Annotation of /FigKernelPackages/Observation.pm

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1 :	mkubal	1.1	package Observation;
2 :
3 :	mkubal	1.19	use lib '/vol/ontologies';
4 :			use DBMaster;
5 :	mkubal	1.34	use Data::Dumper;
6 :	mkubal	1.19
7 :	mkubal	1.1	require Exporter;
8 :			@EXPORT_OK = qw(get_objects);
9 :
10 :	arodri7	1.16	use FIG_Config;
11 :	mkubal	1.30	#use strict;
12 :	arodri7	1.16	#use warnings;
13 :	arodri7	1.9	use HTML;
14 :	mkubal	1.1
15 :			1;
16 :
17 :	arodri7	1.39	# $Id: Observation.pm,v 1.38 2007/09/10 15:10:04 arodri7 Exp $
18 :	mkubal	1.1
19 :			=head1 NAME
20 :
21 :			Observation -- A presentation layer for observations in SEED.
22 :
23 :			=head1 DESCRIPTION
24 :
25 :			The SEED environment contains various sources of information for sequence features. The purpose of this library is to provide a
26 :			single interface to this data.
27 :
28 :			The data can be used to display information for a given sequence feature (protein or other, but primarily information is computed for proteins).
29 :
30 :			=cut
31 :
32 :			=head1 BACKGROUND
33 :
34 :			=head2 Data incorporated in the Observations
35 :
36 :			As the goal of this library is to provide an integrated view, we combine diverse sources of evidence.
37 :
38 :			=head3 SEED core evidence
39 :
40 :			The core SEED data structures provided by FIG.pm. These are Similarities, BBHs and PCHs.
41 :
42 :			=head3 Attribute based Evidence
43 :
44 :			We use the SEED attribute infrastructure to store information computed by a variety of computational procedures.
45 :
46 :			These are e.g. InterPro hits via InterProScan (ipr), NCBI Conserved Domain Database Hits via PSSM(cdd),
47 :			PFAM hits via HMM(pfam), SignalP results(signalp), and various others.
48 :
49 :			=head1 METHODS
50 :
51 :			The public methods this package provides are listed below:
52 :
53 :
54 :	mkubal	1.24	=head3 context()
55 :
56 :			Returns close or diverse for purposes of displaying genomic context
57 :	mkubal	1.1
58 :			=cut
59 :
60 :	mkubal	1.24	sub context {
61 :	mkubal	1.1	my ($self) = @_;
62 :
63 :	mkubal	1.24	return $self->{context};
64 :	mkubal	1.1	}
65 :
66 :	mkubal	1.24	=head3 rows()
67 :	mkubal	1.1
68 :	mkubal	1.24	each row in a displayed table
69 :	mkubal	1.1
70 :	mkubal	1.24	=cut
71 :
72 :			sub rows {
73 :			my ($self) = @_;
74 :
75 :			return $self->{rows};
76 :			}
77 :
78 :			=head3 acc()
79 :
80 :			A valid accession or remote ID (in the style of a db_xref) or a valid local ID (FID) in case this is supported.
81 :	mkubal	1.1
82 :			=cut
83 :
84 :	mkubal	1.24	sub acc {
85 :	mkubal	1.1	my ($self) = @_;
86 :	mkubal	1.24	return $self->{acc};
87 :	mkubal	1.1	}
88 :
89 :			=head3 class()
90 :
91 :			The class of evidence (required). This is usually simply the name of the tool or the name of the SEED data structure.
92 :			B<Please note> the connection of class and display_method and URL.
93 :	mkubal	1.7
94 :	mkubal	1.1	Current valid classes are:
95 :
96 :			=over 9
97 :
98 :	arodri7	1.9	=item IDENTICAL (seq)
99 :
100 :	mkubal	1.3	=item SIM (seq)
101 :	mkubal	1.1
102 :	mkubal	1.3	=item BBH (seq)
103 :	mkubal	1.1
104 :	mkubal	1.3	=item PCH (fc)
105 :	mkubal	1.1
106 :	mkubal	1.3	=item FIGFAM (seq)
107 :	mkubal	1.1
108 :	mkubal	1.3	=item IPR (dom)
109 :	mkubal	1.1
110 :	mkubal	1.3	=item CDD (dom)
111 :	mkubal	1.1
112 :	mkubal	1.3	=item PFAM (dom)
113 :	mkubal	1.1
114 :	mkubal	1.12	=item SIGNALP_CELLO_TMPRED (loc)
115 :	mkubal	1.1
116 :	mkubal	1.20	=item PDB (seq)
117 :
118 :	mkubal	1.3	=item TMHMM (loc)
119 :	mkubal	1.1
120 :	mkubal	1.3	=item HMMTOP (loc)
121 :	mkubal	1.1
122 :			=back
123 :
124 :			=cut
125 :
126 :			sub class {
127 :			my ($self) = @_;
128 :
129 :			return $self->{class};
130 :			}
131 :
132 :			=head3 type()
133 :
134 :			The type of evidence (required).
135 :
136 :			Where type is one of the following:
137 :
138 :			=over 8
139 :
140 :			=item seq=Sequence similarity
141 :
142 :			=item dom=domain based match
143 :
144 :			=item loc=Localization of the feature
145 :
146 :			=item fc=Functional coupling.
147 :
148 :			=back
149 :
150 :			=cut
151 :
152 :			sub type {
153 :			my ($self) = @_;
154 :
155 :	arodri7	1.26	return $self->{type};
156 :	mkubal	1.1	}
157 :
158 :			=head3 start()
159 :
160 :			Start of hit in query sequence.
161 :
162 :			=cut
163 :
164 :			sub start {
165 :			my ($self) = @_;
166 :
167 :			return $self->{start};
168 :			}
169 :
170 :			=head3 end()
171 :
172 :			End of the hit in query sequence.
173 :
174 :			=cut
175 :
176 :			sub stop {
177 :			my ($self) = @_;
178 :
179 :			return $self->{stop};
180 :			}
181 :
182 :	arodri7	1.11	=head3 start()
183 :
184 :			Start of hit in query sequence.
185 :
186 :			=cut
187 :
188 :			sub qstart {
189 :			my ($self) = @_;
190 :
191 :			return $self->{qstart};
192 :			}
193 :
194 :			=head3 qstop()
195 :
196 :			End of the hit in query sequence.
197 :
198 :			=cut
199 :
200 :			sub qstop {
201 :			my ($self) = @_;
202 :
203 :			return $self->{qstop};
204 :			}
205 :
206 :			=head3 hstart()
207 :
208 :			Start of hit in hit sequence.
209 :
210 :			=cut
211 :
212 :			sub hstart {
213 :			my ($self) = @_;
214 :
215 :			return $self->{hstart};
216 :			}
217 :
218 :			=head3 end()
219 :
220 :			End of the hit in hit sequence.
221 :
222 :			=cut
223 :
224 :			sub hstop {
225 :			my ($self) = @_;
226 :
227 :			return $self->{hstop};
228 :			}
229 :
230 :			=head3 qlength()
231 :
232 :			length of the query sequence in similarities
233 :
234 :			=cut
235 :
236 :			sub qlength {
237 :			my ($self) = @_;
238 :
239 :			return $self->{qlength};
240 :			}
241 :
242 :			=head3 hlength()
243 :
244 :			length of the hit sequence in similarities
245 :
246 :			=cut
247 :
248 :			sub hlength {
249 :			my ($self) = @_;
250 :
251 :			return $self->{hlength};
252 :			}
253 :
254 :	mkubal	1.1	=head3 evalue()
255 :
256 :			E-value or P-Value if present.
257 :
258 :			=cut
259 :
260 :			sub evalue {
261 :			my ($self) = @_;
262 :
263 :			return $self->{evalue};
264 :			}
265 :
266 :			=head3 score()
267 :
268 :			Score if present.
269 :
270 :			=cut
271 :
272 :			sub score {
273 :			my ($self) = @_;
274 :			return $self->{score};
275 :			}
276 :
277 :	mkubal	1.12	=head3 display()
278 :	mkubal	1.1
279 :	mkubal	1.12	will be different for each type
280 :	mkubal	1.1
281 :			=cut
282 :
283 :	mkubal	1.7	sub display {
284 :	mkubal	1.1
285 :	mkubal	1.7	die "Abstract Method Called\n";
286 :	mkubal	1.1
287 :			}
288 :
289 :	mkubal	1.24	=head3 display_table()
290 :	mkubal	1.7
291 :	mkubal	1.24	will be different for each type
292 :	mkubal	1.1
293 :	mkubal	1.24	=cut
294 :	mkubal	1.1
295 :	mkubal	1.24	sub display_table {
296 :
297 :			die "Abstract Table Method Called\n";
298 :	mkubal	1.1
299 :			}
300 :
301 :			=head3 get_objects()
302 :
303 :			This is the B<REAL WORKHORSE> method of this Package.
304 :
305 :			=cut
306 :
307 :			sub get_objects {
308 :	mkubal	1.24	my ($self,$fid,$scope) = @_;
309 :	mkubal	1.7
310 :			my $objects = [];
311 :			my @matched_datasets=();
312 :	arodri7	1.28	my $fig = new FIG;
313 :	mkubal	1.1
314 :	mkubal	1.7	# call function that fetches attribute based observations
315 :			# returns an array of arrays of hashes
316 :
317 :	mkubal	1.24	if($scope){
318 :			get_cluster_observations($fid,\@matched_datasets,$scope);
319 :	mkubal	1.7	}
320 :			else{
321 :			my %domain_classes;
322 :	arodri7	1.28	my @attributes = $fig->get_attributes($fid);
323 :	mkubal	1.24	$domain_classes{'CDD'} = 1;
324 :	arodri7	1.33	get_identical_proteins($fid,\@matched_datasets);
325 :	arodri7	1.28	get_attribute_based_domain_observations($fid,\%domain_classes,\@matched_datasets,\@attributes);
326 :	mkubal	1.24	get_sims_observations($fid,\@matched_datasets);
327 :			get_functional_coupling($fid,\@matched_datasets);
328 :	arodri7	1.28	get_attribute_based_location_observations($fid,\@matched_datasets,\@attributes);
329 :			get_pdb_observations($fid,\@matched_datasets,\@attributes);
330 :	mkubal	1.1	}
331 :	mkubal	1.7
332 :			foreach my $dataset (@matched_datasets) {
333 :			my $object;
334 :			if($dataset->{'type'} eq "dom"){
335 :			$object = Observation::Domain->new($dataset);
336 :			}
337 :	arodri7	1.9	if($dataset->{'class'} eq "PCH"){
338 :			$object = Observation::FC->new($dataset);
339 :			}
340 :			if ($dataset->{'class'} eq "IDENTICAL"){
341 :			$object = Observation::Identical->new($dataset);
342 :			}
343 :	mkubal	1.12	if ($dataset->{'class'} eq "SIGNALP_CELLO_TMPRED"){
344 :			$object = Observation::Location->new($dataset);
345 :			}
346 :	arodri7	1.10	if ($dataset->{'class'} eq "SIM"){
347 :			$object = Observation::Sims->new($dataset);
348 :			}
349 :	arodri7	1.15	if ($dataset->{'class'} eq "CLUSTER"){
350 :			$object = Observation::Cluster->new($dataset);
351 :			}
352 :	mkubal	1.20	if ($dataset->{'class'} eq "PDB"){
353 :			$object = Observation::PDB->new($dataset);
354 :			}
355 :
356 :	mkubal	1.7	push (@$objects, $object);
357 :	mkubal	1.1	}
358 :	mkubal	1.7
359 :			return $objects;
360 :	mkubal	1.1
361 :			}
362 :
363 :	arodri7	1.28	=head3 display_housekeeping
364 :			This method returns the housekeeping data for a given peg in a table format
365 :
366 :			=cut
367 :			sub display_housekeeping {
368 :			my ($self,$fid) = @_;
369 :			my $fig = new FIG;
370 :			my $content;
371 :
372 :			my $org_name = $fig->org_of($fid);
373 :			my $org_id = $fig->orgid_of_orgname($org_name);
374 :			my $loc = $fig->feature_location($fid);
375 :			my($contig, $beg, $end) = $fig->boundaries_of($loc);
376 :			my $strand = ($beg <= $end)? '+' : '-';
377 :			my @subsystems = $fig->subsystems_for_peg($fid);
378 :			my $function = $fig->function_of($fid);
379 :			my @aliases = $fig->feature_aliases($fid);
380 :			my $taxonomy = $fig->taxonomy_of($org_id);
381 :			my @ecs = ($function =~ /$EC\s(\d+\.[-\d+]+\.[-\d+]+\.[-\d+]+)$/g);
382 :
383 :			$content .= qq(<b>General Protein Data</b><br><br><br><table border="0">);
384 :			$content .= qq(<tr width=15%><td >FIG ID</td><td>$fid</td></tr>\n);
