Annotation of /FigKernelPackages/Observation.pm

Revision 1.55 - (view) (download) (as text)

1 :	mkubal	1.1	package Observation;
2 :
3 :	paczian	1.54	#use lib '/vol/ontologies';
4 :	mkubal	1.19	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 :	paczian	1.44	use WebColors;
11 :	paczian	1.52	use WebConfig;
12 :	paczian	1.44
13 :	arodri7	1.16	use FIG_Config;
14 :	mkubal	1.30	#use strict;
15 :	arodri7	1.16	#use warnings;
16 :	arodri7	1.9	use HTML;
17 :	arodri7	1.55	use FFs;
18 :	mkubal	1.1
19 :			1;
20 :
21 :			=head1 NAME
22 :
23 :			Observation -- A presentation layer for observations in SEED.
24 :
25 :			=head1 DESCRIPTION
26 :
27 :			The SEED environment contains various sources of information for sequence features. The purpose of this library is to provide a
28 :			single interface to this data.
29 :
30 :			The data can be used to display information for a given sequence feature (protein or other, but primarily information is computed for proteins).
31 :
32 :			=cut
33 :
34 :			=head1 BACKGROUND
35 :
36 :			=head2 Data incorporated in the Observations
37 :
38 :			As the goal of this library is to provide an integrated view, we combine diverse sources of evidence.
39 :
40 :			=head3 SEED core evidence
41 :
42 :			The core SEED data structures provided by FIG.pm. These are Similarities, BBHs and PCHs.
43 :
44 :			=head3 Attribute based Evidence
45 :
46 :			We use the SEED attribute infrastructure to store information computed by a variety of computational procedures.
47 :
48 :			These are e.g. InterPro hits via InterProScan (ipr), NCBI Conserved Domain Database Hits via PSSM(cdd),
49 :			PFAM hits via HMM(pfam), SignalP results(signalp), and various others.
50 :
51 :			=head1 METHODS
52 :
53 :			The public methods this package provides are listed below:
54 :
55 :
56 :	mkubal	1.24	=head3 context()
57 :
58 :			Returns close or diverse for purposes of displaying genomic context
59 :	mkubal	1.1
60 :			=cut
61 :
62 :	mkubal	1.24	sub context {
63 :	mkubal	1.1	my ($self) = @_;
64 :
65 :	mkubal	1.24	return $self->{context};
66 :	mkubal	1.1	}
67 :
68 :	mkubal	1.24	=head3 rows()
69 :	mkubal	1.1
70 :	mkubal	1.24	each row in a displayed table
71 :	mkubal	1.1
72 :	mkubal	1.24	=cut
73 :
74 :			sub rows {
75 :			my ($self) = @_;
76 :
77 :			return $self->{rows};
78 :			}
79 :
80 :			=head3 acc()
81 :
82 :			A valid accession or remote ID (in the style of a db_xref) or a valid local ID (FID) in case this is supported.
83 :	mkubal	1.1
84 :			=cut
85 :
86 :	mkubal	1.24	sub acc {
87 :	mkubal	1.1	my ($self) = @_;
88 :	mkubal	1.24	return $self->{acc};
89 :	mkubal	1.1	}
90 :
91 :	arodri7	1.40	=head3 query()
92 :
93 :			The query id
94 :
95 :			=cut
96 :
97 :			sub query {
98 :			my ($self) = @_;
99 :			return $self->{query};
100 :			}
101 :
102 :
103 :	mkubal	1.1	=head3 class()
104 :
105 :			The class of evidence (required). This is usually simply the name of the tool or the name of the SEED data structure.
106 :			B<Please note> the connection of class and display_method and URL.
107 :	mkubal	1.7
108 :	mkubal	1.1	Current valid classes are:
109 :
110 :			=over 9
111 :
112 :	arodri7	1.9	=item IDENTICAL (seq)
113 :
114 :	mkubal	1.3	=item SIM (seq)
115 :	mkubal	1.1
116 :	mkubal	1.3	=item BBH (seq)
117 :	mkubal	1.1
118 :	mkubal	1.3	=item PCH (fc)
119 :	mkubal	1.1
120 :	mkubal	1.3	=item FIGFAM (seq)
121 :	mkubal	1.1
122 :	mkubal	1.3	=item IPR (dom)
123 :	mkubal	1.1
124 :	mkubal	1.3	=item CDD (dom)
125 :	mkubal	1.1
126 :	mkubal	1.3	=item PFAM (dom)
127 :	mkubal	1.1
128 :	mkubal	1.12	=item SIGNALP_CELLO_TMPRED (loc)
129 :	mkubal	1.1
130 :	mkubal	1.20	=item PDB (seq)
131 :
132 :	mkubal	1.3	=item TMHMM (loc)
133 :	mkubal	1.1
134 :	mkubal	1.3	=item HMMTOP (loc)
135 :	mkubal	1.1
136 :			=back
137 :
138 :			=cut
139 :
140 :			sub class {
141 :			my ($self) = @_;
142 :
143 :			return $self->{class};
144 :			}
145 :
146 :			=head3 type()
147 :
148 :			The type of evidence (required).
149 :
150 :			Where type is one of the following:
151 :
152 :			=over 8
153 :
154 :			=item seq=Sequence similarity
155 :
156 :			=item dom=domain based match
157 :
158 :			=item loc=Localization of the feature
159 :
160 :			=item fc=Functional coupling.
161 :
162 :			=back
163 :
164 :			=cut
165 :
166 :			sub type {
167 :			my ($self) = @_;
168 :
169 :	arodri7	1.26	return $self->{type};
170 :	mkubal	1.1	}
171 :
172 :			=head3 start()
173 :
174 :			Start of hit in query sequence.
175 :
176 :			=cut
177 :
178 :			sub start {
179 :			my ($self) = @_;
180 :
181 :			return $self->{start};
182 :			}
183 :
184 :			=head3 end()
185 :
186 :			End of the hit in query sequence.
187 :
188 :			=cut
189 :
190 :			sub stop {
191 :			my ($self) = @_;
192 :
193 :			return $self->{stop};
194 :			}
195 :
196 :	arodri7	1.11	=head3 start()
197 :
198 :			Start of hit in query sequence.
199 :
200 :			=cut
201 :
202 :			sub qstart {
203 :			my ($self) = @_;
204 :
205 :			return $self->{qstart};
206 :			}
207 :
208 :			=head3 qstop()
209 :
210 :			End of the hit in query sequence.
211 :
212 :			=cut
213 :
214 :			sub qstop {
215 :			my ($self) = @_;
216 :
217 :			return $self->{qstop};
218 :			}
219 :
220 :			=head3 hstart()
221 :
222 :			Start of hit in hit sequence.
223 :
224 :			=cut
225 :
226 :			sub hstart {
227 :			my ($self) = @_;
228 :
229 :			return $self->{hstart};
230 :			}
231 :
232 :			=head3 end()
233 :
234 :			End of the hit in hit sequence.
235 :
236 :			=cut
237 :
238 :			sub hstop {
239 :			my ($self) = @_;
240 :
241 :			return $self->{hstop};
242 :			}
243 :
244 :			=head3 qlength()
245 :
246 :			length of the query sequence in similarities
247 :
248 :			=cut
249 :
250 :			sub qlength {
251 :			my ($self) = @_;
252 :
253 :			return $self->{qlength};
254 :			}
255 :
256 :			=head3 hlength()
257 :
258 :			length of the hit sequence in similarities
259 :
260 :			=cut
261 :
262 :			sub hlength {
263 :			my ($self) = @_;
264 :
265 :			return $self->{hlength};
266 :			}
267 :
268 :	mkubal	1.1	=head3 evalue()
269 :
270 :			E-value or P-Value if present.
271 :
272 :			=cut
273 :
274 :			sub evalue {
275 :			my ($self) = @_;
276 :
277 :			return $self->{evalue};
278 :			}
279 :
280 :			=head3 score()
281 :
282 :			Score if present.
283 :
284 :			=cut
285 :
286 :			sub score {
287 :			my ($self) = @_;
288 :			return $self->{score};
289 :			}
290 :
291 :	mkubal	1.12	=head3 display()
292 :	mkubal	1.1
293 :	mkubal	1.12	will be different for each type
294 :	mkubal	1.1
295 :			=cut
296 :
297 :	mkubal	1.7	sub display {
298 :	mkubal	1.1
299 :	mkubal	1.7	die "Abstract Method Called\n";
300 :	mkubal	1.1
301 :			}
302 :
303 :	mkubal	1.24	=head3 display_table()
304 :	mkubal	1.7
305 :	mkubal	1.24	will be different for each type
306 :	mkubal	1.1
307 :	mkubal	1.24	=cut
308 :	mkubal	1.1
309 :	mkubal	1.24	sub display_table {
310 :
311 :			die "Abstract Table Method Called\n";
312 :	mkubal	1.1
313 :			}
314 :
315 :			=head3 get_objects()
316 :
317 :			This is the B<REAL WORKHORSE> method of this Package.
318 :
319 :			=cut
320 :
321 :			sub get_objects {
322 :	arodri7	1.41	my ($self,$fid,$fig,$scope) = @_;
323 :	paczian	1.44
324 :	mkubal	1.7	my $objects = [];
325 :			my @matched_datasets=();
326 :	mkubal	1.1
327 :	mkubal	1.7	# call function that fetches attribute based observations
328 :			# returns an array of arrays of hashes
329 :
330 :	mkubal	1.24	if($scope){
331 :			get_cluster_observations($fid,\@matched_datasets,$scope);
332 :	mkubal	1.7	}
333 :			else{
334 :			my %domain_classes;
335 :	arodri7	1.28	my @attributes = $fig->get_attributes($fid);
336 :	mkubal	1.24	$domain_classes{'CDD'} = 1;
337 :	arodri7	1.41	$domain_classes{'PFAM'} = 1;
338 :			get_identical_proteins($fid,\@matched_datasets,$fig);
339 :			get_attribute_based_domain_observations($fid,\%domain_classes,\@matched_datasets,\@attributes,$fig);
340 :			get_sims_observations($fid,\@matched_datasets,$fig);
341 :			get_functional_coupling($fid,\@matched_datasets,$fig);
342 :			get_attribute_based_location_observations($fid,\@matched_datasets,\@attributes,$fig);
343 :			get_pdb_observations($fid,\@matched_datasets,\@attributes,$fig);
344 :	mkubal	1.1	}
345 :	mkubal	1.7
346 :			foreach my $dataset (@matched_datasets) {
347 :			my $object;
348 :			if($dataset->{'type'} eq "dom"){
349 :			$object = Observation::Domain->new($dataset);
350 :			}
351 :	arodri7	1.41	elsif($dataset->{'class'} eq "PCH"){
352 :	arodri7	1.9	$object = Observation::FC->new($dataset);
353 :			}
354 :	arodri7	1.41	elsif ($dataset->{'class'} eq "IDENTICAL"){
355 :	arodri7	1.9	$object = Observation::Identical->new($dataset);
356 :			}
357 :	arodri7	1.41	elsif ($dataset->{'class'} eq "SIGNALP_CELLO_TMPRED"){
358 :	mkubal	1.12	$object = Observation::Location->new($dataset);
359 :			}
360 :	arodri7	1.41	elsif ($dataset->{'class'} eq "SIM"){
361 :	arodri7	1.10	$object = Observation::Sims->new($dataset);
362 :			}
363 :	arodri7	1.41	elsif ($dataset->{'class'} eq "CLUSTER"){
364 :	arodri7	1.15	$object = Observation::Cluster->new($dataset);
365 :			}
366 :	arodri7	1.41	elsif ($dataset->{'class'} eq "PDB"){
367 :	mkubal	1.20	$object = Observation::PDB->new($dataset);
368 :			}
369 :
370 :	mkubal	1.7	push (@$objects, $object);
371 :	mkubal	1.1	}
372 :	mkubal	1.7
373 :			return $objects;
374 :	mkubal	1.1
375 :			}
376 :
377 :	arodri7	1.28	=head3 display_housekeeping
378 :			This method returns the housekeeping data for a given peg in a table format
379 :
380 :			=cut
381 :			sub display_housekeeping {
382 :	arodri7	1.41	my ($self,$fid,$fig) = @_;
383 :			my $content = [];
384 :			my $row = [];
385 :	arodri7	1.28
386 :			my $org_name = $fig->org_of($fid);
387 :	arodri7	1.45	my $org_id = $fig->genome_of($fid);
388 :	arodri7	1.28	my $function = $fig->function_of($fid);
389 :	arodri7	1.41	#my $taxonomy = $fig->taxonomy_of($org_id);
390 :			my $length = $fig->translation_length($fid);
391 :
392 :			push (@$row, $org_name);
393 :			push (@$row, $fid);
394 :			push (@$row, $length);
395 :			push (@$row, $function);
396 :
397 :			# initialize the table for commentary and annotations
398 :			#$content .= qq(<b>My Sequence Data</b><br><table border="0">);
399 :			#$content .= qq(<tr width=15%><td >FIG ID</td><td>$fid</td></tr>\n);
400 :			#$content .= qq(<tr width=15%><td >Organism Name</td><td>$org_name</td></tr>\n);
401 :			#$content .= qq(<tr><td width=15%>Taxonomy</td><td>$taxonomy</td></tr>\n);
402 :			#$content .= qq(<tr width=15%><td>Function</td><td>$function</td></tr>\n);
403 :			#$content .= qq(<tr width=15%><td>Sequence Length</td><td>$length aa</td></tr>\n);
404 :			#$content .= qq(</table><p>\n);
405 :
406 :			push(@$content, $row);
407 :	arodri7	1.28
408 :			return ($content);
409 :			}
410 :
411 :			=head3 get_sims_summary
412 :			This method uses as input the similarities of a peg and creates a tree view of their taxonomy
413 :
414 :			=cut
415 :
416 :			sub get_sims_summary {
417 :	arodri7	1.53	my ($observation, $dataset, $fig) = @_;
418 :	arodri7	1.28	my %families;
419 :	arodri7	1.53	my $taxes = $fig->taxonomy_list();
420 :
421 :	arodri7	1.42	foreach my $thing (@$dataset) {
422 :	arodri7	1.53	my ($id, $evalue);
423 :			if ($thing =~ /fig\\|/){
424 :			$id = $thing;
425 :			$evalue = -1;
426 :			}
427 :			else{
428 :			next if ($thing->class ne "SIM");
429 :			$id = $thing->acc;
430 :			$evalue = $thing->evalue;
431 :			}
432 :	arodri7	1.42	next if ($id !~ /fig\\|/);
433 :			next if ($fig->is_deleted_fid($id));
434 :	arodri7	1.53
435 :	arodri7	1.42	my $genome = $fig->genome_of($id);
436 :	arodri7	1.45	#my ($genome1) = ($genome) =~ /(.*)\./;
437 :	arodri7	1.53	my $taxonomy = $taxes->{$genome};
438 :	arodri7	1.28	my $parent_tax = "Root";
439 :	arodri7	1.38	my @currLineage = ($parent_tax);
440 :	arodri7	1.53	push (@{$families{figs}{$parent_tax}}, $id);
441 :			my $level = 2;
442 :	arodri7	1.28	foreach my $tax (split(/\; /, $taxonomy)){
443 :	arodri7	1.53	push (@{$families{children}{$parent_tax}}, $tax) if ($tax ne $parent_tax);
444 :			push (@{$families{figs}{$tax}}, $id) if ($tax ne $parent_tax);
445 :			$families{level}{$tax} = $level;
446 :	arodri7	1.38	push (@currLineage, $tax);
447 :	arodri7	1.28	$families{parent}{$tax} = $parent_tax;
448 :	arodri7	1.38	$families{lineage}{$tax} = join(";", @currLineage);
449 :	arodri7	1.39	if (defined ($families{evalue}{$tax})){
450 :	arodri7	1.53	if ($evalue < $families{evalue}{$tax}){
451 :	arodri7	1.42	$families{evalue}{$tax} = $evalue;
452 :			$families{color}{$tax} = &get_taxcolor($evalue);
453 :	arodri7	1.39	}
454 :			}
455 :			else{
456 :	arodri7	1.42	$families{evalue}{$tax} = $evalue;
457 :			$families{color}{$tax} = &get_taxcolor($evalue);
458 :	arodri7	1.39	}
459 :
460 :	arodri7	1.28	$parent_tax = $tax;
461 :	arodri7	1.53	$level++;
462 :	arodri7	1.28	}
463 :			}
464 :
465 :			foreach my $key (keys %{$families{children}}){
466 :			$families{count}{$key} = @{$families{children}{$key}};
467 :
468 :			my %saw;
469 :			my @out = grep(!$saw{$_}++, @{$families{children}{$key}});
470 :			$families{children}{$key} = \@out;
471 :			}
472 :	arodri7	1.53
473 :			return \%families;
474 :	arodri7	1.28	}
475 :
476 :	mkubal	1.1	=head1 Internal Methods
477 :
478 :			These methods are not meant to be used outside of this package.
