cgi-bin/phenome/locus_display.pl

   1 use strict;
   2 use warnings;
   3 use CXGN::Page;
   4
   5 use CXGN::Apache::Error;
   6 use CXGN::DB::Connection;
   7 use CXGN::People::PageComment;
   8 use CXGN::People;
   9 use CXGN::Contact;
  10 use CXGN::Page::FormattingHelpers qw(
  11         info_section_html
  12         page_title_html
  13         columnar_table_html
  14         info_table_html
  15         html_optional_show
  16         html_alternate_show
  17         tooltipped_text
  18       );
  19 use CXGN::Page::Widgets qw / collapser /;
  20 use CXGN::Phenome::Locus;
  21 use CXGN::Phenome::Locus::LinkageGroup;
  22
  23 use CXGN::Cview::ChrMarkerImage;
  24 use CXGN::Cview::MapFactory;
  25 use CXGN::Marker;
  26 use CXGN::Cview::Marker::RangeMarker;
  27 use CXGN::Map;
  28
  29 use CXGN::Chado::CV;
  30 use CXGN::Chado::Feature;
  31 use CXGN::Chado::Publication;
  32 use CXGN::Chado::Pubauthor;
  33
  34
  35 use CXGN::Sunshine::Browser;
  36 use CXGN::Tools::Identifiers qw/parse_identifier/;
  37 use CXGN::Tools::List qw/distinct/;
  38
  39 use CXGN::Phenome::Locus::LocusPage;
  40 use SGN::Image;
  41 use HTML::Entities;
  42
  43 my $d = CXGN::Debug->new();
  44 ##$d->set_debug( 1 );
  45
  46
  47 my $page= CXGN::Page->new("Locus display", "Naama");
  48 my $dbh=$page->get_dbh();
  49
  50 my $time = time();
  51 $d->d("start time = $time ! \n");
  52
  53 my %args = $page->cgi_params();
  54 my $locus_id = $args{locus_id};
  55
  56 my $person_id = CXGN::Login->new($dbh)->has_session();
  57 my $user = CXGN::People::Person->new($dbh, $person_id);
  58 my $user_type = $user->get_user_type();
  59 my $script = "/phenome/locus_display.pl?locus_id=$locus_id";
  60
  61 unless ( ( $locus_id =~ m /^\d+$/ ) || ($args{action} eq 'new' && !$locus_id) ) {
  62     $c->throw(is_error=>0,
  63               message=>"No locus exists for identifier $locus_id",
  64         );
  65     $d->d("No locus exists for identifier $locus_id");
  66 }
  67
  68 my $locus= CXGN::Phenome::Locus->new( $dbh, $locus_id  );
  69 if ( $locus->get_obsolete() eq 't' && $user_type ne 'curator' )
  70 {
  71     $d->d("locus is obsolete!!" );
  72
  73     $c->throw(is_error=>0,
  74               title => 'Obsolete locus',
  75               message=>"Locus $locus_id is obsolete!",
  76               developer_message => 'only curators can see obsolete loci',
  77               notify => 0,   #< does not send an error email
  78         );
  79     #$page->message_page("Locus $locus_id is obsolete!");
  80 }
  81
  82
  83 my $locus_name = $locus->get_locus_name();
  84 my $organism   = $locus->get_common_name();
  85
  86 $page->jsan_use("CXGN.Phenome.Tools");
  87 $page->jsan_use("CXGN.Phenome.Locus");
  88 $page->jsan_use("MochiKit.DOM");
  89 $page->jsan_use("Prototype");
  90 $page->jsan_use("jQuery");
  91 $page->jsan_use("thickbox");
  92 $page->jsan_use("MochiKit.Async");
  93 $page->jsan_use("CXGN.Sunshine.NetworkBrowser");
  94 $page->jsan_use("CXGN.Phenome.Locus.LocusPage");
  95 $page->jsan_use("CXGN.Page.Form.JSFormPage");
  96
  97 #used to show certain elements to only the proper users
  98
  99 my @owners   = $locus->get_owners();
 100
 101 my $action = $args{action};
 102
 103 if ( !$locus->get_locus_id() && $action ne 'new' && $action ne 'store' ) {
 104     $c->throw(is_error=>0, message=>'No locus exists for this identifier',);
 105     $d->d('No locus exists for this identifier');
 106     #$page->message_page("No locus exists for this identifier");
 107 }
 108
 109 $page->header("SGN $organism locus: $locus_name");
 110
 111 print page_title_html("$organism \t'$locus_name'\n");
 112
 113 print CXGN::Phenome::Locus::LocusPage::initialize($locus_id);
 114
 115 $d->d("!!!Printing page title :  " . ( time() - $time ) . "\n");
 116 ####################################################
 117 #get all dbxref  annotations: pubmed, ncbi sequences, GO, PO, tgrc link
 118 ####################################################
 119 my @allele_objs = $locus->get_alleles();    #array of allele objects
 120 my ( $tgrc, $pubs, $pub_count, $genbank, $gb_count, $onto_ref ) =
 121     get_dbxref_info($locus, @allele_objs);
 122
 123 $d->d( "!!!Got all dbxrefs! :  " . ( time() - $time ) . "\n");
 124
 125 ##############################
 126     #display locus details section
 127 #############################
 128 my $curator_html;
 129 my ( $synonyms, $symbol, $symbol_link, $activity, $description, $lg_name,
 130      $arm, $locus_details );
 131 my $editor_note =
 132     qq |<a href="/phenome/editors_note.pl">Note to Editors</a>|;
 133 my $guide_html =
 134     qq|<a href="http://docs.google.com/View?docid=ddhncntn_0cz2wj6">Annotation guidelines</a>|;
 135
 136 my $locus_html= qq| <table width="100%"><tr><td>|
 137     . CXGN::Phenome::Locus::LocusPage::init_locus_form($locus_id);
 138 #Only show if you are a curator or the object owner and there is no registry already assocaited with the locus
 139 if (
 140     (
 141      $user_type eq 'curator'
 142          || grep { /^$person_id$/ } @owners
 143     )
 144     && !( $locus->get_associated_registry() )
 145     )
 146 {
 147     if ($locus_name) { $locus_html .= associate_registry($locus, $person_id); }
 148     else {
 149         $curator_html .=
 150             qq |<span class = "ghosted"> [Associate registry name]</span> |;
 151     }
 152 }
 153
 154 #merge locus form
 155 if ( $user_type eq 'curator' ) {
 156     $curator_html .= "<br />" . merge_locus($locus, $person_id);
 157 }
 158
 159 my $locus_synonym_count = scalar( $locus->get_locus_aliases('f', 'f') ) || "";
 160 $locus_html .=
 161     qq { <br /><br /><b>Locus synonyms</b> <b>$locus_synonym_count:</b> };
 162
 163 foreach my $synonym ( $locus->get_locus_aliases('f','f') ) {
 164     $locus_html .= $synonym->get_locus_alias() . "  ";
 165 }
 166
 167 if ($locus_name) {
 168     $locus_html .=
 169         qq|<a href="locus_synonym.pl?locus_id=$locus_id&amp;action=new">[Add/Remove]</a><br />|;
 170
 171     $locus_html .= "<br />" . $tgrc;
 172
 173     #print editors info
 174     $locus_html .= print_locus_editor_info($locus) . "<br>";
 175
 176     #change ownership:
 177     if ( $user_type eq 'curator' ) {
 178         $curator_html .= assign_owner($locus);
 179     }
 180     if (   ( !( grep { $_ =~ /^$person_id$/ } @owners ) )
 181            && ( $user_type ne 'curator' ) )
 182     {
 183
 184         $locus_html .=
 185             qq|<a href="claim_locus_ownership.pl?locus_id=$locus_id&amp;action=confirm"> [Request editor privileges]</a><br /><br />|;
 186     }
 187
