lib/CXGN/Cview/Chromosome_viewer.pm

   1
   2 use strict;
   3
   4 package CXGN::Cview::Chromosome_viewer;
   5
   6 use CXGN::VHost;
   7 use CXGN::DB::Connection;
   8 use File::Spec;
   9 use CXGN::Tools::WebImageCache;
  10 use CXGN::Cview::Map::Tools;
  11 use CXGN::Cview;
  12 use CXGN::Cview::Utils qw | set_marker_color get_maps_select get_chromosome_links|;
  13 use CXGN::Cview::MapImage;
  14 use CXGN::Cview::Chromosome;
  15 use CXGN::Cview::Chromosome::Physical;
  16 use CXGN::Cview::Chromosome::PachyteneIdiogram;
  17 use CXGN::Cview::IL;
  18 use CXGN::Cview::ChrLink;
  19 use CXGN::Cview::MapFactory;
  20
  21
  22 use base qw | CXGN::DB::Object |;
  23
  24 return 1;
  25
  26 =head1 NAME
  27
  28 CXGN::Cview::Chromosome_viewer -- a module to display comparative chromosome maps
  29
  30 =head1 SYNOPSIS
  31
  32  my $viewer = chromosome_viewer -> new();
  33  $viewer -> set_map_id($map_id);
  34  $viewer -> set_map_version_id($map_version_id);
  35  $viewer -> set_ref_chr($chr_nr);
  36  $viewer -> set_cM($cM);
  37  $viewer -> set_zoom($zoom);
  38  $viewer -> set_show_physical($show_physical);
  39  $viewer -> set_show_ruler($show_ruler);
  40  $viewer -> set_show_IL($show_IL);
  41  $viewer -> set_comp_map_id($comp_map_id);
  42  $viewer -> set_comp_map_version_id($comp_map_version_id);
  43  $viewer -> set_comp_chr($comp_chr);
  44  $viewer -> set_color_model($color_model);
  45  if ($map_chr_select) {
  46      my ($comp_map_id, $comp_chr) = split / /, $map_chr_select;
  47      $viewer->set_comp_map_id($comp_map_id);
  48      $viewer->set_comp_chr($comp_chr);
  49  }
  50  $viewer -> set_cM_start($cM_start);
  51  $viewer -> set_cM_end($cM_end);
  52  $viewer -> set_confidence($confidence);
  53  $viewer -> set_show_zoomed($show_zoomed);
  54  $viewer -> set_hilite_zoomed($zoomed_hilite_start, $zoomed_hilite_end);
  55  $viewer -> set_force($force);
  56
  57  $viewer -> generate_page();
  58
  59 =head1 DESCRIPTION
  60
  61 =head2 Image Caching
  62
  63 Chromosome_viewer caches the images it produces using CXGN::Tools::WebImageCache. The expiration time is set to a day or so.
  64
  65 The cache for the image generated by any given URL can be reset by setting the force parameter to 1.
  66
  67
  68 =head1 AUTHOR(S)
  69
  70 Lukas Mueller (lam87@cornell.edu)
  71
  72 =head1 FUNCTIONS
  73
  74 The following functions are defined in the class:
  75
  76 =cut
  77
  78
  79 =head2 function new()
  80
  81   Synopsis:     generates a new chromosome_viewer object
  82   Parameters:   $dbh - a database handle
  83   Returns:      an object handle
  84   Side effects: sets some useful default values, creates an SGN page object and
  85                 establishes a connection to the database through the page object.
  86   Status:       implemented
  87   Example:
  88
  89 =cut
  90
  91
  92 sub new {
  93     my $class = shift;
  94     my $dbh = shift;
  95
  96     if (! $dbh) { die "Chromosome_viewer now takes a dbh parameter."; }
  97     my $self = $class->SUPER::new($dbh, @_);
  98
  99     $self -> {unzoomedheight} = 20; # how many cM are seen at zoom level 1
 100 #    $self -> {raster_size} = 5;    # the default raster size for genetic maps
 101                                     # for sequence-based maps this will be changed to 1
 102                                     # later on.
 103     $self->set_temp_dir("/tmp");    # set some default for the temp_dir. However, this
 104                                     # should be visible by apache (which tmp isn't).
 105     return $self;
 106 }
 107
 108 =head2 function _adjust_parameters()
 109
 110   Synopsis:     adjusts parameters; needs to be called before calling generate_image
 111   Parameters:   none
 112   Returns:      nothing
 113   Side effects: adjusts parameters to make program more robust against out-of-range
 114                 parameters
 115   Status:       implemented
 116   Example:
 117   Notes:        this function is only used internally
 118
 119 =cut
 120
 121 sub _adjust_parameters {
 122     my $self = shift;
 123
 124     # initialize some variables to prevent undefined blabla errors
 125     $self->{fatal_errors}="";
 126     if (!$self->get_ref_chr()) { $self->set_ref_chr(1); }
 127     if (!$self->get_hilite()) { $self->set_hilite(""); }
 128     if (!($self->get_cM_start())) { $self->set_cM_start(0); }
 129
 130 #    print STDERR "\n *** Map ID is : ".($self->get_map_id())." ***\n";
 131
 132     # It's possible for our objects to have empty strings for map_id attributes.
 133     # The following weirdness preserves the interface invariant that get_map_id sets
 134     # a desirable default map_id.
 135
 136     my $map_id = $self->get_map_id();
 137
 138     if ($self->get_map_version_id()) {
 139         $self->set_map_id(0);
 140     }
 141
 142     if ($self->get_comp_map_version_id()) {
 143         $self->set_comp_map_id(0);
 144     }
 145
 146     if (!$self->get_map_version_id() && $map_id eq '') {
 147         $self->set_map_id(undef);
 148         $map_id = $self->get_map_id();
 149     }
 150
 151     # generate the map objects
 152     #
 153     my $map_factory = CXGN::Cview::MapFactory->new($self->get_dbh(), $self->get_db_backend());
 154 #    print STDERR "Generating MapFactory with id ".$self->get_map_version_id()."\n";
 155 #    print STDERR "IS A ".ref($map_factory)."\n";
 156
 157     $self->set_ref_map( $map_factory->create( {map_version_id => $self->get_map_version_id(), map_id => $self->get_map_id()} ));
 158
 159     if (!$self->get_ref_map()) {
 160         # if an illegal map id was supplied, create a default map.
 161         $self->set_ref_map( $map_factory->create({map_id=> CXGN::Cview::Map::Tools::current_tomato_map_id()}) );
 162         $self->append_error("Note: Displaying default map, F2-2000.");
 163     }
 164
 165     $self->{ref_map_name}=$self->get_ref_map()->get_short_name();
 166     $self->set_map_version_id($self->get_ref_map()->get_id());
 167     $self->{ref_map_type}=$self->get_ref_map()->get_type();
 168
 169     if ($self->get_comp_map_id() || $self->get_comp_map_version_id()) {
 170         $self->set_comp_map( $map_factory->create( { map_version_id =>$self->get_comp_map_version_id(), map_id => $self->get_comp_map_id() } ) );
 171                                             #   { map_id => $self->get_comp_map_id(),
 172                                         #        map_version_id => $self->get_comp_map_version_id(),
 173                                          #    }
 174                                           #     ));
 175     }
 176
 177
 178     # define the comparison map
 179     #
 180     if ($self->get_comp_map()) {
 181         $self->{comp_map_name} = $self->get_comp_map()->get_short_name();
 182         $self->set_comp_map_version_id($self->get_comp_map()->get_id());
 183         $self->{comp_map_type} = $self->get_comp_map()->get_type();
 184 #    @{$self->{comp_chromo_names}} = $self->get_chr_names($self->get_comp_map_id());
 185         @{$self->{comp_chromo_names}} = $self->get_comp_map()->get_chromosome_names();
 186         #$self->{comp_max_chr} = $self->get_chr_count($self->get_comp_map_id());
 187         $self->{comp_max_chr} = scalar(@{$self->{comp_chromo_names}});
 188     }
 189
 190     # test if the supplied chromosome is a legal chromosome on the specific map.
 191     # if not, try to find a close match.
 192     #
 193     #if (!$self->is_ok_chr($self->get_map_id(), $self->get_ref_chr())) {
 194     if (!$self->get_ref_map()->has_linkage_group($self->get_ref_chr())) {
 195 #       print STDERR "chr ".$self->get_ref_chr()." is not a valid chromosome\n";
 196         my $old_chr = $self->get_ref_chr();
 197         my $chr = $old_chr;
 198         $chr =~ s/.*(\d{1,2}.*)/$1/;
 199         #if (!$self->is_ok_chr($self->get_map_id(), $chr)) {
 200         if (!$self->get_ref_map()->has_linkage_group($chr)) {
 201             $chr =~ s/.*(\d).*/$1/;
 202         }
 203         if (!$self->get_ref_map()->has_linkage_group($chr)) {
 204             #$self->append_errors("The specified chromosome ($old_chr) was not found on map $self->{ref_map_name}!<br /><br />");
 205             $self->set_ref_chr(1);
 206         }
 207         else {
 208             $self->set_ref_chr($chr);
 209             $self->append_error("The chromosome/linkage group $old_chr does not seem to exist on map ".$self->get_ref_map()->get_short_name().". The closest we could find was $chr, displayed below.<br /><br />");
 210         }
 211     }
 212
 213
 214     # if no map_id was supplied, we show the F2.2000 as default
 215     #
 216     if (!$self->get_map_id()) { $self->set_map_id(CXGN::Cview::Map::Tools::current_tomato_map_id()); }
 217
 218 #    @{$self->{chromo_names}} = $self->get_chr_names($self->{map_id});
 219     @{$self->{chromo_names}} = $self->get_ref_map()->get_chromosome_names();
 220
 221     #$self->{max_chr} = $self->get_chr_count($self->get_map_id());;
 222     # get the number of chromosomes of the map.
 223     #
 224     $self->{max_chr} = scalar($self->get_ref_map()->get_chromosome_count());
 225
 226     if ($self->get_ref_chr()<0) { $self->set_ref_chr(abs($self->get_ref_chr())); }
 227
 228      # set the default zoom size in MB for sequence maps
 229      #
 230     $self->{unzoomedheight}=$self->get_ref_map()->initial_zoom_height();
 231 #       $self->{unzoomedheight}=4;
 232 #     }
 233
 234     #
 235     # adjust cM_start and cM_end if the chromosome was clicked.
 236     #
 237 #    if ((($self->get_cM_start()==0) && ($self->get_cM_end()==0)) || ($self->get_cM_end()-$self->get_cM_start()==0)) {
 238
 239     $self->set_ref_chr_len($self->get_ref_map()->get_chr_len_by_name($self->get_ref_chr()));
 240     if ($self->get_cM_start() > $self->get_cM_end()) {
 241         $self->set_cM_start($self->get_cM_end());
 242         $self->set_cM_end($self->get_cM_start() + $self->get_ref_map()->initial_zoom_height());
 243     }
 244
 245     $self->{zoom_length} = $self->get_cM_end() - $self->get_cM_start();
 246
 247     if ($self->{zoom_length} == 0) {
 248         $self->{zoom_length} = $self->get_ref_map()->initial_zoom_height();
 249     }
 250
 251     if ($self->get_clicked()) {
 252
 253
 254         #die "Was going to reset cM_start and cM_end (cM defined... ".($self->get_cM()).")\n";
 255         my $start = $self->get_cM()-($self->{zoom_length}/2);
 256         my $end = $self->get_cM()+($self->{zoom_length}/2);
 257
 258         if ($start < 0 ) {
 259             $start = 0;
 260             $end = $self->{zoom_length};
 261         }
 262
 263 #       print STDERR "REF CHR: ".$self->get_ref_chr()."\n";
 264
 265         if ($end > $self->get_ref_chr_len()) {
 266             $end = $self->get_ref_chr_len();
 267             $start = $end - $self->{zoom_length};
 268         }
 269
 270         $self->set_cM_start($start);
 271         $self->set_cM_end($end);
 272
 273     }
 274 #    $self->set_clicked(0);
 275
 276     # adjust the cM start value if it is below zero. This could (but shouldn't) happen
 277     # during scrolling and zooming operations.
 278     #
 279     if ($self->get_cM_start() < 0) {
 280         $self->set_cM_start(0);
 281         $self->set_cM_end($self->{zoom_length});
 282         $self->set_cM(($self->get_cM_start()+$self->get_cM_end())/2);
 283     }
 284     if ($self->get_cM_end() > $self->get_ref_chr_len()) {
 285         my $end =  $self->get_ref_chr_len();
 286         $self->set_cM_end($end);
 287         $self->set_cM_start($end-$self->{zoom_length});
 288     }
 289
 290     if (!$self->{ref_map_name}) { $self->{fatal_errors} .= "Fatal error: The map id you entered is invalid.<br />"; }
 291
 292     if ($self->get_show_physical() && (!$self->get_ref_map()->has_physical())) {
 293         $self->append_error("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 /> ");
 294         $self->set_show_physical(0);
 295     }
 296
 297     my $message="";
 298     if ($self->get_confidence()==0) { $message= "I(LOD<2) and above [all]"; }
 299     elsif ($self->get_confidence()==1) { $message = "I(LOD2) and above"; }
 300     elsif ($self->get_confidence()==2) { $message = "CF(LOD3) and above"; }
 301     elsif ($self->get_confidence()==3) { $message = "F(LOD>=3)"; }
 302     if ($self->get_confidence()>-2) { $self->append_error("Only showing confidence of $message\n<p />"); }
 303
 304     # note: the force parameter is not part of the state hashref, because it
 305     # would change the key and thus the cache file name.
