lib/SGN/View/Toolbar.pm

   1 package SGN::View::Toolbar;
   2 use Moose;
   3
   4 extends 'Catalyst::View';
   5
   6 has 'toolbar_data' => (
   7     is       => 'rw',
   8     isa      => 'ArrayRef',
   9     required => 1,
  10     default  => \&default_toolbar_data
  11 );
  12
  13 sub default_toolbar_data {
  14     [
  15         {
  16             name => 'search',
  17             link => '/search/direct_search.pl?search=loci',
  18             desc => 'Search our database.',
  19             menu => [
  20
  21                 {
  22                     name => 'Organisms',
  23                     link => '/search/organisms',
  24                     desc => 'search for organisms'
  25                 },
  26                 {
  27                     name => 'Genes',
  28                     link => '/search/locus',
  29                     desc => 'Gene search.'
  30                 },
  31                 {
  32                     name => 'Genome features',
  33                     link => '/search/features',
  34                     desc => 'Search for many types of annotations and sequences.'
  35                 },
  36                 {
  37                     name => 'Phenotypes',
  38                     link => '/search/stocks',
  39                     desc => 'Search for mutants, accessions, and traits.'
  40                 },
  41                 {
  42                     name => 'QTLs',
  43                     link => '/search/phenotypes/qtl',
  44                     desc => 'A web interface for uploading QTL raw data, on-the-fly QTL mapping and search interface for QTLs.'
  45                 },
  46               #   {
  47 #                     name => 'Genomic Selection',
  48 #                     link => '/solgs/search/',
  49 #                     desc => 'A tool for estimating breeding values using rrBlUP.'
  50 #                 },
  51                 {
  52                     name => 'Unigenes',
  53                     link => '/search/transcripts/unigene',
  54                     desc => 'Unigene search.'
  55                 },
  56                 {
  57                     name => "Gene Families",
  58                     link => "/search/family",
  59                     desc => "Unigene family search."
  60                 },
  61                 {
  62                     name => 'Markers',
  63                     link => '/search/markers',
  64                     desc => 'Marker search.'
  65                 },
  66                 {
  67                     name => 'BACs',
  68                     link => '/search/genomic/clones',
  69                     desc => 'BAC (Bacterial Artificial Chromosome) search.'
  70                 },
  71                 {
  72                     name => 'ESTs and libraries',
  73                     link => '/search/transcripts/est',
  74                     desc =>
  75 'Find EST (Expressed Sequence Tag) libraries by keyword, e.g. library name, organism, tissue, development stage, or authors.'
  76                 },
  77                 {
  78                     name => 'Insitu database',
  79                     link => '/insitu/',
  80                     desc =>
  81 'A database of in-situ images which can be updated by users, with image add, delete and annotation editing functions. The current images were generated by the floral genome project (FGP). For more information on the floral genome project, visit http://floralgenome.org/ and http://pgn.cornell.edu/.'
  82                 },
  83                 {
  84                     name => 'Images',
  85                     link => '/search/images',
  86                     desc => 'Search images contained in the SGN database.'
  87                 },
  88                 {
  89                     name => 'Expression',
  90                     link => '/search/expression',
  91                     desc => 'Search images contained in the SGN database.'
  92                 },
  93                 {
  94                     name => 'People',
  95                     link => '/search/people',
  96                     desc => 'Search database of researchers who use SGN.'