 188     my $created_date = $locus->get_create_date();
 189     $created_date = substr $created_date, 0, 10;
 190     my $modified_date = $locus->get_modification_date() || "";
 191     $modified_date = substr $modified_date, 0, 10;
 192
 193     my $updated_by = $locus->get_updated_by();
 194     my $updated =
 195         CXGN::People::Person->new( $locus->get_dbh(), $updated_by );
 196     my $u_first_name = $updated->get_first_name();
 197     my $u_last_name  = $updated->get_last_name();
 198     $locus_html .= qq |Created on: $created_date |;
 199     if ($modified_date) {
 200         $locus_html .=
 201             qq |  Last updated on: $modified_date  by  <a href="/solpeople/personal-info.pl?sp_person_id=$updated_by">$u_first_name $u_last_name</a><br />|;
 202     }
 203
 204     #build a chromosome, map/s and marker/s objects
 205     $locus_html .= get_location($locus);
 206 }
 207
 208 my $name = $locus->get_associated_registry();
 209 if ($name) {
 210     $locus_html .= "This locus is associated with registry name: $name<br />";
 211 }
 212
 213 ##############history ############
 214
 215 if ( $user_type eq 'curator'
 216      || grep { /^$person_id$/ } @owners )
 217 {
 218     my $history_data = print_locus_history($locus) || "";
 219     $locus_html .= $history_data;
 220 }
 221 my $locus_xml = $locus_id ? qq |<a href = "generic_gene_page.pl?locus_id=$locus_id">Download GMOD XML</a>|
 222     : qq |<span class="ghosted">Download GMOD XML</span>|;
 223
 224     #print locus details section
 225     print info_section_html(
 226         title    => 'Locus details',
 227         subtitle => $locus_xml . " |" . " "
 228         . $editor_note . " " . "|" . " "
 229         . $guide_html,
 230         contents => $locus_html,
 231     );
 232     if ($curator_html) {
 233         print info_section_html(
 234             title       => 'Curator tools',
 235             subtitle    => "",
 236             contents    => $curator_html,
 237             collapsible => 1,
 238             collapsed   => 1,
 239         );
 240     }
 241     print STDERR "!!!Printing locus_details :  " . ( time() - $time ) . "\n";
 242
 243 ##########
 244 ## Notes and Figures
 245 ##########
 246     #
 247     my $figure_html     = "";
 248     my $m_figure_html   = "";
 249     my $figure_subtitle = "";
 250     my $figures_count;
 251     my @more_is;
 252
 253
 254     if (
 255         $locus_name
 256         && (   $user_type eq 'submitter'
 257             || $user_type eq 'curator'
 258             || $user_type eq 'sequencer' )
 259       )
 260     {
 261         $figure_subtitle .= associated_figures($locus, $person_id);
 262     }
 263     else {
 264         $figure_subtitle .=
 265           qq|<span class= "ghosted">[Add notes, figures or images]</span> |;
 266     }
 267
 268     my @figures = $locus->get_figure_ids();
 269
 270     if (@figures) {    # don't display anything for empty list of figures
 271         $figure_html .= qq|<table cellpadding="5">|;
 272         foreach my $figure_id (@figures) {
 273             $figures_count++;
 274             my $figure= SGN::Image->new($locus->get_dbh(), $figure_id);
 275             my $figure_name        = $figure->get_name();
 276             my $figure_description = $figure->get_description();
 277             my $figure_img  = $figure->get_image_url("medium");
 278             my $small_image = $figure->get_image_url("thumbnail");
 279             my $image_page  = "/image/index.pl?image_id=$figure_id";
 280
 281             my $thickbox =
 282 qq|<a href="$figure_img"  title="<a href=$image_page>Go to image page ($figure_name)</a>" class="thickbox" rel="gallery-figures"><img src="$small_image" alt="$figure_description" /></a> |;
 283             my $fhtml =
 284                 qq|<tr><td width=120>|
 285               . $thickbox
 286               . $figure_name
 287               . "</td><td>"
 288               . $figure_description
 289               . "</td></tr>";
 290             if ( $figures_count < 3 ) { $figure_html .= $fhtml; }
 291             else {
 292                 push @more_is, $fhtml;
 293             }    #more than 3 figures- show these in a hidden div
 294         }
 295         $figure_html .= "</table>";  #close the table tag or the first 3 figures
 296     }
 297     $m_figure_html .=
 298       "<table cellpadding=5>";  #open table tag for the hidden figures #4 and on
 299     my $more = scalar(@more_is);
 300     foreach (@more_is) { $m_figure_html .= $_; }
 301
 302     $m_figure_html .= "</table>";    #close tabletag for the hidden figures
 303     my $more_images;
 304     if (@more_is) {    #html_optional_show if there are more than 3 figures
 305         $more_images = html_optional_show(
 306             "Images",
 307             "<b>See $more more figures...</b>",
 308             qq| $m_figure_html |,
 309             0,                        #< do not show by default
 310             'abstract_optional_show', #< don't use the default button-like style
 311         );
 312     }
 313     print info_section_html(
 314         title       => "Notes and figures (" . scalar(@figures) . ")",
 315         subtitle    => $figure_subtitle,
 316         contents    => $figure_html . $more_images,
 317         collapsible => 1,
 318         collapsed   => 1,
 319     );
 320     print STDERR "!!!Printing notes and figures :  "
 321       . ( time() - $time ) . "\n";
 322
 323 #################################
 324     #display individuals section
 325 #################################
 326     my $individuals_html = "";
 327     my $ind_subtitle     = "";
 328     if (
 329         $locus_name
 330         && (   $user_type eq 'curator'
 331             || $user_type eq 'submitter'
 332             || $user_type eq 'sequencer' )
 333       )
 334     {
 335         $ind_subtitle .=
 336 qq| <a href="javascript:Tools.toggleContent('associateIndividualForm', 'locus_accessions')">[Associate accession]</a> |;
 337         $individuals_html = associate_individual($locus, $person_id);
 338     }
 339     else {
 340         $ind_subtitle .=
 341           qq|<span class= "ghosted">[Associate accession]</span> |;
 342     }
 343     my ( $html, $ind_count ) = get_individuals_html($locus, $user_type);
 344     $individuals_html .= $html;
 345
 346     print info_section_html(
 347         title       => "Accessions and images  ($ind_count)",
 348         subtitle    => $ind_subtitle,
 349         contents    => $individuals_html,
 350         id          => "locus_accessions",
 351         collapsible => 1,
 352         collapsed   => 1,
