lib/CXGN/Cview/ChromosomeViewer.pm

   1 package CXGN::Cview::ChromosomeViewer;
   2 use strict;
   3 use warnings;
   4
   5 use File::Spec;
   6
   7 use CXGN::DB::Connection;
   8 use CXGN::Tools::WebImageCache;
   9 use CXGN::Cview::Map::Tools;
  10 use CXGN::Cview;
  11 use CXGN::Cview::Utils qw|set_marker_color get_maps_select get_chromosome_links|;
  12 use CXGN::Cview::MapImage;
  13 use CXGN::Cview::Chromosome;
  14 use CXGN::Cview::Chromosome::Physical;
  15 use CXGN::Cview::Chromosome::PachyteneIdiogram;
  16 use CXGN::Cview::IL;
  17 use CXGN::Cview::ChrLink;
  18 use CXGN::Cview::MapFactory;
  19
  20 use base qw| CXGN::DB::Object |;
  21
  22 =head1 NAME
  23
  24 CXGN::Cview::ChromosomeViewer -- a module to display comparative chromosome maps
  25
  26 =head1 SYNOPSIS
  27
  28  my $viewer = CXGN::Cview::ChromosomeViewer->new;
  29  $viewer->set_map_id($map_id);
  30  $viewer->set_map_version_id($map_version_id);
  31  $viewer->set_ref_chr($chr_nr);
  32  $viewer->set_cM($cM);
  33  $viewer->set_zoom($zoom);
  34  $viewer->set_show_physical($show_physical);
  35  $viewer->set_show_ruler($show_ruler);
  36  $viewer->set_show_IL($show_IL);
  37  $viewer->set_comp_map_id($comp_map_id);
  38  $viewer->set_comp_map_version_id($comp_map_version_id);
  39  $viewer->set_comp_chr($comp_chr);
  40  $viewer->set_color_model($color_model);
  41  if ($map_chr_select) {
  42      my ($comp_map_id, $comp_chr) = split / /, $map_chr_select;
  43      $viewer->set_comp_map_id($comp_map_id);
  44      $viewer->set_comp_chr($comp_chr);
  45  }
  46  $viewer->set_cM_start($cM_start);
  47  $viewer->set_cM_end($cM_end);
  48  $viewer->set_confidence($confidence);
  49  $viewer->set_show_zoomed($show_zoomed);
  50  $viewer->set_hilite_zoomed($zoomed_hilite_start, $zoomed_hilite_end);
  51  $viewer->set_force($force);
  52
  53  $viewer->generate_page();
  54
  55 =head1 DESCRIPTION
  56
  57 =head2 Image Caching
  58
  59 ChromosomeViewer caches the images it produces using CXGN::Tools::WebImageCache. The expiration time is set to a day or so.
  60
  61 The cache for the image generated by any given URL can be reset by setting the force parameter to 1.
  62
  63
  64 =head1 AUTHOR(S)
  65
  66 Lukas Mueller (lam87@cornell.edu)
  67
  68 =head1 FUNCTIONS
  69
  70 The following functions are defined in the class:
  71
  72 =cut
  73
  74 =head2 function new()
  75
  76   Synopsis:     generates a new chromosome_viewer object
  77   Parameters:   $dbh - a database handle
  78   Returns:      an object handle
  79   Side effects: sets some useful default values, creates an SGN page object and
  80                 establishes a connection to the database through the page object.
  81   Status:       implemented
  82   Example:
  83
  84 =cut
  85
  86 sub new {
  87     my $class = shift;
  88     my $dbh   = shift;
  89
  90     if ( !$dbh ) { die "ChromosomeViewer now takes a dbh parameter."; }
  91     my $self = $class->SUPER::new( $dbh, @_ );
  92
  93     $self->{unzoomedheight} = 20;    # how many cM are seen at zoom level 1
  94
  95   #    $self -> {raster_size} = 5;    # the default raster size for genetic maps
  96   # for sequence-based maps this will be changed to 1
  97   # later on.
  98     $self->set_temp_dir("/tmp")
  99       ;    # set some default for the temp_dir. However, this
 100            # should be visible by apache (which tmp isn't).
 101     return $self;
 102 }
 103
 104 =head2 function _adjust_parameters()
 105
 106   Synopsis:     adjusts parameters; needs to be called before calling generate_image
 107   Parameters:   none
 108   Returns:      nothing
 109   Side effects: adjusts parameters to make program more robust against out-of-range
 110                 parameters
 111   Status:       implemented
 112   Example:
 113   Notes:        this function is only used internally
 114
 115 =cut
 116
 117 sub _adjust_parameters {
 118     my $self = shift;
 119
 120     # initialize some variables to prevent undefined blabla errors
 121     $self->{fatal_errors} = "";
 122     if ( !$self->get_ref_chr() )      { $self->set_ref_chr(1); }
 123     if ( !$self->get_hilite() )       { $self->set_hilite(""); }
 124     if ( !( $self->get_cM_start() ) ) { $self->set_cM_start(0); }
 125
 126     #    print STDERR "\n *** Map ID is : ".($self->get_map_id())." ***\n";
 127
 128 # It's possible for our objects to have empty strings for map_id attributes.
 129 # The following weirdness preserves the interface invariant that get_map_id sets
 130 # a desirable default map_id.
 131
 132     my $map_id = $self->get_map_id();
 133
 134     if ( $self->get_map_version_id() ) {
 135         $self->set_map_id(0);
 136     }
 137
 138     if ( $self->get_comp_map_version_id() ) {
 139         $self->set_comp_map_id(0);
 140     }
 141
 142     if ( !$self->get_map_version_id() && $map_id eq '' ) {
 143         $self->set_map_id(undef);
 144         $map_id = $self->get_map_id();
 145     }
 146
 147     # generate the map objects
 148     #
 149     my $map_factory =
 150       CXGN::Cview::MapFactory->new( $self->get_dbh(), { cview_db_backend=>$self->get_db_backend() });
 151
 152 #    print STDERR "Generating MapFactory with id ".$self->get_map_version_id()."\n";
 153 #    print STDERR "IS A ".ref($map_factory)."\n";
 154
 155     $self->set_ref_map(
 156         $map_factory->create(
 157             {
 158                 map_version_id => $self->get_map_version_id(),
 159                 map_id         => $self->get_map_id()
 160             }
 161         )
 162     );
 163
 164     if ( !$self->get_ref_map() ) {
 165
 166         # if an illegal map id was supplied, create a default map.
 167         $self->set_ref_map(
 168             $map_factory->create(
 169                 { map_id => CXGN::Cview::Map::Tools::current_tomato_map_id() }
 170             )
 171         );
 172         $self->append_error("Note: Displaying default map, F2-2000.");
 173     }
 174
 175     $self->{ref_map_name} = $self->get_ref_map()->get_short_name();
 176     $self->set_map_version_id( $self->get_ref_map()->get_id() );
 177     $self->{ref_map_type} = $self->get_ref_map()->get_type();
 178
 179     if ( $self->get_comp_map_id() || $self->get_comp_map_version_id() ) {
 180         $self->set_comp_map(
 181             $map_factory->create(
 182                 {
 183                     map_version_id => $self->get_comp_map_version_id(),
 184                     map_id         => $self->get_comp_map_id()
 185                 }
 186             )
 187         );
 188
 189         #   { map_id => $self->get_comp_map_id(),
 190         #        map_version_id => $self->get_comp_map_version_id(),
 191         #    }
 192         #     ));
 193     }
 194
 195     # define the comparison map
 196     #
 197     if ( $self->get_comp_map() ) {
 198         $self->{comp_map_name} = $self->get_comp_map()->get_short_name();
 199         $self->set_comp_map_version_id( $self->get_comp_map()->get_id() );
 200         $self->{comp_map_type} = $self->get_comp_map()->get_type();
 201
 202 #    @{$self->{comp_chromo_names}} = $self->get_chr_names($self->get_comp_map_id());
 203         @{ $self->{comp_chromo_names} } =
 204           $self->get_comp_map()->get_chromosome_names();
 205
 206         #$self->{comp_max_chr} = $self->get_chr_count($self->get_comp_map_id());
 207         $self->{comp_max_chr} = scalar( @{ $self->{comp_chromo_names} } );
 208     }
 209
 210     # test if the supplied chromosome is a legal chromosome on the specific map.
 211     # if not, try to find a close match.
 212     #
 213     #if (!$self->is_ok_chr($self->get_map_id(), $self->get_ref_chr())) {
 214     if ( !$self->get_ref_map()->has_linkage_group( $self->get_ref_chr() ) ) {
 215
 216       # print STDERR "chr ".$self->get_ref_chr()." is not a valid chromosome\n";
 217         my $old_chr = $self->get_ref_chr();
 218         my $chr     = $old_chr;
 219         $chr =~ s/.*(\d{1,2}.*)/$1/;
 220
 221         #if (!$self->is_ok_chr($self->get_map_id(), $chr)) {
 222         if ( !$self->get_ref_map()->has_linkage_group($chr) ) {
 223             $chr =~ s/.*(\d).*/$1/;
 224         }
 225         if ( !$self->get_ref_map()->has_linkage_group($chr) ) {
 226
 227 #$self->append_errors("The specified chromosome ($old_chr) was not found on map $self->{ref_map_name}!<br /><br />");
 228             $self->set_ref_chr(1);
 229         }
 230         else {
 231             $self->set_ref_chr($chr);
 232             $self->append_error(
 233 "The chromosome/linkage group $old_chr does not seem to exist on map "
 234                   . $self->get_ref_map()->get_short_name()
 235                   . ". The closest we could find was $chr, displayed below.<br /><br />"
 236             );
 237         }
 238     }
 239
 240     # if no map_id was supplied, we show the F2.2000 as default
 241     #
 242     if ( !$self->get_map_id() ) {
 243         $self->set_map_id( CXGN::Cview::Map::Tools::current_tomato_map_id() );
 244     }
 245
 246     #    @{$self->{chromo_names}} = $self->get_chr_names($self->{map_id});
 247     @{ $self->{chromo_names} } = $self->get_ref_map()->get_chromosome_names();
 248
 249     #$self->{max_chr} = $self->get_chr_count($self->get_map_id());;
 250     # get the number of chromosomes of the map.
 251     #
 252     $self->{max_chr} = scalar( $self->get_ref_map()->get_chromosome_count() );
 253
 254     if ( $self->get_ref_chr() < 0 ) {
 255         $self->set_ref_chr( abs( $self->get_ref_chr() ) );
 256     }
 257
 258     # set the default zoom size in MB for sequence maps
 259     #
 260     $self->{unzoomedheight} = $self->get_ref_map()->initial_zoom_height();
 261
 262     #   $self->{unzoomedheight}=4;
 263     #     }
 264
 265 #
 266 # adjust cM_start and cM_end if the chromosome was clicked.
 267 #
 268 #    if ((($self->get_cM_start()==0) && ($self->get_cM_end()==0)) || ($self->get_cM_end()-$self->get_cM_start()==0)) {
 269
 270     $self->set_ref_chr_len(
 271         $self->get_ref_map()->get_chr_len_by_name( $self->get_ref_chr() ) );
 272     if ( $self->get_cM_start() > $self->get_cM_end() ) {
 273         $self->set_cM_start( $self->get_cM_end() );
 274         $self->set_cM_end( $self->get_cM_start() +
 275               $self->get_ref_map()->initial_zoom_height() );
 276     }
 277
 278     $self->{zoom_length} = $self->get_cM_end() - $self->get_cM_start();
 279
 280     if ( $self->{zoom_length} == 0 ) {
 281         $self->{zoom_length} = $self->get_ref_map()->initial_zoom_height();
 282     }
 283
 284     if ( $self->get_clicked() ) {
 285
 286 #die "Was going to reset cM_start and cM_end (cM defined... ".($self->get_cM()).")\n";
 287         my $start = $self->get_cM() - ( $self->{zoom_length} / 2 );
 288         my $end   = $self->get_cM() + ( $self->{zoom_length} / 2 );
 289
 290         if ( $start < 0 ) {
 291             $start = 0;
 292             $end   = $self->{zoom_length};
 293         }
 294
 295         #       print STDERR "REF CHR: ".$self->get_ref_chr()."\n";
 296
 297         if ( $end > $self->get_ref_chr_len() ) {
 298             $end   = $self->get_ref_chr_len();
 299             $start = $end - $self->{zoom_length};
 300         }
 301
 302         $self->set_cM_start($start);
 303         $self->set_cM_end($end);
 304
 305     }
 306
 307     #    $self->set_clicked(0);
 308
 309 # adjust the cM start value if it is below zero. This could (but shouldn't) happen
 310 # during scrolling and zooming operations.
 311 #
 312     if ( $self->get_cM_start() < 0 ) {
 313         $self->set_cM_start(0);
 314         $self->set_cM_end( $self->{zoom_length} );
 315         $self->set_cM( ( $self->get_cM_start() + $self->get_cM_end() ) / 2 );
 316     }
 317     if ( $self->get_cM_end() > $self->get_ref_chr_len() ) {
 318         my $end = $self->get_ref_chr_len();
 319         $self->set_cM_end($end);
 320         $self->set_cM_start( $end - $self->{zoom_length} );
 321     }
 322
 323     if ( !$self->{ref_map_name} ) {
 324         $self->{fatal_errors} .=
 325           "Fatal error: The map id you entered is invalid.<br />";
 326     }
 327
 328     if ( $self->get_show_physical()
 329         && ( !$self->get_ref_map()->has_physical() ) )
 330     {
 331         $self->append_error(
 332 "Note: You selected to show physical maps for a map that does not have an associated physical map. The physical map has been turned off.<p /> "
 333         );
 334         $self->set_show_physical(0);
 335     }
 336
 337     my $message = "";
 338     if ( $self->get_confidence() == 0 ) {
 339         $message = "I(LOD<2) and above [all]";
 340     }
 341     elsif ( $self->get_confidence() == 1 ) { $message = "I(LOD2) and above"; }
 342     elsif ( $self->get_confidence() == 2 ) { $message = "CF(LOD3) and above"; }
 343     elsif ( $self->get_confidence() == 3 ) { $message = "F(LOD>=3)"; }
 344     if    ( $self->get_confidence() > -2 ) {
 345         $self->append_error("Only showing confidence of $message\n<p />");
 346     }
 347
 348     # note: the force parameter is not part of the state hashref, because it
 349     # would change the key and thus the cache file name.
