Annotation of /FigKernelPackages/FIG.pm

Revision 1.563 - (view) (download) (as text)

1 :	overbeek	1.549
2 :	olson	1.404	#
3 :			# Copyright (c) 2003-2006 University of Chicago and Fellowship
4 :			# for Interpretations of Genomes. All Rights Reserved.
5 :			#
6 :			# This file is part of the SEED Toolkit.
7 :	parrello	1.518	#
8 :	olson	1.404	# The SEED Toolkit is free software. You can redistribute
9 :			# it and/or modify it under the terms of the SEED Toolkit
10 :	parrello	1.518	# Public License.
11 :	olson	1.404	#
12 :			# You should have received a copy of the SEED Toolkit Public License
13 :			# along with this program; if not write to the University of Chicago
14 :			# at info@ci.uchicago.edu or the Fellowship for Interpretation of
15 :			# Genomes at veronika@thefig.info or download a copy from
16 :			# http://www.theseed.org/LICENSE.TXT.
17 :			#
18 :
19 :	efrank	1.1	package FIG;
20 :
21 :	olson	1.111	use strict;
22 :
23 :	overbeek	1.453	use FIG_Config;
24 :
25 :			#
26 :			# See if we need to use fcntl-based file locking. If so, import
27 :			# the package and override the global definition of flock.
28 :			# This is in place at least initially for the GPFS-based install on
29 :			# the NMPDR cluster.
30 :			#
31 :
32 :			use FileLocking;
33 :
34 :	overbeek	1.135	use Fcntl qw/:flock/; # import LOCK_* constants
35 :
36 :	olson	1.116	use POSIX;
37 :	olson	1.158	use IPC::Open2;
38 :	olson	1.329	use MIME::Base64;
39 :	olson	1.330	use File::Basename;
40 :	olson	1.359	use FileHandle;
41 :	parrello	1.394	use File::Copy;
42 :	olson	1.417	use SOAP::Lite;
43 :	parrello	1.420	use File::Path;
44 :	overbeek	1.484	use LWP::UserAgent;
45 :	olson	1.116
46 :	efrank	1.1	use DBrtns;
47 :			use Sim;
48 :	olson	1.361	use Annotation;
49 :	efrank	1.1	use Blast;
50 :	overbeek	1.322	use FullLocation;
51 :	overbeek	1.36	use tree_utilities;
52 :	olson	1.93	use Subsystem;
53 :	olson	1.162	use SeedDas;
54 :	olson	1.183	use Construct;
55 :	parrello	1.200	use FIGRules;
56 :	parrello	1.210	use Tracer;
57 :	olson	1.297	use GenomeIDMap;
58 :	parrello	1.539	use RemoteCustomAttributes;
59 :	olson	1.260
60 :	olson	1.356	our $haveDateParse;
61 :			eval {
62 :			require Date::Parse;
63 :			import Date::Parse;
64 :			$haveDateParse = 1;
65 :	parrello	1.540	require CustomAttributes;
66 :			import CustomAttributes;
67 :	olson	1.356	};
68 :
69 :	olson	1.245	eval { require FigGFF; };
70 :	parrello	1.390	if ($@ and T(1)) {
71 :	olson	1.260	warn $@;
72 :			}
73 :	olson	1.79
74 :			#
75 :			# Conditionally evaluate this in case its prerequisites are not available.
76 :			#
77 :
78 :	olson	1.356	our $ClearinghouseOK;
79 :			eval {
80 :	olson	1.79	require Clearinghouse;
81 :	olson	1.356	$ClearinghouseOK = 1;
82 :	olson	1.79	};
83 :	efrank	1.1
84 :	olson	1.10	use IO::Socket;
85 :
86 :	efrank	1.1	use FileHandle;
87 :
88 :	olson	1.530	use Carp qw(confess croak carp cluck);
89 :	efrank	1.1	use Data::Dumper;
90 :	overbeek	1.25	use Time::Local;
91 :	olson	1.93	use File::Spec;
92 :	olson	1.123	use File::Copy;
93 :	olson	1.112	#
94 :			# Try to load the RPC stuff; it might fail on older versions of the software.
95 :			#
96 :			eval {
97 :			require FIGrpc;
98 :			};
99 :
100 :			my $xmlrpc_available = 1;
101 :	parrello	1.287	if ($@ ne "") {
102 :	olson	1.112	$xmlrpc_available = 0;
103 :			}
104 :
105 :	efrank	1.1
106 :	olson	1.111	use FIGAttributes;
107 :			use base 'FIGAttributes';
108 :
109 :			use vars qw(%_FunctionAttributes);
110 :
111 :			use Data::Dumper;
112 :
113 :	olson	1.124	#
114 :			# Force all new files to be all-writable.
115 :			#
116 :
117 :			umask 0;
118 :
119 :	parrello	1.210	=head1 FIG Genome Annotation System
120 :
121 :			=head2 Introduction
122 :
123 :			This is the main object for access to the SEED data store. The data store
124 :			itself is a combination of flat files and a database. The flat files can
125 :			be moved easily between systems and the database rebuilt as needed.
126 :
127 :			A reduced set of this object's functions are available via the B<SFXlate>
128 :			object. The SFXlate object uses a single database to represent all its
129 :			genomic information. It provides a much smaller capability for updating
130 :			the data, and eliminates all similarities except for bidirectional best
131 :			hits.
132 :
133 :			The key to making the FIG system work is proper configuration of the
134 :			C<FIG_Config.pm> file. This file contains names and URLs for the key
135 :			directories as well as the type and login information for the database.
136 :
137 :	parrello	1.287	FIG was designed to operate as a series of peer instances. Each instance is
138 :			updated independently by its owner, and the instances can be synchronized
139 :			using a process called a I<peer-to-peer update>. The terms
140 :			I<SEED instance> and I<peer> are used more-or-less interchangeably.
141 :
142 :			The POD documentation for this module is still in progress, and is provided
143 :			on an AS IS basis without warranty. If you have a correction and you're
144 :			not a developer, EMAIL the details to B<bruce@gigabarb.com> and I'll fold
145 :			it in.
146 :
147 :			B<NOTE>: The usage example for each method specifies whether it is static
148 :
149 :			FIG::something
150 :
151 :			or dynamic
152 :
153 :			$fig->something
154 :
155 :			If the method is static and has no parameters (C<FIG::something()>) it can
156 :	parrello	1.298	also be invoked dynamically. This is a general artifact of the
157 :	parrello	1.287	way PERL implements object-oriented programming.
158 :
159 :			=head2 Hiding/Caching in a FIG object
160 :
161 :			We save the DB handle, cache taxonomies, and put a few other odds and ends in the
162 :			FIG object. We expect users to invoke these services using the object $fig constructed
163 :			using:
164 :
165 :			use FIG;
166 :			my $fig = new FIG;
167 :
168 :			$fig is then used as the basic mechanism for accessing FIG services. It is, of course,
169 :			just a hash that is used to retain/cache data. The most commonly accessed item is the
170 :			DB filehandle, which is accessed via $self->db_handle.
171 :
172 :			We cache genus/species expansions, taxonomies, distances (very crudely estimated) estimated
173 :			between genomes, and a variety of other things.
174 :
175 :	parrello	1.210	=cut
176 :
177 :	parrello	1.287
178 :	parrello	1.210	#: Constructor FIG->new();
179 :
180 :			=head2 Public Methods
181 :
182 :			=head3 new
183 :
184 :			C<< my $fig = FIG->new(); >>
185 :
186 :	parrello	1.298	This is the constructor for a FIG object. It uses no parameters. If tracing
187 :			has not yet been turned on, it will be turned on here. The tracing type and
188 :			level are specified by the configuration variables C<$FIG_Config::trace_levels>
189 :	parrello	1.301	and C<$FIG_Config::trace_type>. These defaults can be overridden using the
190 :			environment variables C<Trace> and C<TraceType>, respectively.
191 :	parrello	1.210
192 :			=cut
193 :
194 :	efrank	1.1	sub new {
195 :			my($class) = @_;
196 :
197 :	olson	1.102	#
198 :			# Check to see if we have a FIG_URL environment variable set.
199 :			# If we do, don't actually create a FIG object, but rather
200 :			# create a FIGrpc and return that as the return from this constructor.
201 :			#
202 :	parrello	1.390	if ($ENV{FIG_URL} && $xmlrpc_available) {
203 :	parrello	1.210	my $figrpc = new FIGrpc($ENV{FIG_URL});
204 :			return $figrpc;
205 :	olson	1.102	}
206 :	parrello	1.355	Trace("Connecting to the database.") if T(2);
207 :	parrello	1.287	# Connect to the database, then return ourselves.
208 :	efrank	1.1	my $rdbH = new DBrtns;
209 :	overbeek	1.453
210 :			my $self = {
211 :	parrello	1.210	_dbf => $rdbH,
212 :	overbeek	1.453	};
213 :	parrello	1.542	if ($FIG_Config::attrOld) {
214 :			# Use the old attribute system. This is normally only done if we
215 :			# need to reload.
216 :	parrello	1.563	Trace("Legacy attribute system chosen using the override feature.") if T(3);
217 :	parrello	1.542	} elsif ($FIG_Config::attrURL) {
218 :	parrello	1.563	Trace("Remote attribute server $FIG_Config::attrURL chosen.") if T(3);
219 :	parrello	1.539	$self->{_ca} = RemoteCustomAttributes->new($FIG_Config::attrURL);
220 :			} elsif ($FIG_Config::attrDbName) {
221 :	parrello	1.563	Trace("Local attribute database $FIG_Config::attrDbName chosen.") if T(3);
222 :	parrello	1.538	$self->{_ca} = CustomAttributes->new();
223 :			}
224 :	overbeek	1.453
225 :			#
226 :			# If we have a readonly-database defined in the config,
227 :			# create a handle for that as well.
228 :			#
229 :
230 :			if (defined($FIG_Config::readonly_dbhost))
231 :			{
232 :	parrello	1.485	my $ro = new DBrtns($FIG_Config::dbms, $FIG_Config::readonly_db, $FIG_Config::readonly_dbuser,
233 :			$FIG_Config::readonly_dbpass, $FIG_Config::readonly_dbport, $FIG_Config::readonly_dbhost,
234 :			$FIG_Config::readonly_dbsock);
235 :			$self->{_ro_dbf} = $ro;
236 :	overbeek	1.453
237 :	parrello	1.485	#
238 :			# Oh ick. All of the queries made go through the one dbf that a FIG holds. We want
239 :			# to redirect the select queries through this readonly object. We'll need
240 :			# to tell the main handle about the readonly one, and let it decide.
241 :			#
242 :
243 :			$rdbH->set_readonly_handle($ro);
244 :	overbeek	1.453	}
245 :
246 :			return bless $self, $class;
247 :	efrank	1.1	}
248 :
249 :	mkubal	1.546	=head3 go_number_to_term
250 :
251 :			Returns GO term for GO number from go_number_to_term table in database
252 :
253 :			=cut
254 :
255 :			sub go_number_to_term {
256 :			my($self,$id) = @_;
257 :			my $rdbH = $self->db_handle;
258 :	overbeek	1.548	my $relational_db_response = $rdbH->SQL("SELECT go_desc FROM go_terms where go_id = \'$id\'");
259 :	mkubal	1.546	return (@$relational_db_response == 1) ? $relational_db_response->[0]->[0] : "";
260 :			return "";
261 :			}
262 :	overbeek	1.454
263 :	overbeek	1.548	sub go_number_to_info {
264 :			my($self,$id) = @_;
265 :			my $rdbH = $self->db_handle;
266 :			my $relational_db_response = $rdbH->SQL("SELECT go_desc,go_type,obsolete FROM go_terms where go_id = \'$id\'");
267 :			return (@$relational_db_response == 1) ? $relational_db_response->[0] : "";
268 :			return "";
269 :			}
270 :
271 :
272 :	parrello	1.287	=head3 db_handle
273 :
274 :			C<< my $dbh = $fig->db_handle; >>
275 :
276 :			Return the handle to the internal B<DBrtns> object. This allows direct access to
277 :			the database methods.
278 :
279 :			=cut
280 :
281 :			sub db_handle {
282 :			my($self) = @_;
283 :			return $self->{_dbf};
284 :			}
285 :
286 :	overbeek	1.293	sub table_exists {
287 :			my($self,$table) = @_;
288 :
289 :			my $rdbH = $self->db_handle;
290 :			return $rdbH->table_exists($table);
291 :			}
292 :	parrello	1.292
293 :	parrello	1.287	=head3 cached
294 :
295 :			C<< my $x = $fig->cached($name); >>
296 :
297 :			Return a reference to a hash containing transient data. If no hash exists with the
298 :			specified name, create an empty one under that name and return it.
299 :
300 :			The idea behind this method is to allow clients to cache data in the FIG object for
301 :			later use. (For example, a method might cache feature data so that it can be
302 :			retrieved later without using the database.) This facility should be used sparingly,
303 :			since different clients may destroy each other's data if they use the same name.
304 :
305 :			=over 4
306 :
307 :			=item name
308 :
309 :			Name assigned to the cached data.
310 :
311 :			=item RETURN
312 :
313 :			Returns a reference to a hash that is permanently associated with the specified name.
314 :			If no such hash exists, an empty one will be created for the purpose.
315 :
316 :			=back
317 :
318 :			=cut
319 :
320 :			sub cached {
321 :			my($self,$what) = @_;
322 :
323 :			my $x = $self->{$what};
324 :			if (! $x) {
325 :			$x = $self->{$what} = {};
326 :			}
327 :			return $x;
328 :			}
329 :	parrello	1.210
330 :			=head3 get_system_name
331 :
332 :			C<< my $name = $fig->get_system_name; >>
333 :
334 :			Returns C<seed>, indicating that this is object is using the SEED
335 :			database. The same method on an SFXlate object will return C<sprout>.
336 :
337 :			=cut
338 :			#: Return Type $;
339 :			sub get_system_name {
340 :	olson	1.207	return "seed";
341 :	olson	1.205	}
342 :	parrello	1.210
343 :	parrello	1.287	=head3 DESTROY
344 :
345 :			The destructor releases the database handle.
346 :
347 :			=cut
348 :	olson	1.205
349 :	parrello	1.287	sub DESTROY {
350 :	efrank	1.1	my($self) = @_;
351 :			my($rdbH);
352 :
353 :	parrello	1.210	if ($rdbH = $self->db_handle) {
354 :			$rdbH->DESTROY;
355 :	efrank	1.1	}
356 :			}
357 :
358 :	parrello	1.355	=head3 same_seqs
359 :
360 :			C<< my $sameFlag = FIG::same_seqs($s1, $s2); >>
361 :
362 :			Return TRUE if the specified protein sequences are considered equivalent and FALSE
363 :			otherwise. The sequences should be presented in I<nr-analysis> form, which is in
364 :			reverse order and upper case with the stop codon omitted.
365 :
366 :			The sequences will be considered equivalent if the shorter matches the initial
367 :			portion of the long one and is no more than 30% smaller. Since the sequences are
368 :			in nr-analysis form, the equivalent start potions means that the sequences
369 :			have the same tail. The importance of the tail is that the stop point of a PEG
370 :			is easier to find than the start point, so a same tail means that the two
371 :			sequences are equivalent except for the choice of start point.
372 :
373 :			=over 4
374 :
375 :			=item s1
376 :
377 :			First protein sequence, reversed and with the stop codon removed.
378 :
379 :			=item s2
380 :
381 :			Second protein sequence, reversed and with the stop codon removed.
382 :
383 :			=item RETURN
384 :
385 :			Returns TRUE if the two protein sequences are equivalent, else FALSE.
386 :
387 :			=back
388 :
389 :			=cut
390 :
391 :			sub same_seqs {
392 :			my ($s1,$s2) = @_;
393 :
394 :			my $ln1 = length($s1);
395 :			my $ln2 = length($s2);
396 :
397 :			return ((abs($ln1-$ln2) < (0.3 * (($ln1 < $ln2) ? $ln1 : $ln2))) &&
398 :			((($ln1 <= $ln2) && (index($s2,$s1) == 0)) \|\|
399 :			(($ln1 > $ln2) && (index($s1,$s2) == 0))));
400 :			}
401 :
402 :	overbeek	1.520	=head3 is_locked_fid
403 :
404 :			C<< $fig->is_locked_fid($fid); >>
405 :
406 :			returns 1 iff $fid is locked
407 :
408 :			=cut
409 :
410 :			sub is_locked_fid {
411 :			my($self,$fid) = @_;
412 :
413 :	overbeek	1.523	if (! $self->table_exists('fid_locks')) { return 0 }
414 :	overbeek	1.520	my $rdbH = $self->db_handle;
415 :			my $relational_db_response = $rdbH->SQL("SELECT fid FROM fid_locks WHERE fid = \'$fid\' ");
416 :			return (@$relational_db_response > 0) ? 1 : 0;
417 :			}
418 :
419 :			=head3 lock_fid
420 :
421 :			C<< $fig->lock_fid($user,$fid); >>
422 :
423 :			Sets a lock on annotations for $fid.
424 :
425 :			=cut
426 :
427 :			sub lock_fid {
428 :			my($self,$user,$fid) = @_;
429 :
430 :	overbeek	1.523	if (! $self->table_exists('fid_locks')) { return 0 }
431 :	overbeek	1.521	if ((! $user) \|\| ($fid !~ /^fig\\|\d+\.\d+/)) { return 0 }
432 :	overbeek	1.553	if ($self->is_locked_fid($fid)) { return 1 }
433 :	overbeek	1.521
434 :	overbeek	1.520	my $func = $self->function_of($fid);
435 :			$self->add_annotation($fid,$user,"locked assignments to '$func'");
436 :
437 :			my $rdbH = $self->db_handle;
438 :			my $relational_db_response = $rdbH->SQL("SELECT fid FROM fid_locks WHERE fid = \'$fid\' ");
439 :			if (! (@$relational_db_response > 0))
440 :			{
441 :			$rdbH->SQL("INSERT INTO fid_locks ( fid ) VALUES ( '$fid' )");
442 :			if ($fid =~ /^fig\\|(\d+\.\d+)\.([^\.]+)/)
443 :			{
444 :			my $genome = $1;
445 :			my $type = $2;
446 :			if (open(TMP,">>$FIG_Config::organisms/$genome/Features/$type/locks"))
447 :			{
448 :			print TMP "$fid\t1\n";
449 :			}
450 :			close(TMP);
451 :			}
452 :			}
453 :			}
454 :
455 :			=head3 unlock_fid
456 :
457 :			C<< $fig->unlock_fid($user,$fid); >>
458 :
459 :			Sets a unlock on annotations for $fid.
460 :
461 :			=cut
462 :
463 :			sub unlock_fid {
464 :			my($self,$user,$fid) = @_;
465 :
466 :	overbeek	1.523	if (! $self->table_exists('fid_locks')) { return 0 }
467 :	overbeek	1.521	if ((! $user) \|\| ($fid !~ /^fig\\|\d+\.\d+/)) { return 0 }
468 :	overbeek	1.553	if (! $self->is_locked_fid($fid)) { return 1 }
469 :	overbeek	1.521
470 :	overbeek	1.520	$self->add_annotation($fid,$user,"unlocked assignments");
471 :			my $rdbH = $self->db_handle;
472 :			my $relational_db_response = $rdbH->SQL("SELECT fid FROM fid_locks WHERE fid = '$fid' ");
473 :			$rdbH->SQL("DELETE FROM fid_locks WHERE ( fid = '$fid' )");
474 :			if ($fid =~ /^fig\\|(\d+\.\d+)\.([^\.]+)/)
475 :			{
476 :			my $genome = $1;
477 :			my $type = $2;
478 :			if (open(TMP,">>$FIG_Config::organisms/$genome/Features/$type/locks"))
479 :			{
480 :			print TMP "$fid\t0\n";
481 :			}
482 :			close(TMP);
483 :			}
484 :			}
485 :
486 :	parrello	1.210	=head3 delete_genomes
487 :
488 :			C<< $fig->delete_genomes(\@genomes); >>
489 :
490 :			Delete the specified genomes from the data store. This requires making
491 :			system calls to move and delete files.
492 :
493 :			=cut
494 :			#: Return Type ;
495 :	overbeek	1.429	################################# make damn sure that you have enough disk ######################
496 :			### The following code represents a serious, major update. Normally, one simply "marks" deleted
497 :			### genomes, which is quick and does not require halting the system.