 306     #
 307     my $state_hashref = {
 308                          chr_nr => $self->get_ref_chr(),
 309                          map_version_id => $self->get_map_version_id(),
 310                          cM     => $self->{cM},
 311                          show_ruler => $self->{show_ruler},
 312                          show_IL => $self->{show_IL},
 313                          show_offsets => $self->get_show_offsets(),
 314                          comp_map_version_id => $self->get_comp_map_version_id(),
 315                          comp_chr => $self->{comp_chr},
 316                          color_model => $self->{color_model},
 317                          show_physical => $self->{show_physical},
 318                          size => $self->{size},
 319                          show_zoomed => $self->{show_zoomed},
 320                          confidence => $self->{confidence},
 321                          hilite => $self->{hilite},
 322                          marker_type => $self->{display_marker_type},
 323                          cM_start => $self->get_cM_start(),
 324                          cM_end => $self->get_cM_end(),
 325                          #clicked => $self->get_clicked(),
 326
 327                      };
 328
 329 #    print STDERR "STATE HASHREF CONTENTS: \n";
 330 #    foreach my $k (%$state_hashref) {
 331 ##      print STDERR "$k = $$state_hashref{$k}.\n";
 332 #    }
 333     $self->set_state_hashref($state_hashref);
 334
 335 }
 336
 337
 338 =head2 function generate_page()
 339
 340   Synopsis:     generates the  page to STDOUT in html
 341   Parameters:   none
 342   Returns:      nothing
 343   Side effects:
 344   Status:       implemented
 345   Example:
 346
 347 =cut
 348
 349 sub generate_page {
 350     my $self = shift;
 351    if ($self->{fatal_errors}) { return; }
 352
 353     $self->_adjust_parameters();
 354
 355     $self->get_image();
 356     $self->display_toolbar();
 357
 358 }
 359
 360 =head2 function get_image()
 361
 362   Synopsis:     generates the viewer image as a png file
 363   Parameters:   none
 364   Returns:      an array with the image path (semi-absolute) and the image url
 365   Side effects: creates the image and stores it into a file
 366   Status:       implemented
 367   Example:
 368
 369 =cut
 370
 371 sub get_image {
 372     my $self = shift;
 373
 374     my $cache = CXGN::Tools::WebImageCache->new();
 375     my $state_hashref = $self->get_state_hashref();
 376 #    my $vhost_conf=CXGN::VHost->new();
 377     my @sorted_values = map { $state_hashref->{$_} } sort keys %$state_hashref;
 378     my $key = join "-", @sorted_values;
 379 #    print STDERR "USING KEY: $key\n";
 380     $cache->set_key($key);
 381     $cache->set_expiration_time(86400);
 382     $cache->set_basedir($self->get_basedir());
 383     #vhost_conf->get_conf('basepath'));
 384     $cache->set_temp_dir($self->get_temp_dir());
 385 #File::Spec->catfile($vhost_conf->get_conf('tempfiles_subdir'), "/cview"));
 386     $cache->set_map_name("imagemap");
 387     $cache->set_force( $self->get_force() );
 388
 389     if (! $cache->is_valid()) {
 390         $self->generate_image();
 391         $cache->set_image_data( $self->{map}->render_png_string() );
 392         $cache->set_image_map_data( $self->{map}->get_image_map("imagemap") );
 393     }
 394     $self->{image_html}= $cache->get_image_html();
 395 }
 396
 397
 398
 399 sub generate_image {
 400     my $self = shift;
 401
 402     my $x_distance = 120; # the number of pixels the different elements are spaced
 403     my $element_count = 0.5; # the number of elements currently placed
 404
 405     my $map_width = 500;
 406
 407     if ($self->get_show_zoomed()) {
 408         $map_width+=$x_distance;
 409     }
 410     if ($self->get_show_IL()) { $map_width+=$x_distance; }
 411
 412     #print STDERR "Size requested: $self->{size}\n";
 413     if ($self->get_size() =~ /small/i) {
 414         $self->{map_height} = 300;
 415         $self->set_chr_height(230);
 416     }
 417     elsif ($self->get_size()=~ /large/i) {
 418         $self->{map_height} = 800;
 419         $self->set_chr_height(650);
 420     }
 421     else {
 422         $self->{map_height} = 470;
 423         $self->set_chr_height(400);
 424     }
 425
 426     #print STDERR "Chr height: $self->{chr_height}\n";
 427     $self->{map} = CXGN::Cview::MapImage -> new("", $map_width, $self->{map_height});
 428
 429     # show IL lines if requested
 430     #
 431     if ($self->get_show_IL() && $self->get_ref_map()->has_IL()) {
 432         my $map_factory = CXGN::Cview::MapFactory->new($self->get_dbh(), $self->get_db_backend());
 433         #print STDERR "Current map_id = ".$self->get_map_id()."\n";
 434         my $IL_map = $map_factory->create({ map_version_id=>"il6.".($self->get_map_id()) });
 435         $self->{IL} = $IL_map->get_chromosome($self->get_ref_chr());
 436
 437         $self->{IL} -> set_height($self->get_chr_height());
 438         $self->{IL} -> set_horizontal_offset($x_distance*$element_count, 40);
 439         $self->{IL} -> set_vertical_offset(40);
 440         $self->{IL} -> set_caption("IL");
 441
 442         $self->{map}->add_chromosome($self->{IL});
 443         $element_count=$element_count+0.95;
 444     }
 445
 446     elsif ($self->get_show_IL() && !$self->get_ref_map()->has_IL()) {
 447         $self->append_error("You chose to display the IL information for a map that has no associated IL information.
 448                            The IL display has been turned off.<P>");
 449         $self->set_show_IL(0);
 450     }
 451
 452     # show the physical map if requested
 453     #
 454     if ($self->get_show_physical()) {
 455         my $map_factory = CXGN::Cview::MapFactory->new($self->get_dbh(), $self->get_db_backend());
 456
 457         my $physical_map = $map_factory -> create ( {map_version_id => "p9"});
 458
 459         # we get the overview chromosome, because it is more compact for the comparison
 460         #
 461         $self->{p} = $physical_map->get_overview_chromosome($self->get_ref_chr());
 462         $self->{p}->set_horizontal_offset($x_distance*$element_count);
 463         $self->{p}->set_vertical_offset(40);
 464         $self->{p}->set_height($self->get_chr_height());
 465
 466         $self->{map}->add_physical($self->{p});
 467     }
 468
 469     # add the chromosome
 470     #
 471     $element_count++;
 472
 473     $self->{c1} = $self->get_ref_map()->get_chromosome($self->get_ref_chr());
 474     #if ($self->get_show_offsets()) { $self->{c1}->set_display_marker_offset(); }
 475     #
 476     # adjust the appearance of the chromosome
 477     #
 478     $self->{c1}->set_height($self->get_chr_height());
 479     $self->{c1}->set_vertical_offset(40);
 480     $self->{c1}->set_horizontal_offset($x_distance * $element_count);
 481     $self->{c1}->set_caption($self->get_ref_chr());
 482     $self->{c1}->set_labels_left();
 483     $self->{c1}->set_units( $self->get_ref_map()->get_units() );
 484     $self->{c1}->set_width( $self->get_ref_map()->get_preferred_chromosome_width() );
 485
 486     $self->append_error($self->get_ref_map()->get_messages());
 487     my @m = $self->{c1}->get_markers();
 488     #
 489     # get the markers and determine the highest confidence level
 490     #
 491     my $highest = -1;
 492     foreach my $m (@m) {
 493         if ($m->get_confidence()>$highest) { $highest = $m->get_confidence(); }
 494     }
 495     my @fm = ();
 496     foreach my $m (@m) {
 497         if ($m->get_confidence() == $highest) { push @fm, $m; }
 498
 499     }
 500
 501     my $interval = 0;
 502     if ($self->get_ref_map()->collapsed_marker_count()) {
 503         $interval = @fm/$self->get_ref_map()->collapsed_marker_count();
 504     }
 505
 506
 507     if (@m<$self->get_ref_map()->collapsed_marker_count()) { $interval=1; }
 508     my $frame_marker_count =0;
 509     for (my $i=0; $i<@m; $i++) {
 510         $m[$i]->hide_label();
 511         #
 512         # show label if it is hilited...
 513         #
 514         my $marker_name = $m[$i]->get_name();
 515         if ($self->get_hilite()=~ /\b$marker_name\b/i) {
 516             $m[$i]->show_label();
 517             $m[$i]->hilite();
 518         }
 519         #
 520         # otherwise only show one in $interval markers of the
 521         # highest confidence
 522         #
 523         if ($interval >0) {
 524             if ($m[$i]->get_confidence() == $highest) {
 525                 if ($interval > 1) {
 526                     if ($frame_marker_count % $interval==0) {
 527                         $m[$i] -> show_label();
 528                     }
 529
 530                 }
 531                 else { $m[$i]->show_label(); }
 532                 $frame_marker_count++;
 533             }
 534         }
 535
 536         #else { $m[$i]->set_url("/search/markers/markerinfo.pl?id=".$m[$i]->get_marker_name()); }
 537         set_marker_color($m[$i], $self->get_color_model());
 538         if ($m[$i]->get_confidence() < $self->get_confidence()) { $m[$i]->hide_label(); }
 539     }
 540
 541     #
 542     # make the chromosome clickable using the rasterize function and
 543     # add the url
 544     #
 545     #my $raster_size = int($self->{c1}->get_length() / 20) || 2;
 546     if ($self->get_ref_map()->can_zoom()) {
 547         $self->{c1}->rasterize(1); #$raster_size);
 548         $self->{c1}->set_rasterize_link("view_chromosome.pl?map_version_id=".($self->get_map_version_id())."&amp;chr_nr=".($self->get_ref_chr())."&amp;show_physical=".($self->get_show_physical())."&amp;show_IL=".($self->get_show_IL())."&amp;show_ruler=".($self->get_show_ruler())."&amp;show_offsets=".($self->get_show_offsets())."&amp;color_model=".($self->get_color_model())."&amp;comp_map_version_id=".($self->get_comp_map_version_id())."&amp;comp_chr=".($self->get_comp_chr())."&amp;zoom=".($self->get_zoom())."&amp;size=".($self->get_size())."&amp;hilite=".($self->get_hilite())."&amp;confidence=".($self->get_confidence())."&amp;show_zoomed=1&amp;marker_type=".($self->get_display_marker_type())."&amp;cM_start=".($self->get_cM_start())."&amp;cM_end=".($self->get_cM_end())."&amp;clicked=1&amp;cM=");
 549     }
 550
 551     $self->{map} -> add_chromosome($self->{c1});
 552     #
 553     # show the ruler if requested
 554     #
 555     if ($self->get_show_ruler()) {
 556         $self->{r} = $self->{c1}->get_ruler();
 557         $self->{r}->set_horizontal_offset($x_distance/6);
 558         $self->{r}->set_vertical_offset(40);
 559         $self->{r}->set_height($self->get_chr_height());
 560         $self->{r}->set_start_value(0);
 561         $self->{r}->set_end_value($self->{c1}->get_length());
 562         $self->{map}->add_ruler($self->{r});
 563     }
 564     #
 565     # draw the chromosome section if a chromosome section was requested
 566     # (that is, if cM is defined)
 567     #
 568
 569     my $x_offset = 200;
 570     my @m2; # the markers on c2. Keep for later use.
 571     if ($self->{show_zoomed} && $self->get_ref_map()->can_zoom()) {
 572
 573         $element_count++;
 574
 575         #$self->{c2} = CXGN::Cview::Chromosome -> new ($self->get_ref_chr(), $self->get_chr_height(), $x_distance*$element_count, 40);
 576         $self->{c2} = $self->get_ref_map()->get_chromosome_section($self->get_ref_chr(), $self->get_cM_start(), $self->get_cM_end(), $self->get_comp_chr());
 577         if ($self->get_show_offsets()) { $self->{c2}->set_display_marker_offset(); }
 578         $self->{c2}->set_height($self->get_chr_height());
 579         $self->{c2}->set_vertical_offset(40);
 580         $self->{c2}->set_hilite($self->get_hilite_zoomed());
 581         $self->{c2}->set_horizontal_offset($x_distance*$element_count);
 582
 583
 584         # because we have incomplete length information from the query above,
 585         # we set the length of the zoomed in chromosome
 586         # to be the same as the comparison chromosome (the length is simply
 587         # the marker position of the bottom marker)
 588         #
 589         $self->{c2}->set_length($self->{c1}->get_length());
 590         #
 591         # correct the cM_start and cM_end if out of range
 592         #
 593         #if ($self->get_cM_start() < 0) { $self->set_cM_start(0); }
 594         if ($self->get_cM_end()>$self->{c2}->get_length()) {
 595             $self->set_cM_end($self->{c2}->get_length());
 596         }
 597         $self->{c2} ->set_units( $self->get_ref_map()->get_units() );
 598         $self->{c2} ->set_color(255, 220 ,220);
 599         @m2 = $self->{c2}->get_markers();
 600
 601         #
 602         # go through the markers and show them according to confidence filter,
 603         # add mark for overgo information etc.