 350     #
 351     my $state_hashref = {
 352         chr_nr              => $self->get_ref_chr(),
 353         map_version_id      => $self->get_map_version_id(),
 354         cM                  => $self->{cM},
 355         show_ruler          => $self->{show_ruler},
 356         show_IL             => $self->{show_IL},
 357         show_offsets        => $self->get_show_offsets(),
 358         comp_map_version_id => $self->get_comp_map_version_id(),
 359         comp_chr            => $self->{comp_chr},
 360         color_model         => $self->{color_model},
 361         show_physical       => $self->{show_physical},
 362         size                => $self->{size},
 363         show_zoomed         => $self->{show_zoomed},
 364         confidence          => $self->{confidence},
 365         hilite              => $self->{hilite},
 366         marker_type         => $self->{display_marker_type},
 367         cM_start            => $self->get_cM_start(),
 368         cM_end              => $self->get_cM_end(),
 369
 370         #clicked => $self->get_clicked(),
 371
 372     };
 373
 374     #    print STDERR "STATE HASHREF CONTENTS: \n";
 375     #    foreach my $k (%$state_hashref) {
 376 ##      print STDERR "$k = $$state_hashref{$k}.\n";
 377     #    }
 378     $self->set_state_hashref($state_hashref);
 379
 380 }
 381
 382 =head2 function generate_page()
 383
 384   Synopsis:     generates the  page to STDOUT in html
 385   Parameters:   none
 386   Returns:      nothing
 387   Side effects:
 388   Status:       implemented
 389   Example:
 390
 391 =cut
 392
 393 sub generate_page {
 394     my $self = shift;
 395     if ( $self->{fatal_errors} ) { return; }
 396
 397     $self->_adjust_parameters();
 398
 399     $self->get_image();
 400     $self->display_toolbar();
 401
 402 }
 403
 404 =head2 function get_image()
 405
 406   Synopsis:     generates the viewer image as a png file
 407   Parameters:   none
 408   Returns:      an array with the image path (semi-absolute) and the image url
 409   Side effects: creates the image and stores it into a file
 410   Status:       implemented
 411   Example:
 412
 413 =cut
 414
 415 sub get_image {
 416     my $self = shift;
 417
 418     my $cache         = CXGN::Tools::WebImageCache->new();
 419     my $state_hashref = $self->get_state_hashref();
 420
 421     my @sorted_values = map {
 422         if ( exists( $state_hashref->{$_} ) && defined( $state_hashref->{$_} ) )
 423         {
 424             $state_hashref->{$_};
 425         }
 426     } sort keys %$state_hashref;
 427     my $key = join "-", @sorted_values;
 428
 429     #    print STDERR "USING KEY: $key\n";
 430     $cache->set_key($key);
 431     $cache->set_expiration_time(86400);
 432     $cache->set_basedir( $self->get_basedir() );
 433
 434     $cache->set_temp_dir( $self->get_temp_dir() );
 435
 436     $cache->set_map_name("imagemap");
 437     $cache->set_force( $self->get_force() );
 438
 439     if ( !$cache->is_valid() ) {
 440         $self->generate_image();
 441         $cache->set_image_data( $self->{map}->render_png_string() );
 442         $cache->set_image_map_data( $self->{map}->get_image_map("imagemap") );
 443     }
 444     $self->{image_html} = $cache->get_image_html();
 445 }
 446
 447 sub generate_image {
 448     my $self = shift;
 449
 450     my $x_distance =
 451       120;    # the number of pixels the different elements are spaced
 452     my $element_count = 0.5;    # the number of elements currently placed
 453
 454     my $map_width = 500;
 455
 456     if ( $self->get_show_zoomed() ) {
 457         $map_width += $x_distance;
 458     }
 459     if ( $self->get_show_IL() ) { $map_width += $x_distance; }
 460
 461     #print STDERR "Size requested: $self->{size}\n";
 462     if ( $self->get_size() =~ /small/i ) {
 463         $self->{map_height} = 300;
 464         $self->set_chr_height(230);
 465     }
 466     elsif ( $self->get_size() =~ /large/i ) {
 467         $self->{map_height} = 800;
 468         $self->set_chr_height(650);
 469     }
 470     else {
 471         $self->{map_height} = 470;
 472         $self->set_chr_height(400);
 473     }
 474
 475     #print STDERR "Chr height: $self->{chr_height}\n";
 476     $self->{map} =
 477       CXGN::Cview::MapImage->new( "", $map_width, $self->{map_height} );
 478
 479     # show IL lines if requested
 480     #
 481     if ( $self->get_show_IL() && $self->get_ref_map()->has_IL() ) {
 482         my $map_factory =
 483           CXGN::Cview::MapFactory->new( $self->get_dbh(),
 484             { cview_db_backend => $self->get_db_backend()} );
 485
 486         #print STDERR "Current map_id = ".$self->get_map_id()."\n";
 487         my $IL_map = $map_factory->create(
 488             { map_version_id => "il6." . ( $self->get_map_id() ) } );
 489         $self->{IL} = $IL_map->get_chromosome( $self->get_ref_chr() );
 490
 491         $self->{IL}->set_height( $self->get_chr_height() );
 492         $self->{IL}->set_horizontal_offset( $x_distance * $element_count, 40 );
 493         $self->{IL}->set_vertical_offset(40);
 494         $self->{IL}->set_caption("IL");
 495
 496         $self->{map}->add_chromosome( $self->{IL} );
 497         $element_count = $element_count + 0.95;
 498     }
 499
 500     elsif ( $self->get_show_IL() && !$self->get_ref_map()->has_IL() ) {
 501         $self->append_error(
 502 "You chose to display the IL information for a map that has no associated IL information.
 503                            The IL display has been turned off.<P>"
 504         );
 505         $self->set_show_IL(0);
 506     }
 507
 508     # show the physical map if requested
 509     #
 510     if ( $self->get_show_physical() ) {
 511         my $map_factory =
 512           CXGN::Cview::MapFactory->new( $self->get_dbh(),
 513             { cview_db_backend => $self->get_db_backend()} );
 514
 515         my $physical_map = $map_factory->create( { map_version_id => "p9" } );
 516
 517  # we get the overview chromosome, because it is more compact for the comparison
 518  #
 519         $self->{p} =
 520           $physical_map->get_overview_chromosome( $self->get_ref_chr() );
 521         $self->{p}->set_horizontal_offset( $x_distance * $element_count );
 522         $self->{p}->set_vertical_offset(40);
 523         $self->{p}->set_height( $self->get_chr_height() );
 524
 525         $self->{map}->add_physical( $self->{p} );
 526     }
 527
 528     # add the chromosome
 529     #
 530     $element_count++;
 531
 532     $self->{c1} = $self->get_ref_map()->get_chromosome( $self->get_ref_chr() );
 533
 534    #if ($self->get_show_offsets()) { $self->{c1}->set_display_marker_offset(); }
 535    #
 536    # adjust the appearance of the chromosome
 537    #
 538     $self->{c1}->set_height( $self->get_chr_height() );
 539     $self->{c1}->set_vertical_offset(40);
 540     $self->{c1}->set_horizontal_offset( $x_distance * $element_count );
 541     $self->{c1}->set_caption( $self->get_ref_chr() );
 542     $self->{c1}->set_labels_left();
 543
 544     $self->{c1}->set_units( $self->get_ref_map->get_units() );
 545     $self->{c1}
 546       ->set_width( $self->get_ref_map()->get_preferred_chromosome_width() );
 547
 548     $self->append_error( $self->get_ref_map()->get_messages() );
 549     my @m = $self->{c1}->get_markers();
 550
 551     #
 552     # get the markers and determine the highest confidence level
 553     #
 554     my $highest = -1;
 555     foreach my $m (@m) {
 556         if ( $m->get_confidence() > $highest ) {
 557             $highest = $m->get_confidence();
 558         }
 559     }
 560     my @fm = ();
 561     foreach my $m (@m) {
 562         if ( $m->get_confidence() == $highest ) { push @fm, $m; }
 563
 564     }
 565
 566     my $interval = 0;
 567     if ( $self->get_ref_map()->collapsed_marker_count() ) {
 568         $interval = @fm / $self->get_ref_map()->collapsed_marker_count();
 569     }
 570
 571     if ( @m < $self->get_ref_map()->collapsed_marker_count() ) {
 572         $interval = 1;
 573     }
 574     my $frame_marker_count = 0;
 575     for ( my $i = 0 ; $i < @m ; $i++ ) {
 576         $m[$i]->hide_label();
 577
 578         #
 579         # show label if it is hilited...
 580         #
 581         my $marker_name = $m[$i]->get_name();
 582         if ( $self->get_hilite() =~ /\b$marker_name\b/i ) {
 583             $m[$i]->show_label();
 584             $m[$i]->hilite();
 585         }
 586
 587         #
 588         # otherwise only show one in $interval markers of the
 589         # highest confidence
 590         #
 591         if ( $interval > 0 ) {
 592             if ( $m[$i]->get_confidence() == $highest ) {
 593                 if ( $interval > 1 ) {
 594                     if ( $frame_marker_count % $interval == 0 ) {
 595                         $m[$i]->show_label();
 596                     }
 597
 598                 }
 599                 else { $m[$i]->show_label(); }
 600                 $frame_marker_count++;
 601             }
 602         }
 603
 604         set_marker_color( $m[$i], $self->get_color_model() );
 605         if ( $m[$i]->get_confidence() < $self->get_confidence() ) {
 606             $m[$i]->hide_label();
 607         }
 608     }
 609
 610     #
 611     # make the chromosome clickable using the rasterize function and
 612     # add the url
 613     #
 614     #my $raster_size = int($self->{c1}->get_length() / 20) || 2;
 615     if ( $self->get_ref_map()->can_zoom() ) {
 616         $self->{c1}->rasterize(1);    #$raster_size);
 617         $self->{c1}->set_rasterize_link( "view_chromosome.pl?map_version_id="
 618               . ( $self->get_map_version_id() )
 619               . "&amp;chr_nr="
 620               . ( $self->get_ref_chr() )
 621               . "&amp;show_physical="
 622               . ( $self->get_show_physical() )
 623               . "&amp;show_IL="
 624               . ( $self->get_show_IL() )
 625               . "&amp;show_ruler="
 626               . ( $self->get_show_ruler() )
 627               . "&amp;show_offsets="
 628               . ( $self->get_show_offsets() )
 629               . "&amp;color_model="
 630               . ( $self->get_color_model() )
 631               . "&amp;comp_map_version_id="
 632               . ( $self->get_comp_map_version_id() )
 633               . "&amp;comp_chr="
 634               . ( $self->get_comp_chr() )
 635               . "&amp;zoom="
 636               . ( $self->get_zoom() )
 637               . "&amp;size="
 638               . ( $self->get_size() )
 639               . "&amp;hilite="
 640               . ( $self->get_hilite() )
 641               . "&amp;confidence="
 642               . ( $self->get_confidence() )
 643               . "&amp;show_zoomed=1&amp;marker_type="
 644               . ( $self->get_display_marker_type() )
 645               . "&amp;cM_start="
 646               . ( $self->get_cM_start() )
 647               . "&amp;cM_end="
 648               . ( $self->get_cM_end() )
 649               . "&amp;clicked=1&amp;cM=" );
 650     }
 651
 652     $self->{map}->add_chromosome( $self->{c1} );
 653
 654     #
 655     # show the ruler if requested
 656     #
 657     if ( $self->get_show_ruler() ) {
 658         $self->{r} = $self->{c1}->get_ruler();
 659         $self->{r}->set_horizontal_offset( $x_distance / 6 );
 660         $self->{r}->set_vertical_offset(40);
 661         $self->{r}->set_height( $self->get_chr_height() );
 662         $self->{r}->set_start_value(0);
 663         $self->{r}->set_end_value( $self->{c1}->get_length() );
 664         $self->{r}->set_units( $self->get_ref_map()->get_units() );
 665         $self->{map}->add_ruler( $self->{r} );
 666     }
 667
 668     #
 669     # draw the chromosome section if a chromosome section was requested
 670     # (that is, if cM is defined)
 671     #
 672
 673     my $x_offset = 200;
 674     my @m2;    # the markers on c2. Keep for later use.
 675     if ( $self->{show_zoomed} && $self->get_ref_map()->can_zoom() ) {
 676
 677         $element_count++;
 678
 679 #$self->{c2} = CXGN::Cview::Chromosome -> new ($self->get_ref_chr(), $self->get_chr_height(), $x_distance*$element_count, 40);
 680         $self->{c2} = $self->get_ref_map()->get_chromosome_section(
 681             $self->get_ref_chr(), $self->get_cM_start(),
 682             $self->get_cM_end(),  $self->get_comp_chr()
 683         );
 684         if ( $self->get_show_offsets() ) {
 685             $self->{c2}->set_display_marker_offset();
 686         }
 687         $self->{c2}->set_height( $self->get_chr_height() );
 688         $self->{c2}->set_vertical_offset(40);
 689         $self->{c2}->set_hilite( $self->get_hilite_zoomed() );
 690         $self->{c2}->set_horizontal_offset( $x_distance * $element_count );
 691         $self->{c2}->set_units( $self->{c1}->get_units() );
 692
 693         # because we have incomplete length information from the query above,
 694         # we set the length of the zoomed in chromosome
 695         # to be the same as the comparison chromosome (the length is simply
 696         # the marker position of the bottom marker)
 697         #
 698         $self->{c2}->set_length( $self->{c1}->get_length() );
 699
 700         #
 701         # correct the cM_start and cM_end if out of range
 702         #
 703         #if ($self->get_cM_start() < 0) { $self->set_cM_start(0); }
 704         if ( $self->get_cM_end() > $self->{c2}->get_length() ) {
 705             $self->set_cM_end( $self->{c2}->get_length() );
 706         }
 707
 708         #       $self->{c2}->set_units( $self->{c1}->get_units() );
 709         $self->{c2}->set_color( 255, 220, 220 );
 710         @m2 = $self->{c2}->get_markers();
 711
 712         #
 713         # go through the markers and show them according to confidence filter,
 714         # add mark for overgo information etc.