385 :			$content .= qq(<tr width=15%><td >Organism Name</td><td>$org_name,  $org_id</td></tr>\n);
386 :			$content .= qq(<tr><td width=15%>Taxonomy</td><td>$taxonomy</td></tr>\n);
387 :			$content .= qq(<tr width=15%><td>FIG Organism ID</td><td>$org_id</td></tr>\n);
388 :			$content .= qq(<tr width=15%><td>Gene Location</td><td>Contig $contig [$beg,$end], Strand $strand</td></tr>\n);;
389 :			$content .= qq(<tr width=15%><td>Function</td><td>$function</td></tr>\n);
390 :			if ( @ecs ) {
391 :			$content .= qq(<tr><td>EC:</td><td>);
392 :			foreach my $ec ( @ecs ) {
393 :			my $ec_name = $fig->ec_name($ec);
394 :			$content .= join(" -- ", $ec, $ec_name) . "<br>\n";
395 :			}
396 :			$content .= qq(</td></tr>\n);
397 :			}
398 :
399 :			if ( @subsystems ) {
400 :			$content .= qq(<tr><td>Subsystems</td><td>);
401 :			foreach my $subsystem ( @subsystems ) {
402 :			$content .= join(" -- ", @$subsystem) . "<br>\n";
403 :			}
404 :			}
405 :
406 :			my %groups;
407 :			if ( @aliases ) {
408 :			# get the db for each alias
409 :			foreach my $alias (@aliases){
410 :			$groups{$alias} = &get_database($alias);
411 :			}
412 :
413 :			# group ids by aliases
414 :			my %db_aliases;
415 :			foreach my $key (sort {$groups{$a} cmp $groups{$b}} keys %groups){
416 :			push (@{$db_aliases{$groups{$key}}}, $key);
417 :			}
418 :
419 :
420 :			$content .= qq(<tr><td>Aliases</td><td><table border="0">);
421 :			foreach my $key (sort keys %db_aliases){
422 :			$content .= qq(<tr><td>$key:</td><td>) . join(", ", @{$db_aliases{$key}}) . qq(</td></tr\n);
423 :			}
424 :			$content .= qq(</td></tr></table>\n);
425 :			}
426 :
427 :			$content .= qq(</table><p>\n);
428 :
429 :			return ($content);
430 :			}
431 :
432 :			=head3 get_sims_summary
433 :			This method uses as input the similarities of a peg and creates a tree view of their taxonomy
434 :
435 :			=cut
436 :
437 :			sub get_sims_summary {
438 :	arodri7	1.39	my ($observation, $fid, $taxes) = @_;
439 :	arodri7	1.28	my $fig = new FIG;
440 :			my %families;
441 :	arodri7	1.38	my @sims= $fig->nsims($fid,20000,10,"fig");
442 :	arodri7	1.28
443 :			foreach my $sim (@sims){
444 :			next if ($sim->[1] !~ /fig\\|/);
445 :			my $genome = $fig->genome_of($sim->[1]);
446 :	arodri7	1.39	my ($genome1) = ($genome) =~ /(.*)\./;
447 :			my $taxonomy = $taxes->{$genome1};
448 :			#my $taxonomy = $fig->taxonomy_of($fig->genome_of($sim->[1])); # use this if the taxonomies have been updated
449 :	arodri7	1.28	my $parent_tax = "Root";
450 :	arodri7	1.38	my @currLineage = ($parent_tax);
451 :	arodri7	1.28	foreach my $tax (split(/\; /, $taxonomy)){
452 :			push (@{$families{children}{$parent_tax}}, $tax);
453 :	arodri7	1.38	push (@currLineage, $tax);
454 :	arodri7	1.28	$families{parent}{$tax} = $parent_tax;
455 :	arodri7	1.38	$families{lineage}{$tax} = join(";", @currLineage);
456 :	arodri7	1.39	if (defined ($families{evalue}{$tax})){
457 :			if ($sim->[10] < $families{evalue}{$tax}){
458 :			$families{evalue}{$tax} = $sim->[10];
459 :			$families{color}{$tax} = &get_taxcolor($sim->[10]);
460 :			}
461 :			}
462 :			else{
463 :			$families{evalue}{$tax} = $sim->[10];
464 :			$families{color}{$tax} = &get_taxcolor($sim->[10]);
465 :			}
466 :
467 :	arodri7	1.28	$parent_tax = $tax;
468 :			}
469 :			}
470 :
471 :			foreach my $key (keys %{$families{children}}){
472 :			$families{count}{$key} = @{$families{children}{$key}};
473 :
474 :			my %saw;
475 :			my @out = grep(!$saw{$_}++, @{$families{children}{$key}});
476 :			$families{children}{$key} = \@out;
477 :			}
478 :			return (\%families);
479 :			}
480 :
481 :	mkubal	1.1	=head1 Internal Methods
482 :
483 :			These methods are not meant to be used outside of this package.
484 :
485 :			B<Please do not use them outside of this package!>
486 :
487 :			=cut
488 :
489 :	arodri7	1.39	sub get_taxcolor{
490 :			my ($evalue) = @_;
491 :			my $color;
492 :			if ($evalue <= 1e-170){ $color = "#FF2000"; }
493 :			elsif (($evalue <= 1e-120) && ($evalue > 1e-170)){ $color = "#FF3300"; }
494 :			elsif (($evalue <= 1e-90) && ($evalue > 1e-120)){ $color = "#FF6600"; }
495 :			elsif (($evalue <= 1e-70) && ($evalue > 1e-90)){ $color = "#FF9900"; }
496 :			elsif (($evalue <= 1e-40) && ($evalue > 1e-70)){ $color = "#FFCC00"; }
497 :			elsif (($evalue <= 1e-20) && ($evalue > 1e-40)){ $color = "#FFFF00"; }
498 :			elsif (($evalue <= 1e-5) && ($evalue > 1e-20)){ $color = "#CCFF00"; }
499 :			elsif (($evalue <= 1) && ($evalue > 1e-5)){ $color = "#66FF00"; }
500 :			elsif (($evalue <= 10) && ($evalue > 1)){ $color = "#00FF00"; }
501 :			else{ $color = "#6666FF"; }
502 :			return ($color);
503 :			}
504 :
505 :
506 :	mkubal	1.7	sub get_attribute_based_domain_observations{
507 :
508 :			# we read a FIG ID and a reference to an array (of arrays of hashes, see above)
509 :	arodri7	1.28	my ($fid,$domain_classes,$datasets_ref,$attributes_ref) = (@_);
510 :	mkubal	1.7
511 :			my $fig = new FIG;
512 :	arodri7	1.28
513 :			foreach my $attr_ref (@$attributes_ref) {
514 :			# foreach my $attr_ref ($fig->get_attributes($fid)) {
515 :	mkubal	1.7	my $key = @$attr_ref[1];
516 :			my @parts = split("::",$key);
517 :			my $class = $parts[0];
518 :
519 :			if($domain_classes->{$parts[0]}){
520 :			my $val = @$attr_ref[2];
521 :	mkubal	1.8	if($val =~/^(\d+\.\d+\|0\.0);(\d+)-(\d+)/){
522 :	mkubal	1.7	my $raw_evalue = $1;
523 :	mkubal	1.8	my $from = $2;
524 :			my $to = $3;
525 :	mkubal	1.7	my $evalue;
526 :			if($raw_evalue =~/(\d+)\.(\d+)/){
527 :			my $part2 = 1000 - $1;
528 :			my $part1 = $2/100;
529 :			$evalue = $part1."e-".$part2;
530 :			}
531 :			else{
532 :	mkubal	1.8	$evalue = "0.0";
533 :	mkubal	1.7	}
534 :
535 :			my $dataset = {'class' => $class,
536 :			'acc' => $key,
537 :			'type' => "dom" ,
538 :			'evalue' => $evalue,
539 :			'start' => $from,
540 :	mkubal	1.24	'stop' => $to,
541 :			'fig_id' => $fid,
542 :			'score' => $raw_evalue
543 :	mkubal	1.7	};
544 :
545 :			push (@{$datasets_ref} ,$dataset);
546 :			}
547 :			}
548 :			}
549 :			}
550 :	mkubal	1.12
551 :			sub get_attribute_based_location_observations{
552 :
553 :	arodri7	1.28	my ($fid,$datasets_ref, $attributes_ref) = (@_);
554 :	mkubal	1.12	my $fig = new FIG;
555 :
556 :	mkubal	1.30	my $location_attributes = ['SignalP','CELLO','TMPRED','Phobius'];
557 :	mkubal	1.12
558 :	arodri7	1.26	my $dataset = {'type' => "loc",
559 :			'class' => 'SIGNALP_CELLO_TMPRED',
560 :			'fig_id' => $fid
561 :			};
562 :
563 :	arodri7	1.28	foreach my $attr_ref (@$attributes_ref){
564 :			# foreach my $attr_ref ($fig->get_attributes($fid,$location_attributes)) {
565 :	mkubal	1.12	my $key = @$attr_ref[1];
566 :	mkubal	1.30	next if (($key !~ /SignalP/) && ($key !~ /CELLO/) && ($key !~ /TMPRED/) && ($key !~/Phobius/) );
567 :	mkubal	1.12	my @parts = split("::",$key);
568 :			my $sub_class = $parts[0];
569 :			my $sub_key = $parts[1];
570 :			my $value = @$attr_ref[2];
571 :			if($sub_class eq "SignalP"){
572 :			if($sub_key eq "cleavage_site"){
573 :			my @value_parts = split(";",$value);
574 :			$dataset->{'cleavage_prob'} = $value_parts[0];
575 :			$dataset->{'cleavage_loc'} = $value_parts[1];
576 :	arodri7	1.28	# print STDERR "LOC: $value_parts[1]";
577 :	mkubal	1.12	}
578 :			elsif($sub_key eq "signal_peptide"){
579 :			$dataset->{'signal_peptide_score'} = $value;
580 :			}
581 :			}
582 :	mkubal	1.30
583 :	mkubal	1.12	elsif($sub_class eq "CELLO"){
584 :			$dataset->{'cello_location'} = $sub_key;
585 :			$dataset->{'cello_score'} = $value;
586 :			}
587 :	mkubal	1.30
588 :			elsif($sub_class eq "Phobius"){
589 :			if($sub_key eq "transmembrane"){
590 :			$dataset->{'phobius_tm_locations'} = $value;
591 :			}
592 :			elsif($sub_key eq "signal"){
593 :			$dataset->{'phobius_signal_location'} = $value;
594 :			}
595 :			}
596 :
597 :	mkubal	1.12	elsif($sub_class eq "TMPRED"){
598 :	arodri7	1.26	my @value_parts = split(/\;/,$value);
599 :	mkubal	1.12	$dataset->{'tmpred_score'} = $value_parts[0];
600 :			$dataset->{'tmpred_locations'} = $value_parts[1];
601 :			}
602 :			}
603 :
604 :			push (@{$datasets_ref} ,$dataset);
605 :
606 :			}
607 :
608 :	mkubal	1.20	=head3 get_pdb_observations() (internal)
609 :
610 :			This methods sets the type and class for pdb observations
611 :
612 :			=cut
613 :
614 :			sub get_pdb_observations{
615 :	arodri7	1.28	my ($fid,$datasets_ref, $attributes_ref) = (@_);
616 :	mkubal	1.20
617 :			my $fig = new FIG;
618 :
619 :	arodri7	1.28	foreach my $attr_ref (@$attributes_ref){
620 :			#foreach my $attr_ref ($fig->get_attributes($fid,'PDB')) {
621 :	mkubal	1.20
622 :			my $key = @$attr_ref[1];
623 :	arodri7	1.28	next if ( ($key !~ /PDB/));
624 :	mkubal	1.20	my($key1,$key2) =split("::",$key);
625 :			my $value = @$attr_ref[2];
626 :			my ($evalue,$location) = split(";",$value);
627 :
628 :			if($evalue =~/(\d+)\.(\d+)/){
629 :			my $part2 = 1000 - $1;
630 :			my $part1 = $2/100;
631 :			$evalue = $part1."e-".$part2;
632 :			}
633 :
634 :			my($start,$stop) =split("-",$location);
635 :
636 :			my $url = @$attr_ref[3];
637 :			my $dataset = {'class' => 'PDB',
638 :			'type' => 'seq' ,
639 :			'acc' => $key2,
640 :			'evalue' => $evalue,
641 :			'start' => $start,
642 :	mkubal	1.24	'stop' => $stop,
643 :			'fig_id' => $fid
644 :	mkubal	1.20	};
645 :
646 :			push (@{$datasets_ref} ,$dataset);
647 :			}
648 :			}
649 :
650 :	arodri7	1.15	=head3 get_cluster_observations() (internal)
651 :
652 :			This methods sets the type and class for cluster observations
653 :
654 :			=cut
655 :
656 :			sub get_cluster_observations{
657 :	mkubal	1.24	my ($fid,$datasets_ref,$scope) = (@_);
658 :	arodri7	1.15
659 :	arodri7	1.16	my $dataset = {'class' => 'CLUSTER',
660 :	mkubal	1.24	'type' => 'fc',
661 :			'context' => $scope,
662 :			'fig_id' => $fid
663 :	arodri7	1.16	};
664 :	arodri7	1.15	push (@{$datasets_ref} ,$dataset);
665 :			}
666 :
667 :
668 :	mkubal	1.3	=head3 get_sims_observations() (internal)
669 :
670 :			This methods retrieves sims fills the internal data structures.