  97                 },
  98                 {
  99                     name => 'FAQ',
 100                     link => '/help/faq.pl',
 101                     desc => 'Frequently asked questions from users of SGN.',
 102                 },
 103             ]
 104         },
 105         {
 106             name => 'maps',
 107             link => '/cview/',
 108             desc => 'View and compare chromosomes from various organisms.',
 109             menu => [
 110                 {
 111                     name => 'Tomato-EXPEN 2000',
 112                     link =>
 113 '/cview/map.pl?map_id=9&amp;show_offsets=1&amp;show_ruler=1',
 114                     desc =>
 115 'A combined genetic and physical map, showing the association of BACs (Bacterial Artificial Chromosomes) and BAC-Contigs to this genetic map.',
 116                     style => 'color:#400'
 117                 },
 118                 {
 119                     name => 'Tomato-Kazusa/SolCAP',
 120                     link =>
 121 '/cview/map.pl?map_id=31&amp;show_offsets=1&amp;show_ruler=1',
 122                     desc  => '',
 123                     style => 'color:#400'
 124                 },
 125                 {
 126                     name => 'Tomato QTLs',
 127                     link =>
 128 '/cview/map.pl?map_id=34&amp;show_offsets=1&amp;show_ruler=1',
 129                     desc => '',
 130                     style => 'color:#400'
 131
 132                 },
 133                 {
 134                     name => 'Tomato physical map',
 135                     link =>
 136 '/cview/map.pl?map_id=p9&amp;show_offsets=1&amp;show_ruler=1',
 137                     desc =>
 138 'This map is extracted from the S. lycopersicum LA925 x S. pennellii LA716 type F2.2000 genetic map.',
 139                     style => 'color:#400'
 140
 141                 },
 142                 {
 143                     name => 'Tomato FPC contig map',
 144                     link =>
 145 '/cview/map.pl?map_id=c9&amp;show_offsets=1&amp;show_ruler=1',
 146                     desc =>
 147 'This map shows the positions of the Sanger HindIII/MboI FPC contigs relative to the the S. lycopersicum LA925 x S. pennellii LA716 type F2.2000 genetic map.',
 148                     style => 'color:#400'
 149
 150                 },
 151
 152                 {
 153                     name => 'Tomato IL map',
 154                     link =>
 155 '/cview/map.pl?map_id=il6&amp;show_offsets=1&amp;show_ruler=1',
 156                     desc =>
 157 'This map shows the locations of the introgressed fragments of S. pennellii in the S. lycopersicum genome, tied to the 1992 map.',
 158                     style => 'color:#400'
 159                 },
 160
 161                 {
 162                     name => 'Tomato FISH map',
 163                     link => '/cview/map.pl?map_id=13',
 164                     desc =>
 165                       'Map of FISH (Fluorescent In Situ Hybridization) data.',
 166                     style => 'color:#400'
 167                 },
 168
 169                 {
 170                     name => 'Tomato AGP map',
 171                     link => '/cview/map.pl?map_id=agp',
 172                     desc =>
 173 'The Accessioned Golden Path (AGP) map for the tomato genome.',
 174                     style => 'color:#400'
 175                 },
 176                 {
 177                     name  => 'Pepper COSII map',
 178                     link  => '/cview/map.pl?map_version_id=58',
 179                     desc  => 'COSII map',
 180                     style => 'color:#530'
 181                 },
 182
 183                 {
 184                     name => 'Pepper-AC99',
 185                     link => '/cview/map.pl?map_id=11',
 186                     desc =>
 187 'This map is based on 100 individuals from an inter-specific F2 population of Capsicum. annuum cv. NuMex RNaky and Capsicum chinense var PI159234. 426 molecular markers, including 359 SSR markers 3 specific PCR markers and 68 RFLP markers were used to construct this linkage map, with a total length of 1304.8 cM.',
 188                     style => 'color:#530'
 189                 },
 190                 {
 191                     name => 'Pepper-FA03',
 192                     link => '/cview/map.pl?map_id=10',
 193                     desc =>
 194 'This map is based on 100 individuals from an inter-specific F2 population of Capsicum. annuum cv. NuMex RNaky and Capsicum frutescens BG 2814-6. 728 molecular markers, including 489 SSR markers 195 AFLP, 8 specific PCR markers and 36 RFLP were used to construct this linkage map, with a total length of 1358.7 cM.',
 195                     style => 'color:#530'
 196                 },
 197                 {
 198                     name => 'Potato-TXB 1992',
 199                     link => '/cview/map.pl?map_id=3',
 200                     desc =>
 201 'This is a map based on a S. tuberosum x S. berthaultii BC S. tuberosum population reported in Tanksley et al (1992).',
 202                     style => 'color:#220'
 203                 },
 204                 {
 205                     name  => 'Eggplant COSII map',
 206                     link  => '/cview/map.pl?map_version_id=63',
 207                     desc  => 'COSII map',
 208                     style => 'color:#202'
 209                 },
 210                 {
 211                     name => 'Eggplant-LXM 2002',
 212                     link => '/cview/map.pl?map_id=6',
 213                     desc =>