 604         #
 605         for (my $i=0; $i<@m2; $i++) {
 606             #
 607             # hilite markers to be hilited
 608             #
 609             my $marker_name = $m2[$i]->get_name();
 610             if ($self->get_hilite()=~/\b$marker_name\b/i) {
 611                 $m2[$i]->hilite();
 612                 $m2[$i]->get_label()->set_hidden(0);
 613             }
 614             #
 615             # hide markers with confidence below confidence threshold
 616             #
 617             if ($m2[$i]->get_confidence() < $self->{confidence}) {
 618                 $m2[$i]->hide_label();
 619             }
 620             #
 621             # hide markers that are not of the type that should be displayed
 622             #
 623             my $marker_type = $self->get_display_marker_type();
 624             if ($self->get_display_marker_type() && ($m2[$i]->get_marker_type()!~/$marker_type/i)) {
 625                 $m2[$i]->hide_label();
 626             }
 627            set_marker_color($m2[$i], $self->get_color_model());
 628
 629             #
 630             # set the url only if the marker is visible (otherwise imagemap outside the image will be
 631             # generated that confuses some browsers (such as Explorer).
 632             #
 633             if ($m2[$i]->is_visible()) {
 634 #               if (!$m2[$i]->get_url()) { # some url's may already be set in the data adapter.
 635 #                   $m2[$i]->set_url( $self->get_ref_map()->get_marker_link($m2[$i]->get_id()) );
 636 #               }
 637
 638             }
 639             else {
 640                 #$m[$i]->set_url("");
 641                 $m[$i]->hide_mark();
 642             }
 643         }
 644         #
 645         # set up the section and connections to the left hand chromosome
 646         #
 647         $self->{c2} -> set_section($self->get_cM_start(), $self->get_cM_end());
 648         $self->{c1} -> set_hilite_color(255, 220,220);
 649         $self->{c1} -> set_hilite($self->get_cM_start(), $self->get_cM_end());
 650         $self->{link1} = CXGN::Cview::ChrLink -> new ($self->{c1}, $self->get_cM_start(), $self->{c2}, $self->get_cM_start());
 651         $self->{link1} -> set_color(10, 10, 10);
 652         $self->{link2} = CXGN::Cview::ChrLink -> new ($self->{c1}, $self->get_cM_end(), $self->{c2}, $self->get_cM_end());
 653         $self->{link2} -> set_color(10, 10, 10);
 654         $self->{map}->add_chr_link($self->{link1});
 655         $self->{map}->add_chr_link($self->{link2});
 656
 657         $self->{map} -> add_chromosome($self->{c2});
 658     }
 659     #
 660     # draw the map comparison if the map comparison was requested (comp_map comp_chr will be defined).
 661     #
 662     my @m3;
 663     if ($self->get_comp_map() && $self->get_comp_chr()) {
 664
 665         #print STDERR "Generating the comparative map...\n";
 666
 667         $element_count++;
 668
 669         #$self->{c3} = CXGN::Cview::chromosome -> new ($self->get_comp_chr(), $self->{chr_height}, $x_distance * $element_count, 40);
 670
 671         $self->{c3}=$self->get_comp_map()->get_chromosome($self->get_comp_chr());
 672
 673         $self->{c3}->set_height($self->get_chr_height());
 674         $self->{c3}->set_horizontal_offset($x_distance * $element_count);
 675         $self->{c3}->set_vertical_offset(40);
 676         $self->{c3}->set_units( $self->get_comp_map()->get_units() );
 677
 678         #print STDERR "Fetching map $self->{comp_map} chr $self->{comp_chr} from the database...\n";
 679
 680         #print STDERR "Adjusting colors etc...\n";
 681         $self->{c3} ->set_color(150, 150 ,200);
 682         $self->{c3} ->set_caption($self->get_comp_chr());
 683
 684         @m3 = $self->{c3}->get_markers();
 685         #print STDERR "$self->{comp_chr} has ".@m3." markers...\n";
 686         for (my $i=0; $i<@m3; $i++) {
 687
 688             #print STDERR "Marker read:". $m3[$i]->get_name()."\n";
 689             CXGN::Cview::Utils::set_marker_color($m3[$i], $self->get_color_model());
 690             #$m3[$i]->set_url("/search/markers/markerinfo.pl?type=".$m3[$i]->get_marker_type()."&amp;id=".$m3[$i]->get_marker_name());;
 691         }
 692
 693         #print STDERR "Adding the chromosome to the map...\n";
 694         $self->{map}->add_chromosome($self->{c3});
 695         #
 696         # determine if the magnified section exists -- then draw the correspondence lines to that chromosome object (c2)
 697         # else draw them to the original chromosome object (c1).
 698         #
 699         if (exists($self->{c2})) {
 700             $self->{c2}->set_labels_left();
 701
 702             my $link_list = get_chromosome_links($self->{c2}, $self->{c3});
 703             foreach my $clink ($link_list->get_link_list()) {
 704                 $self->{map}->add_chr_link($clink);
 705             }
 706
 707             foreach my $m3 (@m3) {
 708                 $m3->hide_label();
 709                 if ($link_list->has_link($m3->get_marker_name())) {
 710                     $m3->show_label();
 711                 }
 712
 713                 if ($m3->get_confidence < $self->{confidence}) { $m3->hide_label(); }
 714                 my $marker_name = $m3->get_name();
 715                 if ($self->get_hilite()=~/\b$marker_name\b/i) {
 716                     $m3->show_label();
 717                     $m3->hilite();
 718                 }
 719             }
 720         }
 721         else {
 722             #print STDERR "LINKS:::::::::::::::\n";
 723             my $link_list = get_chromosome_links($self->{c1}, $self->{c3});
 724             foreach my $clink ($link_list->get_link_list()) {
 725                 #print STDERR "  adding link...\n";
 726                 $self->{map}->add_chr_link($clink);
 727             }
 728             foreach my $m3 (@m3) {
 729                 $m3->hide_label();
 730                 set_marker_color($m3, $self->get_color_model());
 731
 732                 if ($link_list->has_link($m3->get_marker_name())) {
 733                     $m3->show_label();
 734                 }
 735                 if ($m3->get_confidence < $self->{confidence}) { $m3->hide_label(); }
 736                 if ($m3->get_name() eq $self->get_hilite()) {
 737                     $m3->show_label();
 738                     $m3->hilite();
 739                 }
 740             }
 741         }
 742         $element_count++;
 743         if ($self->get_show_ruler()) {
 744             $self->{r3} = $self->{c3}->get_ruler();
 745             $self->{r3}->set_horizontal_offset($element_count*$x_distance);
 746             $self->{r3}->set_vertical_offset(40);
 747             $self->{r3}->set_height($self->get_chr_height());
 748             $self->{r3}->set_start_value(0);
 749             $self->{r3}->set_end_value($self->{c3}->get_length());
 750
 751             $self->{map}->add_ruler($self->{r3});
 752         }
 753     }
 754 }
 755
 756
 757
 758
 759 =head2 function get_chr_height()
 760
 761   Synopsis:     Accessor for the chr_height property
 762   Arguments:    none
 763   Returns:      the current chr_height
 764   Side effects: The chromosomes are being drawn with the chr_height in pixels
 765   Description:
 766
 767 =cut
 768
 769 sub get_chr_height {
 770     my $self=shift;
 771     return $self->{chr_height};
 772 }
 773
 774 =head2 function set_chr_height()
 775
 776   Synopsis:
 777   Arguments:    the chromosome height in pixels. In small mode, height is 230 pixels, and
 778                 normal mode the height is 400 pixels.
 779   Returns:
 780   Side effects:
 781   Description:
 782
 783 =cut
 784
 785 sub set_chr_height {
 786     my $self=shift;
 787     $self->{chr_height}=shift;
 788 }
 789
 790 =head2 accessors get_ref_map(), set_ref_map()
 791
 792  Usage:
 793  Desc:
 794  Args/Ret:     the reference map as a CXGN::Cview::Map object
 795                of the appropriate sub-class.
 796  Side Effects: this will be the map displayed as the reference
 797                map (on the left).
 798  Example:
 799
 800 =cut
 801
 802 sub get_ref_map {
 803   my $self=shift;
 804   if (!exists($self->{ref_map})) { $self->{ref_map}=undef; }
 805   return $self->{ref_map};
 806
 807 }
 808
 809 sub set_ref_map {
 810   my $self=shift;
 811   $self->{ref_map}=shift;
 812 }
 813
 814 =head2 accessors get_comp_map(), set_comp_map()
 815
 816   Usage:
 817   Property:     the comparison map, as a CXGN::Cview::Map object
 818                 (or subclass thereof)
 819   Desc:
 820   Side Effects:
 821   Example:
 822
 823 =cut
 824
 825 sub get_comp_map {
 826   my $self=shift;
 827   if (!exists($self->{comp_map})) { $self->{comp_map}=undef; }
 828   return $self->{comp_map};
 829
 830 }
 831
 832 sub set_comp_map {
 833   my $self=shift;
 834   $self->{comp_map}=shift;
 835 }
 836
 837
 838
 839
 840 =head2 accessors set_map_id(), get_map_id()