479 :
480 :			B<Please do not use them outside of this package!>
481 :
482 :			=cut
483 :
484 :	arodri7	1.39	sub get_taxcolor{
485 :			my ($evalue) = @_;
486 :			my $color;
487 :	arodri7	1.53	if ($evalue == -1){ $color = "black"; }
488 :			elsif (($evalue <= 1e-170) && ($evalue >= 0)){ $color = "#FF2000"; }
489 :	arodri7	1.39	elsif (($evalue <= 1e-120) && ($evalue > 1e-170)){ $color = "#FF3300"; }
490 :			elsif (($evalue <= 1e-90) && ($evalue > 1e-120)){ $color = "#FF6600"; }
491 :			elsif (($evalue <= 1e-70) && ($evalue > 1e-90)){ $color = "#FF9900"; }
492 :			elsif (($evalue <= 1e-40) && ($evalue > 1e-70)){ $color = "#FFCC00"; }
493 :			elsif (($evalue <= 1e-20) && ($evalue > 1e-40)){ $color = "#FFFF00"; }
494 :			elsif (($evalue <= 1e-5) && ($evalue > 1e-20)){ $color = "#CCFF00"; }
495 :			elsif (($evalue <= 1) && ($evalue > 1e-5)){ $color = "#66FF00"; }
496 :			elsif (($evalue <= 10) && ($evalue > 1)){ $color = "#00FF00"; }
497 :			else{ $color = "#6666FF"; }
498 :			return ($color);
499 :			}
500 :
501 :
502 :	mkubal	1.7	sub get_attribute_based_domain_observations{
503 :
504 :			# we read a FIG ID and a reference to an array (of arrays of hashes, see above)
505 :	arodri7	1.41	my ($fid,$domain_classes,$datasets_ref,$attributes_ref,$fig) = (@_);
506 :	mkubal	1.7
507 :	arodri7	1.28	foreach my $attr_ref (@$attributes_ref) {
508 :	mkubal	1.7	my $key = @$attr_ref[1];
509 :			my @parts = split("::",$key);
510 :			my $class = $parts[0];
511 :	arodri7	1.50	my $name = $parts[1];
512 :			next if (($class eq "PFAM") && ($name !~ /interpro/));
513 :
514 :	mkubal	1.7	if($domain_classes->{$parts[0]}){
515 :			my $val = @$attr_ref[2];
516 :	mkubal	1.8	if($val =~/^(\d+\.\d+\|0\.0);(\d+)-(\d+)/){
517 :	mkubal	1.7	my $raw_evalue = $1;
518 :	mkubal	1.8	my $from = $2;
519 :			my $to = $3;
520 :	mkubal	1.7	my $evalue;
521 :	arodri7	1.50	if(($raw_evalue =~/(\d+)\.(\d+)/) && ($class ne "PFAM")){
522 :	mkubal	1.7	my $part2 = 1000 - $1;
523 :			my $part1 = $2/100;
524 :			$evalue = $part1."e-".$part2;
525 :			}
526 :	arodri7	1.50	elsif(($raw_evalue =~/(\d+)\.(\d+)/) && ($class eq "PFAM")){
527 :			$evalue=$raw_evalue;
528 :			}
529 :	mkubal	1.7	else{
530 :	mkubal	1.8	$evalue = "0.0";
531 :	mkubal	1.7	}
532 :
533 :			my $dataset = {'class' => $class,
534 :			'acc' => $key,
535 :			'type' => "dom" ,
536 :			'evalue' => $evalue,
537 :			'start' => $from,
538 :	mkubal	1.24	'stop' => $to,
539 :			'fig_id' => $fid,
540 :			'score' => $raw_evalue
541 :	mkubal	1.7	};
542 :
543 :			push (@{$datasets_ref} ,$dataset);
544 :			}
545 :			}
546 :			}
547 :			}
548 :	mkubal	1.12
549 :			sub get_attribute_based_location_observations{
550 :
551 :	arodri7	1.41	my ($fid,$datasets_ref, $attributes_ref,$fig) = (@_);
552 :			#my $fig = new FIG;
553 :	mkubal	1.12
554 :	mkubal	1.30	my $location_attributes = ['SignalP','CELLO','TMPRED','Phobius'];
555 :	mkubal	1.12
556 :	arodri7	1.26	my $dataset = {'type' => "loc",
557 :			'class' => 'SIGNALP_CELLO_TMPRED',
558 :			'fig_id' => $fid
559 :			};
560 :
561 :	arodri7	1.28	foreach my $attr_ref (@$attributes_ref){
562 :	mkubal	1.12	my $key = @$attr_ref[1];
563 :	mkubal	1.30	next if (($key !~ /SignalP/) && ($key !~ /CELLO/) && ($key !~ /TMPRED/) && ($key !~/Phobius/) );
564 :	mkubal	1.12	my @parts = split("::",$key);
565 :			my $sub_class = $parts[0];
566 :			my $sub_key = $parts[1];
567 :			my $value = @$attr_ref[2];
568 :			if($sub_class eq "SignalP"){
569 :			if($sub_key eq "cleavage_site"){
570 :			my @value_parts = split(";",$value);
571 :			$dataset->{'cleavage_prob'} = $value_parts[0];
572 :			$dataset->{'cleavage_loc'} = $value_parts[1];
573 :			}
574 :			elsif($sub_key eq "signal_peptide"){
575 :			$dataset->{'signal_peptide_score'} = $value;
576 :			}
577 :			}
578 :	mkubal	1.30
579 :	mkubal	1.12	elsif($sub_class eq "CELLO"){
580 :			$dataset->{'cello_location'} = $sub_key;
581 :			$dataset->{'cello_score'} = $value;
582 :			}
583 :	mkubal	1.30
584 :			elsif($sub_class eq "Phobius"){
585 :			if($sub_key eq "transmembrane"){
586 :			$dataset->{'phobius_tm_locations'} = $value;
587 :			}
588 :			elsif($sub_key eq "signal"){
589 :			$dataset->{'phobius_signal_location'} = $value;
590 :			}
591 :			}
592 :
593 :	mkubal	1.12	elsif($sub_class eq "TMPRED"){
594 :	arodri7	1.26	my @value_parts = split(/\;/,$value);
595 :	mkubal	1.12	$dataset->{'tmpred_score'} = $value_parts[0];
596 :			$dataset->{'tmpred_locations'} = $value_parts[1];
597 :			}
598 :			}
599 :
600 :			push (@{$datasets_ref} ,$dataset);
601 :
602 :			}
603 :
604 :	mkubal	1.20	=head3 get_pdb_observations() (internal)
605 :
606 :			This methods sets the type and class for pdb observations
607 :
608 :			=cut
609 :
610 :			sub get_pdb_observations{
611 :	arodri7	1.41	my ($fid,$datasets_ref, $attributes_ref,$fig) = (@_);
612 :	mkubal	1.20
613 :	arodri7	1.41	#my $fig = new FIG;
614 :	mkubal	1.20
615 :	arodri7	1.28	foreach my $attr_ref (@$attributes_ref){
616 :	mkubal	1.20	my $key = @$attr_ref[1];
617 :	arodri7	1.28	next if ( ($key !~ /PDB/));
618 :	mkubal	1.20	my($key1,$key2) =split("::",$key);
619 :			my $value = @$attr_ref[2];
620 :			my ($evalue,$location) = split(";",$value);
621 :
622 :			if($evalue =~/(\d+)\.(\d+)/){
623 :			my $part2 = 1000 - $1;
624 :			my $part1 = $2/100;
625 :			$evalue = $part1."e-".$part2;
626 :			}
627 :
628 :			my($start,$stop) =split("-",$location);
629 :
630 :			my $url = @$attr_ref[3];
631 :			my $dataset = {'class' => 'PDB',
632 :			'type' => 'seq' ,
633 :			'acc' => $key2,
634 :			'evalue' => $evalue,
635 :			'start' => $start,
636 :	mkubal	1.24	'stop' => $stop,
637 :			'fig_id' => $fid
638 :	mkubal	1.20	};
639 :
640 :			push (@{$datasets_ref} ,$dataset);
641 :			}
642 :			}
643 :
644 :	arodri7	1.15	=head3 get_cluster_observations() (internal)
645 :
646 :			This methods sets the type and class for cluster observations
647 :
648 :			=cut
649 :
650 :			sub get_cluster_observations{
651 :	mkubal	1.24	my ($fid,$datasets_ref,$scope) = (@_);
652 :	arodri7	1.15
653 :	arodri7	1.16	my $dataset = {'class' => 'CLUSTER',
654 :	mkubal	1.24	'type' => 'fc',
655 :			'context' => $scope,
656 :			'fig_id' => $fid
657 :	arodri7	1.16	};
658 :	arodri7	1.15	push (@{$datasets_ref} ,$dataset);
659 :			}
660 :
661 :
662 :	mkubal	1.3	=head3 get_sims_observations() (internal)
663 :
664 :			This methods retrieves sims fills the internal data structures.
665 :
666 :			=cut
667 :
668 :			sub get_sims_observations{
669 :
670 :	arodri7	1.41	my ($fid,$datasets_ref,$fig) = (@_);
671 :			#my $fig = new FIG;
672 :	arodri7	1.42	my @sims= $fig->sims($fid,500,10,"fig");
673 :	mkubal	1.4	my ($dataset);
674 :	arodri7	1.26
675 :			foreach my $sim (@sims){
676 :	arodri7	1.42	next if ($fig->is_deleted_fid($sim->[1]));
677 :	arodri7	1.26	my $hit = $sim->[1];
678 :	arodri7	1.11	my $percent = $sim->[2];
679 :	mkubal	1.4	my $evalue = $sim->[10];
680 :	arodri7	1.11	my $qfrom = $sim->[6];
681 :			my $qto = $sim->[7];
682 :			my $hfrom = $sim->[8];
683 :			my $hto = $sim->[9];
684 :			my $qlength = $sim->[12];
685 :			my $hlength = $sim->[13];
686 :			my $db = get_database($hit);
687 :			my $func = $fig->function_of($hit);
688 :			my $organism = $fig->org_of($hit);
689 :
690 :	arodri7	1.10	$dataset = {'class' => 'SIM',
691 :	arodri7	1.40	'query' => $sim->[0],
692 :	arodri7	1.10	'acc' => $hit,
693 :	arodri7	1.11	'identity' => $percent,
694 :	arodri7	1.10	'type' => 'seq',
695 :			'evalue' => $evalue,
696 :	arodri7	1.11	'qstart' => $qfrom,
697 :			'qstop' => $qto,
698 :			'hstart' => $hfrom,
699 :			'hstop' => $hto,
700 :			'database' => $db,
701 :			'organism' => $organism,
702 :			'function' => $func,
703 :			'qlength' => $qlength,
704 :	mkubal	1.24	'hlength' => $hlength,
705 :			'fig_id' => $fid
706 :	arodri7	1.10	};
707 :
708 :			push (@{$datasets_ref} ,$dataset);
709 :	mkubal	1.3	}
710 :			}
711 :
712 :	arodri7	1.11	=head3 get_database (internal)
713 :			This method gets the database association from the sequence id
714 :
715 :			=cut
716 :
717 :			sub get_database{
718 :			my ($id) = (@_);
719 :
720 :			my ($db);
721 :			if ($id =~ /^fig\\|/) { $db = "FIG" }
722 :			elsif ($id =~ /^gi\\|/) { $db = "NCBI" }
723 :			elsif ($id =~ /^^[NXYZA]P_/) { $db = "RefSeq" }
724 :			elsif ($id =~ /^sp\\|/) { $db = "SwissProt" }
725 :			elsif ($id =~ /^uni\\|/) { $db = "UniProt" }
726 :			elsif ($id =~ /^tigr\\|/) { $db = "TIGR" }
727 :			elsif ($id =~ /^pir\\|/) { $db = "PIR" }
728 :	arodri7	1.28	elsif (($id =~ /^kegg\\|/) \|\| ($id =~ /Spy/)) { $db = "KEGG" }
729 :			elsif ($id =~ /^tr\\|/) { $db = "TrEMBL" }
730 :	arodri7	1.11	elsif ($id =~ /^eric\\|/) { $db = "ASAP" }
731 :			elsif ($id =~ /^img\\|/) { $db = "JGI" }
732 :
733 :			return ($db);
734 :
735 :			}
736 :
737 :	mkubal	1.24
738 :	arodri7	1.5	=head3 get_identical_proteins() (internal)
739 :
740 :			This methods retrieves sims fills the internal data structures.
