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_solgenomics/',
 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                 {
 451                     name => 'Tomato Expression Database (TED)',
 452                     link => '/ted',
 453                     desc => 'The Tomato Expression Database',
 454                 },
 455                 #Systems Biology
 456                 { name => "Systems Biology" },
 457                 {
 458                     name => 'SolCyc Biochemical Pathways',
 459                     link => '/tools/solcyc/',
 460                     desc => 'An interactive map of metabolic pathways.'
 461                 },
 462
 463                 {
 464                     name => 'Coffee Interactomic Data',
 465                     link => '/tools/interactomics',
 466                     desc => 'Coffee Interactome Data with Cytoscape Web Start viewer.'
 467                 },
 468                 {
 469                     name => 'SGN Ontology Browser',
 470                     link => '/tools/onto/',
 471                     desc => 'AJAX ontology browser.'
 472                 },
 473
 474                 { name => "Breeder Tools" },
 475                 {
 476                     name => 'Breeder Home',
 477                     link => '/breeders/home',
 478                     desc => 'Manage a breeding program',
 479                 },
 480                 #Bulk Query
 481                 { name => 'Bulk Query' },
 482
 483                 {
 484                     name => 'FTP Site',
 485                     link => '/tools/bulk?mode=ftp',
 486                     desc =>
 487 '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.'
 488                 },
 489                 {
 490                     name => 'Download Gene Sequences',
 491                     link => '/tools/bulk?mode=genes',
 492                     desc => 'Download nucleotide or protein sequences for a list of genes'
 493                 },
 494                 {
 495                     name => 'Clones, Arrays, Unigenes and BACs',
 496                     link => '/tools/bulk',
 497                     desc =>
 498 'Rather than sifting through SGN page by page, here you can download large quantities of information in a single step.'
 499                 },
 500                 {
 501                     name => 'Unigene Converter',
 502                     link => '/tools/bulk?mode=converter',
 503                     desc => 'get the last version of unigenes and tomato gene ids from a list of unigenes.'
 504                 },
 505 #                 {
 506 #                     name => 'ID Converter (SGN <=> TIGR)',
 507 #                     link => '/tools/convert/input.pl',
 508 #                     desc =>
 509 # '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.'
 510 #                 },
 511
 512                 #Other
 513                 # { name => "Other" },
 514                 # {
 515                 #     name => 'Primer 3',
 516                 #     link => '/primer3/',
 517                 #     desc => 'Pick primers for PCR reactions'
 518                 # },
 519             ]
 520         }
 521     ];
 522 }
 523
 524 =head2 headings
 525
 526     my @headings=$tb->headings();
 527
 528 Returns a list of the names of the main toolbar buttons
 529 ('search','maps','genomes','tools'). These can then be used to
 530 access other parts of this object.
 531
 532 =cut
 533
 534 sub headings {
 535     map { $_->{name} } @{ shift->toolbar_data };
 536 }
 537
 538 =head2 heading_link
 539
 540     print '<a href="'.$_->heading_link($heading).qq|">$_</a>|
 541         for @headings;
 542
 543 Takes a heading (which can be gotten from the headings
 544 function). Returns the stuff that is supposed to go in the href
 545 attribute for this heading.
 546
 547 =cut
 548
 549 sub heading_link {
 550     my $self = shift;
 551     my ($heading) = @_;
 552     for my $heading_hash ( @{ $self->toolbar_data } ) {
 553         if ( $heading_hash->{name} eq $heading ) {
 554             return $heading_hash->{link};
 555         }
 556     }
 557 }
 558
 559 =head2 heading_desc
 560
 561     for my $heading(@headings)
 562     {
 563         print"$heading description: ".$tb->heading_desc($heading);
 564     }
 565
 566 Takes a heading (which can be gotten from the headings function). Returns a description of what the linked-to page is supposed to do.
 567
 568 =cut
 569
 570 sub heading_desc {
 571     my $self = shift;
 572     my ($heading) = @_;
 573     for my $heading_hash ( @{ $self->toolbar_data } ) {
 574         if ( $heading_hash->{name} eq $heading ) {
 575             return $heading_hash->{desc};
 576         }
 577     }
 578 }
 579
 580 =head2 menu_options
 581
 582     for my $heading(@headings)
 583     {
 584         my @menu_options=$tb->menu_options($heading);
 585     }
 586
 587 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.
 588
 589 =cut
 590
 591 sub menu_options {
 592     my $self = shift;
 593     my ($heading) = @_;
 594     for my $heading_hash ( @{ $self->toolbar_data } ) {
 595         if ( $heading_hash->{name} eq $heading ) {
 596
 597 #            the toolbar links don't work if you add tooltips to the toolbar. fix?