 841
 842   Synopsis:     sets the map_id for the reference chromosome
 843   Parameters:   map_id (integer)
 844   Returns:
 845   Side effects: the map corresponding to map_id will be drawn as the reference chromosome
 846   Status:       DEPRECATED. Call $chr_viewer->get_ref_map()->get_id() instead...
 847   Example:
 848
 849 =cut
 850
 851 sub set_map_id {
 852     my $self = shift;
 853     $self->{map_id}=shift;
 854 }
 855
 856 sub get_map_id {
 857     my $self = shift;
 858 #    if (!exists($self->{map_id})) { $self->{map_id}=0; }
 859     if (!exists($self->{map_id})) { $self->{map_id}=0; }
 860     return $self->{map_id};
 861 }
 862
 863 =head2 accessors get_map_version_id(), set_map_version_id()
 864
 865  Usage:
 866  Desc:         the map_version_id of the reference map
 867  Ret:
 868  Args:
 869  Side Effects:
 870  Example:
 871
 872 =cut
 873
 874 sub get_map_version_id {
 875   my $self=shift;
 876   return $self->{map_version_id};
 877
 878 }
 879
 880 sub set_map_version_id {
 881   my $self=shift;
 882   $self->{map_version_id}=shift;
 883 }
 884
 885 =head2 accessors get_comp_map_version_id(), set_comp_map_version_id()
 886
 887  Usage:
 888  Desc:         the map_version_id of the comparison map
 889  Ret:
 890  Args:
 891  Side Effects:
 892  Example:
 893
 894 =cut
 895
 896 sub get_comp_map_version_id {
 897   my $self=shift;
 898   return $self->{comp_map_version_id};
 899
 900 }
 901
 902 sub set_comp_map_version_id {
 903   my $self=shift;
 904   $self->{comp_map_version_id}=shift;
 905 }
 906
 907 =head2 function set_comp_map_id()
 908
 909   Synopsis:     setter function for the map id of the comparison chromosome
 910   Parameters:   the map id (integer)
 911   Returns:      nothing
 912   Side effects: the specified map will be drawn as the reference chromosome
 913   Status:       implemented
 914   Example:
 915
 916 =cut
 917
 918 sub set_comp_map_id {
 919     my $self = shift;
 920     $self->{comp_map_id}=shift;
 921 }
 922
 923 =head2 function get_comp_map_id()
 924
 925   Synopsis:     get the current map id of the comparison chromosome
 926   Parameters:
 927   Returns:      map id of the comparison chromosome
 928   Side effects:
 929   Status:       implemented
 930   Example:
 931
 932 =cut
 933
 934 sub get_comp_map_id {
 935     my $self = shift;
 936     if (!exists($self->{comp_map_id})) { $self->{comp_map_id}=0; }
 937     return $self->{comp_map_id};
 938 }
 939
 940 =head2 function set_ref_chr()
 941
 942   Synopsis:     setter function for the specifying the reference chromosome
 943                 number/linkage group name
 944   Parameters:   the desired chromosome number/linkage group name (string)
 945   Returns:
 946   Side effects: the specified chromosome/linkage group will be displayed as
 947                 the reference chromosome
 948   Status:       implemented
 949   Example:
 950
 951 =cut
 952
 953 sub set_ref_chr {
 954     my $self = shift;
 955     $self->{chr_nr}=shift;
 956 }
 957
 958 =head2 function get_ref_chr()
 959
 960   Synopsis:     accessor function for set_ref_chr
 961   Parameters:
 962   Returns:      the chromosome number/linkage group name for the reference
 963                 chromosome/linkage group
 964   Side effects:
 965   Status:       implemented
 966   Example:
 967
 968 =cut
 969
 970 sub get_ref_chr {
 971     my $self = shift;
 972     if (!exists($self->{chr_nr}) || !defined($self->{chr_nr})) { $self->{chr_nr}=0; }
 973     return $self->{chr_nr};
 974 }
 975
 976 =head2 function set_comp_chr()
 977
 978   Synopsis:     setter function for specifying the comparison chromosome/linkage
 979                 group
 980   Parameters:   chromosome number/linkage group name
 981   Returns:      nothing
 982   Side effects: the corrsponding chromosome will be drawn as the comparison chromosome
 983   Status:       implemented
 984   Example:
 985
 986 =cut
 987
 988 sub set_comp_chr {
 989     my $self = shift;
 990     $self->{comp_chr}=shift;
 991 }
 992
 993 =head2 function get_comp_chr()
 994
 995   Synopsis:     accessor function for set_comp_chr
 996   Parameters:
 997   Returns:
 998   Side effects:
 999   Status:       implemented
1000   Example:
1001
1002 =cut
1003
1004 sub get_comp_chr {
1005     my $self = shift;
1006     if (!exists($self->{comp_chr})) { $self->{comp_chr}=0; }
1007     return $self->{comp_chr};
1008 }
1009
1010 =head2 accessors get_ref_chr_len, set_ref_chr_len
1011
1012  Usage:
1013  Desc:
1014  Property
1015  Side Effects:
1016  Example:
1017
1018 =cut
1019
1020 sub get_ref_chr_len {
1021   my $self = shift;
1022   return $self->{ref_chr_len};
1023 }
1024
1025 sub set_ref_chr_len {
1026   my $self = shift;
1027   $self->{ref_chr_len} = shift;
1028 }
1029
1030
1031
1032 =head2 function set_cM_start()
1033
1034   Synopsis:     for a chromosome section, sets the starting point in cM
1035   Parameters:   cM start position
1036   Returns:      nothing
1037   Side effects: cleans the input to be an integer
1038   Status:       implemented
1039   Example:
1040
1041 =cut
1042
1043 sub set_cM_start {
1044     my $self = shift;
1045     my $cM_start = shift;
1046    $cM_start =~ s/[^0-9.]//g;
1047     #$cM_start =~ s/.*?(\d+\.?\d*).*/$1/;
1048     $self->{cM_start}=abs($cM_start);
1049 }
1050
1051 =head2 function get_cM_start()
1052
1053   Synopsis:     accessor function for the cM_start property
1054   Parameters:
1055   Returns:
1056   Side effects:
1057   Status:       implemented
1058   Example:
1059
1060 =cut
1061
1062 sub get_cM_start {
1063     my $self = shift;
1064     if (!exists($self->{cM_start}) || !defined($self->{cM_start})) { $self->{cM_start}=0; }
1065
1066     return sprintf "%.2f", $self->{cM_start};
1067 }
1068
1069 =head2 function set_cM_end()
1070
1071   Synopsis:     sets the end of a chromosome /linkage group section, in cM
1072   Parameters:   cM of end of section
1073   Returns:      nothing
1074   Side effects: On a chromosome section, this will define the endpoints of the section.
1075                 If set_section has not been called, this will define which section is
1076                 hilited. The cM and zoom property will be automatically re-calculated.
1077   Status:       implemented
1078   Example:
1079
1080 =cut
1081
1082 sub set_cM_end {
1083     my $self = shift;
1084     my $cM_end = shift;
1085    $cM_end =~ s/[^0-9.]//g;
1086     if ($cM_end eq "" || !$cM_end) { $cM_end=0; }
1087     $self->{cM_end}=abs(($cM_end));
1088 }
1089
1090 =head2 function get_cM_end()
1091
1092   Synopsis:     accessor function for the cM_end property
1093   Parameters:
1094   Returns:
1095   Side effects:
1096   Status:       implemented
1097   Example:
1098
1099 =cut
1100
1101 sub get_cM_end {
1102     my $self = shift;
1103     if (!exists($self->{cM_end}) || !defined($self->{cM_end})) { $self->{cM_end}=0; }
1104     return sprintf "%.2f", $self->{cM_end};
1105 }
1106
1107 =head2 function set_cM()
1108
1109   Synopsis:     sets the cM property. This is the approximate location in which
1110                 the user has clicked. If set_cM is set, cM_start and cM_end will be
1111                 calculated automatically using the current zoom levels.
1112   Parameters:   the cM position (integer)
1113   Returns:      nothing
1114   Side effects: recalculates cM_start and cM_end.
1115   Status:       implemented
1116   Example:
1117
1118 =cut
1119
1120 sub set_cM {
1121     my $self = shift;
1122     $self->{cM}=shift;
1123 }
1124
1125 =head2 function get_cM()
1126
1127   Synopsis:     accessor function for the cM property
1128   Parameters:
1129   Returns:
1130   Side effects:
1131   Status:       implemented
1132   Example:
1133
1134 =cut
1135
1136 sub get_cM {
1137     my $self = shift;
1138     if (!exists($self->{cM})) { $self->{cM}=0; }
1139     return $self->{cM};
1140 }
1141
1142 =head2 function set_zoom()
1143
1144   Synopsis:     sets the zoom level on the reference chromosome
1145   Parameters:   zoom level (1..10). 10 is the highest zoom level (most enlarged section
1146                 showing fewer markers). Zoom levels outside the legal range are rounded to
1147                 the nearest legal value.
1148   Returns:      nothing
1149   Side effects:
1150   Status:       Deprecated. Zooming is now implemented by setting cM_start and cM_end
1151   Example:
1152
1153 =cut
1154
1155 sub set_zoom {
1156     my $self = shift;
1157     $self->{zoom}=shift;
1158     if (!exists($self->{zoom}) || $self->{zoom} eq "") { $self->{zoom}=0; }
1159     if ($self->{zoom}==0) { $self->{zoom} =1; }
1160     if ($self->{zoom} > 10) { $self->{zoom} =10; }
1161 }
1162
1163 =head2 function get_zoom()
1164
1165   Synopsis:     accessor function for the zoom property.
1166   Parameters:
1167   Returns:      the current zoom level (1..10)
1168   Side effects:
1169   Status:       Deprecated. Zooming is now implented by directly setting cM_start and cM_end.
1170   Example:
1171
1172 =cut
1173
1174 sub get_zoom {
1175     my $self=shift;
1176     if (!exists($self->{zoom})) { $self->{zoom}=1; }
1177     return $self->{zoom};
1178 }
1179
1180 =head2 accessors get_clicked, set_clicked
1181
1182  Usage:        my $flag = $cv -> get_clicked()
1183  Desc:         returns true if this page should be regenerated
1184                as a response to a user clicking on the chromosome
1185                (instead of using some of the toolbar buttons),
1186                false otherwise.
1187  Property:
1188  Side Effects:
1189  Example:
1190
1191 =cut
1192
1193 sub get_clicked {
1194     my $self = shift;
1195     return $self->{clicked};
1196 }
1197
1198 sub set_clicked {
1199     my $self = shift;
1200     $self->{clicked} = shift;
1201 }
1202
1203
1204
1205 =head2 function get_show_ruler()
1206
1207   Synopsis:     accessor function for the show_ruler property.
1208   Parameters:   none
1209   Returns:      true if ruler is shown, false otherwise
1210   Side effects:
1211   Status:       implemented
1212   Example:
1213
1214 =cut
1215
1216 sub get_show_ruler {
1217     my $self = shift;
1218     if (!exists($self->{show_ruler})) { $self->{show_ruler}=0; }
1219     return $self->{show_ruler};
1220 }
1221
1222 =head2 function set_show_ruler()
1223
1224   Synopsis:     setter function for the show_ruler property.
1225   Parameters:   true or false (0 or 1)
1226   Returns:      nothing
1227   Side effects: true causes the ruler to be displayed for both the reference and comparison map
1228                 (if present), false hides the ruler.
1229   Status:       implemented
1230   Example:
1231
1232 =cut
1233
1234 sub set_show_ruler {
1235     my $self = shift;
1236     $self->{show_ruler} = shift;
1237 }
1238
1239 =head2 function set_show_IL()
1240
1241   Synopsis:     setter function for the show_IL property
1242   Parameters:   true or false
1243   Returns:      nothing
1244   Side effects: if the current reference map has associated IL information, true will
1245                 cause the IL map to be displayed alongside with the chromosome.
1246   Status:       implemented
1247   Example:
1248
1249 =cut
1250
1251 sub set_show_IL {
1252     my $self = shift;
1253     $self->{show_IL}=shift;
1254 }
1255
1256 =head2 function get_show_IL()
1257
1258   Synopsis:     accessor function for the show_IL property
1259   Parameters:   none
1260   Returns:      true or false
1261   Side effects: none
1262   Status:       implemented
1263   Example:
1264
1265 =cut
1266
1267 sub get_show_IL {
1268     my $self = shift;
1269     if (!exists($self->{show_IL})) { $self->{show_IL}=0; }
1270     return $self ->{show_IL};
1271 }
1272
1273 =head2 function set_show_physical()
1274
1275   Synopsis:     true causes the physical map to be displayed if the current reference map
1276                 has an associated physical map
1277   Parameters:   true/false
1278   Returns:      nothing
1279   Side effects:
1280   Status:       implemented
1281   Example:
1282
1283 =cut
1284
1285 sub set_show_physical {
1286     my $self = shift;
1287     $self->{show_physical}=shift;
1288 }
1289
1290 =head2 function get_show_physical()
1291
1292   Synopsis:     true causes the physical map to be displayed if the current reference map
1293                 has an associated physical map
1294   Parameters:   none
1295   Returns:      true/false
1296   Side effects:
1297   Status:       implemented
1298   Example:
1299
1300 =cut
1301
1302 sub get_show_physical {
1303     my $self = shift;
1304     if (!exists($self->{show_physical})) { $self->{show_physical}=0; }
1305     return $self->{show_physical};
1306 }
1307
1308 =head2 accessors set_show_offsets(), get_show_offsets()
1309
1310   Property:     if the offsets should be shown (each marker will display a
1311                 label opposite of the marker label, showing the offset in map
1312                 units for that marker, for the zoomed-in section
1313   Side Effects:
1314   Description:
1315
1316 =cut
1317
1318 sub get_show_offsets {
1319     my $self=shift;
1320     return $self->{show_offsets};
1321 }
1322
1323 sub set_show_offsets {
1324     my $self=shift;
1325     $self->{show_offsets}=shift;
1326 }
1327
1328
1329
1330
1331 =head2 function get_size()
1332
1333   Synopsis:     accessor function for the size property
1334   Parameters:   none
1335   Returns:      "small" or "normal" or "large"
1336   Side effects:
1337   Status:       implemented
1338   Example:
1339
1340 =cut
1341
1342 sub get_size {
1343     my $self = shift;
1344     if (!exists($self->{size})) { $self->{size}=0; }
1345     return $self->{size};
1346 }
1347
1348 =head2 function set_size()
1349
1350   Synopsis:     sets the size of the image
1351   Parameters:   string ("normal", "small" and "large" are currently supported).
1352   Returns:      nothing
1353   Side effects: "smaller" causes the entire map image to be rendered smaller
1354                           (ideal for a laptop monitor)
1355                 "normal" causes the entire map image to be rendered to fit a desktop monitor
1356                 (>=17\")
1357                 "larger" for really large monitors (>20\")
1358   Status:       implemented
1359   Example:
1360
1361 =cut
1362
1363 sub set_size {
1364     my $self = shift;
1365     $self->{size}=shift;
1366 }
1367
1368 =head2 function set_hilite()
1369
1370   Synopsis:     hilites the specified markers on the reference map (unhides if necessary)
1371                 on the zoomed-in map and on the comparison map.
1372   Parameters:   a string, containing an enumeration of marker names to be hilited, separated
1373                 by spaces (although other delimiters will also work such as comma, semicolons,
1374                 etc.)