 214 'This map is based on 58 F2 plants from an interspecific cross between S. linnaeanum (MM195) and S. melongena (MM738) and contains 233 RFLP markers.',
 215                     style => 'color:#202'
 216                 },
 217                 {
 218                     name  => 'Tobacco SSR 2007',
 219                     link  => '/cview/map.pl?map_id=15',
 220                     desc  => 'Nicotiana tabacum',
 221                     style => 'color:#333'
 222                 },
 223                 {
 224                     name => 'Arabidopsis COSII',
 225                     link =>
 226 '/cview/map.pl?map_id=7&amp;show_offsets=1&amp;show_ruler=1',
 227                     desc  => 'Arabidopsis thaliana sequenced-based COSII map.',
 228                     style => 'color:#002800'
 229                 },
 230
 231                 {
 232                     name => 'Comparative viewer...',
 233                     link =>
 234 '/cview/view_chromosome.pl?show_offsets=1&amp;show_ruler=1&amp;show_offsets=1',
 235                     desc =>
 236                       'Compare chromosomes from different maps, side by side.',
 237                     style => 'font-style:italic;'
 238                 },
 239                 {
 240                     name  => 'See all available maps...',
 241                     link  => '/cview/index.pl',
 242                     desc  => 'All chromosome maps that are available on SGN.',
 243                     style => 'font-style:italic'
 244                 }
 245             ]
 246         },
 247         {
 248             name => 'genomes',
 249             link => '/genomes/',
 250             desc => 'Read about sequencing projects.',
 251             menu => [
 252                 {  name => 'Reference genomes' },
 253                 {
 254                     name => 'Tomato',
 255                     link => '/organism/Solanum_lycopersicum/genome',
 256                     desc =>
 257 'The tomato genome has been sequenced by an international consortium.',
 258                 },
 259                {
 260                     name => '<i>Solanum pennellii</i>',
 261                     link => '/organism/Solanum_pennellii/genome',
 262                     desc => 'Wild tomato genome',
 263                 },
 264
 265
 266                 {
 267                     name => 'Potato',
 268                     link => '/organism/Solanum_tuberosum/genome',
 269                     desc => '',
 270                 },
 271                {
 272                     name => 'Pepper',
 273                     link => '/organism/Capsicum_annuum/genome',
 274                     desc => '',
 275                 },
 276                 { name => 'Draft genomes' },
 277                 {
 278                     name => '<i>Solanum pimpinellifolium</i>',
 279                     link => '/organism/Solanum_pimpinellifolium/genome',
 280                     desc => 'Draft genome sequence of tomato\'s closest wild relative.',
 281                 },
 282                 {
 283                     name => '<i>Nicotiana benthamiana</i>',
 284                     link => '/organism/Nicotiana_benthamiana/genome',
 285                     desc => 'Draft sequence for Nicotiana benthamiana, sequenced by labs at the Boyce Thompson Institute',
 286                 },
 287                 {
 288                     name => '<i>Nicotiana tabacum</i> &amp; related',
 289                     link => '/organism/Nicotiana_tabacum/genome',
 290                     desc => 'Draft sequence for Nicotiana tabacum accessions K326, BX, and TN90. Parental genomes <i>Nicotiana sylvestris</i> and <i>Nicotiana tomentosiformis</i>.',
 291                 },
 292
 293                 { name => 'Resequencing projects' },
 294                 {
 295                     name => '<i>Solanum lycopersicum</i> inbreds',
 296                     link => '/organism/Solanum_lycopersicum/inbred_genomes',
 297                     desc => 'Resequencing projects of tomato inbred lines'
 298                 },
 299                  {
 300                     name => '150 Tomato Genome Resequencing Project',
 301                     link => '/organism/Solanum_lycopersicum/tomato_150',
 302                     desc => 'Resequencing project by the University of Wageningen'
 303                 },
 304                 {
 305                     name => 'BGI Tomato 360 genomes',
 306                     link => '/organism/Solanum_lycopersicum/tomato_360',
 307                     desc => 'Resequencing project of 360 tomato varieties by BGI'
 308                 },
 309
 310                 {   name => 'Projects', type => 'title'  },
 311
 312                 {
 313                     name => 'Solanaceae project (SOL)',
 314                     link => '/solanaceae-project/index.pl',
 315                     desc =>
 316 'Over the coming decade the International Solanaceae Genome Project (SOL) will create a coordianted network of knowledge about the Solanaceae family aimed at answering two of the most important questions about life and agriculture: How can a common set of genes/proteins give rise to such a wide range of morphologically and ecologically distinct organisms that occupy our planet? How can a deeper understanding of the genetic basis of diversity be harnessed to better meet the needs of society in an environmentally-friendly way? On this page, you will find more information about the strategy that will be used to answer these questions.'