498 :	overbeek	1.7	sub delete_genomes {
499 :			my($self,$genomes) = @_;
500 :			my $tmpD = "$FIG_Config::temp/tmp.deleted.$$";
501 :			my $tmp_Data = "$FIG_Config::temp/Data.$$";
502 :
503 :			my %to_del = map { $_ => 1 } @$genomes;
504 :			open(TMP,">$tmpD") \|\| die "could not open $tmpD";
505 :
506 :			my $genome;
507 :	parrello	1.287	foreach $genome ($self->genomes) {
508 :			if (! $to_del{$genome}) {
509 :			print TMP "$genome\n";
510 :			}
511 :	overbeek	1.7	}
512 :			close(TMP);
513 :
514 :			&run("extract_genomes $tmpD $FIG_Config::data $tmp_Data");
515 :	overbeek	1.429	print STDERR "Please bring the system down for a bit\n";
516 :			system "echo \"System down due to update of genomes\n\" >> $tmp_Data/Global/why_down";
517 :	parrello	1.200	&run("mv $FIG_Config::data $FIG_Config::data.deleted");
518 :	overbeek	1.47	&run("mv $tmp_Data $FIG_Config::data");
519 :			&run("fig load_all");
520 :	overbeek	1.429	print STDERR "Now, you should think about deleting $FIG_Config::data.deleted\n";
521 :			unlink("$FIG_Config::global/why_down"); ### start allowing CGIs to run
522 :			# &run("rm -rf $FIG_Config::data.deleted");
523 :			}
524 :
525 :			### Mark a genome as deleted, but do not actually clean up anything. That whole event
526 :			### requires "delete_genomes"
527 :			###
528 :			sub mark_deleted_genomes {
529 :	overbeek	1.466	my($self,$user,$genomes) = @_;
530 :	overbeek	1.429	my($genome);
531 :
532 :	overbeek	1.466	foreach $genome (@$genomes)
533 :			{
534 :	parrello	1.485	$self->log_update($user,$genome,$self->genus_species($genome),"Marked Deleted Genome $genome");
535 :	overbeek	1.466	}
536 :			return $self->mark_deleted_genomes_body($user,$genomes);
537 :			}
538 :
539 :			sub mark_deleted_genomes_body {
540 :			my($self,$user,$genomes) = @_;
541 :			my($genome);
542 :	overbeek	1.440
543 :	overbeek	1.429	my $rdbH = $self->db_handle;
544 :
545 :			my $n = 0;
546 :			foreach $genome (@$genomes)
547 :			{
548 :	parrello	1.485	if ($self->is_genome($genome) && open(DEL,">$FIG_Config::organisms/$genome/DELETED"))
549 :	parrello	1.518	{
550 :	parrello	1.485	print DEL "deleted\n";
551 :			$rdbH->SQL("DELETE FROM genome WHERE ( genome = '$genome' )");
552 :			$n++;
553 :			}
554 :			close(DEL);
555 :	overbeek	1.429	}
556 :	overbeek	1.466	$self->{_is_genome} = {};
557 :	overbeek	1.429	return $n;
558 :			}
559 :	parrello	1.518
560 :	overbeek	1.429	sub unmark_deleted_genomes {
561 :	overbeek	1.466	my($self,$user,$genomes) = @_;
562 :	overbeek	1.429	my($genome);
563 :
564 :	overbeek	1.466	foreach $genome (@$genomes)
565 :			{
566 :	parrello	1.485	$self->log_update($user,$genome,$self->genus_species($genome),"Unmarked Deleted Genome $genome");
567 :	overbeek	1.466	}
568 :
569 :	overbeek	1.429	my $rdbH = $self->db_handle;
570 :
571 :			my $n = 0;
572 :			foreach $genome (@$genomes)
573 :			{
574 :	parrello	1.485	if (-s "$FIG_Config::organisms/$genome/DELETED")
575 :			{
576 :			unlink("$FIG_Config::organisms/$genome/DELETED");
577 :			&run("compute_genome_counts $genome");
578 :			$n++;
579 :			}
580 :	overbeek	1.429	}
581 :	overbeek	1.466	$self->{_is_genome} = {};
582 :	overbeek	1.429	return $n;
583 :	overbeek	1.7	}
584 :	parrello	1.200
585 :	overbeek	1.469	sub log_corr {
586 :	overbeek	1.470	my($self,$user,$genome, $mapping,$msg) = @_;
587 :	overbeek	1.469
588 :			my $gs = $self->genus_species($genome);
589 :	overbeek	1.470	$self->log_update($user,$genome,$gs,"Logged correspondence for $genome [$msg]",$mapping);
590 :	overbeek	1.469	}
591 :
592 :	overbeek	1.466	sub replace_genome {
593 :			my($self,$user,$old_genome,$genomeF, $mapping, $force, $skipnr) = @_;
594 :
595 :	parrello	1.518	($genomeF =~ /(\d+\.\d+)$/)
596 :	parrello	1.485	\|\| die "$genomeF must have a valid genome ID as the last part of the path";
597 :	overbeek	1.466	my $genome = $1;
598 :
599 :			open(TMP,"<$genomeF/GENOME") \|\| die "could not open $genome/GENOME";
600 :			my $gs = <TMP>;
601 :			chomp $gs;
602 :			close(TMP);
603 :
604 :			$self->log_update($user,$genome,$gs,"Replaced genome $old_genome with $genome\n$genomeF $force $skipnr",$genomeF,$mapping);
605 :	parrello	1.518
606 :	overbeek	1.466	$self->mark_deleted_genomes($user,[$old_genome]);
607 :			return $self->add_genome_body($user,$genomeF,$force,$skipnr);
608 :			}
609 :
610 :	parrello	1.210	=head3 add_genome
611 :
612 :	overbeek	1.335	C<< my $ok = $fig->add_genome($genomeF, $force, $skipnr); >>
613 :	parrello	1.210
614 :			Add a new genome to the data store. A genome's data is kept in a directory
615 :	parrello	1.287	by itself, underneath the main organism directory. This method essentially
616 :			moves genome data from an external directory to the main directory and
617 :			performs some indexing tasks to integrate it.
618 :	parrello	1.210
619 :			=over 4
620 :
621 :			=item genomeF
622 :
623 :	parrello	1.287	Name of the directory containing the genome files. This should be a
624 :			fully-qualified directory name. The last segment of the directory
625 :			name should be the genome ID.
626 :	parrello	1.210
627 :	overbeek	1.331	=item force
628 :
629 :			This will ignore errors thrown by verify_genome_directory. This is bad, and you should
630 :			never do it, but I am in the situation where I need to move a genome from one machine
631 :			to another, and although I trust the genome I can't.
632 :
633 :	overbeek	1.335	=item skipnr
634 :
635 :	olson	1.478	We don't always want to add the proteins into the nr database. For example wih a metagnome that has been called by blastx. This will just skip appending the proteins into the NR file.
636 :	overbeek	1.335
637 :	parrello	1.210	=item RETURN
638 :
639 :			Returns TRUE if successful, else FALSE.
640 :
641 :			=back
642 :
643 :			=cut
644 :			#: Return Type $;
645 :	efrank	1.1	sub add_genome {
646 :	overbeek	1.466	my($self,$user,$genomeF, $force, $skipnr, $dont_mark_complete) = @_;
647 :
648 :	parrello	1.518	($genomeF =~ /(\d+\.\d+)$/)
649 :	parrello	1.485	\|\| die "$genomeF must have a valid genome ID as the last part of the path";
650 :	overbeek	1.466	my $genome = $1;
651 :
652 :			open(TMP,"<$genomeF/GENOME") \|\| die "could not open $genome/GENOME";
653 :			my $gs = <TMP>;
654 :			chomp $gs;
655 :			close(TMP);
656 :
657 :	olson	1.478	my $rc = $self->add_genome_body($user,$genomeF,$force,$skipnr,$dont_mark_complete);
658 :	overbeek	1.466
659 :	olson	1.478	if ($rc)
660 :			{
661 :	parrello	1.485	$self->log_update($user,$genome,$gs,"Added genome $genome\n$genomeF $force $skipnr",$genomeF);
662 :	olson	1.478	}
663 :	parrello	1.518
664 :	olson	1.478	return $rc;
665 :	overbeek	1.466	}
666 :	efrank	1.1
667 :	overbeek	1.466	sub add_genome_body {
668 :			my($self,$user,$genomeF, $force, $skipnr,$dont_mark_complete) = @_;
669 :	overbeek	1.440
670 :	efrank	1.1	my $rc = 0;
671 :	olson	1.93
672 :			my(undef, $path, $genome) = File::Spec->splitpath($genomeF);
673 :
674 :	parrello	1.287	if ($genome !~ /^\d+\.\d+$/) {
675 :			warn "Invalid genome filename $genomeF\n";
676 :			return $rc;
677 :	olson	1.93	}
678 :
679 :	parrello	1.287	if (-d $FIG_Config::organisms/$genome) {
680 :			warn "Organism already exists for $genome\n";
681 :			return $rc;
682 :	olson	1.93	}
683 :	parrello	1.200
684 :	olson	1.93
685 :			#
686 :			# We're okay, it doesn't exist.
687 :			#
688 :
689 :			my @errors = `$FIG_Config::bin/verify_genome_directory $genomeF`;
690 :
691 :	parrello	1.287	if (@errors) {
692 :	olson	1.478	print STDERR "Errors found while verifying genome directory $genomeF:\n";
693 :			print STDERR join("", @errors);
694 :
695 :			if (!$force)
696 :	parrello	1.485	{
697 :			return $rc;
698 :			}
699 :	olson	1.478	else
700 :	parrello	1.485	{
701 :			warn "Skipped these errors and continued. You should not do this";
702 :			}
703 :	olson	1.93	}
704 :	parrello	1.200
705 :	olson	1.478	my $sysrc = system("cp -r $genomeF $FIG_Config::organisms");
706 :			if ($sysrc != 0)
707 :			{
708 :	parrello	1.485	warn "Failure copying $genomeF to $FIG_Config::organisms\n";
709 :			return $rc;
710 :	olson	1.478	}
711 :			$sysrc = system("chmod -R 777 $FIG_Config::organisms/$genome");
712 :			if ($sysrc != 0)
713 :			{
714 :	parrello	1.485	warn "Command failed: chmod -R 777 $FIG_Config::organisms/$genome\n";
715 :			return $rc;
716 :	olson	1.478	}
717 :	parrello	1.379
718 :	overbeek	1.353	if (-s "$FIG_Config::organisms/$genome/COMPLETE")
719 :			{
720 :	parrello	1.485	if ($dont_mark_complete)
721 :			{
722 :			print STDERR "$genome was marked as \"complete\", but moving to WAS_MARKED_COMPLETE\n";
723 :			rename("$FIG_Config::organisms/$genome/COMPLETE", "$FIG_Config::organisms/$genome/WAS_MARKED_COMPLETE");
724 :			}
725 :			else
726 :			{
727 :			print STDERR "$genome was marked as \"complete\"\n";
728 :			}
729 :	overbeek	1.353	}
730 :			else
731 :			{
732 :	parrello	1.485	#
733 :			# Not marked complete; assess completeness.
734 :			#
735 :	parrello	1.518
736 :	olson	1.478	my $sysrc = system("assess_completeness $FIG_Config::organisms/$genome");
737 :	parrello	1.485	if ($sysrc != 0)
738 :			{
739 :			warn "assess_completeness $FIG_Config::organisms/$genome failed; continuing with installation.\n";
740 :			}
741 :			else
742 :			{
743 :			if (-s "$FIG_Config::organisms/$genome/PROBABLY_COMPLETE")
744 :			{
745 :			print STDERR "Assessed $genome to be probably complete\n";
746 :			if ($dont_mark_complete)
747 :			{
748 :			print STDERR "Not copying PROBABLY_COMPLETE to COMPLETE; this will need to be done later\n";
749 :			}
750 :			else
751 :			{
752 :			my $cp = "cp -p $FIG_Config::organisms/$genome/PROBABLY_COMPLETE " .
753 :			"$FIG_Config::organisms/$genome/COMPLETE";
754 :			$sysrc = system($cp);
755 :			$sysrc == 0 or warn "Command failed, continuing: $cp\n";
756 :			}
757 :			}
758 :			else
759 :			{
760 :			print STDERR "Assessed $genome to not be probably complete\n";
761 :			}
762 :			}
763 :	overbeek	1.353	}
764 :	parrello	1.379
765 :	olson	1.478	$sysrc = system("index_contigs $genome");
766 :			$sysrc == 0 or
767 :	parrello	1.485	warn "index_contigs $genome failed; continuing with installation\n";
768 :	olson	1.478
769 :			$sysrc = system("compute_genome_counts $genome");
770 :			$sysrc == 0 or
771 :	parrello	1.485	warn "compute_genome_counts $genome failed; continuing with installation\n";
772 :	olson	1.478
773 :			$sysrc = system("load_features $genome");
774 :			$sysrc == 0 or
775 :	parrello	1.485	warn "load_features $genome failed; continuing with installation\n";
776 :	parrello	1.379
777 :	olson	1.93	$rc = 1;
778 :	olson	1.478	if (-s "$FIG_Config::organisms/$genome/Features/peg/fasta")
779 :			{
780 :	parrello	1.518
781 :	parrello	1.485	$sysrc = system("index_translations $genome");
782 :			$sysrc == 0 or
783 :			warn "index_translations $genome failed; continuing with installation\n";
784 :	parrello	1.518
785 :	parrello	1.485	my @tmp = `cut -f1 $FIG_Config::organisms/$genome/Features/peg/tbl`;
786 :			if (@tmp == 0)
787 :			{
788 :			warn "Did not find any features in $FIG_Config::organisms/$genome/Features/peg/tbl\n";
789 :			}
790 :			chomp @tmp;
791 :			if (!$skipnr)
792 :			{
793 :			$sysrc = system("cat $FIG_Config::organisms/$genome/Features/peg/fasta >> $FIG_Config::data/Global/nr");
794 :			$sysrc == 0 or warn "error concatenating features ot NR; continuing with installation\n";
795 :	parrello	1.518
796 :	parrello	1.485	# &run("formatdb -i $FIG_Config::data/Global/nr -p T");
797 :			}
798 :			&enqueue_similarities(\@tmp);
799 :	olson	1.93	}
800 :	olson	1.478
801 :	olson	1.93	if ((-s "$FIG_Config::organisms/$genome/assigned_functions") \|\|
802 :	olson	1.478	(-d "$FIG_Config::organisms/$genome/UserModels"))
803 :			{
804 :			$sysrc = system("add_assertions_of_function $genome");
805 :	parrello	1.485	$sysrc == 0 or warn "add_assertions_of_function $genome failed; continuing with installation\n";
806 :	efrank	1.1	}
807 :	parrello	1.200
808 :	efrank	1.1	return $rc;
809 :			}
810 :
811 :	overbeek	1.466	sub get_index {
812 :			my($self,$gs) = @_;
813 :
814 :			my($index,$max);
815 :			$gs \|\| confess "MISSING GS";
816 :
817 :	overbeek	1.467	my $indexF = "$FIG_Config::data/Logs/GenomeLog/index";
818 :	overbeek	1.466	if (open(INDEX,"<$indexF"))
819 :			{
820 :	parrello	1.485	while ((! $index) && ($_ = <INDEX>))
821 :			{
822 :			if ($_ =~ /^(\d+)/)
823 :			{
824 :			$max = $1;
825 :			if (($_ =~ /^(\d+)\t(\S.*\S)/) && ($2 eq $gs))
826 :			{
827 :			$index = $1;
828 :			}
829 :			}
830 :			}
831 :			close(INDEX);
832 :	overbeek	1.466	}
833 :
834 :			if (! $index)
835 :			{
836 :	parrello	1.485	open(INDEX,">>$indexF") \|\| die "could not open $indexF";
837 :			$index = defined($max) ? $max+1 : 1;
838 :			print INDEX "$index\t$gs\n";
839 :			close(INDEX);
840 :			&verify_dir("$FIG_Config::data/Logs/GenomeLog/Entries/$index");
841 :	overbeek	1.466	}
842 :			return $index;
843 :			}
844 :	parrello	1.518
845 :	overbeek	1.440	sub log_update {
846 :	overbeek	1.466	my($self,$user,$genome,$gs,$msg,@data) = @_;
847 :	overbeek	1.440
848 :			my $time_made = time;
849 :	overbeek	1.471	&verify_dir("$FIG_Config::data/Logs/GenomeLog");
850 :	overbeek	1.466	my $index_id = $self->get_index($gs);
851 :			$index_id \|\| die "could not make an index entry for $gs";
852 :	overbeek	1.471	my $gs_dir = "$FIG_Config::data/Logs/GenomeLog/Entries/$index_id";
853 :	overbeek	1.466
854 :	overbeek	1.440	my($i,$file_or_dir,@tars);
855 :			for ($i=0; ($i < @data); $i++)
856 :			{
857 :	parrello	1.485	$file_or_dir = $data[$i];
858 :			my($dir,$file);
859 :			if ($file_or_dir =~ /^(.*)\/([^\/]+)$/)
860 :			{
861 :			($dir,$file) = ($1,$2);
862 :			}
863 :			else
864 :			{
865 :			($dir,$file) = (".",$file_or_dir);
866 :			}
867 :			my $tar = "$gs_dir/$time_made.$i.tgz";
868 :			&run("cd $dir; tar czf $tar $file");
869 :			push(@tars,$tar);
870 :	overbeek	1.440	}
871 :	overbeek	1.466	open(LOG,">>$gs_dir/log")
872 :	parrello	1.485	\|\| die "could not open $gs_dir/log";
873 :	overbeek	1.466	print LOG "$time_made\n$user\n$genome\n$msg\n";
874 :	parrello	1.518	if (@tars > 0)
875 :	overbeek	1.466	{
876 :	parrello	1.485	print LOG join(",",@tars),"\n";
877 :	overbeek	1.466	}
878 :			print LOG "//\n";
879 :	overbeek	1.440	close(LOG);
880 :			}
881 :
882 :	parrello	1.287	=head3 parse_genome_args
883 :
884 :			C<< my ($mode, @genomes) = FIG::parse_genome_args(@args); >>
885 :
886 :			Extract a list of genome IDs from an argument list. If the argument list is empty,
887 :			return all the genomes in the data store.
888 :
889 :			This is a function that is performed by many of the FIG command-line utilities. The
890 :			user has the option of specifying a list of specific genome IDs or specifying none
891 :			in order to get all of them. If your command requires additional arguments in the
892 :			command line, you can still use this method if you shift them out of the argument list
893 :			before calling. The $mode return value will be C<all> if the user asked for all of
894 :			the genomes or C<some> if he specified a list of IDs. This is useful to know if,
895 :			for example, we are loading a table. If we're loading everything, we can delete the
896 :			entire table; if we're only loading some genomes, we must delete them individually.
897 :
898 :			This method uses the genome directory rather than the database because it may be used
899 :			before the database is ready.
900 :
901 :			=over 4
902 :
903 :			=item args1, args2, ... argsN
904 :
905 :			List of genome IDs. If all genome IDs are to be processed, then this list should be
906 :			empty.
907 :
908 :			=item RETURN
909 :
910 :			Returns a list. The first element of the list is C<all> if the user is asking for all
911 :			the genome IDs and C<some> otherwise. The remaining elements of the list are the
912 :			desired genome IDs.
913 :
914 :			=back
915 :
916 :			=cut
917 :
918 :			sub parse_genome_args {
919 :			# Get the parameters.
920 :			my @args = @_;
921 :			# Check the mode.
922 :			my $mode = (@args > 0 ? 'some' : 'all');
923 :			# Build the return list.
924 :			my @retVal = ($mode);
925 :			# Process according to the mode.
926 :			if ($mode eq 'all') {
927 :			# We want all the genomes, so we get them from the organism directory.
928 :			my $orgdir = "$FIG_Config::organisms";
929 :			opendir( GENOMES, $orgdir ) \|\| Confess("Could not open directory $orgdir");
930 :			push @retVal, grep { $_ =~ /^\d/ } readdir( GENOMES );
931 :			closedir( GENOMES );
932 :			} else {
933 :			# We want only the genomes specified by the user.
934 :			push @retVal, @args;
935 :			}
936 :			# Return the result.
937 :			return @retVal;
938 :			}
939 :
940 :			=head3 reload_table
941 :
942 :			C<< $fig->reload_table($mode, $table, $flds, $xflds, $fileName, $keyList, $keyName); >>
943 :
944 :			Reload a database table from a sequential file. If I<$mode> is C<all>, the table
945 :			will be dropped and re-created. If I<$mode> is C<some>, the data for the individual
946 :			items in I<$keyList> will be deleted before the table is loaded. Thus, the load
947 :			process is optimized for the type of reload.
948 :
949 :			=over 4
950 :
951 :			=item mode
952 :
953 :			C<all> if we are reloading the entire table, C<some> if we are only reloading
954 :			specific entries.
955 :
956 :			=item table
957 :
958 :			Name of the table to reload.
959 :
960 :			=item flds
961 :
962 :			String defining the table columns, in SQL format. In general, this is a
963 :			comma-delimited set of field specifiers, each specifier consisting of the
964 :			field name followed by the field type and any optional qualifiers (such as
965 :			C<NOT NULL> or C<DEFAULT>); however, it can be anything that would appear
966 :			between the parentheses in a C<CREATE TABLE> statement. The order in which
967 :			the fields are specified is important, since it is presumed that is the
968 :			order in which they are appearing in the load file.
969 :
970 :			=item xflds
971 :
972 :			Reference to a hash that describes the indexes. The hash is keyed by index name.
973 :			The value is the index's field list. This is a comma-delimited list of field names
974 :			in order from most significant to least significant. If a field is to be indexed
975 :			in descending order, its name should be followed by the qualifier C<DESC>. For
976 :			example, the following I<$xflds> value will create two indexes, one for name followed
977 :			by creation date in reverse chronological order, and one for ID.
978 :
979 :			{ name_index => "name, createDate DESC", id_index => "id" }
980 :
981 :			=item fileName
982 :
983 :			Fully-qualified name of the file containing the data to load. Each line of the
984 :			file must correspond to a record, and the fields must be arranged in order and
985 :	parrello	1.298	tab-delimited. If the file name is omitted, the table is dropped and re-created
986 :			but not loaded.
987 :	parrello	1.287
988 :			=item keyList
989 :
990 :			Reference to a list of the IDs for the objects being reloaded. This parameter is
991 :			only used if I<$mode> is C<some>.
992 :
993 :			=item keyName (optional)
994 :
995 :			Name of the key field containing the IDs in the keylist. If omitted, C<genome> is
996 :			assumed.
997 :
998 :			=back
999 :
1000 :			=cut
1001 :
1002 :			sub reload_table {
1003 :	parrello	1.298	# Get the parameters.
1004 :			my ($self, $mode, $table, $flds, $xflds, $fileName, $keyList, $keyName) = @_;
1005 :	parrello	1.287	if (!defined $keyName) {
1006 :			$keyName = 'genome';
1007 :			}
1008 :			# Get the database handler.
1009 :			my $dbf = $self->{_dbf};
1010 :	parrello	1.298	# Call the DBKernel method.
1011 :			$dbf->reload_table($mode, $table, $flds, $xflds, $fileName, $keyList, $keyName);
1012 :	parrello	1.287	}
1013 :
1014 :	parrello	1.210	=head3 enqueue_similarities
1015 :	olson	1.93
1016 :	parrello	1.287	C<< FIG::enqueue_similarities(\@fids); >>
1017 :
1018 :			Queue the passed Feature IDs for similarity computation. The actual
1019 :			computation is performed by L</create_sim_askfor_pool>. The queue is a
1020 :			persistent text file in the global data directory, and this method
1021 :			essentially writes new IDs on the end of it.
1022 :
1023 :			=over 4
1024 :
1025 :			=item fids
1026 :
1027 :			Reference to a list of feature IDs.
1028 :	olson	1.93
1029 :	parrello	1.287	=back
1030 :	olson	1.93
1031 :			=cut
1032 :	parrello	1.210	#: Return Type ;
1033 :	olson	1.93	sub enqueue_similarities {
1034 :	olson	1.334	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1035 :	efrank	1.1	my($fids) = @_;
1036 :			my $fid;
1037 :
1038 :	olson	1.93	my $sim_q = "$FIG_Config::global/queued_similarities";
1039 :
1040 :			open(TMP,">>$sim_q")
1041 :	parrello	1.287	\|\| die "could not open $sim_q";
1042 :	olson	1.93
1043 :			#
1044 :			# We need to lock here so that if a computation is creating a snapshot of the
1045 :			# queue, we block until it's done.