1375   Returns:      nothing
1376   Side effects: the hilited marker name will appear with a yellow background.
1377   Status:       implemented
1378   Example:
1379
1380 =cut
1381
1382 sub set_hilite {
1383     my $self = shift;
1384     my $hilite = shift;
1385     $hilite =~ tr/\,\.\:\;\// /;
1386     $hilite =~ s/\s+/ /;
1387     $self->{hilite} = $hilite;
1388
1389 }
1390
1391 =head2 function get_hilite()
1392
1393   Synopsis:     accessor function for the hilite property
1394   Parameters:   none
1395   Returns:      the name of the currently hilited marker
1396   Side effects:
1397   Status:       implemented
1398   Example:
1399
1400 =cut
1401
1402 sub get_hilite {
1403     my $self = shift;
1404     if (!exists($self->{hilite})) { $self->{hilite}=""; }
1405     return $self->{hilite};
1406 }
1407
1408 =head2 function set_confidence()
1409
1410   Synopsis:     sets the minimal confidence level to be displayed
1411   Parameters:   confidence level (-1, 0..3)
1412                 -1: uncalculated confidence, 0 - interval marker ... 3 - frame marker
1413   Returns:      nothing
1414   Side effects: markers below the specified confidence level will be hidden
1415   Status:       implemented
1416   Example:
1417
1418 =cut
1419
1420 sub set_confidence {
1421     my $self = shift;
1422     my $confidence = shift;
1423     $confidence =~ s/[A-Za-z]//g;
1424     if ($confidence eq "" || $confidence == undef ) { $confidence =-2; }
1425     $confidence = $confidence +0;
1426     $self->{confidence} = $confidence;
1427 }
1428
1429 =head2 function get_confidence()
1430
1431   Synopsis:     accessor function for the confidence property
1432   Parameters:   none
1433   Returns:      the current lowest confidence level that is displayed
1434                 Normal values for the confidence property are:
1435                 -1: not calculated
1436                 0 ILOD
1437                 1 ILOD2
1438                 2 CFLOD
1439                 3 LOD3
1440                 If the confidence property is not set, it will return -2,
1441                 causing all markers to be displayed.
1442   Side effects: markers with a lower confidence value (see list above) won\'t be
1443                 displayed.
1444   Status:       implemented
1445   Example:
1446
1447 =cut
1448
1449 sub get_confidence {
1450     my $self = shift;
1451     if (!exists($self->{confidence})) { $self->{confidence}=-2; }
1452     return $self->{confidence};
1453 }
1454
1455
1456 =head2 functions set_display_marker_type(), get_display_marker_type()
1457
1458   Synopsis:     $self->set_display_marker_type('COS');
1459   Arguments:    a marker type. Any of COS, RFLP, ...
1460   Returns:      nothing
1461   Side effects: Will also set $self->{error} to indicate to the
1462                 user that marker type subsets are shown.
1463   Description:  if set_display_marker_type is called with a marker
1464                 type argument, only that marker type will be shown
1465                 on the viewer. If called with undef, shows all markers.
1466
1467 =cut
1468
1469 sub set_display_marker_type {
1470     my $self = shift;
1471     my $type = shift;
1472     if ($type && ("RFLP CAPS COS SSR"=~ /\b$type\b/)) {
1473         $self->{display_marker_type}=$type;
1474         $self->append_error("Only markers of the type $self->{display_marker_type} are shown on the zoomed map.<br />");
1475     }
1476 }
1477
1478 sub get_display_marker_type {
1479     my $self = shift;
1480     if (!exists($self->{display_marker_type})) { $self->{display_marker_type}=""; }
1481     return $self->{display_marker_type};
1482 }
1483
1484
1485 =head2 function set_show_zoomed()
1486
1487   Synopsis:     setter function for the show_zoomed property
1488   Parameters:   show_zoomed property (0 or 1)
1489   Returns:      status of the current show_zoomed property (0 or 1)
1490   Side effects: 0 will cause the zoomed in chromosome section not to be drawn
1491                 1 will cause a zoomed in chromosome section to be drawn
1492   Status:       implemented
1493   Example:
1494
1495 =cut
1496
1497 sub set_show_zoomed {
1498     my $self = shift;
1499     $self->{show_zoomed} = shift;
1500 }
1501
1502
1503 =head2 function get_show_zoomed()
1504
1505   Synopsis:     accessor function for the show_zoomed property
1506   Parameters:   none
1507   Returns:      status of the current show_zoomed property (0 or 1)
1508   Side effects: none
1509   Status:       implemented
1510   Example:
1511
1512 =cut
1513
1514
1515 sub get_show_zoomed {
1516     my $self = shift;
1517     if (!exists($self->{show_zoomed})) { $self->{show_zoomed}=0; }
1518     return $self->{show_zoomed};
1519 }
1520
1521 =head2 accessors get_hilite_zoomed(), set_hilite_zoomed()
1522
1523  Usage:        $chr_viewer->set_hilite_zoomed($cM_start, $cM_end)
1524  Desc:         hilites the given region in the zoomed-in section,
1525                using the current hilite color.
1526  Ret:          The getter returns the start and end in cM
1527  Args:         the start in cM [real], the end in cM [real]
1528  Side Effects: hilites the corresponding region
1529   Notes:       the intended use for this is to hilite sections,
1530                such as the boundaries for ILs on the zoomed in
1531                chromosome.
1532
1533 =cut
1534
1535 sub set_hilite_zoomed {
1536     my $self= shift;
1537     $self->{hilite_zoom_start}= shift;
1538     $self->{hilite_zoom_end} = shift;
1539
1540
1541 }
1542
1543 sub get_hilite_zoomed {
1544     my $self = shift;
1545     return ($self->{hilite_zoom_start}, $self->{hilite_zoom_end});
1546 }
1547
1548 =head2 function get_color_model()
1549
1550   Synopsis:
1551   Parameters:   name of color model (currently, confidence and marker_type are supported)
1552   Returns:      nothing
1553   Side effects: sets the color model property to the specified color model
1554   Status:       implemented
1555   Example:
1556
1557 =cut
1558
1559
1560 sub set_color_model {
1561     my $self = shift;
1562     $self->{color_model} = shift;
1563 }
1564
1565 =head2 function get_color_model()
1566
1567   Synopsis:
1568   Parameters:   none
1569   Returns:      the name of the current marker color model
1570   Side effects: none
1571   Status:       implemented
1572   Example:
1573
1574 =cut
1575
1576 sub get_color_model {
1577     my $self = shift;
1578     if (!exists($self->{color_model})) { $self->{color_model}=""; }
1579     return $self->{color_model};
1580 }
1581
1582
1583 =head2 function get_color_legend()
1584
1585   Synopsis:
1586   Parameters:   none
1587   Returns:      a string containing html code for the marker color legend
1588   Side effects: none
1589   Status:       implemented
1590   Example:
1591
1592 =cut
1593
1594 sub get_color_legend {
1595     my $self= shift;
1596     my $string = "";
1597     my $link = "view_chromosome.pl?map_version_id=".$self->get_map_version_id()."&amp;chr_nr=".$self->get_ref_chr()."&amp;show_physical=".$self->get_show_physical."&amp;show_IL=".$self->get_show_IL()."&amp;show_offsets=".$self->get_show_offsets()."&amp;show_ruler=".$self->get_show_ruler()."&amp;color_model=".$self->get_color_model()."&amp;comp_map_version_id=".$self->get_comp_map_version_id()."&amp;comp_chr=".$self->get_comp_chr()."&amp;zoom=".$self->get_zoom()."&amp;size=".$self->get_size()."&amp;cM=".$self->get_cM()."&amp;cM_start=".$self->get_cM_start()."&amp;cM_end=".$self->get_cM_end()."&amp;hilite=".$self->get_hilite()."&amp;show_zoomed=".$self->get_show_zoomed()."";
1598     if ($self->{color_model} eq "marker_types") {
1599
1600
1601
1602         $string = "<b>Marker color by type:</b>
1603                    <a href=\"$link\&marker_type=RFLP\" style=\"color:#FF0000\">RFLP</a> |
1604                    <a href=\"$link\&marker_type=SSR\" style=\"color:#00FF00\">SSR</a> |
1605                    <a href=\"$link\&marker_type=CAPS\" style=\"color:#0000FF\">CAPS</a> |
1606                    <a href=\"$link\&marker_type=COS\" style=\"color:#FF00FF\">COS</a> |
1607                    <font color=#000000>other</font>
1608                            [<a href=\"$link\&marker_type=\" style=\"color:#111111\">show all</a>]";
1609
1610     }
1611     else {
1612         $string = "<b>Marker color by LOD score:</b>
1613                    <a href=\"$link\&amp;confidence=3\" style=\"color:#FF0000\">F(LOD3)</a> |
1614                    <a href=\"$link\&amp;confidence=2\" style=\"color:#00FF00\">CF(LOD>=3</a> |
1615                    <a href=\"$link\&amp;confidence=1\" style=\"color:#0000FF\">I(LOD2)</a> |
1616                    <a href=\"$link\&amp;confidence=0\" style=\"color:#000000\">I(LOD&lt;2)</a> |
1617                    <a href=\"$link\&amp;confidence=-2\" style=\"color:#777777\">uncalculated</a>  ";
1618     }
1619     return $string;
1620 }
1621
1622 =head2 function get_marker_map_links()
1623
1624   Synopsis:
1625   Parameters:   none
1626   Returns:      a string with html code for the marker map links pull down menu.
1627                 if there is no appropriate map linked to the reference map,
1628                 a string is returned that says so.
1629   Side effects: calls the get_chromosome_connections() function of the reference
1630                 map object.
1631   Status:       implemented
1632   Example:
1633   Notes:
1634   Version:
1635
1636 =cut
1637
1638 sub get_marker_map_links {
1639     my $self=shift;
1640     #print STDERR "get_marker_map_links...\n";
1641     # query the database for maps and chromosome that any of the markers of the current chromosome lie on.
1642     #
1643     my $chr_nr = $self->get_ref_chr();
1644     my $F2_2000 = CXGN::Cview::Map::SGN::Genetic->new($self->get_dbh(), CXGN::Cview::Map::Tools::find_current_version( $self->get_dbh(), CXGN::Cview::Map::Tools::current_tomato_map_id()));
1645
1646     my $F2_2000_version_id = $F2_2000->get_id();
1647
1648     my $form="<form style=\"margin-bottom:0\" action=\"/cview/view_chromosome.pl\">
1649         <input type=\"hidden\" name=\"chr_nr\" value=\"".($self->get_ref_chr())."\" />
1650         <input type=\"hidden\" name=\"map_version_id\" value=\"".($self->get_map_version_id())."\" />
1651         <input type=\"hidden\" name=\"zoom\" value=\"".($self->get_zoom())."\" />
1652         <input type=\"hidden\" name=\"show_ruler\" value=\"".($self->get_show_ruler())."\" />
1653         <input type=\"hidden\" name=\"show_IL\" value=\"".($self->get_show_IL())."\" />
1654         <input type=\"hidden\" name=\"show_offsets\" value=\"".($self->get_show_offsets())."\" />
1655         <input type=\"hidden\" name=\"cM_start\" value=\"".($self->get_cM_start())."\" />
1656         <input type=\"hidden\" name=\"cM_end\" value=\"".($self->get_cM_end())."\" />
1657         <input  type=\"hidden\" name=\"show_physical\" value=\"".($self->get_show_physical())."\" />
1658         <input type=\"hidden\" name=\"color_model\" value=\"".($self->get_color_model())."\" />
1659         <input type=\"hidden\" name=\"size\" value=\"".($self->get_size())."\" />
1660         <input type=\"hidden\" name=\"show_zoomed\" value=\"".($self->get_show_zoomed())."\" />
1661         <input type=\"hidden\" name=\"hilite\" value=\"".($self->get_hilite())."\" />
1662         <input type=\"hidden\" name=\"marker_type\" value=\"".($self->get_display_marker_type())."\" /> ";
1663
1664     my @options = $self->get_ref_map()->get_chromosome_connections($self->get_ref_chr());
1665
1666     if (@options) {
1667
1668         $form .= "<select name=\"map_chr_select\">";
1669         foreach my $o (@options) {
1670 #       print STDERR $o->{map_version_id}, $o->{chr_nr}, $o->{short_name}."<br />\n";
1671             my $selected = "";
1672             if ($o->{map_version_id} == $self->get_comp_map_version_id()) {
1673                 $selected = "selected=\"selected\"";
1674             }
1675
1676             $form .= qq {  <option value="$o->{map_version_id} $o->{lg_name}" $selected>Map $o->{short_name} Chromosome $o->{lg_name} ($o->{marker_count} markers)</option> };
1677         }
1678
1679         $form .="</select>\n";
1680         $self->{compare_disabled} = "";
1681     }
1682     else {
1683         $form .= "<select name=\"map_chr_select\" disabled=\"disabled\" >";
1684         $form .= "<option value=\"\" disabld=\"disabled\" >No maps to compare to</option>";
1685         $form .= "</select>\n";
1686         $self->{compare_disabled} = qq{ disabled="disabled" };
1687     }
1688
1689     $form .= "<input type=\"submit\" value=\"Compare\" $self->{compare_disabled} /></form>";
1690
1691     return $form;
1692 }
1693
1694 sub append_error {
1695     my $self = shift;
1696     my $append = shift;
1697     if (!exists($self->{errors})) { $self ->{errors}=""; }
1698     $self->{errors}.=$append;
1699 }
1700
1701 sub get_errors {
1702     my $self = shift;
1703     return $self->{errors};
1704 }
1705
1706 =head2 function get_preceding_chromosome()
1707
1708   Synopsis:     gives the name of the chromosome or linkage group preceding the
1709                 given chromosome
1710   Parameters:   chromosome name / linkage group name
1711   Returns:      the chromosome number or linkage group name preceding this
1712                 chromosome/linkage group
1713   Side effects: none
1714   Status:       implemented
1715   Example:
1716   Notes:
1717   Version:
1718
1719 =cut
1720
1721 sub get_preceding_chromosome {
1722     my $self = shift;
1723     my $chr_nr = shift;
1724     my $chr_count = scalar( @{$self->{chromo_names}} );
1725     my $chr_index = 0;
1726     my $old_chr_index=0;
1727     #
1728     # find current chromosome in chromo_names array (a hash would be more elegant...)