 353     );
 354     print STDERR "!!!Printing individuas section :  "
 355       . ( time() - $time ) . "\n";
 356
 357 #################################
 358     #display alleles section
 359 #################################
 360
 361     my $allele_count = scalar(@allele_objs);
 362
 363     #map the allele objects to an array ref of the alleles data
 364     my @allele_data;
 365     my $allele_data;
 366     my $allele_subtitle;
 367     if (
 368         $locus_name
 369         && (   $user_type eq 'submitter'
 370             || $user_type eq 'curator'
 371             || $user_type eq 'sequencer' )
 372       )
 373     {
 374         $allele_subtitle .=
 375 qq { <a href="allele.pl?locus_id=$locus_id&amp;action=new">[Add new allele]</a>};
 376     }
 377     else {
 378         $allele_subtitle .=
 379           qq | <span class="ghosted">[Add new Allele]</span> |;
 380     }
 381
 382     foreach my $a (@allele_objs) {
 383
 384         my $allele_id = $a->{allele_id};
 385
 386         my $allele_synonyms;
 387         my @allele_aliases = $a->get_allele_aliases();
 388         foreach my $a_synonym (@allele_aliases) {
 389             $allele_synonyms .= $a_synonym->get_allele_alias() . "  ";
 390         }
 391         if ( !$allele_synonyms ) { $allele_synonyms = "[add new]"; }
 392         my $allele_synonym_link =
 393 qq |<a href= "allele_synonym.pl?allele_id=$allele_id&amp;action=new">$allele_synonyms</a> |;
 394         my $allele_edit_link = get_allele_edit_links($a, $user);
 395         my $phenotype        = $a->get_allele_phenotype();
 396         my @individuals      = $a->get_individuals();
 397         my $individual_link  = "";
 398         my $ind_count        = scalar(@individuals);
 399
 400         $individual_link .=
 401 qq|<a href="allele.pl?action=view&amp;allele_id=$allele_id">$ind_count </a>|;
 402
 403         push @allele_data,
 404           [
 405             map { $_ } (
 406                 "<i>" . $a->get_allele_symbol . "</i>",
 407                 $a->get_allele_name,
 408                 $allele_synonym_link,
 409 qq|<div align="left"><a href="allele.pl?action=view&amp;allele_id=$allele_id"> |
 410                   . $phenotype
 411                   . "</a></div>",
 412                 $individual_link,
 413                 $allele_edit_link,
 414             )
 415           ];
 416
 417     }
 418     if (@allele_data) {
 419
 420         $allele_data .= columnar_table_html(
 421             headings => [
 422                 'Allele symbol', 'Allele name',
 423                 'Synonyms',      'Phenotype',
 424                 'Accessions',
 425             ],
 426             data         => \@allele_data,
 427             __alt_freq   => 2,
 428             __alt_width  => 1,
 429             __alt_offset => 3,
 430         );
 431     }
 432
 433     print info_section_html(
 434         title       => "Known alleles ($allele_count)",
 435         subtitle    => $allele_subtitle,
 436         contents    => $allele_data,
 437         collapsible => 1,
 438         collapsed   => 1,
 439     );
 440     print STDERR "!!!Printing alleles :  " . ( time() - $time ) . "\n";
 441
 442
 443
 444     ###########################               ASSOCIATED LOCI
 445     #my @locus_groups= $locus->get_locusgroups();
 446     #my $direction;
 447     my $al_count = $locus->count_associated_loci();
 448
 449     my $associated_locus_sub;
 450     my $associate_locus_form;
 451     if (
 452         (
 453                $user_type eq 'curator'
 454             || $user_type eq 'submitter'
 455             || $user_type eq 'sequencer'
 456         )
 457       )
 458     {
 459
 460         if ($locus_name) {
 461             $associated_locus_sub .=
 462                 qq |<a href="javascript:Tools.toggleContent('associateLocusForm', 'locus2locus');Tools.getOrganisms()">[Associate new locus]</a> |;
 463             $associate_locus_form =
 464                 CXGN::Phenome::Locus::LocusPage::associate_locus_form($locus_id);
 465         }
 466     }
 467 else {
 468     $associated_locus_sub .=
 469         qq |<span class ="ghosted"> [Associate new locus] </span> |;
 470 }
 471
 472 #printing associated loci section dynamically
 473 my $dyn = CXGN::Phenome::Locus::LocusPage::include_locus_network();
 474
 475 print info_section_html(
 476     title       => "Associated loci ($al_count) ",
 477     subtitle    => $associated_locus_sub,
 478     contents    => $associate_locus_form . $dyn,
 479     id          => 'locus2locus',
 480     collapsible => 1,
 481     collapsed   => 1,
 482     );
 483
 484 $d->d( "!!!Printing locus2locus :  " . ( time() - $time ) . "\n");
 485
 486 ##################  SUNSHINE BROWSER
 487
 488 my $locus2locus_graph =
 489     CXGN::Sunshine::Browser::include_on_page( 'locus', $locus_id );
 490
 491 my $networkbrowser_link =
 492     qq { View <b>$locus_name</b> relationships in the stand-alone <a href="/tools/networkbrowser/?type=locus&name=$locus_id">network browser</a>. Please note that this tool is a prototype.<br /><br /><br /> };
 493
 494 if ( $al_count > 0 ) {
 495     print info_section_html(
 496         title       => "Associated loci - graphical view [beta version]",
 497         contents    => $networkbrowser_link . $locus2locus_graph,
 498         id          => 'locus2locus_graph',
 499         collapsible => 1,
 500         collapsed   => 1,
 501         );
 502 }
 503 else {
 504     print info_section_html(
 505         title       => "Associated loci - graphical view",
 506         collapsible => 0,
 507         collapsed   => 1,
 508         id          => 'locus2locus_graph'
 509         );
 510
 511 }
 512
 513
 514 #####################           UNIGENES AND SOLCYC
 515
 516 my @unigenes = $locus->get_unigenes();
 517 my $unigene_count=0;
 518 my $solcyc_count=0;
 519 foreach (@unigenes) {
 520     $unigene_count++ if $_->get_status eq 'C';
 521 }
 522
 523 my $dyn_solcyc = CXGN::Phenome::Locus::LocusPage::include_solcyc_links();
 524
 525 print info_section_html(
 526     title       => "SolCyc links",
 527     contents    => $dyn_solcyc,
 528     id          => 'solcyc',
 529     collapsible => 1,
 530     collapsed   => 1,
 531     );
 532 $d->d( "!!!Got SolCyc links :  " . ( time() - $time ) . "\n");
 533
 534 my $associate_unigene_form;
 535 if (
 536     (
 537      $user_type eq 'curator'
 538      || $user_type eq 'submitter'
 539      || $user_type eq 'sequencer'
 540     )
 541     )
 542 {
 543     if ($locus_name) {
 544         $associate_unigene_form= qq|<a href="javascript:Tools.toggleContent('associateUnigeneForm', 'unigenes' )">[Associate new unigene]</a> |;