 715         #
 716         for ( my $i = 0 ; $i < @m2 ; $i++ ) {
 717
 718             #
 719             # hilite markers to be hilited
 720             #
 721             my $marker_name = $m2[$i]->get_name();
 722             if ( $self->get_hilite() =~ /\b$marker_name\b/i ) {
 723                 $m2[$i]->hilite();
 724                 $m2[$i]->get_label()->set_hidden(0);
 725             }
 726
 727             #
 728             # hide markers with confidence below confidence threshold
 729             #
 730             if ( $m2[$i]->get_confidence() < $self->{confidence} ) {
 731                 $m2[$i]->hide_label();
 732             }
 733
 734             #
 735             # hide markers that are not of the type that should be displayed
 736             #
 737             my $marker_type = $self->get_display_marker_type();
 738             if ( $self->get_display_marker_type()
 739                 && ( $m2[$i]->get_marker_type() !~ /$marker_type/i ) )
 740             {
 741                 $m2[$i]->hide_label();
 742             }
 743             set_marker_color( $m2[$i], $self->get_color_model() );
 744
 745 #
 746 # set the url only if the marker is visible (otherwise imagemap outside the image will be
 747 # generated that confuses some browsers (such as Explorer).
 748 #
 749             if ( $m2[$i]->is_visible() ) {
 750
 751             }
 752             else {
 753
 754                 $m[$i]->hide_mark();
 755             }
 756         }
 757
 758         #
 759         # set up the section and connections to the left hand chromosome
 760         #
 761         $self->{c2}->set_section( $self->get_cM_start(), $self->get_cM_end() );
 762         $self->{c1}->set_hilite_color( 255, 220, 220 );
 763         $self->{c1}->set_hilite( $self->get_cM_start(), $self->get_cM_end() );
 764         $self->{link1} = CXGN::Cview::ChrLink->new(
 765             $self->{c1}, $self->get_cM_start(),
 766             $self->{c2}, $self->get_cM_start()
 767         );
 768         $self->{link1}->set_color( 10, 10, 10 );
 769         $self->{link2} = CXGN::Cview::ChrLink->new(
 770             $self->{c1}, $self->get_cM_end(),
 771             $self->{c2}, $self->get_cM_end()
 772         );
 773         $self->{link2}->set_color( 10, 10, 10 );
 774         $self->{map}->add_chr_link( $self->{link1} );
 775         $self->{map}->add_chr_link( $self->{link2} );
 776
 777         $self->{map}->add_chromosome( $self->{c2} );
 778     }
 779
 780 #
 781 # draw the map comparison if the map comparison was requested (comp_map comp_chr will be defined).
 782 #
 783     my @m3;
 784     if ( $self->get_comp_map() && $self->get_comp_chr() ) {
 785
 786         #print STDERR "Generating the comparative map...\n";
 787
 788         $element_count++;
 789
 790 #$self->{c3} = CXGN::Cview::chromosome -> new ($self->get_comp_chr(), $self->{chr_height}, $x_distance * $element_count, 40);
 791
 792         $self->{c3} =
 793           $self->get_comp_map()->get_chromosome( $self->get_comp_chr() );
 794
 795         $self->{c3}->set_height( $self->get_chr_height() );
 796         $self->{c3}->set_horizontal_offset( $x_distance * $element_count );
 797         $self->{c3}->set_vertical_offset(40);
 798         $self->{c3}->set_units( $self->get_comp_map()->get_units() );
 799
 800 #print STDERR "Fetching map $self->{comp_map} chr $self->{comp_chr} from the database...\n";
 801
 802         #print STDERR "Adjusting colors etc...\n";
 803         $self->{c3}->set_color( 150, 150, 200 );
 804         $self->{c3}->set_caption( $self->get_comp_chr() );
 805
 806         @m3 = $self->{c3}->get_markers();
 807
 808         #print STDERR "$self->{comp_chr} has ".@m3." markers...\n";
 809         for ( my $i = 0 ; $i < @m3 ; $i++ ) {
 810
 811             #print STDERR "Marker read:". $m3[$i]->get_name()."\n";
 812             CXGN::Cview::Utils::set_marker_color( $m3[$i],
 813                 $self->get_color_model() );
 814
 815         }
 816
 817         #print STDERR "Adding the chromosome to the map...\n";
 818         $self->{map}->add_chromosome( $self->{c3} );
 819
 820 #
 821 # determine if the magnified section exists -- then draw the correspondence lines to that chromosome object (c2)
 822 # else draw them to the original chromosome object (c1).
 823 #
 824         if ( exists( $self->{c2} ) ) {
 825             $self->{c2}->set_labels_left();
 826
 827             my $link_list = get_chromosome_links( $self->{c2}, $self->{c3} );
 828             foreach my $clink ( $link_list->get_link_list() ) {
 829                 $self->{map}->add_chr_link($clink);
 830             }
 831
 832             foreach my $m3 (@m3) {
 833                 $m3->hide_label();
 834                 if ( $link_list->has_link( $m3->get_marker_name() ) ) {
 835                     $m3->show_label();
 836                 }
 837
 838                 if ( $m3->get_confidence < $self->{confidence} ) {
 839                     $m3->hide_label();
 840                 }
 841                 my $marker_name = $m3->get_name();
 842                 if ( $self->get_hilite() =~ /\b$marker_name\b/i ) {
 843                     $m3->show_label();
 844                     $m3->hilite();
 845                 }
 846             }
 847         }
 848         else {
 849
 850             #print STDERR "LINKS:::::::::::::::\n";
 851             my $link_list = get_chromosome_links( $self->{c1}, $self->{c3} );
 852             foreach my $clink ( $link_list->get_link_list() ) {
 853
 854                 #print STDERR "  adding link...\n";
 855                 $self->{map}->add_chr_link($clink);
 856             }
 857             foreach my $m3 (@m3) {
 858                 $m3->hide_label();
 859                 set_marker_color( $m3, $self->get_color_model() );
 860
 861                 if ( $link_list->has_link( $m3->get_marker_name() ) ) {
 862                     $m3->show_label();
 863                 }
 864                 if ( $m3->get_confidence < $self->{confidence} ) {
 865                     $m3->hide_label();
 866                 }
 867                 if ( $m3->get_name() eq $self->get_hilite() ) {
 868                     $m3->show_label();
 869                     $m3->hilite();
 870                 }
 871             }
 872         }
 873         $element_count++;
 874         if ( $self->get_show_ruler() ) {
 875             $self->{r3} = $self->{c3}->get_ruler();
 876             $self->{r3}->set_horizontal_offset( $element_count * $x_distance );
 877             $self->{r3}->set_vertical_offset(40);
 878             $self->{r3}->set_height( $self->get_chr_height() );
 879             $self->{r3}->set_start_value(0);
 880             $self->{r3}->set_end_value( $self->{c3}->get_length() );
 881
 882             $self->{map}->add_ruler( $self->{r3} );
 883         }
 884     }
 885 }
 886
 887 =head2 function get_chr_height()
 888
 889   Synopsis:     Accessor for the chr_height property
 890   Arguments:    none
 891   Returns:      the current chr_height
 892   Side effects: The chromosomes are being drawn with the chr_height in pixels
 893   Description:
 894
 895 =cut
 896
 897 sub get_chr_height {
 898     my $self = shift;
 899     return $self->{chr_height};
 900 }
 901
 902 =head2 function set_chr_height()
 903
 904   Synopsis:
 905   Arguments:    the chromosome height in pixels. In small mode, height is 230 pixels, and
 906                 normal mode the height is 400 pixels.
 907   Returns:
 908   Side effects:
 909   Description:
 910
 911 =cut
 912
 913 sub set_chr_height {
 914     my $self = shift;
 915     $self->{chr_height} = shift;
 916 }
 917
 918 =head2 accessors get_ref_map(), set_ref_map()
 919
 920  Usage:
 921  Desc:
 922  Args/Ret:     the reference map as a CXGN::Cview::Map object
 923                of the appropriate sub-class.
 924  Side Effects: this will be the map displayed as the reference
 925                map (on the left).
 926  Example:
 927
 928 =cut
 929
 930 sub get_ref_map {
 931     my $self = shift;
 932     if ( !exists( $self->{ref_map} ) ) { $self->{ref_map} = undef; }
 933     return $self->{ref_map};
 934
 935 }
 936
 937 sub set_ref_map {
 938     my $self = shift;
 939     $self->{ref_map} = shift;
 940 }
 941
 942 =head2 accessors get_comp_map(), set_comp_map()
 943
 944   Usage:
 945   Property:     the comparison map, as a CXGN::Cview::Map object
 946                 (or subclass thereof)
 947   Desc:
 948   Side Effects:
 949   Example:
 950
 951 =cut
 952
 953 sub get_comp_map {
 954     my $self = shift;
 955     if ( !exists( $self->{comp_map} ) || !defined( $self->{comp_map} ) ) {
 956         $self->{comp_map} = undef;
 957     }
 958     return $self->{comp_map};
 959
 960 }
 961
 962 sub set_comp_map {
 963     my $self = shift;
 964     $self->{comp_map} = shift;
 965 }
 966
 967 =head2 accessors set_map_id(), get_map_id()
 968
 969   Synopsis:     sets the map_id for the reference chromosome
 970   Parameters:   map_id (integer)
 971   Returns:
 972   Side effects: the map corresponding to map_id will be drawn as the reference chromosome
 973   Status:       DEPRECATED. Call $chr_viewer->get_ref_map()->get_id() instead...
 974   Example:
 975
 976 =cut
 977
 978 sub set_map_id {
 979     my $self = shift;
 980     $self->{map_id} = shift;
 981 }
 982
 983 sub get_map_id {
 984     my $self = shift;
 985
 986     #    if (!exists($self->{map_id})) { $self->{map_id}=0; }
 987     if ( !exists( $self->{map_id} ) || !defined( $self->{map_id} ) ) {
 988         $self->{map_id} = 0;
 989     }
 990     return $self->{map_id};
 991 }
 992
 993 =head2 accessors get_default_map_id, set_default_map_id
 994
 995  Usage:
 996  Desc:
 997  Property
 998  Side Effects:
 999  Example:
1000
1001 =cut
1002
1003 sub get_default_map_id {
1004   my $self = shift;
1005   return $self->{default_map_id};
1006 }
1007
1008 sub set_default_map_id {
1009   my $self = shift;
1010   $self->{default_map_id} = shift;
1011 }
1012
1013
1014 =head2 accessors get_map_version_id(), set_map_version_id()
1015
1016  Usage:
1017  Desc:         the map_version_id of the reference map
1018  Ret:
1019  Args:
1020  Side Effects:
1021  Example:
1022
1023 =cut
1024
1025 sub get_map_version_id {
1026     my $self = shift;
1027     return $self->{map_version_id};
1028
1029 }
1030
1031 sub set_map_version_id {
1032     my $self = shift;
1033     $self->{map_version_id} = shift;
1034 }
1035
1036 =head2 accessors get_comp_map_version_id(), set_comp_map_version_id()
1037
1038  Usage:
1039  Desc:         the map_version_id of the comparison map
1040  Ret:
1041  Args:
1042  Side Effects:
1043  Example:
1044
1045 =cut
1046
1047 sub get_comp_map_version_id {
1048     my $self = shift;
1049     if (   !exists( $self->{comp_map_version_id} )
1050         || !defined( $self->{comp_map_version_id} ) )
1051     {
1052         $self->{comp_map_version_id} = '';
1053     }
1054     return $self->{comp_map_version_id};
1055
1056 }
1057
1058 sub set_comp_map_version_id {
1059     my $self = shift;
1060     $self->{comp_map_version_id} = shift;
1061 }
1062
1063 =head2 function set_comp_map_id()
1064
1065   Synopsis:     setter function for the map id of the comparison chromosome
1066   Parameters:   the map id (integer)
1067   Returns:      nothing
1068   Side effects: the specified map will be drawn as the reference chromosome
1069   Status:       implemented
1070   Example:
1071
1072 =cut
1073
1074 sub set_comp_map_id {
1075     my $self = shift;
1076     $self->{comp_map_id} = shift;
1077 }
1078
1079 =head2 function get_comp_map_id()
1080
1081   Synopsis:     get the current map id of the comparison chromosome
1082   Parameters:
1083   Returns:      map id of the comparison chromosome
1084   Side effects:
1085   Status:       implemented
1086   Example:
1087
1088 =cut
1089
1090 sub get_comp_map_id {
1091     my $self = shift;
1092     if ( !exists( $self->{comp_map_id} ) || !defined( $self->{comp_map_id} ) ) {
1093         $self->{comp_map_id} = 0;
1094     }
1095     return $self->{comp_map_id};
1096 }
1097
1098 =head2 function set_ref_chr()
1099
1100   Synopsis:     setter function for the specifying the reference chromosome
1101                 number/linkage group name
1102   Parameters:   the desired chromosome number/linkage group name (string)
1103   Returns:
1104   Side effects: the specified chromosome/linkage group will be displayed as
1105                 the reference chromosome
1106   Status:       implemented
1107   Example:
1108
1109 =cut
1110
1111 sub set_ref_chr {
1112     my $self = shift;
1113     $self->{chr_nr} = shift;
1114 }
1115
1116 =head2 function get_ref_chr()
1117
1118   Synopsis:     accessor function for set_ref_chr
1119   Parameters:
1120   Returns:      the chromosome number/linkage group name for the reference
1121                 chromosome/linkage group
1122   Side effects:
1123   Status:       implemented
1124   Example:
1125
1126 =cut
1127
1128 sub get_ref_chr {
1129     my $self = shift;
1130     if ( !exists( $self->{chr_nr} ) || !defined( $self->{chr_nr} ) ) {
1131         $self->{chr_nr} = 0;
1132     }
1133     return $self->{chr_nr};
1134 }
1135
1136 =head2 function set_comp_chr()
1137
1138   Synopsis:     setter function for specifying the comparison chromosome/linkage
1139                 group
1140   Parameters:   chromosome number/linkage group name
1141   Returns:      nothing
1142   Side effects: the corrsponding chromosome will be drawn as the comparison chromosome
1143   Status:       implemented
1144   Example:
1145
1146 =cut
1147
1148 sub set_comp_chr {
1149     my $self = shift;
1150     $self->{comp_chr} = shift;
1151 }
1152
1153 =head2 function get_comp_chr()
1154
1155   Synopsis:     accessor function for set_comp_chr
1156   Parameters:
1157   Returns:
1158   Side effects:
1159   Status:       implemented
1160   Example:
1161
1162 =cut
1163
1164 sub get_comp_chr {
1165     my $self = shift;
1166     if ( !exists( $self->{comp_chr} ) || !defined( $self->{comp_chr} ) ) {
1167         $self->{comp_chr} = 0;
1168     }
1169     return $self->{comp_chr};
1170 }
1171
1172 =head2 accessors get_ref_chr_len, set_ref_chr_len
1173
1174  Usage:
1175  Desc:
1176  Property
1177  Side Effects:
1178  Example:
1179
1180 =cut
1181
1182 sub get_ref_chr_len {
1183     my $self = shift;
1184     if ( !exists( $self->{ref_chr_len} ) || !defined( $self->{ref_chr_len} ) ) {
1185         $self->{ref_chr_len} = '';
1186     }
1187     return $self->{ref_chr_len};
1188 }
1189
1190 sub set_ref_chr_len {
1191     my $self = shift;
1192     $self->{ref_chr_len} = shift;
1193 }
1194
1195 =head2 function set_cM_start()
1196
1197   Synopsis:     for a chromosome section, sets the starting point in cM
1198   Parameters:   cM start position
1199   Returns:      nothing
1200   Side effects: cleans the input to be an integer
1201   Status:       implemented
1202   Example:
1203
1204 =cut
1205
1206 sub set_cM_start {
1207     my $self     = shift;
1208     my $cM_start = shift;
1209     $cM_start =~ s/[^0-9.]//g;
1210
1211     #$cM_start =~ s/.*?(\d+\.?\d*).*/$1/;
1212     $self->{cM_start} = abs($cM_start);
1213 }
1214
1215 =head2 function get_cM_start()
1216
1217   Synopsis:     accessor function for the cM_start property
1218   Parameters:
1219   Returns:
1220   Side effects:
1221   Status:       implemented
1222   Example:
1223
1224 =cut
1225
1226 sub get_cM_start {
1227     my $self = shift;
1228     if ( !exists( $self->{cM_start} ) || !defined( $self->{cM_start} ) ) {
1229         $self->{cM_start} = 0;
1230     }
1231
1232     return sprintf "%.2f", $self->{cM_start};
1233 }
1234
1235 =head2 function set_cM_end()