1046 :			#
1047 :
1048 :			flock(TMP, LOCK_EX) or die "Cannot lock $sim_q\n";
1049 :	overbeek	1.442	seek(TMP, 0, 2);
1050 :	olson	1.93
1051 :	parrello	1.287	foreach $fid (@$fids) {
1052 :			print TMP "$fid\n";
1053 :	efrank	1.1	}
1054 :			close(TMP);
1055 :	olson	1.10	}
1056 :
1057 :	olson	1.281	=head3 export_similarity_request
1058 :
1059 :			Creates a similarity computation request from the queued similarities and
1060 :	parrello	1.287	the current NR.
1061 :	olson	1.281
1062 :			We keep track of the exported requests in case one gets lost.
1063 :
1064 :			=cut
1065 :
1066 :	parrello	1.287	sub export_similarity_request {
1067 :	overbeek	1.439	my($self, $user_req_dir) = @_;
1068 :
1069 :			my $nr_file = "$user_req_dir/nr";
1070 :			my $fasta_file = "$user_req_dir/fasta";
1071 :			my $peg_syn_file = "$user_req_dir/peg.synonyms";
1072 :	olson	1.281
1073 :			my $req_dir = "$FIG_Config::fig/var/sim_requests";
1074 :			&verify_dir("$FIG_Config::fig/var");
1075 :			&verify_dir($req_dir);
1076 :
1077 :			$req_dir = "$req_dir/" . time;
1078 :			&verify_dir($req_dir);
1079 :
1080 :			#
1081 :			# Open all of our output files before zeroing out the sim queue, in case
1082 :			# there is a problem.
1083 :			#
1084 :
1085 :			open(my $user_fasta_fh, ">$fasta_file") or confess "Cannot open $fasta_file for writing: $!";
1086 :			open(my $fasta_fh, ">$req_dir/fasta.in");
1087 :
1088 :			open(my $user_nr_fh, ">$nr_file") or confess "Cannot open $nr_file for writing: $!";
1089 :			open(my $nr_fh, ">$req_dir/nr") or confess "Cannot open $req_dir/nr for writing: $!";
1090 :
1091 :	overbeek	1.439	open(my $user_peg_syn_fh, ">$peg_syn_file") or confess "Cannot open $peg_syn_file for writing: $!";
1092 :			open(my $peg_syn_fh, ">$req_dir/peg.synonyms") or confess "Cannot open $req_dir/peg.synonyms for writing: $!";
1093 :
1094 :	olson	1.281	open(my $nr_read_fh, "<$FIG_Config::data/Global/nr") or die "Cannot open $FIG_Config::data/Global/nr for reading: $!";
1095 :	overbeek	1.439	open(my $peg_syn_read_fh, "<$FIG_Config::data/Global/peg.synonyms") or die "Cannot open $FIG_Config::data/Global/peg.synonyms for reading: $!";
1096 :	parrello	1.287
1097 :	olson	1.281	my $sim_q = "$FIG_Config::global/queued_similarities";
1098 :
1099 :			#
1100 :			# We need to lock here so that if a computation is creating a snapshot of the
1101 :			# queue, we block until it's done.
1102 :			#
1103 :
1104 :			open(my $sim_q_lock, ">>$sim_q") or confess "could not open $sim_q";
1105 :			flock($sim_q_lock, LOCK_EX) or confess "Cannot lock $sim_q\n";
1106 :
1107 :			#
1108 :			# Everything open & locked, start copying.
1109 :			#
1110 :	parrello	1.287
1111 :	olson	1.281	copy("$sim_q", "$req_dir/q") or confess "Copy $sim_q $req_dir/q failed: $!";
1112 :	overbeek	1.439	copy("$sim_q", "$user_req_dir/q") or confess "Copy $sim_q $user_req_dir/q failed: $!";
1113 :	parrello	1.287
1114 :	overbeek	1.442	#
1115 :			# Copy the contents of the sim queue to the "expected import" queue;
1116 :			# this is a list of pegs for which we expect sims to be computed and installed
1117 :			# at some point.
1118 :			#
1119 :			# We also lock on the pending queue file.
1120 :			#
1121 :	parrello	1.518
1122 :	overbeek	1.442	if (not(open(SQ, "<$sim_q")))
1123 :			{
1124 :	parrello	1.485	warn "Cannot open $sim_q for reading: $!\n";
1125 :	overbeek	1.442	}
1126 :			else
1127 :			{
1128 :	parrello	1.485	if (open(AW, ">>$FIG_Config::global/pending_similarities"))
1129 :			{
1130 :			flock(AW, LOCK_EX);
1131 :			seek(AW, 0, 2);
1132 :
1133 :			while (<SQ>)
1134 :			{
1135 :			print AW @_;
1136 :			}
1137 :			close(AW);
1138 :			}
1139 :			else
1140 :			{
1141 :			warn "Could not open $FIG_Config::global/pending_similarities: $!\n";
1142 :			}
1143 :			close(SQ);
1144 :	overbeek	1.442	}
1145 :	parrello	1.518
1146 :	olson	1.281	my($buf);
1147 :	parrello	1.287	while (1) {
1148 :			my $n = read($nr_read_fh, $buf, 4096);
1149 :			defined($n) or confess "Error reading nr: $!";
1150 :			last unless $n;
1151 :			syswrite($user_nr_fh, $buf) or confess "Error writing $nr_file: $!";
1152 :			syswrite($nr_fh, $buf) or confess "Error writing $req_dir/nr: $!";
1153 :	olson	1.281	}
1154 :
1155 :			close($nr_read_fh);
1156 :			close($nr_fh);
1157 :			close($user_nr_fh);
1158 :
1159 :	overbeek	1.439	while (1) {
1160 :			my $n = read($peg_syn_read_fh, $buf, 4096);
1161 :			defined($n) or confess "Error reading peg.synonyms: $!";
1162 :			last unless $n;
1163 :			syswrite($user_peg_syn_fh, $buf) or confess "Error writing $peg_syn_file: $!";
1164 :			syswrite($peg_syn_fh, $buf) or confess "Error writing $req_dir/peg.synonyms: $!";
1165 :			}
1166 :
1167 :			close($peg_syn_read_fh);
1168 :			close($peg_syn_fh);
1169 :			close($user_peg_syn_fh);
1170 :	parrello	1.518
1171 :	olson	1.281	#
1172 :			# We can zero out the queue and unlock now.
1173 :			#
1174 :
1175 :			open(F, ">$sim_q") or die "Cannot open $sim_q to truncate it: $!\n";
1176 :			close(F);
1177 :	parrello	1.287
1178 :	olson	1.281	close($sim_q_lock);
1179 :
1180 :			#
1181 :			# Generate the fasta input from the queued ids.
1182 :			#
1183 :
1184 :			open(my $q_fh, "<$req_dir/q");
1185 :	parrello	1.287	while (my $id = <$q_fh>) {
1186 :			chomp $id;
1187 :	olson	1.281
1188 :	parrello	1.287	my $seq = $self->get_translation($id);
1189 :	olson	1.281
1190 :	parrello	1.287	display_id_and_seq($id, \$seq, $user_fasta_fh);
1191 :			display_id_and_seq($id, \$seq, $fasta_fh);
1192 :	olson	1.281	}
1193 :			close($q_fh);
1194 :
1195 :			close($user_fasta_fh);
1196 :			close($fasta_fh);
1197 :			}
1198 :
1199 :	parrello	1.210	=head3 create_sim_askfor_pool
1200 :	olson	1.93
1201 :	parrello	1.287	C<< $fig->create_sim_askfor_pool($chunk_size); >>
1202 :	olson	1.93
1203 :	parrello	1.287	Creates an askfor pool, which a snapshot of the current NR and similarity
1204 :			queue. This process clears the old queue.
1205 :	olson	1.123
1206 :			The askfor pool needs to keep track of which sequences need to be
1207 :			calculated, which have been handed out, etc. To simplify this task we
1208 :	olson	1.279	chunk the sequences into fairly small numbers (20k characters) and
1209 :	olson	1.123	allocate work on a per-chunk basis. We make use of the relational
1210 :			database to keep track of chunk status as well as the seek locations
1211 :			into the file of sequence data. The initial creation of the pool
1212 :			involves indexing the sequence data with seek offsets and lengths and
1213 :			populating the sim_askfor_index table with this information and with
1214 :			initial status information.
1215 :	olson	1.93
1216 :	parrello	1.287	=over 4
1217 :
1218 :			=item chunk_size
1219 :
1220 :			Number of features to put into a processing chunk. The default is 15.
1221 :
1222 :			=back
1223 :
1224 :	parrello	1.200	=cut
1225 :	parrello	1.210	#: Return Type $;
1226 :	parrello	1.287	sub create_sim_askfor_pool {
1227 :	olson	1.123	my($self, $chunk_size) = @_;
1228 :
1229 :	olson	1.279	$chunk_size = 20000 unless $chunk_size =~ /^\d+$/;
1230 :	olson	1.93
1231 :	olson	1.279	my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1232 :	olson	1.93	&verify_dir($pool_dir);
1233 :
1234 :			#
1235 :			# Lock the pool directory.
1236 :			#
1237 :			open(my $lock, ">$pool_dir/lockfile");
1238 :
1239 :			flock($lock, LOCK_EX);
1240 :
1241 :			my $num = 0;
1242 :	parrello	1.287	if (open(my $toc, "<$pool_dir/TOC")) {
1243 :			while (<$toc>) {
1244 :			chomp;
1245 :			# print STDERR "Have toc entry $_\n";
1246 :			my ($idx, $time, $str) = split(/\s+/, $_, 3);
1247 :	olson	1.93
1248 :	parrello	1.287	$num = max($num, $idx);
1249 :			}
1250 :			close($toc);
1251 :	olson	1.93	}
1252 :			$num++;
1253 :			open(my $toc, ">>$pool_dir/TOC") or die "Cannot write $pool_dir/TOC: $!\n";
1254 :
1255 :			print $toc "$num ", time(), " New toc entry\n";
1256 :			close($toc);
1257 :
1258 :	olson	1.123	my $cpool_id = sprintf "%04d", $num;
1259 :			my $cpool_dir = "$pool_dir/$cpool_id";
1260 :	olson	1.93
1261 :			#
1262 :			# All set, create the directory for this pool.
1263 :			#
1264 :
1265 :			&verify_dir($cpool_dir);
1266 :
1267 :			#
1268 :			# Now we can copy the nr and sim queue here.
1269 :			# Do this stuff inside an eval so we can clean up
1270 :			# the lockfile.
1271 :			#
1272 :
1273 :			eval {
1274 :	parrello	1.287	my $sim_q = "$FIG_Config::global/queued_similarities";
1275 :	olson	1.93
1276 :	parrello	1.287	copy("$sim_q", "$cpool_dir/q");
1277 :			copy("$FIG_Config::data/Global/nr", "$cpool_dir/nr");
1278 :	olson	1.93
1279 :	parrello	1.287	open(F, ">$sim_q") or die "Cannot open $sim_q to truncate it: $!\n";
1280 :			close(F);
1281 :	olson	1.93	};
1282 :	parrello	1.200
1283 :	olson	1.93	unlink("$pool_dir/lockfile");
1284 :			close($lock);
1285 :	olson	1.123
1286 :			#
1287 :			# We've created our pool; we can now run the formatdb and
1288 :			# extract the sequences for the blast run.
1289 :			#
1290 :	parrello	1.287	my $child_pid = $self->run_in_background(
1291 :			sub {
1292 :			#
1293 :			# Need to close db or there's all sorts of trouble.
1294 :			#
1295 :
1296 :			my $cmd = "$FIG_Config::ext_bin/formatdb -i $cpool_dir/nr -p T -l $cpool_dir/formatdb.log";
1297 :			print "Will run '$cmd'\n";
1298 :			&run($cmd);
1299 :			print "finished. Logfile:\n";
1300 :			print &FIG::file_read("$cpool_dir/formatdb.log");
1301 :			unlink("$cpool_dir/formatdb.pid");
1302 :			});
1303 :	olson	1.279	warn "Running formatdb in background job $child_pid\n";
1304 :	olson	1.123	open(FPID, ">$cpool_dir/formatdb.pid");
1305 :			print FPID "$child_pid\n";
1306 :			close(FPID);
1307 :
1308 :			my $db = $self->db_handle();
1309 :	parrello	1.287	if (!$db->table_exists("sim_queue")) {
1310 :			$db->create_table(tbl => "sim_queue",
1311 :			flds => "qid varchar(32), chunk_id INTEGER, seek INTEGER, len INTEGER, " .
1312 :			"assigned BOOL, finished BOOL, output_file varchar(255), " .
1313 :	parrello	1.485	"worker_pid INTEGER, start_time timestamp, " .
1314 :	parrello	1.287	"assignment_expires INTEGER, worker_info varchar(255)"
1315 :			);
1316 :	olson	1.123	}
1317 :
1318 :			#
1319 :			# Write the fasta input file. Keep track of how many have been written,
1320 :			# and write seek info into the database as appropriate.
1321 :			#
1322 :
1323 :			open(my $seq_fh, ">$cpool_dir/fasta.in");
1324 :
1325 :			my($chunk_idx, $chunk_begin, $seq_idx);
1326 :
1327 :	olson	1.279	my $cur_size = 0;
1328 :
1329 :	olson	1.123	$chunk_idx = 0;
1330 :			$chunk_begin = 0;
1331 :			$seq_idx = 0;
1332 :
1333 :	olson	1.279	my $tmpfile = "$FIG_Config::temp/simseek.$$";
1334 :			open(my $tmpfh, ">$tmpfile") or confess "Cannot open tmpfile $tmpfile: $!";
1335 :
1336 :	olson	1.123	open(my $q_fh, "<$cpool_dir/q");
1337 :	parrello	1.287	while (my $id = <$q_fh>) {
1338 :			chomp $id;
1339 :	olson	1.123
1340 :	parrello	1.287	my $seq = $self->get_translation($id);
1341 :	olson	1.123
1342 :	parrello	1.287	#
1343 :			# check if we're at the beginning of a chunk
1344 :			#
1345 :
1346 :			print $seq_fh ">$id\n$seq\n";
1347 :
1348 :			#
1349 :			# Check if we're at the end of a chunk
1350 :			#
1351 :
1352 :			$cur_size += length($seq);
1353 :			if ($cur_size >= $chunk_size) {
1354 :			my $chunk_end = tell($seq_fh);
1355 :			my $chunk_len = $chunk_end - $chunk_begin;
1356 :
1357 :	olson	1.430	print $tmpfh join("\t", $cpool_id, $chunk_idx, $chunk_begin, $chunk_len, 'FALSE', 'FALSE',
1358 :	parrello	1.485	'\N', '\N', '\N', '\N', '\N'), "\n";
1359 :	parrello	1.287	$chunk_idx++;
1360 :			$chunk_begin = $chunk_end;
1361 :			$cur_size = 0;
1362 :			}
1363 :			$seq_idx++;
1364 :	olson	1.123	}
1365 :
1366 :	parrello	1.287	if ($cur_size > 0) {
1367 :			my $chunk_end = tell($seq_fh);
1368 :			my $chunk_len = $chunk_end - $chunk_begin;
1369 :	olson	1.123
1370 :	olson	1.430	print $tmpfh join("\t", $cpool_id, $chunk_idx, $chunk_begin, $chunk_len, 'FALSE', 'FALSE',
1371 :	parrello	1.485	'\N', '\N', '\N', '\N', '\N'), "\n";
1372 :	olson	1.123	}
1373 :
1374 :			close($q_fh);
1375 :			close($seq_fh);
1376 :	olson	1.279	close($tmpfh);
1377 :	olson	1.123
1378 :	olson	1.279	warn "Write seqs from $tmpfile\n";
1379 :	olson	1.123
1380 :	olson	1.279	$self->db_handle->load_table(tbl => 'sim_queue',
1381 :	parrello	1.298	file => $tmpfile);
1382 :	parrello	1.200
1383 :	olson	1.430	# unlink($tmpfile);
1384 :	parrello	1.287
1385 :	olson	1.279	# for my $seek (@seeks)
1386 :			# {
1387 :	parrello	1.298	# my($cpool_id, $chunk_idx, $chunk_begin, $chunk_len) = @$seek;
1388 :	olson	1.279
1389 :	parrello	1.298	# $db->SQL("insert into sim_queue (qid, chunk_id, seek, len, assigned, finished) " .
1390 :			# "values('$cpool_id', $chunk_idx, $chunk_begin, $chunk_len, FALSE, FALSE)");
1391 :	olson	1.279	# }
1392 :	parrello	1.200
1393 :	olson	1.123	return $cpool_id;
1394 :			}
1395 :
1396 :	parrello	1.210	#=head3 get_sim_queue
1397 :			#
1398 :			#usage: get_sim_queue($pool_id, $all_sims)
1399 :			#
1400 :			#Returns the sims in the given pool. If $all_sims is true, return the entire queue. Otherwise,
1401 :			#just return the sims awaiting processing.
1402 :			#
1403 :			#=cut
1404 :	olson	1.123
1405 :	parrello	1.287	sub get_sim_queue {
1406 :	olson	1.123	my($self, $pool_id, $all_sims) = @_;
1407 :	olson	1.279	}
1408 :
1409 :	parrello	1.287	=head3 get_sim_work
1410 :	olson	1.279
1411 :	parrello	1.287	C<< my ($nrPath, $fasta) = $fig->get_sim_work(); >>
1412 :	olson	1.279
1413 :			Get the next piece of sim computation work to be performed. Returned are
1414 :			the path to the NR and a string containing the fasta data.
1415 :
1416 :			=cut
1417 :
1418 :	parrello	1.287	sub get_sim_work {
1419 :
1420 :			my ($self) = @_;
1421 :	olson	1.279
1422 :			#
1423 :			# For now, just don't care about order of data that we get back.
1424 :			#
1425 :
1426 :			my $db = $self->db_handle();
1427 :			my $lock = FIG::SimLock->new;
1428 :
1429 :			my $work = $db->SQL(qq(SELECT qid, chunk_id, seek, len
1430 :	parrello	1.298	FROM sim_queue
1431 :	olson	1.430	WHERE not finished AND not assigned
1432 :	parrello	1.298	LIMIT 1));
1433 :	olson	1.279	print "Got work ", Dumper($work), "\n";
1434 :
1435 :	parrello	1.287	if (not $work or @$work == 0) {
1436 :			return undef;
1437 :	olson	1.279	}
1438 :
1439 :			my($cpool_id, $chunk_id, $seek, $len) = @{$work->[0]};
1440 :	parrello	1.287
1441 :	olson	1.279	my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1442 :			my $cpool_dir = "$pool_dir/$cpool_id";
1443 :
1444 :			my $nr = "$cpool_dir/nr";
1445 :			open(my $fh, "<$cpool_dir/fasta.in");
1446 :			seek($fh, $seek, 0);
1447 :			my $fasta;
1448 :			read($fh, $fasta, $len);
1449 :
1450 :	olson	1.430	$db->SQL(qq(UPDATE sim_queue
1451 :	parrello	1.485	SET assigned = true
1452 :			WHERE qid = ? AND chunk_id = ?), undef,
1453 :			$cpool_id, $chunk_id);
1454 :	olson	1.430
1455 :	olson	1.279	return($cpool_id, $chunk_id, $nr, $fasta, "$cpool_dir/out.$chunk_id");
1456 :			}
1457 :
1458 :	olson	1.430	sub sim_work_working
1459 :			{
1460 :			my($self, $pool, $chunk, $host, $pid) = @_;
1461 :
1462 :			my $db = $self->db_handle();
1463 :			my $lock = FIG::SimLock->new;
1464 :
1465 :			my $res = $db->SQL(qq(UPDATE sim_queue
1466 :	parrello	1.485	SET worker_pid = ?, start_time = NOW(), worker_info = ?
1467 :			WHERE qid = ? AND chunk_id = ?),
1468 :	parrello	1.518	undef,
1469 :	parrello	1.485	$pid, $host, $pool, $chunk);
1470 :	olson	1.430	}
1471 :
1472 :	olson	1.279	=head3 sim_work_done
1473 :
1474 :	parrello	1.287	C<< $fig->sim_work_done($pool_id, $chunk_id, $out_file); >>
1475 :
1476 :	olson	1.279	Declare that the work in pool_id/chunk_id has been completed, and output written
1477 :			to the pool directory (get_sim_work gave it the path).
1478 :
1479 :	parrello	1.287	=over 4
1480 :
1481 :			=item pool_id
1482 :
1483 :			The ID number of the pool containing the work that just completed.
1484 :
1485 :			=item chunk_id
1486 :
1487 :			The ID number of the chunk completed.
1488 :
1489 :			=item out_file
1490 :
1491 :			The file into which the work was placed.
1492 :
1493 :			=back
1494 :
1495 :	olson	1.279	=cut
1496 :
1497 :	parrello	1.287	sub sim_work_done {
1498 :			my ($self, $pool_id, $chunk_id, $out_file) = @_;
1499 :	olson	1.279
1500 :	parrello	1.287	if (! -f $out_file) {
1501 :			Confess("sim_work_done: output file $out_file does not exist");
1502 :	olson	1.279	}
1503 :
1504 :			my $db = $self->db_handle();
1505 :			my $lock = FIG::SimLock->new;
1506 :
1507 :			my $dbh = $db->{_dbh};
1508 :
1509 :			my $rows = $dbh->do(qq(UPDATE sim_queue
1510 :	parrello	1.298	SET finished = TRUE, output_file = ?
1511 :			WHERE qid = ? and chunk_id = ?), undef, $out_file, $pool_id, $chunk_id);
1512 :	parrello	1.287	if ($rows != 1) {
1513 :			if ($dbh->errstr) {
1514 :			Confess("Update not able to set finished=TRUE: ", $dbh->errstr);
1515 :			} else {
1516 :			Confess("Update not able to set finished=TRUE");
1517 :			}
1518 :	olson	1.279	}
1519 :			#
1520 :			# Determine if this was the last piece of work for this pool. If so, we can
1521 :	parrello	1.287	# schedule the postprocessing work.