 545         $associate_unigene_form .=
 546             CXGN::Phenome::Locus::LocusPage::associate_unigene_form($locus_id);
 547     }
 548 }
 549 my $sequence_links;
 550 if ($locus_name) {
 551     if ( !$genbank ) {
 552         $genbank = qq|<span class=\"ghosted\">none </span>|;
 553     }
 554     $genbank .=
 555         qq|<a href="/chado/add_feature.pl?type=locus&amp;type_id=$locus_id&amp;refering_page=$script&amp;action=new">[Associate new genbank sequence]</a><br />|;
 556
 557
 558     #printing associated unigenes section dynamically
 559     my $dyn_unigenes = CXGN::Phenome::Locus::LocusPage::include_locus_unigenes();
 560     $d->d( "!!!Got unigenes :  " . ( time() - $time ) . "\n");
 561
 562     $sequence_links = info_table_html(
 563         'SGN Unigenes'       => $dyn_unigenes . $associate_unigene_form,
 564         'GenBank Accessions' => $genbank,
 565         'Genome Matches'     => genomic_annots_html($locus),
 566         __border             => 0,
 567        );
 568 }
 569 my $seq_count = $gb_count + $unigene_count;
 570 print info_section_html(
 571     title       => "Sequence annotations ($seq_count)",
 572     contents    => $sequence_links,
 573     id          => 'unigenes',
 574     collapsible => 1,
 575     collapsed   => 1,
 576     );
 577 $d->d("!!!got sequence :  " . ( time() - $time ) . "\n");
 578
 579 ##########literature ########################################
 580 my ( $pub_links, $pub_subtitle );
 581 if ($pubs) {
 582     $pub_links = info_table_html(
 583         "  "     => $pubs,
 584         __border => 0,
 585         );
 586 }
 587
 588 if (
 589     $locus_name
 590     && (   $user_type eq 'curator'
 591            || $user_type eq 'submitter'
 592            || $user_type eq 'sequencer' )
 593     )
 594 {
 595     $pub_subtitle .=
 596         qq|<a href="/chado/add_publication.pl?type=locus&amp;type_id=$locus_id&amp;refering_page=$script&amp;action=new"> [Associate publication] </a>|;
 597 }
 598 else {
 599     $pub_subtitle =
 600         qq|<span class=\"ghosted\">[Associate publication]</span>|;
 601 }
 602
 603 my $disabled = "true";
 604 if ($person_id) { $disabled = "false"; }
 605 $pub_subtitle .=
 606     qq | <a href="javascript:void(0)"onclick="window.open('locus_pub_rank.pl?locus_id=$locus_id','publication_list','width=600,height=400,status=1,location=1,scrollbars=1')">[Matching publications]</a> |;
 607
 608 $d->d("!!!Printing pub links :  " . ( time() - $time ) . "\n");
 609
 610 print info_section_html(
 611     title       => "Literature annotation ($pub_count)",
 612     subtitle    => $pub_subtitle,
 613     contents    => $pub_links,
 614     collapsible => 1,
 615     collapsed   => 1,
 616     );
 617
 618 ######################################## Ontology details ##############
 619
 620 my $ont_count = $locus->count_ontology_annotations(); #= scalar(@$onto_ref);
 621
 622 my $ontology_add_link = "";
 623 my $ontology_subtitle;
 624 if (
 625     (
 626      $user_type eq 'curator'
 627      || $user_type eq 'submitter'
 628      || $user_type eq 'sequencer'
 629     )
 630     )
 631 {
 632     if ($locus_name) {
 633         $ontology_subtitle .=
 634             qq|<a href="javascript:Tools.toggleContent('associateOntologyForm', 'locus_ontology')">[Add ontology annotations]</a> |;
 635         $ontology_add_link =
 636             CXGN::Phenome::Locus::LocusPage::associate_ontology_form(
 637                 $locus_id);
 638     }
 639 }
 640 else {
 641     $ontology_subtitle =
 642         qq |<span class = "ghosted"> [Add ontology annotations]</span> |;
 643 }
 644
 645 my $dyn_ontology_info =
 646     CXGN::Phenome::Locus::LocusPage::include_locus_ontology();
 647
 648 print info_section_html(
 649     title       => "Ontology annotations ($ont_count)",
 650     subtitle    => $ontology_subtitle,
 651     contents    => $ontology_add_link . $dyn_ontology_info,
 652     id          => "locus_ontology",
 653     collapsible => 1,
 654     collapsed   => 1,
 655     );
 656
 657 $d->d( "!!!Printing ontology links! :  " . ( time() - $time ) . "\n");
 658
 659 ####add page comments
 660 if ($locus_name) {
 661     my $page_comment_obj =
 662         CXGN::People::PageComment->new( $locus->get_dbh(), "locus",
 663                                         $locus_id );
 664     print $page_comment_obj->get_html();
 665 }
 666
 667 $page->footer();
 668
 669
 670
 671 #########################################################
 672 #functions used in the locus page:
 673 ##
 674
 675 sub empty_search {
 676     my ($page) = @_;
 677
 678     #  $page->header();
 679
 680     print <<EOF;
 681
 682   <b>No locus was specified or this locus ID does not exist</b>
 683
 684 EOF
 685
 686 exit 0;
 687 }
 688
 689 sub get_allele_edit_links {
 690     my $allele   = shift;
 691     my $user= shift;
 692     my $login_user_id    = $user->get_sp_person_id();
 693     my $locus    = $allele->get_locus();
 694     my $locus_id = $locus->get_locus_id();
 695
 696     my $allele_edit_link = "";
 697
 698     my $allele_id        = $allele->get_allele_id();
 699     if (   ( $allele->get_sp_person_id() == $login_user_id )
 700         || ( $user->get_user_type() eq 'curator' ) )
 701     {
 702         $allele_edit_link =
 703 qq | <a href="allele.pl?action=edit&amp;allele_id=$allele_id">[Edit]</a> |;
 704     }
 705     else { $allele_edit_link = qq | <span class="ghosted">[Edit]</span> |; }
 706 }
 707
 708 sub get_location {
 709     my $locus = shift;
 710
 711     my $lg_name = $locus->get_linkage_group();
 712     my $arm     = $locus->get_lg_arm();
 713     my $location_html;
 714     my @locus_marker_objs =
 715         $locus->get_locus_markers();    #array of locus_marker objects
 716     foreach my $lmo (@locus_marker_objs) {
 717         my $marker_id = $lmo->get_marker_id();    #{marker_id};
 718         my $marker =
 719             CXGN::Marker->new( $locus->get_dbh(), $marker_id )
 720             ;                                       #a new marker object
 721
 722         my $marker_name = $marker->name_that_marker();
 723         my $experiments = $marker->current_mapping_experiments();
 724         if (    $experiments
 725                 and @{$experiments}
 726                 and grep { $_->{location} } @{$experiments} )
 727         {
 728             my $count = 1;
 729             for my $experiment ( @{$experiments} ) {
 730                 if ( my $loc = $experiment->{location} ) {
 731                     my $map_version_id = $loc->map_version_id();