1236
1237   Synopsis:     sets the end of a chromosome /linkage group section, in cM
1238   Parameters:   cM of end of section
1239   Returns:      nothing
1240   Side effects: On a chromosome section, this will define the endpoints of the section.
1241                 If set_section has not been called, this will define which section is
1242                 hilited. The cM and zoom property will be automatically re-calculated.
1243   Status:       implemented
1244   Example:
1245
1246 =cut
1247
1248 sub set_cM_end {
1249     my $self   = shift;
1250     my $cM_end = shift;
1251     $cM_end =~ s/[^0-9.]//g;
1252     if ( !defined($cM_end) || !$cM_end ) { $cM_end = 0; }
1253     $self->{cM_end} = abs( ($cM_end) );
1254 }
1255
1256 =head2 function get_cM_end()
1257
1258   Synopsis:     accessor function for the cM_end property
1259   Parameters:
1260   Returns:
1261   Side effects:
1262   Status:       implemented
1263   Example:
1264
1265 =cut
1266
1267 sub get_cM_end {
1268     my $self = shift;
1269     if ( !exists( $self->{cM_end} ) || !defined( $self->{cM_end} ) ) {
1270         $self->{cM_end} = 0;
1271     }
1272     return sprintf "%.2f", $self->{cM_end};
1273 }
1274
1275 =head2 function set_cM()
1276
1277   Synopsis:     sets the cM property. This is the approximate location in which
1278                 the user has clicked. If set_cM is set, cM_start and cM_end will be
1279                 calculated automatically using the current zoom levels.
1280   Parameters:   the cM position (integer)
1281   Returns:      nothing
1282   Side effects: recalculates cM_start and cM_end.
1283   Status:       implemented
1284   Example:
1285
1286 =cut
1287
1288 sub set_cM {
1289     my $self = shift;
1290     $self->{cM} = shift;
1291 }
1292
1293 =head2 function get_cM()
1294
1295   Synopsis:     accessor function for the cM property
1296   Parameters:
1297   Returns:
1298   Side effects:
1299   Status:       implemented
1300   Example:
1301
1302 =cut
1303
1304 sub get_cM {
1305     my $self = shift;
1306     if ( !exists( $self->{cM} ) || !defined( $self->{cM} ) ) {
1307         $self->{cM} = 0;
1308     }
1309     return $self->{cM};
1310 }
1311
1312 =head2 function set_zoom()
1313
1314   Synopsis:     sets the zoom level on the reference chromosome
1315   Parameters:   zoom level (1..10). 10 is the highest zoom level (most enlarged section
1316                 showing fewer markers). Zoom levels outside the legal range are rounded to
1317                 the nearest legal value.
1318   Returns:      nothing
1319   Side effects:
1320   Status:       Deprecated. Zooming is now implemented by setting cM_start and cM_end
1321   Example:
1322
1323 =cut
1324
1325 sub set_zoom {
1326     my $self = shift;
1327     $self->{zoom} = shift;
1328     if (   !exists( $self->{zoom} )
1329         || !defined( $self->{zoom} )
1330         || $self->{zoom} eq "" )
1331     {
1332         $self->{zoom} = 0;
1333     }
1334     if ( $self->{zoom} == 0 ) { $self->{zoom} = 1; }
1335     if ( $self->{zoom} > 10 ) { $self->{zoom} = 10; }
1336 }
1337
1338 =head2 function get_zoom()
1339
1340   Synopsis:     accessor function for the zoom property.
1341   Parameters:
1342   Returns:      the current zoom level (1..10)
1343   Side effects:
1344   Status:       Deprecated. Zooming is now implented by directly setting cM_start and cM_end.
1345   Example:
1346
1347 =cut
1348
1349 sub get_zoom {
1350     my $self = shift;
1351     if ( !exists( $self->{zoom} ) || !defined( $self->{zoom} ) ) {
1352         $self->{zoom} = 1;
1353     }
1354     return $self->{zoom};
1355 }
1356
1357 =head2 accessors get_clicked, set_clicked
1358
1359  Usage:        my $flag = $cv -> get_clicked()
1360  Desc:         returns true if this page should be regenerated
1361                as a response to a user clicking on the chromosome
1362                (instead of using some of the toolbar buttons),
1363                false otherwise.
1364  Property:
1365  Side Effects:
1366  Example:
1367
1368 =cut
1369
1370 sub get_clicked {
1371     my $self = shift;
1372     if ( !exists( $self->{clicked} ) || !defined( $self->{clicked} ) ) {
1373         $self->{clicked} = 0;
1374     }
1375     return $self->{clicked};
1376 }
1377
1378 sub set_clicked {
1379     my $self = shift;
1380     $self->{clicked} = shift;
1381 }
1382
1383 =head2 function get_show_ruler()
1384
1385   Synopsis:     accessor function for the show_ruler property.
1386   Parameters:   none
1387   Returns:      true if ruler is shown, false otherwise
1388   Side effects:
1389   Status:       implemented
1390   Example:
1391
1392 =cut
1393
1394 sub get_show_ruler {
1395     my $self = shift;
1396     if ( !exists( $self->{show_ruler} ) || !defined( $self->{show_ruler} ) ) {
1397         $self->{show_ruler} = 0;
1398     }
1399     return $self->{show_ruler};
1400 }
1401
1402 =head2 function set_show_ruler()
1403
1404   Synopsis:     setter function for the show_ruler property.
1405   Parameters:   true or false (0 or 1)
1406   Returns:      nothing
1407   Side effects: true causes the ruler to be displayed for both the reference and comparison map
1408                 (if present), false hides the ruler.
1409   Status:       implemented
1410   Example:
1411
1412 =cut
1413
1414 sub set_show_ruler {
1415     my $self = shift;
1416     $self->{show_ruler} = shift;
1417 }
1418
1419 =head2 function set_show_IL()
1420
1421   Synopsis:     setter function for the show_IL property
1422   Parameters:   true or false
1423   Returns:      nothing
1424   Side effects: if the current reference map has associated IL information, true will
1425                 cause the IL map to be displayed alongside with the chromosome.
1426   Status:       implemented
1427   Example:
1428
1429 =cut
1430
1431 sub set_show_IL {
1432     my $self = shift;
1433     $self->{show_IL} = shift;
1434 }
1435
1436 =head2 function get_show_IL()
1437
1438   Synopsis:     accessor function for the show_IL property
1439   Parameters:   none
1440   Returns:      true or false
1441   Side effects: none
1442   Status:       implemented
1443   Example:
1444
1445 =cut
1446
1447 sub get_show_IL {
1448     my $self = shift;
1449     if ( !exists( $self->{show_IL} ) || !defined( $self->{show_IL} ) ) {
1450         $self->{show_IL} = 0;
1451     }
1452     return $self->{show_IL};
1453 }
1454
1455 =head2 function set_show_physical()
1456
1457   Synopsis:     true causes the physical map to be displayed if the current reference map
1458                 has an associated physical map
1459   Parameters:   true/false
1460   Returns:      nothing
1461   Side effects:
1462   Status:       implemented
1463   Example:
1464
1465 =cut
1466
1467 sub set_show_physical {
1468     my $self = shift;
1469     $self->{show_physical} = shift;
1470 }
1471
1472 =head2 function get_show_physical()
1473
1474   Synopsis:     true causes the physical map to be displayed if the current reference map
1475                 has an associated physical map
1476   Parameters:   none
1477   Returns:      true/false
1478   Side effects:
1479   Status:       implemented
1480   Example:
1481
1482 =cut
1483
1484 sub get_show_physical {
1485     my $self = shift;
1486     if (   !exists( $self->{show_physical} )
1487         || !defined( $self->{show_physical} ) )
1488     {
1489         $self->{show_physical} = 0;
1490     }
1491     return $self->{show_physical};
1492 }
1493
1494 =head2 accessors set_show_offsets(), get_show_offsets()
1495
1496   Property:     if the offsets should be shown (each marker will display a
1497                 label opposite of the marker label, showing the offset in map
1498                 units for that marker, for the zoomed-in section
1499   Side Effects:
1500   Description:
1501
1502 =cut
1503
1504 sub get_show_offsets {
1505     my $self = shift;
1506     if ( !exists( $self->{show_offsets} ) || !defined( $self->{show_offsets} ) )
1507     {
1508         $self->{show_offsets} = 0;
1509     }
1510     return $self->{show_offsets};
1511 }
1512
1513 sub set_show_offsets {
1514     my $self = shift;
1515     $self->{show_offsets} = shift;
1516 }
1517
1518 =head2 function get_size()
1519
1520   Synopsis:     accessor function for the size property
1521   Parameters:   none
1522   Returns:      "small" or "normal" or "large"
1523   Side effects:
1524   Status:       implemented
1525   Example:
1526
1527 =cut
1528
1529 sub get_size {
1530     my $self = shift;
1531     if ( !exists( $self->{size} ) or !defined( $self->{size} ) ) {
1532         $self->{size} = 0;
1533     }
1534     return $self->{size};
1535 }
1536
1537 =head2 function set_size()
1538
1539   Synopsis:     sets the size of the image
1540   Parameters:   string ("normal", "small" and "large" are currently supported).
1541   Returns:      nothing
1542   Side effects: "smaller" causes the entire map image to be rendered smaller
1543                           (ideal for a laptop monitor)
1544                 "normal" causes the entire map image to be rendered to fit a desktop monitor
1545                 (>=17\")
1546                 "larger" for really large monitors (>20\")
1547   Status:       implemented
1548   Example:
1549
1550 =cut
1551
1552 sub set_size {
1553     my $self = shift;
1554     $self->{size} = shift;
1555 }
1556
1557 =head2 function set_hilite()
1558
1559   Synopsis:     hilites the specified markers on the reference map (unhides if necessary)
1560                 on the zoomed-in map and on the comparison map.
1561   Parameters:   a string, containing an enumeration of marker names to be hilited, separated
1562                 by spaces (although other delimiters will also work such as comma, semicolons,
1563                 etc.)
1564   Returns:      nothing
1565   Side effects: the hilited marker name will appear with a yellow background.
1566   Status:       implemented
1567   Example:
1568
1569 =cut
1570
1571 sub set_hilite {
1572     my $self = shift;
1573     my $hilite = shift || '';
1574     $hilite =~ tr/\,\.\:\;\// /;
1575     $hilite =~ s/\s+/ /;
1576     $self->{hilite} = $hilite;
1577
1578 }
1579
1580 =head2 function get_hilite()
1581
1582   Synopsis:     accessor function for the hilite property
1583   Parameters:   none
1584   Returns:      the name of the currently hilited marker
1585   Side effects:
1586   Status:       implemented
1587   Example:
1588
1589 =cut
1590
1591 sub get_hilite {
1592     my $self = shift;
1593     if ( !exists( $self->{hilite} ) || !defined( $self->{hilite} ) ) {
1594         $self->{hilite} = "";
1595     }
1596     return $self->{hilite};
1597 }
1598
1599 =head2 function set_confidence()
1600
1601   Synopsis:     sets the minimal confidence level to be displayed
1602   Parameters:   confidence level (-1, 0..3)
1603                 -1: uncalculated confidence, 0 - interval marker ... 3 - frame marker
1604   Returns:      nothing
1605   Side effects: markers below the specified confidence level will be hidden
1606   Status:       implemented
1607   Example:
1608
1609 =cut
1610
1611 sub set_confidence {
1612     my $self = shift;
1613     my $confidence = shift || '';
1614     $confidence =~ s/[A-Za-z]//g;
1615     if ( !defined($confidence) || $confidence eq "" ) { $confidence = -2; }
1616     $confidence = $confidence + 0;
1617     $self->{confidence} = $confidence;
1618 }
1619
1620 =head2 function get_confidence()
1621
1622   Synopsis:     accessor function for the confidence property
1623   Parameters:   none
1624   Returns:      the current lowest confidence level that is displayed
1625                 Normal values for the confidence property are:
1626                 -1: not calculated
1627                 0 ILOD
1628                 1 ILOD2
1629                 2 CFLOD
1630                 3 LOD3
1631                 If the confidence property is not set, it will return -2,
1632                 causing all markers to be displayed.
