in FIG.pm and fixed Blast.pm

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Fri Mar 26 21:38:38 2004 UTC (15 years, 8 months ago) by olson
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Changes since 1.51: +18 -0 lines
Diff to previous 1.51
Make get_local_hostname check for a FIGdisk/config/hostname file and use
that as the local hostname if present.

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Fri Mar 26 13:01:46 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.50: +11 -2 lines
Diff to previous 1.50
better peg mapping when importing spreadsheets

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Thu Mar 25 17:10:50 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.49: +11 -0 lines
Diff to previous 1.49
includes errors

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Thu Mar 25 13:48:27 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.48: +3 -1 lines
Diff to previous 1.48
improvements on importing subsystems

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Wed Mar 24 00:05:40 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.47: +1 -1 lines
Diff to previous 1.47
export subsystems stuff

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Tue Mar 23 21:54:03 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.46: +7 -1 lines
Diff to previous 1.46
Broke a semicolon-chained set of commands in &delete_genomes() into separate &run() invocations, so that if any of them fail, the delete operation will abort. -- /gdp

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 22 02:33:57 2004 UTC (15 years, 8 months ago) by gdpusch
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Changes since 1.45: +1 -1 lines
Diff to previous 1.45
Fixed failure to declare two variables in routine &read_fasta_record(). -- /gdp

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Mon Mar 22 01:51:30 2004 UTC (15 years, 8 months ago) by gdpusch
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Changes since 1.44: +58 -1 lines
Diff to previous 1.44
Added routine &read_fasta_record(). -- /gdp

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Fri Mar 19 21:58:31 2004 UTC (15 years, 8 months ago) by golsen
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Changes since 1.43: +24 -13 lines
Diff to previous 1.43
Relative base address support and cgi_url() based on current http request

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Fri Mar 19 18:45:36 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.42: +39 -22 lines
Diff to previous 1.42
fixes to coupling and protein.cgi

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Thu Mar 18 16:02:32 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.41: +19 -0 lines
Diff to previous 1.41
add versions to spreadsheets

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 18 13:16:40 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.40: +1 -1 lines
Diff to previous 1.40
exchangable flags on spreadsheet

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Wed Mar 17 20:18:22 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.39: +105 -6 lines
Diff to previous 1.39
for Gordon and Mike

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 17 18:17:34 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.38: +107 -0 lines
Diff to previous 1.38
basic export of subsystems stuff

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Mon Mar 15 23:06:47 2004 UTC (15 years, 8 months ago) by olson
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Changes since 1.37: +33 -0 lines
Diff to previous 1.37
Add get_seed_id()

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Mon Mar 15 04:37:50 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.36: +2 -4 lines
Diff to previous 1.36
new spreadsheet

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Sun Mar 14 03:46:16 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.35: +298 -188 lines
Diff to previous 1.35
fixes

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Tue Mar 9 23:19:23 2004 UTC (15 years, 8 months ago) by overbeek
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Changes since 1.34: +97 -0 lines
Diff to previous 1.34
fixed distances and spreadsheet

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Fri Mar 5 22:17:16 2004 UTC (15 years, 9 months ago) by overbeek
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Changes since 1.33: +25 -0 lines
Diff to previous 1.33
support gi and NP numbers for access to fig IDs

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Wed Mar 3 14:56:43 2004 UTC (15 years, 9 months ago) by overbeek
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Changes since 1.32: +48 -1 lines
Diff to previous 1.32
add merged annotations

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Wed Mar 3 12:49:23 2004 UTC (15 years, 9 months ago) by overbeek
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Changes since 1.31: +4 -2 lines
Diff to previous 1.31
fixes from DOE meeting

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Thu Feb 19 12:55:35 2004 UTC (15 years, 9 months ago) by overbeek
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Changes since 1.30: +1 -1 lines
Diff to previous 1.30
fix bug due to change in sims

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Tue Feb 17 22:23:36 2004 UTC (15 years, 9 months ago) by overbeek
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Changes since 1.29: +9 -5 lines
Diff to previous 1.29
preserve translation through similarities

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Sun Feb 15 17:12:54 2004 UTC (15 years, 9 months ago) by overbeek
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Changes since 1.28: +7 -4 lines
Diff to previous 1.28
added Gary Olsen changes

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Tue Feb 10 22:35:57 2004 UTC (15 years, 9 months ago) by olson
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Changes since 1.27: +19 -1 lines
Diff to previous 1.27
in get_local_hostname, ensure that we get a FQDN. If we don't, just bail and
use our IP address.