741 :
742 :			=cut
743 :
744 :			sub get_identical_proteins{
745 :
746 :	arodri7	1.41	my ($fid,$datasets_ref,$fig) = (@_);
747 :			#my $fig = new FIG;
748 :	mkubal	1.24	my $funcs_ref;
749 :	arodri7	1.5
750 :			my @maps_to = grep { $_ ne $fid and $_ !~ /^xxx/ } map { $_->[0] } $fig->mapped_prot_ids($fid);
751 :			foreach my $id (@maps_to) {
752 :			my ($tmp, $who);
753 :	arodri7	1.33	if (($id ne $fid) && ($tmp = $fig->function_of($id))) {
754 :	arodri7	1.11	$who = &get_database($id);
755 :	mkubal	1.24	push(@$funcs_ref, [$id,$who,$tmp]);
756 :	arodri7	1.5	}
757 :			}
758 :
759 :	mkubal	1.24	my $dataset = {'class' => 'IDENTICAL',
760 :			'type' => 'seq',
761 :			'fig_id' => $fid,
762 :			'rows' => $funcs_ref
763 :			};
764 :
765 :			push (@{$datasets_ref} ,$dataset);
766 :
767 :	arodri7	1.5
768 :			}
769 :
770 :	arodri7	1.6	=head3 get_functional_coupling() (internal)
771 :
772 :			This methods retrieves the functional coupling of a protein given a peg ID
773 :
774 :			=cut
775 :
776 :			sub get_functional_coupling{
777 :
778 :	arodri7	1.41	my ($fid,$datasets_ref,$fig) = (@_);
779 :			#my $fig = new FIG;
780 :	arodri7	1.6	my @funcs = ();
781 :
782 :			# initialize some variables
783 :			my($sc,$neigh);
784 :
785 :			# set default parameters for coupling and evidence
786 :			my ($bound,$sim_cutoff,$coupling_cutoff) = (5000, 1.0e-10, 4);
787 :
788 :			# get the fc data
789 :			my @fc_data = $fig->coupling_and_evidence($fid,$bound,$sim_cutoff,$coupling_cutoff,1);
790 :
791 :			# retrieve data
792 :			my @rows = map { ($sc,$neigh) = @$_;
793 :			[$sc,$neigh,scalar $fig->function_of($neigh)]
794 :			} @fc_data;
795 :
796 :	mkubal	1.24	my $dataset = {'class' => 'PCH',
797 :			'type' => 'fc',
798 :			'fig_id' => $fid,
799 :			'rows' => \@rows
800 :			};
801 :
802 :			push (@{$datasets_ref} ,$dataset);
803 :	arodri7	1.9
804 :	arodri7	1.6	}
805 :	arodri7	1.5
806 :	mkubal	1.1	=head3 new (internal)
807 :
808 :			Instantiate a new object.
809 :
810 :			=cut
811 :
812 :			sub new {
813 :	mkubal	1.7	my ($class,$dataset) = @_;
814 :
815 :			my $self = { class => $dataset->{'class'},
816 :	mkubal	1.24	type => $dataset->{'type'},
817 :			fig_id => $dataset->{'fig_id'},
818 :			score => $dataset->{'score'},
819 :	arodri7	1.10	};
820 :	mkubal	1.7
821 :			bless($self,$class);
822 :	mkubal	1.1
823 :			return $self;
824 :			}
825 :
826 :	arodri7	1.11	=head3 identity (internal)
827 :
828 :			Returns the % identity of the similar sequence
829 :
830 :			=cut
831 :
832 :			sub identity {
833 :			my ($self) = @_;
834 :
835 :			return $self->{identity};
836 :			}
837 :
838 :	mkubal	1.24	=head3 fig_id (internal)
839 :
840 :			=cut
841 :
842 :			sub fig_id {
843 :			my ($self) = @_;
844 :			return $self->{fig_id};
845 :			}
846 :
847 :	mkubal	1.1	=head3 feature_id (internal)
848 :
849 :
850 :			=cut
851 :
852 :			sub feature_id {
853 :			my ($self) = @_;
854 :
855 :			return $self->{feature_id};
856 :			}
857 :	arodri7	1.5
858 :			=head3 id (internal)
859 :
860 :			Returns the ID of the identical sequence
861 :
862 :			=cut
863 :
864 :			sub id {
865 :			my ($self) = @_;
866 :
867 :			return $self->{id};
868 :			}
869 :
870 :			=head3 organism (internal)
871 :
872 :			Returns the organism of the identical sequence
873 :
874 :			=cut
875 :
876 :			sub organism {
877 :			my ($self) = @_;
878 :
879 :			return $self->{organism};
880 :			}
881 :
882 :	arodri7	1.9	=head3 function (internal)
883 :
884 :			Returns the function of the identical sequence
885 :
886 :			=cut
887 :
888 :			sub function {
889 :			my ($self) = @_;
890 :
891 :			return $self->{function};
892 :			}
893 :
894 :	arodri7	1.5	=head3 database (internal)
895 :
896 :			Returns the database of the identical sequence
897 :
898 :			=cut
899 :
900 :			sub database {
901 :			my ($self) = @_;
902 :
903 :			return $self->{database};
904 :			}
905 :
906 :	mkubal	1.20	############################################################
907 :			############################################################
908 :			package Observation::PDB;
909 :
910 :			use base qw(Observation);
911 :
912 :			sub new {
913 :
914 :			my ($class,$dataset) = @_;
915 :			my $self = $class->SUPER::new($dataset);
916 :			$self->{acc} = $dataset->{'acc'};
917 :			$self->{evalue} = $dataset->{'evalue'};
918 :			$self->{start} = $dataset->{'start'};
919 :			$self->{stop} = $dataset->{'stop'};
920 :			bless($self,$class);
921 :			return $self;
922 :			}
923 :
924 :			=head3 display()
925 :
926 :			displays data stored in best_PDB attribute and in Ontology server for given PDB id
927 :
928 :			=cut
929 :
930 :			sub display{
931 :	arodri7	1.41	my ($self,$gd,$fig) = @_;
932 :	mkubal	1.20
933 :	mkubal	1.24	my $fid = $self->fig_id;
934 :	paczian	1.52	my $dbmaster = DBMaster->new(-database =>'Ontology',
935 :			-host => $WebConfig::DBHOST,
936 :			-user => $WebConfig::DBUSER,
937 :			-password => $WebConfig::DBPWD);
938 :	mkubal	1.20
939 :			my $acc = $self->acc;
940 :
941 :			my ($pdb_description,$pdb_source,$pdb_ligand);
942 :			my $pdb_objs = $dbmaster->pdb->get_objects( { 'id' => $acc } );
943 :			if(!scalar(@$pdb_objs)){
944 :			$pdb_description = "not available";
945 :			$pdb_source = "not available";
946 :			$pdb_ligand = "not available";
947 :			}
948 :			else{
949 :			my $pdb_obj = $pdb_objs->[0];
950 :			$pdb_description = $pdb_obj->description;
951 :			$pdb_source = $pdb_obj->source;
952 :			$pdb_ligand = $pdb_obj->ligand;
953 :			}
954 :	arodri7	1.6
955 :	mkubal	1.20	my $lines = [];
956 :			my $line_data = [];
957 :			my $line_config = { 'title' => "PDB hit for $fid",
958 :	paczian	1.47	'hover_title' => 'PDB',
959 :	mkubal	1.20	'short_title' => "best PDB",
960 :			'basepair_offset' => '1' };
961 :
962 :	arodri7	1.41	#my $fig = new FIG;
963 :	mkubal	1.20	my $seq = $fig->get_translation($fid);
964 :			my $fid_stop = length($seq);
965 :
966 :			my $fid_element_hash = {
967 :			"title" => $fid,
968 :			"start" => '1',
969 :			"end" => $fid_stop,
970 :			"color"=> '1',
971 :			"zlayer" => '1'
972 :			};
973 :
974 :			push(@$line_data,$fid_element_hash);
975 :
976 :			my $links_list = [];
977 :			my $descriptions = [];
978 :
979 :			my $name;
980 :			$name = {"title" => 'id',
981 :			"value" => $acc};
982 :			push(@$descriptions,$name);
983 :
984 :			my $description;
985 :			$description = {"title" => 'pdb description',
986 :			"value" => $pdb_description};
987 :			push(@$descriptions,$description);
988 :
989 :			my $score;
990 :			$score = {"title" => "score",
991 :			"value" => $self->evalue};
992 :			push(@$descriptions,$score);
993 :
994 :			my $start_stop;
995 :			my $start_stop_value = $self->start."_".$self->stop;
996 :			$start_stop = {"title" => "start-stop",
997 :			"value" => $start_stop_value};
998 :			push(@$descriptions,$start_stop);
999 :
1000 :			my $source;
1001 :			$source = {"title" => "source",
1002 :			"value" => $pdb_source};
1003 :			push(@$descriptions,$source);
1004 :
1005 :			my $ligand;
1006 :			$ligand = {"title" => "pdb ligand",
1007 :			"value" => $pdb_ligand};
1008 :			push(@$descriptions,$ligand);
1009 :
1010 :			my $link;
1011 :			my $link_url ="http://www.rcsb.org/pdb/explore/explore.do?structureId=".$acc;
1012 :
1013 :			$link = {"link_title" => $acc,
1014 :			"link" => $link_url};
1015 :			push(@$links_list,$link);
1016 :
1017 :			my $pdb_element_hash = {
1018 :			"title" => "PDB homology",
1019 :			"start" => $self->start,
1020 :			"end" => $self->stop,
1021 :			"color"=> '6',
1022 :			"zlayer" => '3',
1023 :			"links_list" => $links_list,
1024 :			"description" => $descriptions};
1025 :
1026 :			push(@$line_data,$pdb_element_hash);
1027 :			$gd->add_line($line_data, $line_config);
1028 :
1029 :			return $gd;
1030 :			}
1031 :
1032 :			1;
1033 :	arodri7	1.11
1034 :	arodri7	1.9	############################################################
1035 :			############################################################
1036 :			package Observation::Identical;
1037 :
1038 :			use base qw(Observation);
1039 :
1040 :			sub new {
1041 :
1042 :			my ($class,$dataset) = @_;
1043 :			my $self = $class->SUPER::new($dataset);
1044 :	mkubal	1.24	$self->{rows} = $dataset->{'rows'};
1045 :
1046 :	arodri7	1.9	bless($self,$class);
1047 :			return $self;
1048 :			}
1049 :
1050 :	mkubal	1.24	=head3 display_table()
1051 :	arodri7	1.6
1052 :			If available use the function specified here to display the "raw" observation.
1053 :			This code will display a table for the identical protein
1054 :
1055 :
1056 :	arodri7	1.9	B<Please note> that URL linked to in display_method() is an external component and needs to added to the code for every class of evi
1057 :			dence.
1058 :	arodri7	1.6
1059 :			=cut
1060 :
1061 :
1062 :	mkubal	1.24	sub display_table{
1063 :	arodri7	1.41	my ($self,$fig) = @_;
1064 :	mkubal	1.24
1065 :	arodri7	1.41	#my $fig = new FIG;
1066 :	mkubal	1.24	my $fid = $self->fig_id;
1067 :			my $rows = $self->rows;
1068 :			my $cgi = new CGI;
1069 :	arodri7	1.6	my $all_domains = [];
1070 :			my $count_identical = 0;
1071 :	arodri7	1.9	my $content;
1072 :	mkubal	1.24	foreach my $row (@$rows) {
1073 :			my $id = $row->[0];
1074 :			my $who = $row->[1];
1075 :			my $assignment = $row->[2];
1076 :	arodri7	1.26	my $organism = $fig->org_of($id);
1077 :	arodri7	1.9	my $single_domain = [];
1078 :	mkubal	1.24	push(@$single_domain,$who);
1079 :			push(@$single_domain,&HTML::set_prot_links($cgi,$id));
1080 :			push(@$single_domain,$organism);
1081 :			push(@$single_domain,$assignment);
1082 :	arodri7	1.9	push(@$all_domains,$single_domain);
1083 :	mkubal	1.24	$count_identical++;
1084 :	arodri7	1.6	}
1085 :
1086 :			if ($count_identical >0){
1087 :	arodri7	1.9	$content = $all_domains;
1088 :	arodri7	1.6	}
1089 :			else{
1090 :	arodri7	1.9	$content = "<p>This PEG does not have any essentially identical proteins</p>";
1091 :	arodri7	1.6	}
1092 :			return ($content);
1093 :			}
1094 :	mkubal	1.7
1095 :	arodri7	1.9	1;
1096 :
1097 :			#########################################
1098 :			#########################################
1099 :			package Observation::FC;
1100 :			1;
1101 :
1102 :			use base qw(Observation);
1103 :
1104 :			sub new {
1105 :
1106 :			my ($class,$dataset) = @_;
1107 :			my $self = $class->SUPER::new($dataset);
1108 :	mkubal	1.24	$self->{rows} = $dataset->{'rows'};
1109 :	arodri7	1.9
1110 :			bless($self,$class);
1111 :			return $self;
1112 :			}
1113 :
1114 :	mkubal	1.24	=head3 display_table()
1115 :	arodri7	1.9
1116 :			If available use the function specified here to display the "raw" observation.
1117 :			This code will display a table for the identical protein
1118 :
1119 :
1120 :			B<Please note> that URL linked to in display_method() is an external component and needs to added to the code for every class of evi
1121 :			dence.