1633   Side effects: markers with a lower confidence value (see list above) won\'t be
1634                 displayed.
1635   Status:       implemented
1636   Example:
1637
1638 =cut
1639
1640 sub get_confidence {
1641     my $self = shift;
1642     if ( !exists( $self->{confidence} ) || !defined( $self->{confidence} ) ) {
1643         $self->{confidence} = -2;
1644     }
1645     return $self->{confidence};
1646 }
1647
1648 =head2 functions set_display_marker_type(), get_display_marker_type()
1649
1650   Synopsis:     $self->set_display_marker_type('COS');
1651   Arguments:    a marker type. Any of COS, RFLP, ...
1652   Returns:      nothing
1653   Side effects: Will also set $self->{error} to indicate to the
1654                 user that marker type subsets are shown.
1655   Description:  if set_display_marker_type is called with a marker
1656                 type argument, only that marker type will be shown
1657                 on the viewer. If called with undef, shows all markers.
1658
1659 =cut
1660
1661 sub set_display_marker_type {
1662     my $self = shift;
1663     my $type = shift;
1664     if ( $type && ( "RFLP CAPS COS SSR" =~ /\b$type\b/ ) ) {
1665         $self->{display_marker_type} = $type;
1666         $self->append_error(
1667 "Only markers of the type $self->{display_marker_type} are shown on the zoomed map.<br />"
1668         );
1669     }
1670 }
1671
1672 sub get_display_marker_type {
1673     my $self = shift;
1674     if (   !exists( $self->{display_marker_type} )
1675         || !defined( $self->{display_marker_type} ) )
1676     {
1677         $self->{display_marker_type} = "";
1678     }
1679     return $self->{display_marker_type};
1680 }
1681
1682 =head2 function set_show_zoomed()
1683
1684   Synopsis:     setter function for the show_zoomed property
1685   Parameters:   show_zoomed property (0 or 1)
1686   Returns:      status of the current show_zoomed property (0 or 1)
1687   Side effects: 0 will cause the zoomed in chromosome section not to be drawn
1688                 1 will cause a zoomed in chromosome section to be drawn
1689   Status:       implemented
1690   Example:
1691
1692 =cut
1693
1694 sub set_show_zoomed {
1695     my $self = shift;
1696     $self->{show_zoomed} = shift;
1697 }
1698
1699 =head2 function get_show_zoomed()
1700
1701   Synopsis:     accessor function for the show_zoomed property
1702   Parameters:   none
1703   Returns:      status of the current show_zoomed property (0 or 1)
1704   Side effects: none
1705   Status:       implemented
1706   Example:
1707
1708 =cut
1709
1710 sub get_show_zoomed {
1711     my $self = shift;
1712     if ( !exists( $self->{show_zoomed} ) || !defined( $self->{show_zoomed} ) ) {
1713         $self->{show_zoomed} = 0;
1714     }
1715     return $self->{show_zoomed};
1716 }
1717
1718 =head2 accessors get_hilite_zoomed(), set_hilite_zoomed()
1719
1720  Usage:        $chr_viewer->set_hilite_zoomed($cM_start, $cM_end)
1721  Desc:         hilites the given region in the zoomed-in section,
1722                using the current hilite color.
1723  Ret:          The getter returns the start and end in cM
1724  Args:         the start in cM [real], the end in cM [real]
1725  Side Effects: hilites the corresponding region
1726   Notes:       the intended use for this is to hilite sections,
1727                such as the boundaries for ILs on the zoomed in
1728                chromosome.
1729
1730 =cut
1731
1732 sub set_hilite_zoomed {
1733     my $self = shift;
1734     $self->{hilite_zoom_start} = shift;
1735     $self->{hilite_zoom_end}   = shift;
1736
1737 }
1738
1739 sub get_hilite_zoomed {
1740     my $self = shift;
1741     if (   !exists( $self->{hilite_zoom_start} )
1742         || !defined( $self->{hilite_zoom_start} ) )
1743     {
1744         $self->{hilite_zoom_start} = '';
1745     }
1746     if (   !exists( $self->{hilite_zoom_end} )
1747         || !defined( $self->{hilite_zoom_end} ) )
1748     {
1749         $self->{hilite_zoom_end} = '';
1750     }
1751     return ( $self->{hilite_zoom_start}, $self->{hilite_zoom_end} );
1752 }
1753
1754 =head2 function get_color_model()
1755
1756   Synopsis:
1757   Parameters:   name of color model (currently, confidence and marker_type are supported)
1758   Returns:      nothing
1759   Side effects: sets the color model property to the specified color model
1760   Status:       implemented
1761   Example:
1762
1763 =cut
1764
1765 sub set_color_model {
1766     my $self = shift;
1767     $self->{color_model} = shift;
1768 }
1769
1770 =head2 function get_color_model()
1771
1772   Synopsis:
1773   Parameters:   none
1774   Returns:      the name of the current marker color model
1775   Side effects: none
1776   Status:       implemented
1777   Example:
1778
1779 =cut
1780
1781 sub get_color_model {
1782     my $self = shift;
1783     if ( !exists( $self->{color_model} ) || !defined( $self->{color_model} ) ) {
1784         $self->{color_model} = "";
1785     }
1786     return $self->{color_model};
1787 }
1788
1789 =head2 function get_color_legend()
1790
1791   Synopsis:
1792   Parameters:   none
1793   Returns:      a string containing html code for the marker color legend
1794   Side effects: none
1795   Status:       implemented
1796   Example:
1797
1798 =cut
1799
1800 sub get_color_legend {
1801     my $self   = shift;
1802     my $string = "";
1803     my $link =
1804         "view_chromosome.pl?map_version_id="
1805       . $self->get_map_version_id()
1806       . "&amp;chr_nr="
1807       . $self->get_ref_chr()
1808       . "&amp;show_physical="
1809       . $self->get_show_physical
1810       . "&amp;show_IL="
1811       . $self->get_show_IL()
1812       . "&amp;show_offsets="
1813       . $self->get_show_offsets()
1814       . "&amp;show_ruler="
1815       . $self->get_show_ruler()
1816       . "&amp;color_model="
1817       . $self->get_color_model()
1818       . "&amp;comp_map_version_id="
1819       . $self->get_comp_map_version_id()
1820       . "&amp;comp_chr="
1821       . $self->get_comp_chr()
1822       . "&amp;zoom="
1823       . $self->get_zoom()
1824       . "&amp;size="
1825       . $self->get_size()
1826       . "&amp;cM="
1827       . $self->get_cM()
1828       . "&amp;cM_start="
1829       . $self->get_cM_start()
1830       . "&amp;cM_end="
1831       . $self->get_cM_end()
1832       . "&amp;hilite="
1833       . $self->get_hilite()
1834       . "&amp;show_zoomed="
1835       . $self->get_show_zoomed() . "";
1836     if ( $self->{color_model} eq "marker_types" ) {
1837
1838         $string = "<b>Marker color by type:</b>
1839                    <a href=\"$link\&marker_type=RFLP\" style=\"color:#FF0000\">RFLP</a> |
1840                    <a href=\"$link\&marker_type=SSR\" style=\"color:#00FF00\">SSR</a> |
1841                    <a href=\"$link\&marker_type=CAPS\" style=\"color:#0000FF\">CAPS</a> |
1842                    <a href=\"$link\&marker_type=COS\" style=\"color:#FF00FF\">COS</a> |
1843                    <font color=#000000>other</font>
1844                            [<a href=\"$link\&marker_type=\" style=\"color:#111111\">show all</a>]";
1845
1846     }
1847     else {
1848         $string = "<b>Marker color by LOD score:</b>
1849                    <a href=\"$link\&amp;confidence=3\" style=\"color:#FF0000\">F(LOD3)</a> |
1850                    <a href=\"$link\&amp;confidence=2\" style=\"color:#00FF00\">CF(LOD>=3</a> |
1851                    <a href=\"$link\&amp;confidence=1\" style=\"color:#0000FF\">I(LOD2)</a> |
1852                    <a href=\"$link\&amp;confidence=0\" style=\"color:#000000\">I(LOD&lt;2)</a> |
1853                    <a href=\"$link\&amp;confidence=-2\" style=\"color:#777777\">uncalculated</a>  ";
1854     }
1855     return $string;
1856 }
1857
1858 =head2 function get_marker_map_links()
1859
1860   Synopsis:
1861   Parameters:   none
1862   Returns:      a string with html code for the marker map links pull down menu.
1863                 if there is no appropriate map linked to the reference map,
1864                 a string is returned that says so.
1865   Side effects: calls the get_chromosome_connections() function of the reference
1866                 map object.
1867   Status:       implemented
1868   Example:
1869   Notes:
1870   Version:
1871
1872 =cut
1873
1874 sub get_marker_map_links {
1875     my $self = shift;
1876
1877 #print STDERR "get_marker_map_links...\n";
1878 # query the database for maps and chromosome that any of the markers of the current chromosome lie on.
1879 #
1880     my $chr_nr  = $self->get_ref_chr();
1881     my $default_map = CXGN::Cview::Map::SGN::Genetic->new(
1882         $self->get_dbh(),
1883         CXGN::Cview::Map::Tools::find_current_version(
1884             $self->get_dbh(), #CXGN::Cview::Map::Tools::current_tomato_map_id()
1885             $self->get_default_map_id(),
1886         ),
1887     );
1888
1889     my $default_map_version_id = $default_map->get_id();
1890
1891     my $form =
1892       "<form style=\"margin-bottom:0\" action=\"/cview/view_chromosome.pl\">
1893         <input type=\"hidden\" name=\"chr_nr\" value=\""
1894       . ( $self->get_ref_chr() ) . "\" />
1895         <input type=\"hidden\" name=\"map_version_id\" value=\""
1896       . ( $self->get_map_version_id() ) . "\" />
1897         <input type=\"hidden\" name=\"zoom\" value=\"" . ( $self->get_zoom() ) . "\" />
1898         <input type=\"hidden\" name=\"show_ruler\" value=\""
1899       . ( $self->get_show_ruler() ) . "\" />
1900         <input type=\"hidden\" name=\"show_IL\" value=\""
1901       . ( $self->get_show_IL() ) . "\" />
1902         <input type=\"hidden\" name=\"show_offsets\" value=\""
1903       . ( $self->get_show_offsets() ) . "\" />
1904         <input type=\"hidden\" name=\"cM_start\" value=\""
1905       . ( $self->get_cM_start() ) . "\" />
1906         <input type=\"hidden\" name=\"cM_end\" value=\""
1907       . ( $self->get_cM_end() ) . "\" />
1908         <input  type=\"hidden\" name=\"show_physical\" value=\""
1909       . ( $self->get_show_physical() ) . "\" />
1910         <input type=\"hidden\" name=\"color_model\" value=\""
1911       . ( $self->get_color_model() ) . "\" />
1912         <input type=\"hidden\" name=\"size\" value=\""
1913       . ( $self->get_size() ) . "\" />
1914         <input type=\"hidden\" name=\"show_zoomed\" value=\""
1915       . ( $self->get_show_zoomed() ) . "\" />
1916         <input type=\"hidden\" name=\"hilite\" value=\""
1917       . ( $self->get_hilite() ) . "\" />
1918         <input type=\"hidden\" name=\"marker_type\" value=\""
1919       . ( $self->get_display_marker_type() ) . "\" /> ";
1920
1921     my @options =
1922       $self->get_ref_map()->get_chromosome_connections( $self->get_ref_chr() );
1923
1924     if (@options) {
1925
1926         $form .= "<select name=\"map_chr_select\">";
1927         foreach my $o (@options) {
1928
1929  #      print STDERR $o->{map_version_id}, $o->{chr_nr}, $o->{short_name}."<br />\n";
1930             my $selected = "";
1931
1932             if ( defined( $self->get_comp_map_version_id() )
1933                 && $o->{map_version_id} eq $self->get_comp_map_version_id() )
1934             {
1935                 $selected = "selected=\"selected\"";
1936             }
1937
1938             $form .=
1939 qq {  <option value="$o->{map_version_id} $o->{lg_name}" $selected>Map $o->{short_name} Chromosome $o->{lg_name} ($o->{marker_count} markers)</option> };
1940         }
1941
1942         $form .= "</select>\n";
1943         $self->{compare_disabled} = "";
1944     }
1945     else {
1946         $form .= "<select name=\"map_chr_select\" disabled=\"disabled\" >";
1947         $form .=
1948 "<option value=\"\" disabld=\"disabled\" >No maps to compare to</option>";
1949         $form .= "</select>\n";
1950         $self->{compare_disabled} = qq{ disabled="disabled" };
1951     }
1952
1953     $form .=
1954 "<input type=\"submit\" value=\"Compare\" $self->{compare_disabled} /></form>";
1955
1956     return $form;
1957 }
1958
1959 sub append_error {
1960     my $self = shift;
1961     my $append = shift || '';
1962     if ( !exists( $self->{errors} ) || !defined( $self->{errors} ) ) {
1963         $self->{errors} = "";
1964     }
1965     $self->{errors} .= $append;
1966 }
1967
1968 sub get_errors {
1969     my $self = shift;
1970     return $self->{errors};
1971 }
1972
1973 =head2 function get_preceding_chromosome()
1974
1975   Synopsis:     gives the name of the chromosome or linkage group preceding the
1976                 given chromosome
1977   Parameters:   chromosome name / linkage group name
1978   Returns:      the chromosome number or linkage group name preceding this
1979                 chromosome/linkage group
1980   Side effects: none
1981   Status:       implemented
1982   Example:
1983   Notes:
1984   Version:
1985
1986 =cut
1987
1988 sub get_preceding_chromosome {
1989     my $self          = shift;
1990     my $chr_nr        = shift;
1991     my $chr_count     = scalar( @{ $self->{chromo_names} } );
1992     my $chr_index     = 0;
1993     my $old_chr_index = 0;
1994
1995 #
1996 # find current chromosome in chromo_names array (a hash would be more elegant...)