 317                 },
 318
 319                 {
 320                     name => 'SOL-100 Project',
 321                     link => '/organism/sol100/view',
 322                     desc => 'The SOL community aims to create a common Solanaceae-based genomic framework that includes sequences and phenotypes of 100 genomes encompassing the phylogenetic diversity of the group.',
 323                 },
 324
 325                 {
 326                     name => 'International Tomato Sequencing Project',
 327                     link => '/organism/Solanum_lycopersicum/genome',
 328                     desc =>
 329 'The gene-rich euchromatic portion of the tomato genome is being sequenced by an international consortium. This page gives more information about the progress of the sequencing effort.'
 330                 },
 331                  {
 332                     name => 'U.S. tomato sequencing project',
 333                     link => '/about/us_tomato_sequencing.pl',
 334                     desc => 'An overview of the US Tomato Sequencing Project'
 335                 },
 336                 {
 337                     name => '<i>Nicotiana benthamiana</i> BTI site',
 338                     link => 'http://bti.cornell.edu/research/projects/nicotiana-benthamiana',
 339                     desc => 'BTI project for the Nicotiana benthamiana Draft sequence',
 340                 },
 341
 342             ]
 343         },
 344         {
 345             name => 'tools',
 346             link => '/tools/',
 347             desc => 'Tools for biologists.',
 348             menu => [
 349
 350                 #Sequence Analysis
 351                 { name => 'Sequence Analysis' },
 352                 {
 353                     name => 'BLAST',
 354                     link => '/tools/blast/',
 355                     desc =>
 356 'Compare a given sequence to known sequences using the Basic Local Alignment Search Tool, NCBI BLAST v. 2.2.9 [May-01-2004]'
 357                 },
 358                 {
 359                     name => 'VIGS Tool',
 360                     link => 'http://vigs.solgenomics.net/',
 361                     desc =>
 362 'Determine which genes a probe will silence using VIGS.',
 363                     target => '_blank',
 364
 365                 },
 366
 367                 {
 368                     name => 'Alignment Analyzer',
 369                     link => '/tools/align_viewer/',
 370                     desc =>
 371 'Calculate alignments using Muscle v3.6, or view existing alignments using our navigator.'
 372                 },
 373                 {
 374                     name => 'Tree Browser',
 375                     link => '/tools/tree_browser/',
 376                     desc =>
 377 'Visualize and manipulate phylogenetic trees from a newick-formatted string.'
 378                 },
 379 #                 {
 380 #                     name => 'Intron Finder',
 381 #                     link => '/tools/intron_detection/find_introns.pl',
 382 #                     desc =>
 383 # 'The SGN Intron Finder works by doing a BLAST search for <em>Arabidopsis thaliana</em> proteins that are similar to the translated protein sequence of the DNA input.'
 384 #                 },
 385
 386                 #Mapping
 387                 { name => 'Mapping' },
 388                 {
 389                     name => 'Genome Browser (Jbrowse)',
 390                     link => '/jbrowse/',
 391                     desc => 'browse genomic annotations using the fast Jbrowse browser',
 392                 },
 393
 394                 # {
 395                 #     name => 'Genome Browser (Gbrowse)',
 396                 #     link => '/gbrowse/bin/gbrowse/',
 397                 #     desc => 'browse genomic annotations using GBrowse',
 398                 # },
 399                 # {
 400                 #     name => 'Comparative Genome Browser',
 401                 #     link => 'http://solgenomics.net/gbrowse2/bin/gbrowse_syn/sol2/?search_src=pot;name=ST3.10ch01:1..90000000',
 402                 #     desc => 'Compare genomes using GBrowse_syn',
 403                 # },
 404                 {
 405                     name => 'Comparative Map Viewer',
 406                     link =>
 407 '/cview/view_chromosome.pl?show_offsets=1&amp;show_ruler=1&amp;show_offsets=1',
 408                     desc =>
 409                       'Compare chromosomes from different maps, side by side.',
 410                 },
 411                 {
 412                     name => 'CAPS Designer',
 413                     link => '/tools/caps_designer/caps_input.pl',
 414                     desc =>
 415 'Designs CAPS (Cleaved Amplified Polymorphic Sequence) assays for up to twelve sequences. Two types of nucleotide inputs are accepted: fasta sequences and clustal aligment. It generates a list of polymorphic enzymes that cut the sequences into different length products.'
