Annotation of /FigKernelPackages/FIG.pm

Revision 1.388 - (view) (download) (as text)

1 :	efrank	1.1	package FIG;
2 :
3 :	olson	1.111	use strict;
4 :
5 :	overbeek	1.135	use Fcntl qw/:flock/; # import LOCK_* constants
6 :
7 :	olson	1.116	use POSIX;
8 :	olson	1.158	use IPC::Open2;
9 :	olson	1.329	use MIME::Base64;
10 :	olson	1.330	use File::Basename;
11 :	olson	1.359	use FileHandle;
12 :	olson	1.116
13 :	efrank	1.1	use DBrtns;
14 :			use Sim;
15 :	olson	1.361	use Annotation;
16 :	efrank	1.1	use Blast;
17 :			use FIG_Config;
18 :	overbeek	1.322	use FullLocation;
19 :	overbeek	1.36	use tree_utilities;
20 :	olson	1.93	use Subsystem;
21 :	olson	1.162	use SeedDas;
22 :	olson	1.183	use Construct;
23 :	parrello	1.200	use FIGRules;
24 :	parrello	1.210	use Tracer;
25 :	olson	1.297	use GenomeIDMap;
26 :	olson	1.260
27 :	olson	1.356	our $haveDateParse;
28 :			eval {
29 :			require Date::Parse;
30 :			import Date::Parse;
31 :			$haveDateParse = 1;
32 :			};
33 :
34 :	olson	1.245	eval { require FigGFF; };
35 :	parrello	1.287	if ($@ and $ENV{USER} eq "olson") {
36 :	olson	1.260	warn $@;
37 :			}
38 :	olson	1.79
39 :			#
40 :			# Conditionally evaluate this in case its prerequisites are not available.
41 :			#
42 :
43 :	olson	1.356	our $ClearinghouseOK;
44 :			eval {
45 :	olson	1.79	require Clearinghouse;
46 :	olson	1.356	$ClearinghouseOK = 1;
47 :	olson	1.79	};
48 :	efrank	1.1
49 :	olson	1.10	use IO::Socket;
50 :
51 :	efrank	1.1	use FileHandle;
52 :
53 :			use Carp;
54 :			use Data::Dumper;
55 :	overbeek	1.25	use Time::Local;
56 :	olson	1.93	use File::Spec;
57 :	olson	1.123	use File::Copy;
58 :	olson	1.112	#
59 :			# Try to load the RPC stuff; it might fail on older versions of the software.
60 :			#
61 :			eval {
62 :			require FIGrpc;
63 :			};
64 :
65 :			my $xmlrpc_available = 1;
66 :	parrello	1.287	if ($@ ne "") {
67 :	olson	1.112	$xmlrpc_available = 0;
68 :			}
69 :
70 :	efrank	1.1
71 :	olson	1.111	use FIGAttributes;
72 :			use base 'FIGAttributes';
73 :
74 :			use vars qw(%_FunctionAttributes);
75 :
76 :			use Data::Dumper;
77 :
78 :	olson	1.124	#
79 :			# Force all new files to be all-writable.
80 :			#
81 :
82 :			umask 0;
83 :
84 :	parrello	1.210	=head1 FIG Genome Annotation System
85 :
86 :			=head2 Introduction
87 :
88 :			This is the main object for access to the SEED data store. The data store
89 :			itself is a combination of flat files and a database. The flat files can
90 :			be moved easily between systems and the database rebuilt as needed.
91 :
92 :			A reduced set of this object's functions are available via the B<SFXlate>
93 :			object. The SFXlate object uses a single database to represent all its
94 :			genomic information. It provides a much smaller capability for updating
95 :			the data, and eliminates all similarities except for bidirectional best
96 :			hits.
97 :
98 :			The key to making the FIG system work is proper configuration of the
99 :			C<FIG_Config.pm> file. This file contains names and URLs for the key
100 :			directories as well as the type and login information for the database.
101 :
102 :	parrello	1.287	FIG was designed to operate as a series of peer instances. Each instance is
103 :			updated independently by its owner, and the instances can be synchronized
104 :			using a process called a I<peer-to-peer update>. The terms
105 :			I<SEED instance> and I<peer> are used more-or-less interchangeably.
106 :
107 :			The POD documentation for this module is still in progress, and is provided
108 :			on an AS IS basis without warranty. If you have a correction and you're
109 :			not a developer, EMAIL the details to B<bruce@gigabarb.com> and I'll fold
110 :			it in.
111 :
112 :			B<NOTE>: The usage example for each method specifies whether it is static
113 :
114 :			FIG::something
115 :
116 :			or dynamic
117 :
118 :			$fig->something
119 :
120 :			If the method is static and has no parameters (C<FIG::something()>) it can
121 :	parrello	1.298	also be invoked dynamically. This is a general artifact of the
122 :	parrello	1.287	way PERL implements object-oriented programming.
123 :
124 :	parrello	1.355	=head2 Tracing
125 :
126 :			The FIG object supports tracing using the B<Tracer> module. If tracing is
127 :			inactive when the FIG object is constructed, it will call B<TSetup> using
128 :			parameters specified either in the environment variables or in the
129 :			C<FIG_Config> module. Most command-line tools should call B<TSetup> before
130 :			constructing a FIG object so that the tracing configuration can be specified
131 :			as command-line options. If the prior call to B<TSetup> has not occurred,
132 :			then the environment variables C<Trace> and C<TraceType> will be examined.
133 :			If those do not exist, the global variables I<$FIG_Config::trace_levels> and
134 :			I<$FIG_Config::trace_type> will be used.
135 :
136 :			C<Trace> and I<$FIG_Config::trace_type> specify the tracing level and categories.
137 :			Only tracing calls for the specified categories with a level less than or equal
138 :			to the trace level will be displayed. The higher the trace level or the more
139 :			the categories, the more messages will be displayed. For example, the
140 :			following Unix command will set up for tracing at level 3 for the categories
141 :			C<SQL> and C<Sprout>.
142 :
143 :			env Trace="3 SQL Sprout"
144 :
145 :			In most cases, the category names is the same as the name of the Perl package
146 :			from which the trace call was made. An asterisk (C<*>) can be used to turn on
147 :			tracing for all categories.
148 :
149 :			env Trace="2 *"
150 :
151 :			turns on tracing at level 2 for everything.
152 :
153 :			C<TraceType> and C<$FIG_Config::trace_type> determine where the tracing is going
154 :			to show up. A full treatment of all the options can be found in the documentation
155 :			for the B<Tracer> module. The most common options, however, are C<WARN>, which
156 :			converts all trace messages to warnings, and C<TEXT>, which writes them to the
157 :			standard output. The default is C<WARN>, the theory being that this is the best
158 :			option during web page construction.
159 :
160 :	parrello	1.287	=head2 Hiding/Caching in a FIG object
161 :
162 :			We save the DB handle, cache taxonomies, and put a few other odds and ends in the
163 :			FIG object. We expect users to invoke these services using the object $fig constructed
164 :			using:
165 :
166 :			use FIG;
167 :			my $fig = new FIG;
168 :
169 :			$fig is then used as the basic mechanism for accessing FIG services. It is, of course,
170 :			just a hash that is used to retain/cache data. The most commonly accessed item is the
171 :			DB filehandle, which is accessed via $self->db_handle.
172 :
173 :			We cache genus/species expansions, taxonomies, distances (very crudely estimated) estimated
174 :			between genomes, and a variety of other things.
175 :
176 :	parrello	1.210	=cut
177 :
178 :	parrello	1.287
179 :	parrello	1.210	#: Constructor FIG->new();
180 :
181 :			=head2 Public Methods
182 :
183 :			=head3 new
184 :
185 :			C<< my $fig = FIG->new(); >>
186 :
187 :	parrello	1.298	This is the constructor for a FIG object. It uses no parameters. If tracing
188 :			has not yet been turned on, it will be turned on here. The tracing type and
189 :			level are specified by the configuration variables C<$FIG_Config::trace_levels>
190 :	parrello	1.301	and C<$FIG_Config::trace_type>. These defaults can be overridden using the
191 :			environment variables C<Trace> and C<TraceType>, respectively.
192 :	parrello	1.210
193 :			=cut
194 :
195 :	efrank	1.1	sub new {
196 :			my($class) = @_;
197 :
198 :	olson	1.102	#
199 :			# Check to see if we have a FIG_URL environment variable set.
200 :			# If we do, don't actually create a FIG object, but rather
201 :			# create a FIGrpc and return that as the return from this constructor.
202 :			#
203 :	parrello	1.210	if ($ENV{FIG_URL} ne "" && $xmlrpc_available) {
204 :			my $figrpc = new FIGrpc($ENV{FIG_URL});
205 :			return $figrpc;
206 :	olson	1.102	}
207 :	parrello	1.292	# Here we have the normal case. Check for default tracing. We only do this if
208 :			# the proper parameters are present and nobody else has set up tracing yet.
209 :	parrello	1.355	if (Tracer::Setups() == 0 && (defined $FIG_Config::trace_levels \|\| exists $ENV{Trace})) {
210 :	parrello	1.301	# Tracing is not active and the user has specified tracing levels, so it's safe for
211 :			# us to set it up using our own rules. First, the trace type: the default is WARN.
212 :			my $trace_type;
213 :			if (exists($ENV{TraceType})) {
214 :			$trace_type = $ENV{TraceType};
215 :			} elsif (defined($FIG_Config::trace_type)) {
216 :			$trace_type = $FIG_Config::trace_type;
217 :			} else {
218 :			$trace_type = "WARN";
219 :			}
220 :			# Now the trace levels. The environment variable wins over the FIG_Config value.
221 :			my $trace_levels = (exists($ENV{Trace}) ? $ENV{Trace} : $FIG_Config::trace_levels);
222 :			TSetup($trace_levels, $trace_type);
223 :	parrello	1.287	}
224 :	parrello	1.355	Trace("Connecting to the database.") if T(2);
225 :	parrello	1.287	# Connect to the database, then return ourselves.
226 :	efrank	1.1	my $rdbH = new DBrtns;
227 :			bless {
228 :	parrello	1.210	_dbf => $rdbH,
229 :			}, $class;
230 :	efrank	1.1	}
231 :
232 :	parrello	1.287	=head3 db_handle
233 :
234 :			C<< my $dbh = $fig->db_handle; >>
235 :
236 :			Return the handle to the internal B<DBrtns> object. This allows direct access to
237 :			the database methods.
238 :
239 :			=cut
240 :
241 :			sub db_handle {
242 :			my($self) = @_;
243 :			return $self->{_dbf};
244 :			}
245 :
246 :	overbeek	1.293	sub table_exists {
247 :			my($self,$table) = @_;
248 :
249 :			my $rdbH = $self->db_handle;
250 :			return $rdbH->table_exists($table);
251 :			}
252 :	parrello	1.292
253 :	parrello	1.287	=head3 cached
254 :
255 :			C<< my $x = $fig->cached($name); >>
256 :
257 :			Return a reference to a hash containing transient data. If no hash exists with the
258 :			specified name, create an empty one under that name and return it.
259 :
260 :			The idea behind this method is to allow clients to cache data in the FIG object for
261 :			later use. (For example, a method might cache feature data so that it can be
262 :			retrieved later without using the database.) This facility should be used sparingly,
263 :			since different clients may destroy each other's data if they use the same name.
264 :
265 :			=over 4
266 :
267 :			=item name
268 :
269 :			Name assigned to the cached data.
270 :
271 :			=item RETURN
272 :
273 :			Returns a reference to a hash that is permanently associated with the specified name.
274 :			If no such hash exists, an empty one will be created for the purpose.
275 :
276 :			=back
277 :
278 :			=cut
279 :
280 :			sub cached {
281 :			my($self,$what) = @_;
282 :
283 :			my $x = $self->{$what};
284 :			if (! $x) {
285 :			$x = $self->{$what} = {};
286 :			}
287 :			return $x;
288 :			}
289 :	parrello	1.210
290 :			=head3 get_system_name
291 :
292 :			C<< my $name = $fig->get_system_name; >>
293 :
294 :			Returns C<seed>, indicating that this is object is using the SEED
295 :			database. The same method on an SFXlate object will return C<sprout>.
296 :
297 :			=cut
298 :			#: Return Type $;
299 :			sub get_system_name {
300 :	olson	1.207	return "seed";
301 :	olson	1.205	}
302 :	parrello	1.210
303 :	parrello	1.287	=head3 DESTROY
304 :
305 :			The destructor releases the database handle.
306 :
307 :			=cut
308 :	olson	1.205
309 :	parrello	1.287	sub DESTROY {
310 :	efrank	1.1	my($self) = @_;
311 :			my($rdbH);
312 :
313 :	parrello	1.210	if ($rdbH = $self->db_handle) {
314 :			$rdbH->DESTROY;
315 :	efrank	1.1	}
316 :			}
317 :
318 :	parrello	1.355	=head3 same_seqs
319 :
320 :			C<< my $sameFlag = FIG::same_seqs($s1, $s2); >>
321 :
322 :			Return TRUE if the specified protein sequences are considered equivalent and FALSE
323 :			otherwise. The sequences should be presented in I<nr-analysis> form, which is in
324 :			reverse order and upper case with the stop codon omitted.
325 :
326 :			The sequences will be considered equivalent if the shorter matches the initial
327 :			portion of the long one and is no more than 30% smaller. Since the sequences are
328 :			in nr-analysis form, the equivalent start potions means that the sequences
329 :			have the same tail. The importance of the tail is that the stop point of a PEG
330 :			is easier to find than the start point, so a same tail means that the two
331 :			sequences are equivalent except for the choice of start point.
332 :
333 :			=over 4
334 :
335 :			=item s1
336 :
337 :			First protein sequence, reversed and with the stop codon removed.
338 :
339 :			=item s2
340 :
341 :			Second protein sequence, reversed and with the stop codon removed.
342 :
343 :			=item RETURN
344 :
345 :			Returns TRUE if the two protein sequences are equivalent, else FALSE.
346 :
347 :			=back
348 :
349 :			=cut
350 :
351 :			sub same_seqs {
352 :			my ($s1,$s2) = @_;
353 :
354 :			my $ln1 = length($s1);
355 :			my $ln2 = length($s2);
356 :
357 :			return ((abs($ln1-$ln2) < (0.3 * (($ln1 < $ln2) ? $ln1 : $ln2))) &&
358 :			((($ln1 <= $ln2) && (index($s2,$s1) == 0)) \|\|
359 :			(($ln1 > $ln2) && (index($s1,$s2) == 0))));
360 :			}
361 :
362 :	parrello	1.210	=head3 delete_genomes
363 :
364 :			C<< $fig->delete_genomes(\@genomes); >>
365 :
366 :			Delete the specified genomes from the data store. This requires making
367 :			system calls to move and delete files.
368 :
369 :			=cut
370 :			#: Return Type ;
371 :	overbeek	1.7	sub delete_genomes {
372 :			my($self,$genomes) = @_;
373 :			my $tmpD = "$FIG_Config::temp/tmp.deleted.$$";
374 :			my $tmp_Data = "$FIG_Config::temp/Data.$$";
375 :
376 :			my %to_del = map { $_ => 1 } @$genomes;
377 :			open(TMP,">$tmpD") \|\| die "could not open $tmpD";
378 :
379 :			my $genome;
380 :	parrello	1.287	foreach $genome ($self->genomes) {
381 :			if (! $to_del{$genome}) {
382 :			print TMP "$genome\n";
383 :			}
384 :	overbeek	1.7	}
385 :			close(TMP);
386 :
387 :			&run("extract_genomes $tmpD $FIG_Config::data $tmp_Data");
388 :	parrello	1.200
389 :	overbeek	1.47	# &run("mv $FIG_Config::data $FIG_Config::data.deleted; mv $tmp_Data $FIG_Config::data; fig load_all; rm -rf $FIG_Config::data.deleted");
390 :	parrello	1.200
391 :			&run("mv $FIG_Config::data $FIG_Config::data.deleted");
392 :	overbeek	1.47	&run("mv $tmp_Data $FIG_Config::data");
393 :			&run("fig load_all");
394 :			&run("rm -rf $FIG_Config::data.deleted");
395 :	overbeek	1.7	}
396 :	parrello	1.200
397 :	parrello	1.210	=head3 add_genome
398 :
399 :	overbeek	1.335	C<< my $ok = $fig->add_genome($genomeF, $force, $skipnr); >>
400 :	parrello	1.210
401 :			Add a new genome to the data store. A genome's data is kept in a directory
402 :	parrello	1.287	by itself, underneath the main organism directory. This method essentially
403 :			moves genome data from an external directory to the main directory and
404 :			performs some indexing tasks to integrate it.
405 :	parrello	1.210
406 :			=over 4
407 :
408 :			=item genomeF
409 :
410 :	parrello	1.287	Name of the directory containing the genome files. This should be a
411 :			fully-qualified directory name. The last segment of the directory
412 :			name should be the genome ID.
413 :	parrello	1.210
414 :	overbeek	1.331	=item force
415 :
416 :			This will ignore errors thrown by verify_genome_directory. This is bad, and you should
417 :			never do it, but I am in the situation where I need to move a genome from one machine
418 :			to another, and although I trust the genome I can't.
419 :
420 :	overbeek	1.335	=item skipnr
421 :
422 :			We don't always want to add the pooteins 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.
423 :
424 :	parrello	1.210	=item RETURN
425 :
426 :			Returns TRUE if successful, else FALSE.
427 :
428 :			=back
429 :
430 :			=cut
431 :			#: Return Type $;
432 :	efrank	1.1	sub add_genome {
433 :	overbeek	1.335	my($self,$genomeF, $force, $skipnr) = @_;
434 :	efrank	1.1
435 :			my $rc = 0;
436 :	olson	1.93
437 :			my(undef, $path, $genome) = File::Spec->splitpath($genomeF);
438 :
439 :	parrello	1.287	if ($genome !~ /^\d+\.\d+$/) {
440 :			warn "Invalid genome filename $genomeF\n";
441 :			return $rc;
442 :	olson	1.93	}
443 :
444 :	parrello	1.287	if (-d $FIG_Config::organisms/$genome) {
445 :			warn "Organism already exists for $genome\n";
446 :			return $rc;
447 :	olson	1.93	}
448 :	parrello	1.200
449 :	olson	1.93
450 :			#
451 :			# We're okay, it doesn't exist.
452 :			#
453 :
454 :			my @errors = `$FIG_Config::bin/verify_genome_directory $genomeF`;
455 :
456 :	parrello	1.287	if (@errors) {
457 :			warn "Errors found while verifying genome directory $genomeF:\n";
458 :			print join("", @errors);
459 :	overbeek	1.331	if (!$force) {return $rc}
460 :	parrello	1.365	else {warn "Skipped these errors and continued. You should not do this"}
461 :	olson	1.93	}
462 :	parrello	1.200
463 :	olson	1.93	&run("cp -r $genomeF $FIG_Config::organisms");
464 :			&run("chmod -R 777 $FIG_Config::organisms/$genome");
465 :	parrello	1.379
466 :	overbeek	1.353	if (-s "$FIG_Config::organisms/$genome/COMPLETE")
467 :			{
468 :	parrello	1.365	print STDERR "$genome was marked as \"complete\"\n";
469 :	overbeek	1.353	}
470 :			else
471 :			{
472 :	parrello	1.365	&run("assess_completeness $genome");
473 :			if (-s "$FIG_Config::organisms/$genome/PROBABLY_COMPLETE")
474 :			{
475 :			print STDERR "Assessed $genome to be probably complete\n";
476 :			&run("cp -p $FIG_Config::organisms/$genome/PROBABLY_COMPLETE $FIG_Config::organisms/$genome/COMPLETE");
477 :			}
478 :			else
479 :			{
480 :			print STDERR "Assessed $genome to not be probably complete\n";
481 :			}
482 :	overbeek	1.353	}
483 :	parrello	1.379
484 :	olson	1.93	&run("index_contigs $genome");
485 :			&run("compute_genome_counts $genome");
486 :			&run("load_features $genome");
487 :	parrello	1.379
488 :	olson	1.93	$rc = 1;
489 :	parrello	1.287	if (-s "$FIG_Config::organisms/$genome/Features/peg/fasta") {
490 :			&run("index_translations $genome");
491 :			my @tmp = `cut -f1 $FIG_Config::organisms/$genome/Features/peg/tbl`;
492 :			chomp @tmp;
493 :	overbeek	1.335	&run("cat $FIG_Config::organisms/$genome/Features/peg/fasta >> $FIG_Config::data/Global/nr") if (!$skipnr);
494 :	overbeek	1.370	# &run("formatdb -i $FIG_Config::data/Global/nr -p T") if (!$skipnr);
495 :	parrello	1.287	&enqueue_similarities(\@tmp);
496 :	olson	1.93	}
497 :			if ((-s "$FIG_Config::organisms/$genome/assigned_functions") \|\|
498 :	parrello	1.287	(-d "$FIG_Config::organisms/$genome/UserModels")) {
499 :			&run("add_assertions_of_function $genome");
500 :	efrank	1.1	}
501 :	parrello	1.200
502 :	efrank	1.1	return $rc;
503 :			}
504 :
505 :	parrello	1.287	=head3 parse_genome_args
506 :
507 :			C<< my ($mode, @genomes) = FIG::parse_genome_args(@args); >>
508 :
509 :			Extract a list of genome IDs from an argument list. If the argument list is empty,
510 :			return all the genomes in the data store.
511 :
512 :			This is a function that is performed by many of the FIG command-line utilities. The
513 :			user has the option of specifying a list of specific genome IDs or specifying none
514 :			in order to get all of them. If your command requires additional arguments in the
515 :			command line, you can still use this method if you shift them out of the argument list
516 :			before calling. The $mode return value will be C<all> if the user asked for all of
517 :			the genomes or C<some> if he specified a list of IDs. This is useful to know if,
518 :			for example, we are loading a table. If we're loading everything, we can delete the
519 :			entire table; if we're only loading some genomes, we must delete them individually.
520 :
521 :			This method uses the genome directory rather than the database because it may be used
522 :			before the database is ready.
523 :
524 :			=over 4
525 :
526 :			=item args1, args2, ... argsN
527 :
528 :			List of genome IDs. If all genome IDs are to be processed, then this list should be
529 :			empty.
530 :
531 :			=item RETURN
532 :
533 :			Returns a list. The first element of the list is C<all> if the user is asking for all
534 :			the genome IDs and C<some> otherwise. The remaining elements of the list are the
535 :			desired genome IDs.