671 :
672 :			=cut
673 :
674 :			sub get_sims_observations{
675 :
676 :			my ($fid,$datasets_ref) = (@_);
677 :	mkubal	1.4	my $fig = new FIG;
678 :	arodri7	1.38	my @sims= $fig->nsims($fid,500,10,"fig");
679 :	mkubal	1.4	my ($dataset);
680 :	arodri7	1.26
681 :			my %id_list;
682 :	mkubal	1.3	foreach my $sim (@sims){
683 :	mkubal	1.4	my $hit = $sim->[1];
684 :	arodri7	1.26
685 :			next if ($hit !~ /^fig\\|/);
686 :			my @aliases = $fig->feature_aliases($hit);
687 :			foreach my $alias (@aliases){
688 :			$id_list{$alias} = 1;
689 :			}
690 :			}
691 :
692 :			my %already;
693 :			my (@new_sims, @uniprot);
694 :			foreach my $sim (@sims){
695 :			my $hit = $sim->[1];
696 :			my ($id) = ($hit) =~ /\\|(.*)/;
697 :			next if (defined($already{$id}));
698 :			next if (defined($id_list{$hit}));
699 :			push (@new_sims, $sim);
700 :			$already{$id} = 1;
701 :			}
702 :
703 :			foreach my $sim (@new_sims){
704 :			my $hit = $sim->[1];
705 :	arodri7	1.11	my $percent = $sim->[2];
706 :	mkubal	1.4	my $evalue = $sim->[10];
707 :	arodri7	1.11	my $qfrom = $sim->[6];
708 :			my $qto = $sim->[7];
709 :			my $hfrom = $sim->[8];
710 :			my $hto = $sim->[9];
711 :			my $qlength = $sim->[12];
712 :			my $hlength = $sim->[13];
713 :			my $db = get_database($hit);
714 :			my $func = $fig->function_of($hit);
715 :			my $organism = $fig->org_of($hit);
716 :
717 :	arodri7	1.10	$dataset = {'class' => 'SIM',
718 :			'acc' => $hit,
719 :	arodri7	1.11	'identity' => $percent,
720 :	arodri7	1.10	'type' => 'seq',
721 :			'evalue' => $evalue,
722 :	arodri7	1.11	'qstart' => $qfrom,
723 :			'qstop' => $qto,
724 :			'hstart' => $hfrom,
725 :			'hstop' => $hto,
726 :			'database' => $db,
727 :			'organism' => $organism,
728 :			'function' => $func,
729 :			'qlength' => $qlength,
730 :	mkubal	1.24	'hlength' => $hlength,
731 :			'fig_id' => $fid
732 :	arodri7	1.10	};
733 :
734 :			push (@{$datasets_ref} ,$dataset);
735 :	mkubal	1.3	}
736 :			}
737 :
738 :	arodri7	1.11	=head3 get_database (internal)
739 :			This method gets the database association from the sequence id
740 :
741 :			=cut
742 :
743 :			sub get_database{
744 :			my ($id) = (@_);
745 :
746 :			my ($db);
747 :			if ($id =~ /^fig\\|/) { $db = "FIG" }
748 :			elsif ($id =~ /^gi\\|/) { $db = "NCBI" }
749 :			elsif ($id =~ /^^[NXYZA]P_/) { $db = "RefSeq" }
750 :			elsif ($id =~ /^sp\\|/) { $db = "SwissProt" }
751 :			elsif ($id =~ /^uni\\|/) { $db = "UniProt" }
752 :			elsif ($id =~ /^tigr\\|/) { $db = "TIGR" }
753 :			elsif ($id =~ /^pir\\|/) { $db = "PIR" }
754 :	arodri7	1.28	elsif (($id =~ /^kegg\\|/) \|\| ($id =~ /Spy/)) { $db = "KEGG" }
755 :			elsif ($id =~ /^tr\\|/) { $db = "TrEMBL" }
756 :	arodri7	1.11	elsif ($id =~ /^eric\\|/) { $db = "ASAP" }
757 :			elsif ($id =~ /^img\\|/) { $db = "JGI" }
758 :
759 :			return ($db);
760 :
761 :			}
762 :
763 :	mkubal	1.24
764 :	arodri7	1.5	=head3 get_identical_proteins() (internal)
765 :
766 :			This methods retrieves sims fills the internal data structures.
767 :
768 :			=cut
769 :
770 :			sub get_identical_proteins{
771 :
772 :			my ($fid,$datasets_ref) = (@_);
773 :			my $fig = new FIG;
774 :	mkubal	1.24	my $funcs_ref;
775 :	arodri7	1.5
776 :	arodri7	1.33	# my %id_list;
777 :	arodri7	1.5	my @maps_to = grep { $_ ne $fid and $_ !~ /^xxx/ } map { $_->[0] } $fig->mapped_prot_ids($fid);
778 :	arodri7	1.33	# my @aliases = $fig->feature_aliases($fid);
779 :			# foreach my $alias (@aliases){
780 :			# $id_list{$alias} = 1;
781 :			# }
782 :	arodri7	1.26
783 :	arodri7	1.5	foreach my $id (@maps_to) {
784 :			my ($tmp, $who);
785 :	arodri7	1.33	if (($id ne $fid) && ($tmp = $fig->function_of($id))) {
786 :			# if (($id ne $fid) && ($tmp = $fig->function_of($id)) && (! defined ($id_list{$id}))) {
787 :	arodri7	1.11	$who = &get_database($id);
788 :	mkubal	1.24	push(@$funcs_ref, [$id,$who,$tmp]);
789 :	arodri7	1.5	}
790 :			}
791 :
792 :			my ($dataset);
793 :	mkubal	1.24	my $dataset = {'class' => 'IDENTICAL',
794 :			'type' => 'seq',
795 :			'fig_id' => $fid,
796 :			'rows' => $funcs_ref
797 :			};
798 :
799 :			push (@{$datasets_ref} ,$dataset);
800 :
801 :	arodri7	1.5
802 :			}
803 :
804 :	arodri7	1.6	=head3 get_functional_coupling() (internal)
805 :
806 :			This methods retrieves the functional coupling of a protein given a peg ID
807 :
808 :			=cut
809 :
810 :			sub get_functional_coupling{
811 :
812 :			my ($fid,$datasets_ref) = (@_);
813 :			my $fig = new FIG;
814 :			my @funcs = ();
815 :
816 :			# initialize some variables
817 :			my($sc,$neigh);
818 :
819 :			# set default parameters for coupling and evidence
820 :			my ($bound,$sim_cutoff,$coupling_cutoff) = (5000, 1.0e-10, 4);
821 :
822 :			# get the fc data
823 :			my @fc_data = $fig->coupling_and_evidence($fid,$bound,$sim_cutoff,$coupling_cutoff,1);
824 :
825 :			# retrieve data
826 :			my @rows = map { ($sc,$neigh) = @$_;
827 :			[$sc,$neigh,scalar $fig->function_of($neigh)]
828 :			} @fc_data;
829 :
830 :			my ($dataset);
831 :	mkubal	1.24	my $dataset = {'class' => 'PCH',
832 :			'type' => 'fc',
833 :			'fig_id' => $fid,
834 :			'rows' => \@rows
835 :			};
836 :
837 :			push (@{$datasets_ref} ,$dataset);
838 :	arodri7	1.9
839 :	arodri7	1.6	}
840 :	arodri7	1.5
841 :	mkubal	1.1	=head3 new (internal)
842 :
843 :			Instantiate a new object.
844 :
845 :			=cut
846 :
847 :			sub new {
848 :	mkubal	1.7	my ($class,$dataset) = @_;
849 :
850 :			my $self = { class => $dataset->{'class'},
851 :	mkubal	1.24	type => $dataset->{'type'},
852 :			fig_id => $dataset->{'fig_id'},
853 :			score => $dataset->{'score'},
854 :	arodri7	1.10	};
855 :	mkubal	1.7
856 :			bless($self,$class);
857 :	mkubal	1.1
858 :			return $self;
859 :			}
860 :
861 :	arodri7	1.11	=head3 identity (internal)
862 :
863 :			Returns the % identity of the similar sequence
864 :
865 :			=cut
866 :
867 :			sub identity {
868 :			my ($self) = @_;
869 :
870 :			return $self->{identity};
871 :			}
872 :
873 :	mkubal	1.24	=head3 fig_id (internal)
874 :
875 :			=cut
876 :
877 :			sub fig_id {
878 :			my ($self) = @_;
879 :			return $self->{fig_id};
880 :			}
881 :
882 :	mkubal	1.1	=head3 feature_id (internal)
883 :
884 :
885 :			=cut
886 :
887 :			sub feature_id {
888 :			my ($self) = @_;
889 :
890 :			return $self->{feature_id};
891 :			}
892 :	arodri7	1.5
893 :			=head3 id (internal)
894 :
895 :			Returns the ID of the identical sequence
896 :
897 :			=cut
898 :
899 :			sub id {
900 :			my ($self) = @_;
901 :
902 :			return $self->{id};
903 :			}
904 :
905 :			=head3 organism (internal)
906 :
907 :			Returns the organism of the identical sequence
908 :
909 :			=cut
910 :
911 :			sub organism {
912 :			my ($self) = @_;
913 :
914 :			return $self->{organism};
915 :			}
916 :
917 :	arodri7	1.9	=head3 function (internal)
918 :
919 :			Returns the function of the identical sequence
920 :
921 :			=cut
922 :
923 :			sub function {
924 :			my ($self) = @_;
925 :
926 :			return $self->{function};
927 :			}
928 :
929 :	arodri7	1.5	=head3 database (internal)
930 :
931 :			Returns the database of the identical sequence
932 :
933 :			=cut
934 :
935 :			sub database {
936 :			my ($self) = @_;
937 :
938 :			return $self->{database};
939 :			}
940 :
941 :	mkubal	1.24	sub score {
942 :			my ($self) = @_;
943 :
944 :			return $self->{score};
945 :			}
946 :
947 :	mkubal	1.20	############################################################
948 :			############################################################
949 :			package Observation::PDB;
950 :
951 :			use base qw(Observation);
952 :
953 :			sub new {
954 :
955 :			my ($class,$dataset) = @_;
956 :			my $self = $class->SUPER::new($dataset);
957 :			$self->{acc} = $dataset->{'acc'};
958 :			$self->{evalue} = $dataset->{'evalue'};
959 :			$self->{start} = $dataset->{'start'};
960 :			$self->{stop} = $dataset->{'stop'};
961 :			bless($self,$class);
962 :			return $self;
963 :			}
964 :
965 :			=head3 display()
966 :
967 :			displays data stored in best_PDB attribute and in Ontology server for given PDB id
968 :
969 :			=cut
970 :
971 :			sub display{
972 :	mkubal	1.24	my ($self,$gd) = @_;
973 :	mkubal	1.20
974 :	mkubal	1.24	my $fid = $self->fig_id;
975 :	mkubal	1.20	my $dbmaster = DBMaster->new(-database =>'Ontology');
976 :
977 :			my $acc = $self->acc;
978 :
979 :			my ($pdb_description,$pdb_source,$pdb_ligand);
980 :			my $pdb_objs = $dbmaster->pdb->get_objects( { 'id' => $acc } );
981 :			if(!scalar(@$pdb_objs)){
982 :			$pdb_description = "not available";
983 :			$pdb_source = "not available";
984 :			$pdb_ligand = "not available";
985 :			}
986 :			else{
987 :			my $pdb_obj = $pdb_objs->[0];
988 :			$pdb_description = $pdb_obj->description;
989 :			$pdb_source = $pdb_obj->source;
990 :			$pdb_ligand = $pdb_obj->ligand;
991 :			}
992 :	arodri7	1.6
993 :	mkubal	1.20	my $lines = [];
994 :			my $line_data = [];
995 :			my $line_config = { 'title' => "PDB hit for $fid",
996 :			'short_title' => "best PDB",
997 :			'basepair_offset' => '1' };
998 :
999 :			my $fig = new FIG;
1000 :			my $seq = $fig->get_translation($fid);
1001 :			my $fid_stop = length($seq);
1002 :
1003 :			my $fid_element_hash = {
1004 :			"title" => $fid,
1005 :			"start" => '1',
1006 :			"end" => $fid_stop,
1007 :			"color"=> '1',
1008 :			"zlayer" => '1'
1009 :			};
1010 :
1011 :			push(@$line_data,$fid_element_hash);
1012 :
1013 :			my $links_list = [];
1014 :			my $descriptions = [];
1015 :
1016 :			my $name;
1017 :			$name = {"title" => 'id',
1018 :			"value" => $acc};
1019 :			push(@$descriptions,$name);
1020 :
1021 :			my $description;
1022 :			$description = {"title" => 'pdb description',
1023 :			"value" => $pdb_description};
1024 :			push(@$descriptions,$description);
1025 :
1026 :			my $score;
1027 :			$score = {"title" => "score",
1028 :			"value" => $self->evalue};
1029 :			push(@$descriptions,$score);
1030 :
1031 :			my $start_stop;
1032 :			my $start_stop_value = $self->start."_".$self->stop;
1033 :			$start_stop = {"title" => "start-stop",
1034 :			"value" => $start_stop_value};
1035 :			push(@$descriptions,$start_stop);
1036 :
1037 :			my $source;
1038 :			$source = {"title" => "source",
1039 :			"value" => $pdb_source};
1040 :			push(@$descriptions,$source);
1041 :
1042 :			my $ligand;
1043 :			$ligand = {"title" => "pdb ligand",
1044 :			"value" => $pdb_ligand};
1045 :			push(@$descriptions,$ligand);
1046 :
1047 :			my $link;
1048 :			my $link_url ="http://www.rcsb.org/pdb/explore/explore.do?structureId=".$acc;
1049 :
1050 :			$link = {"link_title" => $acc,
1051 :			"link" => $link_url};
1052 :			push(@$links_list,$link);
1053 :
1054 :			my $pdb_element_hash = {
1055 :			"title" => "PDB homology",
1056 :			"start" => $self->start,
1057 :			"end" => $self->stop,
1058 :			"color"=> '6',
1059 :			"zlayer" => '3',
1060 :			"links_list" => $links_list,
1061 :			"description" => $descriptions};
1062 :
1063 :			push(@$line_data,$pdb_element_hash);
1064 :			$gd->add_line($line_data, $line_config);
1065 :
1066 :			return $gd;
1067 :			}
1068 :
1069 :			1;
1070 :	arodri7	1.11
1071 :	arodri7	1.9	############################################################
1072 :			############################################################
1073 :			package Observation::Identical;
1074 :
1075 :			use base qw(Observation);
1076 :
1077 :			sub new {
1078 :
1079 :			my ($class,$dataset) = @_;
1080 :			my $self = $class->SUPER::new($dataset);
1081 :	mkubal	1.24	$self->{rows} = $dataset->{'rows'};
1082 :
1083 :	arodri7	1.9	bless($self,$class);
1084 :			return $self;
1085 :			}
1086 :
1087 :	mkubal	1.24	=head3 display_table()
1088 :	arodri7	1.6
1089 :			If available use the function specified here to display the "raw" observation.