 416                 },
 417 #                 {
 418 #                     name => 'Seed BAC Finder',
 419 #                     link => '/tools/seedbac/',
 420 #                     desc =>
 421 # 'Lists all anchored BACs for a given chromosome to help identify seed BACs, or suggests a seed BAC given a marker name. '
 422 #                 },
 423                 {
 424                     name => 'solQTL: QTL Mapping',
 425                     link => '/search/phenotypes/qtl',
 426                     desc =>
 427 'A web interface for uploading raw QTL data, on-the-fly QTL mapping, linking predicted QTLs to relevant genetic and genomic data in SGN, and search interface for QTLs.'
 428                 },
 429  #                {
 430 #                     name => 'solGS: Genomic Selection',
 431 #                     link => '/solgs/search',
 432 #                     desc =>
 433 #                         'Builds genomic selection models and predicts genomic estimated breeding values. Prediction is done using Ridge Regression - Best Linear Unbiased Prediction (RR-BLUP).'
 434 #                 },
 435                 #Molecular Biology
 436                 { name => "Molecular Biology" },
 437
 438 #                {
 439 #                    name => 'Signal Peptide Finder',
 440 #                    link => '/tools/sigpep_finder/input.pl',
 441 #                    desc =>
 442 #'This method of searching for signal sequences is designed to complement SignalP, and has similar success rates.'
 443  #               },
 444                 {
 445                     name => 'In Silico PCR',
 446                     link => '/tools/insilicopcr',
 447                     desc => 'In Silico PCR tool based on BLAST'
 448                 },
 449                 {
 450                     name => 'Tomato Expression Atlas (TEA)',
 451                     link =>'http://tea.solgenomics.net/',
 452                     desc => 'The Tomato Expression Atlas',
 453                 },
 454                 {
 455                     name => 'Tomato Expression Database (TED)',
 456                     link => '/ted',
 457                     desc => 'The Tomato Expression Database',
 458                 },
 459                 #Systems Biology
 460                 { name => "Systems Biology" },
 461                 {
 462                     name => 'SolCyc Biochemical Pathways',
 463                     link => '/tools/solcyc/',
 464                     desc => 'An interactive map of metabolic pathways.'
 465                 },
 466
 467                 {
 468                     name => 'Coffee Interactomic Data',
 469                     link => '/tools/interactomics',
 470                     desc => 'Coffee Interactome Data with Cytoscape Web Start viewer.'
 471                 },
 472                 {
 473                     name => 'SGN Ontology Browser',
 474                     link => '/tools/onto/',
 475                     desc => 'AJAX ontology browser.'
 476                 },
 477
 478                 { name => "Breeder Tools" },
 479                 {
 480                     name => 'Breeder Home',
 481                     link => '/breeders/home',
 482                     desc => 'Manage a breeding program',
 483                 },
 484                 #Bulk Query
 485                 { name => 'Bulk Query' },
 486
 487                 {
 488                     name => 'FTP Site',
 489                     link => '/tools/bulk?mode=ftp',
 490                     desc =>
 491 'FTP (File Transfer Protocol) is more efficient than HTTP (HyperText Transfer Protocol) for transferring large files. Many of our larger archive files are accessible here.'
 492                 },
 493                 {
 494                     name => 'Download Gene Sequences',
 495                     link => '/tools/bulk?mode=genes',
 496                     desc => 'Download nucleotide or protein sequences for a list of genes'
 497                 },
 498                 {
 499                     name => 'Clones, Arrays, Unigenes and BACs',
 500                     link => '/tools/bulk',
 501                     desc =>
 502 'Rather than sifting through SGN page by page, here you can download large quantities of information in a single step.'