536 :
537 :			=back
538 :
539 :			=cut
540 :
541 :			sub parse_genome_args {
542 :			# Get the parameters.
543 :			my @args = @_;
544 :			# Check the mode.
545 :			my $mode = (@args > 0 ? 'some' : 'all');
546 :			# Build the return list.
547 :			my @retVal = ($mode);
548 :			# Process according to the mode.
549 :			if ($mode eq 'all') {
550 :			# We want all the genomes, so we get them from the organism directory.
551 :			my $orgdir = "$FIG_Config::organisms";
552 :			opendir( GENOMES, $orgdir ) \|\| Confess("Could not open directory $orgdir");
553 :			push @retVal, grep { $_ =~ /^\d/ } readdir( GENOMES );
554 :			closedir( GENOMES );
555 :			} else {
556 :			# We want only the genomes specified by the user.
557 :			push @retVal, @args;
558 :			}
559 :			# Return the result.
560 :			return @retVal;
561 :			}
562 :
563 :			=head3 reload_table
564 :
565 :			C<< $fig->reload_table($mode, $table, $flds, $xflds, $fileName, $keyList, $keyName); >>
566 :
567 :			Reload a database table from a sequential file. If I<$mode> is C<all>, the table
568 :			will be dropped and re-created. If I<$mode> is C<some>, the data for the individual
569 :			items in I<$keyList> will be deleted before the table is loaded. Thus, the load
570 :			process is optimized for the type of reload.
571 :
572 :			=over 4
573 :
574 :			=item mode
575 :
576 :			C<all> if we are reloading the entire table, C<some> if we are only reloading
577 :			specific entries.
578 :
579 :			=item table
580 :
581 :			Name of the table to reload.
582 :
583 :			=item flds
584 :
585 :			String defining the table columns, in SQL format. In general, this is a
586 :			comma-delimited set of field specifiers, each specifier consisting of the
587 :			field name followed by the field type and any optional qualifiers (such as
588 :			C<NOT NULL> or C<DEFAULT>); however, it can be anything that would appear
589 :			between the parentheses in a C<CREATE TABLE> statement. The order in which
590 :			the fields are specified is important, since it is presumed that is the
591 :			order in which they are appearing in the load file.
592 :
593 :			=item xflds
594 :
595 :			Reference to a hash that describes the indexes. The hash is keyed by index name.
596 :			The value is the index's field list. This is a comma-delimited list of field names
597 :			in order from most significant to least significant. If a field is to be indexed
598 :			in descending order, its name should be followed by the qualifier C<DESC>. For
599 :			example, the following I<$xflds> value will create two indexes, one for name followed
600 :			by creation date in reverse chronological order, and one for ID.
601 :
602 :			{ name_index => "name, createDate DESC", id_index => "id" }
603 :
604 :			=item fileName
605 :
606 :			Fully-qualified name of the file containing the data to load. Each line of the
607 :			file must correspond to a record, and the fields must be arranged in order and
608 :	parrello	1.298	tab-delimited. If the file name is omitted, the table is dropped and re-created
609 :			but not loaded.
610 :	parrello	1.287
611 :			=item keyList
612 :
613 :			Reference to a list of the IDs for the objects being reloaded. This parameter is
614 :			only used if I<$mode> is C<some>.
615 :
616 :			=item keyName (optional)
617 :
618 :			Name of the key field containing the IDs in the keylist. If omitted, C<genome> is
619 :			assumed.
620 :
621 :			=back
622 :
623 :			=cut
624 :
625 :			sub reload_table {
626 :	parrello	1.298	# Get the parameters.
627 :			my ($self, $mode, $table, $flds, $xflds, $fileName, $keyList, $keyName) = @_;
628 :	parrello	1.287	if (!defined $keyName) {
629 :			$keyName = 'genome';
630 :			}
631 :			# Get the database handler.
632 :			my $dbf = $self->{_dbf};
633 :	parrello	1.298	# Call the DBKernel method.
634 :			$dbf->reload_table($mode, $table, $flds, $xflds, $fileName, $keyList, $keyName);
635 :	parrello	1.287	}
636 :
637 :	parrello	1.210	=head3 enqueue_similarities
638 :	olson	1.93
639 :	parrello	1.287	C<< FIG::enqueue_similarities(\@fids); >>
640 :
641 :			Queue the passed Feature IDs for similarity computation. The actual
642 :			computation is performed by L</create_sim_askfor_pool>. The queue is a
643 :			persistent text file in the global data directory, and this method
644 :			essentially writes new IDs on the end of it.
645 :
646 :			=over 4
647 :
648 :			=item fids
649 :
650 :			Reference to a list of feature IDs.
651 :	olson	1.93
652 :	parrello	1.287	=back
653 :	olson	1.93
654 :			=cut
655 :	parrello	1.210	#: Return Type ;
656 :	olson	1.93	sub enqueue_similarities {
657 :	olson	1.334	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
658 :	efrank	1.1	my($fids) = @_;
659 :			my $fid;
660 :
661 :	olson	1.93	my $sim_q = "$FIG_Config::global/queued_similarities";
662 :
663 :			open(TMP,">>$sim_q")
664 :	parrello	1.287	\|\| die "could not open $sim_q";
665 :	olson	1.93
666 :			#
667 :			# We need to lock here so that if a computation is creating a snapshot of the
668 :			# queue, we block until it's done.
669 :			#
670 :
671 :			flock(TMP, LOCK_EX) or die "Cannot lock $sim_q\n";
672 :
673 :	parrello	1.287	foreach $fid (@$fids) {
674 :			print TMP "$fid\n";
675 :	efrank	1.1	}
676 :			close(TMP);
677 :	olson	1.10	}
678 :
679 :	olson	1.281	=head3 export_similarity_request
680 :
681 :			Creates a similarity computation request from the queued similarities and
682 :	parrello	1.287	the current NR.
683 :	olson	1.281
684 :			We keep track of the exported requests in case one gets lost.
685 :
686 :			=cut
687 :
688 :	parrello	1.287	sub export_similarity_request {
689 :	olson	1.281	my($self, $nr_file, $fasta_file) = @_;
690 :
691 :			my $req_dir = "$FIG_Config::fig/var/sim_requests";
692 :			&verify_dir("$FIG_Config::fig/var");
693 :			&verify_dir($req_dir);
694 :
695 :			$req_dir = "$req_dir/" . time;
696 :			&verify_dir($req_dir);
697 :
698 :			#
699 :			# Open all of our output files before zeroing out the sim queue, in case
700 :			# there is a problem.
701 :			#
702 :
703 :			open(my $user_fasta_fh, ">$fasta_file") or confess "Cannot open $fasta_file for writing: $!";
704 :			open(my $fasta_fh, ">$req_dir/fasta.in");
705 :
706 :			open(my $user_nr_fh, ">$nr_file") or confess "Cannot open $nr_file for writing: $!";
707 :			open(my $nr_fh, ">$req_dir/nr") or confess "Cannot open $req_dir/nr for writing: $!";
708 :
709 :			open(my $nr_read_fh, "<$FIG_Config::data/Global/nr") or die "Cannot open $FIG_Config::data/Global/nr for reading: $!";
710 :	parrello	1.287
711 :	olson	1.281	my $sim_q = "$FIG_Config::global/queued_similarities";
712 :
713 :			#
714 :			# We need to lock here so that if a computation is creating a snapshot of the
715 :			# queue, we block until it's done.
716 :			#
717 :
718 :			open(my $sim_q_lock, ">>$sim_q") or confess "could not open $sim_q";
719 :			flock($sim_q_lock, LOCK_EX) or confess "Cannot lock $sim_q\n";
720 :
721 :			#
722 :			# Everything open & locked, start copying.
723 :			#
724 :	parrello	1.287
725 :	olson	1.281	copy("$sim_q", "$req_dir/q") or confess "Copy $sim_q $req_dir/q failed: $!";
726 :	parrello	1.287
727 :	olson	1.281	my($buf);
728 :	parrello	1.287	while (1) {
729 :			my $n = read($nr_read_fh, $buf, 4096);
730 :			defined($n) or confess "Error reading nr: $!";
731 :			last unless $n;
732 :			syswrite($user_nr_fh, $buf) or confess "Error writing $nr_file: $!";
733 :			syswrite($nr_fh, $buf) or confess "Error writing $req_dir/nr: $!";
734 :	olson	1.281	}
735 :
736 :			close($nr_read_fh);
737 :			close($nr_fh);
738 :			close($user_nr_fh);
739 :
740 :			#
741 :			# We can zero out the queue and unlock now.
742 :			#
743 :
744 :			open(F, ">$sim_q") or die "Cannot open $sim_q to truncate it: $!\n";
745 :			close(F);
746 :	parrello	1.287
747 :	olson	1.281	close($sim_q_lock);
748 :
749 :			#
750 :			# Generate the fasta input from the queued ids.
751 :			#
752 :
753 :			open(my $q_fh, "<$req_dir/q");
754 :	parrello	1.287	while (my $id = <$q_fh>) {
755 :			chomp $id;
756 :	olson	1.281
757 :	parrello	1.287	my $seq = $self->get_translation($id);
758 :	olson	1.281
759 :	parrello	1.287	display_id_and_seq($id, \$seq, $user_fasta_fh);
760 :			display_id_and_seq($id, \$seq, $fasta_fh);
761 :	olson	1.281	}
762 :			close($q_fh);
763 :
764 :			close($user_fasta_fh);
765 :			close($fasta_fh);
766 :			}
767 :
768 :	parrello	1.210	=head3 create_sim_askfor_pool
769 :	olson	1.93
770 :	parrello	1.287	C<< $fig->create_sim_askfor_pool($chunk_size); >>
771 :	olson	1.93
772 :	parrello	1.287	Creates an askfor pool, which a snapshot of the current NR and similarity
773 :			queue. This process clears the old queue.
774 :	olson	1.123
775 :			The askfor pool needs to keep track of which sequences need to be
776 :			calculated, which have been handed out, etc. To simplify this task we
777 :	olson	1.279	chunk the sequences into fairly small numbers (20k characters) and
778 :	olson	1.123	allocate work on a per-chunk basis. We make use of the relational
779 :			database to keep track of chunk status as well as the seek locations
780 :			into the file of sequence data. The initial creation of the pool
781 :			involves indexing the sequence data with seek offsets and lengths and
782 :			populating the sim_askfor_index table with this information and with
783 :			initial status information.
784 :	olson	1.93
785 :	parrello	1.287	=over 4
786 :
787 :			=item chunk_size
788 :
789 :			Number of features to put into a processing chunk. The default is 15.
790 :
791 :			=back
792 :
793 :	parrello	1.200	=cut
794 :	parrello	1.210	#: Return Type $;
795 :	parrello	1.287	sub create_sim_askfor_pool {
796 :	olson	1.123	my($self, $chunk_size) = @_;
797 :
798 :	olson	1.279	$chunk_size = 20000 unless $chunk_size =~ /^\d+$/;
799 :	olson	1.93
800 :	olson	1.279	my $pool_dir = "$FIG_Config::fig/var/sim_pools";
801 :	olson	1.93	&verify_dir($pool_dir);
802 :
803 :			#
804 :			# Lock the pool directory.
805 :			#
806 :			open(my $lock, ">$pool_dir/lockfile");
807 :
808 :			flock($lock, LOCK_EX);
809 :
810 :			my $num = 0;
811 :	parrello	1.287	if (open(my $toc, "<$pool_dir/TOC")) {
812 :			while (<$toc>) {
813 :			chomp;
814 :			# print STDERR "Have toc entry $_\n";
815 :			my ($idx, $time, $str) = split(/\s+/, $_, 3);
816 :	olson	1.93
817 :	parrello	1.287	$num = max($num, $idx);
818 :			}
819 :			close($toc);
820 :	olson	1.93	}
821 :			$num++;
822 :			open(my $toc, ">>$pool_dir/TOC") or die "Cannot write $pool_dir/TOC: $!\n";
823 :
824 :			print $toc "$num ", time(), " New toc entry\n";
825 :			close($toc);
826 :
827 :	olson	1.123	my $cpool_id = sprintf "%04d", $num;
828 :			my $cpool_dir = "$pool_dir/$cpool_id";
829 :	olson	1.93
830 :			#
831 :			# All set, create the directory for this pool.
832 :			#
833 :
834 :			&verify_dir($cpool_dir);
835 :
836 :			#
837 :			# Now we can copy the nr and sim queue here.
838 :			# Do this stuff inside an eval so we can clean up
839 :			# the lockfile.
840 :			#
841 :
842 :			eval {
843 :	parrello	1.287	my $sim_q = "$FIG_Config::global/queued_similarities";
844 :	olson	1.93
845 :	parrello	1.287	copy("$sim_q", "$cpool_dir/q");
846 :			copy("$FIG_Config::data/Global/nr", "$cpool_dir/nr");
847 :	olson	1.93
848 :	parrello	1.287	open(F, ">$sim_q") or die "Cannot open $sim_q to truncate it: $!\n";
849 :			close(F);
850 :	olson	1.93	};
851 :	parrello	1.200
852 :	olson	1.93	unlink("$pool_dir/lockfile");
853 :			close($lock);
854 :	olson	1.123
855 :			#
856 :			# We've created our pool; we can now run the formatdb and
857 :			# extract the sequences for the blast run.
858 :			#
859 :	parrello	1.287	my $child_pid = $self->run_in_background(
860 :			sub {
861 :			#
862 :			# Need to close db or there's all sorts of trouble.
863 :			#
864 :
865 :			my $cmd = "$FIG_Config::ext_bin/formatdb -i $cpool_dir/nr -p T -l $cpool_dir/formatdb.log";
866 :			print "Will run '$cmd'\n";
867 :			&run($cmd);
868 :			print "finished. Logfile:\n";
869 :			print &FIG::file_read("$cpool_dir/formatdb.log");
870 :			unlink("$cpool_dir/formatdb.pid");
871 :			});
872 :	olson	1.279	warn "Running formatdb in background job $child_pid\n";
873 :	olson	1.123	open(FPID, ">$cpool_dir/formatdb.pid");
874 :			print FPID "$child_pid\n";
875 :			close(FPID);
876 :
877 :			my $db = $self->db_handle();
878 :	parrello	1.287	if (!$db->table_exists("sim_queue")) {
879 :			$db->create_table(tbl => "sim_queue",
880 :			flds => "qid varchar(32), chunk_id INTEGER, seek INTEGER, len INTEGER, " .
881 :			"assigned BOOL, finished BOOL, output_file varchar(255), " .
882 :			"assignment_expires INTEGER, worker_info varchar(255)"
883 :			);
884 :	olson	1.123	}
885 :
886 :			#
887 :			# Write the fasta input file. Keep track of how many have been written,
888 :			# and write seek info into the database as appropriate.
889 :			#
890 :
891 :			open(my $seq_fh, ">$cpool_dir/fasta.in");
892 :
893 :			my($chunk_idx, $chunk_begin, $seq_idx);
894 :
895 :	olson	1.279	my $cur_size = 0;
896 :
897 :	olson	1.123	$chunk_idx = 0;
898 :			$chunk_begin = 0;
899 :			$seq_idx = 0;
900 :
901 :			my(@seeks);
902 :
903 :	olson	1.279	my $tmpfile = "$FIG_Config::temp/simseek.$$";
904 :			open(my $tmpfh, ">$tmpfile") or confess "Cannot open tmpfile $tmpfile: $!";
905 :
906 :	olson	1.123	open(my $q_fh, "<$cpool_dir/q");
907 :	parrello	1.287	while (my $id = <$q_fh>) {
908 :			chomp $id;
909 :	olson	1.123
910 :	parrello	1.287	my $seq = $self->get_translation($id);
911 :	olson	1.123
912 :	parrello	1.287	#
913 :			# check if we're at the beginning of a chunk
914 :			#
915 :
916 :			print $seq_fh ">$id\n$seq\n";
917 :
918 :			#
919 :			# Check if we're at the end of a chunk
920 :			#
921 :
922 :			$cur_size += length($seq);
923 :			if ($cur_size >= $chunk_size) {
924 :			my $chunk_end = tell($seq_fh);
925 :			my $chunk_len = $chunk_end - $chunk_begin;
926 :
927 :			push(@seeks, [$cpool_id, $chunk_idx, $chunk_begin, $chunk_len]);
928 :			print $tmpfh join("\t", $cpool_id, $chunk_idx, $chunk_begin, $chunk_len, 'FALSE', 'FALSE'), "\n";
929 :			$chunk_idx++;
930 :			$chunk_begin = $chunk_end;
931 :			$cur_size = 0;
932 :			}
933 :			$seq_idx++;
934 :	olson	1.123	}
935 :
936 :	parrello	1.287	if ($cur_size > 0) {
937 :			my $chunk_end = tell($seq_fh);
938 :			my $chunk_len = $chunk_end - $chunk_begin;
939 :	olson	1.123
940 :	parrello	1.287	print $tmpfh join("\t", $cpool_id, $chunk_idx, $chunk_begin, $chunk_len, 'FALSE', 'FALSE'), "\n";
941 :			push(@seeks, [$cpool_id, $chunk_idx, $chunk_begin, $chunk_len]);
942 :	olson	1.123	}
943 :
944 :			close($q_fh);
945 :			close($seq_fh);
946 :	olson	1.279	close($tmpfh);
947 :	olson	1.123
948 :	olson	1.279	warn "Write seqs from $tmpfile\n";
949 :	olson	1.123
950 :	olson	1.279	$self->db_handle->load_table(tbl => 'sim_queue',
951 :	parrello	1.298	file => $tmpfile);
952 :	parrello	1.200
953 :	olson	1.279	unlink($tmpfile);
954 :	parrello	1.287
955 :	olson	1.279	# for my $seek (@seeks)
956 :			# {
957 :	parrello	1.298	# my($cpool_id, $chunk_idx, $chunk_begin, $chunk_len) = @$seek;
958 :	olson	1.279
959 :	parrello	1.298	# $db->SQL("insert into sim_queue (qid, chunk_id, seek, len, assigned, finished) " .
960 :			# "values('$cpool_id', $chunk_idx, $chunk_begin, $chunk_len, FALSE, FALSE)");
961 :	olson	1.279	# }
962 :	parrello	1.200
963 :	olson	1.123	return $cpool_id;
964 :			}
965 :
966 :	parrello	1.210	#=head3 get_sim_queue
967 :			#
968 :			#usage: get_sim_queue($pool_id, $all_sims)
969 :			#
970 :			#Returns the sims in the given pool. If $all_sims is true, return the entire queue. Otherwise,
971 :			#just return the sims awaiting processing.
972 :			#
973 :			#=cut
974 :	olson	1.123
975 :	parrello	1.287	sub get_sim_queue {
976 :	olson	1.123	my($self, $pool_id, $all_sims) = @_;
977 :	olson	1.279	}
978 :
979 :	parrello	1.287	=head3 get_sim_work
980 :	olson	1.279
981 :	parrello	1.287	C<< my ($nrPath, $fasta) = $fig->get_sim_work(); >>
982 :	olson	1.279
983 :			Get the next piece of sim computation work to be performed. Returned are
984 :			the path to the NR and a string containing the fasta data.
985 :
986 :			=cut
987 :
988 :	parrello	1.287	sub get_sim_work {
989 :
990 :			my ($self) = @_;
991 :	olson	1.279
992 :			#
993 :			# For now, just don't care about order of data that we get back.
994 :			#
995 :
996 :			my $db = $self->db_handle();
997 :			my $lock = FIG::SimLock->new;
998 :
999 :			my $work = $db->SQL(qq(SELECT qid, chunk_id, seek, len
1000 :	parrello	1.298	FROM sim_queue
1001 :			WHERE not finished
1002 :			LIMIT 1));
1003 :	olson	1.279	print "Got work ", Dumper($work), "\n";
1004 :
1005 :	parrello	1.287	if (not $work or @$work == 0) {
1006 :			return undef;
1007 :	olson	1.279	}
1008 :
1009 :			my($cpool_id, $chunk_id, $seek, $len) = @{$work->[0]};
1010 :	parrello	1.287
1011 :	olson	1.279	my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1012 :			my $cpool_dir = "$pool_dir/$cpool_id";
1013 :
1014 :			my $nr = "$cpool_dir/nr";
1015 :			open(my $fh, "<$cpool_dir/fasta.in");
1016 :			seek($fh, $seek, 0);
1017 :			my $fasta;
1018 :			read($fh, $fasta, $len);
1019 :
1020 :			return($cpool_id, $chunk_id, $nr, $fasta, "$cpool_dir/out.$chunk_id");
1021 :			}
1022 :
1023 :			=head3 sim_work_done
1024 :
1025 :	parrello	1.287	C<< $fig->sim_work_done($pool_id, $chunk_id, $out_file); >>
1026 :
1027 :	olson	1.279	Declare that the work in pool_id/chunk_id has been completed, and output written
1028 :			to the pool directory (get_sim_work gave it the path).
1029 :
1030 :	parrello	1.287	=over 4
1031 :
1032 :			=item pool_id
1033 :
1034 :			The ID number of the pool containing the work that just completed.
1035 :
1036 :			=item chunk_id
1037 :
1038 :			The ID number of the chunk completed.
1039 :
1040 :			=item out_file
1041 :
1042 :			The file into which the work was placed.
1043 :
1044 :			=back
1045 :
1046 :	olson	1.279	=cut
1047 :
1048 :	parrello	1.287	sub sim_work_done {
1049 :			my ($self, $pool_id, $chunk_id, $out_file) = @_;
1050 :	olson	1.279
1051 :	parrello	1.287	if (! -f $out_file) {
1052 :			Confess("sim_work_done: output file $out_file does not exist");
1053 :	olson	1.279	}
1054 :
1055 :			my $db = $self->db_handle();
1056 :			my $lock = FIG::SimLock->new;
1057 :
1058 :			my $dbh = $db->{_dbh};
1059 :
1060 :			my $rows = $dbh->do(qq(UPDATE sim_queue
1061 :	parrello	1.298	SET finished = TRUE, output_file = ?
1062 :			WHERE qid = ? and chunk_id = ?), undef, $out_file, $pool_id, $chunk_id);
1063 :	parrello	1.287	if ($rows != 1) {
1064 :			if ($dbh->errstr) {
1065 :			Confess("Update not able to set finished=TRUE: ", $dbh->errstr);
1066 :			} else {
1067 :			Confess("Update not able to set finished=TRUE");
1068 :			}
1069 :	olson	1.279	}
1070 :			#
1071 :			# Determine if this was the last piece of work for this pool. If so, we can
1072 :	parrello	1.287	# schedule the postprocessing work.