1522 :	olson	1.279	#
1523 :			# Note we're still holding the lock.
1524 :			#
1525 :
1526 :			my $out = $db->SQL(qq(SELECT chunk_id
1527 :	parrello	1.298	FROM sim_queue
1528 :			WHERE qid = ? AND not finished), undef, $pool_id);
1529 :	parrello	1.287	if (@$out == 0) {
1530 :			#
1531 :			# Pool is done.
1532 :			#
1533 :			$self->schedule_sim_pool_postprocessing($pool_id);
1534 :	olson	1.279	}
1535 :	olson	1.123	}
1536 :
1537 :	olson	1.279	=head3 schedule_sim_pool_postprocessing
1538 :
1539 :	parrello	1.287	C<< $fig->schedule_sim_pool_postprocessing($pool_id); >>
1540 :
1541 :			Schedule a job to do the similarity postprocessing for the specified pool.
1542 :
1543 :			=over 4
1544 :
1545 :			=item pool_id
1546 :
1547 :			ID of the pool whose similarity postprocessing needs to be scheduled.
1548 :	olson	1.279
1549 :	parrello	1.287	=back
1550 :	olson	1.279
1551 :			=cut
1552 :
1553 :	parrello	1.287	sub schedule_sim_pool_postprocessing {
1554 :
1555 :	olson	1.279	my($self, $pool_id) = @_;
1556 :
1557 :			my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1558 :			my $cpool_dir = "$pool_dir/$pool_id";
1559 :
1560 :			my $js = JobScheduler->new();
1561 :			my $job = $js->job_create();
1562 :
1563 :			my $spath = $job->get_script_path();
1564 :			open(my $sfh, ">$spath");
1565 :			print $sfh <<END;
1566 :			#!/bin/sh
1567 :			. $FIG_Config::fig_disk/config/fig-user-env.sh
1568 :			$FIG_Config::bin/postprocess_computed_sims $pool_id
1569 :			END
1570 :
1571 :			close($sfh);
1572 :			chmod(0775, $spath);
1573 :
1574 :			#
1575 :			# Write the job ID to the subsystem queue dir.
1576 :			#
1577 :
1578 :			open(J, ">$cpool_dir/postprocess_jobid");
1579 :			print J $job->get_id(), "\n";
1580 :			close(J);
1581 :
1582 :			$job->enqueue();
1583 :			}
1584 :
1585 :			=head3 postprocess_computed_sims
1586 :
1587 :	parrello	1.287	C<< $fig->postprocess_computed_sims($pool_id); >>
1588 :
1589 :			Set up to reduce, reformat, and split the similarities in a given pool. We build
1590 :			a pipe to this pipeline:
1591 :	olson	1.279
1592 :			reduce_sims peg.synonyms 300 \| reformat_sims nr \| split_sims dest prefix
1593 :
1594 :	parrello	1.287	Then we put the new sims in the pool directory, and then copy to NewSims.
1595 :
1596 :			=over 4
1597 :
1598 :			=item pool_id
1599 :
1600 :			ID of the pool whose similarities are to be post-processed.
1601 :
1602 :			=back
1603 :	olson	1.279
1604 :			=cut
1605 :
1606 :	parrello	1.287	sub postprocess_computed_sims {
1607 :	olson	1.279	my($self, $pool_id) = @_;
1608 :
1609 :			#
1610 :			# We don't lock here because the job is already done, and we
1611 :			# shouldn't (ha, ha) ever postprocess twice.
1612 :			#
1613 :
1614 :			my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1615 :			my $cpool_dir = "$pool_dir/$pool_id";
1616 :
1617 :			my $sim_dir = "$cpool_dir/NewSims";
1618 :			&verify_dir($sim_dir);
1619 :
1620 :			#
1621 :			# Open the processing pipeline.
1622 :			#
1623 :
1624 :			my $reduce = "$FIG_Config::bin/reduce_sims $FIG_Config::global/peg.synonyms 300";
1625 :			my $reformat = "$FIG_Config::bin/reformat_sims $cpool_dir/nr";
1626 :			my $split = "$FIG_Config::bin/split_sims $sim_dir sims.$pool_id";
1627 :			open(my $process, "\| $reduce \| $reformat \| $split");
1628 :
1629 :			#
1630 :			# Iterate over all the sims files, taken from the database.
1631 :			#
1632 :
1633 :			my $dbh = $self->db_handle()->{_dbh};
1634 :			my $files = $dbh->selectcol_arrayref(qq(SELECT output_file
1635 :	parrello	1.298	FROM sim_queue
1636 :			WHERE qid = ? and output_file IS NOT NULL
1637 :			ORDER BY chunk_id), undef, $pool_id);
1638 :	parrello	1.287	for my $file (@$files) {
1639 :			my $buf;
1640 :			open(my $fh, "<$file") or confess "Cannot sim input file $file: $!";
1641 :			while (read($fh, $buf, 4096)) {
1642 :			print $process $buf;
1643 :			}
1644 :			close($fh);
1645 :	olson	1.279	}
1646 :			my $res = close($process);
1647 :	parrello	1.287	if (!$res) {
1648 :			if ($!) {
1649 :			confess "Error closing process pipeline: $!";
1650 :			} else {
1651 :			confess "Process pipeline exited with status $?";
1652 :			}
1653 :	olson	1.279	}
1654 :
1655 :			#
1656 :			# If we got here, it worked. Copy the new sims files over to NewSims.
1657 :			#
1658 :
1659 :			opendir(my $simdh, $sim_dir) or confess "Cannot open $sim_dir: $!";
1660 :			my @new_sims = grep { $_ !~ /^\./ } readdir($simdh);
1661 :			closedir($simdh);
1662 :
1663 :			&verify_dir("$FIG_Config::data/NewSims");
1664 :
1665 :	parrello	1.287	for my $sim_file (@new_sims) {
1666 :			my $target = "$FIG_Config::data/NewSims/$sim_file";
1667 :			if (-s $target) {
1668 :			Confess("$target already exists");
1669 :			}
1670 :			print "copying sim file $sim_file\n";
1671 :			&FIG::run("cp $sim_dir/$sim_file $target");
1672 :			&FIG::run("$FIG_Config::bin/index_sims $target");
1673 :	olson	1.279	}
1674 :			}
1675 :
1676 :	parrello	1.210	=head3 get_active_sim_pools
1677 :	olson	1.123
1678 :	parrello	1.287	C<< @pools = $fig->get_active_sim_pools(); >>
1679 :	olson	1.123
1680 :	parrello	1.287	Return a list of the pool IDs for the sim processing queues that have
1681 :			entries awaiting computation.
1682 :	olson	1.123
1683 :			=cut
1684 :	parrello	1.210	#: Return Type @;
1685 :	parrello	1.287	sub get_active_sim_pools {
1686 :	olson	1.123	my($self) = @_;
1687 :
1688 :			my $dbh = $self->db_handle();
1689 :
1690 :			my $res = $dbh->SQL("select distinct qid from sim_queue where not finished");
1691 :			return undef unless $res;
1692 :
1693 :			return map { $_->[0] } @$res;
1694 :			}
1695 :
1696 :	parrello	1.376	=head3 compute_clusters
1697 :
1698 :			C<< my @clusterList = $fig->compute_clusters(\@pegList, $subsystem, $distance); >>
1699 :
1700 :			Partition a list of PEGs into sections that are clustered close together on
1701 :			the genome. The basic algorithm used builds a graph connecting PEGs to
1702 :			other PEGs close by them on the genome. Each connected subsection of the graph
1703 :			is then separated into a cluster. Singleton clusters are thrown away, and
1704 :			the remaining ones are sorted by length. All PEGs in the incoming list
1705 :			should belong to the same genome, but this is not a requirement. PEGs on
1706 :			different genomes will simply find themselves in different clusters.
1707 :
1708 :			=over 4
1709 :
1710 :			=item pegList
1711 :
1712 :			Reference to a list of PEG IDs.
1713 :
1714 :			=item subsystem
1715 :
1716 :			Subsystem object for the relevant subsystem. This parameter is not used, but is
1717 :			required for compatability with Sprout.
1718 :
1719 :			=item distance (optional)
1720 :
1721 :			The maximum distance between PEGs that makes them considered close. If omitted,
1722 :			the distance is 5000 bases.
1723 :
1724 :			=item RETURN
1725 :
1726 :			Returns a list of lists. Each sub-list is a cluster of PEGs.
1727 :
1728 :			=back
1729 :
1730 :			=cut
1731 :
1732 :			sub compute_clusters {
1733 :			# Get the parameters.
1734 :			my ($self, $pegList, $subsystem, $distance) = @_;
1735 :			if (! defined $distance) {
1736 :			$distance = 5000;
1737 :			}
1738 :	overbeek	1.434
1739 :			my($peg,%by_contig);
1740 :			foreach $peg (@$pegList)
1741 :			{
1742 :	parrello	1.485	my $loc;
1743 :			if ($loc = $self->feature_location($peg))
1744 :			{
1745 :	parrello	1.488	my ($contig,$beg,$end) = $self->boundaries_of($loc);
1746 :	parrello	1.485	my $genome = &FIG::genome_of($peg);
1747 :			push(@{$by_contig{"$genome\t$contig"}},[($beg+$end)/2,$peg]);
1748 :			}
1749 :	overbeek	1.434	}
1750 :
1751 :	parrello	1.376	my @clusters = ();
1752 :	overbeek	1.434	foreach my $tuple (keys(%by_contig))
1753 :			{
1754 :	parrello	1.485	my $x = $by_contig{$tuple};
1755 :			my @pegs = sort { $a->[0] <=> $b->[0] } @$x;
1756 :			while ($x = shift @pegs)
1757 :			{
1758 :			my $clust = [$x->[1]];
1759 :			while ((@pegs > 0) && (abs($pegs[0]->[0] - $x->[0]) <= $distance))
1760 :			{
1761 :			$x = shift @pegs;
1762 :			push(@$clust,$x->[1]);
1763 :			}
1764 :	parrello	1.518
1765 :	parrello	1.485	if (@$clust > 1)
1766 :			{
1767 :			push(@clusters,$clust);
1768 :			}
1769 :			}
1770 :	parrello	1.376	}
1771 :	overbeek	1.434	return sort { @$b <=> @$a } @clusters;
1772 :	parrello	1.376	}
1773 :
1774 :	parrello	1.210	=head3 get_sim_pool_info
1775 :	olson	1.123
1776 :	parrello	1.287	C<< my ($total_entries, $n_finished, $n_assigned, $n_unassigned) = $fig->get_sim_pool_info($pool_id); >>
1777 :
1778 :			Return information about the given sim pool.
1779 :
1780 :			=over 4
1781 :
1782 :			=item pool_id
1783 :
1784 :			Pool ID of the similarity processing queue whose information is desired.
1785 :
1786 :			=item RETURN
1787 :
1788 :			Returns a four-element list. The first is the number of features in the
1789 :			queue; the second is the number of features that have been processed; the
1790 :			third is the number of features that have been assigned to a
1791 :			processor, and the fourth is the number of features left over.
1792 :	olson	1.123
1793 :	parrello	1.287	=back
1794 :	olson	1.123
1795 :			=cut
1796 :	parrello	1.210	#: Return Type @;
1797 :	parrello	1.287	sub get_sim_pool_info {
1798 :
1799 :	olson	1.123	my($self, $pool_id) = @_;
1800 :			my($dbh, $res, $total_entries, $n_finished, $n_assigned, $n_unassigned);
1801 :
1802 :			$dbh = $self->db_handle();
1803 :
1804 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id'");
1805 :	parrello	1.200	$total_entries = $res->[0]->[0];
1806 :	olson	1.123
1807 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and finished");
1808 :			$n_finished = $res->[0]->[0];
1809 :
1810 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and assigned and not finished");
1811 :			$n_assigned = $res->[0]->[0];
1812 :
1813 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and not finished and not assigned");
1814 :			$n_unassigned = $res->[0]->[0];
1815 :
1816 :			return ($total_entries, $n_finished, $n_assigned, $n_unassigned);
1817 :	olson	1.93	}
1818 :
1819 :	parrello	1.210	#=head3 get_sim_chunk
1820 :			#
1821 :			#usage: get_sim_chunk($n_seqs, $worker_id)
1822 :			#
1823 :			#Returns a chunk of $n_seqs of work.
1824 :			#
1825 :			#From Ross, about how sims are processed:
1826 :			#
1827 :			#Here is how I process them:
1828 :			#
1829 :			#
1830 :			# bash$ cd /Volumes/seed/olson/Sims/June22.out
1831 :			# bash$ for i in really*
1832 :			# > do
1833 :			# > cat < $i >> /Volumes/laptop/new.sims
1834 :			# > done
1835 :			#
1836 :			#
1837 :			#Then, I need to "reformat" them by adding to columns to each one
1838 :			# and split the result into files of about 3M each This I do using
1839 :			#
1840 :			#reduce_sims /Volumes/laptop/NR/NewNR/peg.synonyms.june21 300 < /Volumes/laptop/new.sims \|
1841 :			# reformat_sims /Volumes/laptop/NR/NewNR/checked.nr.june21 > /Volumes/laptop/reformated.sims
1842 :			#rm /Volumes/laptop/new.sims
1843 :			#split_sims /Volumes/laptop/NewSims sims.june24 reformated.sims
1844 :			#rm reformatted.sims
1845 :			#
1846 :			#=cut
1847 :	olson	1.93
1848 :	parrello	1.287	sub get_sim_chunk {
1849 :	parrello	1.210	my($self, $n_seqs, $worker_id) = @_;
1850 :			}
1851 :	olson	1.123
1852 :	parrello	1.210	=head3 get_local_hostname
1853 :	parrello	1.200
1854 :	parrello	1.287	C<< my $result = FIG::get_local_hostname(); >>
1855 :
1856 :			Return the local host name for the current processor. The name may be
1857 :			stored in a configuration file, or we may have to get it from the
1858 :			operating system.
1859 :	olson	1.123
1860 :	olson	1.93	=cut
1861 :	parrello	1.213	#: Return Type $;
1862 :	olson	1.10	sub get_local_hostname {
1863 :	olson	1.52
1864 :			#
1865 :			# See if there is a FIGdisk/config/hostname file. If there
1866 :			# is, force the hostname to be that.
1867 :			#
1868 :
1869 :			my $hostfile = "$FIG_Config::fig_disk/config/hostname";
1870 :	parrello	1.287	if (-f $hostfile) {
1871 :			my $fh;
1872 :			if (open($fh, $hostfile)) {
1873 :			my $hostname = <$fh>;
1874 :			chomp($hostname);
1875 :			return $hostname;
1876 :			}
1877 :	olson	1.52	}
1878 :	parrello	1.200
1879 :	olson	1.10	#
1880 :			# First check to see if we our hostname is correct.
1881 :			#
1882 :			# Map it to an IP address, and try to bind to that ip.
1883 :			#
1884 :
1885 :	overbeek	1.435	local $/ = "\n";
1886 :
1887 :	olson	1.10	my $tcp = getprotobyname('tcp');
1888 :	parrello	1.200
1889 :	olson	1.10	my $hostname = `hostname`;
1890 :	overbeek	1.435	chomp $hostname;
1891 :	olson	1.10
1892 :			my @hostent = gethostbyname($hostname);
1893 :
1894 :	parrello	1.287	if (@hostent > 0) {
1895 :			my $sock;
1896 :			my $ip = $hostent[4];
1897 :
1898 :			socket($sock, PF_INET, SOCK_STREAM, $tcp);
1899 :			if (bind($sock, sockaddr_in(0, $ip))) {
1900 :			#
1901 :			# It worked. Reverse-map back to a hopefully fqdn.
1902 :			#
1903 :
1904 :			my @rev = gethostbyaddr($ip, AF_INET);
1905 :			if (@rev > 0) {
1906 :			my $host = $rev[0];
1907 :			#
1908 :			# Check to see if we have a FQDN.
1909 :			#
1910 :
1911 :			if ($host =~ /\./) {
1912 :			#
1913 :			# Good.
1914 :			#
1915 :			return $host;
1916 :			} else {
1917 :			#
1918 :			# We didn't get a fqdn; bail and return the IP address.
1919 :			#
1920 :			return get_hostname_by_adapter()
1921 :			}
1922 :			} else {
1923 :			return inet_ntoa($ip);
1924 :			}
1925 :			} else {
1926 :			#
1927 :			# Our hostname must be wrong; we can't bind to the IP
1928 :			# address it maps to.
1929 :			# Return the name associated with the adapter.
1930 :			#
1931 :			return get_hostname_by_adapter()
1932 :			}
1933 :			} else {
1934 :			#
1935 :			# Our hostname isn't known to DNS. This isn't good.
1936 :			# Return the name associated with the adapter.
1937 :			#
1938 :			return get_hostname_by_adapter()
1939 :			}
1940 :			}
1941 :
1942 :			=head3 get_hostname_by_adapter
1943 :	parrello	1.200
1944 :	parrello	1.287	C<< my $name = FIG::get_hostname_by_adapter(); >>
1945 :	olson	1.10
1946 :	parrello	1.287	Return the local host name for the current network environment.
1947 :	parrello	1.213
1948 :			=cut
1949 :			#: Return Type $;
1950 :	olson	1.10	sub get_hostname_by_adapter {
1951 :			#
1952 :			# Attempt to determine our local hostname based on the
1953 :			# network environment.
1954 :			#
1955 :			# This implementation reads the routing table for the default route.
1956 :			# We then look at the interface config for the interface that holds the default.
1957 :			#
1958 :			#
1959 :			# Linux routing table:
1960 :			# [olson@yips 0.0.0]$ netstat -rn
1961 :			# Kernel IP routing table
1962 :			# Destination Gateway Genmask Flags MSS Window irtt Iface
1963 :			# 140.221.34.32 0.0.0.0 255.255.255.224 U 0 0 0 eth0
1964 :			# 169.254.0.0 0.0.0.0 255.255.0.0 U 0 0 0 eth0
1965 :			# 127.0.0.0 0.0.0.0 255.0.0.0 U 0 0 0 lo
1966 :			# 0.0.0.0 140.221.34.61 0.0.0.0 UG 0 0 0 eth0
1967 :	parrello	1.200	#
1968 :	olson	1.10	# Mac routing table:
1969 :	parrello	1.200	#
1970 :	olson	1.10	# bash-2.05a$ netstat -rn
1971 :			# Routing tables
1972 :	parrello	1.200	#
1973 :	olson	1.10	# Internet:
1974 :			# Destination Gateway Flags Refs Use Netif Expire
1975 :			# default 140.221.11.253 UGSc 12 120 en0
1976 :			# 127.0.0.1 127.0.0.1 UH 16 8415486 lo0
1977 :			# 140.221.8/22 link#4 UCS 12 0 en0
1978 :			# 140.221.8.78 0:6:5b:f:51:c4 UHLW 0 183 en0 408
1979 :			# 140.221.8.191 0:3:93:84:ab:e8 UHLW 0 92 en0 622
1980 :			# 140.221.8.198 0:e0:98:8e:36:e2 UHLW 0 5 en0 691
1981 :			# 140.221.9.6 0:6:5b:f:51:d6 UHLW 1 63 en0 1197
1982 :			# 140.221.10.135 0:d0:59:34:26:34 UHLW 2 2134 en0 1199
1983 :			# 140.221.10.152 0:30:1b:b0:ec:dd UHLW 1 137 en0 1122
1984 :			# 140.221.10.153 127.0.0.1 UHS 0 0 lo0
1985 :			# 140.221.11.37 0:9:6b:53:4e:4b UHLW 1 624 en0 1136
1986 :			# 140.221.11.103 0:30:48:22:59:e6 UHLW 3 973 en0 1016
1987 :			# 140.221.11.224 0:a:95:6f:7:10 UHLW 1 1 en0 605
1988 :			# 140.221.11.237 0:1:30:b8:80:c0 UHLW 0 0 en0 1158
1989 :			# 140.221.11.250 0:1:30:3:1:0 UHLW 0 0 en0 1141
1990 :			# 140.221.11.253 0:d0:3:e:70:a UHLW 13 0 en0 1199
1991 :			# 169.254 link#4 UCS 0 0 en0
1992 :	parrello	1.200	#
1993 :	olson	1.10	# Internet6:
1994 :			# Destination Gateway Flags Netif Expire
1995 :			# UH lo0
1996 :			# fe80::%lo0/64 Uc lo0
1997 :			# link#1 UHL lo0
1998 :			# fe80::%en0/64 link#4 UC en0
1999 :			# 0:a:95:a8:26:68 UHL lo0
2000 :			# ff01::/32 U lo0
2001 :			# ff02::%lo0/32 UC lo0
2002 :			# ff02::%en0/32 link#4 UC en0
2003 :
2004 :			my($fh);
2005 :
2006 :	parrello	1.287	if (!open($fh, "netstat -rn \|")) {
2007 :			warn "Cannot run netstat to determine local IP address\n";
2008 :			return "localhost";
2009 :	olson	1.10	}
2010 :
2011 :			my $interface_name;
2012 :	parrello	1.200
2013 :	parrello	1.287	while (<$fh>) {
2014 :			my @cols = split();
2015 :	olson	1.10
2016 :	parrello	1.287	if ($cols[0] eq "default" \|\| $cols[0] eq "0.0.0.0") {
2017 :			$interface_name = $cols[$#cols];
2018 :			}
2019 :	olson	1.10	}
2020 :			close($fh);
2021 :	parrello	1.200
2022 :	olson	1.11	# print "Default route on $interface_name\n";
2023 :	olson	1.10
2024 :			#
2025 :			# Find ifconfig.