1122 :
1123 :			=cut
1124 :
1125 :	mkubal	1.24	sub display_table {
1126 :	arodri7	1.9
1127 :	arodri7	1.41	my ($self,$dataset,$fig) = @_;
1128 :	mkubal	1.24	my $fid = $self->fig_id;
1129 :			my $rows = $self->rows;
1130 :			my $cgi = new CGI;
1131 :	arodri7	1.9	my $functional_data = [];
1132 :			my $count = 0;
1133 :			my $content;
1134 :
1135 :	mkubal	1.24	foreach my $row (@$rows) {
1136 :	arodri7	1.9	my $single_domain = [];
1137 :			$count++;
1138 :
1139 :			# construct the score link
1140 :	mkubal	1.24	my $score = $row->[0];
1141 :			my $toid = $row->[1];
1142 :	paczian	1.44	my $link = $cgi->url(-relative => 1) . "?page=Annotation&feature=$fid";
1143 :			my $sc_link = "<a href='$link'>$score</a>";
1144 :	arodri7	1.9
1145 :			push(@$single_domain,$sc_link);
1146 :	mkubal	1.24	push(@$single_domain,$row->[1]);
1147 :			push(@$single_domain,$row->[2]);
1148 :	arodri7	1.9	push(@$functional_data,$single_domain);
1149 :			}
1150 :
1151 :			if ($count >0){
1152 :			$content = $functional_data;
1153 :			}
1154 :			else
1155 :			{
1156 :			$content = "<p>This PEG does not have any functional coupling</p>";
1157 :			}
1158 :			return ($content);
1159 :			}
1160 :
1161 :
1162 :			#########################################
1163 :			#########################################
1164 :	mkubal	1.7	package Observation::Domain;
1165 :
1166 :			use base qw(Observation);
1167 :
1168 :			sub new {
1169 :
1170 :			my ($class,$dataset) = @_;
1171 :			my $self = $class->SUPER::new($dataset);
1172 :			$self->{evalue} = $dataset->{'evalue'};
1173 :			$self->{acc} = $dataset->{'acc'};
1174 :			$self->{start} = $dataset->{'start'};
1175 :			$self->{stop} = $dataset->{'stop'};
1176 :
1177 :			bless($self,$class);
1178 :			return $self;
1179 :			}
1180 :
1181 :			sub display {
1182 :			my ($thing,$gd) = @_;
1183 :			my $lines = [];
1184 :	arodri7	1.27	# my $line_config = { 'title' => $thing->acc,
1185 :			# 'short_title' => $thing->type,
1186 :			# 'basepair_offset' => '1' };
1187 :	mkubal	1.7	my $color = "4";
1188 :
1189 :			my $line_data = [];
1190 :			my $links_list = [];
1191 :			my $descriptions = [];
1192 :	mkubal	1.19
1193 :			my $db_and_id = $thing->acc;
1194 :			my ($db,$id) = split("::",$db_and_id);
1195 :	arodri7	1.41
1196 :	paczian	1.52	my $dbmaster = DBMaster->new(-database =>'Ontology',
1197 :			-host => $WebConfig::DBHOST,
1198 :			-user => $WebConfig::DBUSER,
1199 :			-password => $WebConfig::DBPWD);
1200 :	mkubal	1.7
1201 :	mkubal	1.19	my ($name_title,$name_value,$description_title,$description_value);
1202 :			if($db eq "CDD"){
1203 :			my $cdd_objs = $dbmaster->cdd->get_objects( { 'id' => $id } );
1204 :			if(!scalar(@$cdd_objs)){
1205 :			$name_title = "name";
1206 :			$name_value = "not available";
1207 :			$description_title = "description";
1208 :			$description_value = "not available";
1209 :			}
1210 :			else{
1211 :			my $cdd_obj = $cdd_objs->[0];
1212 :			$name_title = "name";
1213 :			$name_value = $cdd_obj->term;
1214 :			$description_title = "description";
1215 :			$description_value = $cdd_obj->description;
1216 :			}
1217 :			}
1218 :	arodri7	1.41	elsif($db =~ /PFAM/){
1219 :	arodri7	1.50	my ($new_id) = ($id) =~ /(.*?)_/;
1220 :			my $pfam_objs = $dbmaster->pfam->get_objects( { 'id' => $new_id } );
1221 :	arodri7	1.41	if(!scalar(@$pfam_objs)){
1222 :			$name_title = "name";
1223 :			$name_value = "not available";
1224 :			$description_title = "description";
1225 :			$description_value = "not available";
1226 :			}
1227 :			else{
1228 :			my $pfam_obj = $pfam_objs->[0];
1229 :	arodri7	1.50	$name_title = "name";
1230 :			$name_value = $pfam_obj->term;
1231 :	arodri7	1.41	#$description_title = "description";
1232 :			#$description_value = $pfam_obj->description;
1233 :			}
1234 :			}
1235 :
1236 :			my $short_title = $thing->acc;
1237 :			$short_title =~ s/::/ - /ig;
1238 :	arodri7	1.50	my $new_short_title=$short_title;
1239 :			if ($short_title =~ /interpro/){
1240 :			($new_short_title) = ($short_title) =~ /(.*?)_/;
1241 :			}
1242 :	arodri7	1.41	my $line_config = { 'title' => $name_value,
1243 :	paczian	1.47	'hover_title', => 'Domain',
1244 :	arodri7	1.50	'short_title' => $new_short_title,
1245 :	arodri7	1.27	'basepair_offset' => '1' };
1246 :	mkubal	1.7
1247 :	mkubal	1.19	my $name;
1248 :	arodri7	1.50	my ($new_id) = ($id) =~ /(.*?)_/;
1249 :	arodri7	1.41	$name = {"title" => $db,
1250 :	arodri7	1.50	"value" => $new_id};
1251 :	mkubal	1.19	push(@$descriptions,$name);
1252 :
1253 :	arodri7	1.41	# my $description;
1254 :			# $description = {"title" => $description_title,
1255 :			# "value" => $description_value};
1256 :			# push(@$descriptions,$description);
1257 :	mkubal	1.7
1258 :			my $score;
1259 :			$score = {"title" => "score",
1260 :			"value" => $thing->evalue};
1261 :			push(@$descriptions,$score);
1262 :
1263 :	arodri7	1.41	my $location;
1264 :			$location = {"title" => "location",
1265 :			"value" => $thing->start . " - " . $thing->stop};
1266 :			push(@$descriptions,$location);
1267 :
1268 :	mkubal	1.7	my $link_id;
1269 :	arodri7	1.41	if ($thing->acc =~/::(.*)/){
1270 :	mkubal	1.7	$link_id = $1;
1271 :			}
1272 :
1273 :			my $link;
1274 :	mkubal	1.12	my $link_url;
1275 :			if ($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"}
1276 :	arodri7	1.53	elsif($thing->class eq "PFAM"){$link_url = "http://pfam.sanger.ac.uk/family?acc=$link_id"}
1277 :	mkubal	1.12	else{$link_url = "NO_URL"}
1278 :
1279 :	mkubal	1.7	$link = {"link_title" => $thing->acc,
1280 :	mkubal	1.12	"link" => $link_url};
1281 :	mkubal	1.7	push(@$links_list,$link);
1282 :
1283 :			my $element_hash = {
1284 :	arodri7	1.41	"title" => $name_value,
1285 :	mkubal	1.7	"start" => $thing->start,
1286 :			"end" => $thing->stop,
1287 :			"color"=> $color,
1288 :			"zlayer" => '2',
1289 :			"links_list" => $links_list,
1290 :			"description" => $descriptions};
1291 :
1292 :			push(@$line_data,$element_hash);
1293 :			$gd->add_line($line_data, $line_config);
1294 :
1295 :			return $gd;
1296 :
1297 :			}
1298 :	arodri7	1.28
1299 :			sub display_table {
1300 :			my ($self,$dataset) = @_;
1301 :			my $cgi = new CGI;
1302 :			my $data = [];
1303 :			my $count = 0;
1304 :			my $content;
1305 :
1306 :			foreach my $thing (@$dataset) {
1307 :			next if ($thing->type !~ /dom/);
1308 :			my $single_domain = [];
1309 :			$count++;
1310 :
1311 :			my $db_and_id = $thing->acc;
1312 :			my ($db,$id) = split("::",$db_and_id);
1313 :
1314 :	paczian	1.52	my $dbmaster = DBMaster->new(-database =>'Ontology',
1315 :			-host => $WebConfig::DBHOST,
1316 :			-user => $WebConfig::DBUSER,
1317 :			-password => $WebConfig::DBPWD);
1318 :	arodri7	1.28
1319 :			my ($name_title,$name_value,$description_title,$description_value);
1320 :			if($db eq "CDD"){
1321 :			my $cdd_objs = $dbmaster->cdd->get_objects( { 'id' => $id } );
1322 :			if(!scalar(@$cdd_objs)){
1323 :			$name_title = "name";
1324 :			$name_value = "not available";
1325 :			$description_title = "description";
1326 :			$description_value = "not available";
1327 :			}
1328 :			else{
1329 :			my $cdd_obj = $cdd_objs->[0];
1330 :			$name_title = "name";
1331 :			$name_value = $cdd_obj->term;
1332 :			$description_title = "description";
1333 :			$description_value = $cdd_obj->description;
1334 :			}
1335 :			}
1336 :	arodri7	1.51	elsif($db =~ /PFAM/){
1337 :			my ($new_id) = ($id) =~ /(.*?)_/;
1338 :			my $pfam_objs = $dbmaster->pfam->get_objects( { 'id' => $new_id } );
1339 :			if(!scalar(@$pfam_objs)){
1340 :			$name_title = "name";
1341 :			$name_value = "not available";
1342 :			$description_title = "description";
1343 :			$description_value = "not available";
1344 :			}
1345 :			else{
1346 :			my $pfam_obj = $pfam_objs->[0];
1347 :			$name_title = "name";
1348 :			$name_value = $pfam_obj->term;
1349 :			#$description_title = "description";
1350 :			#$description_value = $pfam_obj->description;
1351 :			}
1352 :			}
1353 :	arodri7	1.28
1354 :			my $location = $thing->start . " - " . $thing->stop;
1355 :
1356 :			push(@$single_domain,$db);
1357 :			push(@$single_domain,$thing->acc);
1358 :			push(@$single_domain,$name_value);
1359 :			push(@$single_domain,$location);
1360 :			push(@$single_domain,$thing->evalue);
1361 :			push(@$single_domain,$description_value);
1362 :			push(@$data,$single_domain);
1363 :			}
1364 :
1365 :			if ($count >0){
1366 :			$content = $data;
1367 :			}
1368 :			else
1369 :			{
1370 :			$content = "<p>This PEG does not have any similarities to domains</p>";
1371 :			}
1372 :			}
1373 :
1374 :	mkubal	1.7
1375 :	arodri7	1.10	#########################################
1376 :			#########################################
1377 :	mkubal	1.12	package Observation::Location;
1378 :
1379 :			use base qw(Observation);
1380 :
1381 :			sub new {
1382 :
1383 :			my ($class,$dataset) = @_;
1384 :			my $self = $class->SUPER::new($dataset);
1385 :			$self->{cleavage_prob} = $dataset->{'cleavage_prob'};
1386 :			$self->{cleavage_loc} = $dataset->{'cleavage_loc'};
1387 :			$self->{signal_peptide_score} = $dataset->{'signal_peptide_score'};
1388 :			$self->{cello_location} = $dataset->{'cello_location'};
1389 :			$self->{cello_score} = $dataset->{'cello_score'};
1390 :			$self->{tmpred_score} = $dataset->{'tmpred_score'};
1391 :			$self->{tmpred_locations} = $dataset->{'tmpred_locations'};
1392 :	mkubal	1.30	$self->{phobius_signal_location} = $dataset->{'phobius_signal_location'};
1393 :			$self->{phobius_tm_locations} = $dataset->{'phobius_tm_locations'};
1394 :	mkubal	1.12
1395 :			bless($self,$class);
1396 :			return $self;
1397 :			}
1398 :
1399 :	mkubal	1.36	sub display_cello {
1400 :	arodri7	1.45	my ($thing) = @_;
1401 :	mkubal	1.36	my $html;
1402 :			my $cello_location = $thing->cello_location;
1403 :			my $cello_score = $thing->cello_score;
1404 :			if($cello_location){
1405 :	arodri7	1.40	$html .= "<p><font type=verdana size=-2>Subcellular location prediction: $cello_location, score: $cello_score</font> </p>";
1406 :			#$html .= "<p>CELLO score: $cello_score </p>";
1407 :	mkubal	1.36	}
1408 :			return ($html);
1409 :			}
1410 :
1411 :	mkubal	1.12	sub display {
1412 :	arodri7	1.41	my ($thing,$gd,$fig) = @_;
1413 :	mkubal	1.12
1414 :	mkubal	1.24	my $fid = $thing->fig_id;
1415 :	arodri7	1.41	#my $fig= new FIG;
1416 :	mkubal	1.12	my $length = length($fig->get_translation($fid));
1417 :
1418 :			my $cleavage_prob;
1419 :			if($thing->cleavage_prob){$cleavage_prob = $thing->cleavage_prob;}
1420 :			my ($cleavage_loc_begin,$cleavage_loc_end) = split("-",$thing->cleavage_loc);
1421 :			my $signal_peptide_score = $thing->signal_peptide_score;
1422 :			my $cello_location = $thing->cello_location;
1423 :			my $cello_score = $thing->cello_score;
1424 :			my $tmpred_score = $thing->tmpred_score;
1425 :			my @tmpred_locations = split(",",$thing->tmpred_locations);
1426 :
1427 :	mkubal	1.30	my $phobius_signal_location = $thing->phobius_signal_location;
1428 :			my @phobius_tm_locations = split(",",$thing->phobius_tm_locations);
1429 :
1430 :	mkubal	1.12	my $lines = [];
1431 :
1432 :			#color is
1433 :	arodri7	1.28	my $color = "6";
1434 :	mkubal	1.36
1435 :			=pod=
1436 :
1437 :	mkubal	1.12	if($cello_location){
1438 :			my $cello_descriptions = [];
1439 :	arodri7	1.28	my $line_data =[];
1440 :
1441 :			my $line_config = { 'title' => 'Localization Evidence',
1442 :			'short_title' => 'CELLO',
1443 :	paczian	1.48	'hover_title' => 'Localization',
1444 :	arodri7	1.28	'basepair_offset' => '1' };
1445 :
1446 :	mkubal	1.12	my $description_cello_location = {"title" => 'Best Cello Location',
1447 :			"value" => $cello_location};
1448 :
1449 :			push(@$cello_descriptions,$description_cello_location);
1450 :
1451 :			my $description_cello_score = {"title" => 'Cello Score',
1452 :			"value" => $cello_score};
1453 :
1454 :			push(@$cello_descriptions,$description_cello_score);
1455 :
1456 :			my $element_hash = {
1457 :			"title" => "CELLO",
1458 :	mkubal	1.34	"color"=> $color,
1459 :	mkubal	1.12	"start" => "1",
1460 :			"end" => $length + 1,
1461 :	arodri7	1.28	"zlayer" => '1',
1462 :	mkubal	1.12	"description" => $cello_descriptions};
1463 :
1464 :			push(@$line_data,$element_hash);
1465 :	arodri7	1.28	$gd->add_line($line_data, $line_config);
1466 :	mkubal	1.12	}
1467 :
1468 :	arodri7	1.28	$color = "2";
1469 :	mkubal	1.12	if($tmpred_score){
1470 :	arodri7	1.28	my $line_data =[];
1471 :			my $line_config = { 'title' => 'Localization Evidence',
1472 :			'short_title' => 'Transmembrane',
1473 :			'basepair_offset' => '1' };
1474 :
1475 :	mkubal	1.12	foreach my $tmpred (@tmpred_locations){
1476 :			my $descriptions = [];
1477 :			my ($begin,$end) =split("-",$tmpred);
1478 :			my $description_tmpred_score = {"title" => 'TMPRED score',
1479 :			"value" => $tmpred_score};
1480 :
1481 :			push(@$descriptions,$description_tmpred_score);
1482 :
1483 :			my $element_hash = {
1484 :			"title" => "transmembrane location",
1485 :			"start" => $begin + 1,
1486 :			"end" => $end + 1,
1487 :			"color"=> $color,
1488 :			"zlayer" => '5',
1489 :	mkubal	1.34	"type" => 'box',
1490 :	mkubal	1.12	"description" => $descriptions};
1491 :
1492 :			push(@$line_data,$element_hash);
1493 :	arodri7	1.28
1494 :	mkubal	1.12	}
1495 :	arodri7	1.28	$gd->add_line($line_data, $line_config);
1496 :	mkubal	1.12	}
1497 :	arodri7	1.40	=cut
1498 :	mkubal	1.12
1499 :	mkubal	1.30	if((scalar(@phobius_tm_locations) > 0) \|\| $phobius_signal_location){
1500 :			my $line_data =[];
1501 :	arodri7	1.40	my $line_config = { 'title' => 'Localization Evidence, Transmembrane and Signal Peptide',
1502 :			'short_title' => 'TM and SP',
1503 :	paczian	1.48	'hover_title' => 'Localization',