1090 :			This code will display a table for the identical protein
1091 :
1092 :
1093 :	arodri7	1.9	B<Please note> that URL linked to in display_method() is an external component and needs to added to the code for every class of evi
1094 :			dence.
1095 :	arodri7	1.6
1096 :			=cut
1097 :
1098 :
1099 :	mkubal	1.24	sub display_table{
1100 :			my ($self) = @_;
1101 :
1102 :			my $fig = new FIG;
1103 :			my $fid = $self->fig_id;
1104 :			my $rows = $self->rows;
1105 :			my $cgi = new CGI;
1106 :	arodri7	1.6	my $all_domains = [];
1107 :			my $count_identical = 0;
1108 :	arodri7	1.9	my $content;
1109 :	mkubal	1.24	foreach my $row (@$rows) {
1110 :			my $id = $row->[0];
1111 :			my $who = $row->[1];
1112 :			my $assignment = $row->[2];
1113 :	arodri7	1.26	my $organism = $fig->org_of($id);
1114 :	arodri7	1.9	my $single_domain = [];
1115 :	mkubal	1.24	push(@$single_domain,$who);
1116 :			push(@$single_domain,&HTML::set_prot_links($cgi,$id));
1117 :			push(@$single_domain,$organism);
1118 :			push(@$single_domain,$assignment);
1119 :	arodri7	1.9	push(@$all_domains,$single_domain);
1120 :	mkubal	1.24	$count_identical++;
1121 :	arodri7	1.6	}
1122 :
1123 :			if ($count_identical >0){
1124 :	arodri7	1.9	$content = $all_domains;
1125 :	arodri7	1.6	}
1126 :			else{
1127 :	arodri7	1.9	$content = "<p>This PEG does not have any essentially identical proteins</p>";
1128 :	arodri7	1.6	}
1129 :			return ($content);
1130 :			}
1131 :	mkubal	1.7
1132 :	arodri7	1.9	1;
1133 :
1134 :			#########################################
1135 :			#########################################
1136 :			package Observation::FC;
1137 :			1;
1138 :
1139 :			use base qw(Observation);
1140 :
1141 :			sub new {
1142 :
1143 :			my ($class,$dataset) = @_;
1144 :			my $self = $class->SUPER::new($dataset);
1145 :	mkubal	1.24	$self->{rows} = $dataset->{'rows'};
1146 :	arodri7	1.9
1147 :			bless($self,$class);
1148 :			return $self;
1149 :			}
1150 :
1151 :	mkubal	1.24	=head3 display_table()
1152 :	arodri7	1.9
1153 :			If available use the function specified here to display the "raw" observation.
1154 :			This code will display a table for the identical protein
1155 :
1156 :
1157 :			B<Please note> that URL linked to in display_method() is an external component and needs to added to the code for every class of evi
1158 :			dence.
1159 :
1160 :			=cut
1161 :
1162 :	mkubal	1.24	sub display_table {
1163 :	arodri7	1.9
1164 :	mkubal	1.24	my ($self,$dataset) = @_;
1165 :			my $fid = $self->fig_id;
1166 :			my $rows = $self->rows;
1167 :			my $cgi = new CGI;
1168 :	arodri7	1.9	my $functional_data = [];
1169 :			my $count = 0;
1170 :			my $content;
1171 :
1172 :	mkubal	1.24	foreach my $row (@$rows) {
1173 :	arodri7	1.9	my $single_domain = [];
1174 :			$count++;
1175 :
1176 :			# construct the score link
1177 :	mkubal	1.24	my $score = $row->[0];
1178 :			my $toid = $row->[1];
1179 :	arodri7	1.9	my $link = $cgi->url(-relative => 1) . "?user=master&request=show_coupling_evidence&prot=$fid&to=$toid&SPROUT=";
1180 :			my $sc_link = "<a href=$link>$score</a>";
1181 :
1182 :			push(@$single_domain,$sc_link);
1183 :	mkubal	1.24	push(@$single_domain,$row->[1]);
1184 :			push(@$single_domain,$row->[2]);
1185 :	arodri7	1.9	push(@$functional_data,$single_domain);
1186 :			}
1187 :
1188 :			if ($count >0){
1189 :			$content = $functional_data;
1190 :			}
1191 :			else
1192 :			{
1193 :			$content = "<p>This PEG does not have any functional coupling</p>";
1194 :			}
1195 :			return ($content);
1196 :			}
1197 :
1198 :
1199 :			#########################################
1200 :			#########################################
1201 :	mkubal	1.7	package Observation::Domain;
1202 :
1203 :			use base qw(Observation);
1204 :
1205 :			sub new {
1206 :
1207 :			my ($class,$dataset) = @_;
1208 :			my $self = $class->SUPER::new($dataset);
1209 :			$self->{evalue} = $dataset->{'evalue'};
1210 :			$self->{acc} = $dataset->{'acc'};
1211 :			$self->{start} = $dataset->{'start'};
1212 :			$self->{stop} = $dataset->{'stop'};
1213 :
1214 :			bless($self,$class);
1215 :			return $self;
1216 :			}
1217 :
1218 :			sub display {
1219 :			my ($thing,$gd) = @_;
1220 :			my $lines = [];
1221 :	arodri7	1.27	# my $line_config = { 'title' => $thing->acc,
1222 :			# 'short_title' => $thing->type,
1223 :			# 'basepair_offset' => '1' };
1224 :	mkubal	1.7	my $color = "4";
1225 :
1226 :			my $line_data = [];
1227 :			my $links_list = [];
1228 :			my $descriptions = [];
1229 :	mkubal	1.19
1230 :			my $db_and_id = $thing->acc;
1231 :			my ($db,$id) = split("::",$db_and_id);
1232 :
1233 :			my $dbmaster = DBMaster->new(-database =>'Ontology');
1234 :	mkubal	1.7
1235 :	mkubal	1.19	my ($name_title,$name_value,$description_title,$description_value);
1236 :			if($db eq "CDD"){
1237 :			my $cdd_objs = $dbmaster->cdd->get_objects( { 'id' => $id } );
1238 :			if(!scalar(@$cdd_objs)){
1239 :			$name_title = "name";
1240 :			$name_value = "not available";
1241 :			$description_title = "description";
1242 :			$description_value = "not available";
1243 :			}
1244 :			else{
1245 :			my $cdd_obj = $cdd_objs->[0];
1246 :			$name_title = "name";
1247 :			$name_value = $cdd_obj->term;
1248 :			$description_title = "description";
1249 :			$description_value = $cdd_obj->description;
1250 :			}
1251 :			}
1252 :	arodri7	1.27
1253 :			my $line_config = { 'title' => $thing->acc,
1254 :			'short_title' => $name_value,
1255 :			'basepair_offset' => '1' };
1256 :	mkubal	1.7
1257 :	mkubal	1.19	my $name;
1258 :			$name = {"title" => $name_title,
1259 :			"value" => $name_value};
1260 :			push(@$descriptions,$name);
1261 :
1262 :			my $description;
1263 :			$description = {"title" => $description_title,
1264 :			"value" => $description_value};
1265 :			push(@$descriptions,$description);
1266 :	mkubal	1.7
1267 :			my $score;
1268 :			$score = {"title" => "score",
1269 :			"value" => $thing->evalue};
1270 :			push(@$descriptions,$score);
1271 :
1272 :			my $link_id;
1273 :	mkubal	1.12	if ($thing->acc =~/\w+::(\d+)/){
1274 :	mkubal	1.7	$link_id = $1;
1275 :			}
1276 :
1277 :			my $link;
1278 :	mkubal	1.12	my $link_url;
1279 :			if ($thing->class eq "CDD"){$link_url = "http://0-www.ncbi.nlm.nih.gov.library.vu.edu.au:80/Structure/cdd/cddsrv.cgi?uid=$link_id"}
1280 :			elsif($thing->class eq "PFAM"){$link_url = "http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?$link_id"}
1281 :			else{$link_url = "NO_URL"}
1282 :
1283 :	mkubal	1.7	$link = {"link_title" => $thing->acc,
1284 :	mkubal	1.12	"link" => $link_url};
1285 :	mkubal	1.7	push(@$links_list,$link);
1286 :
1287 :			my $element_hash = {
1288 :			"title" => $thing->type,
1289 :			"start" => $thing->start,
1290 :			"end" => $thing->stop,
1291 :			"color"=> $color,
1292 :			"zlayer" => '2',
1293 :			"links_list" => $links_list,
1294 :			"description" => $descriptions};
1295 :
1296 :			push(@$line_data,$element_hash);
1297 :			$gd->add_line($line_data, $line_config);
1298 :
1299 :			return $gd;
1300 :
1301 :			}
1302 :	arodri7	1.28
1303 :			sub display_table {
1304 :			my ($self,$dataset) = @_;
1305 :			my $cgi = new CGI;
1306 :			my $data = [];
1307 :			my $count = 0;
1308 :			my $content;
1309 :
1310 :			foreach my $thing (@$dataset) {
1311 :			next if ($thing->type !~ /dom/);
1312 :			my $single_domain = [];
1313 :			$count++;
1314 :
1315 :			my $db_and_id = $thing->acc;
1316 :			my ($db,$id) = split("::",$db_and_id);
1317 :
1318 :			my $dbmaster = DBMaster->new(-database =>'Ontology');
1319 :
1320 :			my ($name_title,$name_value,$description_title,$description_value);
1321 :			if($db eq "CDD"){
1322 :			my $cdd_objs = $dbmaster->cdd->get_objects( { 'id' => $id } );
1323 :			if(!scalar(@$cdd_objs)){
1324 :			$name_title = "name";
1325 :			$name_value = "not available";
1326 :			$description_title = "description";
1327 :			$description_value = "not available";
1328 :			}
1329 :			else{
1330 :			my $cdd_obj = $cdd_objs->[0];
1331 :			$name_title = "name";
1332 :			$name_value = $cdd_obj->term;
1333 :			$description_title = "description";
1334 :			$description_value = $cdd_obj->description;
1335 :			}
1336 :			}
1337 :
1338 :			my $location = $thing->start . " - " . $thing->stop;
1339 :
1340 :			push(@$single_domain,$db);
1341 :			push(@$single_domain,$thing->acc);
1342 :			push(@$single_domain,$name_value);
1343 :			push(@$single_domain,$location);
1344 :			push(@$single_domain,$thing->evalue);
1345 :			push(@$single_domain,$description_value);
1346 :			push(@$data,$single_domain);
1347 :			}
1348 :
1349 :			if ($count >0){
1350 :			$content = $data;
1351 :			}
1352 :			else
1353 :			{
1354 :			$content = "<p>This PEG does not have any similarities to domains</p>";
1355 :			}
1356 :			}
1357 :
1358 :	mkubal	1.7
1359 :	arodri7	1.10	#########################################
1360 :			#########################################
1361 :	mkubal	1.12	package Observation::Location;
1362 :
1363 :			use base qw(Observation);
1364 :
1365 :			sub new {
1366 :
1367 :			my ($class,$dataset) = @_;
1368 :			my $self = $class->SUPER::new($dataset);
1369 :			$self->{cleavage_prob} = $dataset->{'cleavage_prob'};
1370 :			$self->{cleavage_loc} = $dataset->{'cleavage_loc'};
1371 :			$self->{signal_peptide_score} = $dataset->{'signal_peptide_score'};