1073 :	olson	1.279	#
1074 :			# Note we're still holding the lock.
1075 :			#
1076 :
1077 :			my $out = $db->SQL(qq(SELECT chunk_id
1078 :	parrello	1.298	FROM sim_queue
1079 :			WHERE qid = ? AND not finished), undef, $pool_id);
1080 :	parrello	1.287	if (@$out == 0) {
1081 :			#
1082 :			# Pool is done.
1083 :			#
1084 :			$self->schedule_sim_pool_postprocessing($pool_id);
1085 :	olson	1.279	}
1086 :	olson	1.123	}
1087 :
1088 :	olson	1.279	=head3 schedule_sim_pool_postprocessing
1089 :
1090 :	parrello	1.287	C<< $fig->schedule_sim_pool_postprocessing($pool_id); >>
1091 :
1092 :			Schedule a job to do the similarity postprocessing for the specified pool.
1093 :
1094 :			=over 4
1095 :
1096 :			=item pool_id
1097 :
1098 :			ID of the pool whose similarity postprocessing needs to be scheduled.
1099 :	olson	1.279
1100 :	parrello	1.287	=back
1101 :	olson	1.279
1102 :			=cut
1103 :
1104 :	parrello	1.287	sub schedule_sim_pool_postprocessing {
1105 :
1106 :	olson	1.279	my($self, $pool_id) = @_;
1107 :
1108 :			my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1109 :			my $cpool_dir = "$pool_dir/$pool_id";
1110 :
1111 :			my $js = JobScheduler->new();
1112 :			my $job = $js->job_create();
1113 :
1114 :			my $spath = $job->get_script_path();
1115 :			open(my $sfh, ">$spath");
1116 :			print $sfh <<END;
1117 :			#!/bin/sh
1118 :			. $FIG_Config::fig_disk/config/fig-user-env.sh
1119 :			$FIG_Config::bin/postprocess_computed_sims $pool_id
1120 :			END
1121 :
1122 :			close($sfh);
1123 :			chmod(0775, $spath);
1124 :
1125 :			#
1126 :			# Write the job ID to the subsystem queue dir.
1127 :			#
1128 :
1129 :			open(J, ">$cpool_dir/postprocess_jobid");
1130 :			print J $job->get_id(), "\n";
1131 :			close(J);
1132 :
1133 :			$job->enqueue();
1134 :			}
1135 :
1136 :			=head3 postprocess_computed_sims
1137 :
1138 :	parrello	1.287	C<< $fig->postprocess_computed_sims($pool_id); >>
1139 :
1140 :			Set up to reduce, reformat, and split the similarities in a given pool. We build
1141 :			a pipe to this pipeline:
1142 :	olson	1.279
1143 :			reduce_sims peg.synonyms 300 \| reformat_sims nr \| split_sims dest prefix
1144 :
1145 :	parrello	1.287	Then we put the new sims in the pool directory, and then copy to NewSims.
1146 :
1147 :			=over 4
1148 :
1149 :			=item pool_id
1150 :
1151 :			ID of the pool whose similarities are to be post-processed.
1152 :
1153 :			=back
1154 :	olson	1.279
1155 :			=cut
1156 :
1157 :	parrello	1.287	sub postprocess_computed_sims {
1158 :	olson	1.279	my($self, $pool_id) = @_;
1159 :
1160 :			#
1161 :			# We don't lock here because the job is already done, and we
1162 :			# shouldn't (ha, ha) ever postprocess twice.
1163 :			#
1164 :
1165 :			my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1166 :			my $cpool_dir = "$pool_dir/$pool_id";
1167 :
1168 :			my $sim_dir = "$cpool_dir/NewSims";
1169 :			&verify_dir($sim_dir);
1170 :
1171 :			#
1172 :			# Open the processing pipeline.
1173 :			#
1174 :
1175 :			my $reduce = "$FIG_Config::bin/reduce_sims $FIG_Config::global/peg.synonyms 300";
1176 :			my $reformat = "$FIG_Config::bin/reformat_sims $cpool_dir/nr";
1177 :			my $split = "$FIG_Config::bin/split_sims $sim_dir sims.$pool_id";
1178 :			open(my $process, "\| $reduce \| $reformat \| $split");
1179 :
1180 :			#
1181 :			# Iterate over all the sims files, taken from the database.
1182 :			#
1183 :
1184 :			my $dbh = $self->db_handle()->{_dbh};
1185 :			my $files = $dbh->selectcol_arrayref(qq(SELECT output_file
1186 :	parrello	1.298	FROM sim_queue
1187 :			WHERE qid = ? and output_file IS NOT NULL
1188 :			ORDER BY chunk_id), undef, $pool_id);
1189 :	parrello	1.287	for my $file (@$files) {
1190 :			my $buf;
1191 :			open(my $fh, "<$file") or confess "Cannot sim input file $file: $!";
1192 :			while (read($fh, $buf, 4096)) {
1193 :			print $process $buf;
1194 :			}
1195 :			close($fh);
1196 :	olson	1.279	}
1197 :			my $res = close($process);
1198 :	parrello	1.287	if (!$res) {
1199 :			if ($!) {
1200 :			confess "Error closing process pipeline: $!";
1201 :			} else {
1202 :			confess "Process pipeline exited with status $?";
1203 :			}
1204 :	olson	1.279	}
1205 :
1206 :			#
1207 :			# If we got here, it worked. Copy the new sims files over to NewSims.
1208 :			#
1209 :
1210 :			opendir(my $simdh, $sim_dir) or confess "Cannot open $sim_dir: $!";
1211 :			my @new_sims = grep { $_ !~ /^\./ } readdir($simdh);
1212 :			closedir($simdh);
1213 :
1214 :			&verify_dir("$FIG_Config::data/NewSims");
1215 :
1216 :	parrello	1.287	for my $sim_file (@new_sims) {
1217 :			my $target = "$FIG_Config::data/NewSims/$sim_file";
1218 :			if (-s $target) {
1219 :			Confess("$target already exists");
1220 :			}
1221 :			print "copying sim file $sim_file\n";
1222 :			&FIG::run("cp $sim_dir/$sim_file $target");
1223 :			&FIG::run("$FIG_Config::bin/index_sims $target");
1224 :	olson	1.279	}
1225 :			}
1226 :
1227 :	parrello	1.210	=head3 get_active_sim_pools
1228 :	olson	1.123
1229 :	parrello	1.287	C<< @pools = $fig->get_active_sim_pools(); >>
1230 :	olson	1.123
1231 :	parrello	1.287	Return a list of the pool IDs for the sim processing queues that have
1232 :			entries awaiting computation.
1233 :	olson	1.123
1234 :			=cut
1235 :	parrello	1.210	#: Return Type @;
1236 :	parrello	1.287	sub get_active_sim_pools {
1237 :	olson	1.123	my($self) = @_;
1238 :
1239 :			my $dbh = $self->db_handle();
1240 :
1241 :			my $res = $dbh->SQL("select distinct qid from sim_queue where not finished");
1242 :			return undef unless $res;
1243 :
1244 :			return map { $_->[0] } @$res;
1245 :			}
1246 :
1247 :	parrello	1.376	=head3 compute_clusters
1248 :
1249 :			C<< my @clusterList = $fig->compute_clusters(\@pegList, $subsystem, $distance); >>
1250 :
1251 :			Partition a list of PEGs into sections that are clustered close together on
1252 :			the genome. The basic algorithm used builds a graph connecting PEGs to
1253 :			other PEGs close by them on the genome. Each connected subsection of the graph
1254 :			is then separated into a cluster. Singleton clusters are thrown away, and
1255 :			the remaining ones are sorted by length. All PEGs in the incoming list
1256 :			should belong to the same genome, but this is not a requirement. PEGs on
1257 :			different genomes will simply find themselves in different clusters.
1258 :
1259 :			=over 4
1260 :
1261 :			=item pegList
1262 :
1263 :			Reference to a list of PEG IDs.
1264 :
1265 :			=item subsystem
1266 :
1267 :			Subsystem object for the relevant subsystem. This parameter is not used, but is
1268 :			required for compatability with Sprout.
1269 :
1270 :			=item distance (optional)
1271 :
1272 :			The maximum distance between PEGs that makes them considered close. If omitted,
1273 :			the distance is 5000 bases.
1274 :
1275 :			=item RETURN
1276 :
1277 :			Returns a list of lists. Each sub-list is a cluster of PEGs.
1278 :
1279 :			=back
1280 :
1281 :			=cut
1282 :
1283 :			sub compute_clusters {
1284 :			# Get the parameters.
1285 :			my ($self, $pegList, $subsystem, $distance) = @_;
1286 :			if (! defined $distance) {
1287 :			$distance = 5000;
1288 :			}
1289 :			# Create a hash of the PEG IDs we're considering for cluster membership.
1290 :			my %myPeg = map { $_ => 1 } @{$pegList};
1291 :			# This next hash serves as our connection graph. We map each PEG to a list of
1292 :			# the PEGs that are near it. The GREP filter insures that a PEG is not
1293 :			# connected to itself and that only PEGs from the caller's list are
1294 :			# included.
1295 :			my %conn = ();
1296 :			for my $peg (keys %myPeg) {
1297 :			$conn{$peg} =
1298 :			[grep { $myPeg{$_} && ($_ ne $peg) } $self->close_genes($peg, $distance)];
1299 :			}
1300 :			# Our third and final hash tracks the PEGs we've already processed. This prevents
1301 :			# a PEG from being put in more than one cluster or in the same cluster twice.
1302 :			my %seen = ();
1303 :			# Now we create the list of clusters.
1304 :			my @clusters = ();
1305 :			# Loop through the pegs.
1306 :			for my $peg (keys %myPeg) {
1307 :			# Only proceed if this PEG has not been put into a cluster.
1308 :			if (! $seen{$peg}) {
1309 :			# Create a new cluster for this PEG.
1310 :			my $subList = [$peg];
1311 :			# Denote we've seen it.
1312 :			$seen{$peg} = 1;
1313 :			# Now we recursively build this cluster. The "$subList" acts as a
1314 :			# queue. We run through it from the beginning, adding connected
1315 :			# pegs to the list. The process stops when we run out of new PEGs to
1316 :			# add.
1317 :			for (my $i=0; $i < @$subList; $i++) {
1318 :			# Get a list of the PEGs connected to the current cluster PEG.
1319 :			# Only PEGs we haven't clustered yet will be processed.
1320 :			my $subPeg = $subList->[$i];
1321 :			my @tmp = grep { ! $seen{$_} } @{$conn{$subPeg}};
1322 :			# Only proceed if we found at least one new PEG.
1323 :			if (@tmp > 0) {
1324 :			# For each new PEG, denote we've seen it and
1325 :			# stuff it into the queue.
1326 :			for my $peg1 (@tmp) { $seen{$peg1} = 1 }
1327 :			push @$subList, @tmp;
1328 :			}
1329 :			}
1330 :			# If the queue we've built is not a singleton, we push it on
1331 :			# the master cluster list.
1332 :			if (@$subList > 1) {
1333 :			push @clusters, $subList;
1334 :			}
1335 :			}
1336 :			}
1337 :			# Sort the clusters by length. The shortest clusters will be bubbled to
1338 :			# the front.
1339 :			my @retVal = sort { @$a <=> @$b } @clusters;
1340 :			# Return the sorted and pruned cluster list.
1341 :			return @retVal;
1342 :			}
1343 :
1344 :	parrello	1.210	=head3 get_sim_pool_info
1345 :	olson	1.123
1346 :	parrello	1.287	C<< my ($total_entries, $n_finished, $n_assigned, $n_unassigned) = $fig->get_sim_pool_info($pool_id); >>
1347 :
1348 :			Return information about the given sim pool.
1349 :
1350 :			=over 4
1351 :
1352 :			=item pool_id
1353 :
1354 :			Pool ID of the similarity processing queue whose information is desired.
1355 :
1356 :			=item RETURN
1357 :
1358 :			Returns a four-element list. The first is the number of features in the
1359 :			queue; the second is the number of features that have been processed; the
1360 :			third is the number of features that have been assigned to a
1361 :			processor, and the fourth is the number of features left over.
1362 :	olson	1.123
1363 :	parrello	1.287	=back
1364 :	olson	1.123
1365 :			=cut
1366 :	parrello	1.210	#: Return Type @;
1367 :	parrello	1.287	sub get_sim_pool_info {
1368 :
1369 :	olson	1.123	my($self, $pool_id) = @_;
1370 :			my($dbh, $res, $total_entries, $n_finished, $n_assigned, $n_unassigned);
1371 :
1372 :			$dbh = $self->db_handle();
1373 :
1374 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id'");
1375 :	parrello	1.200	$total_entries = $res->[0]->[0];
1376 :	olson	1.123
1377 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and finished");
1378 :			$n_finished = $res->[0]->[0];
1379 :
1380 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and assigned and not finished");
1381 :			$n_assigned = $res->[0]->[0];
1382 :
1383 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and not finished and not assigned");
1384 :			$n_unassigned = $res->[0]->[0];
1385 :
1386 :			return ($total_entries, $n_finished, $n_assigned, $n_unassigned);
1387 :	olson	1.93	}
1388 :
1389 :	parrello	1.210	#=head3 get_sim_chunk
1390 :			#
1391 :			#usage: get_sim_chunk($n_seqs, $worker_id)
1392 :			#
1393 :			#Returns a chunk of $n_seqs of work.
1394 :			#
1395 :			#From Ross, about how sims are processed:
1396 :			#
1397 :			#Here is how I process them:
1398 :			#
1399 :			#
1400 :			# bash$ cd /Volumes/seed/olson/Sims/June22.out
1401 :			# bash$ for i in really*
1402 :			# > do
1403 :			# > cat < $i >> /Volumes/laptop/new.sims
1404 :			# > done
1405 :			#
1406 :			#
1407 :			#Then, I need to "reformat" them by adding to columns to each one
1408 :			# and split the result into files of about 3M each This I do using
1409 :			#
1410 :			#reduce_sims /Volumes/laptop/NR/NewNR/peg.synonyms.june21 300 < /Volumes/laptop/new.sims \|
1411 :			# reformat_sims /Volumes/laptop/NR/NewNR/checked.nr.june21 > /Volumes/laptop/reformated.sims
1412 :			#rm /Volumes/laptop/new.sims
1413 :			#split_sims /Volumes/laptop/NewSims sims.june24 reformated.sims
1414 :			#rm reformatted.sims
1415 :			#
1416 :			#=cut
1417 :	olson	1.93
1418 :	parrello	1.287	sub get_sim_chunk {
1419 :	parrello	1.210	my($self, $n_seqs, $worker_id) = @_;
1420 :			}
1421 :	olson	1.123
1422 :	parrello	1.210	=head3 get_local_hostname
1423 :	parrello	1.200
1424 :	parrello	1.287	C<< my $result = FIG::get_local_hostname(); >>
1425 :
1426 :			Return the local host name for the current processor. The name may be
1427 :			stored in a configuration file, or we may have to get it from the
1428 :			operating system.
1429 :	olson	1.123
1430 :	olson	1.93	=cut
1431 :	parrello	1.213	#: Return Type $;
1432 :	olson	1.10	sub get_local_hostname {
1433 :	olson	1.52
1434 :			#
1435 :			# See if there is a FIGdisk/config/hostname file. If there
1436 :			# is, force the hostname to be that.
1437 :			#
1438 :
1439 :			my $hostfile = "$FIG_Config::fig_disk/config/hostname";
1440 :	parrello	1.287	if (-f $hostfile) {
1441 :			my $fh;
1442 :			if (open($fh, $hostfile)) {
1443 :			my $hostname = <$fh>;
1444 :			chomp($hostname);
1445 :			return $hostname;
1446 :			}
1447 :	olson	1.52	}
1448 :	parrello	1.200
1449 :	olson	1.10	#
1450 :			# First check to see if we our hostname is correct.
1451 :			#
1452 :			# Map it to an IP address, and try to bind to that ip.
1453 :			#
1454 :
1455 :			my $tcp = getprotobyname('tcp');
1456 :	parrello	1.200
1457 :	olson	1.10	my $hostname = `hostname`;
1458 :	golsen	1.44	chomp($hostname);
1459 :	olson	1.10
1460 :			my @hostent = gethostbyname($hostname);
1461 :
1462 :	parrello	1.287	if (@hostent > 0) {
1463 :			my $sock;
1464 :			my $ip = $hostent[4];
1465 :
1466 :			socket($sock, PF_INET, SOCK_STREAM, $tcp);
1467 :			if (bind($sock, sockaddr_in(0, $ip))) {
1468 :			#
1469 :			# It worked. Reverse-map back to a hopefully fqdn.
1470 :			#
1471 :
1472 :			my @rev = gethostbyaddr($ip, AF_INET);
1473 :			if (@rev > 0) {
1474 :			my $host = $rev[0];
1475 :			#
1476 :			# Check to see if we have a FQDN.
1477 :			#
1478 :
1479 :			if ($host =~ /\./) {
1480 :			#
1481 :			# Good.
1482 :			#
1483 :			return $host;
1484 :			} else {
1485 :			#
1486 :			# We didn't get a fqdn; bail and return the IP address.
1487 :			#
1488 :			return get_hostname_by_adapter()
1489 :			}
1490 :			} else {
1491 :			return inet_ntoa($ip);
1492 :			}
1493 :			} else {
1494 :			#
1495 :			# Our hostname must be wrong; we can't bind to the IP
1496 :			# address it maps to.
1497 :			# Return the name associated with the adapter.
1498 :			#
1499 :			return get_hostname_by_adapter()
1500 :			}
1501 :			} else {
1502 :			#
1503 :			# Our hostname isn't known to DNS. This isn't good.
1504 :			# Return the name associated with the adapter.
1505 :			#
1506 :			return get_hostname_by_adapter()
1507 :			}
1508 :			}
1509 :
1510 :			=head3 get_hostname_by_adapter
1511 :	parrello	1.200
1512 :	parrello	1.287	C<< my $name = FIG::get_hostname_by_adapter(); >>
1513 :	olson	1.10
1514 :	parrello	1.287	Return the local host name for the current network environment.
1515 :	parrello	1.213
1516 :			=cut
1517 :			#: Return Type $;
1518 :	olson	1.10	sub get_hostname_by_adapter {
1519 :			#
1520 :			# Attempt to determine our local hostname based on the
1521 :			# network environment.
1522 :			#
1523 :			# This implementation reads the routing table for the default route.
1524 :			# We then look at the interface config for the interface that holds the default.
1525 :			#
1526 :			#
1527 :			# Linux routing table:
1528 :			# [olson@yips 0.0.0]$ netstat -rn
1529 :			# Kernel IP routing table
1530 :			# Destination Gateway Genmask Flags MSS Window irtt Iface
1531 :			# 140.221.34.32 0.0.0.0 255.255.255.224 U 0 0 0 eth0
1532 :			# 169.254.0.0 0.0.0.0 255.255.0.0 U 0 0 0 eth0
1533 :			# 127.0.0.0 0.0.0.0 255.0.0.0 U 0 0 0 lo
1534 :			# 0.0.0.0 140.221.34.61 0.0.0.0 UG 0 0 0 eth0
1535 :	parrello	1.200	#
1536 :	olson	1.10	# Mac routing table:
1537 :	parrello	1.200	#
1538 :	olson	1.10	# bash-2.05a$ netstat -rn
1539 :			# Routing tables
1540 :	parrello	1.200	#
1541 :	olson	1.10	# Internet:
1542 :			# Destination Gateway Flags Refs Use Netif Expire
1543 :			# default 140.221.11.253 UGSc 12 120 en0
1544 :			# 127.0.0.1 127.0.0.1 UH 16 8415486 lo0
1545 :			# 140.221.8/22 link#4 UCS 12 0 en0
1546 :			# 140.221.8.78 0:6:5b:f:51:c4 UHLW 0 183 en0 408
1547 :			# 140.221.8.191 0:3:93:84:ab:e8 UHLW 0 92 en0 622
1548 :			# 140.221.8.198 0:e0:98:8e:36:e2 UHLW 0 5 en0 691
1549 :			# 140.221.9.6 0:6:5b:f:51:d6 UHLW 1 63 en0 1197
1550 :			# 140.221.10.135 0:d0:59:34:26:34 UHLW 2 2134 en0 1199
1551 :			# 140.221.10.152 0:30:1b:b0:ec:dd UHLW 1 137 en0 1122
1552 :			# 140.221.10.153 127.0.0.1 UHS 0 0 lo0
1553 :			# 140.221.11.37 0:9:6b:53:4e:4b UHLW 1 624 en0 1136
1554 :			# 140.221.11.103 0:30:48:22:59:e6 UHLW 3 973 en0 1016
1555 :			# 140.221.11.224 0:a:95:6f:7:10 UHLW 1 1 en0 605
1556 :			# 140.221.11.237 0:1:30:b8:80:c0 UHLW 0 0 en0 1158
1557 :			# 140.221.11.250 0:1:30:3:1:0 UHLW 0 0 en0 1141
1558 :			# 140.221.11.253 0:d0:3:e:70:a UHLW 13 0 en0 1199
1559 :			# 169.254 link#4 UCS 0 0 en0
1560 :	parrello	1.200	#
1561 :	olson	1.10	# Internet6:
1562 :			# Destination Gateway Flags Netif Expire
1563 :			# UH lo0
1564 :			# fe80::%lo0/64 Uc lo0
1565 :			# link#1 UHL lo0
1566 :			# fe80::%en0/64 link#4 UC en0
1567 :			# 0:a:95:a8:26:68 UHL lo0
1568 :			# ff01::/32 U lo0
1569 :			# ff02::%lo0/32 UC lo0
1570 :			# ff02::%en0/32 link#4 UC en0
1571 :
1572 :			my($fh);
1573 :
1574 :	parrello	1.287	if (!open($fh, "netstat -rn \|")) {
1575 :			warn "Cannot run netstat to determine local IP address\n";
1576 :			return "localhost";
1577 :	olson	1.10	}
1578 :
1579 :			my $interface_name;
1580 :	parrello	1.200
1581 :	parrello	1.287	while (<$fh>) {
1582 :			my @cols = split();
1583 :	olson	1.10
1584 :	parrello	1.287	if ($cols[0] eq "default" \|\| $cols[0] eq "0.0.0.0") {
1585 :			$interface_name = $cols[$#cols];
1586 :			}
1587 :	olson	1.10	}
1588 :			close($fh);
1589 :	parrello	1.200
1590 :	olson	1.11	# print "Default route on $interface_name\n";
1591 :	olson	1.10
1592 :			#
1593 :			# Find ifconfig.