1504 :	mkubal	1.30	'basepair_offset' => '1' };
1505 :
1506 :			foreach my $tm_loc (@phobius_tm_locations){
1507 :			my $descriptions = [];
1508 :	arodri7	1.40	my $description_phobius_tm_locations = {"title" => 'transmembrane location',
1509 :	mkubal	1.30	"value" => $tm_loc};
1510 :			push(@$descriptions,$description_phobius_tm_locations);
1511 :
1512 :			my ($begin,$end) =split("-",$tm_loc);
1513 :
1514 :			my $element_hash = {
1515 :	arodri7	1.40	"title" => "Phobius",
1516 :	mkubal	1.30	"start" => $begin + 1,
1517 :			"end" => $end + 1,
1518 :			"color"=> '6',
1519 :			"zlayer" => '4',
1520 :			"type" => 'bigbox',
1521 :			"description" => $descriptions};
1522 :
1523 :			push(@$line_data,$element_hash);
1524 :
1525 :			}
1526 :
1527 :			if($phobius_signal_location){
1528 :			my $descriptions = [];
1529 :			my $description_phobius_signal_location = {"title" => 'Phobius Signal Location',
1530 :			"value" => $phobius_signal_location};
1531 :			push(@$descriptions,$description_phobius_signal_location);
1532 :
1533 :
1534 :			my ($begin,$end) =split("-",$phobius_signal_location);
1535 :			my $element_hash = {
1536 :			"title" => "phobius signal locations",
1537 :			"start" => $begin + 1,
1538 :			"end" => $end + 1,
1539 :			"color"=> '1',
1540 :			"zlayer" => '5',
1541 :			"type" => 'box',
1542 :			"description" => $descriptions};
1543 :			push(@$line_data,$element_hash);
1544 :			}
1545 :
1546 :			$gd->add_line($line_data, $line_config);
1547 :			}
1548 :
1549 :	arodri7	1.40	=head3
1550 :	arodri7	1.28	$color = "1";
1551 :	mkubal	1.12	if($signal_peptide_score){
1552 :	arodri7	1.28	my $line_data = [];
1553 :	mkubal	1.12	my $descriptions = [];
1554 :	arodri7	1.28
1555 :			my $line_config = { 'title' => 'Localization Evidence',
1556 :			'short_title' => 'SignalP',
1557 :	paczian	1.48	'hover_title' => 'Localization',
1558 :	arodri7	1.28	'basepair_offset' => '1' };
1559 :
1560 :	mkubal	1.12	my $description_signal_peptide_score = {"title" => 'signal peptide score',
1561 :			"value" => $signal_peptide_score};
1562 :
1563 :			push(@$descriptions,$description_signal_peptide_score);
1564 :
1565 :			my $description_cleavage_prob = {"title" => 'cleavage site probability',
1566 :			"value" => $cleavage_prob};
1567 :
1568 :			push(@$descriptions,$description_cleavage_prob);
1569 :
1570 :			my $element_hash = {
1571 :			"title" => "SignalP",
1572 :			"start" => $cleavage_loc_begin - 2,
1573 :	arodri7	1.28	"end" => $cleavage_loc_end + 1,
1574 :	mkubal	1.12	"type" => 'bigbox',
1575 :			"color"=> $color,
1576 :			"zlayer" => '10',
1577 :			"description" => $descriptions};
1578 :
1579 :			push(@$line_data,$element_hash);
1580 :	arodri7	1.28	$gd->add_line($line_data, $line_config);
1581 :	mkubal	1.12	}
1582 :	arodri7	1.40	=cut
1583 :
1584 :	mkubal	1.12	return ($gd);
1585 :
1586 :			}
1587 :
1588 :			sub cleavage_loc {
1589 :			my ($self) = @_;
1590 :
1591 :			return $self->{cleavage_loc};
1592 :			}
1593 :
1594 :			sub cleavage_prob {
1595 :			my ($self) = @_;
1596 :
1597 :			return $self->{cleavage_prob};
1598 :			}
1599 :
1600 :			sub signal_peptide_score {
1601 :			my ($self) = @_;
1602 :
1603 :			return $self->{signal_peptide_score};
1604 :			}
1605 :
1606 :			sub tmpred_score {
1607 :			my ($self) = @_;
1608 :
1609 :			return $self->{tmpred_score};
1610 :			}
1611 :
1612 :			sub tmpred_locations {
1613 :			my ($self) = @_;
1614 :
1615 :			return $self->{tmpred_locations};
1616 :			}
1617 :
1618 :			sub cello_location {
1619 :			my ($self) = @_;
1620 :
1621 :			return $self->{cello_location};
1622 :			}
1623 :
1624 :			sub cello_score {
1625 :			my ($self) = @_;
1626 :
1627 :			return $self->{cello_score};
1628 :			}
1629 :
1630 :	mkubal	1.30	sub phobius_signal_location {
1631 :			my ($self) = @_;
1632 :			return $self->{phobius_signal_location};
1633 :			}
1634 :
1635 :			sub phobius_tm_locations {
1636 :			my ($self) = @_;
1637 :			return $self->{phobius_tm_locations};
1638 :			}
1639 :
1640 :
1641 :	mkubal	1.12
1642 :			#########################################
1643 :			#########################################
1644 :	arodri7	1.10	package Observation::Sims;
1645 :
1646 :			use base qw(Observation);
1647 :
1648 :			sub new {
1649 :
1650 :			my ($class,$dataset) = @_;
1651 :			my $self = $class->SUPER::new($dataset);
1652 :	arodri7	1.11	$self->{identity} = $dataset->{'identity'};
1653 :	arodri7	1.10	$self->{acc} = $dataset->{'acc'};
1654 :	arodri7	1.40	$self->{query} = $dataset->{'query'};
1655 :	arodri7	1.10	$self->{evalue} = $dataset->{'evalue'};
1656 :	arodri7	1.11	$self->{qstart} = $dataset->{'qstart'};
1657 :			$self->{qstop} = $dataset->{'qstop'};
1658 :			$self->{hstart} = $dataset->{'hstart'};
1659 :			$self->{hstop} = $dataset->{'hstop'};
1660 :			$self->{database} = $dataset->{'database'};
1661 :			$self->{organism} = $dataset->{'organism'};
1662 :			$self->{function} = $dataset->{'function'};
1663 :			$self->{qlength} = $dataset->{'qlength'};
1664 :			$self->{hlength} = $dataset->{'hlength'};
1665 :	arodri7	1.10
1666 :			bless($self,$class);
1667 :			return $self;
1668 :			}
1669 :
1670 :	arodri7	1.25	=head3 display()
1671 :
1672 :			If available use the function specified here to display a graphical observation.
1673 :			This code will display a graphical view of the similarities using the genome drawer object
1674 :
1675 :			=cut
1676 :
1677 :			sub display {
1678 :	arodri7	1.41	my ($self,$gd,$array,$fig) = @_;
1679 :			#my $fig = new FIG;
1680 :	arodri7	1.25
1681 :	arodri7	1.41	my @ids;
1682 :			foreach my $thing(@$array){
1683 :			next if ($thing->class ne "SIM");
1684 :			push (@ids, $thing->acc);
1685 :			}
1686 :	arodri7	1.25
1687 :	arodri7	1.41	my %in_subs = $fig->subsystems_for_pegs(\@ids);
1688 :	arodri7	1.55
1689 :			my %sims_objects_evalue;
1690 :			my $count = 0;
1691 :	arodri7	1.41	foreach my $thing (@$array){
1692 :			if ($thing->class eq "SIM"){
1693 :	arodri7	1.55	$sims_objects_evalue{$count} = $thing->evalue;
1694 :			}
1695 :			$count++;
1696 :			}
1697 :	arodri7	1.41
1698 :	arodri7	1.55	foreach my $index (sort {$sims_objects_evalue{$a}<=>$sims_objects_evalue{$b}} keys %sims_objects_evalue){
1699 :			# foreach my $thing ( @$array){
1700 :			my $thing = $array->[$index];
1701 :			if ($thing->class eq "SIM"){
1702 :	arodri7	1.41	my $peg = $thing->acc;
1703 :			my $query = $thing->query;
1704 :
1705 :			my $organism = $thing->organism;
1706 :			my $genome = $fig->genome_of($peg);
1707 :			my ($org_tax) = ($genome) =~ /(.*)\./;
1708 :			my $function = $thing->function;
1709 :			my $abbrev_name = $fig->abbrev($organism);
1710 :			my $align_start = $thing->qstart;
1711 :			my $align_stop = $thing->qstop;
1712 :			my $hit_start = $thing->hstart;
1713 :			my $hit_stop = $thing->hstop;
1714 :
1715 :			my $tax_link = "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=" . $org_tax;
1716 :
1717 :			my $line_config = { 'title' => "$organism [$org_tax]",
1718 :			'short_title' => "$abbrev_name",
1719 :			'title_link' => '$tax_link',
1720 :			'basepair_offset' => '0'
1721 :			};
1722 :
1723 :			my $line_data = [];
1724 :
1725 :			my $element_hash;
1726 :			my $links_list = [];
1727 :			my $descriptions = [];
1728 :
1729 :			# get subsystem information
1730 :	paczian	1.44	my $url_link = "?page=Annotation&feature=".$peg;
1731 :	arodri7	1.41	my $link;
1732 :			$link = {"link_title" => $peg,
1733 :			"link" => $url_link};
1734 :			push(@$links_list,$link);
1735 :
1736 :			#my @subsystems = $fig->peg_to_subsystems($peg);
1737 :			my @subs = @{$in_subs{$peg}} if (defined $in_subs{$peg});
1738 :			my @subsystems;
1739 :
1740 :			foreach my $array (@subs){
1741 :			my $subsystem = $$array[0];
1742 :			push(@subsystems,$subsystem);
1743 :			my $link;
1744 :	paczian	1.44	$link = {"link" => "?page=Subsystems&subsystem=$subsystem",
1745 :	arodri7	1.41	"link_title" => $subsystem};
1746 :			push(@$links_list,$link);
1747 :			}
1748 :
1749 :			$link = {"link_title" => "view blast alignment",
1750 :			"link" => "$FIG_Config::cgi_url/seedviewer.cgi?page=ToolResult&tool=bl2seq&peg1=$query&peg2=$peg"};
1751 :			push (@$links_list,$link);
1752 :
1753 :			my $description_function;
1754 :			$description_function = {"title" => "function",
1755 :			"value" => $function};
1756 :			push(@$descriptions,$description_function);
1757 :
1758 :			my ($description_ss, $ss_string);
1759 :			$ss_string = join (",", @subsystems);
1760 :			$description_ss = {"title" => "subsystems",
1761 :			"value" => $ss_string};
1762 :			push(@$descriptions,$description_ss);
1763 :
1764 :			my $description_loc;
1765 :			$description_loc = {"title" => "location start",
1766 :			"value" => $hit_start};
1767 :			push(@$descriptions, $description_loc);
1768 :
1769 :			$description_loc = {"title" => "location stop",
1770 :			"value" => $hit_stop};
1771 :			push(@$descriptions, $description_loc);
1772 :
1773 :			my $evalue = $thing->evalue;
1774 :			while ($evalue =~ /-0/)
1775 :			{
1776 :			my ($chunk1, $chunk2) = split(/-/, $evalue);
1777 :			$chunk2 = substr($chunk2,1);
1778 :			$evalue = $chunk1 . "-" . $chunk2;
1779 :			}
1780 :
1781 :			my $color = &color($evalue);
1782 :
1783 :			my $description_eval = {"title" => "E-Value",
1784 :			"value" => $evalue};
1785 :			push(@$descriptions, $description_eval);
1786 :
1787 :			my $identity = $self->identity;
1788 :			my $description_identity = {"title" => "Identity",
1789 :			"value" => $identity};
1790 :			push(@$descriptions, $description_identity);
1791 :
1792 :			$element_hash = {
1793 :			"title" => $peg,
1794 :			"start" => $align_start,
1795 :			"end" => $align_stop,
1796 :			"type"=> 'box',
1797 :			"color"=> $color,
1798 :			"zlayer" => "2",
1799 :			"links_list" => $links_list,
1800 :			"description" => $descriptions
1801 :			};
1802 :			push(@$line_data,$element_hash);
1803 :			$gd->add_line($line_data, $line_config);
1804 :			}
1805 :	arodri7	1.25	}
1806 :			return ($gd);
1807 :			}
1808 :
1809 :	mkubal	1.34	=head3 display_domain_composition()
1810 :
1811 :			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
1812 :
1813 :			=cut
1814 :
1815 :			sub display_domain_composition {
1816 :	arodri7	1.41	my ($self,$gd,$fig) = @_;
1817 :	mkubal	1.34
1818 :	arodri7	1.45	#$fig = new FIG;
1819 :	mkubal	1.34	my $peg = $self->acc;
1820 :
1821 :			my $line_data = [];
1822 :			my $links_list = [];
1823 :			my $descriptions = [];
1824 :
1825 :			my @domain_query_results =$fig->get_attributes($peg,"CDD");
1826 :	arodri7	1.45	#my @domain_query_results = ();
1827 :	mkubal	1.34	foreach $dqr (@domain_query_results){
1828 :			my $key = @$dqr[1];
1829 :			my @parts = split("::",$key);
1830 :			my $db = $parts[0];
1831 :			my $id = $parts[1];
1832 :			my $val = @$dqr[2];
1833 :			my $from;
1834 :			my $to;
1835 :			my $evalue;
1836 :
1837 :			if($val =~/^(\d+\.\d+\|0\.0);(\d+)-(\d+)/){
1838 :			my $raw_evalue = $1;
1839 :			$from = $2;
1840 :			$to = $3;
1841 :			if($raw_evalue =~/(\d+)\.(\d+)/){
1842 :			my $part2 = 1000 - $1;
1843 :			my $part1 = $2/100;
1844 :			$evalue = $part1."e-".$part2;
1845 :			}
1846 :			else{
1847 :			$evalue = "0.0";
1848 :			}
1849 :			}
1850 :
1851 :	paczian	1.52	my $dbmaster = DBMaster->new(-database =>'Ontology',
1852 :			-host => $WebConfig::DBHOST,
1853 :			-user => $WebConfig::DBUSER,
1854 :			-password => $WebConfig::DBPWD);
1855 :	mkubal	1.34	my ($name_value,$description_value);
1856 :
1857 :			if($db eq "CDD"){
1858 :			my $cdd_objs = $dbmaster->cdd->get_objects( { 'id' => $id } );
1859 :			if(!scalar(@$cdd_objs)){
1860 :			$name_title = "name";
1861 :			$name_value = "not available";
1862 :			$description_title = "description";
1863 :			$description_value = "not available";
1864 :			}
1865 :			else{
1866 :			my $cdd_obj = $cdd_objs->[0];
1867 :			$name_value = $cdd_obj->term;
1868 :			$description_value = $cdd_obj->description;
1869 :			}
1870 :			}
1871 :
1872 :			my $domain_name;
1873 :			$domain_name = {"title" => "name",
1874 :	arodri7	1.45	"value" => $name_value};
1875 :	mkubal	1.34	push(@$descriptions,$domain_name);
1876 :
1877 :			my $description;
1878 :			$description = {"title" => "description",
1879 :			"value" => $description_value};
1880 :			push(@$descriptions,$description);
1881 :
1882 :			my $score;
1883 :			$score = {"title" => "score",
1884 :			"value" => $evalue};
1885 :			push(@$descriptions,$score);
1886 :
1887 :			my $link_id = $id;
1888 :			my $link;
1889 :			my $link_url;
1890 :			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"}
1891 :	arodri7	1.53	elsif($db eq "PFAM"){$link_url = "http://pfam.sanger.ac.uk/family?acc=$link_id"}
1892 :	mkubal	1.34	else{$link_url = "NO_URL"}
1893 :
1894 :			$link = {"link_title" => $name_value,
1895 :			"link" => $link_url};
1896 :			push(@$links_list,$link);
1897 :
1898 :			my $domain_element_hash = {
1899 :			"title" => $peg,
1900 :			"start" => $from,
1901 :			"end" => $to,
1902 :			"type"=> 'box',
1903 :			"zlayer" => '4',
1904 :			"links_list" => $links_list,
1905 :			"description" => $descriptions
1906 :			};
1907 :
1908 :			push(@$line_data,$domain_element_hash);
1909 :
1910 :			#just one CDD domain for now, later will add option for multiple domains from selected DB
1911 :			last;
1912 :			}
1913 :
1914 :			my $line_config = { 'title' => $peg,
1915 :	paczian	1.47	'hover_title' => 'Domain',
1916 :	mkubal	1.34	'short_title' => $peg,
1917 :			'basepair_offset' => '1' };
1918 :	arodri7	1.45
1919 :	mkubal	1.34	$gd->add_line($line_data, $line_config);
1920 :
1921 :			return ($gd);
1922 :
1923 :			}
1924 :
1925 :	mkubal	1.24	=head3 display_table()
1926 :	arodri7	1.10
1927 :			If available use the function specified here to display the "raw" observation.