1997 #
1998     for ( my $i = 0 ; $i < ( @{ $self->{chromo_names} } ) ; $i++ ) {
1999         if ( ${ $self->{chromo_names} }[$i] eq $chr_nr ) {
2000             $old_chr_index = $i;
2001         }
2002     }
2003
2004     if   ( $old_chr_index == 0 ) { $chr_index = $chr_count - 1; }
2005     else                         { $chr_index = $old_chr_index - 1; }
2006     return ${ $self->{chromo_names} }[$chr_index];
2007 }
2008
2009 =head2 function get_next_chromosome()
2010
2011   Synopsis:     gives the name of the chromosome or linkage group following the given
2012                 chromosome
2013   Parameters:   chromosome name / linkage group name
2014   Returns:      the chromosome number or linkage group name following this
2015                 chromosome/linkage group
2016   Side effects: none
2017   Status:       implemented
2018   Example:
2019   Notes:
2020   Version:
2021
2022 =cut
2023
2024 sub get_next_chromosome {
2025     my $self          = shift;
2026     my $chr_nr        = shift;
2027     my $chr_count     = scalar( @{ $self->{chromo_names} } );
2028     my $chr_index     = 0;
2029     my $old_chr_index = 0;
2030     for ( my $i = 0 ; $i < ( @{ $self->{chromo_names} } ) ; $i++ ) {
2031         if ( ${ $self->{chromo_names} }[$i] eq $chr_nr ) {
2032             $old_chr_index = $i;
2033         }
2034     }
2035
2036     if ( $old_chr_index == ( $chr_count - 1 ) ) { $chr_index = 0; }
2037     else { $chr_index = $old_chr_index + 1; }
2038     return ${ $self->{chromo_names} }[$chr_index];
2039 }
2040
2041 sub get_preceding_comp_chromosome {
2042     my $self   = shift;
2043     my $chr_nr = shift;
2044     if ( !( $self->get_comp_map() ) ) {
2045         return "?";
2046     }
2047     my $chr_count     = scalar( @{ $self->{comp_chromo_names} } );
2048     my $chr_index     = 0;
2049     my $old_chr_index = 0;
2050
2051     for ( my $i = 0 ; $i < ( @{ $self->{comp_chromo_names} } ) ; $i++ ) {
2052         if ( ${ $self->{comp_chromo_names} }[$i] eq $chr_nr ) {
2053             $old_chr_index = $i;
2054         }
2055     }
2056
2057     if   ( $old_chr_index == 0 ) { $chr_index = $chr_count - 1; }
2058     else                         { $chr_index = $old_chr_index - 1; }
2059     return ${ $self->{comp_chromo_names} }[$chr_index];
2060 }
2061
2062 sub get_next_comp_chromosome {
2063     my $self   = shift;
2064     my $chr_nr = shift;
2065     if ( !( $self->get_comp_map() ) ) {
2066         return "?";
2067     }
2068     else {
2069         my $chr_count     = scalar( @{ $self->{comp_chromo_names} } );
2070         my $chr_index     = 0;
2071         my $old_chr_index = 0;
2072         for ( my $i = 0 ; $i < ( @{ $self->{comp_chromo_names} } ) ; $i++ ) {
2073             if ( ${ $self->{comp_chromo_names} }[$i] eq $chr_nr ) {
2074                 $old_chr_index = $i;
2075             }
2076         }
2077
2078         if ( $old_chr_index == ( $chr_count - 1 ) ) { $chr_index = 0; }
2079         else { $chr_index = $old_chr_index + 1; }
2080         return ${ $self->{comp_chromo_names} }[$chr_index];
2081     }
2082
2083 }
2084
2085 =head2 function display_toolbar()
2086
2087   Synopsis:     displays the toolbar by printing html to STDOUT
2088   Parameters:   none
2089   Returns:      nothing
2090   Side effects: prints html code to STDOUT
2091   Status:       implemented
2092   Example:
2093
2094 =cut
2095
2096 sub display_toolbar {
2097     my $self = shift;
2098
2099    #$self->{scrolldown} = $self->{cM}+2*$self->{unzoomedheight}/$self->{zoom}/3;
2100
2101     $self->{scrolldown_start} =
2102       $self->get_cM_start() + ( $self->{zoom_length} / 2 );
2103     $self->{scrolldown_end} =
2104       $self->get_cM_end() + ( $self->{zoom_length} / 2 );
2105     if ( $self->{scrolldown_end} > $self->get_ref_chr_len() ) {
2106
2107         $self->{scrolldown_end} = $self->get_ref_chr_len();
2108         $self->{scrolldown_start} =
2109           $self->{scrolldown_end} - $self->{zoom_length};
2110     }
2111
2112    #$self->{scrollup}   = $self->{cM}-2*$self->{unzoomedheight}/$self->{zoom}/3;
2113     $self->{scrollup_start} =
2114       $self->get_cM_start() - ( $self->{zoom_length} / 2 );
2115     $self->{scrollup_end} = $self->get_cM_end() - ( $self->{zoom_length} / 2 );
2116     if ( $self->{scrollup_start} < 0 ) {
2117         $self->{scrollup_start} = 0;
2118         $self->{scrollup_end}   = $self->{zoom_length};
2119     }
2120
2121     if ( $self->{zoom_length} == 0 ) { die "ZOOM LENGTH IS 0!\n"; }
2122
2123     #$self->{zoom_in}    = $self->{zoom}+1;
2124     $self->{zoom_in_start} =
2125       $self->get_cM_start() + ( $self->{zoom_length} / 4 );
2126     $self->{zoom_in_end} = $self->get_cM_end() - ( $self->{zoom_length} / 4 );
2127
2128     #$self->{zoom_out}   = $self->{zoom}-1;
2129     $self->{zoom_out_start} =
2130       $self->get_cM_start() - ( $self->{zoom_length} / 4 );
2131     $self->{zoom_out_end} = $self->get_cM_end + ( $self->{zoom_length} / 4 );
2132
2133     if ( $self->{zoom_out_end} > $self->get_ref_chr_len() ) {
2134         $self->{zoom_out_end}   = $self->get_ref_chr_len();
2135         $self->{zoom_out_start} = $self->{zoom_out_end} - $self->{zoom_length};
2136     }
2137
2138     # set buttons to disabled when no zoomed-in chromosome is displayed.
2139     if ( !$self->{show_zoomed} || !$self->get_ref_map()->can_zoom() ) {
2140         $self->{zoom_in_disabled}     = "disabled=\"disabled\"";
2141         $self->{zoom_out_disabled}    = "disabled=\"disabled\"";
2142         $self->{scroll_up_disabled}   = "disabled=\"disabled\"";
2143         $self->{scroll_down_disabled} = "disabled=\"disabled\"";
2144     }
2145
2146     #    if (!$self->map_has_physical($self->{map_id})) {
2147     if ( !$self->get_ref_map()->has_physical() ) {
2148         $self->{physical_disabled} = "disabled=\"disabled\"";
2149     }
2150
2151     if ( !$self->get_ref_map()->has_IL() ) {
2152         $self->{IL_disabled} = qq { disabled="disabled" };
2153     }
2154     else {
2155         $self->{IL_disabled} = "";
2156     }
2157
2158     if ( $self->{show_zoomed} ) {
2159
2160         #$self->{zoom_in_disabled} = "";
2161         $self->{enable_zoom_text}      = "Hide zoomed";
2162         $self->{enable_zoom_value}     = 0;
2163         $self->{toggle_zoomed_section} = 0;
2164     }
2165     else {
2166         $self->{zoom_in_disabled}      = " disabled=\"disabled\" ";
2167         $self->{enable_zoom_text}      = "Show zoomed";
2168         $self->{enable_zoom_value}     = 1;
2169         $self->{toggle_zoomed_section} = 10;
2170     }
2171     if ( !$self->get_ref_map->can_zoom() ) {
2172         $self->{zoomed_button_enabled} = " disabled=\"disabled\" ";
2173     }
2174
2175 #    $self->{next_chromosome} = $self->{chr_nr} + 1;
2176 #    if ($self->{next_chromosome} > $self->{max_chr}) { $self->{next_chromosome} = 1; }
2177
2178     $self->{next_chromosome} =
2179       $self->get_next_chromosome( $self->get_ref_chr() );
2180
2181 #   $self->{preceding_chromosome} = $self->{chr_nr}-1;
2182 #   if ($self->{preceding_chromosome} == 0)  { $self->{preceding_chromosome} = $self->{max_chr}; }
2183
2184     $self->{preceding_chromosome} =
2185       $self->get_preceding_chromosome( $self->get_ref_chr() );
2186
2187 #    $self->{next_comp_chr} = $self->{comp_chr} + 1;
2188 #    if ($self->{next_comp_chr} > $self->{comp_max_chr}) { $self->{next_comp_chr} = 1; }
2189
2190     $self->{next_comp_chr} =
2191       $self->get_next_comp_chromosome( $self->get_comp_chr() );
2192
2193 #   $self->{preceding_comp_chr} = $self -> {comp_chr} -1;
2194 #   if ($self->{preceding_comp_chr} ==0 ) { $self->{preceding_comp_chr} = $self->{comp_max_chr}; }
2195     $self->{preceding_comp_chr} =
2196       $self->get_preceding_comp_chromosome( $self->get_comp_chr() );
2197
2198     #    $self->{imagemap} =    $self->{map}->get_image_map("imagemap");
2199
2200     $self->{marker_map_links} = $self->get_marker_map_links();
2201
2202     my $comp_map_caption   = "";
2203     my $chromo_designation = "chr";
2204     if ( $self->get_comp_chr() =~ /[A-Za-z]/ ) {
2205         $chromo_designation = "linkage group";
2206     }
2207     if ( $self->get_comp_map_version_id() ) {
2208         $comp_map_caption =
2209 "<td>Comparing to $chromo_designation <b>$self->{comp_chr}</b> of map&nbsp;</td><td bgcolor=\"#9999CC\"><a href=\"/cview/map.pl?map_version_id=$self->{comp_map_version_id}\"><b>$self->{comp_map_name}</b></a>&nbsp;</td>";
2210     }
2211
2212     # some legends need to know the state of the script...
2213     $self->get_ref_map()->get_legend()
2214       ->set_state_hashref( $self->get_state_hashref() );
2215     $self->get_ref_map()->get_legend()->set_mode( $self->get_color_model() );
2216     my $color_legend    = $self->get_ref_map()->get_legend()->get_legend_html();
2217     my $toggle_ruler    = !( $self->{show_ruler} );
2218     my $toggle_physical = !( $self->{show_physical} );
2219     my $toggle_IL       = !( $self->{show_IL} );
2220     my $toggle_offsets  = !( $self->get_show_offsets() );
2221
2222     my $toggle_size_select = qq { <select name="size" > };
2223
2224     my @selected = ( '', '', '' );
2225     if    ( $self->{size} =~ /small/i ) { $selected[0] = qq { selected="1" }; }
2226     elsif ( $self->{size} =~ /large/i ) { $selected[2] = qq { selected="1" }; }
2227     else                                { $selected[1] = qq { selected="1" }; }
2228     $toggle_size_select .=
2229       qq { <option value="small" $selected[0] >Small</option> };
2230     $toggle_size_select .=
2231       qq { <option value="normal" $selected[1] >Normal</option> };
2232     $toggle_size_select .=
2233       qq { <option value="large" $selected[2] >Large</option> };
2234     $toggle_size_select .= qq { </select> };
2235
2236     if ( !$self->get_comp_map_version_id() ) {
2237         $self->{hide_comparison} = "disabled=\"disabled\"";
2238     }
2239
2240     $self->{maps_select} =
2241       CXGN::Cview::Utils::get_maps_select( $self->get_dbh(),
2242         $self->get_ref_map()->get_id(), undef, $self->get_db_backend);
2243
2244     my $view_entire_map_link = "&nbsp;View entire comparative map";
2245     if ( $self->get_comp_map_version_id() ) {
2246         $view_entire_map_link =
2247             "&nbsp;<a href=\"/cview/view_maps.pl?center_map_version_id="
2248           . ( $self->get_ref_map()->get_id() )
2249           . "&amp;right_map_version_id=$self->{comp_map_version_id}\">View entire comparative map</a>";
2250     }
2251
2252     $self->{url_map_name} = $self->{ref_map_name};
2253     $self->{url_map_name} =~ s/ /\+/g;
2254
2255     my $show_marker_link = "Show markers between 0 and 0 cM";
2256     if ( $self->{show_zoomed} && $self->get_ref_map()->can_zoom() ) {
2257         $show_marker_link = "<a href=\"/search/markers/markersearch.pl?