1594 :			#
1595 :
1596 :			my $ifconfig;
1597 :
1598 :	parrello	1.287	for my $dir ((split(":", $ENV{PATH}), "/sbin", "/usr/sbin")) {
1599 :			if (-x "$dir/ifconfig") {
1600 :			$ifconfig = "$dir/ifconfig";
1601 :			last;
1602 :			}
1603 :	olson	1.10	}
1604 :
1605 :	parrello	1.287	if ($ifconfig eq "") {
1606 :			warn "Ifconfig not found\n";
1607 :			return "localhost";
1608 :	olson	1.10	}
1609 :	olson	1.11	# print "Foudn $ifconfig\n";
1610 :	olson	1.10
1611 :	parrello	1.287	if (!open($fh, "$ifconfig $interface_name \|")) {
1612 :			warn "Could not run $ifconfig: $!\n";
1613 :			return "localhost";
1614 :	olson	1.10	}
1615 :
1616 :			my $ip;
1617 :	parrello	1.287	while (<$fh>) {
1618 :			#
1619 :			# Mac:
1620 :			# inet 140.221.10.153 netmask 0xfffffc00 broadcast 140.221.11.255
1621 :			# Linux:
1622 :			# inet addr:140.221.34.37 Bcast:140.221.34.63 Mask:255.255.255.224
1623 :			#
1624 :
1625 :			chomp;
1626 :			s/^\s*//;
1627 :
1628 :			# print "Have '$_'\n";
1629 :			if (/inet\s+addr:(\d+\.\d+\.\d+\.\d+)\s+/) {
1630 :			#
1631 :			# Linux hit.
1632 :			#
1633 :			$ip = $1;
1634 :			# print "Got linux $ip\n";
1635 :			last;
1636 :			} elsif (/inet\s+(\d+\.\d+\.\d+\.\d+)\s+/) {
1637 :			#
1638 :			# Mac hit.
1639 :			#
1640 :			$ip = $1;
1641 :			# print "Got mac $ip\n";
1642 :			last;
1643 :			}
1644 :	olson	1.10	}
1645 :			close($fh);
1646 :
1647 :	parrello	1.287	if ($ip eq "") {
1648 :			warn "Didn't find an IP\n";
1649 :			return "localhost";
1650 :	olson	1.10	}
1651 :
1652 :			return $ip;
1653 :	efrank	1.1	}
1654 :
1655 :	parrello	1.213	=head3 get_seed_id
1656 :
1657 :	parrello	1.287	C<< my $id = FIG::get_seed_id(); >>
1658 :
1659 :			Return the Universally Unique ID for this SEED instance. If one
1660 :			does not exist, it will be created.
1661 :	parrello	1.213
1662 :			=cut
1663 :			#: Return type $;
1664 :	olson	1.38	sub get_seed_id {
1665 :			#
1666 :			# Retrieve the seed identifer from FIGdisk/config/seed_id.
1667 :			#
1668 :			# If it's not there, create one, and make it readonly.
1669 :			#
1670 :			my $id;
1671 :			my $id_file = "$FIG_Config::fig_disk/config/seed_id";
1672 :	parrello	1.287	if (! -f $id_file) {
1673 :			my $newid = `uuidgen`;
1674 :			if (!$newid) {
1675 :			die "Cannot run uuidgen: $!";
1676 :			}
1677 :	olson	1.38
1678 :	parrello	1.287	chomp($newid);
1679 :			my $fh = new FileHandle(">$id_file");
1680 :			if (!$fh) {
1681 :			die "error creating $id_file: $!";
1682 :			}
1683 :			print $fh "$newid\n";
1684 :			$fh->close();
1685 :			chmod(0444, $id_file);
1686 :	olson	1.38	}
1687 :			my $fh = new FileHandle("<$id_file");
1688 :			$id = <$fh>;
1689 :			chomp($id);
1690 :			return $id;
1691 :			}
1692 :
1693 :	parrello	1.287	=head3 get_release_info
1694 :	olson	1.155
1695 :	parrello	1.287	C<< my ($name, $id, $inst, $email, $parent_id, $description) = FIG::get_release_info(); >>
1696 :	olson	1.155
1697 :	parrello	1.287	Return the current data release information..
1698 :	olson	1.195
1699 :			The release info comes from the file FIG/Data/RELEASE. It is formatted as:
1700 :
1701 :	parrello	1.287	<release-name>
1702 :			<unique id>
1703 :			<institution>
1704 :			<contact email>
1705 :			<unique id of data release this release derived from>
1706 :			<description>
1707 :	olson	1.195
1708 :			For instance:
1709 :
1710 :	parrello	1.287	-----
1711 :			SEED Data Release, 09/15/2004.
1712 :			4148208C-1DF2-11D9-8417-000A95D52EF6
1713 :			ANL/FIG
1714 :			olson@mcs.anl.gov
1715 :
1716 :			Test release.
1717 :			-----
1718 :	olson	1.195
1719 :			If no RELEASE file exists, this routine will create one with a new unique ID. This
1720 :			lets a peer optimize the data transfer by being able to cache ID translations
1721 :			from this instance.
1722 :	olson	1.155
1723 :			=cut
1724 :	parrello	1.213	#: Return Type @;
1725 :	parrello	1.287	sub get_release_info {
1726 :	olson	1.196	my($fig, $no_create) = @_;
1727 :	olson	1.195
1728 :			my $rel_file = "$FIG_Config::data/RELEASE";
1729 :
1730 :	parrello	1.287	if (! -f $rel_file and !$no_create) {
1731 :	parrello	1.298	#
1732 :			# Create a new one.
1733 :			#
1734 :	olson	1.195
1735 :	parrello	1.287	my $newid = `uuidgen`;
1736 :			if (!$newid) {
1737 :			die "Cannot run uuidgen: $!";
1738 :			}
1739 :	olson	1.195
1740 :	parrello	1.287	chomp($newid);
1741 :	olson	1.195
1742 :	parrello	1.287	my $relinfo = "Automatically generated release info " . localtime();
1743 :			my $inst = "Unknown";
1744 :			my $contact = "Unknown";
1745 :			my $parent = "";
1746 :			my( $a, $b, $e, $v, $env ) = $fig->genome_counts;
1747 :			my $description = "Automatically generated release info\n";
1748 :			$description .= "Contains $a archaeal, $b bacterial, $e eukaryal, $v viral and $env environmental genomes.\n";
1749 :
1750 :			my $fh = new FileHandle(">$rel_file");
1751 :			if (!$fh) {
1752 :			warn "error creating $rel_file: $!";
1753 :			return undef;
1754 :			}
1755 :			print $fh "$relinfo\n";
1756 :			print $fh "$newid\n";
1757 :			print $fh "$inst\n";
1758 :			print $fh "$contact\n";
1759 :			print $fh "$parent\n";
1760 :			print $fh $description;
1761 :			$fh->close();
1762 :			chmod(0444, $rel_file);
1763 :	olson	1.195	}
1764 :
1765 :	parrello	1.287	if (open(my $fh, $rel_file)) {
1766 :			my(@lines) = <$fh>;
1767 :			close($fh);
1768 :	parrello	1.200
1769 :	parrello	1.287	chomp(@lines);
1770 :	parrello	1.200
1771 :	parrello	1.287	my($info, $id, $inst, $contact, $parent, @desc) = @lines;
1772 :	olson	1.195
1773 :	parrello	1.287	return ($info, $id, $inst, $contact, $parent, join("\n", @desc));
1774 :	olson	1.195	}
1775 :	olson	1.155
1776 :			return undef;
1777 :			}
1778 :
1779 :	parrello	1.376	=head3 FIG
1780 :
1781 :			C<< my $realFig = $fig->FIG(); >>
1782 :
1783 :			Return this object. This method is provided for compatability with SFXlate.
1784 :
1785 :			=cut
1786 :
1787 :			sub FIG {
1788 :			my ($self) = @_;
1789 :			return $self;
1790 :			}
1791 :
1792 :	parrello	1.287	=head3 get_peer_last_update
1793 :	olson	1.155
1794 :	parrello	1.287	C<< my $date = $fig->get_peer_last_update($peer_id); >>
1795 :	parrello	1.213
1796 :	olson	1.155	Return the timestamp from the last successful peer-to-peer update with
1797 :	parrello	1.287	the given peer. If the specified peer has made updates, comparing this
1798 :			timestamp to the timestamp of the updates can tell you whether or not
1799 :			the updates have been integrated into your SEED data store.
1800 :	olson	1.155
1801 :			We store this information in FIG/Data/Global/Peers/<peer-id>.
1802 :
1803 :	parrello	1.287	=over 4
1804 :
1805 :			=item peer_id
1806 :
1807 :			Universally Unique ID for the desired peer.
1808 :
1809 :			=item RETURN
1810 :
1811 :			Returns the date/time stamp for the last peer-to-peer updated performed
1812 :			with the identified SEED instance.
1813 :
1814 :			=back
1815 :
1816 :	olson	1.155	=cut
1817 :	parrello	1.213	#: Return Type $;
1818 :	parrello	1.287	sub get_peer_last_update {
1819 :	olson	1.155	my($self, $peer_id) = @_;
1820 :
1821 :			my $dir = "$FIG_Config::data/Global/Peers";
1822 :			&verify_dir($dir);
1823 :			$dir .= "/$peer_id";
1824 :			&verify_dir($dir);
1825 :
1826 :			my $update_file = "$dir/last_update";
1827 :	parrello	1.287	if (-f $update_file) {
1828 :			my $time = file_head($update_file, 1);
1829 :			chomp $time;
1830 :			return $time;
1831 :			} else {
1832 :			return undef;
1833 :	olson	1.155	}
1834 :			}
1835 :
1836 :	parrello	1.287	=head3 set_peer_last_update
1837 :	parrello	1.213
1838 :	parrello	1.287	C<< $fig->set_peer_last_update($peer_id, $time); >>
1839 :	parrello	1.213
1840 :	parrello	1.287	Manually set the update timestamp for a specified peer. This informs
1841 :			the SEED that you have all of the assignments and updates from a
1842 :			particular SEED instance as of a certain date.
1843 :	parrello	1.213
1844 :			=cut
1845 :			#: Return Type ;
1846 :
1847 :	parrello	1.287	sub set_peer_last_update {
1848 :	olson	1.155	my($self, $peer_id, $time) = @_;
1849 :
1850 :			my $dir = "$FIG_Config::data/Global/Peers";
1851 :			&verify_dir($dir);
1852 :			$dir .= "/$peer_id";
1853 :			&verify_dir($dir);
1854 :
1855 :			my $update_file = "$dir/last_update";
1856 :			open(F, ">$update_file");
1857 :			print F "$time\n";
1858 :			close(F);
1859 :			}
1860 :
1861 :	redwards	1.302	=head3 clean_spaces
1862 :
1863 :	parrello	1.320	Remove any extra spaces from input fields. This will (currently) remove ^\s, \s$, and concatenate multiple spaces into one.
1864 :	redwards	1.302
1865 :			my $input=$fig->clean_spaces($cgi->param('input'));
1866 :
1867 :			=cut
1868 :
1869 :			sub clean_spaces
1870 :			{
1871 :			my ($self, $s)=@_;
1872 :			# note at the moment I do not use \s because that recognizes \t and \n too. This should only remove multiple spaces.
1873 :	parrello	1.320	$s =~ s/^ +//;
1874 :	redwards	1.302	$s =~ s/ +$//;
1875 :			$s =~ s/ +/ /g;
1876 :			return $s;
1877 :			}
1878 :
1879 :
1880 :
1881 :	parrello	1.213	=head3 cgi_url
1882 :
1883 :	parrello	1.287	C<< my $url = FIG::$fig->cgi_url(); >>
1884 :
1885 :			Return the URL for the CGI script directory.
1886 :	parrello	1.213
1887 :			=cut
1888 :			#: Return Type $;
1889 :	efrank	1.1	sub cgi_url {
1890 :	overbeek	1.377	# return &plug_url($FIG_Config::cgi_url);
1891 :
1892 :			#
1893 :			# In order to globally make relative references work properly, return ".".
1894 :			# This might break some stuff in p2p, but this will get us most of the way there.
1895 :			# The things that break we can repair by inspecting the value of $ENV{SCRIPT_NAME}
1896 :			#
1897 :			return ".";
1898 :	efrank	1.1	}
1899 :	parrello	1.200
1900 :	overbeek	1.382	=head3 top_link
1901 :
1902 :			C<< my $url = FIG::top_link(); >>
1903 :
1904 :			Return the relative URL for the top of the CGI script directory.
1905 :
1906 :			We determine this based on the SCRIPT_NAME environment variable, falling
1907 :			back to FIG_Config::cgi_base if necessary.
1908 :
1909 :			=cut
1910 :
1911 :			sub top_link
1912 :			{
1913 :
1914 :			#
1915 :			# Determine if this is a toplevel cgi or one in one of the subdirs (currently
1916 :			# just /p2p).
1917 :			#
1918 :
1919 :			my @parts = split(/\//, $ENV{SCRIPT_NAME});
1920 :			my $top;
1921 :			if ($parts[-2] eq 'FIG')
1922 :			{
1923 :			$top = '.';
1924 :			# warn "toplevel @parts\n";
1925 :			}
1926 :			elsif ($parts[-3] eq 'FIG')
1927 :			{
1928 :			$top = '..';
1929 :			# warn "subdir @parts\n";
1930 :			}
1931 :			else
1932 :			{
1933 :			$top = $FIG_Config::cgi_base;
1934 :			# warn "other @parts\n";
1935 :			}
1936 :
1937 :			return $top;
1938 :			}
1939 :
1940 :	parrello	1.213	=head3 temp_url
1941 :
1942 :	parrello	1.287	C<< my $url = FIG::temp_url(); >>
1943 :
1944 :			Return the URL of the temporary file directory.
1945 :	parrello	1.213
1946 :			=cut
1947 :			#: Return Type $;
1948 :	efrank	1.1	sub temp_url {
1949 :	overbeek	1.377	# return &plug_url($FIG_Config::temp_url);
1950 :
1951 :			#
1952 :			# Similarly, make this relative.
1953 :			#
1954 :			return "../FIG-Tmp";
1955 :	efrank	1.1	}
1956 :	parrello	1.200
1957 :	parrello	1.213	=head3 plug_url
1958 :
1959 :	parrello	1.287	C<< my $url2 = $fig->plug_url($url); >>
1960 :
1961 :			or
1962 :
1963 :			C<< my $url2 = $fig->plug_url($url); >>
1964 :
1965 :			Change the domain portion of a URL to point to the current domain. This essentially
1966 :			relocates URLs into the current environment.
1967 :
1968 :			=over 4
1969 :
1970 :			=item url
1971 :
1972 :			URL to relocate.
1973 :
1974 :			=item RETURN
1975 :
1976 :			Returns a new URL with the base portion converted to the current operating host.
1977 :			If the URL does not begin with C<http://>, the URL will be returned unmodified.
1978 :
1979 :			=back
1980 :	parrello	1.213
1981 :			=cut
1982 :			#: Return Type $;
1983 :	efrank	1.1	sub plug_url {
1984 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1985 :	efrank	1.1	my($url) = @_;
1986 :
1987 :	golsen	1.44	my $name;
1988 :
1989 :			# Revised by GJO
1990 :			# First try to get url from the current http request
1991 :
1992 :			if ( defined( $ENV{ 'HTTP_HOST' } ) # This is where $cgi->url gets its value
1993 :			&& ( $name = $ENV{ 'HTTP_HOST' } )
1994 :			&& ( $url =~ s~^http://[^/]*~http://$name~ ) # ~ is delimiter
1995 :			) {}
1996 :
1997 :			# Otherwise resort to alternative sources
1998 :
1999 :			elsif ( ( $name = &get_local_hostname )
2000 :			&& ( $url =~ s~^http://[^/]*~http://$name~ ) # ~ is delimiter
2001 :			) {}
2002 :
2003 :	efrank	1.1	return $url;
2004 :			}
2005 :
2006 :	parrello	1.213	=head3 file_read
2007 :
2008 :	parrello	1.287	C<< my $text = $fig->file_read($fileName); >>
2009 :
2010 :			or
2011 :
2012 :			C<< my @lines = $fig->file_read($fileName); >>
2013 :
2014 :			or
2015 :
2016 :			C<< my $text = FIG::file_read($fileName); >>
2017 :
2018 :			or
2019 :
2020 :			C<< my @lines = FIG::file_read($fileName); >>
2021 :
2022 :			Read an entire file into memory. In a scalar context, the file is returned
2023 :			as a single text string with line delimiters included. In a list context, the
2024 :			file is returned as a list of lines, each line terminated by a line
2025 :			delimiter. (For a method that automatically strips the line delimiters,
2026 :			use C<Tracer::GetFile>.)
2027 :
2028 :			=over 4
2029 :
2030 :			=item fileName
2031 :
2032 :			Fully-qualified name of the file to read.
2033 :
2034 :			=item RETURN
2035 :
2036 :			In a list context, returns a list of the file lines. In a scalar context, returns
2037 :			a string containing all the lines of the file with delimiters included.
2038 :	parrello	1.213
2039 :	parrello	1.287	=back
2040 :	parrello	1.213
2041 :			=cut
2042 :			#: Return Type $;
2043 :			#: Return Type @;
2044 :	parrello	1.287	sub file_read {
2045 :
2046 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2047 :	parrello	1.287	my($fileName) = @_;
2048 :			return file_head($fileName, '*');
2049 :	olson	1.90
2050 :			}
2051 :
2052 :
2053 :	parrello	1.213	=head3 file_head
2054 :
2055 :	parrello	1.287	C<< my $text = $fig->file_head($fileName, $count); >>
2056 :
2057 :			or
2058 :
2059 :			C<< my @lines = $fig->file_head($fileName, $count); >>
2060 :	parrello	1.213
2061 :	parrello	1.287	or
2062 :	parrello	1.213
2063 :	parrello	1.287	C<< my $text = FIG::file_head($fileName, $count); >>
2064 :	olson	1.90
2065 :	parrello	1.287	or
2066 :	olson	1.90
2067 :	parrello	1.287	C<< my @lines = FIG::file_head($fileName, $count); >>
2068 :	olson	1.90
2069 :	parrello	1.287	Read a portion of a file into memory. In a scalar context, the file portion is
2070 :			returned as a single text string with line delimiters included. In a list
2071 :			context, the file portion is returned as a list of lines, each line terminated
2072 :			by a line delimiter.
2073 :	olson	1.155
2074 :	parrello	1.287	=over 4
2075 :	olson	1.90
2076 :	parrello	1.287	=item fileName
2077 :	olson	1.90
2078 :	parrello	1.287	Fully-qualified name of the file to read.
2079 :	efrank	1.1
2080 :	parrello	1.287	=item count (optional)
2081 :	efrank	1.1
2082 :	parrello	1.287	Number of lines to read from the file. If omitted, C<1> is assumed. If the
2083 :			non-numeric string C<*> is specified, the entire file will be read.
2084 :	efrank	1.1
2085 :	parrello	1.287	=item RETURN
2086 :	efrank	1.1
2087 :	parrello	1.287	In a list context, returns a list of the desired file lines. In a scalar context, returns
2088 :			a string containing the desired lines of the file with delimiters included.
2089 :	efrank	1.1
2090 :	parrello	1.287	=back
2091 :	efrank	1.1
2092 :			=cut
2093 :	parrello	1.287	#: Return Type $;
2094 :			#: Return Type @;
2095 :			sub file_head {
2096 :	efrank	1.1
2097 :	parrello	1.287	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2098 :			my($file, $count) = @_;
2099 :	efrank	1.1
2100 :	parrello	1.287	my ($n, $allFlag);
2101 :			if ($count eq '*') {
2102 :	olson	1.304	Trace("Full file read for \"$file\".") if T(3);
2103 :	parrello	1.287	$allFlag = 1;
2104 :			$n = 0;
2105 :			} else {
2106 :			$allFlag = 0;
2107 :			$n = (!$count ? 1 : $count);
2108 :	olson	1.304	Trace("Reading $n record(s) from \"$file\".") if T(3);
2109 :	parrello	1.287	}
2110 :	efrank	1.1
2111 :	parrello	1.287	if (open(my $fh, "<$file")) {
2112 :	parrello	1.298	my(@ret, $i);
2113 :	parrello	1.287	$i = 0;
2114 :			while (<$fh>) {
2115 :			push(@ret, $_);
2116 :			$i++;
2117 :			last if !$allFlag && $i >= $n;
2118 :			}
2119 :			close($fh);
2120 :			if (wantarray) {
2121 :			return @ret;
2122 :			} else {
2123 :			return join("", @ret);
2124 :			}
2125 :	efrank	1.1	}
2126 :			}
2127 :
2128 :			################ Basic Routines [ existed since WIT ] ##########################
2129 :
2130 :	parrello	1.287	=head3 min
2131 :
2132 :			C<< my $min = FIG::min(@x); >>
2133 :
2134 :			or
2135 :
2136 :			C<< my $min = $fig->min(@x); >>
2137 :
2138 :			Return the minimum numeric value from a list.
2139 :
2140 :			=over 4
2141 :
2142 :			=item x1, x2, ... xN
2143 :	efrank	1.1
2144 :	parrello	1.287	List of numbers to process.
2145 :	efrank	1.1
2146 :	parrello	1.287	=item RETURN
2147 :	efrank	1.1
2148 :	parrello	1.287	Returns the numeric value of the list entry possessing the lowest value. Returns
2149 :			C<undef> if the list is empty.
2150 :	efrank	1.1
2151 :	parrello	1.287	=back
2152 :	efrank	1.1
2153 :			=cut
2154 :	parrello	1.213	#: Return Type $;
2155 :	efrank	1.1	sub min {
2156 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2157 :	efrank	1.1	my(@x) = @_;
2158 :			my($min,$i);
2159 :
2160 :			(@x > 0) \|\| return undef;
2161 :			$min = $x[0];
2162 :	parrello	1.287	for ($i=1; ($i < @x); $i++) {
2163 :			$min = ($min > $x[$i]) ? $x[$i] : $min;
2164 :	efrank	1.1	}
2165 :			return $min;
2166 :			}
2167 :
2168 :	parrello	1.287	=head3 max
2169 :
2170 :			C<< my $max = FIG::max(@x); >>
2171 :
2172 :			or
2173 :
2174 :			C<< my $max = $fig->max(@x); >>
2175 :	efrank	1.1
2176 :	parrello	1.287	Return the maximum numeric value from a list.