1928 :			This code will display a table for the similarities protein
1929 :
1930 :			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.
1931 :
1932 :			=cut
1933 :
1934 :	mkubal	1.24	sub display_table {
1935 :	arodri7	1.41	my ($self,$dataset, $scroll_list, $query_fid,$lineages,$fig) = @_;
1936 :	paczian	1.52
1937 :	arodri7	1.10	my $data = [];
1938 :			my $count = 0;
1939 :			my $content;
1940 :	arodri7	1.41	#my $fig = new FIG;
1941 :	mkubal	1.24	my $cgi = new CGI;
1942 :	arodri7	1.28	my @ids;
1943 :	arodri7	1.53	$lineages = $fig->taxonomy_list();
1944 :
1945 :	arodri7	1.10	foreach my $thing (@$dataset) {
1946 :	arodri7	1.28	next if ($thing->class ne "SIM");
1947 :			push (@ids, $thing->acc);
1948 :			}
1949 :
1950 :	arodri7	1.31	my (%box_column, %subsystems_column, %evidence_column, %e_identical);
1951 :	arodri7	1.41	my @attributes = $fig->get_attributes(\@ids);
1952 :	arodri7	1.35
1953 :			# get the column for the subsystems
1954 :	arodri7	1.41	%subsystems_column = &get_subsystems_column(\@ids,$fig);
1955 :	arodri7	1.35
1956 :			# get the column for the evidence codes
1957 :	arodri7	1.41	%evidence_column = &get_evidence_column(\@ids, \@attributes,$fig);
1958 :	arodri7	1.35
1959 :			# get the column for pfam_domain
1960 :	arodri7	1.41	%pfam_column = &get_pfam_column(\@ids, \@attributes,$fig);
1961 :
1962 :			my %e_identical = &get_essentially_identical($query_fid,$dataset,$fig);
1963 :			my $alias_col = &get_aliases(\@ids,$fig);
1964 :	arodri7	1.42	#my $alias_col = {};
1965 :	arodri7	1.31
1966 :	arodri7	1.53	my $figfam_data = "$FIG_Config::FigfamsData";
1967 :	arodri7	1.55	my $figfams = new FFs($figfam_data);
1968 :			# my $ff_hash = $figfams->families_containing_peg_bulk(\@ids);
1969 :
1970 :			my %sims_objects_evalue;
1971 :			my $simcount = 0;
1972 :			foreach my $thing (@$dataset){
1973 :			if ($thing->class eq "SIM"){
1974 :			$sims_objects_evalue{$simcount} = $thing->evalue;
1975 :			}
1976 :			$simcount++;
1977 :			}
1978 :
1979 :			foreach my $index (sort {$sims_objects_evalue{$a}<=>$sims_objects_evalue{$b}} keys %sims_objects_evalue){
1980 :			# foreach my $thing ( @$dataset){
1981 :			my $thing = $dataset->[$index];
1982 :	arodri7	1.53
1983 :	arodri7	1.28	next if ($thing->class ne "SIM");
1984 :	arodri7	1.10	my $single_domain = [];
1985 :			$count++;
1986 :
1987 :	arodri7	1.41	my $id = $thing->acc;
1988 :	arodri7	1.45	my $taxid = $fig->genome_of($id);
1989 :	arodri7	1.11	my $iden = $thing->identity;
1990 :			my $ln1 = $thing->qlength;
1991 :			my $ln2 = $thing->hlength;
1992 :			my $b1 = $thing->qstart;
1993 :			my $e1 = $thing->qstop;
1994 :			my $b2 = $thing->hstart;
1995 :			my $e2 = $thing->hstop;
1996 :			my $d1 = abs($e1 - $b1) + 1;
1997 :			my $d2 = abs($e2 - $b2) + 1;
1998 :			my $reg1 = "$b1-$e1 (<b>$d1/$ln1</b>)";
1999 :			my $reg2 = "$b2-$e2 (<b>$d2/$ln2</b>)";
2000 :
2001 :	arodri7	1.29	# checkbox column
2002 :			my $field_name = "tables_" . $id;
2003 :			my $pair_name = "visual_" . $id;
2004 :			my $box_col = qq(<input type=checkbox name=seq value="$id" id="$field_name" onClick="VisualCheckPair('$field_name', '$pair_name');">);
2005 :	arodri7	1.40	my ($tax) = ($id) =~ /fig\\|(.*?)\./;
2006 :	arodri7	1.31
2007 :			# get the linked fig id
2008 :			my $fig_col;
2009 :			if (defined ($e_identical{$id})){
2010 :	paczian	1.44	$fig_col = "<a href='?page=Annotation&feature=$id'>$id</a>";#&HTML::set_prot_links($cgi,$id) . "*";
2011 :	arodri7	1.31	}
2012 :			else{
2013 :	paczian	1.44	$fig_col = "<a href='?page=Annotation&feature=$id'>$id</a>";#&HTML::set_prot_links($cgi,$id);
2014 :	arodri7	1.28	}
2015 :
2016 :	arodri7	1.41	push (@$single_domain, $box_col, $fig_col, $thing->evalue,
2017 :			"$iden\%", $reg1, $reg2, $thing->organism, $thing->function); # permanent columns
2018 :
2019 :	arodri7	1.55	my ($ff) = $figfams->families_containing_peg($id);
2020 :
2021 :	arodri7	1.35	foreach my $col (sort keys %$scroll_list){
2022 :			if ($col =~ /associated_subsystem/) {push(@$single_domain,$subsystems_column{$id});}
2023 :			elsif ($col =~ /evidence/) {push(@$single_domain,$evidence_column{$id});}
2024 :			elsif ($col =~ /pfam_domains/) {push(@$single_domain,$pfam_column{$id});}
2025 :	arodri7	1.41	elsif ($col =~ /ncbi_id/) {push(@$single_domain,$alias_col->{$id}->{"NCBI"});}
2026 :			elsif ($col =~ /refseq_id/) {push(@$single_domain,$alias_col->{$id}->{"RefSeq"});}
2027 :			elsif ($col =~ /swissprot_id/) {push(@$single_domain,$alias_col->{$id}->{"SwissProt"});}
2028 :			elsif ($col =~ /uniprot_id/) {push(@$single_domain,$alias_col->{$id}->{"UniProt"});}
2029 :			elsif ($col =~ /tigr_id/) {push(@$single_domain,$alias_col->{$id}->{"TIGR"});}
2030 :			elsif ($col =~ /pir_id/) {push(@$single_domain,$alias_col->{$id}->{"PIR"});}
2031 :			elsif ($col =~ /kegg_id/) {push(@$single_domain,$alias_col->{$id}->{"KEGG"});}
2032 :	arodri7	1.42	#elsif ($col =~ /trembl_id/) {push(@$single_domain,$alias_col->{$id}->{"TrEMBL"});}
2033 :	arodri7	1.41	elsif ($col =~ /asap_id/) {push(@$single_domain,$alias_col->{$id}->{"ASAP"});}
2034 :			elsif ($col =~ /jgi_id/) {push(@$single_domain,$alias_col->{$id}->{"JGI"});}
2035 :	arodri7	1.53	elsif ($col =~ /taxonomy/) {push(@$single_domain,$lineages->{$tax});}
2036 :			#elsif ($col =~ /taxonomy/) {push(@$single_domain,$fig->taxonomy_of($taxid));}
2037 :	arodri7	1.55	#elsif ($col =~ /figfam/) {push(@$single_domain,"<a href='?page=FigFamViewer&figfam=" . $ff_hash->{$id} . "' target='_new'>" . $ff_hash->{$id} . "</a>");}
2038 :			elsif ($col =~ /figfam/) {push(@$single_domain,"<a href='?page=FigFamViewer&figfam=" . $ff . "' target='_new'>" . $ff . "</a>");}
2039 :	arodri7	1.32	}
2040 :	arodri7	1.10	push(@$data,$single_domain);
2041 :			}
2042 :	arodri7	1.26	if ($count >0 ){
2043 :			$content = $data;
2044 :	arodri7	1.10	}
2045 :	arodri7	1.26	else{
2046 :	arodri7	1.10	$content = "<p>This PEG does not have any similarities</p>";
2047 :			}
2048 :			return ($content);
2049 :			}
2050 :	arodri7	1.11
2051 :	arodri7	1.29	sub get_box_column{
2052 :			my ($ids) = @_;
2053 :			my %column;
2054 :			foreach my $id (@$ids){
2055 :			my $field_name = "tables_" . $id;
2056 :			my $pair_name = "visual_" . $id;
2057 :			$column{$id} = qq(<input type=checkbox name=seq value="$id" id="$field_name" onClick="VisualCheckPair('$field_name', '$pair_name');">);
2058 :			}
2059 :			return (%column);
2060 :			}
2061 :
2062 :			sub get_subsystems_column{
2063 :	arodri7	1.41	my ($ids,$fig) = @_;
2064 :	arodri7	1.29
2065 :	arodri7	1.41	#my $fig = new FIG;
2066 :	arodri7	1.29	my $cgi = new CGI;
2067 :			my %in_subs = $fig->subsystems_for_pegs($ids);
2068 :			my %column;
2069 :			foreach my $id (@$ids){
2070 :	arodri7	1.32	my @in_sub = @{$in_subs{$id}} if (defined $in_subs{$id});
2071 :			my @subsystems;
2072 :
2073 :	arodri7	1.29	if (@in_sub > 0) {
2074 :	arodri7	1.32	foreach my $array(@in_sub){
2075 :	arodri7	1.41	my $ss = $$array[0];
2076 :			$ss =~ s/_/ /ig;
2077 :			push (@subsystems, "-" . $ss);
2078 :	arodri7	1.32	}
2079 :			my $in_sub_line = join ("<br>", @subsystems);
2080 :			$column{$id} = $in_sub_line;
2081 :	arodri7	1.29	} else {
2082 :			$column{$id} = " ";
2083 :			}
2084 :			}
2085 :			return (%column);
2086 :			}
2087 :
2088 :	arodri7	1.31	sub get_essentially_identical{
2089 :	arodri7	1.41	my ($fid,$dataset,$fig) = @_;
2090 :			#my $fig = new FIG;
2091 :
2092 :	arodri7	1.31	my %id_list;
2093 :	arodri7	1.41	#my @maps_to = grep { $_ ne $fid and $_ !~ /^xxx/ } map { $_->[0] } $fig->mapped_prot_ids($fid);
2094 :	arodri7	1.31
2095 :	arodri7	1.41	foreach my $thing (@$dataset){
2096 :			if($thing->class eq "IDENTICAL"){
2097 :			my $rows = $thing->rows;
2098 :			my $count_identical = 0;
2099 :			foreach my $row (@$rows) {
2100 :			my $id = $row->[0];
2101 :			if (($id ne $fid) && ($fig->function_of($id))) {
2102 :			$id_list{$id} = 1;
2103 :			}
2104 :			}
2105 :			}
2106 :	arodri7	1.31	}
2107 :	arodri7	1.41
2108 :			# foreach my $id (@maps_to) {
2109 :			# if (($id ne $fid) && ($fig->function_of($id))) {
2110 :			# $id_list{$id} = 1;
2111 :			# }
2112 :			# }
2113 :	arodri7	1.31	return(%id_list);
2114 :			}
2115 :
2116 :
2117 :	arodri7	1.29	sub get_evidence_column{
2118 :	arodri7	1.41	my ($ids, $attributes,$fig) = @_;
2119 :			#my $fig = new FIG;
2120 :	arodri7	1.29	my $cgi = new CGI;
2121 :			my (%column, %code_attributes);
2122 :
2123 :	arodri7	1.41	my @codes = grep { $_->[1] =~ /^evidence_code/i } @$attributes;
2124 :	arodri7	1.29	foreach my $key (@codes){
2125 :			push (@{$code_attributes{$$key[0]}}, $key);
2126 :			}
2127 :
2128 :			foreach my $id (@$ids){
2129 :			# add evidence code with tool tip
2130 :			my $ev_codes="   ";
2131 :
2132 :	arodri7	1.41	my @codes = @{$code_attributes{$id}} if (defined @{$code_attributes{$id}});
2133 :			my @ev_codes = ();
2134 :			foreach my $code (@codes) {
2135 :			my $pretty_code = $code->[2];
2136 :			if ($pretty_code =~ /;/) {
2137 :			my ($cd, $ss) = split(";", $code->[2]);
2138 :			$ss =~ s/_/ /g;
2139 :			$pretty_code = $cd;# . " in " . $ss;
2140 :			}
2141 :			push(@ev_codes, $pretty_code);
2142 :			}
2143 :	arodri7	1.29
2144 :			if (scalar(@ev_codes) && $ev_codes[0]) {
2145 :			my $ev_code_help=join("<br />", map {&HTML::evidence_codes_explain($_)} @ev_codes);
2146 :			$ev_codes = $cgi->a(
2147 :			{
2148 :			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));
2149 :			}
2150 :			$column{$id}=$ev_codes;
2151 :			}
2152 :			return (%column);
2153 :			}
2154 :
2155 :	arodri7	1.33	sub get_pfam_column{
2156 :	arodri7	1.41	my ($ids, $attributes,$fig) = @_;
2157 :			#my $fig = new FIG;
2158 :	arodri7	1.33	my $cgi = new CGI;
2159 :	arodri7	1.40	my (%column, %code_attributes, %attribute_locations);
2160 :	paczian	1.52	my $dbmaster = DBMaster->new(-database =>'Ontology',
2161 :			-host => $WebConfig::DBHOST,
2162 :			-user => $WebConfig::DBUSER,
2163 :			-password => $WebConfig::DBPWD);
2164 :	arodri7	1.33
2165 :	arodri7	1.41	my @codes = grep { $_->[1] =~ /^PFAM/i } @$attributes;
2166 :	arodri7	1.33	foreach my $key (@codes){
2167 :	arodri7	1.41	my $name = $key->[1];
2168 :			if ($name =~ /_/){
2169 :			($name) = ($key->[1]) =~ /(.*?)_/;
2170 :			}
2171 :			push (@{$code_attributes{$key->[0]}}, $name);
2172 :			push (@{$attribute_location{$key->[0]}{$name}}, $key->[2]);
2173 :	arodri7	1.33	}
2174 :
2175 :			foreach my $id (@$ids){
2176 :	arodri7	1.41	# add evidence code
2177 :	arodri7	1.33	my $pfam_codes="   ";
2178 :			my @pfam_codes = "";
2179 :			my %description_codes;
2180 :
2181 :			if ($id =~ /^fig\\|\d+\.\d+\.peg\.\d+$/) {
2182 :	arodri7	1.40	my @ncodes = @{$code_attributes{$id}} if (defined @{$code_attributes{$id}});
2183 :	arodri7	1.33	@pfam_codes = ();
2184 :	arodri7	1.40
2185 :			# get only unique values