 732                     my $lg_name        = $loc->lg_name();
 733
 734                     if ($map_version_id) {
 735                         my $map_factory =
 736                             CXGN::Cview::MapFactory->new( $locus->get_dbh() );
 737                         my $map = $map_factory->create(
 738                             { map_version_id => $map_version_id } );
 739                         my $map_version_id = $map->get_id();
 740                         my $map_name       = $map->get_short_name();
 741
 742                         my $chromosome =
 743                             CXGN::Cview::ChrMarkerImage->new( "", 100, 150,
 744                                                               $locus->get_dbh(), $lg_name, $map, $marker_name );
 745                         my ( $image_path, $image_url ) =
 746                             $chromosome->get_image_filename();
 747                         my $chr_link =
 748                             qq|<img src="$image_url" usemap="#map$count" border="0" alt="" />|;
 749                         $chr_link .=
 750                             $chromosome->get_image_map("map$count") . "<br />";
 751                         $chr_link .= $map_name;
 752                         $count++;
 753
 754                         $location_html .= "<td>" . $chr_link . "</td>";
 755                     }
 756                 }
 757             }
 758         }
 759     }
 760
 761 #draw chromosome with marker-range for loci w/o associated marker, only a chromosome arm annotation
 762     if ( scalar(@locus_marker_objs) == 0 && $lg_name ) {
 763         my $organism = $locus->get_common_name();
 764         my %org_hash = (
 765             'Tomato'   => 9,    #F2 2000 map
 766             'Potato'   => 3,
 767             'Eggplant' => 6,
 768             'Pepper'   => 10
 769             );
 770         my $map_id      = $org_hash{$organism};
 771         my $map_factory = CXGN::Cview::MapFactory->new( $locus->get_dbh() );
 772
 773         my $map = $map_factory->create( { map_id => $map_id } );
 774         if ($map) {
 775             my $map_name = $map->get_short_name();
 776             my ( $north, $south, $center ) = $map->get_centromere($lg_name);
 777
 778             my $dummy_name;
 779             $dummy_name = "$arm arm" if $arm;
 780             my $chr_image =
 781                 CXGN::Cview::ChrMarkerImage->new( "", 150, 150, $locus->get_dbh(),
 782                                                   $lg_name, $map, $dummy_name );
 783
 784             my ($chr) = $chr_image->get_chromosomes();
 785
 786             my $range_marker = CXGN::Cview::Marker::RangeMarker->new($chr);
 787
 788             my ( $offset, $nrange, $srange );
 789             if ( $arm eq 'short' ) {
 790                 $offset = $nrange = $srange = $center / 2;
 791             }
 792             elsif ( $arm eq 'long' ) {
 793                 my $stelomere = $chr->get_length();
 794                 $offset = ( $center + $stelomere ) / 2;
 795                 $nrange = $srange = ( $stelomere - $center ) / 2;
 796             }
 797
 798             $range_marker->set_offset($offset);    #center of north/south arm
 799             $range_marker->set_north_range($nrange);
 800             $range_marker->set_south_range($srange);
 801             $range_marker->set_marker_name($dummy_name);
 802             if ( !$dummy_name ) { $range_marker->hide_label(); }
 803
 804             #$range_marker->show_label();
 805             #}else {
 806             $range_marker->set_label_spacer(20);
 807
 808             $range_marker->get_label()->set_name($dummy_name);
 809             $range_marker->get_label->set_stacking_level(2);
 810
 811             $chr->add_marker($range_marker);
 812
 813             my ( $image_path, $image_url ) = $chr_image->get_image_filename();
 814             my $chr_link =
 815                 qq|<img src="$image_url" usemap="#chr_arm_map" border="0" alt="" />|;
 816             $chr_link .= $chr_image->get_image_map("chr_arm_map") . "<br />";
 817             $chr_link .= $map_name;
 818
 819             $location_html .= "<td>" . $chr_link . "</td>";
 820         }
 821     }
 822
 823     $location_html .= "</td></tr></table>";
 824     return $location_html;
 825 }    #get_location
 826
 827 sub print_locus_history {
 828     my $locus = shift;
 829     my @history;
 830     my $history_data;
 831     my $print_history;
 832     my @history_objs = $locus->show_history();   #array of locus_history objects
 833
 834     foreach my $h (@history_objs) {
 835
 836         my $created_date = $h->get_create_date();
 837         $created_date = substr $created_date, 0, 10;
 838
 839         my $history_id    = $h->{locus_history_id};
 840         my $updated_by_id = $h->{updated_by};
 841         my $updated =
 842             CXGN::People::Person->new( $locus->get_dbh(), $updated_by_id );
 843         my $u_first_name = $updated->get_first_name();
 844         my $u_last_name  = $updated->get_last_name();
 845         my $up_person_link =
 846             qq |<a href="/solpeople/personal-info.pl?sp_person_id=$updated_by_id">$u_first_name $u_last_name</a> ($created_date)|;
 847
 848         push @history,
 849         [
 850          map { $_ } (
 851              $h->get_locus_symbol,  $h->get_locus_name,
 852              $h->get_gene_activity, $h->get_description,
 853              $h->get_linkage_group, $h->get_lg_arm,
 854              $up_person_link,
 855          )
 856         ];
 857     }
 858
 859     if (@history) {
 860
 861         $history_data .= columnar_table_html(
 862             headings => [
 863                 'Symbol',     'Name', 'Activity', 'Description',
 864                 'Chromosome', 'Arm',  'Updated by',
 865             ],
 866             data         => \@history,
 867             __alt_freq   => 2,
 868             __alt_width  => 1,
 869             __alt_offset => 3,
 870             );
 871         $print_history = html_optional_show(
 872             'locus_history',
 873             'Show locus history',
 874             qq|<div class="minorbox">$history_data</div> |,
 875             );
 876     }
 877
 878     return $print_history;
 879 }    #print_locus_history
 880
 881 sub get_dbxref_info {
 882     my $locus      = shift;
 883     my $locus_name = $locus->get_locus_name();
 884     my %dbs        = $locus->get_dbxref_lists()
 885         ;    #hash of arrays. keys=dbname values= dbxref objects
 886     my (@alleles) = @_;    #$locus->get_alleles();
 887     #add the allele dbxrefs to the locus dbxrefs hash...