2177 :	efrank	1.1
2178 :	parrello	1.287	=over 4
2179 :
2180 :			=item x1, x2, ... xN
2181 :
2182 :			List of numbers to process.
2183 :
2184 :			=item RETURN
2185 :
2186 :			Returns the numeric value of t/he list entry possessing the highest value. Returns
2187 :			C<undef> if the list is empty.
2188 :	efrank	1.1
2189 :	parrello	1.287	=back
2190 :	efrank	1.1
2191 :			=cut
2192 :	parrello	1.213	#: Return Type $;
2193 :	efrank	1.1	sub max {
2194 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2195 :	efrank	1.1	my(@x) = @_;
2196 :			my($max,$i);
2197 :
2198 :			(@x > 0) \|\| return undef;
2199 :			$max = $x[0];
2200 :	parrello	1.287	for ($i=1; ($i < @x); $i++) {
2201 :			$max = ($max < $x[$i]) ? $x[$i] : $max;
2202 :	efrank	1.1	}
2203 :			return $max;
2204 :			}
2205 :
2206 :	parrello	1.287	=head3 between
2207 :	efrank	1.1
2208 :	parrello	1.287	C<< my $flag = FIG::between($x, $y, $z); >>
2209 :	efrank	1.1
2210 :	parrello	1.287	or
2211 :
2212 :			C<< my $flag = $fig->between($x, $y, $z); >>
2213 :
2214 :			Determine whether or not $y is between $x and $z.
2215 :
2216 :			=over 4
2217 :
2218 :			=item x
2219 :
2220 :			First edge number.
2221 :
2222 :			=item y
2223 :	efrank	1.1
2224 :	parrello	1.287	Number to examine.
2225 :
2226 :			=item z
2227 :
2228 :			Second edge number.
2229 :
2230 :			=item RETURN
2231 :
2232 :			Return TRUE if the number I<$y> is between the numbers I<$x> and I<$z>. The check
2233 :			is inclusive (that is, if I<$y> is equal to I<$x> or I<$z> the function returns
2234 :			TRUE), and the order of I<$x> and I<$z> does not matter. If I<$x> is lower than
2235 :			I<$z>, then the return is TRUE if I<$x> <= I<$y> <= I<$z>. If I<$z> is lower,
2236 :			then the return is TRUE if I<$x> >= I$<$y> >= I<$z>.
2237 :
2238 :			=back
2239 :	efrank	1.1
2240 :			=cut
2241 :	parrello	1.213	#: Return Type $;
2242 :	efrank	1.1	sub between {
2243 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2244 :	efrank	1.1	my($x,$y,$z) = @_;
2245 :
2246 :	parrello	1.287	if ($x < $z) {
2247 :			return (($x <= $y) && ($y <= $z));
2248 :			} else {
2249 :			return (($x >= $y) && ($y >= $z));
2250 :	efrank	1.1	}
2251 :			}
2252 :
2253 :	parrello	1.287	=head3 standard_genetic_code
2254 :	efrank	1.1
2255 :	parrello	1.287	C<< my $code = FIG::standard_genetic_code(); >>
2256 :	efrank	1.1
2257 :	parrello	1.287	Return a hash containing the standard translation of nucleotide triples to proteins.
2258 :			Methods such as L</translate> can take a translation scheme as a parameter. This method
2259 :			returns the default translation scheme. The scheme is implemented as a reference to a
2260 :			hash that contains nucleotide triplets as keys and has protein letters as values.
2261 :	efrank	1.1
2262 :			=cut
2263 :	parrello	1.213	#: Return Type $;
2264 :	efrank	1.1	sub standard_genetic_code {
2265 :	parrello	1.200
2266 :	efrank	1.1	my $code = {};
2267 :
2268 :			$code->{"AAA"} = "K";
2269 :			$code->{"AAC"} = "N";
2270 :			$code->{"AAG"} = "K";
2271 :			$code->{"AAT"} = "N";
2272 :			$code->{"ACA"} = "T";
2273 :			$code->{"ACC"} = "T";
2274 :			$code->{"ACG"} = "T";
2275 :			$code->{"ACT"} = "T";
2276 :			$code->{"AGA"} = "R";
2277 :			$code->{"AGC"} = "S";
2278 :			$code->{"AGG"} = "R";
2279 :			$code->{"AGT"} = "S";
2280 :			$code->{"ATA"} = "I";
2281 :			$code->{"ATC"} = "I";
2282 :			$code->{"ATG"} = "M";
2283 :			$code->{"ATT"} = "I";
2284 :			$code->{"CAA"} = "Q";
2285 :			$code->{"CAC"} = "H";
2286 :			$code->{"CAG"} = "Q";
2287 :			$code->{"CAT"} = "H";
2288 :			$code->{"CCA"} = "P";
2289 :			$code->{"CCC"} = "P";
2290 :			$code->{"CCG"} = "P";
2291 :			$code->{"CCT"} = "P";
2292 :			$code->{"CGA"} = "R";
2293 :			$code->{"CGC"} = "R";
2294 :			$code->{"CGG"} = "R";
2295 :			$code->{"CGT"} = "R";
2296 :			$code->{"CTA"} = "L";
2297 :			$code->{"CTC"} = "L";
2298 :			$code->{"CTG"} = "L";
2299 :			$code->{"CTT"} = "L";
2300 :			$code->{"GAA"} = "E";
2301 :			$code->{"GAC"} = "D";
2302 :			$code->{"GAG"} = "E";
2303 :			$code->{"GAT"} = "D";
2304 :			$code->{"GCA"} = "A";
2305 :			$code->{"GCC"} = "A";
2306 :			$code->{"GCG"} = "A";
2307 :			$code->{"GCT"} = "A";
2308 :			$code->{"GGA"} = "G";
2309 :			$code->{"GGC"} = "G";
2310 :			$code->{"GGG"} = "G";
2311 :			$code->{"GGT"} = "G";
2312 :			$code->{"GTA"} = "V";
2313 :			$code->{"GTC"} = "V";
2314 :			$code->{"GTG"} = "V";
2315 :			$code->{"GTT"} = "V";
2316 :			$code->{"TAA"} = "*";
2317 :			$code->{"TAC"} = "Y";
2318 :			$code->{"TAG"} = "*";
2319 :			$code->{"TAT"} = "Y";
2320 :			$code->{"TCA"} = "S";
2321 :			$code->{"TCC"} = "S";
2322 :			$code->{"TCG"} = "S";
2323 :			$code->{"TCT"} = "S";
2324 :			$code->{"TGA"} = "*";
2325 :			$code->{"TGC"} = "C";
2326 :			$code->{"TGG"} = "W";
2327 :			$code->{"TGT"} = "C";
2328 :			$code->{"TTA"} = "L";
2329 :			$code->{"TTC"} = "F";
2330 :			$code->{"TTG"} = "L";
2331 :			$code->{"TTT"} = "F";
2332 :	parrello	1.200
2333 :	efrank	1.1	return $code;
2334 :			}
2335 :
2336 :	parrello	1.287	=head3 translate
2337 :
2338 :			C<< my $aa_seq = &FIG::translate($dna_seq, $code, $fix_start); >>
2339 :
2340 :			Translate a DNA sequence to a protein sequence using the specified genetic code.
2341 :			If I<$fix_start> is TRUE, will translate an initial C<TTG> or C<GTG> code to
2342 :			C<M>. (In the standard genetic code, these two combinations normally translate
2343 :			to C<V> and C<L>, respectively.)
2344 :
2345 :			=over 4
2346 :	efrank	1.1
2347 :	parrello	1.287	=item dna_seq
2348 :	efrank	1.1
2349 :	parrello	1.287	DNA sequence to translate. Note that the DNA sequence can only contain
2350 :			known nucleotides.
2351 :	efrank	1.1
2352 :	parrello	1.287	=item code
2353 :	efrank	1.1
2354 :	parrello	1.287	Reference to a hash specifying the translation code. The hash is keyed by
2355 :			nucleotide triples, and the value for each key is the corresponding protein
2356 :			letter. If this parameter is omitted, the L</standard_genetic_code> will be
2357 :			used.
2358 :	efrank	1.1
2359 :	parrello	1.287	=item fix_start
2360 :
2361 :			TRUE if the first triple is to get special treatment, else FALSE. If TRUE,
2362 :			then a value of C<TTG> or C<GTG> in the first position will be translated to
2363 :			C<M> instead of the value specified in the translation code.
2364 :
2365 :			=item RETURN
2366 :
2367 :			Returns a string resulting from translating each nucleotide triple into a
2368 :			protein letter.
2369 :
2370 :			=back
2371 :
2372 :			=cut
2373 :			#: Return Type $;
2374 :			sub translate {
2375 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2376 :
2377 :			my( $dna,$code,$start ) = @_;
2378 :			my( $i,$j,$ln );
2379 :			my( $x,$y );
2380 :			my( $prot );
2381 :
2382 :			if (! defined($code)) {
2383 :			$code = &FIG::standard_genetic_code;
2384 :	efrank	1.1	}
2385 :			$ln = length($dna);
2386 :			$prot = "X" x ($ln/3);
2387 :			$dna =~ tr/a-z/A-Z/;
2388 :
2389 :	parrello	1.287	for ($i=0,$j=0; ($i < ($ln-2)); $i += 3,$j++) {
2390 :			$x = substr($dna,$i,3);
2391 :			if ($y = $code->{$x}) {
2392 :			substr($prot,$j,1) = $y;
2393 :	efrank	1.1	}
2394 :			}
2395 :	parrello	1.200
2396 :	parrello	1.287	if (($start) && ($ln >= 3) && (substr($dna,0,3) =~ /^[GT]TG$/)) {
2397 :			substr($prot,0,1) = 'M';
2398 :	efrank	1.1	}
2399 :			return $prot;
2400 :			}
2401 :
2402 :	parrello	1.287	=head3 reverse_comp
2403 :
2404 :			C<< my $dnaR = FIG::reverse_comp($dna); >>
2405 :
2406 :			or
2407 :
2408 :			C<< my $dnaR = $fig->reverse_comp($dna); >>
2409 :
2410 :			Return the reverse complement os the specified DNA sequence.
2411 :	efrank	1.1
2412 :	parrello	1.287	NOTE: for extremely long DNA strings, use L</rev_comp>, which allows you to
2413 :			pass the strings around in the form of pointers.
2414 :	efrank	1.1
2415 :	parrello	1.287	=over 4
2416 :
2417 :			=item dna
2418 :	efrank	1.1
2419 :	parrello	1.287	DNA sequence whose reverse complement is desired.
2420 :
2421 :			=item RETURN
2422 :
2423 :			Returns the reverse complement of the incoming DNA sequence.
2424 :
2425 :			=back
2426 :	efrank	1.1
2427 :			=cut
2428 :	parrello	1.213	#: Return Type $;
2429 :	efrank	1.1	sub reverse_comp {
2430 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2431 :	efrank	1.1	my($seq) = @_;
2432 :
2433 :			return ${&rev_comp(\$seq)};
2434 :			}
2435 :
2436 :	parrello	1.287	=head3 rev_comp
2437 :
2438 :			C<< my $dnaRP = FIG::rev_comp(\$dna); >>
2439 :
2440 :			or
2441 :
2442 :			C<< my $dnaRP = $fig->rev_comp(\$dna); >>
2443 :
2444 :			Return the reverse complement of the specified DNA sequence. The DNA sequence
2445 :			is passed in as a string reference rather than a raw string for performance
2446 :			reasons. If this is unnecessary, use L</reverse_comp>, which processes strings
2447 :			instead of references to strings.
2448 :
2449 :			=over 4
2450 :
2451 :			=item dna
2452 :
2453 :			Reference to the DNA sequence whose reverse complement is desired.
2454 :
2455 :			=item RETURN
2456 :
2457 :			Returns a reference to the reverse complement of the incoming DNA sequence.
2458 :
2459 :			=back
2460 :	parrello	1.213
2461 :			=cut
2462 :			#: Return Type $;
2463 :	efrank	1.1	sub rev_comp {
2464 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2465 :	efrank	1.1	my( $seqP ) = @_;
2466 :			my( $rev );
2467 :
2468 :			$rev = reverse( $$seqP );
2469 :	overbeek	1.317	$rev =~ tr/A-Z/a-z/;
2470 :			$rev =~ tr/acgtumrwsykbdhv/tgcaakywsrmvhdb/;
2471 :	efrank	1.1	return \$rev;
2472 :			}
2473 :
2474 :	parrello	1.287	=head3 verify_dir
2475 :
2476 :			C<< FIG::verify_dir($dir); >>
2477 :	efrank	1.1
2478 :	parrello	1.287	or
2479 :	efrank	1.1
2480 :	parrello	1.287	C<< $fig->verify_dir($dir); >>
2481 :	efrank	1.1
2482 :	parrello	1.287	Insure that the specified directory exists. If it must be created, the permissions will
2483 :			be set to C<0777>.
2484 :	efrank	1.1
2485 :			=cut
2486 :
2487 :			sub verify_dir {
2488 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2489 :	efrank	1.1	my($dir) = @_;
2490 :
2491 :	parrello	1.287	if (-d $dir) {
2492 :			return
2493 :			}
2494 :			if ($dir =~ /^(.*)\/[^\/]+$/) {
2495 :			&verify_dir($1);
2496 :	efrank	1.1	}
2497 :	parrello	1.287	mkdir($dir,0777) \|\| Confess("Could not make directory $dir: $!");
2498 :	efrank	1.1	}
2499 :
2500 :	parrello	1.287	=head3 run
2501 :	efrank	1.1
2502 :	parrello	1.287	C<< FIG::run($cmd); >>
2503 :	overbeek	1.283
2504 :	parrello	1.287	or
2505 :
2506 :			C<< $fig->run($cmd); >>
2507 :	overbeek	1.283
2508 :	parrello	1.287	Run a command. If the command fails, the error will be traced.
2509 :	overbeek	1.283
2510 :			=cut
2511 :
2512 :	parrello	1.287	sub run {
2513 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2514 :			my($cmd) = @_;
2515 :
2516 :	overbeek	1.363	if ($ENV{FIG_VERBOSE}) {
2517 :	parrello	1.287	my @tmp = `date`;
2518 :			chomp @tmp;
2519 :			print STDERR "$tmp[0]: running $cmd\n";
2520 :			}
2521 :			Trace("Running command: $cmd") if T(3);
2522 :			(system($cmd) == 0) \|\| Confess("FAILED: $cmd");
2523 :			}
2524 :
2525 :	olson	1.388	=head3 run_gathering_output
2526 :
2527 :			C<< FIG::run_gathering_output($cmd, @args); >>
2528 :
2529 :			or
2530 :
2531 :			C<< $fig->run_gathering_output($cmd, @args); >>
2532 :
2533 :			Run a command, gathering the output. This is similar to the backtick
2534 :			operator, but it does not invoke the shell. Note that the argument list
2535 :			must be explicitly passed one command line argument per argument to
2536 :			run_gathering_output.
2537 :
2538 :			If the command fails, the error will be traced.
2539 :
2540 :			=cut
2541 :
2542 :			sub run_gathering_output {
2543 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2544 :			my($cmd, @args) = @_;
2545 :
2546 :			#
2547 :			# Run the command in a safe fork-with-pipe/exec.
2548 :			#
2549 :
2550 :			my $pid = open(PROC_READ, "-\|");
2551 :
2552 :			if ($pid == 0)
2553 :			{
2554 :			exec { $cmd } $cmd, @args;
2555 :			die "could not execute $cmd @args: $!\n";
2556 :			}
2557 :
2558 :			if (wantarray)
2559 :			{
2560 :			my @out;
2561 :			while (<PROC_READ>)
2562 :			{
2563 :			push(@out, $_);
2564 :			}
2565 :			if (!close(PROC_READ))
2566 :			{
2567 :			Confess("FAILED: $cmd @args with error return $?");
2568 :			}
2569 :			return @out;
2570 :			}
2571 :			else
2572 :			{
2573 :			my $out = '';
2574 :
2575 :			while (<PROC_READ>)
2576 :			{
2577 :			$out .= $_;
2578 :			}
2579 :			if (!close(PROC_READ))
2580 :			{
2581 :			Confess("FAILED: $cmd @args with error return $?");
2582 :			}
2583 :			return $out;
2584 :			}
2585 :			}
2586 :
2587 :	parrello	1.287	=head3 augment_path
2588 :
2589 :			C<< FIG::augment_path($dirName); >>
2590 :	overbeek	1.283
2591 :	parrello	1.287	Add a directory to the system path.
2592 :	overbeek	1.283
2593 :	parrello	1.287	This method adds a new directory to the front of the system path. It looks in the
2594 :			configuration file to determine whether this is Windows or Unix, and uses the
2595 :			appropriate separator.
2596 :	efrank	1.1
2597 :	parrello	1.287	=over 4
2598 :	efrank	1.1
2599 :	parrello	1.287	=item dirName
2600 :
2601 :			Name of the directory to add to the path.
2602 :
2603 :			=back
2604 :	efrank	1.1
2605 :			=cut
2606 :
2607 :	parrello	1.287	sub augment_path {
2608 :			my ($dirName) = @_;
2609 :			if ($FIG_Config::win_mode) {
2610 :			$ENV{PATH} = "$dirName;$ENV{PATH}";
2611 :			} else {
2612 :			$ENV{PATH} = "$dirName:$ENV{PATH}";
2613 :	overbeek	1.278	}
2614 :	efrank	1.1	}
2615 :
2616 :	parrello	1.287	=head3 read_fasta_record
2617 :	gdpusch	1.45
2618 :	parrello	1.287	C<< my ($seq_id, $seq_pointer, $comment) = FIG::read_fasta_record(\*FILEHANDLE); >>
2619 :	gdpusch	1.45
2620 :	parrello	1.287	or
2621 :	gdpusch	1.45
2622 :	parrello	1.287	C<< my ($seq_id, $seq_pointer, $comment) = $fig->read_fasta_record(\*FILEHANDLE); >>
2623 :	gdpusch	1.45
2624 :	parrello	1.287	Read and parse the next logical record of a FASTA file. A FASTA logical record
2625 :			consists of multiple lines of text. The first line begins with a C<< > >> symbol
2626 :			and contains the sequence ID followed by an optional comment. (NOTE: comments
2627 :			are currently deprecated, because not all tools handle them properly.) The
2628 :			remaining lines contain the sequence data.
2629 :
2630 :			This method uses a trick to smooth its operation: the line terminator character
2631 :			is temporarily changed to C<< \n> >> so that a single read operation brings in
2632 :			the entire logical record.
2633 :	gdpusch	1.45
2634 :	parrello	1.287	=over 4
2635 :	gdpusch	1.45
2636 :	parrello	1.287	=item FILEHANDLE
2637 :	gdpusch	1.45
2638 :	parrello	1.287	Open handle of the FASTA file. If not specified, C<STDIN> is assumed.
2639 :
2640 :			=item RETURN
2641 :
2642 :			If we are at the end of the file, returns C<undef>. Otherwise, returns a
2643 :			three-element list. The first element is the sequence ID, the second is
2644 :			a pointer to the sequence data (that is, a string reference as opposed to
2645 :			as string), and the third is the comment.
2646 :
2647 :			=back
2648 :	gdpusch	1.45
2649 :			=cut
2650 :	parrello	1.213	#: Return Type @;
2651 :	parrello	1.287	sub read_fasta_record {
2652 :
2653 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2654 :	gdpusch	1.45	my ($file_handle) = @_;
2655 :	parrello	1.287	my ($old_end_of_record, $fasta_record, @lines, $head, $sequence, $seq_id, $comment, @parsed_fasta_record);
2656 :	parrello	1.200
2657 :	gdpusch	1.45	if (not defined($file_handle)) { $file_handle = \*STDIN; }
2658 :	parrello	1.200
2659 :	gdpusch	1.45	$old_end_of_record = $/;
2660 :			$/ = "\n>";
2661 :	parrello	1.200
2662 :	parrello	1.287	if (defined($fasta_record = <$file_handle>)) {
2663 :			chomp $fasta_record;
2664 :			@lines = split( /\n/, $fasta_record );
2665 :			$head = shift @lines;
2666 :			$head =~ s/^>?//;
2667 :			$head =~ m/^(\S+)/;
2668 :			$seq_id = $1;
2669 :			if ($head =~ m/^\S+\s+(.*)$/) { $comment = $1; } else { $comment = ""; }
2670 :			$sequence = join( "", @lines );
2671 :			@parsed_fasta_record = ( $seq_id, \$sequence, $comment );
2672 :			} else {
2673 :			@parsed_fasta_record = ();
2674 :	gdpusch	1.45	}
2675 :	parrello	1.200
2676 :	gdpusch	1.45	$/ = $old_end_of_record;
2677 :	parrello	1.200
2678 :	gdpusch	1.45	return @parsed_fasta_record;
2679 :			}
2680 :
2681 :	parrello	1.287	=head3 display_id_and_seq
2682 :
2683 :			C<< FIG::display_id_and_seq($id_and_comment, $seqP, $fh); >>
2684 :
2685 :			or
2686 :
2687 :	parrello	1.355	C<< $fig->display_id_and_seq($id_and_comment, \$seqP, $fh); >>
2688 :	parrello	1.287
2689 :			Display a fasta ID and sequence to the specified open file. This method is designed
2690 :			to work well with L</read_fasta_sequence> and L</rev_comp>, because it takes as
2691 :			input a string pointer rather than a string. If the file handle is omitted it
2692 :			defaults to STDOUT.
2693 :
2694 :			The output is formatted into a FASTA record. The first line of the output is
2695 :			preceded by a C<< > >> symbol, and the sequence is split into 60-character
2696 :			chunks displayed one per line. Thus, this method can be used to produce
2697 :			FASTA files from data gathered by the rest of the system.
2698 :
2699 :			=over 4
2700 :
2701 :			=item id_and_comment
2702 :
2703 :			The sequence ID and (optionally) the comment from the sequence's FASTA record.
2704 :			The ID
2705 :	gdpusch	1.45
2706 :	parrello	1.287	=item seqP
2707 :	efrank	1.1
2708 :	parrello	1.287	Reference to a string containing the sequence. The sequence is automatically
2709 :			formatted into 60-character chunks displayed one per line.
2710 :	efrank	1.1
2711 :	parrello	1.287	=item fh
2712 :	efrank	1.1
2713 :	parrello	1.287	Open file handle to which the ID and sequence should be output. If omitted,
2714 :	parrello	1.355	C<\*STDOUT> is assumed.