2026 :			#
2027 :
2028 :			my $ifconfig;
2029 :
2030 :	parrello	1.287	for my $dir ((split(":", $ENV{PATH}), "/sbin", "/usr/sbin")) {
2031 :			if (-x "$dir/ifconfig") {
2032 :			$ifconfig = "$dir/ifconfig";
2033 :			last;
2034 :			}
2035 :	olson	1.10	}
2036 :
2037 :	parrello	1.287	if ($ifconfig eq "") {
2038 :			warn "Ifconfig not found\n";
2039 :			return "localhost";
2040 :	olson	1.10	}
2041 :	olson	1.11	# print "Foudn $ifconfig\n";
2042 :	olson	1.10
2043 :	parrello	1.287	if (!open($fh, "$ifconfig $interface_name \|")) {
2044 :			warn "Could not run $ifconfig: $!\n";
2045 :			return "localhost";
2046 :	olson	1.10	}
2047 :
2048 :			my $ip;
2049 :	parrello	1.287	while (<$fh>) {
2050 :			#
2051 :			# Mac:
2052 :			# inet 140.221.10.153 netmask 0xfffffc00 broadcast 140.221.11.255
2053 :			# Linux:
2054 :			# inet addr:140.221.34.37 Bcast:140.221.34.63 Mask:255.255.255.224
2055 :			#
2056 :
2057 :			chomp;
2058 :			s/^\s*//;
2059 :
2060 :			# print "Have '$_'\n";
2061 :			if (/inet\s+addr:(\d+\.\d+\.\d+\.\d+)\s+/) {
2062 :			#
2063 :			# Linux hit.
2064 :			#
2065 :			$ip = $1;
2066 :			# print "Got linux $ip\n";
2067 :			last;
2068 :			} elsif (/inet\s+(\d+\.\d+\.\d+\.\d+)\s+/) {
2069 :			#
2070 :			# Mac hit.
2071 :			#
2072 :			$ip = $1;
2073 :			# print "Got mac $ip\n";
2074 :			last;
2075 :			}
2076 :	olson	1.10	}
2077 :			close($fh);
2078 :
2079 :	parrello	1.287	if ($ip eq "") {
2080 :			warn "Didn't find an IP\n";
2081 :			return "localhost";
2082 :	olson	1.10	}
2083 :
2084 :			return $ip;
2085 :	efrank	1.1	}
2086 :
2087 :	parrello	1.213	=head3 get_seed_id
2088 :
2089 :	parrello	1.287	C<< my $id = FIG::get_seed_id(); >>
2090 :
2091 :			Return the Universally Unique ID for this SEED instance. If one
2092 :			does not exist, it will be created.
2093 :	parrello	1.213
2094 :			=cut
2095 :			#: Return type $;
2096 :	olson	1.38	sub get_seed_id {
2097 :			#
2098 :			# Retrieve the seed identifer from FIGdisk/config/seed_id.
2099 :			#
2100 :			# If it's not there, create one, and make it readonly.
2101 :			#
2102 :			my $id;
2103 :			my $id_file = "$FIG_Config::fig_disk/config/seed_id";
2104 :	parrello	1.287	if (! -f $id_file) {
2105 :			my $newid = `uuidgen`;
2106 :			if (!$newid) {
2107 :			die "Cannot run uuidgen: $!";
2108 :			}
2109 :	olson	1.38
2110 :	parrello	1.287	chomp($newid);
2111 :			my $fh = new FileHandle(">$id_file");
2112 :			if (!$fh) {
2113 :			die "error creating $id_file: $!";
2114 :			}
2115 :			print $fh "$newid\n";
2116 :			$fh->close();
2117 :			chmod(0444, $id_file);
2118 :	olson	1.38	}
2119 :			my $fh = new FileHandle("<$id_file");
2120 :			$id = <$fh>;
2121 :			chomp($id);
2122 :			return $id;
2123 :			}
2124 :
2125 :	parrello	1.287	=head3 get_release_info
2126 :	olson	1.155
2127 :	parrello	1.287	C<< my ($name, $id, $inst, $email, $parent_id, $description) = FIG::get_release_info(); >>
2128 :	olson	1.155
2129 :	parrello	1.287	Return the current data release information..
2130 :	olson	1.195
2131 :			The release info comes from the file FIG/Data/RELEASE. It is formatted as:
2132 :
2133 :	parrello	1.287	<release-name>
2134 :			<unique id>
2135 :			<institution>
2136 :			<contact email>
2137 :			<unique id of data release this release derived from>
2138 :			<description>
2139 :	olson	1.195
2140 :			For instance:
2141 :
2142 :	parrello	1.287	-----
2143 :			SEED Data Release, 09/15/2004.
2144 :			4148208C-1DF2-11D9-8417-000A95D52EF6
2145 :			ANL/FIG
2146 :			olson@mcs.anl.gov
2147 :
2148 :			Test release.
2149 :			-----
2150 :	olson	1.195
2151 :			If no RELEASE file exists, this routine will create one with a new unique ID. This
2152 :			lets a peer optimize the data transfer by being able to cache ID translations
2153 :			from this instance.
2154 :	olson	1.155
2155 :			=cut
2156 :	parrello	1.213	#: Return Type @;
2157 :	parrello	1.287	sub get_release_info {
2158 :	olson	1.196	my($fig, $no_create) = @_;
2159 :	olson	1.195
2160 :			my $rel_file = "$FIG_Config::data/RELEASE";
2161 :
2162 :	parrello	1.287	if (! -f $rel_file and !$no_create) {
2163 :	parrello	1.298	#
2164 :			# Create a new one.
2165 :			#
2166 :	olson	1.195
2167 :	parrello	1.287	my $newid = `uuidgen`;
2168 :			if (!$newid) {
2169 :			die "Cannot run uuidgen: $!";
2170 :			}
2171 :	olson	1.195
2172 :	parrello	1.287	chomp($newid);
2173 :	olson	1.195
2174 :	parrello	1.287	my $relinfo = "Automatically generated release info " . localtime();
2175 :			my $inst = "Unknown";
2176 :			my $contact = "Unknown";
2177 :			my $parent = "";
2178 :			my( $a, $b, $e, $v, $env ) = $fig->genome_counts;
2179 :			my $description = "Automatically generated release info\n";
2180 :			$description .= "Contains $a archaeal, $b bacterial, $e eukaryal, $v viral and $env environmental genomes.\n";
2181 :
2182 :			my $fh = new FileHandle(">$rel_file");
2183 :			if (!$fh) {
2184 :			warn "error creating $rel_file: $!";
2185 :			return undef;
2186 :			}
2187 :			print $fh "$relinfo\n";
2188 :			print $fh "$newid\n";
2189 :			print $fh "$inst\n";
2190 :			print $fh "$contact\n";
2191 :			print $fh "$parent\n";
2192 :			print $fh $description;
2193 :			$fh->close();
2194 :			chmod(0444, $rel_file);
2195 :	olson	1.195	}
2196 :
2197 :	parrello	1.287	if (open(my $fh, $rel_file)) {
2198 :			my(@lines) = <$fh>;
2199 :			close($fh);
2200 :	parrello	1.200
2201 :	parrello	1.287	chomp(@lines);
2202 :	parrello	1.200
2203 :	parrello	1.287	my($info, $id, $inst, $contact, $parent, @desc) = @lines;
2204 :	olson	1.195
2205 :	parrello	1.287	return ($info, $id, $inst, $contact, $parent, join("\n", @desc));
2206 :	olson	1.195	}
2207 :	olson	1.155
2208 :			return undef;
2209 :			}
2210 :
2211 :	parrello	1.406	=head3 Title
2212 :
2213 :			C<< my $title = $fig->Title(); >>
2214 :
2215 :			Return the title of this database. For SEED, this will return SEED, for Sprout
2216 :			it will return NMPDR, and so forth.
2217 :
2218 :			=cut
2219 :
2220 :			sub Title {
2221 :			return "SEED";
2222 :			}
2223 :
2224 :	parrello	1.376	=head3 FIG
2225 :
2226 :			C<< my $realFig = $fig->FIG(); >>
2227 :
2228 :			Return this object. This method is provided for compatability with SFXlate.
2229 :
2230 :			=cut
2231 :
2232 :			sub FIG {
2233 :			my ($self) = @_;
2234 :			return $self;
2235 :			}
2236 :
2237 :	parrello	1.287	=head3 get_peer_last_update
2238 :	olson	1.155
2239 :	parrello	1.287	C<< my $date = $fig->get_peer_last_update($peer_id); >>
2240 :	parrello	1.213
2241 :	olson	1.155	Return the timestamp from the last successful peer-to-peer update with
2242 :	parrello	1.287	the given peer. If the specified peer has made updates, comparing this
2243 :			timestamp to the timestamp of the updates can tell you whether or not
2244 :			the updates have been integrated into your SEED data store.
2245 :	olson	1.155
2246 :			We store this information in FIG/Data/Global/Peers/<peer-id>.
2247 :
2248 :	parrello	1.287	=over 4
2249 :
2250 :			=item peer_id
2251 :
2252 :			Universally Unique ID for the desired peer.
2253 :
2254 :			=item RETURN
2255 :
2256 :			Returns the date/time stamp for the last peer-to-peer updated performed
2257 :			with the identified SEED instance.
2258 :
2259 :			=back
2260 :
2261 :	olson	1.155	=cut
2262 :	parrello	1.213	#: Return Type $;
2263 :	parrello	1.287	sub get_peer_last_update {
2264 :	olson	1.155	my($self, $peer_id) = @_;
2265 :
2266 :			my $dir = "$FIG_Config::data/Global/Peers";
2267 :			&verify_dir($dir);
2268 :			$dir .= "/$peer_id";
2269 :			&verify_dir($dir);
2270 :
2271 :			my $update_file = "$dir/last_update";
2272 :	parrello	1.287	if (-f $update_file) {
2273 :			my $time = file_head($update_file, 1);
2274 :			chomp $time;
2275 :			return $time;
2276 :			} else {
2277 :			return undef;
2278 :	olson	1.155	}
2279 :			}
2280 :
2281 :	parrello	1.287	=head3 set_peer_last_update
2282 :	parrello	1.213
2283 :	parrello	1.287	C<< $fig->set_peer_last_update($peer_id, $time); >>
2284 :	parrello	1.213
2285 :	parrello	1.287	Manually set the update timestamp for a specified peer. This informs
2286 :			the SEED that you have all of the assignments and updates from a
2287 :			particular SEED instance as of a certain date.
2288 :	parrello	1.213
2289 :			=cut
2290 :			#: Return Type ;
2291 :
2292 :	parrello	1.287	sub set_peer_last_update {
2293 :	olson	1.155	my($self, $peer_id, $time) = @_;
2294 :
2295 :			my $dir = "$FIG_Config::data/Global/Peers";
2296 :			&verify_dir($dir);
2297 :			$dir .= "/$peer_id";
2298 :			&verify_dir($dir);
2299 :
2300 :			my $update_file = "$dir/last_update";
2301 :			open(F, ">$update_file");
2302 :			print F "$time\n";
2303 :			close(F);
2304 :			}
2305 :
2306 :	redwards	1.302	=head3 clean_spaces
2307 :
2308 :	parrello	1.320	Remove any extra spaces from input fields. This will (currently) remove ^\s, \s$, and concatenate multiple spaces into one.
2309 :	redwards	1.302
2310 :			my $input=$fig->clean_spaces($cgi->param('input'));
2311 :
2312 :			=cut
2313 :
2314 :			sub clean_spaces
2315 :			{
2316 :			my ($self, $s)=@_;
2317 :			# note at the moment I do not use \s because that recognizes \t and \n too. This should only remove multiple spaces.
2318 :	parrello	1.320	$s =~ s/^ +//;
2319 :	redwards	1.302	$s =~ s/ +$//;
2320 :			$s =~ s/ +/ /g;
2321 :			return $s;
2322 :			}
2323 :
2324 :
2325 :
2326 :	parrello	1.213	=head3 cgi_url
2327 :
2328 :	parrello	1.287	C<< my $url = FIG::$fig->cgi_url(); >>
2329 :
2330 :			Return the URL for the CGI script directory.
2331 :	parrello	1.213
2332 :			=cut
2333 :			#: Return Type $;
2334 :	efrank	1.1	sub cgi_url {
2335 :	overbeek	1.377	# return &plug_url($FIG_Config::cgi_url);
2336 :
2337 :			#
2338 :			# In order to globally make relative references work properly, return ".".
2339 :			# This might break some stuff in p2p, but this will get us most of the way there.
2340 :			# The things that break we can repair by inspecting the value of $ENV{SCRIPT_NAME}
2341 :			#
2342 :			return ".";
2343 :	efrank	1.1	}
2344 :	parrello	1.200
2345 :	overbeek	1.382	=head3 top_link
2346 :
2347 :			C<< my $url = FIG::top_link(); >>
2348 :
2349 :			Return the relative URL for the top of the CGI script directory.
2350 :
2351 :			We determine this based on the SCRIPT_NAME environment variable, falling
2352 :			back to FIG_Config::cgi_base if necessary.
2353 :
2354 :			=cut
2355 :
2356 :			sub top_link
2357 :			{
2358 :	parrello	1.518
2359 :	overbeek	1.382	#
2360 :			# Determine if this is a toplevel cgi or one in one of the subdirs (currently
2361 :			# just /p2p).
2362 :			#
2363 :
2364 :			my @parts = split(/\//, $ENV{SCRIPT_NAME});
2365 :			my $top;
2366 :			if ($parts[-2] eq 'FIG')
2367 :			{
2368 :	parrello	1.485	$top = '.';
2369 :			# warn "toplevel @parts\n";
2370 :	overbeek	1.382	}
2371 :			elsif ($parts[-3] eq 'FIG')
2372 :			{
2373 :	parrello	1.485	$top = '..';
2374 :			# warn "subdir @parts\n";
2375 :	overbeek	1.382	}
2376 :			else
2377 :			{
2378 :	parrello	1.485	$top = $FIG_Config::cgi_base;
2379 :			# warn "other @parts\n";
2380 :	overbeek	1.382	}
2381 :
2382 :			return $top;
2383 :			}
2384 :
2385 :	parrello	1.213	=head3 temp_url
2386 :
2387 :	parrello	1.287	C<< my $url = FIG::temp_url(); >>
2388 :
2389 :			Return the URL of the temporary file directory.
2390 :	parrello	1.213
2391 :			=cut
2392 :			#: Return Type $;
2393 :	efrank	1.1	sub temp_url {
2394 :	overbeek	1.377	# return &plug_url($FIG_Config::temp_url);
2395 :
2396 :			#
2397 :			# Similarly, make this relative.
2398 :			#
2399 :			return "../FIG-Tmp";
2400 :	efrank	1.1	}
2401 :	parrello	1.200
2402 :	parrello	1.213	=head3 plug_url
2403 :
2404 :	parrello	1.287	C<< my $url2 = $fig->plug_url($url); >>
2405 :
2406 :			or
2407 :
2408 :			C<< my $url2 = $fig->plug_url($url); >>
2409 :
2410 :			Change the domain portion of a URL to point to the current domain. This essentially
2411 :			relocates URLs into the current environment.
2412 :
2413 :			=over 4
2414 :
2415 :			=item url
2416 :
2417 :			URL to relocate.
2418 :
2419 :			=item RETURN
2420 :
2421 :			Returns a new URL with the base portion converted to the current operating host.
2422 :			If the URL does not begin with C<http://>, the URL will be returned unmodified.
2423 :
2424 :			=back
2425 :	parrello	1.213
2426 :			=cut
2427 :			#: Return Type $;
2428 :	efrank	1.1	sub plug_url {
2429 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2430 :	efrank	1.1	my($url) = @_;
2431 :
2432 :	golsen	1.44	my $name;
2433 :
2434 :			# Revised by GJO
2435 :			# First try to get url from the current http request
2436 :
2437 :			if ( defined( $ENV{ 'HTTP_HOST' } ) # This is where $cgi->url gets its value
2438 :			&& ( $name = $ENV{ 'HTTP_HOST' } )
2439 :			&& ( $url =~ s~^http://[^/]*~http://$name~ ) # ~ is delimiter
2440 :			) {}
2441 :
2442 :			# Otherwise resort to alternative sources
2443 :
2444 :			elsif ( ( $name = &get_local_hostname )
2445 :			&& ( $url =~ s~^http://[^/]*~http://$name~ ) # ~ is delimiter
2446 :			) {}
2447 :
2448 :	efrank	1.1	return $url;
2449 :			}
2450 :
2451 :	parrello	1.213	=head3 file_read
2452 :
2453 :	parrello	1.287	C<< my $text = $fig->file_read($fileName); >>
2454 :
2455 :			or
2456 :
2457 :			C<< my @lines = $fig->file_read($fileName); >>
2458 :
2459 :			or
2460 :
2461 :			C<< my $text = FIG::file_read($fileName); >>
2462 :
2463 :			or
2464 :
2465 :			C<< my @lines = FIG::file_read($fileName); >>
2466 :
2467 :			Read an entire file into memory. In a scalar context, the file is returned
2468 :			as a single text string with line delimiters included. In a list context, the
2469 :			file is returned as a list of lines, each line terminated by a line
2470 :			delimiter. (For a method that automatically strips the line delimiters,
2471 :			use C<Tracer::GetFile>.)
2472 :
2473 :			=over 4
2474 :
2475 :			=item fileName
2476 :
2477 :			Fully-qualified name of the file to read.
2478 :
2479 :			=item RETURN
2480 :
2481 :			In a list context, returns a list of the file lines. In a scalar context, returns
2482 :			a string containing all the lines of the file with delimiters included.
2483 :	parrello	1.213
2484 :	parrello	1.287	=back
2485 :	parrello	1.213
2486 :			=cut
2487 :			#: Return Type $;
2488 :			#: Return Type @;
2489 :	parrello	1.287	sub file_read {
2490 :
2491 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2492 :	parrello	1.287	my($fileName) = @_;
2493 :			return file_head($fileName, '*');
2494 :	olson	1.90
2495 :			}
2496 :
2497 :
2498 :	parrello	1.213	=head3 file_head
2499 :
2500 :	parrello	1.287	C<< my $text = $fig->file_head($fileName, $count); >>
2501 :
2502 :			or
2503 :
2504 :			C<< my @lines = $fig->file_head($fileName, $count); >>
2505 :	parrello	1.213
2506 :	parrello	1.287	or
2507 :	parrello	1.213
2508 :	parrello	1.287	C<< my $text = FIG::file_head($fileName, $count); >>
2509 :	olson	1.90
2510 :	parrello	1.287	or
2511 :	olson	1.90
2512 :	parrello	1.287	C<< my @lines = FIG::file_head($fileName, $count); >>
2513 :	olson	1.90
2514 :	parrello	1.287	Read a portion of a file into memory. In a scalar context, the file portion is
2515 :			returned as a single text string with line delimiters included. In a list
2516 :			context, the file portion is returned as a list of lines, each line terminated
2517 :			by a line delimiter.
2518 :	olson	1.155
2519 :	parrello	1.287	=over 4
2520 :	olson	1.90
2521 :	parrello	1.287	=item fileName
2522 :	olson	1.90
2523 :	parrello	1.287	Fully-qualified name of the file to read.
2524 :	efrank	1.1
2525 :	parrello	1.287	=item count (optional)
2526 :	efrank	1.1
2527 :	parrello	1.287	Number of lines to read from the file. If omitted, C<1> is assumed. If the
2528 :			non-numeric string C<*> is specified, the entire file will be read.
2529 :	efrank	1.1
2530 :	parrello	1.287	=item RETURN
2531 :	efrank	1.1
2532 :	parrello	1.287	In a list context, returns a list of the desired file lines. In a scalar context, returns
2533 :			a string containing the desired lines of the file with delimiters included.
2534 :	efrank	1.1
2535 :	parrello	1.287	=back
2536 :	efrank	1.1
2537 :			=cut
2538 :	parrello	1.287	#: Return Type $;
2539 :			#: Return Type @;
2540 :			sub file_head {
2541 :	efrank	1.1
2542 :	parrello	1.287	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2543 :			my($file, $count) = @_;
2544 :	efrank	1.1
2545 :	parrello	1.287	my ($n, $allFlag);
2546 :			if ($count eq '*') {
2547 :	olson	1.304	Trace("Full file read for \"$file\".") if T(3);
2548 :	parrello	1.287	$allFlag = 1;
2549 :			$n = 0;
2550 :			} else {
2551 :			$allFlag = 0;
2552 :			$n = (!$count ? 1 : $count);
2553 :	olson	1.304	Trace("Reading $n record(s) from \"$file\".") if T(3);
2554 :	parrello	1.287	}
2555 :	efrank	1.1
2556 :	parrello	1.287	if (open(my $fh, "<$file")) {
2557 :	parrello	1.298	my(@ret, $i);
2558 :	parrello	1.287	$i = 0;
2559 :			while (<$fh>) {
2560 :			push(@ret, $_);
2561 :			$i++;
2562 :			last if !$allFlag && $i >= $n;
2563 :			}
2564 :			close($fh);
2565 :			if (wantarray) {
2566 :			return @ret;
2567 :			} else {
2568 :			return join("", @ret);
2569 :			}
2570 :	efrank	1.1	}
2571 :			}
2572 :
2573 :			################ Basic Routines [ existed since WIT ] ##########################
2574 :
2575 :	parrello	1.287	=head3 min
2576 :
2577 :			C<< my $min = FIG::min(@x); >>
2578 :
2579 :			or
2580 :
2581 :			C<< my $min = $fig->min(@x); >>
2582 :
2583 :			Return the minimum numeric value from a list.
2584 :
2585 :			=over 4
2586 :
2587 :			=item x1, x2, ... xN
2588 :	efrank	1.1
2589 :	parrello	1.287	List of numbers to process.
2590 :	efrank	1.1
2591 :	parrello	1.287	=item RETURN
2592 :	efrank	1.1
2593 :	parrello	1.287	Returns the numeric value of the list entry possessing the lowest value. Returns
2594 :			C<undef> if the list is empty.
2595 :	efrank	1.1
2596 :	parrello	1.287	=back
2597 :	efrank	1.1
2598 :			=cut
2599 :	parrello	1.213	#: Return Type $;
2600 :	efrank	1.1	sub min {
2601 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2602 :	efrank	1.1	my(@x) = @_;
2603 :			my($min,$i);
2604 :
2605 :			(@x > 0) \|\| return undef;
2606 :			$min = $x[0];
2607 :	parrello	1.287	for ($i=1; ($i < @x); $i++) {
2608 :			$min = ($min > $x[$i]) ? $x[$i] : $min;
2609 :	efrank	1.1	}
2610 :			return $min;
2611 :			}
2612 :
2613 :	parrello	1.287	=head3 max
2614 :
2615 :			C<< my $max = FIG::max(@x); >>
2616 :
2617 :			or
2618 :
2619 :			C<< my $max = $fig->max(@x); >>
2620 :	efrank	1.1
2621 :	parrello	1.287	Return the maximum numeric value from a list.