1372 :			$self->{cello_location} = $dataset->{'cello_location'};
1373 :			$self->{cello_score} = $dataset->{'cello_score'};
1374 :			$self->{tmpred_score} = $dataset->{'tmpred_score'};
1375 :			$self->{tmpred_locations} = $dataset->{'tmpred_locations'};
1376 :	mkubal	1.30	$self->{phobius_signal_location} = $dataset->{'phobius_signal_location'};
1377 :			$self->{phobius_tm_locations} = $dataset->{'phobius_tm_locations'};
1378 :	mkubal	1.12
1379 :			bless($self,$class);
1380 :			return $self;
1381 :			}
1382 :
1383 :	mkubal	1.36	sub display_cello {
1384 :			my ($thing) = @_;
1385 :			my $html;
1386 :			my $cello_location = $thing->cello_location;
1387 :			my $cello_score = $thing->cello_score;
1388 :			if($cello_location){
1389 :			$html .= "<p>CELLO prediction: $cello_location </p>";
1390 :			$html .= "<p>CELLO score: $cello_score </p>";
1391 :			}
1392 :			return ($html);
1393 :			}
1394 :
1395 :	mkubal	1.12	sub display {
1396 :	mkubal	1.24	my ($thing,$gd) = @_;
1397 :	mkubal	1.12
1398 :	mkubal	1.24	my $fid = $thing->fig_id;
1399 :	mkubal	1.12	my $fig= new FIG;
1400 :			my $length = length($fig->get_translation($fid));
1401 :
1402 :			my $cleavage_prob;
1403 :			if($thing->cleavage_prob){$cleavage_prob = $thing->cleavage_prob;}
1404 :			my ($cleavage_loc_begin,$cleavage_loc_end) = split("-",$thing->cleavage_loc);
1405 :			my $signal_peptide_score = $thing->signal_peptide_score;
1406 :			my $cello_location = $thing->cello_location;
1407 :			my $cello_score = $thing->cello_score;
1408 :			my $tmpred_score = $thing->tmpred_score;
1409 :			my @tmpred_locations = split(",",$thing->tmpred_locations);
1410 :
1411 :	mkubal	1.30	my $phobius_signal_location = $thing->phobius_signal_location;
1412 :			my @phobius_tm_locations = split(",",$thing->phobius_tm_locations);
1413 :
1414 :	mkubal	1.12	my $lines = [];
1415 :
1416 :			#color is
1417 :	arodri7	1.28	my $color = "6";
1418 :	mkubal	1.36
1419 :			=pod=
1420 :
1421 :	mkubal	1.12	if($cello_location){
1422 :			my $cello_descriptions = [];
1423 :	arodri7	1.28	my $line_data =[];
1424 :
1425 :			my $line_config = { 'title' => 'Localization Evidence',
1426 :			'short_title' => 'CELLO',
1427 :			'basepair_offset' => '1' };
1428 :
1429 :	mkubal	1.12	my $description_cello_location = {"title" => 'Best Cello Location',
1430 :			"value" => $cello_location};
1431 :
1432 :			push(@$cello_descriptions,$description_cello_location);
1433 :
1434 :			my $description_cello_score = {"title" => 'Cello Score',
1435 :			"value" => $cello_score};
1436 :
1437 :			push(@$cello_descriptions,$description_cello_score);
1438 :
1439 :			my $element_hash = {
1440 :			"title" => "CELLO",
1441 :	mkubal	1.34	"color"=> $color,
1442 :	mkubal	1.12	"start" => "1",
1443 :			"end" => $length + 1,
1444 :	arodri7	1.28	"zlayer" => '1',
1445 :	mkubal	1.12	"description" => $cello_descriptions};
1446 :
1447 :			push(@$line_data,$element_hash);
1448 :	arodri7	1.28	$gd->add_line($line_data, $line_config);
1449 :	mkubal	1.12	}
1450 :
1451 :	mkubal	1.36	=cut
1452 :
1453 :	arodri7	1.28	$color = "2";
1454 :	mkubal	1.12	if($tmpred_score){
1455 :	arodri7	1.28	my $line_data =[];
1456 :			my $line_config = { 'title' => 'Localization Evidence',
1457 :			'short_title' => 'Transmembrane',
1458 :			'basepair_offset' => '1' };
1459 :
1460 :	mkubal	1.12	foreach my $tmpred (@tmpred_locations){
1461 :			my $descriptions = [];
1462 :			my ($begin,$end) =split("-",$tmpred);
1463 :			my $description_tmpred_score = {"title" => 'TMPRED score',
1464 :			"value" => $tmpred_score};
1465 :
1466 :			push(@$descriptions,$description_tmpred_score);
1467 :
1468 :			my $element_hash = {
1469 :			"title" => "transmembrane location",
1470 :			"start" => $begin + 1,
1471 :			"end" => $end + 1,
1472 :			"color"=> $color,
1473 :			"zlayer" => '5',
1474 :	mkubal	1.34	"type" => 'box',
1475 :	mkubal	1.12	"description" => $descriptions};
1476 :
1477 :			push(@$line_data,$element_hash);
1478 :	arodri7	1.28
1479 :	mkubal	1.12	}
1480 :	arodri7	1.28	$gd->add_line($line_data, $line_config);
1481 :	mkubal	1.12	}
1482 :
1483 :	mkubal	1.30	if((scalar(@phobius_tm_locations) > 0) \|\| $phobius_signal_location){
1484 :			my $line_data =[];
1485 :			my $line_config = { 'title' => 'Localization Evidence',
1486 :			'short_title' => 'Phobius',
1487 :			'basepair_offset' => '1' };
1488 :
1489 :			foreach my $tm_loc (@phobius_tm_locations){
1490 :			my $descriptions = [];
1491 :			my $description_phobius_tm_locations = {"title" => 'Phobius TM Location',
1492 :			"value" => $tm_loc};
1493 :			push(@$descriptions,$description_phobius_tm_locations);
1494 :
1495 :			my ($begin,$end) =split("-",$tm_loc);
1496 :
1497 :			my $element_hash = {
1498 :			"title" => "phobius transmembrane location",
1499 :			"start" => $begin + 1,
1500 :			"end" => $end + 1,
1501 :			"color"=> '6',
1502 :			"zlayer" => '4',
1503 :			"type" => 'bigbox',
1504 :			"description" => $descriptions};
1505 :
1506 :			push(@$line_data,$element_hash);
1507 :
1508 :			}
1509 :
1510 :			if($phobius_signal_location){
1511 :			my $descriptions = [];
1512 :			my $description_phobius_signal_location = {"title" => 'Phobius Signal Location',
1513 :			"value" => $phobius_signal_location};
1514 :			push(@$descriptions,$description_phobius_signal_location);
1515 :
1516 :
1517 :			my ($begin,$end) =split("-",$phobius_signal_location);
1518 :			my $element_hash = {
1519 :			"title" => "phobius signal locations",
1520 :			"start" => $begin + 1,
1521 :			"end" => $end + 1,
1522 :			"color"=> '1',
1523 :			"zlayer" => '5',
1524 :			"type" => 'box',
1525 :			"description" => $descriptions};
1526 :			push(@$line_data,$element_hash);
1527 :			}
1528 :
1529 :			$gd->add_line($line_data, $line_config);
1530 :			}
1531 :
1532 :
1533 :	arodri7	1.28	$color = "1";
1534 :	mkubal	1.12	if($signal_peptide_score){
1535 :	arodri7	1.28	my $line_data = [];
1536 :	mkubal	1.12	my $descriptions = [];
1537 :	arodri7	1.28
1538 :			my $line_config = { 'title' => 'Localization Evidence',
1539 :			'short_title' => 'SignalP',
1540 :			'basepair_offset' => '1' };
1541 :
1542 :	mkubal	1.12	my $description_signal_peptide_score = {"title" => 'signal peptide score',
1543 :			"value" => $signal_peptide_score};
1544 :
1545 :			push(@$descriptions,$description_signal_peptide_score);
1546 :
1547 :			my $description_cleavage_prob = {"title" => 'cleavage site probability',
1548 :			"value" => $cleavage_prob};
1549 :
1550 :			push(@$descriptions,$description_cleavage_prob);
1551 :
1552 :			my $element_hash = {
1553 :			"title" => "SignalP",
1554 :			"start" => $cleavage_loc_begin - 2,
1555 :	arodri7	1.28	"end" => $cleavage_loc_end + 1,
1556 :	mkubal	1.12	"type" => 'bigbox',
1557 :			"color"=> $color,
1558 :			"zlayer" => '10',
1559 :			"description" => $descriptions};
1560 :
1561 :			push(@$line_data,$element_hash);
1562 :	arodri7	1.28	$gd->add_line($line_data, $line_config);
1563 :	mkubal	1.12	}
1564 :
1565 :			return ($gd);
1566 :
1567 :			}
1568 :
1569 :			sub cleavage_loc {
1570 :			my ($self) = @_;
1571 :
1572 :			return $self->{cleavage_loc};
1573 :			}
1574 :
1575 :			sub cleavage_prob {
1576 :			my ($self) = @_;
1577 :
1578 :			return $self->{cleavage_prob};
1579 :			}
1580 :
1581 :			sub signal_peptide_score {
1582 :			my ($self) = @_;
1583 :
1584 :			return $self->{signal_peptide_score};
1585 :			}
1586 :
1587 :			sub tmpred_score {
1588 :			my ($self) = @_;
1589 :
1590 :			return $self->{tmpred_score};
1591 :			}
1592 :
1593 :			sub tmpred_locations {
1594 :			my ($self) = @_;
1595 :
1596 :			return $self->{tmpred_locations};
1597 :			}
1598 :
1599 :			sub cello_location {
1600 :			my ($self) = @_;
1601 :
1602 :			return $self->{cello_location};
1603 :			}
1604 :
1605 :			sub cello_score {
1606 :			my ($self) = @_;
1607 :
1608 :			return $self->{cello_score};
1609 :			}
1610 :
1611 :	mkubal	1.30	sub phobius_signal_location {
1612 :			my ($self) = @_;
1613 :			return $self->{phobius_signal_location};
1614 :			}
1615 :
1616 :			sub phobius_tm_locations {
1617 :			my ($self) = @_;
1618 :			return $self->{phobius_tm_locations};
1619 :			}
1620 :
1621 :
1622 :	mkubal	1.12
1623 :			#########################################
1624 :			#########################################
1625 :	arodri7	1.10	package Observation::Sims;
1626 :
1627 :			use base qw(Observation);
1628 :
1629 :			sub new {
1630 :
1631 :			my ($class,$dataset) = @_;
1632 :			my $self = $class->SUPER::new($dataset);
1633 :	arodri7	1.11	$self->{identity} = $dataset->{'identity'};
1634 :	arodri7	1.10	$self->{acc} = $dataset->{'acc'};
1635 :			$self->{evalue} = $dataset->{'evalue'};
1636 :	arodri7	1.11	$self->{qstart} = $dataset->{'qstart'};
1637 :			$self->{qstop} = $dataset->{'qstop'};
1638 :			$self->{hstart} = $dataset->{'hstart'};
1639 :			$self->{hstop} = $dataset->{'hstop'};
1640 :			$self->{database} = $dataset->{'database'};
1641 :			$self->{organism} = $dataset->{'organism'};
1642 :			$self->{function} = $dataset->{'function'};
1643 :			$self->{qlength} = $dataset->{'qlength'};
1644 :			$self->{hlength} = $dataset->{'hlength'};
1645 :	arodri7	1.10
1646 :			bless($self,$class);
1647 :			return $self;
1648 :			}
1649 :
1650 :	arodri7	1.25	=head3 display()
1651 :
1652 :			If available use the function specified here to display a graphical observation.