 503                 },
 504                 {
 505                     name => 'Unigene Converter',
 506                     link => '/tools/bulk?mode=converter',
 507                     desc => 'get the last version of unigenes and tomato gene ids from a list of unigenes.'
 508                 },
 509 #                 {
 510 #                     name => 'ID Converter (SGN <=> TIGR)',
 511 #                     link => '/tools/convert/input.pl',
 512 #                     desc =>
 513 # 'The Institute for Genomic Research and SGN maintain independent unigene databases, entries in which tend to have common member ESTs (Expressed Sequence Tags), although they tend not to correspond completely. This tool uses common members to convert back and forth between the two identifier sets.'
 514 #                 },
 515
 516                 #Other
 517                 # { name => "Other" },
 518                 # {
 519                 #     name => 'Primer 3',
 520                 #     link => '/primer3/',
 521                 #     desc => 'Pick primers for PCR reactions'
 522                 # },
 523             ]
 524         }
 525     ];
 526 }
 527
 528 =head2 headings
 529
 530     my @headings=$tb->headings();
 531
 532 Returns a list of the names of the main toolbar buttons
 533 ('search','maps','genomes','tools'). These can then be used to
 534 access other parts of this object.
 535
 536 =cut
 537
 538 sub headings {
 539     map { $_->{name} } @{ shift->toolbar_data };
 540 }
 541
 542 =head2 heading_link
 543
 544     print '<a href="'.$_->heading_link($heading).qq|">$_</a>|
 545         for @headings;
 546
 547 Takes a heading (which can be gotten from the headings
 548 function). Returns the stuff that is supposed to go in the href
 549 attribute for this heading.
 550
 551 =cut
 552
 553 sub heading_link {
 554     my $self = shift;
 555     my ($heading) = @_;
 556     for my $heading_hash ( @{ $self->toolbar_data } ) {
 557         if ( $heading_hash->{name} eq $heading ) {
 558             return $heading_hash->{link};
 559         }
 560     }
 561 }
 562
 563 =head2 heading_desc
 564
 565     for my $heading(@headings)
 566     {
 567         print"$heading description: ".$tb->heading_desc($heading);
 568     }
 569
 570 Takes a heading (which can be gotten from the headings function). Returns a description of what the linked-to page is supposed to do.
 571
 572 =cut
 573
 574 sub heading_desc {
 575     my $self = shift;
 576     my ($heading) = @_;
 577     for my $heading_hash ( @{ $self->toolbar_data } ) {
 578         if ( $heading_hash->{name} eq $heading ) {
 579             return $heading_hash->{desc};
 580         }
 581     }
 582 }
 583
 584 =head2 menu_options
 585
 586     for my $heading(@headings)
 587     {
 588         my @menu_options=$tb->menu_options($heading);
 589     }
 590
 591 Takes a heading (which can be gotten from the headings function). Returns a list of the names of the options below that heading ('Genes','Unigenes','Markers','BACs','Annotations','ESTs and libraries','People'). Like the list returned by the headings function, these can then be used to access other information from this object.
 592
 593 =cut
 594
 595 sub menu_options {
 596     my $self = shift;
 597     my ($heading) = @_;
 598     for my $heading_hash ( @{ $self->toolbar_data } ) {
 599         if ( $heading_hash->{name} eq $heading ) {
 600
 601 #            the toolbar links don't work if you add tooltips to the toolbar. fix?
 602 #            my @menu_options=map {CXGN::Page::FormattingHelpers::tooltipped_text($_->{name},$_->{desc},'toolbar_help')} @{$heading_hash->{menu}};
 603             my @menu_options = map { $_->{name} } @{ $heading_hash->{menu} };
 604             return @menu_options;
 605         }
 606     }
 607 }
 608
 609 =head2 option_link
 610
 611     for my $heading(@headings)
 612     {
 613         my @menu_options=$tb->menu_options($heading);
 614         for my $option(@menu_options)
 615         {
 616             print"<a href=\"".$tb->option_link($heading,$option)."\">$option</a>";