2715 :	parrello	1.287
2716 :			=back
2717 :	efrank	1.1
2718 :			=cut
2719 :
2720 :	parrello	1.287	sub display_id_and_seq {
2721 :	mkubal	1.53
2722 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2723 :	parrello	1.287
2724 :	overbeek	1.326	my( $id, $seqP, $fh ) = @_;
2725 :	parrello	1.200
2726 :	efrank	1.1	if (! defined($fh) ) { $fh = \*STDOUT; }
2727 :	parrello	1.200
2728 :	efrank	1.1	print $fh ">$id\n";
2729 :	overbeek	1.326	&display_seq($seqP, $fh);
2730 :	efrank	1.1	}
2731 :
2732 :	parrello	1.355	=head3 display_seq
2733 :	parrello	1.287
2734 :	parrello	1.355	C<< FIG::display_seq(\$seqP, $fh); >>
2735 :	parrello	1.287
2736 :			or
2737 :
2738 :	parrello	1.355	C<< $fig->display_seq(\$seqP, $fh); >>
2739 :	parrello	1.287
2740 :			Display a fasta sequence to the specified open file. This method is designed
2741 :			to work well with L</read_fasta_sequence> and L</rev_comp>, because it takes as
2742 :			input a string pointer rather than a string. If the file handle is omitted it
2743 :			defaults to STDOUT.
2744 :
2745 :			The sequence is split into 60-character chunks displayed one per line for
2746 :			readability.
2747 :
2748 :			=over 4
2749 :
2750 :			=item seqP
2751 :
2752 :			Reference to a string containing the sequence.
2753 :
2754 :			=item fh
2755 :
2756 :			Open file handle to which the sequence should be output. If omitted,
2757 :			C<STDOUT> is assumed.
2758 :
2759 :			=back
2760 :
2761 :			=cut
2762 :
2763 :	efrank	1.1	sub display_seq {
2764 :	parrello	1.287
2765 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2766 :	parrello	1.287
2767 :	overbeek	1.326	my ( $seqP, $fh ) = @_;
2768 :	efrank	1.1	my ( $i, $n, $ln );
2769 :	parrello	1.200
2770 :	efrank	1.1	if (! defined($fh) ) { $fh = \*STDOUT; }
2771 :
2772 :	overbeek	1.326	$n = length($$seqP);
2773 :	efrank	1.1	# confess "zero-length sequence ???" if ( (! defined($n)) \|\| ($n == 0) );
2774 :	parrello	1.287	for ($i=0; ($i < $n); $i += 60) {
2775 :			if (($i + 60) <= $n) {
2776 :	overbeek	1.326	$ln = substr($$seqP,$i,60);
2777 :	parrello	1.287	} else {
2778 :	overbeek	1.326	$ln = substr($$seqP,$i,($n-$i));
2779 :	parrello	1.287	}
2780 :			print $fh "$ln\n";
2781 :	efrank	1.1	}
2782 :			}
2783 :
2784 :			########## I commented the pods on the following routines out, since they should not
2785 :			########## be part of the SOAP/WSTL interface
2786 :			#=pod
2787 :			#
2788 :	parrello	1.287	#=head3 file2N
2789 :	efrank	1.1	#
2790 :			#usage: $n = $fig->file2N($file)
2791 :			#
2792 :			#In some of the databases I need to store filenames, which can waste a lot of
2793 :			#space. Hence, I maintain a database for converting filenames to/from integers.
2794 :			#
2795 :			#=cut
2796 :			#
2797 :	parrello	1.328	sub file2N :Scalar {
2798 :	efrank	1.1	my($self,$file) = @_;
2799 :			my($relational_db_response);
2800 :
2801 :			my $rdbH = $self->db_handle;
2802 :
2803 :			if (($relational_db_response = $rdbH->SQL("SELECT fileno FROM file_table WHERE ( file = \'$file\')")) &&
2804 :	parrello	1.298	(@$relational_db_response == 1)) {
2805 :	parrello	1.287	return $relational_db_response->[0]->[0];
2806 :			} elsif (($relational_db_response = $rdbH->SQL("SELECT MAX(fileno) FROM file_table ")) && (@$relational_db_response == 1) && ($relational_db_response->[0]->[0])) {
2807 :			my $fileno = $relational_db_response->[0]->[0] + 1;
2808 :			if ($rdbH->SQL("INSERT INTO file_table ( file, fileno ) VALUES ( \'$file\', $fileno )")) {
2809 :			return $fileno;
2810 :			}
2811 :			} elsif ($rdbH->SQL("INSERT INTO file_table ( file, fileno ) VALUES ( \'$file\', 1 )")) {
2812 :			return 1;
2813 :	efrank	1.1	}
2814 :			return undef;
2815 :			}
2816 :
2817 :			#=pod
2818 :			#
2819 :	parrello	1.287	#=head3 N2file
2820 :	efrank	1.1	#
2821 :			#usage: $filename = $fig->N2file($n)
2822 :			#
2823 :			#In some of the databases I need to store filenames, which can waste a lot of
2824 :			#space. Hence, I maintain a database for converting filenames to/from integers.
2825 :			#
2826 :			#=cut
2827 :			#
2828 :	overbeek	1.364	sub N2file :Scalar
2829 :			{
2830 :	efrank	1.1	my($self,$fileno) = @_;
2831 :	overbeek	1.364
2832 :			#
2833 :			# Cache outputs. This results in a huge savings of time when files are
2834 :			# accessed multiple times (as in when a bunch of sims are requested).
2835 :			#
2836 :
2837 :	parrello	1.379
2838 :	overbeek	1.364	my $fcache = $self->cached("_n2file");
2839 :	parrello	1.379
2840 :	overbeek	1.364	my $fname;
2841 :			if (defined($fname = $fcache->{$fileno}))
2842 :			{
2843 :	parrello	1.365	return $fname;
2844 :	overbeek	1.364	}
2845 :	efrank	1.1
2846 :			my $rdbH = $self->db_handle;
2847 :	parrello	1.379
2848 :	overbeek	1.364	my $relational_db_response = $rdbH->SQL("SELECT file FROM file_table WHERE ( fileno = $fileno )");
2849 :	efrank	1.1
2850 :	overbeek	1.364	if ($relational_db_response and @$relational_db_response == 1)
2851 :			{
2852 :	parrello	1.365	$fname = $relational_db_response->[0]->[0];
2853 :			$fcache->{$fileno} = $fname;
2854 :			return $fname;
2855 :	efrank	1.1	}
2856 :			return undef;
2857 :			}
2858 :
2859 :
2860 :			#=pod
2861 :			#
2862 :	parrello	1.287	#=head3 openF
2863 :	efrank	1.1	#
2864 :			#usage: $fig->openF($filename)
2865 :			#
2866 :			#Parts of the system rely on accessing numerous different files. The most obvious case is
2867 :			#the situation with similarities. It is important that the system be able to run in cases in
2868 :			#which an arbitrary number of files cannot be open simultaneously. This routine (with closeF) is
2869 :			#a hack to handle this. I should probably just pitch them and insist that the OS handle several
2870 :			#hundred open filehandles.
2871 :			#
2872 :			#=cut
2873 :			#
2874 :			sub openF {
2875 :			my($self,$file) = @_;
2876 :			my($fxs,$x,@fxs,$fh);
2877 :
2878 :			$fxs = $self->cached('_openF');
2879 :	parrello	1.287	if ($x = $fxs->{$file}) {
2880 :			$x->[1] = time();
2881 :			return $x->[0];
2882 :	efrank	1.1	}
2883 :	parrello	1.200
2884 :	efrank	1.1	@fxs = keys(%$fxs);
2885 :	parrello	1.287	if (defined($fh = new FileHandle "<$file")) {
2886 :			if (@fxs >= 50) {
2887 :			@fxs = sort { $fxs->{$a}->[1] <=> $fxs->{$b}->[1] } @fxs;
2888 :			$x = $fxs->{$fxs[0]};
2889 :			undef $x->[0];
2890 :			delete $fxs->{$fxs[0]};
2891 :			}
2892 :			$fxs->{$file} = [$fh,time()];
2893 :			return $fh;
2894 :	efrank	1.1	}
2895 :			return undef;
2896 :			}
2897 :
2898 :			#=pod
2899 :			#
2900 :	parrello	1.287	#=head3 closeF
2901 :	efrank	1.1	#
2902 :			#usage: $fig->closeF($filename)
2903 :			#
2904 :			#Parts of the system rely on accessing numerous different files. The most obvious case is
2905 :			#the situation with similarities. It is important that the system be able to run in cases in
2906 :			#which an arbitrary number of files cannot be open simultaneously. This routine (with openF) is
2907 :			#a hack to handle this. I should probably just pitch them and insist that the OS handle several
2908 :			#hundred open filehandles.
2909 :			#
2910 :			#=cut
2911 :			#
2912 :			sub closeF {
2913 :			my($self,$file) = @_;
2914 :			my($fxs,$x);
2915 :
2916 :	parrello	1.287	if (($fxs = $self->{_openF}) && ($x = $fxs->{$file})) {
2917 :			undef $x->[0];
2918 :			delete $fxs->{$file};
2919 :	efrank	1.1	}
2920 :			}
2921 :
2922 :	parrello	1.287	=head3 ec_name
2923 :
2924 :			C<< my $enzymatic_function = $fig->ec_name($ec); >>
2925 :	efrank	1.1
2926 :	parrello	1.287	Returns the enzymatic name corresponding to the specified enzyme code.
2927 :	efrank	1.1
2928 :	parrello	1.287	=over 4
2929 :
2930 :			=item ec
2931 :	efrank	1.1
2932 :	parrello	1.287	Code number for the enzyme whose name is desired. The code number is actually
2933 :			a string of digits and periods (e.g. C<1.2.50.6>).
2934 :
2935 :			=item RETURN
2936 :
2937 :			Returns the name of the enzyme specified by the indicated code, or a null string
2938 :			if the code is not found in the database.
2939 :
2940 :			=back
2941 :	efrank	1.1
2942 :			=cut
2943 :
2944 :			sub ec_name {
2945 :			my($self,$ec) = @_;
2946 :
2947 :			($ec =~ /^\d+\.\d+\.\d+\.\d+$/) \|\| return "";
2948 :			my $rdbH = $self->db_handle;
2949 :			my $relational_db_response = $rdbH->SQL("SELECT name FROM ec_names WHERE ( ec = \'$ec\' )");
2950 :
2951 :			return (@$relational_db_response == 1) ? $relational_db_response->[0]->[0] : "";
2952 :			return "";
2953 :			}
2954 :
2955 :	parrello	1.287	=head3 all_roles
2956 :	efrank	1.1
2957 :	parrello	1.287	C<< my @roles = $fig->all_roles; >>
2958 :	efrank	1.1
2959 :	parrello	1.287	Return a list of the known roles. Currently, this is a list of the enzyme codes and names.
2960 :	efrank	1.1
2961 :	parrello	1.287	The return value is a list of list references. Each element of the big list contains an
2962 :			enzyme code (EC) followed by the enzymatic name.
2963 :	efrank	1.1
2964 :			=cut
2965 :
2966 :			sub all_roles {
2967 :			my($self) = @_;
2968 :
2969 :			my $rdbH = $self->db_handle;
2970 :			my $relational_db_response = $rdbH->SQL("SELECT ec,name FROM ec_names");
2971 :
2972 :			return @$relational_db_response;
2973 :			}
2974 :
2975 :	parrello	1.287	=head3 expand_ec
2976 :	efrank	1.1
2977 :	parrello	1.287	C<< my $expanded_ec = $fig->expand_ec($ec); >>
2978 :	efrank	1.1
2979 :			Expands "1.1.1.1" to "1.1.1.1 - alcohol dehydrogenase" or something like that.
2980 :
2981 :			=cut
2982 :
2983 :			sub expand_ec {
2984 :			my($self,$ec) = @_;
2985 :			my($name);
2986 :
2987 :			return ($name = $self->ec_name($ec)) ? "$ec - $name" : $ec;
2988 :			}
2989 :
2990 :	parrello	1.287	=head3 clean_tmp
2991 :	efrank	1.1
2992 :	parrello	1.287	C<< FIG::clean_tmp(); >>
2993 :	efrank	1.1
2994 :	parrello	1.287	Delete temporary files more than two days old.
2995 :	efrank	1.1
2996 :			We store temporary files in $FIG_Config::temp. There are specific classes of files
2997 :			that are created and should be saved for at least a few days. This routine can be
2998 :			invoked to clean out those that are over two days old.
2999 :
3000 :			=cut
3001 :
3002 :			sub clean_tmp {
3003 :
3004 :			my($file);
3005 :	parrello	1.287	if (opendir(TMP,"$FIG_Config::temp")) {
3006 :			# change the pattern to pick up other files that need to be cleaned up
3007 :			my @temp = grep { $_ =~ /^(Geno\|tmp)/ } readdir(TMP);
3008 :			foreach $file (@temp) {
3009 :			if (-M "$FIG_Config::temp/$file" > 2) {
3010 :			unlink("$FIG_Config::temp/$file");
3011 :			}
3012 :			}
3013 :	efrank	1.1	}
3014 :			}
3015 :
3016 :			################ Routines to process genomes and genome IDs ##########################
3017 :
3018 :
3019 :	parrello	1.287	=head3 genomes
3020 :	efrank	1.1
3021 :	parrello	1.287	C<< my @genome_ids = $fig->genomes($complete, $restrictions, $domain); >>
3022 :	efrank	1.1
3023 :	parrello	1.287	Return a list of genome IDs. If called with no parameters, all genome IDs
3024 :			in the database will be returned.
3025 :	efrank	1.1
3026 :			Genomes are assigned ids of the form X.Y where X is the taxonomic id maintained by
3027 :			NCBI for the species (not the specific strain), and Y is a sequence digit assigned to
3028 :			this particular genome (as one of a set with the same genus/species). Genomes also
3029 :			have versions, but that is a separate issue.
3030 :
3031 :	parrello	1.287	=over 4
3032 :
3033 :			=item complete
3034 :
3035 :			TRUE if only complete genomes should be returned, else FALSE.
3036 :
3037 :			=item restrictions
3038 :
3039 :			TRUE if only restriction genomes should be returned, else FALSE.
3040 :
3041 :			=item domain
3042 :
3043 :			Name of the domain from which the genomes should be returned. Possible values are
3044 :			C<Bacteria>, C<Virus>, C<Eukaryota>, C<unknown>, C<Archaea>, and
3045 :			C<Environmental Sample>. If no domain is specified, all domains will be
3046 :			eligible.
3047 :
3048 :			=item RETURN
3049 :
3050 :			Returns a list of all the genome IDs with the specified characteristics.
3051 :
3052 :			=back
3053 :
3054 :	efrank	1.1	=cut
3055 :	parrello	1.320	#: Return Type @;
3056 :	parrello	1.328	sub genomes :Remote :List {
3057 :	golsen	1.150	my( $self, $complete, $restrictions, $domain ) = @_;
3058 :	overbeek	1.13
3059 :			my $rdbH = $self->db_handle;
3060 :
3061 :			my @where = ();
3062 :	parrello	1.287	if ($complete) {
3063 :			push(@where, "( complete = \'1\' )")
3064 :	overbeek	1.13	}
3065 :
3066 :	parrello	1.287	if ($restrictions) {
3067 :			push(@where, "( restrictions = \'1\' )")
3068 :	overbeek	1.13	}
3069 :	golsen	1.150
3070 :	parrello	1.287	if ($domain) {
3071 :			push( @where, "( maindomain = '$domain' )" )
3072 :	golsen	1.150	}
3073 :
3074 :	overbeek	1.13	my $relational_db_response;
3075 :	parrello	1.287	if (@where > 0) {
3076 :			my $where = join(" AND ",@where);
3077 :			$relational_db_response = $rdbH->SQL("SELECT genome FROM genome where $where");
3078 :			} else {
3079 :			$relational_db_response = $rdbH->SQL("SELECT genome FROM genome");
3080 :	overbeek	1.13	}
3081 :			my @genomes = sort { $a <=> $b } map { $_->[0] } @$relational_db_response;
3082 :	efrank	1.1	return @genomes;
3083 :			}
3084 :
3085 :	parrello	1.287	=head3 is_complete
3086 :
3087 :			C<< my $flag = $fig->is_complete($genome); >>
3088 :
3089 :			Return TRUE if the genome with the specified ID is complete, else FALSE.
3090 :
3091 :			=over 4
3092 :
3093 :			=item genome
3094 :
3095 :			ID of the relevant genome.
3096 :
3097 :			=item RETURN
3098 :
3099 :			Returns TRUE if there is a complete genome in the database with the specified ID,
3100 :			else FALSE.
3101 :
3102 :			=back
3103 :
3104 :			=cut
3105 :
3106 :	overbeek	1.180	sub is_complete {
3107 :			my($self,$genome) = @_;
3108 :
3109 :			my $rdbH = $self->db_handle;
3110 :			my $relational_db_response = $rdbH->SQL("SELECT genome FROM genome where (genome = '$genome') AND (complete = '1')");
3111 :			return (@$relational_db_response == 1)
3112 :	parrello	1.287	}
3113 :
3114 :			=head3 genome_counts
3115 :
3116 :			C<< my ($arch, $bact, $euk, $vir, $env, $unk) = $fig->genome_counts($complete); >>
3117 :
3118 :			Count the number of genomes in each domain. If I<$complete> is TRUE, only complete
3119 :			genomes will be included in the counts.
3120 :
3121 :			=over 4
3122 :
3123 :			=item complete
3124 :
3125 :			TRUE if only complete genomes are to be counted, FALSE if all genomes are to be
3126 :			counted
3127 :
3128 :			=item RETURN
3129 :
3130 :			A six-element list containing the number of genomes in each of six categories--
3131 :			Archaea, Bacteria, Eukaryota, Viral, Environmental, and Unknown, respectively.
3132 :
3133 :			=back
3134 :
3135 :			=cut
3136 :	golsen	1.150
3137 :	efrank	1.2	sub genome_counts {
3138 :	overbeek	1.13	my($self,$complete) = @_;
3139 :			my($x,$relational_db_response);
3140 :	efrank	1.2
3141 :	overbeek	1.13	my $rdbH = $self->db_handle;
3142 :
3143 :	parrello	1.287	if ($complete) {
3144 :			$relational_db_response = $rdbH->SQL("SELECT genome, maindomain FROM genome where complete = '1'");
3145 :			} else {
3146 :			$relational_db_response = $rdbH->SQL("SELECT genome,maindomain FROM genome");
3147 :	overbeek	1.13	}
3148 :
3149 :	gdpusch	1.107	my ($arch, $bact, $euk, $vir, $env, $unk) = (0, 0, 0, 0, 0, 0);
3150 :	parrello	1.287	if (@$relational_db_response > 0) {
3151 :			foreach $x (@$relational_db_response) {
3152 :			if ($x->[1] =~ /^archaea/i) { ++$arch }
3153 :			elsif ($x->[1] =~ /^bacter/i) { ++$bact }
3154 :			elsif ($x->[1] =~ /^eukar/i) { ++$euk }
3155 :			elsif ($x->[1] =~ /^vir/i) { ++$vir }
3156 :			elsif ($x->[1] =~ /^env/i) { ++$env }
3157 :			else { ++$unk }
3158 :	parrello	1.298	}
3159 :	efrank	1.2	}
3160 :	parrello	1.200
3161 :	gdpusch	1.107	return ($arch, $bact, $euk, $vir, $env, $unk);
3162 :			}
3163 :
3164 :
3165 :	parrello	1.287	=head3 genome_domain
3166 :
3167 :			C<< my $domain = $fig->genome_domain($genome_id); >>
3168 :
3169 :			Find the domain of a genome.
3170 :	gdpusch	1.107
3171 :	parrello	1.287	=over 4
3172 :
3173 :			=item genome_id
3174 :	gdpusch	1.107
3175 :	parrello	1.287	ID of the genome whose domain is desired.
3176 :	gdpusch	1.107
3177 :	parrello	1.287	=item RETURN
3178 :
3179 :			Returns the name of the genome's domain (archaea, bacteria, etc.), or C<undef> if
3180 :			the genome is not in the database.
3181 :	gdpusch	1.107
3182 :	parrello	1.292	=back
3183 :
3184 :	gdpusch	1.107	=cut
3185 :
3186 :			sub genome_domain {
3187 :			my($self,$genome) = @_;
3188 :			my $relational_db_response;
3189 :			my $rdbH = $self->db_handle;
3190 :	parrello	1.200
3191 :	parrello	1.287	if ($genome) {
3192 :			if (($relational_db_response = $rdbH->SQL("SELECT genome,maindomain FROM genome WHERE ( genome = \'$genome\' )"))
3193 :			&& (@$relational_db_response == 1)) {
3194 :			# die Dumper($relational_db_response);
3195 :			return $relational_db_response->[0]->[1];
3196 :			}
3197 :	gdpusch	1.107	}
3198 :			return undef;
3199 :	efrank	1.2	}
3200 :
3201 :	gdpusch	1.92
3202 :	parrello	1.287	=head3 genome_pegs
3203 :	gdpusch	1.92
3204 :	parrello	1.287	C<< my $num_pegs = $fig->genome_pegs($genome_id); >>
3205 :	gdpusch	1.92
3206 :	parrello	1.287	Return the number of protein-encoding genes (PEGs) for a specified
3207 :			genome.
3208 :	gdpusch	1.92
3209 :	parrello	1.287	=over 4
3210 :
3211 :			=item genome_id
3212 :
3213 :			ID of the genome whose PEG count is desired.
3214 :
3215 :			=item RETURN
3216 :
3217 :			Returns the number of PEGs for the specified genome, or C<undef> if the genome
3218 :			is not indexed in the database.
3219 :
3220 :			=back
3221 :	gdpusch	1.92
3222 :			=cut
3223 :
3224 :			sub genome_pegs {
3225 :			my($self,$genome) = @_;
3226 :			my $relational_db_response;
3227 :			my $rdbH = $self->db_handle;
3228 :	parrello	1.200
3229 :	parrello	1.287	if ($genome) {
3230 :			if (($relational_db_response = $rdbH->SQL("SELECT pegs FROM genome WHERE ( genome = \'$genome\' )"))
3231 :			&& (@$relational_db_response == 1)) {
3232 :			return $relational_db_response->[0]->[0];
3233 :			}
3234 :	gdpusch	1.92	}
3235 :			return undef;
3236 :			}
3237 :
3238 :
3239 :	parrello	1.287	=head3 genome_rnas
3240 :
3241 :			C<< my $num_rnas = $fig->genome_rnas($genome_id); >>
3242 :
3243 :			Return the number of RNA-encoding genes for a genome.