 888     #This way the alleles associated publications and sequences are also printed on the locus page
 889     #it might be a good idea to pring a link to the allele next to each allele-derived annotation
 890
 891     foreach my $a (@alleles) {
 892         my %a_dbs = $a->get_dbxref_lists();
 893
 894         foreach my $a_db_name ( keys %a_dbs )
 895         {    #add allele_dbxrefs to the locus_dbxrefs list
 896             my %seen = ()
 897                 ; #hash for assisting filtering of duplicated dbxrefs (from allele annotation)
 898             foreach ( @{ $dbs{$a_db_name} } ) {
 899                 $seen{ $_->[0]->get_accession() }++;
 900             }    #populate with the locus_dbxrefs
 901             foreach ( @{ $a_dbs{$a_db_name} } ) {    #and filter duplicates
 902                 push @{ $dbs{$a_db_name} }, $_
 903                     unless $seen{ $_->[0]->get_accession() }++;
 904             }
 905         }
 906     }
 907     my ( $tgrc, $pubs, $genbank );
 908     ##tgrc
 909     foreach ( @{ $dbs{'tgrc'} } ) {
 910         if ( $_->[1] eq '0' ) {
 911             my $url       = $_->[0]->get_urlprefix() . $_->[0]->get_url();
 912             my $accession = $_->[0]->get_accession();
 913             $tgrc .=
 914                 qq|$locus_name is a <a href="$url$accession" target="blank">TGRC gene</a><br />|;
 915         }
 916     }
 917
 918     my $abs_count = 0;
 919     foreach ( @{ $dbs{'PMID'} } ) {
 920         if ( $_->[1] eq '0' ) {    #if the pub is not obsolete
 921             $pubs .= get_pub_info( $_->[0], 'PMID', $abs_count++ );
 922         }
 923     }
 924     foreach ( @{ $dbs{'SGN_ref'} } ) {
 925         $pubs .= get_pub_info( $_->[0], 'SGN_ref', $abs_count++ )
 926             if $_->[1] eq '0';
 927     }
 928
 929     my $gb_count = 0;
 930     foreach ( @{ $dbs{'DB:GenBank_GI'} } ) {
 931         if ( $_->[1] eq '0' ) {
 932             $gb_count++;
 933             my $url = $_->[0]->get_urlprefix() . $_->[0]->get_url();
 934             my $gb_accession =
 935                 $locus->CXGN::Chado::Feature::get_feature_name_by_gi(
 936                     $_->[0]->get_accession() );
 937             my $description = $_->[0]->get_description();
 938             $genbank .=
 939                 qq|<a href="$url$gb_accession" target="blank">$gb_accession</a> $description<br />|;
 940         }
 941     }
 942     my @ont_annot;
 943
 944     # foreach ( @{$dbs{'GO'}}) { push @ont_annot, $_; }
 945     # foreach ( @{$dbs{'PO'}}) { push @ont_annot, $_; }
 946     # foreach ( @{$dbs{'SP'}}) { push @ont_annot, $_; }
 947
 948     return ( $tgrc, $pubs, $abs_count, $genbank, $gb_count, \@ont_annot );
 949 }
 950
 951 ########################
 952
 953 sub abstract_view {
 954     my $pub           = shift;
 955     my $abs_count     = shift;
 956     my $abstract      = encode_entities($pub->get_abstract() );
 957     my $authors       = encode_entities($pub->get_authors_as_string() );
 958     my $journal       = $pub->get_series_name();
 959     my $pyear         = $pub->get_pyear();
 960     my $volume        = $pub->get_volume();
 961     my $issue         = $pub->get_issue();
 962     my $pages         = $pub->get_pages();
 963     my $abstract_view = html_optional_show(
 964         "abstracts$abs_count",
 965         'Show/hide abstract',
 966         qq|$abstract <b> <i>$authors.</i> $journal. $pyear. $volume($issue). $pages.</b>|,
 967         0,                           #< do not show by default
 968         'abstract_optional_show',    #< don't use the default button-like style
 969         );
 970     return $abstract_view;
 971 }    #
 972
 973 sub get_pub_info {
 974     my ( $dbxref, $db, $count ) = @_;
 975     my $pub_info;
 976     my $accession = $dbxref->get_accession();
 977     my $pub_title = $dbxref->get_publication()->get_title();
 978     my $year= $dbxref->get_publication()->get_pyear();
 979     my $pub_id    = $dbxref->get_publication()->get_pub_id();
 980     my $abstract_view =
 981         abstract_view( $dbxref->get_publication(), $count );
 982     $pub_info =
 983         qq|<div><a href="/chado/publication.pl?pub_id=$pub_id" >$db:$accession</a> $pub_title ($year). $abstract_view </div> |;
 984     return $pub_info;
 985 }    #
 986
 987 sub print_locus_editor_info {
 988     my $locus=shift;
 989     my $html   = "Locus editors: ";
 990     my @owners = $locus->get_owners();
 991
 992     foreach my $id (@owners) {
 993         my $person = CXGN::People::Person->new( $locus->get_dbh(), $id );
 994
 995         my $first_name = $person->get_first_name();
 996         my $last_name  = $person->get_last_name();
 997         if ($person->get_user_type() eq 'curator' && scalar(@owners) == 1  ) {
 998             $html .= '<b>No editor assigned</b>';
 999         } else {
1000             $html .=
1001                 qq |<a href="/solpeople/personal-info.pl?sp_person_id=$id">$first_name $last_name</a>;|;
1002         }
1003     }
1004     chop $html;
1005     return $html;
1006 }
1007
1008 sub get_individuals_html {
1009     my $locus        = shift;
1010     my $user_type=shift;
1011     my @individuals = $locus->get_individuals();
1012
1013     my $html;
1014     my %imageHoA
1015       ; # hash of image arrays. Keys are individual_ids, values are arrays of image_ids
1016     my %individualHash;
1017     my %imageHash;
1018     my @no_image;
1019     my $more_html;
1020     my $more;    #count the number of accessions in the optional_show box
1021     my $count
1022       ; # a scalar for checking if there are accessions with images in the optional box
1023
1024     if (@individuals) {
1025         $html      .= "<table>";
1026         $more_html .= "<table>";
1027
1028         my %imageHoA
1029           ; # hash of image arrays. Keys are individual ids values are arrays of image ids
1030         foreach my $i (@individuals) {
1031             my $individual_id   = $i->get_individual_id();
1032             my $individual_name = $i->get_name();
1033             $individualHash{$individual_id} = $individual_name;
1034
1035             my @images =
1036               $i->get_images();    #array of all associated image objects
1037             foreach my $image (@images) {
1038                 my $image_id = $image->get_image_id();
1039
1040                 #my $img_src_tag= $image->get_img_src_tag("thumbnail");
1041                 $imageHash{$image_id} = $image;
1042                 push @{ $imageHoA{$individual_id} }, $image_id;
1043             }
1044
1045             #if there are no associated images with this individual:
1046             if ( !@images ) { push @no_image, $individual_id; }
1047         }
1048         my $ind_count = 0;
1049
1050         # Print the whole thing sorted by number of members and name.