1653 :			This code will display a graphical view of the similarities using the genome drawer object
1654 :
1655 :			=cut
1656 :
1657 :			sub display {
1658 :			my ($self,$gd) = @_;
1659 :
1660 :			my $fig = new FIG;
1661 :			my $peg = $self->acc;
1662 :
1663 :			my $organism = $self->organism;
1664 :	arodri7	1.28	my $genome = $fig->genome_of($peg);
1665 :			my ($org_tax) = ($genome) =~ /(.*)\./;
1666 :	arodri7	1.25	my $function = $self->function;
1667 :			my $abbrev_name = $fig->abbrev($organism);
1668 :			my $align_start = $self->qstart;
1669 :			my $align_stop = $self->qstop;
1670 :			my $hit_start = $self->hstart;
1671 :			my $hit_stop = $self->hstop;
1672 :
1673 :	arodri7	1.28	my $tax_link = "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=" . $org_tax;
1674 :
1675 :			my $line_config = { 'title' => "$organism [$org_tax]",
1676 :	arodri7	1.25	'short_title' => "$abbrev_name",
1677 :	arodri7	1.28	'title_link' => '$tax_link',
1678 :	arodri7	1.25	'basepair_offset' => '0'
1679 :			};
1680 :
1681 :			my $line_data = [];
1682 :
1683 :			my $element_hash;
1684 :			my $links_list = [];
1685 :			my $descriptions = [];
1686 :
1687 :			# get subsystem information
1688 :			my $url_link = "http://seed-viewer.theseed.org/index.cgi?action=ShowAnnotation&prot=".$peg;
1689 :
1690 :			my $link;
1691 :			$link = {"link_title" => $peg,
1692 :			"link" => $url_link};
1693 :			push(@$links_list,$link);
1694 :
1695 :			my @subsystems = $fig->peg_to_subsystems($peg);
1696 :			foreach my $subsystem (@subsystems){
1697 :			my $link;
1698 :			$link = {"link" => "http://seed-viewer.theseed.org/index.cgi?action=ShowSubsystem&subsystem_name=$subsystem",
1699 :			"link_title" => $subsystem};
1700 :			push(@$links_list,$link);
1701 :			}
1702 :
1703 :			my $description_function;
1704 :			$description_function = {"title" => "function",
1705 :			"value" => $function};
1706 :			push(@$descriptions,$description_function);
1707 :
1708 :	arodri7	1.26	my ($description_ss, $ss_string);
1709 :			$ss_string = join (",", @subsystems);
1710 :	arodri7	1.25	$description_ss = {"title" => "subsystems",
1711 :			"value" => $ss_string};
1712 :			push(@$descriptions,$description_ss);
1713 :
1714 :			my $description_loc;
1715 :			$description_loc = {"title" => "location start",
1716 :			"value" => $hit_start};
1717 :			push(@$descriptions, $description_loc);
1718 :
1719 :			$description_loc = {"title" => "location stop",
1720 :			"value" => $hit_stop};
1721 :			push(@$descriptions, $description_loc);
1722 :
1723 :			my $evalue = $self->evalue;
1724 :			while ($evalue =~ /-0/)
1725 :			{
1726 :			my ($chunk1, $chunk2) = split(/-/, $evalue);
1727 :			$chunk2 = substr($chunk2,1);
1728 :			$evalue = $chunk1 . "-" . $chunk2;
1729 :			}
1730 :
1731 :	arodri7	1.26	my $color = &color($evalue);
1732 :	arodri7	1.25
1733 :			my $description_eval = {"title" => "E-Value",
1734 :			"value" => $evalue};
1735 :			push(@$descriptions, $description_eval);
1736 :
1737 :			my $identity = $self->identity;
1738 :			my $description_identity = {"title" => "Identity",
1739 :			"value" => $identity};
1740 :			push(@$descriptions, $description_identity);
1741 :
1742 :			$element_hash = {
1743 :			"title" => $peg,
1744 :			"start" => $align_start,
1745 :			"end" => $align_stop,
1746 :			"type"=> 'box',
1747 :			"color"=> $color,
1748 :			"zlayer" => "2",
1749 :			"links_list" => $links_list,
1750 :			"description" => $descriptions
1751 :			};
1752 :			push(@$line_data,$element_hash);
1753 :			$gd->add_line($line_data, $line_config);
1754 :
1755 :			return ($gd);
1756 :
1757 :			}
1758 :
1759 :	mkubal	1.34	=head3 display_domain_composition()
1760 :
1761 :			If available use the function specified here to display a graphical observation of the CDD(later Pfam or selected) domains that occur in the set of similar proteins
1762 :
1763 :			=cut
1764 :
1765 :			sub display_domain_composition {
1766 :			my ($self,$gd) = @_;
1767 :
1768 :			my $fig = new FIG;
1769 :			my $peg = $self->acc;
1770 :
1771 :			my $line_data = [];
1772 :			my $links_list = [];
1773 :			my $descriptions = [];
1774 :
1775 :			my @domain_query_results =$fig->get_attributes($peg,"CDD");
1776 :
1777 :			foreach $dqr (@domain_query_results){
1778 :			my $key = @$dqr[1];
1779 :			my @parts = split("::",$key);
1780 :			my $db = $parts[0];
1781 :			my $id = $parts[1];
1782 :			my $val = @$dqr[2];
1783 :			my $from;
1784 :			my $to;
1785 :			my $evalue;
1786 :
1787 :			if($val =~/^(\d+\.\d+\|0\.0);(\d+)-(\d+)/){
1788 :			my $raw_evalue = $1;
1789 :			$from = $2;
1790 :			$to = $3;
1791 :			if($raw_evalue =~/(\d+)\.(\d+)/){
1792 :			my $part2 = 1000 - $1;
1793 :			my $part1 = $2/100;
1794 :			$evalue = $part1."e-".$part2;
1795 :			}
1796 :			else{
1797 :			$evalue = "0.0";
1798 :			}
1799 :			}
1800 :
1801 :			my $dbmaster = DBMaster->new(-database =>'Ontology');
1802 :			my ($name_value,$description_value);
1803 :
1804 :			if($db eq "CDD"){
1805 :			my $cdd_objs = $dbmaster->cdd->get_objects( { 'id' => $id } );
1806 :			if(!scalar(@$cdd_objs)){
1807 :			$name_title = "name";
1808 :			$name_value = "not available";
1809 :			$description_title = "description";
1810 :			$description_value = "not available";
1811 :			}
1812 :			else{
1813 :			my $cdd_obj = $cdd_objs->[0];
1814 :			$name_value = $cdd_obj->term;
1815 :			$description_value = $cdd_obj->description;
1816 :			}
1817 :			}
1818 :
1819 :			my $domain_name;
1820 :			$domain_name = {"title" => "name",
1821 :			"value" => $name_value};
1822 :			push(@$descriptions,$domain_name);
1823 :
1824 :			my $description;
1825 :			$description = {"title" => "description",
1826 :			"value" => $description_value};
1827 :			push(@$descriptions,$description);
1828 :
1829 :			my $score;
1830 :			$score = {"title" => "score",
1831 :			"value" => $evalue};
1832 :			push(@$descriptions,$score);
1833 :
1834 :			my $link_id = $id;
1835 :			my $link;
1836 :			my $link_url;
1837 :			if ($db eq "CDD"){$link_url = "http://0-www.ncbi.nlm.nih.gov.library.vu.edu.au:80/Structure/cdd/cddsrv.cgi?uid=$link_id"}
1838 :			elsif($db eq "PFAM"){$link_url = "http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?$link_id"}
1839 :			else{$link_url = "NO_URL"}
1840 :
1841 :			$link = {"link_title" => $name_value,
1842 :			"link" => $link_url};
1843 :			push(@$links_list,$link);
1844 :
1845 :			my $domain_element_hash = {
1846 :			"title" => $peg,
1847 :			"start" => $from,
1848 :			"end" => $to,
1849 :			"type"=> 'box',
1850 :			"zlayer" => '4',
1851 :			"links_list" => $links_list,
1852 :			"description" => $descriptions
1853 :			};
1854 :
1855 :			push(@$line_data,$domain_element_hash);
1856 :
1857 :			#just one CDD domain for now, later will add option for multiple domains from selected DB
1858 :			last;
1859 :			}
1860 :
1861 :			my $line_config = { 'title' => $peg,
1862 :			'short_title' => $peg,
1863 :			'basepair_offset' => '1' };
1864 :
1865 :			$gd->add_line($line_data, $line_config);
1866 :
1867 :			return ($gd);
1868 :
1869 :			}
1870 :
1871 :	mkubal	1.24	=head3 display_table()
1872 :	arodri7	1.10
1873 :			If available use the function specified here to display the "raw" observation.
1874 :			This code will display a table for the similarities protein
1875 :
1876 :			B<Please note> that URL linked to in display_method() is an external component and needs to added to the code for every class of evidence.
1877 :
1878 :			=cut
1879 :
1880 :	mkubal	1.24	sub display_table {
1881 :	arodri7	1.35	my ($self,$dataset, $scroll_list, $query_fid) = @_;
1882 :	mkubal	1.24
1883 :	arodri7	1.10	my $data = [];
1884 :			my $count = 0;
1885 :			my $content;
1886 :	arodri7	1.11	my $fig = new FIG;
1887 :	mkubal	1.24	my $cgi = new CGI;
1888 :	arodri7	1.28	my @ids;
1889 :	arodri7	1.10	foreach my $thing (@$dataset) {
1890 :	arodri7	1.28	next if ($thing->class ne "SIM");
1891 :			push (@ids, $thing->acc);
1892 :			}
1893 :
1894 :	arodri7	1.31	my (%box_column, %subsystems_column, %evidence_column, %e_identical);
1895 :	arodri7	1.35
1896 :			# get the column for the subsystems
1897 :			%subsystems_column = &get_subsystems_column(\@ids);
1898 :
1899 :			# get the column for the evidence codes
1900 :			%evidence_column = &get_evidence_column(\@ids);
1901 :
1902 :			# get the column for pfam_domain
1903 :			%pfam_column = &get_pfam_column(\@ids);
1904 :	arodri7	1.28
1905 :	arodri7	1.31	my %e_identical = &get_essentially_identical($query_fid);
1906 :	arodri7	1.33	my $all_aliases = $fig->feature_aliases_bulk(\@ids);
1907 :	arodri7	1.31
1908 :	arodri7	1.28	foreach my $thing (@$dataset) {
1909 :			next if ($thing->class ne "SIM");
1910 :	arodri7	1.10	my $single_domain = [];
1911 :			$count++;
1912 :
1913 :	arodri7	1.11	my $id = $thing->acc;
1914 :
1915 :			my $iden = $thing->identity;
1916 :			my $ln1 = $thing->qlength;
1917 :			my $ln2 = $thing->hlength;
1918 :			my $b1 = $thing->qstart;
1919 :			my $e1 = $thing->qstop;
1920 :			my $b2 = $thing->hstart;
1921 :			my $e2 = $thing->hstop;
1922 :			my $d1 = abs($e1 - $b1) + 1;
1923 :			my $d2 = abs($e2 - $b2) + 1;
1924 :			my $reg1 = "$b1-$e1 (<b>$d1/$ln1</b>)";
1925 :			my $reg2 = "$b2-$e2 (<b>$d2/$ln2</b>)";
1926 :
1927 :	arodri7	1.29	# checkbox column
1928 :			my $field_name = "tables_" . $id;
1929 :			my $pair_name = "visual_" . $id;
1930 :			my $box_col = qq(<input type=checkbox name=seq value="$id" id="$field_name" onClick="VisualCheckPair('$field_name', '$pair_name');">);
1931 :	arodri7	1.31
1932 :			# get the linked fig id
1933 :			my $fig_col;
1934 :			if (defined ($e_identical{$id})){
1935 :			$fig_col = &HTML::set_prot_links($cgi,$id) . "*";
1936 :			}
1937 :			else{
1938 :			$fig_col = &HTML::set_prot_links($cgi,$id);
1939 :	arodri7	1.28	}
1940 :
1941 :	arodri7	1.29	push(@$single_domain,$box_col); # permanent column
1942 :	arodri7	1.31	push(@$single_domain,$fig_col); # permanent column
1943 :	arodri7	1.29	push(@$single_domain,$thing->evalue); # permanent column
1944 :			push(@$single_domain,"$iden\%"); # permanent column
1945 :			push(@$single_domain,$reg1); # permanent column
1946 :			push(@$single_domain,$reg2); # permanent column
1947 :			push(@$single_domain,$thing->organism); # permanent column
1948 :			push(@$single_domain,$thing->function); # permanent column
1949 :	arodri7	1.35	foreach my $col (sort keys %$scroll_list){
1950 :			if ($col =~ /associated_subsystem/) {push(@$single_domain,$subsystems_column{$id});}
1951 :			elsif ($col =~ /evidence/) {push(@$single_domain,$evidence_column{$id});}
1952 :			elsif ($col =~ /pfam_domains/) {push(@$single_domain,$pfam_column{$id});}
1953 :			elsif ($col =~ /ncbi_id/) {push(@$single_domain,&get_prefer($thing->acc, 'NCBI', $all_aliases));}
1954 :			elsif ($col =~ /refseq_id/) {push(@$single_domain,&get_prefer($thing->acc, 'RefSeq', $all_aliases));}