3244 :			"$genome_id" is indexed in the "genome" database, and 'undef' otherwise.
3245 :	efrank	1.1
3246 :	parrello	1.287	=over 4
3247 :
3248 :			=item genome_id
3249 :
3250 :			ID of the genome whose RNA count is desired.
3251 :
3252 :			=item RETURN
3253 :	gdpusch	1.92
3254 :	parrello	1.287	Returns the number of RNAs for the specified genome, or C<undef> if the genome
3255 :			is not indexed in the database.
3256 :	gdpusch	1.92
3257 :	parrello	1.287	=back
3258 :	gdpusch	1.92
3259 :			=cut
3260 :
3261 :			sub genome_rnas {
3262 :			my($self,$genome) = @_;
3263 :			my $relational_db_response;
3264 :			my $rdbH = $self->db_handle;
3265 :	parrello	1.200
3266 :	parrello	1.287	if ($genome) {
3267 :			if (($relational_db_response = $rdbH->SQL("SELECT rnas FROM genome WHERE ( genome = \'$genome\' )"))
3268 :			&& (@$relational_db_response == 1)) {
3269 :			return $relational_db_response->[0]->[0];
3270 :			}
3271 :	gdpusch	1.92	}
3272 :			return undef;
3273 :			}
3274 :
3275 :
3276 :	parrello	1.287	=head3 genome_szdna
3277 :
3278 :			usage: $szdna = $fig->genome_szdna($genome_id);
3279 :
3280 :			Return the number of DNA base-pairs in a genome's contigs.
3281 :
3282 :			=over 4
3283 :
3284 :			=item genome_id
3285 :
3286 :			ID of the genome whose base-pair count is desired.
3287 :	gdpusch	1.92
3288 :	parrello	1.287	=item RETURN
3289 :	efrank	1.1
3290 :	parrello	1.287	Returns the number of base pairs in the specified genome's contigs, or C<undef>
3291 :			if the genome is not indexed in the database.
3292 :	gdpusch	1.91
3293 :	parrello	1.287	=back
3294 :	gdpusch	1.91
3295 :			=cut
3296 :
3297 :	gdpusch	1.92	sub genome_szdna {
3298 :	gdpusch	1.91	my($self,$genome) = @_;
3299 :			my $relational_db_response;
3300 :			my $rdbH = $self->db_handle;
3301 :	parrello	1.200
3302 :	parrello	1.287	if ($genome) {
3303 :			if (($relational_db_response =
3304 :			$rdbH->SQL("SELECT szdna FROM genome WHERE ( genome = \'$genome\' )"))
3305 :			&& (@$relational_db_response == 1)) {
3306 :
3307 :			return $relational_db_response->[0]->[0];
3308 :
3309 :			}
3310 :	gdpusch	1.91	}
3311 :			return undef;
3312 :			}
3313 :
3314 :	parrello	1.287	=head3 genome_version
3315 :	gdpusch	1.91
3316 :	parrello	1.287	C<< my $version = $fig->genome_version($genome_id); >>
3317 :	gdpusch	1.91
3318 :	parrello	1.287	Return the version number of the specified genome.
3319 :	efrank	1.1
3320 :			Versions are incremented for major updates. They are put in as major
3321 :			updates of the form 1.0, 2.0, ...
3322 :
3323 :			Users may do local "editing" of the DNA for a genome, but when they do,
3324 :			they increment the digits to the right of the decimal. Two genomes remain
3325 :	parrello	1.200	comparable only if the versions match identically. Hence, minor updating should be
3326 :	efrank	1.1	committed only by the person/group responsible for updating that genome.
3327 :
3328 :			We can, of course, identify which genes are identical between any two genomes (by matching
3329 :			the DNA or amino acid sequences). However, the basic intent of the system is to
3330 :			support editing by the main group issuing periodic major updates.
3331 :
3332 :	parrello	1.287	=over 4
3333 :
3334 :			=item genome_id
3335 :
3336 :			ID of the genome whose version is desired.
3337 :
3338 :			=item RETURN
3339 :
3340 :			Returns the version number of the specified genome, or C<undef> if the genome is not in
3341 :			the data store or no version number has been assigned.
3342 :
3343 :			=back
3344 :
3345 :	efrank	1.1	=cut
3346 :
3347 :	parrello	1.328	sub genome_version :Scalar {
3348 :	efrank	1.1	my($self,$genome) = @_;
3349 :
3350 :			my(@tmp);
3351 :			if ((-s "$FIG_Config::organisms/$genome/VERSION") &&
3352 :	parrello	1.298	(@tmp = `cat $FIG_Config::organisms/$genome/VERSION`) &&
3353 :			($tmp[0] =~ /^(\S+)$/)) {
3354 :			return $1;
3355 :	efrank	1.1	}
3356 :			return undef;
3357 :			}
3358 :
3359 :	parrello	1.287	=head3 genome_md5sum
3360 :	olson	1.236
3361 :	parrello	1.287	C<< my $md5sum = $fig->genome_md5sum($genome_id); >>
3362 :	olson	1.236
3363 :	parrello	1.287	Returns the MD5 checksum of the specified genome.
3364 :	olson	1.236
3365 :			The checksum of a genome is defined as the checksum of its signature file. The signature
3366 :			file consists of tab-separated lines, one for each contig, ordered by the contig id.
3367 :	parrello	1.287	Each line contains the contig ID, the length of the contig in nucleotides, and the
3368 :	olson	1.236	MD5 checksum of the nucleotide data, with uppercase letters forced to lower case.
3369 :
3370 :	parrello	1.287	The checksum is indexed in the database. If you know a genome's checksum, you can use
3371 :			the L</genome_with_md5sum> method to find its ID in the database.
3372 :
3373 :			=over 4
3374 :
3375 :			=item genome
3376 :
3377 :			ID of the genome whose checksum is desired.
3378 :
3379 :			=item RETURN
3380 :
3381 :			Returns the specified genome's checksum, or C<undef> if the genome is not in the
3382 :			database.
3383 :
3384 :			=back
3385 :	olson	1.236
3386 :			=cut
3387 :
3388 :	parrello	1.328	sub genome_md5sum :Scalar {
3389 :	olson	1.236	my($self,$genome) = @_;
3390 :			my $relational_db_response;
3391 :			my $rdbH = $self->db_handle;
3392 :
3393 :	parrello	1.287	if ($genome) {
3394 :			if (($relational_db_response =
3395 :			$rdbH->SQL("SELECT md5sum FROM genome_md5sum WHERE ( genome = \'$genome\' )"))
3396 :			&& (@$relational_db_response == 1)) {
3397 :			return $relational_db_response->[0]->[0];
3398 :			}
3399 :	olson	1.236	}
3400 :			return undef;
3401 :			}
3402 :
3403 :	parrello	1.287	=head3 genome_with_md5sum
3404 :
3405 :			C<< my $genome = $fig->genome_with_md5sum($cksum); >>
3406 :
3407 :			Find a genome with the specified checksum.
3408 :
3409 :			The MD5 checksum is computed from the content of the genome (see L</genome_md5sum>). This method
3410 :			can be used to determine if a genome already exists for a specified content.
3411 :
3412 :			=over 4
3413 :
3414 :			=item cksum
3415 :
3416 :			Checksum to use for searching the genome table.
3417 :	olson	1.260
3418 :	parrello	1.287	=item RETURN
3419 :
3420 :			The ID of a genome with the specified checksum, or C<undef> if no such genome exists.
3421 :	olson	1.260
3422 :	parrello	1.287	=back
3423 :	olson	1.260
3424 :			=cut
3425 :
3426 :	parrello	1.328	sub genome_with_md5sum :Scalar {
3427 :	olson	1.260	my($self,$cksum) = @_;
3428 :			my $relational_db_response;
3429 :			my $rdbH = $self->db_handle;
3430 :
3431 :	parrello	1.287	if (($relational_db_response =
3432 :			$rdbH->SQL("SELECT genome FROM genome_md5sum WHERE ( md5sum = \'$cksum\' )"))
3433 :	parrello	1.298	&& (@$relational_db_response == 1)) {
3434 :			return $relational_db_response->[0]->[0];
3435 :	olson	1.260	}
3436 :
3437 :			return undef;
3438 :			}
3439 :
3440 :	parrello	1.287	=head3 contig_md5sum
3441 :
3442 :			C<< my $cksum = $fig->contig_md5sum($genome, $contig); >>
3443 :
3444 :			Return the MD5 checksum for a contig. The MD5 checksum is computed from the content
3445 :			of the contig. This method retrieves the checksum stored in the database. The checksum
3446 :			can be compared to the checksum of an external contig as a cheap way of seeing if they
3447 :			match.
3448 :
3449 :			=over 4
3450 :
3451 :			=item genome
3452 :
3453 :			ID of the genome containing the contig.
3454 :
3455 :			=item contig
3456 :
3457 :			ID of the relevant contig.
3458 :
3459 :			=item RETURN
3460 :
3461 :			Returns the checksum of the specified contig, or C<undef> if the contig is not in the
3462 :			database.
3463 :
3464 :			=back
3465 :
3466 :			=cut
3467 :
3468 :	parrello	1.328	sub contig_md5sum :Scalar {
3469 :	olson	1.237	my($self, $genome, $contig) = @_;
3470 :			my $relational_db_response;
3471 :			my $rdbH = $self->db_handle;
3472 :
3473 :	parrello	1.287	if ($genome) {
3474 :			if (($relational_db_response =
3475 :			$rdbH->SQL(qq(SELECT md5 FROM contig_md5sums WHERE (genome = ? AND contig = ?)), undef, $genome, $contig))
3476 :			&& (@$relational_db_response == 1)) {
3477 :			return $relational_db_response->[0]->[0];
3478 :			}
3479 :	olson	1.237	}
3480 :			return undef;
3481 :			}
3482 :
3483 :	parrello	1.287	=head3 genus_species
3484 :
3485 :			C<< my $gs = $fig->genus_species($genome_id); >>
3486 :
3487 :			Return the genus, species, and possibly also the strain of a specified genome.
3488 :
3489 :			This method converts a genome ID into a more recognizble species name. The species name
3490 :			is stored directly in the genome table of the database. Essentially, if the strain is
3491 :			present in the database, it will be returned by this method, and if it's not present,
3492 :			it won't.
3493 :	efrank	1.1
3494 :	parrello	1.287	=over 4
3495 :
3496 :			=item genome_id
3497 :
3498 :			ID of the genome whose name is desired.
3499 :	efrank	1.1
3500 :	parrello	1.287	=item RETURN
3501 :
3502 :			Returns the scientific species name associated with the specified ID, or C<undef> if the
3503 :			ID is not in the database.
3504 :	efrank	1.1
3505 :	parrello	1.287	=back
3506 :	efrank	1.1
3507 :			=cut
3508 :	parrello	1.320	#: Return Type $;
3509 :	parrello	1.328	sub genus_species :Scalar {
3510 :	efrank	1.1	my ($self,$genome) = @_;
3511 :	overbeek	1.13	my $ans;
3512 :	efrank	1.1
3513 :			my $genus_species = $self->cached('_genus_species');
3514 :	parrello	1.287	if (! ($ans = $genus_species->{$genome})) {
3515 :			my $rdbH = $self->db_handle;
3516 :			my $relational_db_response = $rdbH->SQL("SELECT genome,gname FROM genome");
3517 :			my $pair;
3518 :			foreach $pair (@$relational_db_response) {
3519 :			$genus_species->{$pair->[0]} = $pair->[1];
3520 :			}
3521 :			$ans = $genus_species->{$genome};
3522 :	efrank	1.1	}
3523 :			return $ans;
3524 :			}
3525 :
3526 :	parrello	1.287	=head3 org_of
3527 :
3528 :			C<< my $org = $fig->org_of($prot_id); >>
3529 :
3530 :			Return the genus/species name of the organism containing a protein. Note that in this context
3531 :			I<protein> is not a certain string of amino acids but a protein encoding region on a specific
3532 :			contig.
3533 :
3534 :			For a FIG protein ID (e.g. C<fig\|134537.1.peg.123>), the organism and strain
3535 :			information is always available. In the case of external proteins, we can usually
3536 :			determine an organism, but not anything more precise than genus/species (and
3537 :			often not that). When the organism name is not present, a null string is returned.
3538 :
3539 :			=over 4
3540 :
3541 :			=item prot_id
3542 :	efrank	1.1
3543 :	parrello	1.287	Protein or feature ID.
3544 :	efrank	1.1
3545 :	parrello	1.287	=item RETURN
3546 :
3547 :			Returns the displayable scientific name (genus, species, and strain) of the organism containing
3548 :			the identified PEG. If the name is not available, returns a null string. If the PEG is not found,
3549 :			returns C<undef>.
3550 :	efrank	1.1
3551 :	parrello	1.287	=back
3552 :	efrank	1.1
3553 :			=cut
3554 :
3555 :			sub org_of {
3556 :			my($self,$prot_id) = @_;
3557 :			my $relational_db_response;
3558 :			my $rdbH = $self->db_handle;
3559 :
3560 :	parrello	1.287	if ($prot_id =~ /^fig\\|/) {
3561 :			return $self->is_deleted_fid( $prot_id) ? undef
3562 :			: $self->genus_species( $self->genome_of( $prot_id ) ) \|\| "";
3563 :	efrank	1.1	}
3564 :
3565 :	parrello	1.287	if (($relational_db_response =
3566 :			$rdbH->SQL("SELECT org FROM external_orgs WHERE ( prot = \'$prot_id\' )")) &&
3567 :			(@$relational_db_response >= 1)) {
3568 :			$relational_db_response->[0]->[0] =~ s/^\d+://;
3569 :			return $relational_db_response->[0]->[0];
3570 :	efrank	1.1	}
3571 :			return "";
3572 :			}
3573 :
3574 :	parrello	1.287	=head3 genus_species_domain
3575 :
3576 :			C<< my ($gs, $domain) = $fig->genus_species_domain($genome_id); >>
3577 :
3578 :			Returns a genome's genus and species (and strain if that has been properly
3579 :			recorded) in a printable form, along with its domain. This method is similar
3580 :			to L</genus_species>, except it also returns the domain name (archaea,
3581 :			bacteria, etc.).
3582 :
3583 :			=over 4
3584 :
3585 :			=item genome_id
3586 :
3587 :			ID of the genome whose species and domain information is desired.
3588 :	golsen	1.130
3589 :	parrello	1.287	=item RETURN
3590 :	golsen	1.130
3591 :	parrello	1.287	Returns a two-element list. The first element is the species name and the
3592 :			second is the domain name.
3593 :	golsen	1.130
3594 :	parrello	1.287	=back
3595 :	golsen	1.130
3596 :			=cut
3597 :
3598 :			sub genus_species_domain {
3599 :			my ($self, $genome) = @_;
3600 :
3601 :			my $genus_species_domain = $self->cached('_genus_species_domain');
3602 :	parrello	1.287	if ( ! $genus_species_domain->{ $genome } ) {
3603 :			my $rdbH = $self->db_handle;
3604 :			my $relational_db_response = $rdbH->SQL("SELECT genome,gname,maindomain FROM genome");
3605 :			my $triple;
3606 :			foreach $triple ( @$relational_db_response ) {
3607 :			$genus_species_domain->{ $triple->[0] } = [ $triple->[1], $triple->[2] ];
3608 :			}
3609 :	golsen	1.130	}
3610 :			my $gsdref = $genus_species_domain->{ $genome };
3611 :			return $gsdref ? @$gsdref : ( "", "" );
3612 :			}
3613 :
3614 :	parrello	1.287	=head3 domain_color
3615 :
3616 :			C<< my $web_color = FIG::domain_color($domain); >>
3617 :
3618 :			Return the web color string associated with a specified domain. The colors are
3619 :			extremely subtle (86% luminance), so they absolutely require a black background.
3620 :			Archaea are slightly cyan, bacteria are slightly magenta, eukaryota are slightly
3621 :			yellow, viruses are slightly silver, environmental samples are slightly gray,
3622 :			and unknown or invalid domains are pure white.
3623 :
3624 :			=over 4
3625 :
3626 :			=item domain
3627 :
3628 :			Name of the domain whose color is desired.
3629 :
3630 :			=item RETURN
3631 :
3632 :			Returns a web color string for the specified domain (e.g. C<#FFDDFF> for
3633 :			bacteria).
3634 :
3635 :			=back
3636 :
3637 :			=cut
3638 :	golsen	1.130
3639 :			my %domain_color = ( AR => "#DDFFFF", BA => "#FFDDFF", EU => "#FFFFDD",
3640 :			VI => "#DDDDDD", EN => "#BBBBBB" );
3641 :
3642 :			sub domain_color {
3643 :			my ($domain) = @_;
3644 :			defined $domain \|\| return "#FFFFFF";
3645 :			return $domain_color{ uc substr($domain, 0, 2) } \|\| "#FFFFFF";
3646 :			}
3647 :
3648 :	parrello	1.287	=head3 org_and_color_of
3649 :	golsen	1.130
3650 :	parrello	1.287	C<< my ($org, $color) = $fig->org_and_domain_of($prot_id); >>
3651 :	golsen	1.130
3652 :	parrello	1.287	Return the best guess organism and domain html color string of an organism.
3653 :			In the case of external proteins, we can usually determine an organism, but not
3654 :			anything more precise than genus/species (and often not that).
3655 :
3656 :			=over 4
3657 :
3658 :			=item prot_id
3659 :
3660 :			Relevant protein or feature ID.
3661 :
3662 :			=item RETURN
3663 :	golsen	1.130
3664 :	parrello	1.287	Returns a two-element list. The first element is the displayable organism name, and the second
3665 :			is an HTML color string based on the domain (see L</domain_color>).
3666 :	golsen	1.130
3667 :	parrello	1.287	=back
3668 :	golsen	1.130
3669 :			=cut
3670 :
3671 :			sub org_and_color_of {
3672 :			my($self,$prot_id) = @_;
3673 :			my $relational_db_response;
3674 :			my $rdbH = $self->db_handle;
3675 :
3676 :	parrello	1.287	if ($prot_id =~ /^fig\\|/) {
3677 :			my( $gs, $domain ) = $self->genus_species_domain($self->genome_of($prot_id));
3678 :			return ( $gs, domain_color( $domain ) );
3679 :	golsen	1.130	}
3680 :
3681 :	parrello	1.287	if (($relational_db_response =
3682 :			$rdbH->SQL("SELECT org FROM external_orgs WHERE ( prot = \'$prot_id\' )")) &&
3683 :			(@$relational_db_response >= 1)) {
3684 :			return ($relational_db_response->[0]->[0], "#FFFFFF");
3685 :	golsen	1.130	}
3686 :			return ("", "#FFFFFF");
3687 :			}
3688 :
3689 :	redwards	1.310	=head3 partial_genus_matching
3690 :
3691 :			Return a list of genome IDs that match a partial genus.
3692 :
3693 :	redwards	1.311	For example partial_genus_matching("Listeria") will return all genome IDs that begin with Listeria, and this can also be restricted to complete genomes with another argument like this partial_genus_matching("Listeria", 1)
3694 :	redwards	1.310
3695 :			=cut
3696 :
3697 :			sub partial_genus_matching {
3698 :	redwards	1.311	my ($self, $gen, $complete)=@_;
3699 :			return grep {$self->genus_species($_) =~ /$gen/i} $self->genomes($complete);
3700 :	redwards	1.310	}
3701 :
3702 :
3703 :	parrello	1.287	=head3 abbrev
3704 :
3705 :			C<< my $abbreviated_name = FIG::abbrev($genome_name); >>
3706 :	golsen	1.130
3707 :	parrello	1.287	or
3708 :	efrank	1.1
3709 :	parrello	1.287	C<< my $abbreviated_name = $fig->abbrev($genome_name); >>
3710 :	efrank	1.1
3711 :	parrello	1.287	Abbreviate a genome name to 10 characters or less.
3712 :	efrank	1.1
3713 :			For alignments and such, it is very useful to be able to produce an abbreviation of genus/species.
3714 :			That's what this does. Note that multiple genus/species might reduce to the same abbreviation, so
3715 :			be careful (disambiguate them, if you must).
3716 :
3717 :	parrello	1.287	The abbreviation is formed from the first three letters of the species name followed by the
3718 :			first three letters of the genus name followed by the first three letters of the species name and
3719 :			then the next four nonblank characters.
3720 :
3721 :			=over 4
3722 :
3723 :			=item genome_name
3724 :
3725 :			The name to abbreviate.
3726 :
3727 :			=item RETURN
3728 :
3729 :			An abbreviated version of the specified name.
3730 :
3731 :			=back
3732 :
3733 :	efrank	1.1	=cut
3734 :
3735 :	parrello	1.328	sub abbrev :Scalar {
3736 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3737 :	efrank	1.1	my($genome_name) = @_;
3738 :
3739 :			$genome_name =~ s/^(\S{3})\S+/$1./;
3740 :	overbeek	1.198	$genome_name =~ s/^(\S+)\s+(\S{3})\S+/$1$2./;
3741 :	overbeek	1.257	$genome_name =~ s/ //g;
3742 :	parrello	1.287	if (length($genome_name) > 10) {
3743 :	parrello	1.298	$genome_name = substr($genome_name,0,10);
3744 :	efrank	1.1	}
3745 :			return $genome_name;
3746 :			}
3747 :
3748 :			################ Routines to process Features and Feature IDs ##########################
3749 :
3750 :	parrello	1.287	=head3 ftype
3751 :
3752 :			C<< my $type = FIG::ftype($fid); >>
3753 :	efrank	1.1
3754 :	parrello	1.287	or
3755 :	efrank	1.1
3756 :	parrello	1.287	C<< my $type = $fig->ftype($fid); >>
3757 :	efrank	1.1
3758 :			Returns the type of a feature, given the feature ID. This just amounts
3759 :	parrello	1.287	to lifting it out of the feature ID, since features have IDs of the form
3760 :	efrank	1.1
3761 :	parrello	1.287	fig\|x.y.f.n
3762 :	efrank	1.1
3763 :			where
3764 :			x.y is the genome ID
3765 :	parrello	1.287	f is the type of feature
3766 :	efrank	1.1	n is an integer that is unique within the genome/type
3767 :
3768 :	parrello	1.287	=over 4
3769 :
3770 :			=item fid
3771 :
3772 :			FIG ID of the feature whose type is desired.