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Tue Feb 3 16:45:57 2004 UTC (15 years, 10 months ago) by overbeek
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Changes since 1.26: +9 -0 lines
Diff to previous 1.26
minor fixes

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Mon Jan 26 22:51:32 2004 UTC (15 years, 10 months ago) by overbeek
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Changes since 1.25: +12 -4 lines
Diff to previous 1.25
fixes

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Wed Jan 21 18:27:29 2004 UTC (15 years, 10 months ago) by overbeek
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Changes since 1.24: +1 -0 lines
Diff to previous 1.24
from the Penn trip

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Fri Jan 16 19:37:40 2004 UTC (15 years, 10 months ago) by overbeek
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Changes since 1.23: +2 -2 lines
Diff to previous 1.23
chop delimiter off annotations

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Wed Jan 14 20:20:32 2004 UTC (15 years, 10 months ago) by overbeek
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Changes since 1.22: +9 -99 lines
Diff to previous 1.22
synch up Ross

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Thu Jan 8 16:31:59 2004 UTC (15 years, 11 months ago) by overbeek
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Changes since 1.21: +8 -0 lines
Diff to previous 1.21
handle loops in translation

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Wed Jan 7 03:34:13 2004 UTC (15 years, 11 months ago) by overbeek
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Changes since 1.20: +9 -0 lines
Diff to previous 1.20
make Assignments files have readable names

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Tue Jan 6 23:08:26 2004 UTC (15 years, 11 months ago) by overbeek
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Changes since 1.19: +1 -1 lines
Diff to previous 1.19
fix in extract_genomes

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 6 18:14:48 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.18: +14 -4 lines
Diff to previous 1.18
fix stick behavior for checked sims

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 5 12:26:58 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.17: +2 -1 lines
Diff to previous 1.17
minor bugs

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 3 14:13:48 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.16: +41 -1 lines
Diff to previous 1.16
fix P2P to use get_assignments

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 3 06:03:43 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.15: +25 -20 lines
Diff to previous 1.15
changes to annotations to allow extraction of assignments

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 30 05:21:24 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.14: +2 -2 lines
Diff to previous 1.14
fix order of database loads

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 29 02:22:37 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.13: +17 -12 lines
Diff to previous 1.13
numerous performance issues

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 28 17:11:29 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.12: +55 -18 lines
Diff to previous 1.12
cleanup issues relating to large numbers of partial genomes

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 23 22:38:31 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.11: +1 -1 lines
Diff to previous 1.11
make plugging URLs more robust

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 23 22:29:51 2003 UTC (15 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.10: +5 -5 lines
Diff to previous 1.10
remove prints

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 23 22:28:10 2003 UTC (15 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.9: +207 -0 lines
Diff to previous 1.9
Add IP-determination logic.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 22 01:24:22 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +14 -5 lines
Diff to previous 1.8
add pins and clusters properly

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 21 01:20:59 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +0 -1 lines
Diff to previous 1.7
allow multiple sims files in update_sims

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 20 21:08:43 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +26 -3 lines
Diff to previous 1.6
fixed issues relating to addition/deletion of genomes

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 19 20:09:34 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +0 -18 lines
Diff to previous 1.5
get rid of set_urls, since it will not work anymore

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 5 14:31:23 2003 UTC (16 years ago) by overbeek
Branch: MAIN
CVS Tags: delong-01, delong-02
Changes since 1.4: +1 -1 lines
Diff to previous 1.4
fix permissions on added genome

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 4 21:49:02 2003 UTC (16 years ago) by overbeek
Branch: MAIN
Changes since 1.3: +6 -2 lines
Diff to previous 1.3
fix bug in function translation

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 3 21:24:31 2003 UTC (16 years ago) by overbeek
Branch: MAIN
Changes since 1.2: +4 -3 lines
Diff to previous 1.2
*** empty log message ***

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 3 19:39:29 2003 UTC (16 years ago) by efrank
Branch: MAIN
Changes since 1.1: +25 -5 lines
Diff to previous 1.1

fixed a bunch of changes

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 1 16:54:26 2003 UTC (16 years ago) by efrank
Branch: MAIN
Branch point for: initial
Initial revision

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