2258 w822_pos_start="
2259           . $self->get_cM_start()
2260           . "&amp;w822_pos_end="
2261           . $self->get_cM_end()
2262           . "&amp;w822_maps="
2263           . (
2264             CXGN::Cview::Map::Tools::find_map_id_with_version(
2265                 $self->get_dbh(), $self->get_ref_map()->get_id()
2266             )
2267           )
2268           . "&amp;w822_confs=$self->{confidence}&amp;&amp;w822_submit=Search&amp;w822_chromos="
2269           . $self->get_ref_chr()
2270           . "\"\n>Search markers between "
2271           . ( $self->get_cM_start() ) . " and "
2272           . ( $self->get_cM_end() ) . " "
2273           . $self->get_ref_map()->get_units() . "</a>";
2274     }
2275     $chromo_designation = "chr";
2276     if ( $self->get_ref_chr() =~ /[A-Za-z]/ ) {
2277         $chromo_designation = "linkage group";
2278     }
2279
2280     my $state_hashref = $self->get_state_hashref();
2281
2282     my $scroll_up_button =
2283       CXGN::Cview::Chromosome_view::toolbar_button->new( "Scroll up",
2284         $state_hashref );
2285     $scroll_up_button->set_property( "cM_start", $self->{scrollup_start} );
2286     $scroll_up_button->set_property( "cM_end",   $self->{scrollup_end} );
2287     $scroll_up_button->set_enabled( $self->{scroll_up_disabled} );
2288     my $scroll_up_html = $scroll_up_button->render_string();
2289
2290     my $scroll_down_button =
2291       CXGN::Cview::Chromosome_view::toolbar_button->new( "Scroll down",
2292         $state_hashref );
2293     $scroll_down_button->set_property( "cM_start", $self->{scrolldown_start} );
2294     $scroll_down_button->set_property( "cM_end",   $self->{scrolldown_end} );
2295     $scroll_down_button->set_enabled( $self->{scroll_down_disabled} );
2296     my $scroll_down_html = $scroll_down_button->render_string();
2297
2298     my $zoom_in_button =
2299       CXGN::Cview::Chromosome_view::toolbar_button->new( "Zoom in",
2300         $state_hashref );
2301     $zoom_in_button->set_property( "cM_start", $self->{zoom_in_start} );
2302     $zoom_in_button->set_property( "cM_end",   $self->{zoom_in_end} );
2303     $zoom_in_button->set_enabled( $self->{zoom_in_disabled} );
2304     my $zoom_in_html = $zoom_in_button->render_string();
2305
2306     my $zoom_out_button =
2307       CXGN::Cview::Chromosome_view::toolbar_button->new( "Zoom out",
2308         $state_hashref );
2309     $zoom_out_button->set_property( "cM_start", $self->{zoom_out_start} );
2310     $zoom_out_button->set_property( "cM_end",   $self->{zoom_out_end} );
2311     $zoom_out_button->set_enabled( $self->{zoom_out_disabled} );
2312     my $zoom_out_html = $zoom_out_button->render_string();
2313
2314     my $show_zoomed_button = CXGN::Cview::Chromosome_view::toolbar_button->new(
2315         $self->{enable_zoom_text},
2316         $state_hashref );
2317     $show_zoomed_button->set_enabled( $self->{zoomed_button_enabled} );
2318     $show_zoomed_button->set_property( "show_zoomed",
2319         $self->{toggle_zoomed_section} );
2320
2321     my $show_zoomed_html = $show_zoomed_button->render_string();
2322
2323     my $hide_comparison_button =
2324       CXGN::Cview::Chromosome_view::toolbar_button->new( "Hide comparison",
2325         $state_hashref );
2326     $hide_comparison_button->set_property( "comp_map_version_id", 0 );
2327     $hide_comparison_button->set_property( "comp_chr",            0 );
2328     $hide_comparison_button->set_enabled( $self->{hide_comparison} );
2329     my $hide_comparison_html = $hide_comparison_button->render_string();
2330
2331     my $switch_chromosomes_button =
2332       CXGN::Cview::Chromosome_view::toolbar_button->new( "Switch chromosomes",
2333         $state_hashref );
2334     $switch_chromosomes_button->set_property( "comp_chr",
2335         $self->get_ref_chr() );
2336     $switch_chromosomes_button->set_property( "chr_nr", $self->get_comp_chr() );
2337     $switch_chromosomes_button->set_property( "map_version_id",
2338         $self->get_comp_map_version_id() );
2339     $switch_chromosomes_button->set_property( "", "" );
2340     $switch_chromosomes_button->set_property( "", "" );
2341     $switch_chromosomes_button->set_property( "comp_map_version_id",
2342         $self->get_map_version_id() );
2343     $switch_chromosomes_button->set_enabled( $self->{hide_comparison} );
2344     my $switch_chromosomes_html = $switch_chromosomes_button->render_string();
2345
2346     my $sync_preceding_chr_button =
2347       CXGN::Cview::Chromosome_view::toolbar_button->new( "&lt;&lt;",
2348         $state_hashref );
2349     $sync_preceding_chr_button->set_property( "chr_nr",
2350         $self->{preceding_chromosome} );
2351     $sync_preceding_chr_button->set_property( "comp_chr",
2352         $self->{preceding_comp_chr} );
2353     $sync_preceding_chr_button->set_enabled( $self->{hide_comparison} );
2354     my $sync_preceding_chr_html = $sync_preceding_chr_button->render_string();
2355
2356     my $sync_next_chr_button =
2357       CXGN::Cview::Chromosome_view::toolbar_button->new( "&gt;&gt;",
2358         $state_hashref );
2359     $sync_next_chr_button->set_property( "chr_nr",   $self->{next_chromosome} );
2360     $sync_next_chr_button->set_property( "comp_chr", $self->{next_comp_chr} );
2361     $sync_next_chr_button->set_enabled( $self->{hide_comparison} );
2362     my $sync_next_chr_html = $sync_next_chr_button->render_string();
2363
2364     my $previous_chr_button = CXGN::Cview::Chromosome_view::toolbar_button->new(
2365         $self->{preceding_chromosome} . "&lt;",
2366         $state_hashref );
2367     $previous_chr_button->set_property( "chr_nr",
2368         $self->{preceding_chromosome} );
2369     my $previous_chr_html = $previous_chr_button->render_string();
2370
2371     my $next_chr_button = CXGN::Cview::Chromosome_view::toolbar_button->new(
2372         "&gt;" . $self->{next_chromosome},
2373         $state_hashref );
2374     $next_chr_button->set_property( "chr_nr", $self->{next_chromosome} );
2375     my $next_chr_html = $next_chr_button->render_string();
2376
2377     my $preceding_comp_chr_button =
2378       CXGN::Cview::Chromosome_view::toolbar_button->new(
2379         $self->{preceding_comp_chr} . "&lt;",
2380         $state_hashref );
2381     $preceding_comp_chr_button->set_property( "comp_chr",
2382         $self->{preceding_comp_chr} );
2383     $preceding_comp_chr_button->set_enabled( $self->{hide_comparison} );
2384     my $preceding_comp_chr_html = $preceding_comp_chr_button->render_string();
2385
2386     my $next_comp_chr_button =
2387       CXGN::Cview::Chromosome_view::toolbar_button->new(
2388         "&gt;" . $self->{next_comp_chr},
2389         $state_hashref );
2390     $next_comp_chr_button->set_property( "comp_chr", $self->{next_comp_chr} );
2391     $next_comp_chr_button->set_enabled( $self->{hide_comparison} );
2392     my $next_comp_chr_html = $next_comp_chr_button->render_string();
2393
2394     my $ruler_button =
2395       CXGN::Cview::Chromosome_view::toolbar_button->new( "Ruler",
2396         $state_hashref );
2397     $ruler_button->set_property( "show_ruler", $toggle_ruler );
2398     my $ruler_html = $ruler_button->render_string();
2399
2400     my $physical_map_button =
2401       CXGN::Cview::Chromosome_view::toolbar_button->new( "Physical map",
2402         $state_hashref );
2403     $physical_map_button->set_property( "show_physical", $toggle_physical );
2404     $physical_map_button->set_enabled( $self->{physical_disabled} );
2405     my $physical_map_html = $physical_map_button->render_string();
2406
2407     my $IL_button =
2408       CXGN::Cview::Chromosome_view::toolbar_button->new( "IL", $state_hashref );
2409     $IL_button->set_property( "show_IL", $toggle_IL );
2410     $IL_button->set_enabled( $self->{IL_disabled} );
2411     my $IL_html = $IL_button->render_string();
2412
2413     my $offset_button =
2414       CXGN::Cview::Chromosome_view::toolbar_button->new( "Offsets",
2415         $state_hashref );
2416     $offset_button->set_property( "show_offsets", $toggle_offsets );
2417     $offset_button->set_enabled( $self->{zoom_button_enabled} );
2418     my $offset_html = $offset_button->render_string();
2419
2420 #    my $size_button = CXGN::Cview::Chromosome_view::toolbar_button -> new($size_button_text, $state_hashref);
2421 #    $size_button -> set_property("size", $toggle_size);
2422 #    my $size_html = $size_button -> render_string();
2423
2424     my $errors = $self->get_errors();
2425
2426     my $chr_nr              = $self->get_ref_chr();
2427     my $map_version_id      = $self->get_map_version_id();
2428     my $map_name            = $self->get_ref_map()->get_short_name();
2429     my $zoom                = $self->get_zoom();
2430     my $cM                  = $self->get_cM();
2431     my $show_ruler          = $self->get_show_ruler();
2432     my $show_IL             = $self->get_show_IL();
2433     my $show_offsets        = $self->get_show_offsets();
2434     my $comp_map_version_id = $self->get_comp_map_version_id() || '';
2435     my $comp_chr            = $self->get_comp_chr() || '';
2436     my $color_model         = $self->get_color_model() || '';
2437     my $show_physical       = $self->get_show_physical() || 0;
2438     my $size                = $self->get_size() || 0;
2439     my $show_zoomed         = $self->get_show_zoomed() || 0;
2440     my $confidence          = $self->get_confidence() || -2;
2441     my $hilite              = $self->get_hilite() || '';
2442     my $display_marker_type = $self->get_display_marker_type() || '';
2443     my $cM_start            = $self->get_cM_start() || '';
2444     my $cM_end              = $self->get_cM_end() || '';
2445
2446     my $zoom_range_html = qq {
2447         <form style="margin-bottom:0" >
2448             <input type="hidden" name="map_version_id" value="$map_version_id" />
2449             <input type="hidden" name="chr_nr" value="$chr_nr" size="2" />
2450             <input type="hidden" name="show_ruler" value="$show_ruler" />
2451             <input type="hidden" name="show_IL" value="$show_IL" />
2452             <input type="hidden" name="show_offsets" value="$show_offsets" />
2453             <input type="hidden" name="comp_map_version_id" value="$comp_map_version_id" />
2454             <input type="hidden" name="comp_chr" value="$comp_chr" />
2455             <input type="hidden" name="color_model" value="$color_model" />
2456             <input type="hidden" name="show_physical" value="$show_physical" />
2457             <input type="hidden" name="size" value="$size" />
2458             <input type="hidden" name="show_zoomed" value="1" />
2459             <input type="hidden" name="confidence" value="$confidence" />
2460             <input type="hidden" name="hilite" value="$hilite" />
2461             <input type="hidden" name="marker_type" value="$display_marker_type" />
2462
2463             <b>zoom range:</b> <input name="cM_start" size="3" value="$cM_start" /> to <input name="cM_end" size="3" value="$cM_end" />
2464             <input type="submit" value="show" />
2465             </form>
2466         };
2467
2468     print <<BUTTONS;
2469
2470     $errors
2471
2472
2473     <table summary="" cellpadding="0" cellspacing="0"><tr><td>Viewing $chromo_designation <b>$chr_nr</b> of map &nbsp;</td><td bgcolor="#CC9999"><a href=\"/cview/map.pl?map_version_id=$map_version_id\"><b>$map_name</b></a></td><td>&nbsp;</td>
2474         $comp_map_caption
2475         <td>&nbsp;&nbsp;[<a href="/help/cview.pl">Help</a>]</td>
2476         </tr></table>
2477
2478         <table summary="" cellpadding="0" cellspacing="0"><tr>
2479         <td>
2480
2481         $self->{image_html}
2482
2483         </td></tr></table>
2484
2485             $color_legend
2486
2487
2488 <table summary="" cellpadding="0" cellspacing="0"><tr><td>
2489
2490 $scroll_up_html
2491
2492
2493     </td><td>
2494
2495     $scroll_down_html
2496
2497     </td><td>
2498
2499     $zoom_in_html
2500
2501
2502     </td><td>
2503
2504
2505     $zoom_out_html
2506
2507
2508     </td>
2509
2510     <td>|</td><td>
2511
2512     $show_zoomed_html
2513
2514
2515     </td>
2516
2517     <td width="10">&nbsp;</td><td>
2518
2519     $zoom_range_html
2520     <!-- $show_marker_link -->
2521
2522     </td>
2523
2524     </tr></table>
2525
2526         <table summary="" cellpadding="0" cellspacing="0" border="0">
2527         <tr><td valign="middle" width="120"><b>Compare map to:</b>&nbsp;</td><td valign="middle">$self->{marker_map_links}</td></tr>
2528         </table>
2529
2530         <table summary="" cellpadding="0" cellspacing="0">
2531
2532         <tr><td width="120">&nbsp;</td><td>
2533
2534         $hide_comparison_html
2535
2536
2537 </td>
2538 <td>
2539
2540         $switch_chromosomes_html
2541
2542
2543         </td>
2544
2545
2546
2547         <td>
2548         $view_entire_map_link
2549
2550 </td>
2551
2552         </tr></table>
2553
2554         <table summary=""><tr><td>
2555
2556          <form style="margin-bottom:0"  action="/cview/view_chromosome.pl">
2557
2558          <table summary="" cellpadding="0" border="0" cellspacing="0">
2559          <tr valign="middle"><td valign="middle" width="120">
2560          <b>Jump to map:</b></td><td>$self->{maps_select}</td><td valign="middle">&nbsp;chr&nbsp;</td><td>
2561          <input type="text" name="chr_nr" value="$chr_nr" size="2" />
2562          <input type="hidden" name="zoom" value="$zoom" />
2563          <!-- <input type="hidden" name="cM" value="$cM" /> -->
2564         <input type="hidden" name="cM_start" value="$cM_start" />
2565         <input type="hidden" name="cM_end" value="$cM_end" />
2566          <input type="hidden" name="show_ruler" value="$show_ruler" />
2567          <input type="hidden" name="show_IL" value="$show_IL" />