 598 #            my @menu_options=map {CXGN::Page::FormattingHelpers::tooltipped_text($_->{name},$_->{desc},'toolbar_help')} @{$heading_hash->{menu}};
 599             my @menu_options = map { $_->{name} } @{ $heading_hash->{menu} };
 600             return @menu_options;
 601         }
 602     }
 603 }
 604
 605 =head2 option_link
 606
 607     for my $heading(@headings)
 608     {
 609         my @menu_options=$tb->menu_options($heading);
 610         for my $option(@menu_options)
 611         {
 612             print"<a href=\"".$tb->option_link($heading,$option)."\">$option</a>";
 613         }
 614     }
 615
 616 Takes a heading and an option. Returns the stuff that goes in the href for that option.
 617
 618 =cut
 619
 620 sub option_link {
 621     my $self = shift;
 622     my ( $heading, $option ) = @_;
 623
 624     #print STDERR "option_link received: heading '$heading' option '$option'\n";
 625     for my $heading_hash ( @{ $self->toolbar_data } ) {
 626         if ( $heading_hash->{name} eq $heading ) {
 627             for my $menu_option_hash ( @{ $heading_hash->{menu} } ) {
 628                 if ( $menu_option_hash->{name} eq $option ) {
 629                     my $option_link = $menu_option_hash->{link};
 630                     if ($option_link) { return $option_link }
 631                 }
 632             }
 633         }
 634     }
 635
 636     #die"Option link not found for heading '$heading' option '$option'";
 637 }
 638
 639 sub option_target {
 640     my $self = shift;
 641     my ( $heading, $option ) = @_;
 642
 643     #print STDERR "option_link received: heading '$heading' option '$option'\n";
 644     for my $heading_hash ( @{ $self->toolbar_data } ) {
 645         if ( $heading_hash->{name} eq $heading ) {
 646             for my $menu_option_hash ( @{ $heading_hash->{menu} } ) {
 647                 if ( $menu_option_hash->{name} eq $option ) {
 648                     my $option_target = $menu_option_hash->{target};
 649                     if ($option_target) { return ' target=$option_target ' }
 650                 }
 651             }
 652         }
 653     }
 654
 655 }
 656
 657 =head2 option_style
 658
 659     for my $heading(@headings)
 660     {
 661         my @menu_options=$tb->menu_options($heading);
 662         for my $option(@menu_options)
 663         {
 664             my $style = $tb->option_style($heading,$option);                            print "<span style='$style'>";
 665                                 #print option item
 666                           print "</span>";
 667         }
 668     }
 669
 670 Takes a heading and an option. Returns the stuff that goes in the href for that option. Override me.
 671
 672
 673 =cut
 674
 675 sub option_style {
 676     my $self = shift;
 677     my ( $heading, $option ) = @_;
 678
 679     #print STDERR "option_link received: heading '$heading' option '$option'\n";
 680     for my $heading_hash ( @{ $self->toolbar_data } ) {
 681         if ( $heading_hash->{name} eq $heading ) {
 682             for my $menu_option_hash ( @{ $heading_hash->{menu} } ) {
 683                 if ( $menu_option_hash->{name} eq $option ) {
 684                     my $option_style = $menu_option_hash->{style};
 685                     if ($option_style) { return $option_style }
 686                 }
 687             }
 688         }
 689     }
 690
 691     #die"Option link not found for heading '$heading' option '$option'";
 692 }
 693
 694 =head2 option_desc
 695
 696     for my $heading(@headings)
 697     {
 698         my @menu_options=$tb->menu_options($heading);
 699         for my $option(@menu_options)
 700         {
 701             print"$option description: ".$tb->option_desc($heading,$option);