1729     #
1730     for (my $i=0; $i< (@{$self->{chromo_names}}); $i++) {
1731         if (${$self->{chromo_names}}[$i] eq $chr_nr) {
1732             $old_chr_index=$i;
1733         }
1734     }
1735
1736     if ($old_chr_index==0) { $chr_index = $chr_count-1; }
1737     else { $chr_index = $old_chr_index-1; }
1738     return ${$self->{chromo_names}}[$chr_index];
1739 }
1740
1741 =head2 function get_next_chromosome()
1742
1743   Synopsis:     gives the name of the chromosome or linkage group following the given
1744                 chromosome
1745   Parameters:   chromosome name / linkage group name
1746   Returns:      the chromosome number or linkage group name following this
1747                 chromosome/linkage group
1748   Side effects: none
1749   Status:       implemented
1750   Example:
1751   Notes:
1752   Version:
1753
1754 =cut
1755
1756 sub get_next_chromosome {
1757     my $self = shift;
1758     my $chr_nr = shift;
1759     my $chr_count = scalar( @{$self->{chromo_names}} );
1760     my $chr_index = 0;
1761     my $old_chr_index = 0;
1762     for (my $i=0; $i< (@{$self->{chromo_names}}); $i++) {
1763         if (${$self->{chromo_names}}[$i] eq $chr_nr) {
1764             $old_chr_index=$i;
1765         }
1766     }
1767
1768     if ($old_chr_index == ($chr_count-1)) { $chr_index = 0; }
1769     else { $chr_index = $old_chr_index+1; }
1770     return ${$self->{chromo_names}}[$chr_index];
1771 }
1772
1773 sub get_preceding_comp_chromosome {
1774     my $self = shift;
1775     my $chr_nr = shift;
1776     if (!($self->get_comp_map())) {
1777         return "?";
1778     }
1779     my $chr_count = scalar( @{$self->{comp_chromo_names}} );
1780     my $chr_index = 0;
1781     my $old_chr_index = 0;
1782
1783     for (my $i=0; $i< (@{$self->{comp_chromo_names}}); $i++) {
1784         if (${$self->{comp_chromo_names}}[$i] eq $chr_nr) {
1785             $old_chr_index=$i;
1786         }
1787     }
1788
1789     if ($old_chr_index == 0) { $chr_index = $chr_count-1; }
1790     else { $chr_index = $old_chr_index-1; }
1791     return ${$self->{comp_chromo_names}}[$chr_index];
1792 }
1793
1794 sub get_next_comp_chromosome {
1795     my $self = shift;
1796     my $chr_nr = shift;
1797     if (!($self->get_comp_map())) {
1798         return "?";
1799     }
1800     else {
1801         my $chr_count = scalar( @{$self->{comp_chromo_names}} );
1802         my $chr_index = 0;
1803         my $old_chr_index = 0;
1804         for (my $i=0; $i< (@{$self->{comp_chromo_names}}); $i++) {
1805             if (${$self->{comp_chromo_names}}[$i] eq $chr_nr) {
1806                 $old_chr_index=$i;
1807             }
1808         }
1809
1810
1811         if ($old_chr_index == ($chr_count-1)) { $chr_index = 0; }
1812         else { $chr_index = $old_chr_index+1; }
1813         return ${$self->{comp_chromo_names}}[$chr_index];
1814     }
1815
1816 }
1817
1818 =head2 function display_toolbar()
1819
1820   Synopsis:     displays the toolbar by printing html to STDOUT
1821   Parameters:   none
1822   Returns:      nothing
1823   Side effects: prints html code to STDOUT
1824   Status:       implemented
1825   Example:
1826
1827 =cut
1828
1829 sub display_toolbar {
1830     my $self=shift;
1831     #$self->{scrolldown} = $self->{cM}+2*$self->{unzoomedheight}/$self->{zoom}/3;
1832
1833
1834
1835     $self->{scrolldown_start} = $self->get_cM_start() + ($self->{zoom_length} / 2);
1836     $self->{scrolldown_end}   = $self->get_cM_end() + ($self->{zoom_length} / 2);
1837     if ($self->{scrolldown_end} > $self->get_ref_chr_len()) {
1838
1839         $self->{scrolldown_end}= $self->get_ref_chr_len();
1840         $self->{scrolldown_start} = $self->{scrolldown_end}-$self->{zoom_length};
1841     }
1842     #$self->{scrollup}   = $self->{cM}-2*$self->{unzoomedheight}/$self->{zoom}/3;
1843     $self->{scrollup_start}   = $self->get_cM_start()- ($self->{zoom_length} / 2);
1844     $self->{scrollup_end}    = $self->get_cM_end() - ($self->{zoom_length} /2);
1845     if ($self->{scrollup_start}<0) {
1846         $self->{scrollup_start}=0;
1847         $self->{scrollup_end}=$self->{zoom_length};
1848     }
1849
1850     if ($self->{zoom_length}==0) { die "ZOOM LENGTH IS 0!\n"; }
1851     #$self->{zoom_in}    = $self->{zoom}+1;
1852     $self->{zoom_in_start} = $self->get_cM_start() +($self->{zoom_length}/4);
1853     $self->{zoom_in_end}   = $self->get_cM_end() - ($self->{zoom_length}/4);
1854
1855     #$self->{zoom_out}   = $self->{zoom}-1;
1856     $self->{zoom_out_start}   = $self->get_cM_start() - ($self->{zoom_length}/4);
1857     $self->{zoom_out_end}  = $self->get_cM_end + ($self->{zoom_length}/4);
1858
1859     if ($self->{zoom_out_end} > $self->get_ref_chr_len()) {
1860         $self->{zoom_out_end} = $self->get_ref_chr_len();
1861         $self->{zoom_out_start} = $self->{zoom_out_end} - $self->{zoom_length};
1862     }
1863
1864     # set buttons to disabled when no zoomed-in chromosome is displayed.
1865     if (!$self->{show_zoomed} || !$self->get_ref_map()->can_zoom()) {
1866         $self->{zoom_in_disabled}="disabled=\"disabled\"";
1867         $self->{zoom_out_disabled} = "disabled=\"disabled\"";
1868         $self->{scroll_up_disabled} = "disabled=\"disabled\"";
1869         $self->{scroll_down_disabled} = "disabled=\"disabled\"";
1870     }
1871
1872
1873
1874 #    if (!$self->map_has_physical($self->{map_id})) {
1875     if (!$self->get_ref_map()->has_physical()) {
1876         $self->{physical_disabled} = "disabled=\"disabled\"";
1877     }
1878
1879     if (!$self->get_ref_map()->has_IL()) {
1880         $self->{IL_disabled} = qq { disabled="disabled" };
1881     }
1882     else {
1883         $self->{IL_disabled} = "";
1884     }
1885
1886     if ($self->{show_zoomed}) {
1887         #$self->{zoom_in_disabled} = "";
1888         $self->{enable_zoom_text} = "Hide zoomed";
1889         $self->{enable_zoom_value} = 0;
1890         $self->{toggle_zoomed_section} = 0;
1891     }
1892     else {
1893         $self->{zoom_in_disabled} = " disabled=\"disabled\" ";
1894         $self->{enable_zoom_text} = "Show zoomed";
1895         $self->{enable_zoom_value} =1;
1896         $self->{toggle_zoomed_section} = 10;
1897     }
1898     if (!$self->get_ref_map->can_zoom()) {
1899         $self->{zoomed_button_enabled}= " disabled=\"disabled\" ";
1900     }
1901
1902 #    $self->{next_chromosome} = $self->{chr_nr} + 1;
1903 #    if ($self->{next_chromosome} > $self->{max_chr}) { $self->{next_chromosome} = 1; }
1904
1905     $self->{next_chromosome} = $self->get_next_chromosome($self->get_ref_chr());
1906
1907  #   $self->{preceding_chromosome} = $self->{chr_nr}-1;
1908  #   if ($self->{preceding_chromosome} == 0)  { $self->{preceding_chromosome} = $self->{max_chr}; }
1909
1910     $self->{preceding_chromosome} = $self -> get_preceding_chromosome($self->get_ref_chr());
1911
1912 #    $self->{next_comp_chr} = $self->{comp_chr} + 1;
1913 #    if ($self->{next_comp_chr} > $self->{comp_max_chr}) { $self->{next_comp_chr} = 1; }
1914
1915     $self->{next_comp_chr} = $self->get_next_comp_chromosome($self->get_comp_chr());
1916
1917  #   $self->{preceding_comp_chr} = $self -> {comp_chr} -1;
1918  #   if ($self->{preceding_comp_chr} ==0 ) { $self->{preceding_comp_chr} = $self->{comp_max_chr}; }
1919     $self->{preceding_comp_chr} = $self->get_preceding_comp_chromosome($self->get_comp_chr());
1920
1921
1922 #    $self->{imagemap} =    $self->{map}->get_image_map("imagemap");
1923
1924     $self->{marker_map_links} = $self->get_marker_map_links();
1925
1926     my $comp_map_caption = "";
1927     my $chromo_designation = "chr";
1928     if ($self->get_comp_chr()=~/[A-Za-z]/) { $chromo_designation = "linkage group"; }
1929     if ($self->get_comp_map_version_id()) { $comp_map_caption = "<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>"; }
1930
1931     # some legends need to know the state of the script...
1932     $self->get_ref_map()->get_legend()->set_state_hashref($self->get_state_hashref());
1933     $self->get_ref_map()->get_legend()->set_mode($self->get_color_model());
1934     my $color_legend = $self->get_ref_map()->get_legend()->get_legend_html();
1935     my $toggle_ruler= !($self->{show_ruler});
1936     my $toggle_physical = !($self->{show_physical});
1937     my $toggle_IL = ! ($self->{show_IL});
1938     my $toggle_offsets = ! ($self->get_show_offsets());
1939
1940     my $toggle_size_select = qq { <select name="size" > };
1941
1942     my @selected = ();
1943     if ($self->{size}=~/small/i) {  $selected[0]=qq { selected="1" }; }
1944     elsif ($self->{size}=~/large/i) {  $selected[2]= qq { selected="1" }; }
1945     else { $selected[1]= qq { selected="1" }; }
1946     $toggle_size_select .= qq { <option value="small" $selected[0] >Small</option> };
1947     $toggle_size_select .= qq { <option value="normal" $selected[1] >Normal</option> };
1948     $toggle_size_select .= qq { <option value="large" $selected[2] >Large</option> };
1949     $toggle_size_select .= qq { </select> };
1950
1951     if (!$self->get_comp_map_version_id()) {
1952         $self->{hide_comparison} = "disabled=\"disabled\"";
1953     }
1954
1955     $self->{maps_select} = CXGN::Cview::Utils::get_maps_select($self->get_dbh(), $self->get_ref_map()->get_id());
1956
1957     my $view_entire_map_link = "&nbsp;View entire comparative map";
1958     if ($self->get_comp_map_version_id()) {
1959         $view_entire_map_link = "&nbsp;<a href=\"/cview/view_maps.pl?center_map_version_id=".($self->get_ref_map()->get_id())."&amp;right_map_version_id=$self->{comp_map_version_id}\">View entire comparative map</a>";
1960     }
1961
1962     $self->{url_map_name} = $self->{ref_map_name};
1963     $self->{url_map_name} =~ s/ /\+/g;
1964
1965
1966     my $show_marker_link = "Show markers between 0 and 0 cM";
1967     if ($self->{show_zoomed} && $self->get_ref_map()->can_zoom()) {
1968         $show_marker_link= "<a href=\"/search/markers/markersearch.pl?