2568          <input type="hidden" name="show_offsets" value="$show_offsets" />
2569          <input type="hidden" name="comp_map_version_id" value="$comp_map_version_id" />
2570          <input type="hidden" name="comp_chr" value="$comp_chr" />
2571          <input type="hidden" name="color_model" value="$color_model" />
2572          <input type="hidden" name="show_physical" value="$show_physical" />
2573          <input type="hidden" name="size" value="$size" />
2574          <input type="hidden" name="show_zoomed" value="$show_zoomed" />
2575          <input type="hidden" name="confidence" value="$confidence" />
2576          <input type="hidden" name="hilite" value="$hilite" />
2577          <input type="hidden" name="marker_type" value="$display_marker_type" />
2578          <input type="submit" value="Jump" />
2579          </td>
2580          </tr>
2581          </table>
2582          </form>
2583          </td>
2584
2585          <td width="20">&nbsp;</td>
2586
2587          <td>
2588         <form  style="margin-bottom:0" action="/cview/view_chromosome.pl">
2589         <b>Highlight marker:</b>
2590         <input type="text" name="hilite" value="$hilite" size="5" />
2591         <input type="submit" value="Highlight" />
2592         <input type="hidden" name="zoom" value="$zoom" />
2593         <!-- <input type="hidden" name="cM" value="$cM" /> -->
2594         <input type="hidden" name="cM_start" value="$cM_start" />
2595         <input type="hidden" name="cM_end" value="$cM_end" />
2596         <input type="hidden" name="chr_nr" value="$chr_nr" />
2597         <input type="hidden" name="map_version_id" value="$map_version_id" />
2598         <input type="hidden" name="show_ruler" value="$show_ruler" />
2599         <input type="hidden" name="show_IL" value="$show_IL" />
2600         <input type="hidden" name="show_offsets" value="$show_offsets" />
2601         <input type="hidden" name="comp_map_version_id" value="$comp_map_version_id" />
2602         <input type="hidden" name="comp_chr" value="$comp_chr" />
2603         <input type="hidden" name="color_model" value="$color_model" />
2604         <input type="hidden" name="show_zoomed" value="$show_zoomed" />
2605         <input type="hidden" name="confidence" value="$confidence" />
2606         <input type="hidden" name="show_physical" value="$show_physical" />
2607         <input type="hidden" name="size" value="$size" />
2608         <input type="hidden" name="marker_type" value="$display_marker_type" />
2609         </form>
2610         </td>
2611
2612
2613 </tr>
2614         </table>
2615
2616
2617
2618
2619     <table summary="" cellpadding="0" cellspacing="0" border="0"><tr>
2620     <td width="120">&nbsp;</td>
2621     <td colspan="3" align="center"><b>Reference chromosome</b></td>
2622     <td width="20">&nbsp;</td>
2623     <td colspan="3" align="center"><b>Comparison chromosome</b></td>
2624     </tr>
2625     <tr>
2626     <td width="120">&nbsp;</td>
2627     <td align="right">
2628
2629     <table summary="" cellpadding="0" cellspacing="0" border="0"><tr><td>
2630     $sync_preceding_chr_html
2631     </td><td>
2632     $previous_chr_html
2633     </td></tr></table>
2634
2635     </td>
2636     <td align="center" valign="middle">
2637
2638 BUTTONS
2639
2640     unless ( $chr_nr ne "" ) { $chr_nr = "&nbsp;"; }
2641
2642     print <<BUTTONS;
2643
2644     &nbsp;<b>$chr_nr</b>&nbsp; </td>
2645     <td>
2646
2647     $next_chr_html
2648
2649
2650 </td>
2651 <td width="20">&nbsp;</td>
2652 <td align="right">
2653 $preceding_comp_chr_html
2654
2655
2656     </td>
2657     <td align="center" valign="middle">
2658
2659
2660 BUTTONS
2661
2662     unless ( $comp_chr ne "" ) { $comp_chr = "&nbsp;"; }
2663
2664     print <<BUTTONS;
2665
2666     &nbsp;<b>$comp_chr</b>&nbsp;</td>
2667     <td>
2668
2669     <table summary="" cellpadding="0" cellspacing="0" border="0"><tr><td>
2670     $next_comp_chr_html
2671     </td><td>
2672     $sync_next_chr_html
2673     </td></tr></table>
2674
2675 </td>
2676
2677         </tr></table>
2678
2679         <table summary="" cellpadding="0" cellspacing="0">
2680         <tr><td valign="middle" width="120">
2681         <b>Show/hide:</b></td>
2682         <td>
2683
2684         $ruler_html
2685
2686         </td>
2687         <td>
2688         $offset_html
2689         </td>
2690
2691
2692
2693 <td>
2694
2695         $physical_map_html
2696
2697         </td>
2698
2699         <td>
2700
2701         $IL_html
2702
2703
2704         </td>
2705
2706
2707         <td width="30">&nbsp;</td>
2708         <td valign="middle">&nbsp;<b>image size: </b> </td><td>
2709
2710         <form  style="margin-bottom:0" action="/cview/view_chromosome.pl">
2711         $toggle_size_select
2712         <input type="submit" value="change" />
2713         <input type="hidden" name="zoom" value="$zoom" />
2714         <input type="hidden" name="cM_start" value="$cM_start" />
2715         <input type="hidden" name="cM_end" value="$cM_end" />
2716         <input type="hidden" name="chr_nr" value="$chr_nr" />
2717         <input type="hidden" name="map_version_id" value="$map_version_id" />
2718         <input type="hidden" name="show_ruler" value="$show_ruler" />
2719         <input type="hidden" name="show_IL" value="$show_IL" />
2720         <input type="hidden" name="show_offsets" value="$show_offsets" />
2721         <input type="hidden" name="comp_map_version_id" value="$comp_map_version_id" />
2722         <input type="hidden" name="comp_chr" value="$comp_chr" />
2723         <input type="hidden" name="color_model" value="$color_model" />
2724         <input type="hidden" name="show_zoomed" value="$show_zoomed" />
2725         <input type="hidden" name="confidence" value="$confidence" />
2726         <input type="hidden" name="show_physical" value="$show_physical" />
2727         <input type="hidden" name="marker_type" value="$display_marker_type" />
2728         </form>
2729
2730
2731
2732
2733         </td>
2734 </tr></table>
2735
2736 BUTTONS
2737
2738 }
2739
2740 sub clean_up {
2741     my $self = shift;
2742 }
2743
2744 =head2 accessors set_state_hashref(), get_state_hashref()
2745
2746   Property:     the state_hashref is a hash describing the current
2747                 state of the ChromosomeViewer, essentially collecting
2748                 all the processed page arguments.
2749   Args/Ret:     a hash reference
2750   Side Effects: the state_hashref determines what the toolbar buttons
2751                 and links constructed on the page will contain as
2752                 parameters.
2753
2754 =cut
2755
2756 sub get_state_hashref {
2757     my $self = shift;
2758     return $self->{state_hashref};
2759 }
2760
2761 sub set_state_hashref {
2762     my $self = shift;
2763     $self->{state_hashref} = shift;
2764 }
2765
2766 =head2 accessors set_force(), get_force()
2767
2768   Property:     force - regenerate cached files whatever the
2769                 status of the cache
2770   Args/Ret      true for re-generation, false for letting cache
2771                 decide when to re-generate the images.
2772   Side Effects: true will force regenerate all associated files
2773   Description:
2774
2775 =cut
2776
2777 sub get_force {
2778     my $self = shift;
2779     if ( !exists( $self->{force} ) || !defined( $self->{force} ) ) {
2780         $self->{force} = "";
2781     }
2782     return $self->{force};
2783 }
2784
2785 sub set_force {
2786     my $self = shift;
2787     $self->{force} = shift;
2788 }
2789
2790 =head2 get_temp_dir
2791
2792  Usage:
2793  Desc:
2794  Ret:
2795  Args:
2796  Side Effects:
2797  Example:
2798
2799 =cut
2800
2801 sub get_temp_dir {
2802     my $self = shift;
2803     if ( !exists( $self->{temp_dir} ) ) {
2804         die "ChromosomeViewer: need a temp_dir  for storing images... STOP!\n";
2805     }
2806
2807     return $self->{temp_dir};
2808
2809 }
2810
2811 =head2 set_temp_dir
2812
2813  Usage:
2814  Desc:
2815  Ret:
2816  Args:
2817  Side Effects:
2818  Example:
2819
2820 =cut
2821
2822 sub set_temp_dir {
2823     my $self = shift;
2824     $self->{temp_dir} = shift;
2825 }
2826
2827 =head2 get_basedir
2828
2829  Usage:
2830  Desc:
2831  Ret:
2832  Args:
2833  Side Effects:
2834  Example:
2835
2836 =cut
2837
2838 sub get_basedir {
2839     my $self = shift;
2840     if ( !exists( $self->{basedir} ) ) {
2841         die "ChromosomeViewer: need a basedir for storing images... STOP!\n";
2842     }
2843     return $self->{basedir};
2844
2845 }
2846
2847 =head2 set_basedir
2848
2849  Usage:
2850  Desc:
2851  Ret:
2852  Args:
2853  Side Effects:
2854  Example:
2855
2856 =cut
2857
2858 sub set_basedir {
2859     my $self = shift;
2860     $self->{basedir} = shift;
2861 }
2862
2863 =head2 accessors get_db_backend, set_db_backend
2864
2865  Usage:        $v ->set_db_backend("cxgn");
2866  Desc:         sets the db backend of the comparative viewer.
2867                following values are allowed:
2868                o cxgn - the cxgn database
2869                o cmap - the cmap database
2870                o cxgn_and_cmap - both databases are queried for maps.
2871  Property      a string describing the database backend to be used.
2872  Side Effects: the specified backend will be used
2873
2874 =cut
2875
2876 sub get_db_backend {
2877     my $self = shift;
2878     return $self->{db_backend} || 'cxgn';
2879 }
2880
2881 sub set_db_backend {
2882     my $self = shift;
2883     $self->{db_backend} = shift;
2884 }
2885
2886 =head2 accessors get_context, set_context
2887
2888  Usage:        $cv -> set_context( CXGN::Context->new() );
2889  Property:     A context object
2890  Side Effects: The context object provides things like temp
2891                file locations, etc.
2892  Example:
2893
2894 =cut
2895
2896 sub get_context {
2897     my $self = shift;
2898     return $self->{context};
2899 }
2900
2901 sub set_context {
2902     my $self = shift;
2903     $self->{context} = shift;
2904 }
2905
2906 package CXGN::Cview::Chromosome_view::toolbar_button;
2907
2908 sub new {
2909     my $class = shift;
2910     my $args  = {};
2911     my $self  = bless $args, $class;
2912
2913     my $name = shift;
2914
2915     my $properties_hashref = shift;
2916
2917     $self->set_name($name);
2918
2919     %{ $self->{properties} } = (
2920         'chr_nr'              => "",
2921         'map_version_id'      => "",
2922         'zoom'                => "",
2923         'show_ruler'          => "",
2924         'show_IL'             => "",
2925         'show_offsets'        => "",
2926         'comp_map_version_id' => "",
2927         'comp_chr'            => "",
2928         'color_model'         => "",
2929         'show_zoomed'         => "",
2930         'show_physical'       => "",
2931         'confidence'          => "",
2932         'size'                => "",
2933         'hilite'              => "",
2934         'marker_type'         => "",
2935         'cM_start'            => "",
2936         'cM_end'              => "",
2937         'cM'                  => "",
2938         'clicked'             => "",
2939     );
2940
2941     foreach my $k ( keys(%$properties_hashref) ) {
2942         if ( exists( ${ $self->{properties} }{$k} ) ) {
2943             ${ $self->{properties} }{$k} = $$properties_hashref{$k};
2944         }
2945         else {
2946             print STDERR
2947               "property $k is not supported in toolbar_button package.\n";
2948         }
2949     }
2950     return $self;
2951 }
2952
2953 sub set_name {
2954     my $self = shift;
2955     $self->{name} = shift;
2956 }
2957
2958 sub get_name {
2959     my $self = shift;
2960     return $self->{name};
2961 }
2962
2963 sub set_action {
2964     my $self = shift;
2965     $self->{action} = shift;
2966 }
2967
2968 sub get_action {
2969     my $self = shift;
2970     if ( !exists( $self->{action} ) ) { $self->{action} = ""; }
2971     return $self->{action};
2972 }
2973
2974 sub set_enabled {
2975
2976     # parameter: true or false setting to enabled or disabled
2977     #
2978     my $self = shift;
2979     $self->{enabled} = shift;
2980 }
2981
2982 sub is_enabled {
2983     my $self = shift;
2984     return $self->{enabled};
2985 }
2986
2987 sub set_property {
2988     my $self     = shift;
2989     my $property = shift;
2990     my $value    = shift;
2991     if ( !$value ) { $value = ""; }
2992     if ( !exists( ${ $self->{properties} }{$property} ) ) {
2993         print STDERR
2994           "Warning: toolbar_button: property $property does not exist!\n";
2995         return 0;
2996     }
2997     else {
2998         ${ $self->{properties} }{$property} = $value;
2999         return 1;
3000     }
3001 }
3002
3003 sub render_string {
3004     my $self = shift;
3005
3006     my $action = $self->get_action();
3007
3008     if ( $action eq "" ) {
3009         $action = "#";
3010     }
3011     my $s = "<form style=\"margin-bottom:0\" action=\"$action\">\n";
3012
3013     foreach my $p ( keys %{ $self->{properties} } ) {
3014
3015 #print STDERR "Printing toolbar button: hidden field: $p, $self->{properties}{$p}\n";
3016         if ( exists( $self->{properties}{$p} ) && $self->{properties}{$p} ) {
3017             $s .=
3018 "<input type=\"hidden\" name=\"$p\" value=\"$self->{properties}{$p}\" />\n";
3019         }
3020
3021     }
3022
3023     my $disabled;
3024     if ( $self->is_enabled() ) {
3025         $disabled = "disabled=\"disabled\"";
3026     }
3027     else {
3028         $disabled = "";
3029     }
3030     $s .=
3031         "<input type=\"submit\" value=\""
3032       . $self->get_name()
3033       . "\" $disabled />\n";
3034     $s .= "</form>\n";
3035     return $s;
3036 }
3037
3038 sub render {
3039     my $self = shift;
3040     print $self->render_string();
3041 }
3042
3043 1;