3773 :
3774 :			=item RETURN
3775 :
3776 :			Returns the feature type (e.g. C<peg>, C<rna>, C<pi>, or C<pp>), or C<undef> if the
3777 :			feature ID is not a FIG ID.
3778 :
3779 :			=back
3780 :
3781 :	efrank	1.1	=cut
3782 :
3783 :			sub ftype {
3784 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3785 :	efrank	1.1	my($feature_id) = @_;
3786 :
3787 :	parrello	1.287	if ($feature_id =~ /^fig\\|\d+\.\d+\.([^\.]+)/) {
3788 :	parrello	1.365	return $1;
3789 :	efrank	1.1	}
3790 :			return undef;
3791 :			}
3792 :
3793 :	parrello	1.287	=head3 genome_of
3794 :
3795 :			C<< my $genome_id = $fig->genome_of($fid); >>
3796 :
3797 :			or
3798 :
3799 :			C<< my $genome_id = FIG::genome_of($fid); >>
3800 :
3801 :			Return the genome ID from a feature ID.
3802 :	efrank	1.1
3803 :	parrello	1.287	=over 4
3804 :
3805 :			=item fid
3806 :
3807 :			ID of the feature whose genome ID is desired.
3808 :
3809 :			=item RETURN
3810 :	efrank	1.1
3811 :	parrello	1.287	If the feature ID is a FIG ID, returns the genome ID embedded inside it; otherwise, it
3812 :			returns C<undef>.
3813 :	efrank	1.1
3814 :	parrello	1.287	=back
3815 :	efrank	1.1
3816 :			=cut
3817 :
3818 :
3819 :	parrello	1.328	sub genome_of :Scalar {
3820 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3821 :	parrello	1.200	my $prot_id = (@_ == 1) ? $_[0] : $_[1];
3822 :	efrank	1.1
3823 :			if ($prot_id =~ /^fig\\|(\d+\.\d+)/) { return $1; }
3824 :			return undef;
3825 :			}
3826 :
3827 :	parrello	1.287	=head3 genome_and_peg_of
3828 :
3829 :			C<< my ($genome_id, $peg_number = FIG::genome_and_peg_of($fid); >>
3830 :
3831 :			C<< my ($genome_id, $peg_number = $fig->genome_and_peg_of($fid); >>
3832 :	olson	1.96
3833 :	parrello	1.287	Return the genome ID and peg number from a feature ID.
3834 :	olson	1.96
3835 :	parrello	1.287	=over 4
3836 :
3837 :			=item prot_id
3838 :
3839 :			ID of the feature whose genome and PEG number as desired.
3840 :
3841 :			=item RETURN
3842 :
3843 :			Returns the genome ID and peg number associated with a feature if the feature
3844 :			is represented by a FIG ID, else C<undef>.
3845 :
3846 :			=back
3847 :	olson	1.96
3848 :			=cut
3849 :
3850 :			sub genome_and_peg_of {
3851 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3852 :	parrello	1.200	my $prot_id = (@_ == 1) ? $_[0] : $_[1];
3853 :	olson	1.96
3854 :	parrello	1.287	if ($prot_id =~ /^fig\\|(\d+\.\d+)\.peg\.(\d+)/) {
3855 :	parrello	1.298	return ($1, $2);
3856 :	olson	1.96	}
3857 :			return undef;
3858 :			}
3859 :
3860 :	parrello	1.287	=head3 by_fig_id
3861 :
3862 :			C<< my @sorted_by_fig_id = sort { FIG::by_fig_id($a,$b) } @fig_ids; >>
3863 :
3864 :			Compare two feature IDs.
3865 :
3866 :			This function is designed to assist in sorting features by ID. The sort is by
3867 :			genome ID followed by feature type and then feature number.
3868 :
3869 :			=over 4
3870 :
3871 :			=item a
3872 :	efrank	1.1
3873 :	parrello	1.287	First feature ID.
3874 :	efrank	1.1
3875 :	parrello	1.287	=item b
3876 :	efrank	1.1
3877 :	parrello	1.287	Second feature ID.
3878 :
3879 :			=item RETURN
3880 :
3881 :			Returns a negative number if the first parameter is smaller, zero if both parameters
3882 :			are equal, and a positive number if the first parameter is greater.
3883 :
3884 :			=back
3885 :	efrank	1.1
3886 :			=cut
3887 :
3888 :			sub by_fig_id {
3889 :			my($a,$b) = @_;
3890 :			my($g1,$g2,$t1,$t2,$n1,$n2);
3891 :			if (($a =~ /^fig\\|(\d+\.\d+).([^\.]+)\.(\d+)$/) && (($g1,$t1,$n1) = ($1,$2,$3)) &&
3892 :	parrello	1.298	($b =~ /^fig\\|(\d+\.\d+).([^\.]+)\.(\d+)$/) && (($g2,$t2,$n2) = ($1,$2,$3))) {
3893 :			($g1 <=> $g2) or ($t1 cmp $t2) or ($n1 <=> $n2);
3894 :	parrello	1.287	} else {
3895 :	parrello	1.298	$a cmp $b;
3896 :	efrank	1.1	}
3897 :			}
3898 :
3899 :	olson	1.357	=head3 by_genome_id
3900 :
3901 :			C<< my @sorted_by_genome_id = sort { FIG::by_genome_id($a,$b) } @genome_ids; >>
3902 :
3903 :			Compare two genome IDs.
3904 :
3905 :	parrello	1.379	This function is designed to assist in sorting genomes by ID.
3906 :	olson	1.357
3907 :			=over 4
3908 :
3909 :			=item a
3910 :
3911 :			First genome ID.
3912 :
3913 :			=item b
3914 :
3915 :			Second genome ID.
3916 :
3917 :			=item RETURN
3918 :
3919 :			Returns a negative number if the first parameter is smaller, zero if both parameters
3920 :			are equal, and a positive number if the first parameter is greater.
3921 :
3922 :			=back
3923 :
3924 :			=cut
3925 :
3926 :			sub by_genome_id {
3927 :			my($a,$b) = @_;
3928 :			my($g1,$g2,$s1, $s2);
3929 :			if (($a =~ /^(\d+)\.(\d+)$/) && (($g1, $s1) = ($1, $2)) &&
3930 :	parrello	1.365	($b =~ /^(\d+)\.(\d+)$/) && (($g2, $s2) = ($1, $2))) {
3931 :	olson	1.357	($g1 <=> $g2) or ($s1 <=> $s2);
3932 :			} else {
3933 :			$a cmp $b;
3934 :			}
3935 :			}
3936 :
3937 :	parrello	1.287	=head3 genes_in_region
3938 :	efrank	1.1
3939 :	parrello	1.287	C<< my ($features_in_region, $beg1, $end1) = $fig->genes_in_region($genome, $contig, $beg, $end, size_limit); >>
3940 :	efrank	1.1
3941 :	parrello	1.287	Locate features that overlap a specified region of a contig. This includes features that begin or end
3942 :			outside that region, just so long as some part of the feature can be found in the region of interest.
3943 :	efrank	1.1
3944 :			It is often important to be able to find the genes that occur in a specific region on
3945 :			a chromosome. This routine is designed to provide this information. It returns all genes
3946 :	parrello	1.287	that overlap positions from I<$beg> through I<$end> in the specified contig.
3947 :
3948 :			The I<$size_limit> parameter limits the search process. It is presumed that no features are longer than the
3949 :			specified size limit. A shorter size limit means you'll miss some features; a longer size limit significantly
3950 :			slows the search process. For prokaryotes, a value of C<10000> (the default) seems to work best.
3951 :
3952 :			=over 4
3953 :
3954 :			=item genome
3955 :
3956 :			ID of the genome containing the relevant contig.
3957 :
3958 :			=item contig
3959 :
3960 :			ID of the relevant contig.
3961 :
3962 :			=item beg
3963 :
3964 :			Position of the first base pair in the region of interest.
3965 :
3966 :			=item end
3967 :
3968 :			Position of the last base pair in the region of interest.
3969 :
3970 :			=item size_limit
3971 :
3972 :			Maximum allowable size for a feature. If omitted, C<10000> is assumed.
3973 :
3974 :			=item RETURN
3975 :	efrank	1.1
3976 :	parrello	1.287	Returns a three-element list. The first element is a reference to a list of the feature IDs found. The second
3977 :			element is the position of the leftmost base pair in any feature found. This may be well before the region of
3978 :			interest begins or it could be somewhere inside. The third element is the position of the rightmost base pair
3979 :			in any feature found. Again, this can be somewhere inside the region or it could be well to the right of it.
3980 :
3981 :			=back
3982 :	efrank	1.1
3983 :			=cut
3984 :	parrello	1.213	#: Return Type @;
3985 :	efrank	1.1	sub genes_in_region {
3986 :	parrello	1.287	my($self, $genome, $contig, $beg, $end, $pad) = @_;
3987 :			if (!defined $pad) { $pad = 10000; }
3988 :	efrank	1.1	my($x,$relational_db_response,$feature_id,$b1,$e1,@feat,@tmp,$l,$u);
3989 :
3990 :			my $rdbH = $self->db_handle;
3991 :
3992 :	parrello	1.200	my $minV = $beg - $pad;
3993 :	efrank	1.1	my $maxV = $end + $pad;
3994 :	parrello	1.287	if (($relational_db_response = $rdbH->SQL("SELECT id FROM features "
3995 :			. " WHERE ( minloc > $minV ) AND ( minloc < $maxV ) AND ( maxloc < $maxV) AND "
3996 :			. " ( genome = \'$genome\' ) AND ( contig = \'$contig\' );")) &&
3997 :			(@$relational_db_response >= 1)) {
3998 :			@tmp = sort { ($a->[1] cmp $b->[1]) or (($a->[2]+$a->[3]) <=> ($b->[2]+$b->[3])) }
3999 :			map { $feature_id = $_->[0]; $x = $self->feature_location($feature_id); $x ? [$feature_id,&boundaries_of($x)] : ()
4000 :			} @$relational_db_response;
4001 :	efrank	1.1
4002 :
4003 :	parrello	1.287	($l,$u) = (10000000000,0);
4004 :			foreach $x (@tmp)
4005 :			{
4006 :			($feature_id,undef,$b1,$e1) = @$x;
4007 :			if (&between($beg,&min($b1,$e1),$end) \|\| &between(&min($b1,$e1),$beg,&max($b1,$e1)))
4008 :			{
4009 :			if (! $self->is_deleted_fid($feature_id))
4010 :			{
4011 :			push(@feat,$feature_id);
4012 :			$l = &min($l,&min($b1,$e1));
4013 :			$u = &max($u,&max($b1,$e1));
4014 :			}
4015 :			}
4016 :			}
4017 :			(@feat <= 0) \|\| return ([@feat],$l,$u);
4018 :	efrank	1.1	}
4019 :			return ([],$l,$u);
4020 :			}
4021 :
4022 :	golsen	1.141
4023 :			#=============================================================================
4024 :			# Using the following version is better, but it brings out a very annoying
4025 :			# issue with some genomes. It already exists in the current code (above)
4026 :			# for some genes in some genomes. For example, visit fig\|70601.1.peg.1.
4027 :			# This is true for any genome that has a feature that crosses the origin.
4028 :			# The root of the problem lies in boundaries_of. I am working on a fix that
4029 :			# replaces boundaries_of with a more sophisticated function. When it is
4030 :			# all done, genes_in_retion should behave as desired. -- GJO, Aug. 22, 2004
4031 :			#=============================================================================
4032 :	parrello	1.200	#
4033 :	golsen	1.141	# =pod
4034 :	parrello	1.200	#
4035 :	parrello	1.287	# =head3 genes_in_region
4036 :	parrello	1.200	#
4037 :	golsen	1.141	# usage: ( $features_in_region, $min_coord, $max_coord )
4038 :			# = $fig->genes_in_region( $genome, $contig, $beg, $end )
4039 :	parrello	1.200	#
4040 :	golsen	1.141	# It is often important to be able to find the genes that occur in a specific
4041 :			# region on a chromosome. This routine is designed to provide this information.
4042 :			# It returns all genes that overlap the region ( $genome, $contig, $beg, $end ).
4043 :			# $min_coord is set to the minimum coordinate of the returned genes (which may
4044 :			# preceed the given region), and $max_coord the maximum coordinate. Because
4045 :			# the database is indexed by the leftmost and rightmost coordinates of each
4046 :			# feature, the function makes no assumption about the length of the feature, but
4047 :			# it can (and probably will) miss features spanning multiple contigs.
4048 :	parrello	1.200	#
4049 :	golsen	1.141	# =cut
4050 :	parrello	1.200	#
4051 :			#
4052 :	golsen	1.141	# sub genes_in_region {
4053 :			# my ( $self, $genome, $contig, $beg, $end ) = @_;
4054 :			# my ( $x, $db_response, $feature_id, $b1, $e1, @tmp, @bounds );
4055 :			# my ( $min_coord, $max_coord );
4056 :	parrello	1.200	#
4057 :	golsen	1.141	# my @features = ();
4058 :			# my $rdbH = $self->db_handle;
4059 :	parrello	1.200	#
4060 :	golsen	1.141	# if ( ( $db_response = $rdbH->SQL( "SELECT id
4061 :			# FROM features
4062 :			# WHERE ( contig = '$contig' )
4063 :			# AND ( genome = '$genome' )
4064 :	parrello	1.200	# AND ( minloc <= $end )
4065 :	golsen	1.141	# AND ( maxloc >= $beg );"
4066 :			# )
4067 :			# )
4068 :	parrello	1.365	# && ( @$db_response > 0 )
4069 :	golsen	1.141	# )
4070 :			# {
4071 :			# # The sort is unnecessary, but provides a consistent ordering
4072 :	parrello	1.200	#
4073 :	parrello	1.365	# @tmp = sort { ( $a->[1] cmp $b->[1] ) # contig
4074 :			# \|\| ( ($a->[2] + $a->[3] ) <=> ( $b->[2] + $b->[3] ) ) # midpoint
4075 :	golsen	1.141	# }
4076 :	parrello	1.365	# map { $feature_id = $_->[0];
4077 :			# ( ( ! $self->is_deleted_fid( $feature_id ) ) # not deleted
4078 :	golsen	1.141	# && ( $x = $self->feature_location( $feature_id ) ) # and has location
4079 :			# && ( ( @bounds = boundaries_of( $x ) ) == 3 ) # and has bounds
4080 :	parrello	1.200	# ) ? [ $feature_id, @bounds ] : ()
4081 :	golsen	1.141	# } @$db_response;
4082 :	parrello	1.200	#
4083 :	parrello	1.365	# ( $min_coord, $max_coord ) = ( 10000000000, 0 );
4084 :	parrello	1.200	#
4085 :	parrello	1.365	# foreach $x ( @tmp )
4086 :			# {
4087 :			# ( $feature_id, undef, $b1, $e1 ) = @$x;
4088 :			# push @features, $feature_id;
4089 :			# my ( $min, $max ) = ( $b1 <= $e1 ) ? ( $b1, $e1 ) : ( $e1, $b1 );
4090 :			# ( $min_coord <= $min ) \|\| ( $min_coord = $min );
4091 :			# ( $max_coord >= $max ) \|\| ( $max_coord = $max );
4092 :			# }
4093 :	golsen	1.141	# }
4094 :	parrello	1.200	#
4095 :	golsen	1.141	# return ( @features ) ? ( [ @features ], $min_coord, $max_coord )
4096 :			# : ( [], undef, undef );
4097 :			# }
4098 :
4099 :			# These will be part of the fix to genes_in_region. -- GJO
4100 :
4101 :	parrello	1.287	=head3 regions_spanned
4102 :
4103 :			C<< my ( [ $contig, $beg, $end ], ... ) = $fig->regions_spanned( $loc ); >>
4104 :	golsen	1.141
4105 :	parrello	1.287	or
4106 :	golsen	1.141
4107 :	parrello	1.287	C<< my ( [ $contig, $beg, $end ], ... ) = FIG::regions_spanned( $loc ); >>
4108 :	golsen	1.141
4109 :			The location of a feature in a scalar context is
4110 :
4111 :	parrello	1.287	contig_b1_e1, contig_b2_e2, ... [one contig_b_e for each segment]
4112 :
4113 :			This routine takes as input a scalar location in the above form
4114 :			and reduces it to one or more regions spanned by the gene. This
4115 :			involves combining regions in the location string that are on the
4116 :			same contig and going in the same direction. Unlike L</boundaries_of>,
4117 :			which returns one region in which the entire gene can be found,
4118 :			B<regions_spanned> handles wrapping through the orgin, features
4119 :			split over contigs and exons that are not ordered nicely along
4120 :			the chromosome (ugly but true).
4121 :	golsen	1.141
4122 :	parrello	1.287	=over 4
4123 :
4124 :			=item loc
4125 :
4126 :			The location string for a feature.
4127 :
4128 :			=item RETURN
4129 :
4130 :			Returns a list of list references. Each inner list contains a contig ID, a starting
4131 :			position, and an ending position. The starting position may be numerically greater
4132 :			than the ending position (which indicates a backward-traveling gene). It is
4133 :			guaranteed that the entire feature is covered by the regions in the list.
4134 :
4135 :			=back
4136 :	golsen	1.141
4137 :			=cut
4138 :
4139 :			sub regions_spanned {
4140 :			shift if UNIVERSAL::isa( $_[0], __PACKAGE__ );
4141 :			my( $location ) = ( @_ == 1 ) ? $_[0] : $_[1];
4142 :			defined( $location ) \|\| return undef;
4143 :
4144 :			my @regions = ();
4145 :
4146 :			my ( $cur_contig, $cur_beg, $cur_end, $cur_dir );
4147 :			my ( $contig, $beg, $end, $dir );
4148 :			my @segs = split( /\s,\s/, $location ); # should not have space, but ...
4149 :			@segs \|\| return undef;
4150 :
4151 :			# Process the first segment
4152 :
4153 :			my $seg = shift @segs;
4154 :			( ( $cur_contig, $cur_beg, $cur_end ) = ( $seg =~ /^(\S+)_(\d+)_\d+$/ ) )
4155 :			\|\| return undef;
4156 :			$cur_dir = ( $cur_end >= $cur_beg ) ? 1 : -1;
4157 :
4158 :			foreach $seg ( @segs ) {
4159 :	parrello	1.298	( ( $contig, $beg, $end ) = ( $seg =~ /^(\S+)_(\d+)_\d+$/ ) ) \|\| next;
4160 :			$dir = ( $end >= $beg ) ? 1 : -1;
4161 :	golsen	1.141
4162 :	parrello	1.298	# Is this a continuation? Update end
4163 :	golsen	1.141
4164 :	parrello	1.298	if ( ( $contig eq $cur_contig )
4165 :			&& ( $dir == $cur_dir )
4166 :			&& ( ( ( $dir > 0 ) && ( $end > $cur_end ) )
4167 :			\|\| ( ( $dir < 0 ) && ( $end < $cur_end ) ) )
4168 :			)
4169 :			{
4170 :			$cur_end = $end;
4171 :			}
4172 :	golsen	1.141
4173 :	parrello	1.298	# Not a continuation. Report previous and update current.
4174 :	golsen	1.141
4175 :	parrello	1.298	else
4176 :			{
4177 :			push @regions, [ $cur_contig, $cur_beg, $cur_end ];
4178 :			( $cur_contig, $cur_beg, $cur_end, $cur_dir )
4179 :			= ( $contig, $beg, $end, $dir );
4180 :			}
4181 :	golsen	1.141	}
4182 :
4183 :			# There should alwasy be a valid, unreported region.
4184 :
4185 :			push @regions, [ $cur_contig, $cur_beg, $cur_end ];
4186 :
4187 :			return wantarray ? @regions : \@regions;
4188 :			}
4189 :
4190 :	parrello	1.287	=head3 filter_regions
4191 :
4192 :			C<< my @regions = FIG::filter_regions( $contig, $min, $max, @regions ); >>
4193 :
4194 :			or
4195 :
4196 :			C<< my \@regions = FIG::filter_regions( $contig, $min, $max, @regions ); >>
4197 :
4198 :			or
4199 :
4200 :			C<< my @regions = FIG::filter_regions( $contig, $min, $max, \@regions ); >>
4201 :
4202 :			or
4203 :
4204 :			C<< my \@regions = FIG::filter_regions( $contig, $min, $max, \@regions ); >>
4205 :
4206 :			Filter a list of regions to those that overlap a specified section of a
4207 :			particular contig. Region definitions correspond to those produced
4208 :			by L</regions_spanned>. That is, C<[>I<contig>C<,>I<beg>C<,>I<end>C<]>.
4209 :			In the function call, either I<$contig> or I<$min> and I<$max> can be
4210 :			undefined (permitting anything). So, for example,
4211 :
4212 :			my @regions = FIG::filter_regions(undef, 1, 5000, $regionList);
4213 :
4214 :			would return all regions in C<$regionList> that overlap the first
4215 :			5000 base pairs in any contig. Conversely,
4216 :
4217 :			my @regions = FIG::filter_regions('NC_003904', undef, undef, $regionList);
4218 :	golsen	1.141
4219 :	parrello	1.287	would return all regions on the contig C<NC_003904>.
4220 :	golsen	1.141
4221 :	parrello	1.287	=over 4
4222 :
4223 :			=item contig
4224 :
4225 :			ID of the contig whose regions are to be passed by the filter, or C<undef>
4226 :			if the contig doesn't matter.
4227 :
4228 :			=item min
4229 :
4230 :			Leftmost position of the region used for filtering. Only regions which contain
4231 :			at least one base pair at or beyond this position will be passed. A value
4232 :			of C<undef> is equivalent to zero.
4233 :
4234 :			=item max
4235 :
4236 :			Rightmost position of the region used for filtering. Only regions which contain
4237 :			at least one base pair on or before this position will be passed. A value
4238 :			of C<undef> is equivalent to the length of the contig.
4239 :
4240 :			=item regionList
4241 :	golsen	1.141
4242 :	parrello	1.287	A list of regions, or a reference to a list of regions. Each region is a
4243 :			reference to a three-element list, the first element of which is a contig
4244 :			ID, the second element of which is the start position, and the third
4245 :			element of which is the ending position. (The ending position can be
4246 :			before the starting position if the region is backward-traveling.)
4247 :
4248 :			=item RETURN
4249 :
4250 :			In a scalar context, returns a reference to a list of the filtered regions.
4251 :			In a list context, returns the list itself.