1955 :			elsif ($col =~ /swissprot_id/) {push(@$single_domain,&get_prefer($thing->acc, 'SwissProt', $all_aliases));}
1956 :			elsif ($col =~ /uniprot_id/) {push(@$single_domain,&get_prefer($thing->acc, 'UniProt', $all_aliases));}
1957 :			elsif ($col =~ /tigr_id/) {push(@$single_domain,&get_prefer($thing->acc, 'TIGR', $all_aliases));}
1958 :			elsif ($col =~ /pir_id/) {push(@$single_domain,&get_prefer($thing->acc, 'PIR', $all_aliases));}
1959 :			elsif ($col =~ /kegg_id/) {push(@$single_domain,&get_prefer($thing->acc, 'KEGG', $all_aliases));}
1960 :			elsif ($col =~ /trembl_id/) {push(@$single_domain,&get_prefer($thing->acc, 'TrEMBL', $all_aliases));}
1961 :			elsif ($col =~ /asap_id/) {push(@$single_domain,&get_prefer($thing->acc, 'ASAP', $all_aliases));}
1962 :			elsif ($col =~ /jgi_id/) {push(@$single_domain,&get_prefer($thing->acc, 'JGI', $all_aliases));}
1963 :	arodri7	1.32	}
1964 :	arodri7	1.10	push(@$data,$single_domain);
1965 :			}
1966 :
1967 :	arodri7	1.26	if ($count >0 ){
1968 :			$content = $data;
1969 :	arodri7	1.10	}
1970 :	arodri7	1.26	else{
1971 :	arodri7	1.10	$content = "<p>This PEG does not have any similarities</p>";
1972 :			}
1973 :			return ($content);
1974 :			}
1975 :	arodri7	1.11
1976 :	arodri7	1.29	sub get_box_column{
1977 :			my ($ids) = @_;
1978 :			my %column;
1979 :			foreach my $id (@$ids){
1980 :			my $field_name = "tables_" . $id;
1981 :			my $pair_name = "visual_" . $id;
1982 :			$column{$id} = qq(<input type=checkbox name=seq value="$id" id="$field_name" onClick="VisualCheckPair('$field_name', '$pair_name');">);
1983 :			}
1984 :			return (%column);
1985 :			}
1986 :
1987 :			sub get_subsystems_column{
1988 :			my ($ids) = @_;
1989 :
1990 :			my $fig = new FIG;
1991 :			my $cgi = new CGI;
1992 :			my %in_subs = $fig->subsystems_for_pegs($ids);
1993 :			my %column;
1994 :			foreach my $id (@$ids){
1995 :	arodri7	1.32	my @in_sub = @{$in_subs{$id}} if (defined $in_subs{$id});
1996 :			my @subsystems;
1997 :
1998 :	arodri7	1.29	if (@in_sub > 0) {
1999 :	arodri7	1.32	my $count = 1;
2000 :			foreach my $array(@in_sub){
2001 :			push (@subsystems, $count . ". " . $$array[0]);
2002 :			$count++;
2003 :			}
2004 :			my $in_sub_line = join ("<br>", @subsystems);
2005 :			$column{$id} = $in_sub_line;
2006 :	arodri7	1.29	} else {
2007 :			$column{$id} = " ";
2008 :			}
2009 :			}
2010 :			return (%column);
2011 :			}
2012 :
2013 :	arodri7	1.31	sub get_essentially_identical{
2014 :			my ($fid) = @_;
2015 :			my $fig = new FIG;
2016 :
2017 :			my %id_list;
2018 :			my @maps_to = grep { $_ ne $fid and $_ !~ /^xxx/ } map { $_->[0] } $fig->mapped_prot_ids($fid);
2019 :
2020 :			foreach my $id (@maps_to) {
2021 :			if (($id ne $fid) && ($fig->function_of($id))) {
2022 :			$id_list{$id} = 1;
2023 :			}
2024 :			}
2025 :			return(%id_list);
2026 :			}
2027 :
2028 :
2029 :	arodri7	1.29	sub get_evidence_column{
2030 :			my ($ids) = @_;
2031 :			my $fig = new FIG;
2032 :			my $cgi = new CGI;
2033 :			my (%column, %code_attributes);
2034 :
2035 :			my @codes = grep { $_->[1] =~ /^evidence_code/i } $fig->get_attributes($ids);
2036 :			foreach my $key (@codes){
2037 :			push (@{$code_attributes{$$key[0]}}, $key);
2038 :			}
2039 :
2040 :			foreach my $id (@$ids){
2041 :			# add evidence code with tool tip
2042 :			my $ev_codes="   ";
2043 :			my @ev_codes = "";
2044 :
2045 :			if ($id =~ /^fig\\|\d+\.\d+\.peg\.\d+$/) {
2046 :			my @codes;
2047 :			@codes = @{$code_attributes{$id}} if (defined @{$code_attributes{$id}});
2048 :			@ev_codes = ();
2049 :			foreach my $code (@codes) {
2050 :			my $pretty_code = $code->[2];
2051 :			if ($pretty_code =~ /;/) {
2052 :			my ($cd, $ss) = split(";", $code->[2]);
2053 :			$ss =~ s/_/ /g;
2054 :			$pretty_code = $cd;# . " in " . $ss;
2055 :			}
2056 :			push(@ev_codes, $pretty_code);
2057 :			}
2058 :			}
2059 :
2060 :			if (scalar(@ev_codes) && $ev_codes[0]) {
2061 :			my $ev_code_help=join("<br />", map {&HTML::evidence_codes_explain($_)} @ev_codes);
2062 :			$ev_codes = $cgi->a(
2063 :			{
2064 :			id=>"evidence_codes", onMouseover=>"javascript:if(!this.tooltip) this.tooltip=new Popup_Tooltip(this, 'Evidence Codes', '$ev_code_help', ''); this.tooltip.addHandler(); return false;"}, join("<br />", @ev_codes));
2065 :			}
2066 :			$column{$id}=$ev_codes;
2067 :			}
2068 :			return (%column);
2069 :			}
2070 :
2071 :	arodri7	1.33	sub get_pfam_column{
2072 :			my ($ids) = @_;
2073 :			my $fig = new FIG;
2074 :			my $cgi = new CGI;
2075 :			my (%column, %code_attributes);
2076 :			my $dbmaster = DBMaster->new(-database =>'Ontology');
2077 :
2078 :			my @codes = grep { $_->[1] =~ /^PFAM/i } $fig->get_attributes($ids);
2079 :			foreach my $key (@codes){
2080 :			push (@{$code_attributes{$$key[0]}}, $$key[1]);
2081 :			}
2082 :
2083 :			foreach my $id (@$ids){
2084 :			# add evidence code with tool tip
2085 :			my $pfam_codes="   ";
2086 :			my @pfam_codes = "";
2087 :			my %description_codes;
2088 :
2089 :			if ($id =~ /^fig\\|\d+\.\d+\.peg\.\d+$/) {
2090 :			my @codes;
2091 :			@codes = @{$code_attributes{$id}} if (defined @{$code_attributes{$id}});
2092 :			@pfam_codes = ();
2093 :			foreach my $code (@codes) {
2094 :			my @parts = split("::",$code);
2095 :			my $pfam_link = "<a href=http://www.sanger.ac.uk//cgi-bin/Pfam/getacc?" . $parts[1] . ">$parts[1]</a>";
2096 :			if (defined ($description_codes{$parts[1]})){
2097 :			push(@pfam_codes, "$description_codes{$parts[1]} ($parts[1])");
2098 :			}
2099 :			else {
2100 :			my $description = $dbmaster->pfam->get_objects( { 'id' => $parts[1] } );
2101 :			$description_codes{$parts[1]} = ${$$description[0]}{term};
2102 :			push(@pfam_codes, "${$$description[0]}{term} ($pfam_link)");
2103 :			}
2104 :			}
2105 :			}
2106 :
2107 :			$column{$id}=join("<br><br>", @pfam_codes);
2108 :			}
2109 :			return (%column);
2110 :
2111 :			}
2112 :	mkubal	1.12
2113 :	arodri7	1.28	sub get_prefer {
2114 :	arodri7	1.33	my ($fid, $db, $all_aliases) = @_;
2115 :	arodri7	1.28	my $fig = new FIG;
2116 :	arodri7	1.31	my $cgi = new CGI;
2117 :
2118 :	arodri7	1.33	foreach my $alias (@{$$all_aliases{$fid}}){
2119 :	arodri7	1.28	my $id_db = &Observation::get_database($alias);
2120 :			if ($id_db eq $db){
2121 :	arodri7	1.31	my $acc_col .= &HTML::set_prot_links($cgi,$alias);
2122 :			return ($acc_col);
2123 :	arodri7	1.28	}
2124 :			}
2125 :	arodri7	1.31	return (" ");
2126 :	arodri7	1.28	}
2127 :
2128 :	arodri7	1.33	sub html_enc { $_ = $_[0]; s/\&/&/g; s/\>/>/g; s/\</</g; $_ }
2129 :
2130 :	arodri7	1.26	sub color {
2131 :	arodri7	1.39	my ($evalue) = @_;
2132 :	arodri7	1.26	my $color;
2133 :	arodri7	1.39	if ($evalue <= 1e-170){ $color = 51; }
2134 :			elsif (($evalue <= 1e-120) && ($evalue > 1e-170)){ $color = 52; }
2135 :			elsif (($evalue <= 1e-90) && ($evalue > 1e-120)){ $color = 53; }
2136 :			elsif (($evalue <= 1e-70) && ($evalue > 1e-90)){ $color = 54; }
2137 :			elsif (($evalue <= 1e-40) && ($evalue > 1e-70)){ $color = 55; }
2138 :			elsif (($evalue <= 1e-20) && ($evalue > 1e-40)){ $color = 56; }
2139 :			elsif (($evalue <= 1e-5) && ($evalue > 1e-20)){ $color = 57; }
2140 :			elsif (($evalue <= 1) && ($evalue > 1e-5)){ $color = 58; }
2141 :			elsif (($evalue <= 10) && ($evalue > 1)){ $color = 59; }
2142 :			else{ $color = 60; }
2143 :	arodri7	1.26	return ($color);
2144 :			}
2145 :	arodri7	1.13
2146 :
2147 :			############################
2148 :			package Observation::Cluster;
2149 :
2150 :			use base qw(Observation);
2151 :
2152 :			sub new {
2153 :
2154 :			my ($class,$dataset) = @_;
2155 :			my $self = $class->SUPER::new($dataset);
2156 :	mkubal	1.24	$self->{context} = $dataset->{'context'};
2157 :	arodri7	1.13	bless($self,$class);
2158 :			return $self;
2159 :			}
2160 :
2161 :			sub display {
2162 :	arodri7	1.39	my ($self,$gd,$selected_taxonomies,$taxes) = @_;
2163 :	mkubal	1.24
2164 :			my $fid = $self->fig_id;
2165 :			my $compare_or_coupling = $self->context;
2166 :			my $gd_window_size = $gd->window_size;
2167 :	arodri7	1.13	my $fig = new FIG;
2168 :	mkubal	1.14	my $all_regions = [];
2169 :	arodri7	1.38	my $gene_associations={};
2170 :	arodri7	1.13
2171 :			#get the organism genome
2172 :	mkubal	1.14	my $target_genome = $fig->genome_of($fid);
2173 :	arodri7	1.38	$gene_associations->{$fid}->{"organism"} = $target_genome;
2174 :			$gene_associations->{$fid}->{"main_gene"} = $fid;
2175 :			$gene_associations->{$fid}->{"reverse_flag"} = 0;
2176 :	arodri7	1.13
2177 :			# get location of the gene
2178 :			my $data = $fig->feature_location($fid);
2179 :			my ($contig, $beg, $end);
2180 :	arodri7	1.22	my %reverse_flag;
2181 :	arodri7	1.13
2182 :			if ($data =~ /(.*)_(\d+)_(\d+)$/){
2183 :			$contig = $1;
2184 :			$beg = $2;
2185 :			$end = $3;
2186 :			}
2187 :
2188 :	arodri7	1.22	my $offset;
2189 :	arodri7	1.13	my ($region_start, $region_end);
2190 :			if ($beg < $end)
2191 :			{
2192 :			$region_start = $beg - 4000;
2193 :			$region_end = $end+4000;
2194 :	arodri7	1.22	$offset = ($2+(($3-$2)/2))-($gd_window_size/2);
2195 :	arodri7	1.13	}
2196 :			else
2197 :			{
2198 :	arodri7	1.21	$region_start = $end-4000;
2199 :			$region_end = $beg+4000;
2200 :	arodri7	1.22	$offset = ($3+(($2-$3)/2))-($gd_window_size/2);
2201 :	arodri7	1.25	$reverse_flag{$target_genome} = $fid;
2202 :	arodri7	1.38	$gene_associations->{$fid}->{"reverse_flag"} = 1;
2203 :	arodri7	1.21	}
2204 :	arodri7	1.13
2205 :			# call genes in region
2206 :	arodri7	1.16	my ($target_gene_features, $reg_beg, $reg_end) = $fig->genes_in_region($target_genome, $contig, $region_start, $region_end);
2207 :	mkubal	1.14	push(@$all_regions,$target_gene_features);
2208 :	arodri7	1.16	my (@start_array_region);
2209 :	arodri7	1.22	push (@start_array_region, $offset);
2210 :	mkubal	1.14
2211 :			my %all_genes;
2212 :			my %all_genomes;
2213 :	arodri7	1.38	foreach my $feature (@$target_gene_features){ $all_genes{$feature} = $fid; $gene_associations->{$feature}->{"main_gene"}=$fid;}
2214 :	arodri7	1.16
2215 :	mkubal	1.24	if ($compare_or_coupling eq "diverse")
2216 :	arodri7	1.25	{
2217 :	arodri7	1.21	my @coup = grep { $_->[1]} $fig->coupling_and_evidence($fid,5000,1e-10,4,1);
2218 :
2219 :			my $coup_count = 0;
2220 :
2221 :			foreach my $pair (@{$coup[0]->[2]}) {
2222 :			# last if ($coup_count > 10);
2223 :			my ($peg1,$peg2) = @$pair;
2224 :	arodri7	1.22
2225 :			my ($pair_contig,$pair_beg,$pair_end,$pair_region_start,$pair_region_stop,$pair_genome);
2226 :			$pair_genome = $fig->genome_of($peg1);
2227 :	arodri7	1.21
2228 :			my $location = $fig->feature_location($peg1);
2229 :			if($location =~/(.*)_(\d+)_(\d+)$/){
2230 :			$pair_contig = $1;
2231 :			$pair_beg = $2;
2232 :			$pair_end = $3;
2233 :			if ($pair_beg < $pair_end)