2622 :	efrank	1.1
2623 :	parrello	1.287	=over 4
2624 :
2625 :			=item x1, x2, ... xN
2626 :
2627 :			List of numbers to process.
2628 :
2629 :			=item RETURN
2630 :
2631 :			Returns the numeric value of t/he list entry possessing the highest value. Returns
2632 :			C<undef> if the list is empty.
2633 :	efrank	1.1
2634 :	parrello	1.287	=back
2635 :	efrank	1.1
2636 :			=cut
2637 :	parrello	1.213	#: Return Type $;
2638 :	efrank	1.1	sub max {
2639 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2640 :	efrank	1.1	my(@x) = @_;
2641 :			my($max,$i);
2642 :
2643 :			(@x > 0) \|\| return undef;
2644 :			$max = $x[0];
2645 :	parrello	1.287	for ($i=1; ($i < @x); $i++) {
2646 :			$max = ($max < $x[$i]) ? $x[$i] : $max;
2647 :	efrank	1.1	}
2648 :			return $max;
2649 :			}
2650 :
2651 :	parrello	1.287	=head3 between
2652 :	efrank	1.1
2653 :	parrello	1.287	C<< my $flag = FIG::between($x, $y, $z); >>
2654 :	efrank	1.1
2655 :	parrello	1.287	or
2656 :
2657 :			C<< my $flag = $fig->between($x, $y, $z); >>
2658 :
2659 :			Determine whether or not $y is between $x and $z.
2660 :
2661 :			=over 4
2662 :
2663 :			=item x
2664 :
2665 :			First edge number.
2666 :
2667 :			=item y
2668 :	efrank	1.1
2669 :	parrello	1.287	Number to examine.
2670 :
2671 :			=item z
2672 :
2673 :			Second edge number.
2674 :
2675 :			=item RETURN
2676 :
2677 :			Return TRUE if the number I<$y> is between the numbers I<$x> and I<$z>. The check
2678 :			is inclusive (that is, if I<$y> is equal to I<$x> or I<$z> the function returns
2679 :			TRUE), and the order of I<$x> and I<$z> does not matter. If I<$x> is lower than
2680 :			I<$z>, then the return is TRUE if I<$x> <= I<$y> <= I<$z>. If I<$z> is lower,
2681 :			then the return is TRUE if I<$x> >= I$<$y> >= I<$z>.
2682 :
2683 :			=back
2684 :	efrank	1.1
2685 :			=cut
2686 :	parrello	1.213	#: Return Type $;
2687 :	efrank	1.1	sub between {
2688 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2689 :	efrank	1.1	my($x,$y,$z) = @_;
2690 :
2691 :	parrello	1.287	if ($x < $z) {
2692 :			return (($x <= $y) && ($y <= $z));
2693 :			} else {
2694 :			return (($x >= $y) && ($y >= $z));
2695 :	efrank	1.1	}
2696 :			}
2697 :
2698 :	parrello	1.287	=head3 standard_genetic_code
2699 :	efrank	1.1
2700 :	parrello	1.287	C<< my $code = FIG::standard_genetic_code(); >>
2701 :	efrank	1.1
2702 :	parrello	1.287	Return a hash containing the standard translation of nucleotide triples to proteins.
2703 :			Methods such as L</translate> can take a translation scheme as a parameter. This method
2704 :			returns the default translation scheme. The scheme is implemented as a reference to a
2705 :			hash that contains nucleotide triplets as keys and has protein letters as values.
2706 :	efrank	1.1
2707 :			=cut
2708 :	parrello	1.213	#: Return Type $;
2709 :	efrank	1.1	sub standard_genetic_code {
2710 :	parrello	1.200
2711 :	efrank	1.1	my $code = {};
2712 :
2713 :			$code->{"AAA"} = "K";
2714 :			$code->{"AAC"} = "N";
2715 :			$code->{"AAG"} = "K";
2716 :			$code->{"AAT"} = "N";
2717 :			$code->{"ACA"} = "T";
2718 :			$code->{"ACC"} = "T";
2719 :			$code->{"ACG"} = "T";
2720 :			$code->{"ACT"} = "T";
2721 :			$code->{"AGA"} = "R";
2722 :			$code->{"AGC"} = "S";
2723 :			$code->{"AGG"} = "R";
2724 :			$code->{"AGT"} = "S";
2725 :			$code->{"ATA"} = "I";
2726 :			$code->{"ATC"} = "I";
2727 :			$code->{"ATG"} = "M";
2728 :			$code->{"ATT"} = "I";
2729 :			$code->{"CAA"} = "Q";
2730 :			$code->{"CAC"} = "H";
2731 :			$code->{"CAG"} = "Q";
2732 :			$code->{"CAT"} = "H";
2733 :			$code->{"CCA"} = "P";
2734 :			$code->{"CCC"} = "P";
2735 :			$code->{"CCG"} = "P";
2736 :			$code->{"CCT"} = "P";
2737 :			$code->{"CGA"} = "R";
2738 :			$code->{"CGC"} = "R";
2739 :			$code->{"CGG"} = "R";
2740 :			$code->{"CGT"} = "R";
2741 :			$code->{"CTA"} = "L";
2742 :			$code->{"CTC"} = "L";
2743 :			$code->{"CTG"} = "L";
2744 :			$code->{"CTT"} = "L";
2745 :			$code->{"GAA"} = "E";
2746 :			$code->{"GAC"} = "D";
2747 :			$code->{"GAG"} = "E";
2748 :			$code->{"GAT"} = "D";
2749 :			$code->{"GCA"} = "A";
2750 :			$code->{"GCC"} = "A";
2751 :			$code->{"GCG"} = "A";
2752 :			$code->{"GCT"} = "A";
2753 :			$code->{"GGA"} = "G";
2754 :			$code->{"GGC"} = "G";
2755 :			$code->{"GGG"} = "G";
2756 :			$code->{"GGT"} = "G";
2757 :			$code->{"GTA"} = "V";
2758 :			$code->{"GTC"} = "V";
2759 :			$code->{"GTG"} = "V";
2760 :			$code->{"GTT"} = "V";
2761 :			$code->{"TAA"} = "*";
2762 :			$code->{"TAC"} = "Y";
2763 :			$code->{"TAG"} = "*";
2764 :			$code->{"TAT"} = "Y";
2765 :			$code->{"TCA"} = "S";
2766 :			$code->{"TCC"} = "S";
2767 :			$code->{"TCG"} = "S";
2768 :			$code->{"TCT"} = "S";
2769 :			$code->{"TGA"} = "*";
2770 :			$code->{"TGC"} = "C";
2771 :			$code->{"TGG"} = "W";
2772 :			$code->{"TGT"} = "C";
2773 :			$code->{"TTA"} = "L";
2774 :			$code->{"TTC"} = "F";
2775 :			$code->{"TTG"} = "L";
2776 :			$code->{"TTT"} = "F";
2777 :	parrello	1.200
2778 :	efrank	1.1	return $code;
2779 :			}
2780 :
2781 :	hwang	1.547
2782 :			sub fr_to_go {
2783 :	overbeek	1.548	my($self,$role) = @_;
2784 :	hwang	1.547
2785 :	overbeek	1.549	my $roleQ = quotemeta $role;
2786 :	overbeek	1.548	my $rdbH = $self->db_handle;
2787 :	overbeek	1.549	my $relational_db_response = $rdbH->SQL("SELECT go_id FROM fr2go WHERE role = '$roleQ'");
2788 :	overbeek	1.548	return map { $_->[0] } @{$relational_db_response};
2789 :	hwang	1.547	}
2790 :
2791 :	parrello	1.287	=head3 translate
2792 :
2793 :			C<< my $aa_seq = &FIG::translate($dna_seq, $code, $fix_start); >>
2794 :
2795 :			Translate a DNA sequence to a protein sequence using the specified genetic code.
2796 :			If I<$fix_start> is TRUE, will translate an initial C<TTG> or C<GTG> code to
2797 :			C<M>. (In the standard genetic code, these two combinations normally translate
2798 :			to C<V> and C<L>, respectively.)
2799 :
2800 :			=over 4
2801 :	efrank	1.1
2802 :	parrello	1.287	=item dna_seq
2803 :	efrank	1.1
2804 :	parrello	1.287	DNA sequence to translate. Note that the DNA sequence can only contain
2805 :			known nucleotides.
2806 :	efrank	1.1
2807 :	parrello	1.287	=item code
2808 :	efrank	1.1
2809 :	parrello	1.287	Reference to a hash specifying the translation code. The hash is keyed by
2810 :			nucleotide triples, and the value for each key is the corresponding protein
2811 :			letter. If this parameter is omitted, the L</standard_genetic_code> will be
2812 :			used.
2813 :	efrank	1.1
2814 :	parrello	1.287	=item fix_start
2815 :
2816 :			TRUE if the first triple is to get special treatment, else FALSE. If TRUE,
2817 :			then a value of C<TTG> or C<GTG> in the first position will be translated to
2818 :			C<M> instead of the value specified in the translation code.
2819 :
2820 :			=item RETURN
2821 :
2822 :			Returns a string resulting from translating each nucleotide triple into a
2823 :			protein letter.
2824 :
2825 :			=back
2826 :
2827 :			=cut
2828 :			#: Return Type $;
2829 :			sub translate {
2830 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2831 :
2832 :			my( $dna,$code,$start ) = @_;
2833 :			my( $i,$j,$ln );
2834 :			my( $x,$y );
2835 :			my( $prot );
2836 :
2837 :			if (! defined($code)) {
2838 :			$code = &FIG::standard_genetic_code;
2839 :	efrank	1.1	}
2840 :			$ln = length($dna);
2841 :			$prot = "X" x ($ln/3);
2842 :			$dna =~ tr/a-z/A-Z/;
2843 :
2844 :	parrello	1.287	for ($i=0,$j=0; ($i < ($ln-2)); $i += 3,$j++) {
2845 :			$x = substr($dna,$i,3);
2846 :			if ($y = $code->{$x}) {
2847 :			substr($prot,$j,1) = $y;
2848 :	efrank	1.1	}
2849 :			}
2850 :	parrello	1.200
2851 :	parrello	1.287	if (($start) && ($ln >= 3) && (substr($dna,0,3) =~ /^[GT]TG$/)) {
2852 :			substr($prot,0,1) = 'M';
2853 :	efrank	1.1	}
2854 :			return $prot;
2855 :			}
2856 :
2857 :	parrello	1.287	=head3 reverse_comp
2858 :
2859 :			C<< my $dnaR = FIG::reverse_comp($dna); >>
2860 :
2861 :			or
2862 :
2863 :			C<< my $dnaR = $fig->reverse_comp($dna); >>
2864 :
2865 :			Return the reverse complement os the specified DNA sequence.
2866 :	efrank	1.1
2867 :	parrello	1.287	NOTE: for extremely long DNA strings, use L</rev_comp>, which allows you to
2868 :			pass the strings around in the form of pointers.
2869 :	efrank	1.1
2870 :	parrello	1.287	=over 4
2871 :
2872 :			=item dna
2873 :	efrank	1.1
2874 :	parrello	1.287	DNA sequence whose reverse complement is desired.
2875 :
2876 :			=item RETURN
2877 :
2878 :			Returns the reverse complement of the incoming DNA sequence.
2879 :
2880 :			=back
2881 :	efrank	1.1
2882 :			=cut
2883 :	parrello	1.213	#: Return Type $;
2884 :	efrank	1.1	sub reverse_comp {
2885 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2886 :	efrank	1.1	my($seq) = @_;
2887 :
2888 :			return ${&rev_comp(\$seq)};
2889 :			}
2890 :
2891 :	parrello	1.287	=head3 rev_comp
2892 :
2893 :			C<< my $dnaRP = FIG::rev_comp(\$dna); >>
2894 :
2895 :			or
2896 :
2897 :			C<< my $dnaRP = $fig->rev_comp(\$dna); >>
2898 :
2899 :			Return the reverse complement of the specified DNA sequence. The DNA sequence
2900 :			is passed in as a string reference rather than a raw string for performance
2901 :			reasons. If this is unnecessary, use L</reverse_comp>, which processes strings
2902 :			instead of references to strings.
2903 :
2904 :			=over 4
2905 :
2906 :			=item dna
2907 :
2908 :			Reference to the DNA sequence whose reverse complement is desired.
2909 :
2910 :			=item RETURN
2911 :
2912 :			Returns a reference to the reverse complement of the incoming DNA sequence.
2913 :
2914 :			=back
2915 :	parrello	1.213
2916 :			=cut
2917 :			#: Return Type $;
2918 :	efrank	1.1	sub rev_comp {
2919 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2920 :	efrank	1.1	my( $seqP ) = @_;
2921 :			my( $rev );
2922 :
2923 :			$rev = reverse( $$seqP );
2924 :	overbeek	1.317	$rev =~ tr/A-Z/a-z/;
2925 :			$rev =~ tr/acgtumrwsykbdhv/tgcaakywsrmvhdb/;
2926 :	efrank	1.1	return \$rev;
2927 :			}
2928 :
2929 :	overbeek	1.454	sub verify_external_tool {
2930 :			my(@progs) = @_;
2931 :
2932 :			my $prog;
2933 :			foreach $prog (@progs)
2934 :			{
2935 :			my @tmp = `which $prog`;
2936 :			if ($tmp[0] =~ /^no $prog/)
2937 :			{
2938 :			print STDERR $tmp[0];
2939 :			exit(1);
2940 :			}
2941 :			}
2942 :			}
2943 :
2944 :	parrello	1.287	=head3 verify_dir
2945 :
2946 :			C<< FIG::verify_dir($dir); >>
2947 :	efrank	1.1
2948 :	parrello	1.287	or
2949 :	efrank	1.1
2950 :	parrello	1.287	C<< $fig->verify_dir($dir); >>
2951 :	efrank	1.1
2952 :	parrello	1.287	Insure that the specified directory exists. If it must be created, the permissions will
2953 :			be set to C<0777>.
2954 :	efrank	1.1
2955 :			=cut
2956 :
2957 :			sub verify_dir {
2958 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2959 :	efrank	1.1	my($dir) = @_;
2960 :
2961 :	olson	1.416	if (!defined($dir))
2962 :			{
2963 :	parrello	1.485	Confess("FIG::verify_dir: missing \$dir argument\n");
2964 :	olson	1.416	}
2965 :			if ($dir eq "")
2966 :			{
2967 :	parrello	1.485	confess("FIG::verify_dir: refusing to create a directory named ''\n");
2968 :	olson	1.416	}
2969 :
2970 :	parrello	1.287	if (-d $dir) {
2971 :			return
2972 :			}
2973 :	olson	1.416	if ($dir =~ /^(.*)\/[^\/]+$/ and $1 ne '') {
2974 :	parrello	1.287	&verify_dir($1);
2975 :	efrank	1.1	}
2976 :	overbeek	1.522	mkdir($dir,0777) \|\| confess "Could not make directory $dir: $!";
2977 :	efrank	1.1	}
2978 :
2979 :	parrello	1.287	=head3 run
2980 :	efrank	1.1
2981 :	parrello	1.287	C<< FIG::run($cmd); >>
2982 :	overbeek	1.283
2983 :	parrello	1.287	or
2984 :
2985 :			C<< $fig->run($cmd); >>
2986 :	overbeek	1.283
2987 :	parrello	1.287	Run a command. If the command fails, the error will be traced.
2988 :	overbeek	1.283
2989 :			=cut
2990 :
2991 :	parrello	1.287	sub run {
2992 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2993 :			my($cmd) = @_;
2994 :
2995 :	overbeek	1.363	if ($ENV{FIG_VERBOSE}) {
2996 :	parrello	1.287	my @tmp = `date`;
2997 :			chomp @tmp;
2998 :			print STDERR "$tmp[0]: running $cmd\n";
2999 :			}
3000 :			Trace("Running command: $cmd") if T(3);
3001 :			(system($cmd) == 0) \|\| Confess("FAILED: $cmd");
3002 :			}
3003 :
3004 :	olson	1.388	=head3 run_gathering_output
3005 :
3006 :			C<< FIG::run_gathering_output($cmd, @args); >>
3007 :
3008 :			or
3009 :
3010 :			C<< $fig->run_gathering_output($cmd, @args); >>
3011 :
3012 :			Run a command, gathering the output. This is similar to the backtick
3013 :			operator, but it does not invoke the shell. Note that the argument list
3014 :	parrello	1.518	must be explicitly passed one command line argument per argument to
3015 :	olson	1.388	run_gathering_output.
3016 :
3017 :			If the command fails, the error will be traced.
3018 :
3019 :			=cut
3020 :
3021 :			sub run_gathering_output {
3022 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3023 :			my($cmd, @args) = @_;
3024 :
3025 :			#
3026 :			# Run the command in a safe fork-with-pipe/exec.
3027 :			#
3028 :
3029 :			my $pid = open(PROC_READ, "-\|");
3030 :
3031 :			if ($pid == 0)
3032 :			{
3033 :	parrello	1.485	exec { $cmd } $cmd, @args;
3034 :			die "could not execute $cmd @args: $!\n";
3035 :	olson	1.388	}
3036 :
3037 :			if (wantarray)
3038 :			{
3039 :	parrello	1.485	my @out;
3040 :			while (<PROC_READ>)
3041 :			{
3042 :			push(@out, $_);
3043 :			}
3044 :			if (!close(PROC_READ))
3045 :			{
3046 :			Confess("FAILED: $cmd @args with error return $?");
3047 :			}
3048 :			return @out;
3049 :	olson	1.388	}
3050 :			else
3051 :			{
3052 :	parrello	1.485	my $out = '';
3053 :	parrello	1.518
3054 :	parrello	1.485	while (<PROC_READ>)
3055 :			{
3056 :			$out .= $_;
3057 :			}
3058 :			if (!close(PROC_READ))
3059 :			{
3060 :			Confess("FAILED: $cmd @args with error return $?");
3061 :			}
3062 :			return $out;
3063 :	olson	1.388	}
3064 :			}
3065 :
3066 :	parrello	1.287	=head3 augment_path
3067 :
3068 :			C<< FIG::augment_path($dirName); >>
3069 :	overbeek	1.283
3070 :	parrello	1.287	Add a directory to the system path.
3071 :	overbeek	1.283
3072 :	parrello	1.287	This method adds a new directory to the front of the system path. It looks in the
3073 :			configuration file to determine whether this is Windows or Unix, and uses the
3074 :			appropriate separator.
3075 :	efrank	1.1
3076 :	parrello	1.287	=over 4
3077 :	efrank	1.1
3078 :	parrello	1.287	=item dirName
3079 :
3080 :			Name of the directory to add to the path.
3081 :
3082 :			=back
3083 :	efrank	1.1
3084 :			=cut
3085 :
3086 :	parrello	1.287	sub augment_path {
3087 :			my ($dirName) = @_;
3088 :			if ($FIG_Config::win_mode) {
3089 :			$ENV{PATH} = "$dirName;$ENV{PATH}";
3090 :			} else {
3091 :			$ENV{PATH} = "$dirName:$ENV{PATH}";
3092 :	overbeek	1.278	}
3093 :	efrank	1.1	}
3094 :
3095 :	parrello	1.287	=head3 read_fasta_record
3096 :	gdpusch	1.45
3097 :	parrello	1.287	C<< my ($seq_id, $seq_pointer, $comment) = FIG::read_fasta_record(\*FILEHANDLE); >>
3098 :	gdpusch	1.45
3099 :	parrello	1.287	or
3100 :	gdpusch	1.45
3101 :	parrello	1.287	C<< my ($seq_id, $seq_pointer, $comment) = $fig->read_fasta_record(\*FILEHANDLE); >>
3102 :	gdpusch	1.45
3103 :	parrello	1.287	Read and parse the next logical record of a FASTA file. A FASTA logical record
3104 :			consists of multiple lines of text. The first line begins with a C<< > >> symbol
3105 :			and contains the sequence ID followed by an optional comment. (NOTE: comments
3106 :			are currently deprecated, because not all tools handle them properly.) The
3107 :			remaining lines contain the sequence data.
3108 :
3109 :			This method uses a trick to smooth its operation: the line terminator character
3110 :			is temporarily changed to C<< \n> >> so that a single read operation brings in
3111 :			the entire logical record.
3112 :	gdpusch	1.45
3113 :	parrello	1.287	=over 4
3114 :	gdpusch	1.45
3115 :	parrello	1.287	=item FILEHANDLE
3116 :	gdpusch	1.45
3117 :	parrello	1.287	Open handle of the FASTA file. If not specified, C<STDIN> is assumed.
3118 :
3119 :			=item RETURN
3120 :
3121 :			If we are at the end of the file, returns C<undef>. Otherwise, returns a
3122 :			three-element list. The first element is the sequence ID, the second is
3123 :			a pointer to the sequence data (that is, a string reference as opposed to
3124 :			as string), and the third is the comment.
3125 :
3126 :			=back
3127 :	gdpusch	1.45
3128 :			=cut
3129 :	parrello	1.213	#: Return Type @;
3130 :	parrello	1.287	sub read_fasta_record {
3131 :
3132 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3133 :	gdpusch	1.45	my ($file_handle) = @_;
3134 :	parrello	1.287	my ($old_end_of_record, $fasta_record, @lines, $head, $sequence, $seq_id, $comment, @parsed_fasta_record);
3135 :	parrello	1.200
3136 :	gdpusch	1.45	if (not defined($file_handle)) { $file_handle = \*STDIN; }
3137 :	parrello	1.200
3138 :	gdpusch	1.45	$old_end_of_record = $/;
3139 :			$/ = "\n>";
3140 :	parrello	1.200
3141 :	parrello	1.287	if (defined($fasta_record = <$file_handle>)) {
3142 :			chomp $fasta_record;
3143 :			@lines = split( /\n/, $fasta_record );
3144 :			$head = shift @lines;
3145 :			$head =~ s/^>?//;
3146 :			$head =~ m/^(\S+)/;
3147 :			$seq_id = $1;
3148 :			if ($head =~ m/^\S+\s+(.*)$/) { $comment = $1; } else { $comment = ""; }
3149 :			$sequence = join( "", @lines );
3150 :			@parsed_fasta_record = ( $seq_id, \$sequence, $comment );
3151 :			} else {
3152 :			@parsed_fasta_record = ();
3153 :	gdpusch	1.45	}
3154 :	parrello	1.200
3155 :	gdpusch	1.45	$/ = $old_end_of_record;
3156 :	parrello	1.200
3157 :	gdpusch	1.45	return @parsed_fasta_record;
3158 :			}
3159 :
3160 :	parrello	1.287	=head3 display_id_and_seq
3161 :
3162 :			C<< FIG::display_id_and_seq($id_and_comment, $seqP, $fh); >>
3163 :
3164 :			or
3165 :
3166 :	parrello	1.355	C<< $fig->display_id_and_seq($id_and_comment, \$seqP, $fh); >>
3167 :	parrello	1.287
3168 :			Display a fasta ID and sequence to the specified open file. This method is designed
3169 :			to work well with L</read_fasta_sequence> and L</rev_comp>, because it takes as
3170 :			input a string pointer rather than a string. If the file handle is omitted it
3171 :			defaults to STDOUT.