 617         }
 618     }
 619
 620 Takes a heading and an option. Returns the stuff that goes in the href for that option.
 621
 622 =cut
 623
 624 sub option_link {
 625     my $self = shift;
 626     my ( $heading, $option ) = @_;
 627
 628     #print STDERR "option_link received: heading '$heading' option '$option'\n";
 629     for my $heading_hash ( @{ $self->toolbar_data } ) {
 630         if ( $heading_hash->{name} eq $heading ) {
 631             for my $menu_option_hash ( @{ $heading_hash->{menu} } ) {
 632                 if ( $menu_option_hash->{name} eq $option ) {
 633                     my $option_link = $menu_option_hash->{link};
 634                     if ($option_link) { return $option_link }
 635                 }
 636             }
 637         }
 638     }
 639
 640     #die"Option link not found for heading '$heading' option '$option'";
 641 }
 642
 643 sub option_target {
 644     my $self = shift;
 645     my ( $heading, $option ) = @_;
 646
 647     #print STDERR "option_link received: heading '$heading' option '$option'\n";
 648     for my $heading_hash ( @{ $self->toolbar_data } ) {
 649         if ( $heading_hash->{name} eq $heading ) {
 650             for my $menu_option_hash ( @{ $heading_hash->{menu} } ) {
 651                 if ( $menu_option_hash->{name} eq $option ) {
 652                     my $option_target = $menu_option_hash->{target};
 653                     if ($option_target) { return ' target=$option_target ' }
 654                 }
 655             }
 656         }
 657     }
 658
 659 }
 660
 661 =head2 option_style
 662
 663     for my $heading(@headings)
 664     {
 665         my @menu_options=$tb->menu_options($heading);
 666         for my $option(@menu_options)
 667         {
 668             my $style = $tb->option_style($heading,$option);                            print "<span style='$style'>";
 669                                 #print option item
 670                           print "</span>";
 671         }
 672     }
 673
 674 Takes a heading and an option. Returns the stuff that goes in the href for that option. Override me.
 675
 676
 677 =cut
 678
 679 sub option_style {
 680     my $self = shift;
 681     my ( $heading, $option ) = @_;
 682
 683     #print STDERR "option_link received: heading '$heading' option '$option'\n";
 684     for my $heading_hash ( @{ $self->toolbar_data } ) {
 685         if ( $heading_hash->{name} eq $heading ) {
 686             for my $menu_option_hash ( @{ $heading_hash->{menu} } ) {
 687                 if ( $menu_option_hash->{name} eq $option ) {
 688                     my $option_style = $menu_option_hash->{style};
 689                     if ($option_style) { return $option_style }
 690                 }
 691             }
 692         }
 693     }
 694
 695     #die"Option link not found for heading '$heading' option '$option'";
 696 }
 697
 698 =head2 option_desc
 699
 700     for my $heading(@headings)
 701     {
 702         my @menu_options=$tb->menu_options($heading);
 703         for my $option(@menu_options)
 704         {
 705             print"$option description: ".$tb->option_desc($heading,$option);