2234 :			{
2235 :			$pair_region_start = $pair_beg - 4000;
2236 :			$pair_region_stop = $pair_end+4000;
2237 :	arodri7	1.38	$offset = ($pair_beg+(($pair_end-$pair_beg)/2))-($gd_window_size/2);
2238 :	arodri7	1.21	}
2239 :			else
2240 :			{
2241 :			$pair_region_start = $pair_end-4000;
2242 :			$pair_region_stop = $pair_beg+4000;
2243 :	arodri7	1.38	$offset = ($pair_end+(($pair_beg-$pair_end)/2))-($gd_window_size/2);
2244 :	arodri7	1.25	$reverse_flag{$pair_genome} = $peg1;
2245 :	arodri7	1.21	}
2246 :
2247 :	arodri7	1.22	push (@start_array_region, $offset);
2248 :	arodri7	1.21
2249 :			$all_genomes{$pair_genome} = 1;
2250 :			my ($pair_features) = $fig->genes_in_region($pair_genome, $pair_contig, $pair_region_start, $pair_region_stop);
2251 :			push(@$all_regions,$pair_features);
2252 :	arodri7	1.25	foreach my $pair_feature (@$pair_features){ $all_genes{$pair_feature} = $peg1;}
2253 :	arodri7	1.21	}
2254 :			$coup_count++;
2255 :			}
2256 :			}
2257 :	arodri7	1.37	elsif ($compare_or_coupling eq "sims"){
2258 :			# get the selected boxes
2259 :	arodri7	1.38	#my @selected_taxonomy = ("Streptococcaceae", "Enterobacteriales");
2260 :			my @selected_taxonomy = @$selected_taxonomies;
2261 :	arodri7	1.37
2262 :			# get the similarities and store only the ones that match the lineages selected
2263 :			my @selected_sims;
2264 :	arodri7	1.38	my @sims= $fig->nsims($fid,20000,10,"fig");
2265 :	arodri7	1.37
2266 :	arodri7	1.38	if (@selected_taxonomy > 0){
2267 :			foreach my $sim (@sims){
2268 :			next if ($sim->[1] !~ /fig\\|/);
2269 :			my $genome = $fig->genome_of($sim->[1]);
2270 :	arodri7	1.39	my ($genome1) = ($genome) =~ /(.*)\./;
2271 :			my $lineage = $taxes->{$genome1};
2272 :			#my $lineage = $fig->taxonomy_of($fig->genome_of($sim->[1]));
2273 :	arodri7	1.38	foreach my $taxon(@selected_taxonomy){
2274 :			if ($lineage =~ /$taxon/){
2275 :			push (@selected_sims, $sim->[1]);
2276 :			}
2277 :	arodri7	1.37	}
2278 :	arodri7	1.38	my %saw;
2279 :			@selected_sims = grep(!$saw{$_}++, @selected_sims);
2280 :	arodri7	1.37	}
2281 :			}
2282 :	arodri7	1.16
2283 :	arodri7	1.37	# get the gene context for the sorted matches
2284 :			foreach my $sim_fid(@selected_sims){
2285 :			#get the organism genome
2286 :			my $sim_genome = $fig->genome_of($sim_fid);
2287 :	arodri7	1.38	$gene_associations->{$sim_fid}->{"organism"} = $sim_genome;
2288 :			$gene_associations->{$sim_fid}->{"main_gene"} = $sim_fid;
2289 :			$gene_associations->{$sim_fid}->{"reverse_flag"} = 0;
2290 :	arodri7	1.37
2291 :			# get location of the gene
2292 :			my $data = $fig->feature_location($sim_fid);
2293 :			my ($contig, $beg, $end);
2294 :
2295 :			if ($data =~ /(.*)_(\d+)_(\d+)$/){
2296 :			$contig = $1;
2297 :			$beg = $2;
2298 :			$end = $3;
2299 :			}
2300 :
2301 :			my $offset;
2302 :			my ($region_start, $region_end);
2303 :			if ($beg < $end)
2304 :			{
2305 :			$region_start = $beg - 4000;
2306 :			$region_end = $end+4000;
2307 :	arodri7	1.38	$offset = ($beg+(($end-$beg)/2))-($gd_window_size/2);
2308 :	arodri7	1.37	}
2309 :			else
2310 :			{
2311 :			$region_start = $end-4000;
2312 :			$region_end = $beg+4000;
2313 :	arodri7	1.38	$offset = ($end+(($beg-$end)/2))-($gd_window_size/2);
2314 :			$reverse_flag{$sim_genome} = $sim_fid;
2315 :			$gene_associations->{$sim_fid}->{"reverse_flag"} = 1;
2316 :	arodri7	1.37	}
2317 :
2318 :			# call genes in region
2319 :			my ($sim_gene_features, $reg_beg, $reg_end) = $fig->genes_in_region($sim_genome, $contig, $region_start, $region_end);
2320 :			push(@$all_regions,$sim_gene_features);
2321 :			push (@start_array_region, $offset);
2322 :	arodri7	1.38	foreach my $feature (@$sim_gene_features){ $all_genes{$feature} = $sim_fid;$gene_associations->{$feature}->{"main_gene"}=$sim_fid;}
2323 :			$all_genomes{$sim_genome} = 1;
2324 :	arodri7	1.16	}
2325 :	mkubal	1.14
2326 :			}
2327 :	arodri7	1.21
2328 :	arodri7	1.38	# cluster the genes
2329 :			my @all_pegs = keys %all_genes;
2330 :			my $color_sets = &cluster_genes($fig,\@all_pegs,$fid);
2331 :	arodri7	1.21
2332 :	mkubal	1.14	foreach my $region (@$all_regions){
2333 :			my $sample_peg = @$region[0];
2334 :			my $region_genome = $fig->genome_of($sample_peg);
2335 :			my $region_gs = $fig->genus_species($region_genome);
2336 :	arodri7	1.18	my $abbrev_name = $fig->abbrev($region_gs);
2337 :	arodri7	1.16	my $line_config = { 'title' => $region_gs,
2338 :	arodri7	1.18	'short_title' => $abbrev_name,
2339 :	arodri7	1.16	'basepair_offset' => '0'
2340 :			};
2341 :
2342 :	arodri7	1.22	my $offsetting = shift @start_array_region;
2343 :	arodri7	1.16
2344 :	arodri7	1.25	my $second_line_config = { 'title' => "$region_gs",
2345 :			'short_title' => "",
2346 :	arodri7	1.38	'basepair_offset' => '0',
2347 :			'no_middle_line' => '1'
2348 :	arodri7	1.25	};
2349 :
2350 :	mkubal	1.14	my $line_data = [];
2351 :	arodri7	1.25	my $second_line_data = [];
2352 :
2353 :			# initialize variables to check for overlap in genes
2354 :			my ($prev_start, $prev_stop, $prev_fig, $second_line_flag);
2355 :			my $major_line_flag = 0;
2356 :			my $prev_second_flag = 0;
2357 :
2358 :	arodri7	1.16	foreach my $fid1 (@$region){
2359 :	arodri7	1.25	$second_line_flag = 0;
2360 :	mkubal	1.14	my $element_hash;
2361 :			my $links_list = [];
2362 :			my $descriptions = [];
2363 :	arodri7	1.38
2364 :			my $color = $color_sets->{$fid1};
2365 :	arodri7	1.26
2366 :	arodri7	1.18	# get subsystem information
2367 :			my $function = $fig->function_of($fid1);
2368 :			my $url_link = "http://seed-viewer.theseed.org/index.cgi?action=ShowAnnotation&prot=".$fid1;
2369 :
2370 :			my $link;
2371 :			$link = {"link_title" => $fid1,
2372 :			"link" => $url_link};
2373 :			push(@$links_list,$link);
2374 :
2375 :			my @subsystems = $fig->peg_to_subsystems($fid1);
2376 :			foreach my $subsystem (@subsystems){
2377 :			my $link;
2378 :			$link = {"link" => "http://seed-viewer.theseed.org/index.cgi?action=ShowSubsystem&subsystem_name=$subsystem",
2379 :			"link_title" => $subsystem};
2380 :			push(@$links_list,$link);
2381 :			}
2382 :
2383 :			my $description_function;
2384 :			$description_function = {"title" => "function",
2385 :			"value" => $function};
2386 :			push(@$descriptions,$description_function);
2387 :
2388 :			my $description_ss;
2389 :			my $ss_string = join (",", @subsystems);
2390 :			$description_ss = {"title" => "subsystems",
2391 :			"value" => $ss_string};
2392 :			push(@$descriptions,$description_ss);
2393 :
2394 :	arodri7	1.16
2395 :			my $fid_location = $fig->feature_location($fid1);
2396 :	mkubal	1.14	if($fid_location =~/(.*)_(\d+)_(\d+)$/){
2397 :			my($start,$stop);
2398 :	arodri7	1.22	$start = $2 - $offsetting;
2399 :			$stop = $3 - $offsetting;
2400 :	arodri7	1.25
2401 :			if ( (($prev_start) && ($prev_stop) ) &&
2402 :			( ($start < $prev_start) \|\| ($start < $prev_stop) \|\|
2403 :			($stop < $prev_start) \|\| ($stop < $prev_stop) )){
2404 :			if (($second_line_flag == 0) && ($prev_second_flag == 0)) {
2405 :			$second_line_flag = 1;
2406 :			$major_line_flag = 1;
2407 :			}
2408 :			}
2409 :			$prev_start = $start;
2410 :			$prev_stop = $stop;
2411 :			$prev_fig = $fid1;
2412 :
2413 :			if ((defined($reverse_flag{$region_genome})) && ($reverse_flag{$region_genome} eq $all_genes{$fid1})){
2414 :	arodri7	1.22	$start = $gd_window_size - $start;
2415 :			$stop = $gd_window_size - $stop;
2416 :			}
2417 :
2418 :	mkubal	1.14	$element_hash = {
2419 :	arodri7	1.16	"title" => $fid1,
2420 :	mkubal	1.14	"start" => $start,
2421 :			"end" => $stop,
2422 :			"type"=> 'arrow',
2423 :			"color"=> $color,
2424 :	arodri7	1.18	"zlayer" => "2",
2425 :			"links_list" => $links_list,
2426 :			"description" => $descriptions
2427 :	mkubal	1.14	};
2428 :	arodri7	1.25
2429 :			# if there is an overlap, put into second line
2430 :			if ($second_line_flag == 1){ push(@$second_line_data,$element_hash); $prev_second_flag = 1;}
2431 :			else{ push(@$line_data,$element_hash); $prev_second_flag = 0;}
2432 :	mkubal	1.14	}
2433 :			}
2434 :			$gd->add_line($line_data, $line_config);
2435 :	arodri7	1.25	$gd->add_line($second_line_data, $second_line_config) if ($major_line_flag == 1);
2436 :	mkubal	1.14	}
2437 :			return $gd;
2438 :			}
2439 :
2440 :	arodri7	1.38	sub cluster_genes {
2441 :			my($fig,$all_pegs,$peg) = @_;
2442 :			my(%seen,$i,$j,$k,$x,$cluster,$conn,$pegI,$red_set);
2443 :
2444 :			my @color_sets = ();
2445 :
2446 :			$conn = &get_connections_by_similarity($fig,$all_pegs);
2447 :
2448 :			for ($i=0; ($i < @$all_pegs); $i++) {
2449 :			if ($all_pegs->[$i] eq $peg) { $pegI = $i }
2450 :			if (! $seen{$i}) {
2451 :			$cluster = [$i];
2452 :			$seen{$i} = 1;
2453 :			for ($j=0; ($j < @$cluster); $j++) {
2454 :			$x = $conn->{$cluster->[$j]};
2455 :			foreach $k (@$x) {
2456 :			if (! $seen{$k}) {
2457 :			push(@$cluster,$k);
2458 :			$seen{$k} = 1;
2459 :			}
2460 :			}
2461 :			}
2462 :
2463 :			if ((@$cluster > 1) \|\| ($cluster->[0] eq $pegI)) {
2464 :			push(@color_sets,$cluster);
2465 :			}
2466 :			}
2467 :			}
2468 :			for ($i=0; ($i < @color_sets) && (! &in($pegI,$color_sets[$i])); $i++) {}
2469 :			$red_set = $color_sets[$i];
2470 :			splice(@color_sets,$i,1);
2471 :			@color_sets = sort { @$b <=> @$a } @color_sets;
2472 :			unshift(@color_sets,$red_set);
2473 :
2474 :			my $color_sets = {};
2475 :			for ($i=0; ($i < @color_sets); $i++) {
2476 :			foreach $x (@{$color_sets[$i]}) {
2477 :			$color_sets->{$all_pegs->[$x]} = $i;
2478 :			}
2479 :			}
2480 :			return $color_sets;
2481 :			}
2482 :
2483 :			sub get_connections_by_similarity {
2484 :			my($fig,$all_pegs) = @_;
2485 :			my($i,$j,$tmp,$peg,%pos_of);
2486 :			my($sim,%conn,$x,$y);
2487 :
2488 :			for ($i=0; ($i < @$all_pegs); $i++) {
2489 :			$tmp = $fig->maps_to_id($all_pegs->[$i]);
2490 :			push(@{$pos_of{$tmp}},$i);
2491 :			if ($tmp ne $all_pegs->[$i]) {
2492 :			push(@{$pos_of{$all_pegs->[$i]}},$i);
2493 :			}
2494 :			}
2495 :
2496 :			foreach $y (keys(%pos_of)) {
2497 :			$x = $pos_of{$y};
2498 :			for ($i=0; ($i < @$x); $i++) {
2499 :			for ($j=$i+1; ($j < @$x); $j++) {
2500 :			push(@{$conn{$x->[$i]}},$x->[$j]);
2501 :			push(@{$conn{$x->[$j]}},$x->[$i]);
2502 :			}
2503 :			}
2504 :			}
2505 :
2506 :			for ($i=0; ($i < @$all_pegs); $i++) {
2507 :			foreach $sim ($fig->nsims($all_pegs->[$i],500,10,"raw")) {
2508 :			if (defined($x = $pos_of{$sim->id2})) {
2509 :			foreach $y (@$x) {
2510 :			push(@{$conn{$i}},$y);
2511 :			}
2512 :			}
2513 :			}
2514 :			}
2515 :			return \%conn;
2516 :			}
2517 :
2518 :			sub in {
2519 :			my($x,$xL) = @_;
2520 :			my($i);
2521 :
2522 :			for ($i=0; ($i < @$xL) && ($x != $xL->[$i]); $i++) {}
2523 :			return ($i < @$xL);
2524 :			}

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