 702         }
 703     }
 704
 705 Takes a heading and an option. Returns the stuff that goes in the href for that option.
 706
 707 =cut
 708
 709 sub option_desc {
 710     my $self = shift;
 711     my ( $heading, $option ) = @_;
 712     for my $heading_hash ( @{ $self->toolbar_data } ) {
 713         if ( $heading_hash->{name} eq $heading ) {
 714             for my $menu_option_hash ( @{ $heading_hash->{menu} } ) {
 715                 if ( $menu_option_hash->{name} eq $option ) {
 716                     return $menu_option_hash->{desc};
 717                 }
 718             }
 719         }
 720     }
 721 }
 722
 723 sub as_html {
 724     my $self     = shift;
 725     my @headings = $self->headings();
 726
 727     #decorate the headings array with its menu alignments
 728     @headings = map [ 'center', $_ ], @headings;
 729     if ( @headings > 1 ) {
 730         $headings[0]->[0] = 'left';
 731
 732         #      $headings[-1]->[0] = 'right';
 733     }
 734
 735     my $index        = 0;
 736     my $toolbar_html = <<EOH
 737 <table class="toolbar" summary="" cellspacing="0" cellpadding="0">
 738 <tr class="toolbar_content">
 739   <td class="toolbar_l"><img src="/documents/img/toolbar_l.gif" alt="" /></td>
 740 EOH
 741       . join(
 742         '',
 743         map {
 744             my ( $align, $heading ) = @$_;
 745             my $heading_link = $self->heading_link($heading);
 746             my $popup_menu   = $self->render_menu($heading);
 747             <<EOH
 748   <td class="toolbar_content" onmouseover="CXGN.Page.Toolbar.showmenu('$heading')" onmouseout="CXGN.Page.Toolbar.hidemenu()" style="text-align: $align">
 749     <a class="toolbar_menuname" href="$heading_link">$heading</a>
 750     <div style="position: relative; text-align: left">
 751 $popup_menu
 752     </div>
 753   </td>
 754 EOH
 755           } @headings
 756       )
 757       . <<EOH
 758
 759   <td class="toolbar_search toolbar_content">
 760     <form name="quicksearch" class="quicksearch" action="/search/quick_search.pl">
 761       <input class="quicksearch field" type="text" name="term" size="14" />
 762       <input class="quicksearch imgbutton" type="image" src="/documents/img/sol_search_button.gif" value="sol search" />
 763     </form>
 764   </td>
 765   <td class="toolbar_r" height="1">
 766     <img src="/documents/img/toolbar_r.gif" alt="" />
 767   </td>
 768 </tr>
 769 </table>
 770 <script language="JavaScript" type="text/javascript">
 771 EOH
 772       . join( '', map <<EOH, @headings )
 773   CXGN.Page.Toolbar.addmenu('$_->[1]');
 774 EOH
 775       . <<EOH
 776 </script>
 777 EOH
 778 }
 779
 780 #return HTML for the popup menu for the  menu heading
 781 sub render_menu {
 782     my ( $self, $heading ) = @_;
 783
 784     my @menu_options = $self->menu_options($heading);
 785
 786     return <<EOH
 787     <table cellspacing="0" cellpadding="0" id="$heading" class="toolbar_popmenu">
 788 EOH
 789       . join( '',
 790               map {
 791                   my $menu_option = $_;
 792
 793                   #menu options for each heading, these will be invisible unless hovered over
 794                   my $option_link = $self->option_link( $heading, $menu_option );
 795                   my $option_target = $self->option_target( $heading, $menu_option );
 796                   $option_link &&=
 797                       qq|<a class="toolbar_item" $option_target href="$option_link">$menu_option</a>|;
 798                   $option_link ||= qq|<span class="toolbar_item">$menu_option</span>|;
 799                   my $style = $self->option_style( $heading, $menu_option );
 800                   <<EOH
 801        <tr><td class="toolbar_item">$option_link</td></tr>
 802 EOH
 803               } @menu_options
 804            )
 805       . <<EOH
 806     </table>
 807 EOH
 808 }
 809
 810 sub index_page {
 811     my $self         = shift;
 812     my ($heading)    = @_;
 813     my $content      = '';
 814     my $disp_heading = ucfirst($heading);
 815     for my $option ( $self->menu_options($heading) ) {
 816         my $link = $self->option_link( $heading, $option );
 817         my $desc = $self->option_desc( $heading, $option );
 818         if ($link) {
 819             $content .=
 820 qq|<div style="margin-left:10px"><a href="$link">$option</a> - $desc<br /><br /></div>|;
 821         }
 822         else {
 823             $content .=
 824 "<br /><span style='font-size:1.00em; font-weight:bold'>$option</span> $desc";
 825             $content .= ": $desc" if $desc;
 826             $content .= "<br /><br />";
 827         }
 828     }
 829     return <<END_HEREDOC;
 830 <center>
 831 <table class="boxbgcolor2" width="100%" summary="">
 832 <tr>
 833 <td width="15%">&nbsp;</td>
 834 <td width="70%" class="left">
 835 <div class="boxcontent">
 836 <div class="subheading" style='font-size:1.1em'>
 837 $disp_heading<br />
 838 </div>
 839 <div class="boxsubcontent">
 840 $content
 841 </div>
 842 </div>
 843 </td>
 844 <td width="15%">&nbsp;</td>
 845 </tr>
 846 </table>
 847 </center>
 848 END_HEREDOC
 849 }
 850
 851 1;