1969 w822_pos_start=".$self->get_cM_start()."&amp;w822_pos_end=".$self->get_cM_end()."&amp;w822_maps=".(CXGN::Cview::Map::Tools::find_map_id_with_version($self->get_dbh(), $self->get_ref_map()->get_id()))."&amp;w822_confs=$self->{confidence}&amp;&amp;w822_submit=Search&amp;w822_chromos=".$self->get_ref_chr()."\"\n>Search markers between ".($self->get_cM_start())." and ".($self->get_cM_end())." ".$self->get_ref_map()->get_units()."</a>";
1970     }
1971     $chromo_designation = "chr";
1972     if ($self->get_ref_chr()=~/[A-Za-z]/) { $chromo_designation = "linkage group"; }
1973
1974     my $state_hashref = $self->get_state_hashref();
1975
1976
1977     my $scroll_up_button = CXGN::Cview::Chromosome_view::toolbar_button -> new("Scroll up", $state_hashref);
1978     $scroll_up_button -> set_property("cM_start", $self->{scrollup_start});
1979     $scroll_up_button -> set_property("cM_end", $self->{scrollup_end});
1980     $scroll_up_button -> set_enabled($self->{scroll_up_disabled});
1981     my $scroll_up_html = $scroll_up_button -> render_string();
1982
1983     my $scroll_down_button = CXGN::Cview::Chromosome_view::toolbar_button -> new("Scroll down", $state_hashref);
1984     $scroll_down_button -> set_property("cM_start", $self->{scrolldown_start});
1985     $scroll_down_button -> set_property("cM_end", $self->{scrolldown_end});
1986     $scroll_down_button -> set_enabled($self->{scroll_down_disabled});
1987     my $scroll_down_html = $scroll_down_button -> render_string();
1988
1989     my $zoom_in_button = CXGN::Cview::Chromosome_view::toolbar_button -> new("Zoom in", $state_hashref);
1990     $zoom_in_button -> set_property("cM_start", $self->{zoom_in_start});
1991     $zoom_in_button -> set_property("cM_end", $self->{zoom_in_end});
1992     $zoom_in_button -> set_enabled($self->{zoom_in_disabled});
1993     my $zoom_in_html = $zoom_in_button -> render_string();
1994
1995
1996     my $zoom_out_button = CXGN::Cview::Chromosome_view::toolbar_button -> new("Zoom out", $state_hashref);
1997     $zoom_out_button -> set_property("cM_start", $self->{zoom_out_start});
1998     $zoom_out_button -> set_property("cM_end", $self->{zoom_out_end});
1999     $zoom_out_button -> set_enabled($self->{zoom_out_disabled});
2000     my $zoom_out_html = $zoom_out_button-> render_string();
2001
2002     my $show_zoomed_button = CXGN::Cview::Chromosome_view::toolbar_button -> new($self->{enable_zoom_text}, $state_hashref);
2003     $show_zoomed_button->set_enabled($self->{zoomed_button_enabled});
2004     $show_zoomed_button -> set_property("show_zoomed", $self->{toggle_zoomed_section});
2005
2006     my $show_zoomed_html = $show_zoomed_button -> render_string();
2007
2008     my $hide_comparison_button = CXGN::Cview::Chromosome_view::toolbar_button -> new("Hide comparison", $state_hashref);
2009     $hide_comparison_button -> set_property("comp_map_version_id", 0);
2010     $hide_comparison_button -> set_property("comp_chr", 0);
2011     $hide_comparison_button -> set_enabled($self->{hide_comparison});
2012     my $hide_comparison_html = $hide_comparison_button -> render_string();
2013
2014     my $switch_chromosomes_button = CXGN::Cview::Chromosome_view::toolbar_button -> new("Switch chromosomes", $state_hashref);
2015     $switch_chromosomes_button -> set_property("comp_chr", $self->get_ref_chr());
2016     $switch_chromosomes_button -> set_property("chr_nr", $self->get_comp_chr());
2017     $switch_chromosomes_button -> set_property("map_version_id", $self->get_comp_map_version_id());
2018     $switch_chromosomes_button -> set_property("comp_map_version_id", $self->get_map_version_id());
2019     $switch_chromosomes_button -> set_enabled($self->{hide_comparison});
2020     my $switch_chromosomes_html = $switch_chromosomes_button -> render_string();
2021
2022     my $sync_preceding_chr_button = CXGN::Cview::Chromosome_view::toolbar_button->new("&lt;&lt;", $state_hashref);
2023     $sync_preceding_chr_button ->set_property("chr_nr", $self->{preceding_chromosome});
2024     $sync_preceding_chr_button ->set_property("comp_chr", $self->{preceding_comp_chr});
2025     $sync_preceding_chr_button ->set_enabled($self->{hide_comparison});
2026     my $sync_preceding_chr_html = $sync_preceding_chr_button->render_string();
2027
2028     my $sync_next_chr_button  = CXGN::Cview::Chromosome_view::toolbar_button->new("&gt;&gt;", $state_hashref);
2029     $sync_next_chr_button ->set_property("chr_nr", $self->{next_chromosome});
2030     $sync_next_chr_button ->set_property("comp_chr", $self->{next_comp_chr});
2031     $sync_next_chr_button ->set_enabled($self->{hide_comparison});
2032     my $sync_next_chr_html = $sync_next_chr_button->render_string();
2033
2034     my $previous_chr_button = CXGN::Cview::Chromosome_view::toolbar_button -> new($self->{preceding_chromosome}."&lt;", $state_hashref);
2035     $previous_chr_button -> set_property("chr_nr", $self->{preceding_chromosome});
2036     my $previous_chr_html = $previous_chr_button -> render_string();
2037
2038     my $next_chr_button = CXGN::Cview::Chromosome_view::toolbar_button -> new("&gt;".$self->{next_chromosome}, $state_hashref);
2039     $next_chr_button -> set_property("chr_nr", $self->{next_chromosome});
2040     my $next_chr_html = $next_chr_button -> render_string();
2041
2042     my $preceding_comp_chr_button = CXGN::Cview::Chromosome_view::toolbar_button -> new($self->{preceding_comp_chr}."&lt;", $state_hashref);
2043     $preceding_comp_chr_button -> set_property("comp_chr", $self->{preceding_comp_chr});
2044     $preceding_comp_chr_button -> set_enabled($self->{hide_comparison});
2045     my $preceding_comp_chr_html = $preceding_comp_chr_button -> render_string();
2046
2047     my $next_comp_chr_button = CXGN::Cview::Chromosome_view::toolbar_button -> new("&gt;".$self->{next_comp_chr}, $state_hashref);
2048     $next_comp_chr_button -> set_property("comp_chr", $self->{next_comp_chr});
2049     $next_comp_chr_button -> set_enabled($self->{hide_comparison});
2050     my $next_comp_chr_html = $next_comp_chr_button -> render_string();
2051
2052     my $ruler_button = CXGN::Cview::Chromosome_view::toolbar_button -> new("Ruler", $state_hashref);
2053     $ruler_button -> set_property("show_ruler", $toggle_ruler);
2054     my $ruler_html = $ruler_button->render_string();
2055
2056     my $physical_map_button = CXGN::Cview::Chromosome_view::toolbar_button -> new("Physical map", $state_hashref);
2057     $physical_map_button -> set_property("show_physical", $toggle_physical);
2058     $physical_map_button -> set_enabled($self->{physical_disabled});
2059     my $physical_map_html = $physical_map_button -> render_string();
2060
2061     my $IL_button = CXGN::Cview::Chromosome_view::toolbar_button->new("IL", $state_hashref);
2062     $IL_button -> set_property("show_IL", $toggle_IL);
2063     $IL_button -> set_enabled($self->{IL_disabled});
2064     my $IL_html = $IL_button -> render_string();
2065
2066     my $offset_button = CXGN::Cview::Chromosome_view::toolbar_button->new("Offsets", $state_hashref);
2067     $offset_button -> set_property("show_offsets", $toggle_offsets);
2068     $offset_button -> set_enabled($self->{zoom_button_enabled});
2069     my $offset_html = $offset_button-> render_string();
2070
2071 #    my $size_button = CXGN::Cview::Chromosome_view::toolbar_button -> new($size_button_text, $state_hashref);
2072 #    $size_button -> set_property("size", $toggle_size);
2073 #    my $size_html = $size_button -> render_string();
2074
2075     my $errors = $self->get_errors();
2076
2077     my $chr_nr = $self->get_ref_chr();
2078     my $map_version_id = $self->get_map_version_id();
2079     my $map_name = $self->get_ref_map()->get_short_name();
2080     my $zoom = $self->get_zoom();
2081     my $cM   = $self->get_cM();
2082     my $show_ruler = $self->get_show_ruler();
2083     my $show_IL = $self->get_show_IL();
2084     my $show_offsets = $self->get_show_offsets();
2085     my $comp_map_version_id= $self ->get_comp_map_version_id();
2086     my $comp_chr= $self->get_comp_chr();
2087     my $color_model = $self->get_color_model();
2088     my $show_physical = $self->get_show_physical();
2089     my $size = $self->get_size();
2090     my $show_zoomed = $self->get_show_zoomed();
2091     my $confidence = $self->get_confidence();
2092     my $hilite = $self->get_hilite();
2093     my $display_marker_type = $self->get_display_marker_type();
2094     my $cM_start = $self->get_cM_start();
2095     my $cM_end = $self->get_cM_end();
2096
2097     my $zoom_range_html = qq {
2098         <form style="margin-bottom:0" >
2099             <input type="hidden" name="map_version_id" value="$map_version_id" />
2100             <input type="hidden" name="chr_nr" value="$chr_nr" size="2" />
2101             <input type="hidden" name="show_ruler" value="$show_ruler" />
2102             <input type="hidden" name="show_IL" value="$show_IL" />
2103             <input type="hidden" name="show_offsets" value="$show_offsets" />
2104             <input type="hidden" name="comp_map_version_id" value="$comp_map_version_id" />
2105             <input type="hidden" name="comp_chr" value="$comp_chr" />
2106             <input type="hidden" name="color_model" value="$color_model" />
2107             <input type="hidden" name="show_physical" value="$show_physical" />
2108             <input type="hidden" name="size" value="$size" />
2109             <input type="hidden" name="show_zoomed" value="1" />
2110             <input type="hidden" name="confidence" value="$confidence" />
2111             <input type="hidden" name="hilite" value="$hilite" />
2112             <input type="hidden" name="marker_type" value="$display_marker_type" />
2113
2114             <b>zoom range:</b> <input name="cM_start" size="3" value="$cM_start" /> to <input name="cM_end" size="3" value="$cM_end" />
2115             <input type="submit" value="show" />
2116             </form>
2117         };
2118
2119
2120     print <<BUTTONS;
2121
2122     $errors
2123
2124
2125     <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>
2126         $comp_map_caption
2127         <td>&nbsp;&nbsp;[<a href="/help/cview.pl">Help</a>]</td>
2128         </tr></table>
2129
2130         <table summary="" cellpadding="0" cellspacing="0"><tr>
2131         <td>
2132
2133         $self->{image_html}
2134
2135         </td></tr></table>
2136
2137             $color_legend
2138
2139
2140 <table summary="" cellpadding="0" cellspacing="0"><tr><td>
2141
2142 $scroll_up_html
2143
2144
2145     </td><td>
2146
2147     $scroll_down_html
2148
2149     </td><td>
2150
2151     $zoom_in_html
2152
2153
2154     </td><td>
2155
2156
2157     $zoom_out_html
2158
2159
2160     </td>
2161
2162     <td>|</td><td>
2163
2164     $show_zoomed_html
2165
2166
2167     </td>
2168
2169     <td width="10">&nbsp;</td><td>
2170
2171     $zoom_range_html
2172     <!-- $show_marker_link -->
2173
2174     </td>
2175
2176     </tr></table>
2177
2178         <table summary="" cellpadding="0" cellspacing="0" border="0">
2179         <tr><td valign="middle" width="120"><b>Compare map to:</b>&nbsp;</td><td valign="middle">$self->{marker_map_links}</td></tr>
2180         </table>
2181
2182         <table summary="" cellpadding="0" cellspacing="0">
2183
2184         <tr><td width="120">&nbsp;</td><td>
2185
2186         $hide_comparison_html
2187
2188
2189 </td>
2190 <td>
2191
2192         $switch_chromosomes_html
2193
2194
2195         </td>
2196
2197
2198
2199         <td>
2200         $view_entire_map_link
2201
2202 </td>
2203
2204         </tr></table>
2205
2206         <table summary=""><tr><td>
2207
2208          <form style="margin-bottom:0"  action="/cview/view_chromosome.pl">
2209
2210          <table summary="" cellpadding="0" border="0" cellspacing="0">
2211          <tr valign="middle"><td valign="middle" width="120">
2212          <b>Jump to map:</b></td><td>$self->{maps_select}</td><td valign="middle">&nbsp;chr&nbsp;</td><td>
2213          <input type="text" name="chr_nr" value="$chr_nr" size="2" />
2214          <input type="hidden" name="zoom" value="$zoom" />
2215          <!-- <input type="hidden" name="cM" value="$cM" /> -->
2216         <input type="hidden" name="cM_start" value="$cM_start" />
2217         <input type="hidden" name="cM_end" value="$cM_end" />
2218          <input type="hidden" name="show_ruler" value="$show_ruler" />
2219          <input type="hidden" name="show_IL" value="$show_IL" />
2220          <input type="hidden" name="show_offsets" value="$show_offsets" />
2221          <input type="hidden" name="comp_map_version_id" value="$comp_map_version_id" />