2186 :			my %saw;
2187 :			foreach my $key (@ncodes) {$saw{$key}=1;}
2188 :			@ncodes = keys %saw;
2189 :
2190 :			foreach my $code (@ncodes) {
2191 :	arodri7	1.33	my @parts = split("::",$code);
2192 :	arodri7	1.53	my $pfam_link = "<a href=http://pfam.sanger.ac.uk/family?acc=" . $parts[1] . ">$parts[1]</a>";
2193 :	arodri7	1.40
2194 :			# get the locations for the domain
2195 :			my @locs;
2196 :			foreach my $part (@{$attribute_location{$id}{$code}}){
2197 :			my ($loc) = ($part) =~ /\;(.*)/;
2198 :			push (@locs,$loc);
2199 :			}
2200 :	arodri7	1.41	my %locsaw;
2201 :			foreach my $key (@locs) {$locsaw{$key}=1;}
2202 :			@locs = keys %locsaw;
2203 :
2204 :	arodri7	1.40	my $locations = join (", ", @locs);
2205 :
2206 :	arodri7	1.33	if (defined ($description_codes{$parts[1]})){
2207 :	arodri7	1.40	push(@pfam_codes, "$parts[1] ($locations)");
2208 :	arodri7	1.33	}
2209 :			else {
2210 :			my $description = $dbmaster->pfam->get_objects( { 'id' => $parts[1] } );
2211 :			$description_codes{$parts[1]} = ${$$description[0]}{term};
2212 :	arodri7	1.40	push(@pfam_codes, "$pfam_link ($locations)");
2213 :	arodri7	1.33	}
2214 :			}
2215 :			}
2216 :
2217 :			$column{$id}=join("<br><br>", @pfam_codes);
2218 :			}
2219 :			return (%column);
2220 :
2221 :			}
2222 :	mkubal	1.12
2223 :	arodri7	1.41	sub get_aliases {
2224 :			my ($ids,$fig) = @_;
2225 :	arodri7	1.31
2226 :	arodri7	1.41	my $all_aliases = $fig->feature_aliases_bulk($ids);
2227 :			foreach my $id (@$ids){
2228 :			foreach my $alias (@{$$all_aliases{$id}}){
2229 :			my $id_db = &Observation::get_database($alias);
2230 :			next if ($aliases->{$id}->{$id_db});
2231 :			$aliases->{$id}->{$id_db} = &HTML::set_prot_links($cgi,$alias);
2232 :	arodri7	1.28	}
2233 :			}
2234 :	arodri7	1.41	return ($aliases);
2235 :	arodri7	1.28	}
2236 :
2237 :	arodri7	1.33	sub html_enc { $_ = $_[0]; s/\&/&/g; s/\>/>/g; s/\</</g; $_ }
2238 :
2239 :	arodri7	1.26	sub color {
2240 :	paczian	1.44	my ($evalue) = @_;
2241 :			my $palette = WebColors::get_palette('vitamins');
2242 :	arodri7	1.26	my $color;
2243 :	paczian	1.44	if ($evalue <= 1e-170){ $color = $palette->[0]; }
2244 :			elsif (($evalue <= 1e-120) && ($evalue > 1e-170)){ $color = $palette->[1]; }
2245 :			elsif (($evalue <= 1e-90) && ($evalue > 1e-120)){ $color = $palette->[2]; }
2246 :			elsif (($evalue <= 1e-70) && ($evalue > 1e-90)){ $color = $palette->[3]; }
2247 :			elsif (($evalue <= 1e-40) && ($evalue > 1e-70)){ $color = $palette->[4]; }
2248 :			elsif (($evalue <= 1e-20) && ($evalue > 1e-40)){ $color = $palette->[5]; }
2249 :			elsif (($evalue <= 1e-5) && ($evalue > 1e-20)){ $color = $palette->[6]; }
2250 :			elsif (($evalue <= 1) && ($evalue > 1e-5)){ $color = $palette->[7]; }
2251 :			elsif (($evalue <= 10) && ($evalue > 1)){ $color = $palette->[8]; }
2252 :			else{ $color = $palette->[9]; }
2253 :	arodri7	1.26	return ($color);
2254 :			}
2255 :	arodri7	1.13
2256 :
2257 :			############################
2258 :			package Observation::Cluster;
2259 :
2260 :			use base qw(Observation);
2261 :
2262 :			sub new {
2263 :
2264 :			my ($class,$dataset) = @_;
2265 :			my $self = $class->SUPER::new($dataset);
2266 :	mkubal	1.24	$self->{context} = $dataset->{'context'};
2267 :	arodri7	1.13	bless($self,$class);
2268 :			return $self;
2269 :			}
2270 :
2271 :			sub display {
2272 :	arodri7	1.41	my ($self,$gd,$selected_taxonomies,$taxes,$sims_array,$fig) = @_;
2273 :	mkubal	1.24
2274 :	arodri7	1.53	$taxes = $fig->taxonomy_list();
2275 :
2276 :	mkubal	1.24	my $fid = $self->fig_id;
2277 :			my $compare_or_coupling = $self->context;
2278 :			my $gd_window_size = $gd->window_size;
2279 :	arodri7	1.41	my $range = $gd_window_size;
2280 :	mkubal	1.14	my $all_regions = [];
2281 :	arodri7	1.38	my $gene_associations={};
2282 :	arodri7	1.13
2283 :			#get the organism genome
2284 :	mkubal	1.14	my $target_genome = $fig->genome_of($fid);
2285 :	arodri7	1.38	$gene_associations->{$fid}->{"organism"} = $target_genome;
2286 :			$gene_associations->{$fid}->{"main_gene"} = $fid;
2287 :			$gene_associations->{$fid}->{"reverse_flag"} = 0;
2288 :	arodri7	1.13
2289 :			# get location of the gene
2290 :			my $data = $fig->feature_location($fid);
2291 :			my ($contig, $beg, $end);
2292 :	arodri7	1.22	my %reverse_flag;
2293 :	arodri7	1.13
2294 :			if ($data =~ /(.*)_(\d+)_(\d+)$/){
2295 :			$contig = $1;
2296 :			$beg = $2;
2297 :			$end = $3;
2298 :			}
2299 :
2300 :	arodri7	1.22	my $offset;
2301 :	arodri7	1.13	my ($region_start, $region_end);
2302 :			if ($beg < $end)
2303 :			{
2304 :	arodri7	1.41	$region_start = $beg - ($range);
2305 :			$region_end = $end+ ($range);
2306 :	arodri7	1.22	$offset = ($2+(($3-$2)/2))-($gd_window_size/2);
2307 :	arodri7	1.13	}
2308 :			else
2309 :			{
2310 :	arodri7	1.41	$region_start = $end-($range);
2311 :			$region_end = $beg+($range);
2312 :	arodri7	1.22	$offset = ($3+(($2-$3)/2))-($gd_window_size/2);
2313 :	arodri7	1.25	$reverse_flag{$target_genome} = $fid;
2314 :	arodri7	1.38	$gene_associations->{$fid}->{"reverse_flag"} = 1;
2315 :	arodri7	1.21	}
2316 :	arodri7	1.13
2317 :			# call genes in region
2318 :	arodri7	1.16	my ($target_gene_features, $reg_beg, $reg_end) = $fig->genes_in_region($target_genome, $contig, $region_start, $region_end);
2319 :	arodri7	1.42	#foreach my $feat (@$target_gene_features){
2320 :			# push (@$all_regions, $feat) if ($feat =~ /peg/);
2321 :			#}
2322 :	mkubal	1.14	push(@$all_regions,$target_gene_features);
2323 :	arodri7	1.16	my (@start_array_region);
2324 :	arodri7	1.22	push (@start_array_region, $offset);
2325 :	mkubal	1.14
2326 :			my %all_genes;
2327 :			my %all_genomes;
2328 :	arodri7	1.42	foreach my $feature (@$target_gene_features){
2329 :			#if ($feature =~ /peg/){
2330 :			$all_genes{$feature} = $fid; $gene_associations->{$feature}->{"main_gene"}=$fid;
2331 :			#}
2332 :			}
2333 :
2334 :	arodri7	1.41	my @selected_sims;
2335 :	arodri7	1.16
2336 :	arodri7	1.40	if ($compare_or_coupling eq "sims"){
2337 :	arodri7	1.37	# get the selected boxes
2338 :	arodri7	1.38	my @selected_taxonomy = @$selected_taxonomies;
2339 :	arodri7	1.37
2340 :			# get the similarities and store only the ones that match the lineages selected
2341 :	arodri7	1.41	if (@selected_taxonomy > 0){
2342 :			foreach my $sim (@$sims_array){
2343 :			next if ($sim->class ne "SIM");
2344 :			next if ($sim->acc !~ /fig\\|/);
2345 :	arodri7	1.37
2346 :	arodri7	1.41	#my $genome = $fig->genome_of($sim->[1]);
2347 :			my $genome = $fig->genome_of($sim->acc);
2348 :	arodri7	1.45	#my ($genome1) = ($genome) =~ /(.*)\./;
2349 :	arodri7	1.53	my $lineage = $taxes->{$genome};
2350 :			#my $lineage = $fig->taxonomy_of($fig->genome_of($genome));
2351 :	arodri7	1.38	foreach my $taxon(@selected_taxonomy){
2352 :			if ($lineage =~ /$taxon/){
2353 :	arodri7	1.41	#push (@selected_sims, $sim->[1]);
2354 :			push (@selected_sims, $sim->acc);
2355 :	arodri7	1.38	}
2356 :	arodri7	1.37	}
2357 :			}
2358 :			}
2359 :	arodri7	1.40	else{
2360 :			my $simcount = 0;
2361 :	arodri7	1.41	foreach my $sim (@$sims_array){
2362 :			next if ($sim->class ne "SIM");
2363 :			next if ($sim->acc !~ /fig\\|/);
2364 :
2365 :			push (@selected_sims, $sim->acc);
2366 :	arodri7	1.40	$simcount++;
2367 :			last if ($simcount > 4);
2368 :			}
2369 :			}
2370 :	arodri7	1.16
2371 :	arodri7	1.41	my %saw;
2372 :			@selected_sims = grep(!$saw{$_}++, @selected_sims);
2373 :
2374 :	arodri7	1.37	# get the gene context for the sorted matches
2375 :			foreach my $sim_fid(@selected_sims){
2376 :			#get the organism genome
2377 :			my $sim_genome = $fig->genome_of($sim_fid);
2378 :	arodri7	1.38	$gene_associations->{$sim_fid}->{"organism"} = $sim_genome;
2379 :			$gene_associations->{$sim_fid}->{"main_gene"} = $sim_fid;
2380 :			$gene_associations->{$sim_fid}->{"reverse_flag"} = 0;
2381 :	arodri7	1.37
2382 :			# get location of the gene
2383 :			my $data = $fig->feature_location($sim_fid);
2384 :			my ($contig, $beg, $end);
2385 :
2386 :			if ($data =~ /(.*)_(\d+)_(\d+)$/){
2387 :			$contig = $1;
2388 :			$beg = $2;
2389 :			$end = $3;
2390 :			}
2391 :
2392 :			my $offset;
2393 :			my ($region_start, $region_end);
2394 :			if ($beg < $end)
2395 :			{
2396 :	arodri7	1.41	$region_start = $beg - ($range/2);
2397 :			$region_end = $end+($range/2);
2398 :	arodri7	1.38	$offset = ($beg+(($end-$beg)/2))-($gd_window_size/2);
2399 :	arodri7	1.37	}
2400 :			else
2401 :			{
2402 :	arodri7	1.41	$region_start = $end-($range/2);
2403 :			$region_end = $beg+($range/2);
2404 :	arodri7	1.38	$offset = ($end+(($beg-$end)/2))-($gd_window_size/2);
2405 :			$reverse_flag{$sim_genome} = $sim_fid;
2406 :			$gene_associations->{$sim_fid}->{"reverse_flag"} = 1;
2407 :	arodri7	1.37	}
2408 :
2409 :			# call genes in region
2410 :			my ($sim_gene_features, $reg_beg, $reg_end) = $fig->genes_in_region($sim_genome, $contig, $region_start, $region_end);
2411 :			push(@$all_regions,$sim_gene_features);
2412 :			push (@start_array_region, $offset);
2413 :	arodri7	1.38	foreach my $feature (@$sim_gene_features){ $all_genes{$feature} = $sim_fid;$gene_associations->{$feature}->{"main_gene"}=$sim_fid;}
2414 :			$all_genomes{$sim_genome} = 1;
2415 :	arodri7	1.16	}
2416 :	mkubal	1.14
2417 :			}
2418 :	arodri7	1.41
2419 :	arodri7	1.42	#print STDERR "START CLUSTER OF GENES IN COMP REGION: " . `date`;
2420 :	arodri7	1.38	# cluster the genes
2421 :			my @all_pegs = keys %all_genes;
2422 :			my $color_sets = &cluster_genes($fig,\@all_pegs,$fid);
2423 :	arodri7	1.42	#print STDERR "END CLUSTER OF GENES IN COMP REGION: ". `date`;
2424 :	arodri7	1.41	my %in_subs = $fig->subsystems_for_pegs(\@all_pegs);
2425 :	arodri7	1.21
2426 :	mkubal	1.14	foreach my $region (@$all_regions){
2427 :			my $sample_peg = @$region[0];
2428 :			my $region_genome = $fig->genome_of($sample_peg);
2429 :			my $region_gs = $fig->genus_species($region_genome);
2430 :	arodri7	1.18	my $abbrev_name = $fig->abbrev($region_gs);
2431 :	arodri7	1.45	#my ($genome1) = ($region_genome) =~ /(.*?)\./;
2432 :	arodri7	1.53	my $lineage = $taxes->{$region_genome};
2433 :			#my $lineage = $fig->taxonomy_of($region_genome);
2434 :	arodri7	1.40	#$region_gs .= "Lineage:$lineage";
2435 :	arodri7	1.16	my $line_config = { 'title' => $region_gs,
2436 :	arodri7	1.18	'short_title' => $abbrev_name,
2437 :	arodri7	1.16	'basepair_offset' => '0'
2438 :			};
2439 :
2440 :	arodri7	1.22	my $offsetting = shift @start_array_region;
2441 :	arodri7	1.16
2442 :	arodri7	1.40	my $second_line_config = { 'title' => "$lineage",
2443 :	arodri7	1.25	'short_title' => "",
2444 :	arodri7	1.38	'basepair_offset' => '0',
2445 :			'no_middle_line' => '1'
2446 :	arodri7	1.25	};
2447 :
2448 :	mkubal	1.14	my $line_data = [];
2449 :	arodri7	1.25	my $second_line_data = [];