 706         }
 707     }
 708
 709 Takes a heading and an option. Returns the stuff that goes in the href for that option.
 710
 711 =cut
 712
 713 sub option_desc {
 714     my $self = shift;
 715     my ( $heading, $option ) = @_;
 716     for my $heading_hash ( @{ $self->toolbar_data } ) {
 717         if ( $heading_hash->{name} eq $heading ) {
 718             for my $menu_option_hash ( @{ $heading_hash->{menu} } ) {
 719                 if ( $menu_option_hash->{name} eq $option ) {
 720                     return $menu_option_hash->{desc};
 721                 }
 722             }
 723         }
 724     }
 725 }
 726
 727 sub as_html {
 728     my $self     = shift;
 729     my @headings = $self->headings();
 730
 731     #decorate the headings array with its menu alignments
 732     @headings = map [ 'center', $_ ], @headings;
 733     if ( @headings > 1 ) {
 734         $headings[0]->[0] = 'left';
 735
 736         #      $headings[-1]->[0] = 'right';
 737     }
 738
 739     my $index        = 0;
 740     my $toolbar_html = <<EOH
 741 <table class="toolbar" summary="" cellspacing="0" cellpadding="0">
 742 <tr class="toolbar_content">
 743   <td class="toolbar_l"><img src="/documents/img/toolbar_l.gif" alt="" /></td>
 744 EOH
 745       . join(
 746         '',
 747         map {
 748             my ( $align, $heading ) = @$_;
 749             my $heading_link = $self->heading_link($heading);
 750             my $popup_menu   = $self->render_menu($heading);
 751             <<EOH
 752   <td class="toolbar_content" onmouseover="CXGN.Page.Toolbar.showmenu('$heading')" onmouseout="CXGN.Page.Toolbar.hidemenu()" style="text-align: $align">
 753     <a class="toolbar_menuname" href="$heading_link">$heading</a>
 754     <div style="position: relative; text-align: left">
 755 $popup_menu
 756     </div>
 757   </td>
 758 EOH
 759           } @headings
 760       )
 761       . <<EOH
 762
 763   <td class="toolbar_search toolbar_content">
 764     <form name="quicksearch" class="quicksearch" action="/search/quick_search.pl">
 765       <input class="quicksearch field" type="text" name="term" size="14" />
 766       <input class="quicksearch imgbutton" type="image" src="/documents/img/sol_search_button.gif" value="sol search" />
 767     </form>
 768   </td>
 769   <td class="toolbar_r" height="1">
 770     <img src="/documents/img/toolbar_r.gif" alt="" />
 771   </td>
 772 </tr>
 773 </table>
 774 <script language="JavaScript" type="text/javascript">
 775 EOH
 776       . join( '', map <<EOH, @headings )
 777   CXGN.Page.Toolbar.addmenu('$_->[1]');
 778 EOH
 779       . <<EOH
 780 </script>
 781 EOH
 782 }
 783
 784 #return HTML for the popup menu for the  menu heading
 785 sub render_menu {
 786     my ( $self, $heading ) = @_;
 787
 788     my @menu_options = $self->menu_options($heading);
 789
 790     return <<EOH
 791     <table cellspacing="0" cellpadding="0" id="$heading" class="toolbar_popmenu">
 792 EOH
 793       . join( '',
 794               map {
 795                   my $menu_option = $_;
 796
 797                   #menu options for each heading, these will be invisible unless hovered over
 798                   my $option_link = $self->option_link( $heading, $menu_option );
 799                   my $option_target = $self->option_target( $heading, $menu_option );
 800                   $option_link &&=
 801                       qq|<a class="toolbar_item" $option_target href="$option_link">$menu_option</a>|;
 802                   $option_link ||= qq|<span class="toolbar_item">$menu_option</span>|;
 803                   my $style = $self->option_style( $heading, $menu_option );
 804                   <<EOH
 805        <tr><td class="toolbar_item">$option_link</td></tr>
 806 EOH
 807               } @menu_options
 808            )
 809       . <<EOH
 810     </table>
 811 EOH
 812 }
 813
 814 sub index_page {
 815     my $self         = shift;
 816     my ($heading)    = @_;
 817     my $content      = '';
 818     my $disp_heading = ucfirst($heading);
 819     for my $option ( $self->menu_options($heading) ) {
 820         my $link = $self->option_link( $heading, $option );
 821         my $desc = $self->option_desc( $heading, $option );
 822         if ($link) {
 823             $content .=
 824 qq|<div style="margin-left:10px"><a href="$link">$option</a> - $desc<br /><br /></div>|;
 825         }
 826         else {
 827             $content .=
 828 "<br /><span style='font-size:1.00em; font-weight:bold'>$option</span> $desc";
 829             $content .= ": $desc" if $desc;
 830             $content .= "<br /><br />";
 831         }
 832     }
 833     return <<END_HEREDOC;
 834 <center>
 835 <table class="boxbgcolor2" width="100%" summary="">
 836 <tr>
 837 <td width="15%">&nbsp;</td>
 838 <td width="70%" class="left">
 839 <div class="boxcontent">
 840 <div class="subheading" style='font-size:1.1em'>
 841 $disp_heading<br />
 842 </div>
 843 <div class="boxsubcontent">
 844 $content
 845 </div>
 846 </div>
 847 </td>
 848 <td width="15%">&nbsp;</td>
 849 </tr>
 850 </table>
 851 </center>
 852 END_HEREDOC
 853 }
 854
 855 1;