3172 :
3173 :			The output is formatted into a FASTA record. The first line of the output is
3174 :			preceded by a C<< > >> symbol, and the sequence is split into 60-character
3175 :			chunks displayed one per line. Thus, this method can be used to produce
3176 :			FASTA files from data gathered by the rest of the system.
3177 :
3178 :			=over 4
3179 :
3180 :			=item id_and_comment
3181 :
3182 :			The sequence ID and (optionally) the comment from the sequence's FASTA record.
3183 :			The ID
3184 :	gdpusch	1.45
3185 :	parrello	1.287	=item seqP
3186 :	efrank	1.1
3187 :	parrello	1.287	Reference to a string containing the sequence. The sequence is automatically
3188 :			formatted into 60-character chunks displayed one per line.
3189 :	efrank	1.1
3190 :	parrello	1.287	=item fh
3191 :	efrank	1.1
3192 :	parrello	1.287	Open file handle to which the ID and sequence should be output. If omitted,
3193 :	parrello	1.355	C<\*STDOUT> is assumed.
3194 :	parrello	1.287
3195 :			=back
3196 :	efrank	1.1
3197 :			=cut
3198 :
3199 :	parrello	1.287	sub display_id_and_seq {
3200 :	mkubal	1.53
3201 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3202 :	parrello	1.287
3203 :	overbeek	1.326	my( $id, $seqP, $fh ) = @_;
3204 :	parrello	1.200
3205 :	efrank	1.1	if (! defined($fh) ) { $fh = \*STDOUT; }
3206 :	parrello	1.200
3207 :	efrank	1.1	print $fh ">$id\n";
3208 :	overbeek	1.326	&display_seq($seqP, $fh);
3209 :	efrank	1.1	}
3210 :
3211 :	parrello	1.355	=head3 display_seq
3212 :	parrello	1.287
3213 :	parrello	1.355	C<< FIG::display_seq(\$seqP, $fh); >>
3214 :	parrello	1.287
3215 :			or
3216 :
3217 :	parrello	1.355	C<< $fig->display_seq(\$seqP, $fh); >>
3218 :	parrello	1.287
3219 :			Display a fasta sequence to the specified open file. This method is designed
3220 :			to work well with L</read_fasta_sequence> and L</rev_comp>, because it takes as
3221 :			input a string pointer rather than a string. If the file handle is omitted it
3222 :			defaults to STDOUT.
3223 :
3224 :			The sequence is split into 60-character chunks displayed one per line for
3225 :			readability.
3226 :
3227 :			=over 4
3228 :
3229 :			=item seqP
3230 :
3231 :			Reference to a string containing the sequence.
3232 :
3233 :			=item fh
3234 :
3235 :			Open file handle to which the sequence should be output. If omitted,
3236 :			C<STDOUT> is assumed.
3237 :
3238 :			=back
3239 :
3240 :			=cut
3241 :
3242 :	efrank	1.1	sub display_seq {
3243 :	parrello	1.287
3244 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3245 :	parrello	1.287
3246 :	overbeek	1.326	my ( $seqP, $fh ) = @_;
3247 :	efrank	1.1	my ( $i, $n, $ln );
3248 :	parrello	1.200
3249 :	efrank	1.1	if (! defined($fh) ) { $fh = \*STDOUT; }
3250 :
3251 :	overbeek	1.326	$n = length($$seqP);
3252 :	efrank	1.1	# confess "zero-length sequence ???" if ( (! defined($n)) \|\| ($n == 0) );
3253 :	parrello	1.287	for ($i=0; ($i < $n); $i += 60) {
3254 :			if (($i + 60) <= $n) {
3255 :	overbeek	1.326	$ln = substr($$seqP,$i,60);
3256 :	parrello	1.287	} else {
3257 :	overbeek	1.326	$ln = substr($$seqP,$i,($n-$i));
3258 :	parrello	1.287	}
3259 :			print $fh "$ln\n";
3260 :	efrank	1.1	}
3261 :			}
3262 :
3263 :	overbeek	1.529
3264 :			=head3 flatten_dumper
3265 :
3266 :			C<< FIG::flatten_dumper( $perl_ref_or_object_1, ... ); >>
3267 :
3268 :			C<< $fig->flatten_dumper( $perl_ref_or_object_1, ... ); >>
3269 :
3270 :			Takes a list of perl references or objects, and "flattens" their Data::Dumper() output
3271 :			so that it can be printed on a single line.
3272 :
3273 :			=cut
3274 :
3275 :			sub flatten_dumper {
3276 :			my @x = @_;
3277 :			my $x;
3278 :
3279 :			foreach $x (@x)
3280 :			{
3281 :			$x = Dumper($x);
3282 :
3283 :			$x =~ s/\$VAR\d+\s+\=\s+//o;
3284 :			$x =~ s/\n//gso;
3285 :			$x =~ s/\s+/ /go;
3286 :			$x =~ s/\'//go;
3287 :			# $x =~ s/^[^\(\[\{]+//o;
3288 :			# $x =~ s/[^\)\]\}]+$//o;
3289 :			}
3290 :
3291 :			return @x;
3292 :			}
3293 :
3294 :
3295 :	efrank	1.1	########## I commented the pods on the following routines out, since they should not
3296 :			########## be part of the SOAP/WSTL interface
3297 :			#=pod
3298 :			#
3299 :	parrello	1.287	#=head3 file2N
3300 :	efrank	1.1	#
3301 :			#usage: $n = $fig->file2N($file)
3302 :			#
3303 :			#In some of the databases I need to store filenames, which can waste a lot of
3304 :			#space. Hence, I maintain a database for converting filenames to/from integers.
3305 :			#
3306 :			#=cut
3307 :			#
3308 :	parrello	1.328	sub file2N :Scalar {
3309 :	efrank	1.1	my($self,$file) = @_;
3310 :			my($relational_db_response);
3311 :
3312 :			my $rdbH = $self->db_handle;
3313 :
3314 :	olson	1.403	#
3315 :			# Strip the figdisk path from the file. N2file replaces it if the path
3316 :			# in the database is relative.
3317 :			#
3318 :			$file =~ s,^$FIG_Config::fig_disk/,,;
3319 :
3320 :	efrank	1.1	if (($relational_db_response = $rdbH->SQL("SELECT fileno FROM file_table WHERE ( file = \'$file\')")) &&
3321 :	parrello	1.298	(@$relational_db_response == 1)) {
3322 :	parrello	1.287	return $relational_db_response->[0]->[0];
3323 :			} elsif (($relational_db_response = $rdbH->SQL("SELECT MAX(fileno) FROM file_table ")) && (@$relational_db_response == 1) && ($relational_db_response->[0]->[0])) {
3324 :			my $fileno = $relational_db_response->[0]->[0] + 1;
3325 :			if ($rdbH->SQL("INSERT INTO file_table ( file, fileno ) VALUES ( \'$file\', $fileno )")) {
3326 :			return $fileno;
3327 :			}
3328 :			} elsif ($rdbH->SQL("INSERT INTO file_table ( file, fileno ) VALUES ( \'$file\', 1 )")) {
3329 :			return 1;
3330 :	efrank	1.1	}
3331 :			return undef;
3332 :			}
3333 :
3334 :			#=pod
3335 :			#
3336 :	parrello	1.287	#=head3 N2file
3337 :	efrank	1.1	#
3338 :			#usage: $filename = $fig->N2file($n)
3339 :			#
3340 :			#In some of the databases I need to store filenames, which can waste a lot of
3341 :			#space. Hence, I maintain a database for converting filenames to/from integers.
3342 :			#
3343 :			#=cut
3344 :			#
3345 :	overbeek	1.364	sub N2file :Scalar
3346 :			{
3347 :	efrank	1.1	my($self,$fileno) = @_;
3348 :	overbeek	1.364
3349 :			#
3350 :			# Cache outputs. This results in a huge savings of time when files are
3351 :			# accessed multiple times (as in when a bunch of sims are requested).
3352 :			#
3353 :
3354 :			my $fcache = $self->cached("_n2file");
3355 :	parrello	1.379
3356 :	overbeek	1.364	my $fname;
3357 :			if (defined($fname = $fcache->{$fileno}))
3358 :			{
3359 :	parrello	1.365	return $fname;
3360 :	overbeek	1.364	}
3361 :	efrank	1.1
3362 :			my $rdbH = $self->db_handle;
3363 :	parrello	1.379
3364 :	overbeek	1.364	my $relational_db_response = $rdbH->SQL("SELECT file FROM file_table WHERE ( fileno = $fileno )");
3365 :	efrank	1.1
3366 :	overbeek	1.364	if ($relational_db_response and @$relational_db_response == 1)
3367 :			{
3368 :	parrello	1.365	$fname = $relational_db_response->[0]->[0];
3369 :	olson	1.403
3370 :	parrello	1.420	#
3371 :			# If $fname is relative, prepend the base of the fig_disk.
3372 :			# (Updated to use PERL's system-independent filename utilities.
3373 :			#
3374 :	parrello	1.518
3375 :	parrello	1.420	$fname = File::Spec->rel2abs($fname, $FIG_Config::fig_disk);
3376 :	parrello	1.518
3377 :	parrello	1.365	$fcache->{$fileno} = $fname;
3378 :			return $fname;
3379 :	efrank	1.1	}
3380 :			return undef;
3381 :			}
3382 :
3383 :
3384 :			#=pod
3385 :			#
3386 :	parrello	1.287	#=head3 openF
3387 :	efrank	1.1	#
3388 :			#usage: $fig->openF($filename)
3389 :			#
3390 :			#Parts of the system rely on accessing numerous different files. The most obvious case is
3391 :			#the situation with similarities. It is important that the system be able to run in cases in
3392 :			#which an arbitrary number of files cannot be open simultaneously. This routine (with closeF) is
3393 :			#a hack to handle this. I should probably just pitch them and insist that the OS handle several
3394 :			#hundred open filehandles.
3395 :			#
3396 :			#=cut
3397 :			#
3398 :			sub openF {
3399 :			my($self,$file) = @_;
3400 :			my($fxs,$x,@fxs,$fh);
3401 :
3402 :			$fxs = $self->cached('_openF');
3403 :	parrello	1.287	if ($x = $fxs->{$file}) {
3404 :			$x->[1] = time();
3405 :			return $x->[0];
3406 :	efrank	1.1	}
3407 :	parrello	1.200
3408 :	efrank	1.1	@fxs = keys(%$fxs);
3409 :	parrello	1.287	if (defined($fh = new FileHandle "<$file")) {
3410 :			if (@fxs >= 50) {
3411 :			@fxs = sort { $fxs->{$a}->[1] <=> $fxs->{$b}->[1] } @fxs;
3412 :			$x = $fxs->{$fxs[0]};
3413 :			undef $x->[0];
3414 :			delete $fxs->{$fxs[0]};
3415 :			}
3416 :			$fxs->{$file} = [$fh,time()];
3417 :			return $fh;
3418 :	efrank	1.1	}
3419 :			return undef;
3420 :			}
3421 :
3422 :			#=pod
3423 :			#
3424 :	parrello	1.287	#=head3 closeF
3425 :	efrank	1.1	#
3426 :			#usage: $fig->closeF($filename)
3427 :			#
3428 :			#Parts of the system rely on accessing numerous different files. The most obvious case is
3429 :			#the situation with similarities. It is important that the system be able to run in cases in
3430 :			#which an arbitrary number of files cannot be open simultaneously. This routine (with openF) is
3431 :			#a hack to handle this. I should probably just pitch them and insist that the OS handle several
3432 :			#hundred open filehandles.
3433 :			#
3434 :			#=cut
3435 :			#
3436 :			sub closeF {
3437 :			my($self,$file) = @_;
3438 :			my($fxs,$x);
3439 :
3440 :	parrello	1.287	if (($fxs = $self->{_openF}) && ($x = $fxs->{$file})) {
3441 :			undef $x->[0];
3442 :			delete $fxs->{$file};
3443 :	efrank	1.1	}
3444 :			}
3445 :
3446 :	parrello	1.287	=head3 ec_name
3447 :
3448 :			C<< my $enzymatic_function = $fig->ec_name($ec); >>
3449 :	efrank	1.1
3450 :	parrello	1.287	Returns the enzymatic name corresponding to the specified enzyme code.
3451 :	efrank	1.1
3452 :	parrello	1.287	=over 4
3453 :
3454 :			=item ec
3455 :	efrank	1.1
3456 :	parrello	1.287	Code number for the enzyme whose name is desired. The code number is actually
3457 :			a string of digits and periods (e.g. C<1.2.50.6>).
3458 :
3459 :			=item RETURN
3460 :
3461 :			Returns the name of the enzyme specified by the indicated code, or a null string
3462 :			if the code is not found in the database.
3463 :
3464 :			=back
3465 :	efrank	1.1
3466 :			=cut
3467 :
3468 :			sub ec_name {
3469 :			my($self,$ec) = @_;
3470 :
3471 :			($ec =~ /^\d+\.\d+\.\d+\.\d+$/) \|\| return "";
3472 :			my $rdbH = $self->db_handle;
3473 :			my $relational_db_response = $rdbH->SQL("SELECT name FROM ec_names WHERE ( ec = \'$ec\' )");
3474 :
3475 :			return (@$relational_db_response == 1) ? $relational_db_response->[0]->[0] : "";
3476 :			return "";
3477 :			}
3478 :
3479 :	parrello	1.287	=head3 all_roles
3480 :	efrank	1.1
3481 :	parrello	1.287	C<< my @roles = $fig->all_roles; >>
3482 :	efrank	1.1
3483 :	parrello	1.287	Return a list of the known roles. Currently, this is a list of the enzyme codes and names.
3484 :	efrank	1.1
3485 :	parrello	1.287	The return value is a list of list references. Each element of the big list contains an
3486 :			enzyme code (EC) followed by the enzymatic name.
3487 :	efrank	1.1
3488 :			=cut
3489 :
3490 :			sub all_roles {
3491 :			my($self) = @_;
3492 :
3493 :			my $rdbH = $self->db_handle;
3494 :			my $relational_db_response = $rdbH->SQL("SELECT ec,name FROM ec_names");
3495 :
3496 :			return @$relational_db_response;
3497 :			}
3498 :
3499 :	parrello	1.287	=head3 expand_ec
3500 :	efrank	1.1
3501 :	parrello	1.287	C<< my $expanded_ec = $fig->expand_ec($ec); >>
3502 :	efrank	1.1
3503 :			Expands "1.1.1.1" to "1.1.1.1 - alcohol dehydrogenase" or something like that.
3504 :
3505 :			=cut
3506 :
3507 :			sub expand_ec {
3508 :			my($self,$ec) = @_;
3509 :			my($name);
3510 :
3511 :			return ($name = $self->ec_name($ec)) ? "$ec - $name" : $ec;
3512 :			}
3513 :
3514 :	parrello	1.287	=head3 clean_tmp
3515 :	efrank	1.1
3516 :	parrello	1.287	C<< FIG::clean_tmp(); >>
3517 :	efrank	1.1
3518 :	parrello	1.287	Delete temporary files more than two days old.
3519 :	efrank	1.1
3520 :			We store temporary files in $FIG_Config::temp. There are specific classes of files
3521 :			that are created and should be saved for at least a few days. This routine can be
3522 :			invoked to clean out those that are over two days old.
3523 :
3524 :			=cut
3525 :
3526 :			sub clean_tmp {
3527 :
3528 :			my($file);
3529 :	parrello	1.287	if (opendir(TMP,"$FIG_Config::temp")) {
3530 :			# change the pattern to pick up other files that need to be cleaned up
3531 :			my @temp = grep { $_ =~ /^(Geno\|tmp)/ } readdir(TMP);
3532 :			foreach $file (@temp) {
3533 :			if (-M "$FIG_Config::temp/$file" > 2) {
3534 :			unlink("$FIG_Config::temp/$file");
3535 :			}
3536 :			}
3537 :	efrank	1.1	}
3538 :			}
3539 :
3540 :			################ Routines to process genomes and genome IDs ##########################
3541 :
3542 :
3543 :	parrello	1.287	=head3 genomes
3544 :	efrank	1.1
3545 :	parrello	1.287	C<< my @genome_ids = $fig->genomes($complete, $restrictions, $domain); >>
3546 :	efrank	1.1
3547 :	parrello	1.287	Return a list of genome IDs. If called with no parameters, all genome IDs
3548 :			in the database will be returned.
3549 :	efrank	1.1
3550 :			Genomes are assigned ids of the form X.Y where X is the taxonomic id maintained by
3551 :			NCBI for the species (not the specific strain), and Y is a sequence digit assigned to
3552 :			this particular genome (as one of a set with the same genus/species). Genomes also
3553 :			have versions, but that is a separate issue.
3554 :
3555 :	parrello	1.287	=over 4
3556 :
3557 :			=item complete
3558 :
3559 :			TRUE if only complete genomes should be returned, else FALSE.
3560 :
3561 :			=item restrictions
3562 :
3563 :			TRUE if only restriction genomes should be returned, else FALSE.
3564 :
3565 :			=item domain
3566 :
3567 :			Name of the domain from which the genomes should be returned. Possible values are
3568 :			C<Bacteria>, C<Virus>, C<Eukaryota>, C<unknown>, C<Archaea>, and
3569 :			C<Environmental Sample>. If no domain is specified, all domains will be
3570 :			eligible.
3571 :
3572 :			=item RETURN
3573 :
3574 :			Returns a list of all the genome IDs with the specified characteristics.
3575 :
3576 :			=back
3577 :
3578 :	efrank	1.1	=cut
3579 :	parrello	1.320	#: Return Type @;
3580 :	parrello	1.328	sub genomes :Remote :List {
3581 :	golsen	1.150	my( $self, $complete, $restrictions, $domain ) = @_;
3582 :	overbeek	1.13
3583 :			my $rdbH = $self->db_handle;
3584 :
3585 :			my @where = ();
3586 :	parrello	1.287	if ($complete) {
3587 :			push(@where, "( complete = \'1\' )")
3588 :	overbeek	1.13	}
3589 :
3590 :	parrello	1.287	if ($restrictions) {
3591 :			push(@where, "( restrictions = \'1\' )")
3592 :	overbeek	1.13	}
3593 :	golsen	1.150
3594 :	parrello	1.287	if ($domain) {
3595 :			push( @where, "( maindomain = '$domain' )" )
3596 :	golsen	1.150	}
3597 :
3598 :	overbeek	1.13	my $relational_db_response;
3599 :	parrello	1.287	if (@where > 0) {
3600 :			my $where = join(" AND ",@where);
3601 :			$relational_db_response = $rdbH->SQL("SELECT genome FROM genome where $where");
3602 :			} else {
3603 :			$relational_db_response = $rdbH->SQL("SELECT genome FROM genome");
3604 :	overbeek	1.13	}
3605 :			my @genomes = sort { $a <=> $b } map { $_->[0] } @$relational_db_response;
3606 :	efrank	1.1	return @genomes;
3607 :			}
3608 :
3609 :	parrello	1.287	=head3 is_complete
3610 :
3611 :			C<< my $flag = $fig->is_complete($genome); >>
3612 :
3613 :			Return TRUE if the genome with the specified ID is complete, else FALSE.
3614 :
3615 :			=over 4
3616 :
3617 :			=item genome
3618 :
3619 :			ID of the relevant genome.
3620 :
3621 :			=item RETURN
3622 :
3623 :			Returns TRUE if there is a complete genome in the database with the specified ID,
3624 :			else FALSE.
3625 :
3626 :			=back
3627 :
3628 :			=cut
3629 :
3630 :	overbeek	1.180	sub is_complete {
3631 :			my($self,$genome) = @_;
3632 :
3633 :			my $rdbH = $self->db_handle;
3634 :			my $relational_db_response = $rdbH->SQL("SELECT genome FROM genome where (genome = '$genome') AND (complete = '1')");
3635 :			return (@$relational_db_response == 1)
3636 :	parrello	1.287	}
3637 :
3638 :	parrello	1.490	=head3 is_genome
3639 :
3640 :			C<< my $flag = $fig->is_genome($genome); >>
3641 :
3642 :			Return TRUE if the specified genome exists, else FALSE.
3643 :
3644 :			=over 4
3645 :
3646 :			=item genome
3647 :
3648 :			ID of the genome to test.
3649 :
3650 :			=item RETURN
3651 :
3652 :			Returns TRUE if a genome with the specified ID exists in the data store, else FALSE.
3653 :
3654 :			=back
3655 :
3656 :			=cut
3657 :
3658 :	overbeek	1.421	sub is_genome {
3659 :			my($self,$genome) = @_;
3660 :			my($x,$y);
3661 :
3662 :			if (! ($x = $self->{_is_genome}))
3663 :			{
3664 :			$x = $self->{_is_genome} = {};
3665 :			}
3666 :
3667 :			if (defined($y = $x->{$genome})) { return $y }
3668 :			my $rdbH = $self->db_handle;
3669 :			my $relational_db_response = $rdbH->SQL("SELECT genome FROM genome where (genome = '$genome')");
3670 :			$y = (@$relational_db_response == 1);
3671 :			$x->{$genome} = $y;
3672 :			return $y;
3673 :			}
3674 :
3675 :	parrello	1.287	=head3 genome_counts
3676 :
3677 :			C<< my ($arch, $bact, $euk, $vir, $env, $unk) = $fig->genome_counts($complete); >>
3678 :
3679 :			Count the number of genomes in each domain. If I<$complete> is TRUE, only complete
3680 :			genomes will be included in the counts.