2450 :
2451 :			# initialize variables to check for overlap in genes
2452 :			my ($prev_start, $prev_stop, $prev_fig, $second_line_flag);
2453 :			my $major_line_flag = 0;
2454 :			my $prev_second_flag = 0;
2455 :
2456 :	arodri7	1.16	foreach my $fid1 (@$region){
2457 :	arodri7	1.25	$second_line_flag = 0;
2458 :	mkubal	1.14	my $element_hash;
2459 :			my $links_list = [];
2460 :			my $descriptions = [];
2461 :	arodri7	1.38
2462 :			my $color = $color_sets->{$fid1};
2463 :	arodri7	1.26
2464 :	arodri7	1.18	# get subsystem information
2465 :			my $function = $fig->function_of($fid1);
2466 :	paczian	1.44	my $url_link = "?page=Annotation&feature=".$fid1;
2467 :	arodri7	1.18
2468 :			my $link;
2469 :			$link = {"link_title" => $fid1,
2470 :			"link" => $url_link};
2471 :			push(@$links_list,$link);
2472 :
2473 :	arodri7	1.41	my @subs = @{$in_subs{$fid1}} if (defined $in_subs{$fid1});
2474 :			my @subsystems;
2475 :			foreach my $array (@subs){
2476 :			my $subsystem = $$array[0];
2477 :			my $ss = $subsystem;
2478 :			$ss =~ s/_/ /ig;
2479 :			push (@subsystems, $ss);
2480 :	arodri7	1.18	my $link;
2481 :	paczian	1.44	$link = {"link" => "?page=Subsystems&subsystem=$subsystem",
2482 :	arodri7	1.41	"link_title" => $ss};
2483 :	arodri7	1.18	push(@$links_list,$link);
2484 :			}
2485 :	arodri7	1.41
2486 :			if ($fid1 eq $fid){
2487 :			my $link;
2488 :			$link = {"link_title" => "Annotate this sequence",
2489 :			"link" => "$FIG_Config::cgi_url/seedviewer.cgi?page=Commentary"};
2490 :			push (@$links_list,$link);
2491 :			}
2492 :
2493 :	arodri7	1.18	my $description_function;
2494 :			$description_function = {"title" => "function",
2495 :			"value" => $function};
2496 :			push(@$descriptions,$description_function);
2497 :
2498 :			my $description_ss;
2499 :	arodri7	1.41	my $ss_string = join (", ", @subsystems);
2500 :	arodri7	1.18	$description_ss = {"title" => "subsystems",
2501 :			"value" => $ss_string};
2502 :			push(@$descriptions,$description_ss);
2503 :
2504 :	arodri7	1.16
2505 :			my $fid_location = $fig->feature_location($fid1);
2506 :	mkubal	1.14	if($fid_location =~/(.*)_(\d+)_(\d+)$/){
2507 :			my($start,$stop);
2508 :	arodri7	1.22	$start = $2 - $offsetting;
2509 :			$stop = $3 - $offsetting;
2510 :	arodri7	1.25
2511 :			if ( (($prev_start) && ($prev_stop) ) &&
2512 :			( ($start < $prev_start) \|\| ($start < $prev_stop) \|\|
2513 :			($stop < $prev_start) \|\| ($stop < $prev_stop) )){
2514 :			if (($second_line_flag == 0) && ($prev_second_flag == 0)) {
2515 :			$second_line_flag = 1;
2516 :			$major_line_flag = 1;
2517 :			}
2518 :			}
2519 :			$prev_start = $start;
2520 :			$prev_stop = $stop;
2521 :			$prev_fig = $fid1;
2522 :
2523 :			if ((defined($reverse_flag{$region_genome})) && ($reverse_flag{$region_genome} eq $all_genes{$fid1})){
2524 :	arodri7	1.22	$start = $gd_window_size - $start;
2525 :			$stop = $gd_window_size - $stop;
2526 :			}
2527 :
2528 :	arodri7	1.41	my $title = $fid1;
2529 :			if ($fid1 eq $fid){
2530 :			$title = "My query gene: $fid1";
2531 :			}
2532 :
2533 :	mkubal	1.14	$element_hash = {
2534 :	arodri7	1.41	"title" => $title,
2535 :	mkubal	1.14	"start" => $start,
2536 :			"end" => $stop,
2537 :			"type"=> 'arrow',
2538 :			"color"=> $color,
2539 :	arodri7	1.18	"zlayer" => "2",
2540 :			"links_list" => $links_list,
2541 :			"description" => $descriptions
2542 :	mkubal	1.14	};
2543 :	arodri7	1.25
2544 :			# if there is an overlap, put into second line
2545 :			if ($second_line_flag == 1){ push(@$second_line_data,$element_hash); $prev_second_flag = 1;}
2546 :			else{ push(@$line_data,$element_hash); $prev_second_flag = 0;}
2547 :	arodri7	1.41
2548 :			if ($fid1 eq $fid){
2549 :			$element_hash = {
2550 :			"title" => 'Query',
2551 :			"start" => $start,
2552 :			"end" => $stop,
2553 :			"type"=> 'bigbox',
2554 :			"color"=> $color,
2555 :			"zlayer" => "1"
2556 :			};
2557 :
2558 :			# if there is an overlap, put into second line
2559 :			if ($second_line_flag == 1){ push(@$second_line_data,$element_hash); $prev_second_flag = 1;}
2560 :			else{ push(@$line_data,$element_hash); $prev_second_flag = 0;}
2561 :			}
2562 :	mkubal	1.14	}
2563 :			}
2564 :			$gd->add_line($line_data, $line_config);
2565 :	arodri7	1.40	$gd->add_line($second_line_data, $second_line_config); # if ($major_line_flag == 1);
2566 :	mkubal	1.14	}
2567 :	arodri7	1.41	return ($gd, \@selected_sims);
2568 :	mkubal	1.14	}
2569 :
2570 :	arodri7	1.38	sub cluster_genes {
2571 :			my($fig,$all_pegs,$peg) = @_;
2572 :			my(%seen,$i,$j,$k,$x,$cluster,$conn,$pegI,$red_set);
2573 :
2574 :			my @color_sets = ();
2575 :
2576 :			$conn = &get_connections_by_similarity($fig,$all_pegs);
2577 :
2578 :			for ($i=0; ($i < @$all_pegs); $i++) {
2579 :			if ($all_pegs->[$i] eq $peg) { $pegI = $i }
2580 :			if (! $seen{$i}) {
2581 :			$cluster = [$i];
2582 :			$seen{$i} = 1;
2583 :			for ($j=0; ($j < @$cluster); $j++) {
2584 :			$x = $conn->{$cluster->[$j]};
2585 :			foreach $k (@$x) {
2586 :			if (! $seen{$k}) {
2587 :			push(@$cluster,$k);
2588 :			$seen{$k} = 1;
2589 :			}
2590 :			}
2591 :			}
2592 :
2593 :			if ((@$cluster > 1) \|\| ($cluster->[0] eq $pegI)) {
2594 :			push(@color_sets,$cluster);
2595 :			}
2596 :			}
2597 :			}
2598 :			for ($i=0; ($i < @color_sets) && (! &in($pegI,$color_sets[$i])); $i++) {}
2599 :			$red_set = $color_sets[$i];
2600 :			splice(@color_sets,$i,1);
2601 :			@color_sets = sort { @$b <=> @$a } @color_sets;
2602 :			unshift(@color_sets,$red_set);
2603 :
2604 :			my $color_sets = {};
2605 :			for ($i=0; ($i < @color_sets); $i++) {
2606 :			foreach $x (@{$color_sets[$i]}) {
2607 :			$color_sets->{$all_pegs->[$x]} = $i;
2608 :			}
2609 :			}
2610 :			return $color_sets;
2611 :			}
2612 :
2613 :			sub get_connections_by_similarity {
2614 :			my($fig,$all_pegs) = @_;
2615 :			my($i,$j,$tmp,$peg,%pos_of);
2616 :			my($sim,%conn,$x,$y);
2617 :
2618 :			for ($i=0; ($i < @$all_pegs); $i++) {
2619 :			$tmp = $fig->maps_to_id($all_pegs->[$i]);
2620 :			push(@{$pos_of{$tmp}},$i);
2621 :			if ($tmp ne $all_pegs->[$i]) {
2622 :			push(@{$pos_of{$all_pegs->[$i]}},$i);
2623 :			}
2624 :			}
2625 :
2626 :			foreach $y (keys(%pos_of)) {
2627 :	arodri7	1.41	$x = $pos_of{$y};
2628 :	arodri7	1.38	for ($i=0; ($i < @$x); $i++) {
2629 :			for ($j=$i+1; ($j < @$x); $j++) {
2630 :			push(@{$conn{$x->[$i]}},$x->[$j]);
2631 :			push(@{$conn{$x->[$j]}},$x->[$i]);
2632 :			}
2633 :			}
2634 :			}
2635 :
2636 :			for ($i=0; ($i < @$all_pegs); $i++) {
2637 :	arodri7	1.42	foreach $sim ($fig->sims($all_pegs->[$i],500,10,"raw")) {
2638 :	arodri7	1.38	if (defined($x = $pos_of{$sim->id2})) {
2639 :			foreach $y (@$x) {
2640 :			push(@{$conn{$i}},$y);
2641 :			}
2642 :			}
2643 :			}
2644 :			}
2645 :			return \%conn;
2646 :			}
2647 :
2648 :			sub in {
2649 :			my($x,$xL) = @_;
2650 :			my($i);
2651 :
2652 :			for ($i=0; ($i < @$xL) && ($x != $xL->[$i]); $i++) {}
2653 :			return ($i < @$xL);
2654 :			}
2655 :	arodri7	1.41
2656 :			#############################################
2657 :			#############################################
2658 :			package Observation::Commentary;
2659 :
2660 :			use base qw(Observation);
2661 :
2662 :			=head3 display_protein_commentary()
2663 :
2664 :			=cut
2665 :
2666 :			sub display_protein_commentary {
2667 :			my ($self,$dataset,$mypeg,$fig) = @_;
2668 :
2669 :			my $all_rows = [];
2670 :			my $content;
2671 :			#my $fig = new FIG;
2672 :			my $cgi = new CGI;
2673 :			my $count = 0;
2674 :			my $peg_array = [];
2675 :			my (%evidence_column, %subsystems_column, %e_identical);
2676 :
2677 :			if (@$dataset != 1){
2678 :			foreach my $thing (@$dataset){
2679 :			if ($thing->class eq "SIM"){
2680 :			push (@$peg_array, $thing->acc);
2681 :			}
2682 :			}
2683 :			# get the column for the evidence codes
2684 :			%evidence_column = &Observation::Sims::get_evidence_column($peg_array);
2685 :
2686 :			# get the column for the subsystems
2687 :			%subsystems_column = &Observation::Sims::get_subsystems_column($peg_array,$fig);
2688 :
2689 :			# get essentially identical seqs
2690 :			%e_identical = &Observation::Sims::get_essentially_identical($mypeg,$dataset,$fig);
2691 :			}
2692 :			else{
2693 :			push (@$peg_array, @$dataset);
2694 :			}
2695 :
2696 :			my $selected_sims = [];
2697 :			foreach my $id (@$peg_array){
2698 :			last if ($count > 10);
2699 :			my $row_data = [];
2700 :			my ($set, $org, $ss, $ev, $function, $function_cell, $id_cell);
2701 :			$org = $fig->org_of($id);
2702 :			$function = $fig->function_of($id);
2703 :			if ($mypeg ne $id){
2704 :	paczian	1.47	$function_cell = "<input type='radio' name='function' id='$id' value='$function' onClick=\"clearText('setAnnotation');\">  $function";
2705 :			$id_cell .= "<a href='?page=Annotation&feature=$id'>$id</a>"; # &HTML::set_prot_links($cgi,$id);
2706 :	arodri7	1.41	if (defined($e_identical{$id})) { $id_cell .= "*";}
2707 :			}
2708 :			else{
2709 :			$function_cell = "  $function";
2710 :	paczian	1.47	$id_cell = "<input type='checkbox' name='peg' id='peg$count' value='$id' checked='true'>";
2711 :			$id_cell .= "<a href='?page=Annotation&feature=$id'>$id</a>"; # &HTML::set_prot_links($cgi,$id);
2712 :	arodri7	1.41	}
2713 :
2714 :			push(@$row_data,$id_cell);
2715 :			push(@$row_data,$org);
2716 :			push(@$row_data, $subsystems_column{$id}) if ($mypeg ne $id);
2717 :			push(@$row_data, $evidence_column{$id}) if ($mypeg ne $id);
2718 :			push(@$row_data, $fig->translation_length($id));
2719 :			push(@$row_data,$function_cell);
2720 :			push(@$all_rows,$row_data);
2721 :			push (@$selected_sims, $id);
2722 :			$count++;
2723 :			}
2724 :
2725 :			if ($count >0){
2726 :			$content = $all_rows;
2727 :			}
2728 :			else{
2729 :			$content = "<p>This PEG does not have enough similarities to change the commentary</p>";
2730 :			}
2731 :			return ($content,$selected_sims);
2732 :			}
2733 :
2734 :			sub display_protein_history {
2735 :			my ($self, $id,$fig) = @_;
2736 :			my $all_rows = [];
2737 :			my $content;
2738 :
2739 :			my $cgi = new CGI;
2740 :			my $count = 0;
2741 :			foreach my $feat ($fig->feature_annotations($id)){
2742 :			my $row = [];
2743 :			my $col1 = $feat->[2];
2744 :			my $col2 = $feat->[1];
2745 :			#my $text = "<pre>" . $feat->[3] . "<\pre>";
2746 :			my $text = $feat->[3];
2747 :
2748 :			push (@$row, $col1);
2749 :			push (@$row, $col2);
2750 :			push (@$row, $text);
2751 :			push (@$all_rows, $row);
2752 :			$count++;
2753 :			}
2754 :			if ($count > 0){
2755 :			$content = $all_rows;
2756 :			}
2757 :			else {
2758 :			$content = "There is no history for this PEG";
2759 :			}
2760 :
2761 :			return($content);
2762 :			}

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