1051         for
1052           my $individual_id ( sort { @{ $imageHoA{$b} } <=> @{ $imageHoA{$a} } }
1053             keys %imageHoA )
1054         {
1055             $ind_count++;
1056             my $individual_name = $individualHash{$individual_id};
1057             my $individual_obsolete_link =
1058               get_individual_obsolete_link($locus,$individual_id, $user_type);
1059             my $link =
1060 qq|<a href="individual.pl?individual_id=$individual_id">$individual_name </a>  |;
1061             if ( $ind_count < 4 )
1062             { #print the first 3 individuals by default. The rest will be hidden
1063                 $html .=
1064 qq|<tr valign="top"><td>$link</td> <td> $individual_obsolete_link </td>|;
1065             }
1066             else {
1067                 $count++;
1068                 $more++;
1069                 $more_html .=
1070                   qq|<tr><td>$link </td><td> $individual_obsolete_link</td> |;
1071             }
1072
1073         #print only 5 images, if there are more write the number of total images
1074             my $image_count = ( $#{ $imageHoA{$individual_id} } );    #+1;
1075             if ( $image_count > 4 ) { $image_count = 4; }
1076             for my $i ( 0 .. $image_count ) {
1077                 my $image_id = $imageHoA{$individual_id}[$i];
1078                 #my $image    = $imageHash{$image_id};
1079                 my $image = SGN::Image->new($locus->get_dbh(), $image_id);
1080                 my $small_image  = $image->get_image_url("thumbnail");
1081                 my $medium_image = $image->get_image_url("medium");
1082                 my $image_page   = "/image/index.pl?image_id=$image_id";
1083                 my $thickbox =
1084                     qq|<a href="$medium_image" title="<a href=$image_page>Go to image page </a>" class="thickbox" rel="gallery-images"><img src="$small_image" alt="" /></a> |;
1085                 if ( $ind_count < 4 ) { $html .= qq|<td>$thickbox</td>|; }
1086                 else                  { $more_html .= qq|<td>$thickbox</td>|; }
1087                 $image_count--;
1088             }
1089             if ( $#{ $imageHoA{$individual_id} } > 4 ) {
1090                 my $image_count = ( $#{ $imageHoA{$individual_id} } ) + 1;
1091                 $html .= qq|<td>... (Total $image_count images)</td>|;
1092             }
1093             if   ( $ind_count < 4 ) { $html      .= "</tr>"; }
1094             else                    { $more_html .= "</tr>"; }
1095         }
1096         $html      .= "</table><br />";
1097         $more_html .= "</table><br />";
1098         if ( !$count ) {
1099             my $individual_name;
1100             my $no_image_count = 0;
1101             foreach my $individual_id (@no_image) {
1102                 $no_image_count++;
1103                 my $individual_obsolete_link =
1104                     get_individual_obsolete_link($locus, $individual_id, $user_type);
1105                 if ( $no_image_count < 26 ) {
1106                     $individual_name = $individualHash{$individual_id};
1107                     $html .=
1108                         qq|<a href="individual.pl?individual_id=$individual_id">$individual_name</a>&nbsp$individual_obsolete_link |;
1109                 }
1110                 else {
1111                     $more++;
1112                     $more_html .=
1113                         qq|<a href="individual.pl?individual_id=$individual_id">$individual_name</a>&nbsp$individual_obsolete_link |;
1114                 }
1115             }
1116         }
1117         else {
1118             foreach my $individual_id (@no_image) {
1119                 $more++;
1120                 my $individual_obsolete_link =
1121                     get_individual_obsolete_link($locus, $individual_id, $user_type);
1122                 my $individual_name = $individualHash{$individual_id};
1123                 $more_html .=
1124                     qq|<a href="individual.pl?individual_id=$individual_id">$individual_name</a>&nbsp$individual_obsolete_link |;
1125             }
1126         }
1127     }
1128
1129     if ($more) {
1130         my ( $more_link, $contents ) = collapser(
1131             {
1132                 linktext => "<b> See $more more accessions </b>",
1133
1134                 #hide_state_linktext => $title,
1135                 content   => $more_html,
1136                 collapsed => 1,
1137                 id        => "more_individuals_display"
1138             }
1139             );
1140         $html .= "$more_link\n$contents";
1141     }
1142     return ( $html, scalar(@individuals) );
1143 }    #get_individuals_html
1144
1145 ############################javascript code
1146
1147 sub associate_registry {
1148     my $locus         = shift;
1149     my $locus_id     = $locus->get_locus_id();
1150     my $sp_person_id = shift;
1151
1152     my $associate = qq^
1153
1154         <a href=javascript:Locus.toggleAssociateRegistry()>[Associate a registry name with this locus]</a><br>
1155         <div id='associateRegistryForm' style="display: none">
1156             <div id='registry_search'>
1157                 Registry Name:
1158                 <input type="text"
1159                        style="width: 50%"
1160                        id="registry_input"
1161                        onkeyup="Locus.getRegistries(this.value)">
1162                 <input type="button"
1163                        id="associate_registry_button"
1164                        value="associate registry"
1165                        disabled="true"
1166                        onclick="Locus.associateRegistry('$locus_id','$sp_person_id');this.disabled=false;">
1167
1168                 <select id="registry_select"
1169                         style="width: 100%"
1170                         name="registry_select"
1171                         size=10
1172                         onchange="Locus.updateRegistryInput()">
1173
1174                 </select>
1175
1176                 Click <a href=javascript:Locus.addRegistryView()>here</a> to add a new registry name to our database
1177             </div>
1178
1179             <div id="registry_add" style="display: none">
1180                 <b>Please enter the values for the new registry name below (* is required)</b><br><br>
1181                 <table cellspacing="0" cellpadding="0">
1182                     <tr><td>*Registry Symbol: </td><td width="20">&nbsp;</td>
1183                     <td><input type="text" id="registry_symbol" onblur="Locus.enableButton();" onchange="Locus.enableButton();"></td></tr>
1184                     <tr><td>*Registry Name: </td><td width="20">&nbsp;</td>
1185                     <td><input type="text" id="registry_name" onblur="Locus.enableButton();" onchange="Locus.enableButton();"></td></tr>
1186                 </table>
1187                 Registry Description:<br>
1188                 <textarea id="registry_description" style="width: 100%"></textarea><br>
1189                 <input type="button" disabled="true" id="add_registry_button" value="Add New Registry" onclick="Locus.addRegistry('$locus_id', '$sp_person_id');this.disabled=true;"><br>
1190                 Click <a href=javascript:Locus.searchRegistries()>here</a> to go back to the registry search
1191             </div>
1192         </div>
1193
1194
1195 ^;
1196
1197     return $associate;
1198 }
1199
1200 sub associate_individual {
1201
1202     my $locus         = shift;
1203     my $locus_id     = $locus->get_locus_id();
1204     my $sp_person_id = shift;
1205
1206     my $associate_html = qq^
1207
1208 <div id="associateIndividualForm" style="display: none">
1209     Accession name:
1210     <input type="text"
1211            style="width: 50%"
1212            id="locus_name"