3681 :
3682 :			=over 4
3683 :
3684 :			=item complete
3685 :
3686 :			TRUE if only complete genomes are to be counted, FALSE if all genomes are to be
3687 :			counted
3688 :
3689 :			=item RETURN
3690 :
3691 :			A six-element list containing the number of genomes in each of six categories--
3692 :			Archaea, Bacteria, Eukaryota, Viral, Environmental, and Unknown, respectively.
3693 :
3694 :			=back
3695 :
3696 :			=cut
3697 :	golsen	1.150
3698 :	efrank	1.2	sub genome_counts {
3699 :	overbeek	1.13	my($self,$complete) = @_;
3700 :			my($x,$relational_db_response);
3701 :	efrank	1.2
3702 :	overbeek	1.13	my $rdbH = $self->db_handle;
3703 :
3704 :	parrello	1.287	if ($complete) {
3705 :			$relational_db_response = $rdbH->SQL("SELECT genome, maindomain FROM genome where complete = '1'");
3706 :			} else {
3707 :			$relational_db_response = $rdbH->SQL("SELECT genome,maindomain FROM genome");
3708 :	overbeek	1.13	}
3709 :
3710 :	gdpusch	1.107	my ($arch, $bact, $euk, $vir, $env, $unk) = (0, 0, 0, 0, 0, 0);
3711 :	parrello	1.287	if (@$relational_db_response > 0) {
3712 :			foreach $x (@$relational_db_response) {
3713 :			if ($x->[1] =~ /^archaea/i) { ++$arch }
3714 :			elsif ($x->[1] =~ /^bacter/i) { ++$bact }
3715 :			elsif ($x->[1] =~ /^eukar/i) { ++$euk }
3716 :			elsif ($x->[1] =~ /^vir/i) { ++$vir }
3717 :			elsif ($x->[1] =~ /^env/i) { ++$env }
3718 :			else { ++$unk }
3719 :	parrello	1.298	}
3720 :	efrank	1.2	}
3721 :	parrello	1.200
3722 :	gdpusch	1.107	return ($arch, $bact, $euk, $vir, $env, $unk);
3723 :			}
3724 :
3725 :
3726 :	parrello	1.287	=head3 genome_domain
3727 :
3728 :			C<< my $domain = $fig->genome_domain($genome_id); >>
3729 :
3730 :			Find the domain of a genome.
3731 :	gdpusch	1.107
3732 :	parrello	1.287	=over 4
3733 :
3734 :			=item genome_id
3735 :	gdpusch	1.107
3736 :	parrello	1.287	ID of the genome whose domain is desired.
3737 :	gdpusch	1.107
3738 :	parrello	1.287	=item RETURN
3739 :
3740 :			Returns the name of the genome's domain (archaea, bacteria, etc.), or C<undef> if
3741 :			the genome is not in the database.
3742 :	gdpusch	1.107
3743 :	parrello	1.292	=back
3744 :
3745 :	gdpusch	1.107	=cut
3746 :
3747 :			sub genome_domain {
3748 :			my($self,$genome) = @_;
3749 :			my $relational_db_response;
3750 :			my $rdbH = $self->db_handle;
3751 :	parrello	1.200
3752 :	parrello	1.287	if ($genome) {
3753 :			if (($relational_db_response = $rdbH->SQL("SELECT genome,maindomain FROM genome WHERE ( genome = \'$genome\' )"))
3754 :			&& (@$relational_db_response == 1)) {
3755 :			# die Dumper($relational_db_response);
3756 :			return $relational_db_response->[0]->[1];
3757 :			}
3758 :	gdpusch	1.107	}
3759 :			return undef;
3760 :	efrank	1.2	}
3761 :
3762 :	gdpusch	1.92
3763 :	parrello	1.287	=head3 genome_pegs
3764 :	gdpusch	1.92
3765 :	parrello	1.287	C<< my $num_pegs = $fig->genome_pegs($genome_id); >>
3766 :	gdpusch	1.92
3767 :	parrello	1.287	Return the number of protein-encoding genes (PEGs) for a specified
3768 :			genome.
3769 :	gdpusch	1.92
3770 :	parrello	1.287	=over 4
3771 :
3772 :			=item genome_id
3773 :
3774 :			ID of the genome whose PEG count is desired.
3775 :
3776 :			=item RETURN
3777 :
3778 :			Returns the number of PEGs for the specified genome, or C<undef> if the genome
3779 :			is not indexed in the database.
3780 :
3781 :			=back
3782 :	gdpusch	1.92
3783 :			=cut
3784 :
3785 :			sub genome_pegs {
3786 :			my($self,$genome) = @_;
3787 :			my $relational_db_response;
3788 :			my $rdbH = $self->db_handle;
3789 :	parrello	1.200
3790 :	parrello	1.287	if ($genome) {
3791 :			if (($relational_db_response = $rdbH->SQL("SELECT pegs FROM genome WHERE ( genome = \'$genome\' )"))
3792 :			&& (@$relational_db_response == 1)) {
3793 :			return $relational_db_response->[0]->[0];
3794 :			}
3795 :	gdpusch	1.92	}
3796 :			return undef;
3797 :			}
3798 :
3799 :
3800 :	parrello	1.287	=head3 genome_rnas
3801 :
3802 :			C<< my $num_rnas = $fig->genome_rnas($genome_id); >>
3803 :
3804 :			Return the number of RNA-encoding genes for a genome.
3805 :			"$genome_id" is indexed in the "genome" database, and 'undef' otherwise.
3806 :	efrank	1.1
3807 :	parrello	1.287	=over 4
3808 :
3809 :			=item genome_id
3810 :
3811 :			ID of the genome whose RNA count is desired.
3812 :
3813 :			=item RETURN
3814 :	gdpusch	1.92
3815 :	parrello	1.287	Returns the number of RNAs for the specified genome, or C<undef> if the genome
3816 :			is not indexed in the database.
3817 :	gdpusch	1.92
3818 :	parrello	1.287	=back
3819 :	gdpusch	1.92
3820 :			=cut
3821 :
3822 :			sub genome_rnas {
3823 :			my($self,$genome) = @_;
3824 :			my $relational_db_response;
3825 :			my $rdbH = $self->db_handle;
3826 :	parrello	1.200
3827 :	parrello	1.287	if ($genome) {
3828 :			if (($relational_db_response = $rdbH->SQL("SELECT rnas FROM genome WHERE ( genome = \'$genome\' )"))
3829 :			&& (@$relational_db_response == 1)) {
3830 :			return $relational_db_response->[0]->[0];
3831 :			}
3832 :	gdpusch	1.92	}
3833 :			return undef;
3834 :			}
3835 :
3836 :
3837 :	parrello	1.287	=head3 genome_szdna
3838 :
3839 :			usage: $szdna = $fig->genome_szdna($genome_id);
3840 :
3841 :			Return the number of DNA base-pairs in a genome's contigs.
3842 :
3843 :			=over 4
3844 :
3845 :			=item genome_id
3846 :
3847 :			ID of the genome whose base-pair count is desired.
3848 :	gdpusch	1.92
3849 :	parrello	1.287	=item RETURN
3850 :	efrank	1.1
3851 :	parrello	1.287	Returns the number of base pairs in the specified genome's contigs, or C<undef>
3852 :			if the genome is not indexed in the database.
3853 :	gdpusch	1.91
3854 :	parrello	1.287	=back
3855 :	gdpusch	1.91
3856 :			=cut
3857 :
3858 :	gdpusch	1.92	sub genome_szdna {
3859 :	gdpusch	1.91	my($self,$genome) = @_;
3860 :			my $relational_db_response;
3861 :			my $rdbH = $self->db_handle;
3862 :	parrello	1.200
3863 :	parrello	1.287	if ($genome) {
3864 :			if (($relational_db_response =
3865 :			$rdbH->SQL("SELECT szdna FROM genome WHERE ( genome = \'$genome\' )"))
3866 :			&& (@$relational_db_response == 1)) {
3867 :
3868 :			return $relational_db_response->[0]->[0];
3869 :
3870 :			}
3871 :	gdpusch	1.91	}
3872 :			return undef;
3873 :			}
3874 :
3875 :	parrello	1.287	=head3 genome_version
3876 :	gdpusch	1.91
3877 :	parrello	1.287	C<< my $version = $fig->genome_version($genome_id); >>
3878 :	gdpusch	1.91
3879 :	parrello	1.287	Return the version number of the specified genome.
3880 :	efrank	1.1
3881 :			Versions are incremented for major updates. They are put in as major
3882 :			updates of the form 1.0, 2.0, ...
3883 :
3884 :			Users may do local "editing" of the DNA for a genome, but when they do,
3885 :			they increment the digits to the right of the decimal. Two genomes remain
3886 :	parrello	1.200	comparable only if the versions match identically. Hence, minor updating should be
3887 :	efrank	1.1	committed only by the person/group responsible for updating that genome.
3888 :
3889 :			We can, of course, identify which genes are identical between any two genomes (by matching
3890 :			the DNA or amino acid sequences). However, the basic intent of the system is to
3891 :			support editing by the main group issuing periodic major updates.
3892 :
3893 :	parrello	1.287	=over 4
3894 :
3895 :			=item genome_id
3896 :
3897 :			ID of the genome whose version is desired.
3898 :
3899 :			=item RETURN
3900 :
3901 :			Returns the version number of the specified genome, or C<undef> if the genome is not in
3902 :			the data store or no version number has been assigned.
3903 :
3904 :			=back
3905 :
3906 :	efrank	1.1	=cut
3907 :
3908 :	parrello	1.328	sub genome_version :Scalar {
3909 :	efrank	1.1	my($self,$genome) = @_;
3910 :
3911 :			my(@tmp);
3912 :			if ((-s "$FIG_Config::organisms/$genome/VERSION") &&
3913 :	parrello	1.298	(@tmp = `cat $FIG_Config::organisms/$genome/VERSION`) &&
3914 :			($tmp[0] =~ /^(\S+)$/)) {
3915 :			return $1;
3916 :	efrank	1.1	}
3917 :			return undef;
3918 :			}
3919 :
3920 :	parrello	1.287	=head3 genome_md5sum
3921 :	olson	1.236
3922 :	parrello	1.287	C<< my $md5sum = $fig->genome_md5sum($genome_id); >>
3923 :	olson	1.236
3924 :	parrello	1.287	Returns the MD5 checksum of the specified genome.
3925 :	olson	1.236
3926 :			The checksum of a genome is defined as the checksum of its signature file. The signature
3927 :			file consists of tab-separated lines, one for each contig, ordered by the contig id.
3928 :	parrello	1.287	Each line contains the contig ID, the length of the contig in nucleotides, and the
3929 :	olson	1.236	MD5 checksum of the nucleotide data, with uppercase letters forced to lower case.
3930 :
3931 :	parrello	1.287	The checksum is indexed in the database. If you know a genome's checksum, you can use
3932 :			the L</genome_with_md5sum> method to find its ID in the database.
3933 :
3934 :			=over 4
3935 :
3936 :			=item genome
3937 :
3938 :			ID of the genome whose checksum is desired.
3939 :
3940 :			=item RETURN
3941 :
3942 :			Returns the specified genome's checksum, or C<undef> if the genome is not in the
3943 :			database.
3944 :
3945 :			=back
3946 :	olson	1.236
3947 :			=cut
3948 :
3949 :	parrello	1.328	sub genome_md5sum :Scalar {
3950 :	olson	1.236	my($self,$genome) = @_;
3951 :			my $relational_db_response;
3952 :			my $rdbH = $self->db_handle;
3953 :
3954 :	parrello	1.287	if ($genome) {
3955 :			if (($relational_db_response =
3956 :			$rdbH->SQL("SELECT md5sum FROM genome_md5sum WHERE ( genome = \'$genome\' )"))
3957 :			&& (@$relational_db_response == 1)) {
3958 :			return $relational_db_response->[0]->[0];
3959 :			}
3960 :	olson	1.236	}
3961 :			return undef;
3962 :			}
3963 :
3964 :	parrello	1.287	=head3 genome_with_md5sum
3965 :
3966 :			C<< my $genome = $fig->genome_with_md5sum($cksum); >>
3967 :
3968 :			Find a genome with the specified checksum.
3969 :
3970 :			The MD5 checksum is computed from the content of the genome (see L</genome_md5sum>). This method
3971 :			can be used to determine if a genome already exists for a specified content.
3972 :
3973 :			=over 4
3974 :
3975 :			=item cksum
3976 :
3977 :			Checksum to use for searching the genome table.
3978 :	olson	1.260
3979 :	parrello	1.287	=item RETURN
3980 :
3981 :			The ID of a genome with the specified checksum, or C<undef> if no such genome exists.
3982 :	olson	1.260
3983 :	parrello	1.287	=back
3984 :	olson	1.260
3985 :			=cut
3986 :
3987 :	parrello	1.328	sub genome_with_md5sum :Scalar {
3988 :	olson	1.260	my($self,$cksum) = @_;
3989 :			my $relational_db_response;
3990 :			my $rdbH = $self->db_handle;
3991 :
3992 :	parrello	1.287	if (($relational_db_response =
3993 :			$rdbH->SQL("SELECT genome FROM genome_md5sum WHERE ( md5sum = \'$cksum\' )"))
3994 :	parrello	1.298	&& (@$relational_db_response == 1)) {
3995 :			return $relational_db_response->[0]->[0];
3996 :	olson	1.260	}
3997 :
3998 :			return undef;
3999 :			}
4000 :
4001 :	parrello	1.287	=head3 contig_md5sum
4002 :
4003 :			C<< my $cksum = $fig->contig_md5sum($genome, $contig); >>
4004 :
4005 :			Return the MD5 checksum for a contig. The MD5 checksum is computed from the content
4006 :			of the contig. This method retrieves the checksum stored in the database. The checksum
4007 :			can be compared to the checksum of an external contig as a cheap way of seeing if they
4008 :			match.
4009 :
4010 :			=over 4
4011 :
4012 :			=item genome
4013 :
4014 :			ID of the genome containing the contig.
4015 :
4016 :			=item contig
4017 :
4018 :			ID of the relevant contig.
4019 :
4020 :			=item RETURN
4021 :
4022 :			Returns the checksum of the specified contig, or C<undef> if the contig is not in the
4023 :			database.
4024 :
4025 :			=back
4026 :
4027 :			=cut
4028 :
4029 :	parrello	1.328	sub contig_md5sum :Scalar {
4030 :	olson	1.237	my($self, $genome, $contig) = @_;
4031 :			my $relational_db_response;
4032 :			my $rdbH = $self->db_handle;
4033 :
4034 :	parrello	1.287	if ($genome) {
4035 :			if (($relational_db_response =
4036 :			$rdbH->SQL(qq(SELECT md5 FROM contig_md5sums WHERE (genome = ? AND contig = ?)), undef, $genome, $contig))
4037 :			&& (@$relational_db_response == 1)) {
4038 :			return $relational_db_response->[0]->[0];
4039 :			}
4040 :	olson	1.237	}
4041 :			return undef;
4042 :			}
4043 :
4044 :	parrello	1.287	=head3 genus_species
4045 :
4046 :			C<< my $gs = $fig->genus_species($genome_id); >>
4047 :
4048 :			Return the genus, species, and possibly also the strain of a specified genome.
4049 :
4050 :			This method converts a genome ID into a more recognizble species name. The species name
4051 :			is stored directly in the genome table of the database. Essentially, if the strain is
4052 :			present in the database, it will be returned by this method, and if it's not present,
4053 :			it won't.
4054 :	efrank	1.1
4055 :	parrello	1.287	=over 4
4056 :
4057 :			=item genome_id
4058 :
4059 :			ID of the genome whose name is desired.
4060 :	efrank	1.1
4061 :	parrello	1.287	=item RETURN
4062 :
4063 :			Returns the scientific species name associated with the specified ID, or C<undef> if the
4064 :			ID is not in the database.
4065 :	efrank	1.1
4066 :	parrello	1.287	=back
4067 :	efrank	1.1
4068 :			=cut
4069 :	parrello	1.320	#: Return Type $;
4070 :	parrello	1.328	sub genus_species :Scalar {
4071 :	efrank	1.1	my ($self,$genome) = @_;
4072 :	overbeek	1.13	my $ans;
4073 :	efrank	1.1
4074 :			my $genus_species = $self->cached('_genus_species');
4075 :	parrello	1.287	if (! ($ans = $genus_species->{$genome})) {
4076 :			my $rdbH = $self->db_handle;
4077 :			my $relational_db_response = $rdbH->SQL("SELECT genome,gname FROM genome");
4078 :			my $pair;
4079 :			foreach $pair (@$relational_db_response) {
4080 :			$genus_species->{$pair->[0]} = $pair->[1];
4081 :			}
4082 :			$ans = $genus_species->{$genome};
4083 :	parrello	1.485	if ((! $ans) && open(GEN,"<$FIG_Config::organisms/$genome/GENOME"))
4084 :			{
4085 :			$ans = <GEN>;
4086 :			close(GEN);
4087 :			chomp $ans;
4088 :			$genus_species->{$genome} = $ans;
4089 :			}
4090 :	efrank	1.1	}
4091 :			return $ans;
4092 :			}
4093 :
4094 :	parrello	1.287	=head3 org_of
4095 :
4096 :			C<< my $org = $fig->org_of($prot_id); >>
4097 :
4098 :			Return the genus/species name of the organism containing a protein. Note that in this context
4099 :			I<protein> is not a certain string of amino acids but a protein encoding region on a specific
4100 :			contig.
4101 :
4102 :			For a FIG protein ID (e.g. C<fig\|134537.1.peg.123>), the organism and strain
4103 :			information is always available. In the case of external proteins, we can usually
4104 :			determine an organism, but not anything more precise than genus/species (and
4105 :			often not that). When the organism name is not present, a null string is returned.
4106 :
4107 :			=over 4
4108 :
4109 :			=item prot_id
4110 :	efrank	1.1
4111 :	parrello	1.287	Protein or feature ID.
4112 :	efrank	1.1
4113 :	parrello	1.287	=item RETURN
4114 :
4115 :			Returns the displayable scientific name (genus, species, and strain) of the organism containing
4116 :			the identified PEG. If the name is not available, returns a null string. If the PEG is not found,
4117 :			returns C<undef>.
4118 :	efrank	1.1
4119 :	parrello	1.287	=back
4120 :	efrank	1.1
4121 :			=cut
4122 :
4123 :			sub org_of {
4124 :			my($self,$prot_id) = @_;
4125 :			my $relational_db_response;
4126 :			my $rdbH = $self->db_handle;
4127 :
4128 :	parrello	1.287	if ($prot_id =~ /^fig\\|/) {
4129 :			return $self->is_deleted_fid( $prot_id) ? undef
4130 :			: $self->genus_species( $self->genome_of( $prot_id ) ) \|\| "";
4131 :	efrank	1.1	}
4132 :
4133 :	parrello	1.287	if (($relational_db_response =
4134 :			$rdbH->SQL("SELECT org FROM external_orgs WHERE ( prot = \'$prot_id\' )")) &&
4135 :			(@$relational_db_response >= 1)) {
4136 :			$relational_db_response->[0]->[0] =~ s/^\d+://;
4137 :			return $relational_db_response->[0]->[0];
4138 :	efrank	1.1	}
4139 :			return "";
4140 :			}
4141 :
4142 :	paczian	1.533	sub orgid_of_orgname {
4143 :			my($self,$genome_name) = @_;
4144 :			my $relational_db_response;
4145 :			my $rdbH = $self->db_handle;
4146 :
4147 :			my $genome_nameQ = quotemeta $genome_name;
4148 :
4149 :			if (($relational_db_response =
4150 :			$rdbH->SQL("SELECT genome FROM genome WHERE gname='$genome_nameQ'")) &&
4151 :			(@$relational_db_response >= 1)) {
4152 :			return $relational_db_response->[0]->[0];
4153 :			}
4154 :			return "";
4155 :			}
4156 :
4157 :			sub orgname_of_orgid {
4158 :			my($self,$genome) = @_;
4159 :			my $relational_db_response;
4160 :			my $rdbH = $self->db_handle;
4161 :
4162 :			if (($relational_db_response =
4163 :			$rdbH->SQL("SELECT gname FROM genome WHERE genome='$genome'")) &&
4164 :			(@$relational_db_response >= 1)) {
4165 :			return $relational_db_response->[0]->[0];
4166 :			}
4167 :			return "";
4168 :			}
4169 :
4170 :	parrello	1.287	=head3 genus_species_domain
4171 :
4172 :			C<< my ($gs, $domain) = $fig->genus_species_domain($genome_id); >>
4173 :
4174 :			Returns a genome's genus and species (and strain if that has been properly
4175 :			recorded) in a printable form, along with its domain. This method is similar
4176 :			to L</genus_species>, except it also returns the domain name (archaea,
4177 :			bacteria, etc.).
4178 :
4179 :			=over 4
4180 :
4181 :			=item genome_id
4182 :
4183 :			ID of the genome whose species and domain information is desired.
4184 :	golsen	1.130
4185 :	parrello	1.287	=item RETURN
4186 :	golsen	1.130
4187 :	parrello	1.287	Returns a two-element list. The first element is the species name and the
4188 :			second is the domain name.
4189 :	golsen	1.130
4190 :	parrello	1.287	=back
4191 :	golsen	1.130
4192 :			=cut
4193 :
4194 :			sub genus_species_domain {
4195 :			my ($self, $genome) = @_;
4196 :
4197 :			my $genus_species_domain = $self->cached('_genus_species_domain');
4198 :	parrello	1.287	if ( ! $genus_species_domain->{ $genome } ) {
4199 :			my $rdbH = $self->db_handle;
4200 :			my $relational_db_response = $rdbH->SQL("SELECT genome,gname,maindomain FROM genome");
4201 :			my $triple;
4202 :			foreach $triple ( @$relational_db_response ) {
4203 :			$genus_species_domain->{ $triple->[0] } = [ $triple->[1], $triple->[2] ];
4204 :			}
4205 :	golsen	1.130	}
4206 :			my $gsdref = $genus_species_domain->{ $genome };
4207 :			return $gsdref ? @$gsdref : ( "", "" );
4208 :			}
4209 :
4210 :	parrello	1.287	=head3 domain_color
4211 :
4212 :			C<< my $web_color = FIG::domain_color($domain); >>
4213 :
4214 :			Return the web color string associated with a specified domain. The colors are
4215 :			extremely subtle (86% luminance), so they absolutely require a black background.