1213            onkeyup="Locus.getIndividuals(this.value, '$locus_id');">
1214     <input type="button"
1215            id="associate_individual_button"
1216            value="associate accession"
1217            disabled="true"
1218            onclick="Locus.associateAllele('$sp_person_id');this.disabled=true;">
1219     <select id="individual_select"
1220             style="width: 100%"
1221             onchange="Locus.getAlleles('$locus_id')"
1222             size=10>
1223        </select>
1224
1225     <b>Would you Like to specify an allele?</b>
1226     <select id="allele_select"
1227             style="width: 100%">
1228     </select>
1229
1230 </div>
1231 ^;
1232
1233     return $associate_html;
1234 }
1235
1236
1237 sub assign_owner {
1238     my $locus        = shift;
1239     my $locus_id    = $locus->get_locus_id();
1240     my $object_type = "locus";
1241
1242     my $assign = qq^
1243         <a href=javascript:Tools.toggleAssignFormDisplay()>[Assign a locus owner]</a> Notice: 'user' account will be updated to 'submitter' <br>
1244         <div id='assignOwnerForm' style="display:none">
1245             <div id='user_search'>
1246                 First name or last name:
1247                 <input type="text"
1248                        style="width: 50%"
1249                        id="user_input"
1250                        onkeyup="Tools.getUsers(this.value)">
1251                 <input type="button"
1252                        id="associate_button"
1253                        value="assign owner"
1254                        disabled="true"
1255                        onclick="Tools.assignOwner('$locus_id', '$object_type');this.disabled=false;">
1256
1257                 <select id="user_select"
1258                         style="width: 100%"
1259                         onchange= "Tools.enableButton('associate_button');"
1260                         size=5>
1261                  </select>
1262
1263            </div>
1264            </div>
1265            <BR>
1266
1267 ^;
1268     return $assign;
1269 }
1270
1271 sub associated_figures {
1272
1273     my $locus         = shift;
1274     my $locus_id     = $locus->get_locus_id();
1275     my $sp_person_id = shift;
1276
1277     my $associate_html = qq^
1278        <span>
1279        <a href="/image/add_image.pl?type_id=$locus_id&type=locus&action=new&refering_page=/phenome/locus_display.pl?locus_id=$locus_id">
1280        [Add notes, figures or images]</a></span>
1281 ^;
1282
1283     return $associate_html;
1284 }
1285
1286
1287 sub get_individual_obsolete_link {
1288     my $locus                    = shift;
1289     my $individual_id            = shift;
1290     my $user_type = shift;
1291     my $individual_obsolete_link = "";
1292     my $individual_allele_id = $locus->get_individual_allele_id($individual_id);
1293     if (   ( $user_type eq 'submitter' )
1294            || ( $user_type eq 'curator' )
1295            || ( $user_type eq 'sequencer' ) )
1296     {
1297         $individual_obsolete_link = qq|
1298             <a href="javascript:Locus.obsoleteIndividualAllele('$individual_allele_id')">[Remove]</a>
1299
1300             <div id='obsoleteIndividualAlleleForm' style="display: none">
1301             <div id='individual_allele_id_hidden'>
1302             <input type="hidden"
1303             value=$individual_allele_id
1304             id="$individual_allele_id">
1305             </div>
1306             </div>
1307             |;
1308
1309     }
1310     return $individual_obsolete_link;
1311 }
1312
1313 sub merge_locus {
1314     my $locus        = shift;
1315     my $locus_id    = $locus->get_locus_id();
1316     my $object_type = "locus";
1317     my $common_name = $locus->get_common_name();
1318     my $merge       = qq^
1319         <a href=javascript:Tools.toggleMergeFormDisplay()>[Merge locus]</a> Warning: Merged locus will be set to obsolete! Unobsoleting is possible only directly via the database! <br>
1320         <div id='mergeLocusForm' style="display:none">
1321
1322         <div id='locus_merge'>
1323              <input type="hidden"
1324              value=$common_name
1325              id ="common_name"
1326              >
1327              locus name
1328                 <input type="text"
1329                        style="width: 50%"
1330                        id="locus_input"
1331                        onkeyup="Locus.getMergeLocus(this.value, $locus_id)">
1332                 <input type="button"
1333                        id="merge_locus_button"
1334                        value="merge locus"
1335                        disabled="true"
1336                        onclick="Locus.mergeLocus('$locus_id');this.disabled=false;">
1337
1338                 <select id="locus_list"
1339                         style="width: 100%"
1340                         onchange= "Locus.enableMergeButton();"
1341                         size=5>
1342                  </select>
1343               </div>
1344            </div>
1345            <BR>
1346
1347 ^;
1348     return $merge;
1349 }
1350
1351 #returns string html listing of locus sequence matches found in ITAG gbrowse DBs
1352 sub genomic_annots_html {
1353
1354     my $locus    = shift;
1355     my $locus_id = $locus->get_locus_id();
1356
1357
1358     # look up any gbrowse cross-refs for this locus id, if any
1359     my @xrefs = map {
1360         $_->xrefs({ -types      => ['match'],
1361                     -attributes => { sgn_locus_id => $locus_id },
1362                  }),
1363     } $c->enabled_feature('gbrowse2');
1364
1365     return '<span class="ghosted">None</span>'
1366         unless @xrefs;
1367
1368
1369     # and now convert each of the matched regions into HTML strings
1370     # that display them
1371     return join "\n", map _render_genomic_xref( $_ ), @xrefs;
1372 }
1373
1374 sub _render_genomic_xref {
1375     my ( $xref ) = @_;
1376
1377     # look up all the matching locus sequence names
1378     my @locus_seqnames =
1379         distinct
1380         map {
1381             my $f = $_;
1382             my $p = parse_identifier(
1383                 $f->target->seq_id,
1384                 'sgn_locus_sequence'
1385                ) or die "cannot parse " . $f->target->seq_id;
1386             $p->{ext_id}
1387         }
1388         @{$xref->seqfeatures};
1389
1390     my $linked_img = CGI->a( { href => $xref->url },
1391                               CGI->img({ #style => "border: 1px solid #ddd; border-top: 0; padding: 1em 0; margin:0",
1392                                          style => 'border: none',
1393                                          src   => $xref->preview_image_url })
1394                             );
1395
1396
1397     my $sequences_matched =
1398         @locus_seqnames > 1 ? 'Sequences matched'
1399                             : 'Sequence matched';
1400
1401     return join('',
1402                  '<div style="border: 1px solid #777; padding-bottom: 10px">',
1403                  info_table_html(
1404                      'Annotation Set'     => $xref->data_source->description,
1405                      'Feature(s) matched' => join( ', ', map $_->display_name || $_->primary_id, @{$xref->seqfeatures} ),
1406                      'Reference Sequence' => $xref->seqfeatures->[0]->seq_id,
1407                      $sequences_matched   => join( ', ', @locus_seqnames ),
1408                      #__tableattrs         => qq|summary="" style="margin: 1em auto -1px auto"|,
1409                      __border             => 0,
1410                      __multicol           => 3,
1411                     ),
1412                  '<hr style="width: 95%" />',
1413                  $linked_img,
1414                  '</div>',
1415                 );
1416 }
1417