2222          <input type="hidden" name="comp_chr" value="$comp_chr" />
2223          <input type="hidden" name="color_model" value="$color_model" />
2224          <input type="hidden" name="show_physical" value="$show_physical" />
2225          <input type="hidden" name="size" value="$size" />
2226          <input type="hidden" name="show_zoomed" value="$show_zoomed" />
2227          <input type="hidden" name="confidence" value="$confidence" />
2228          <input type="hidden" name="hilite" value="$hilite" />
2229          <input type="hidden" name="marker_type" value="$display_marker_type" />
2230          <input type="submit" value="Jump" />
2231          </td>
2232          </tr>
2233          </table>
2234          </form>
2235          </td>
2236
2237          <td width="20">&nbsp;</td>
2238
2239          <td>
2240         <form  style="margin-bottom:0" action="/cview/view_chromosome.pl">
2241         <b>Highlight marker:</b>
2242         <input type="text" name="hilite" value="$hilite" size="5" />
2243         <input type="submit" value="Highlight" />
2244         <input type="hidden" name="zoom" value="$zoom" />
2245         <!-- <input type="hidden" name="cM" value="$cM" /> -->
2246         <input type="hidden" name="cM_start" value="$cM_start" />
2247         <input type="hidden" name="cM_end" value="$cM_end" />
2248         <input type="hidden" name="chr_nr" value="$chr_nr" />
2249         <input type="hidden" name="map_version_id" value="$map_version_id" />
2250         <input type="hidden" name="show_ruler" value="$show_ruler" />
2251         <input type="hidden" name="show_IL" value="$show_IL" />
2252         <input type="hidden" name="show_offsets" value="$show_offsets" />
2253         <input type="hidden" name="comp_map_version_id" value="$comp_map_version_id" />
2254         <input type="hidden" name="comp_chr" value="$comp_chr" />
2255         <input type="hidden" name="color_model" value="$color_model" />
2256         <input type="hidden" name="show_zoomed" value="$show_zoomed" />
2257         <input type="hidden" name="confidence" value="$confidence" />
2258         <input type="hidden" name="show_physical" value="$show_physical" />
2259         <input type="hidden" name="size" value="$size" />
2260         <input type="hidden" name="marker_type" value="$display_marker_type" />
2261         </form>
2262         </td>
2263
2264
2265 </tr>
2266         </table>
2267
2268
2269
2270
2271     <table summary="" cellpadding="0" cellspacing="0" border="0"><tr>
2272     <td width="120">&nbsp;</td>
2273     <td colspan="3" align="center"><b>Reference chromosome</b></td>
2274     <td width="20">&nbsp;</td>
2275     <td colspan="3" align="center"><b>Comparison chromosome</b></td>
2276     </tr>
2277     <tr>
2278     <td width="120">&nbsp;</td>
2279     <td align="right">
2280
2281     <table summary="" cellpadding="0" cellspacing="0" border="0"><tr><td>
2282     $sync_preceding_chr_html
2283     </td><td>
2284     $previous_chr_html
2285     </td></tr></table>
2286
2287     </td>
2288     <td align="center" valign="middle">
2289
2290 BUTTONS
2291
2292     unless($chr_nr ne "") {$chr_nr ="&nbsp;";}
2293
2294
2295 print <<BUTTONS;
2296
2297     &nbsp;<b>$chr_nr</b>&nbsp; </td>
2298     <td>
2299
2300     $next_chr_html
2301
2302
2303 </td>
2304 <td width="20">&nbsp;</td>
2305 <td align="right">
2306 $preceding_comp_chr_html
2307
2308
2309     </td>
2310     <td align="center" valign="middle">
2311
2312
2313 BUTTONS
2314
2315     unless($comp_chr ne "") {$comp_chr ="&nbsp;";}
2316
2317
2318 print <<BUTTONS;
2319
2320     &nbsp;<b>$comp_chr</b>&nbsp;</td>
2321     <td>
2322
2323     <table summary="" cellpadding="0" cellspacing="0" border="0"><tr><td>
2324     $next_comp_chr_html
2325     </td><td>
2326     $sync_next_chr_html
2327     </td></tr></table>
2328
2329 </td>
2330
2331         </tr></table>
2332
2333         <table summary="" cellpadding="0" cellspacing="0">
2334         <tr><td valign="middle" width="120">
2335         <b>Show/hide:</b></td>
2336         <td>
2337
2338         $ruler_html
2339
2340         </td>
2341         <td>
2342         $offset_html
2343         </td>
2344
2345
2346
2347 <td>
2348
2349         $physical_map_html
2350
2351         </td>
2352
2353         <td>
2354
2355         $IL_html
2356
2357
2358         </td>
2359
2360
2361         <td width="30">&nbsp;</td>
2362         <td valign="middle">&nbsp;<b>image size: </b> </td><td>
2363
2364         <form  style="margin-bottom:0" action="/cview/view_chromosome.pl">
2365         $toggle_size_select
2366         <input type="submit" value="change" />
2367         <input type="hidden" name="zoom" value="$zoom" />
2368         <input type="hidden" name="cM_start" value="$cM_start" />
2369         <input type="hidden" name="cM_end" value="$cM_end" />
2370         <input type="hidden" name="chr_nr" value="$chr_nr" />
2371         <input type="hidden" name="map_version_id" value="$map_version_id" />
2372         <input type="hidden" name="show_ruler" value="$show_ruler" />
2373         <input type="hidden" name="show_IL" value="$show_IL" />
2374         <input type="hidden" name="show_offsets" value="$show_offsets" />
2375         <input type="hidden" name="comp_map_version_id" value="$comp_map_version_id" />
2376         <input type="hidden" name="comp_chr" value="$comp_chr" />
2377         <input type="hidden" name="color_model" value="$color_model" />
2378         <input type="hidden" name="show_zoomed" value="$show_zoomed" />
2379         <input type="hidden" name="confidence" value="$confidence" />
2380         <input type="hidden" name="show_physical" value="$show_physical" />
2381         <input type="hidden" name="marker_type" value="$display_marker_type" />
2382         </form>
2383
2384
2385
2386
2387         </td>
2388 </tr></table>
2389
2390 BUTTONS
2391
2392
2393 }
2394
2395 sub clean_up {
2396     my $self = shift;
2397 }
2398
2399
2400 =head2 accessors set_state_hashref(), get_state_hashref()
2401
2402   Property:     the state_hashref is a hash describing the current
2403                 state of the Chromosome_viewer, essentially collecting
2404                 all the processed page arguments.
2405   Args/Ret:     a hash reference
2406   Side Effects: the state_hashref determines what the toolbar buttons
2407                 and links constructed on the page will contain as
2408                 parameters.
2409
2410 =cut
2411
2412 sub get_state_hashref {
2413     my $self=shift;
2414     return $self->{state_hashref};
2415 }
2416
2417 sub set_state_hashref {
2418     my $self=shift;
2419     $self->{state_hashref}=shift;
2420 }
2421
2422
2423 =head2 accessors set_force(), get_force()
2424
2425   Property:     force - regenerate cached files whatever the
2426                 status of the cache
2427   Args/Ret      true for re-generation, false for letting cache
2428                 decide when to re-generate the images.
2429   Side Effects: true will force regenerate all associated files
2430   Description:
2431
2432 =cut
2433
2434 sub get_force {
2435     my $self=shift;
2436     if (!exists($self->{force}) || !defined($self->{force})) {
2437         $self->{force}="";
2438     }
2439     return $self->{force};
2440 }
2441
2442 sub set_force {
2443     my $self=shift;
2444     $self->{force}=shift;
2445 }
2446
2447
2448 =head2 get_temp_dir
2449
2450  Usage:
2451  Desc:
2452  Ret:
2453  Args:
2454  Side Effects:
2455  Example:
2456
2457 =cut
2458
2459 sub get_temp_dir {
2460   my $self=shift;
2461   if (!exists($self->{temp_dir})) {
2462       die "Chromosome_viewer: need a temp_dir  for storing images... STOP!\n";
2463   }
2464
2465   return $self->{temp_dir};
2466
2467 }
2468
2469 =head2 set_temp_dir
2470
2471  Usage:
2472  Desc:
2473  Ret:
2474  Args:
2475  Side Effects:
2476  Example:
2477
2478 =cut
2479
2480 sub set_temp_dir {
2481   my $self=shift;
2482   $self->{temp_dir}=shift;
2483 }
2484
2485 =head2 get_basedir
2486
2487  Usage:
2488  Desc:
2489  Ret:
2490  Args:
2491  Side Effects:
2492  Example:
2493
2494 =cut
2495
2496 sub get_basedir {
2497   my $self=shift;
2498   if (!exists($self->{basedir})) {
2499       die "Chromosome_viewer: need a basedir for storing images... STOP!\n";
2500   }
2501   return $self->{basedir};
2502
2503 }
2504
2505 =head2 set_basedir
2506
2507  Usage:
2508  Desc:
2509  Ret:
2510  Args:
2511  Side Effects:
2512  Example:
2513
2514 =cut
2515
2516 sub set_basedir {
2517   my $self=shift;
2518   $self->{basedir}=shift;
2519 }
2520
2521 =head2 accessors get_db_backend, set_db_backend
2522
2523  Usage:        $v ->set_db_backend("cxgn");
2524  Desc:         sets the db backend of the comparative viewer.
2525                following values are allowed:
2526                o cxgn - the cxgn database
2527                o cmap - the cmap database
2528                o cxgn_and_cmap - both databases are queried for maps.
2529  Property      a string describing the database backend to be used.
2530  Side Effects: the specified backend will be used
2531
2532 =cut
2533
2534 sub get_db_backend {
2535   my $self = shift;
2536   return $self->{db_backend};
2537 }
2538
2539 sub set_db_backend {
2540   my $self = shift;
2541   $self->{db_backend} = shift;
2542 }
2543
2544
2545
2546
2547
2548 package CXGN::Cview::Chromosome_view::toolbar_button;
2549
2550 sub new {
2551     my $class = shift;
2552     my $args = {};
2553     my $self = bless $args, $class;
2554
2555     my $name = shift;
2556
2557     my $properties_hashref = shift;
2558
2559     $self->set_name($name);
2560
2561     %{$self->{properties}} = ( 'chr_nr' => "",
2562                                'map_version_id' => "",
2563                                'zoom'   => "",
2564                                'show_ruler' => "",
2565                                'show_IL' => "",
2566                                'show_offsets'=> "",
2567                                'comp_map_version_id' => "",
2568                                'comp_chr' => "",
2569                                'color_model' => "",
2570                                'show_zoomed' => "",
2571                                'show_physical' => "",
2572                                'confidence' => "",
2573                                'size'=> "",
2574                                'hilite' => "",
2575                                'marker_type' => "",
2576                                'cM_start' => "",
2577                                'cM_end' => "",
2578                                'cM' => "",
2579                                'clicked' => "",
2580                            );
2581
2582     foreach my $k (keys(%$properties_hashref)) {
2583         if (exists(${$self->{properties}}{$k})) {
2584             ${$self->{properties}}{$k}=$$properties_hashref{$k};
2585         }
2586         else { print STDERR "property $k is not supported in toolbar_button package.\n"; }
2587     }
2588     return $self;
2589 }
2590
2591 sub set_name {
2592     my $self = shift;
2593     $self->{name}=shift;
2594 }
2595
2596 sub get_name {
2597     my $self = shift;
2598     return $self->{name};
2599 }
2600
2601 sub set_action {
2602     my $self = shift;
2603     $self->{action} = shift;
2604 }
2605
2606 sub get_action {
2607     my $self =shift;
2608     if (!exists($self->{action})) { $self->{action}=""; }
2609     return $self->{action};
2610 }
2611
2612 sub set_enabled {
2613     # parameter: true or false setting to enabled or disabled
2614     #
2615     my $self = shift;
2616     $self->{enabled} = shift;
2617 }
2618
2619 sub is_enabled {
2620     my $self = shift;
2621     return $self->{enabled};
2622 }
2623
2624 sub set_property {
2625     my $self = shift;
2626     my $property = shift;
2627     my $value = shift;
2628     if (!$value) { $value=""; }
2629     if (!exists(${$self->{properties}}{$property})) {
2630         print STDERR "Warning: toolbar_button: property $property does not exist!\n";
2631         return 0;
2632     }
2633     else {
2634         ${$self->{properties}}{$property}=$value;
2635         return 1;
2636     }
2637 }
2638
2639 sub render_string {
2640     my $self = shift;
2641
2642     my $action = $self->get_action();
2643
2644     if ($action eq "") {
2645 $action = "#"
2646 }
2647     my $s = "<form style=\"margin-bottom:0\" action=\"$action\">\n";
2648
2649     foreach my $p (keys %{$self->{properties}}) {
2650         #print STDERR "Printing toolbar button: hidden field: $p, $self->{properties}{$p}\n";
2651         if (exists($self->{properties}{$p}) && $self->{properties}{$p}) {
2652             $s .= "<input type=\"hidden\" name=\"$p\" value=\"$self->{properties}{$p}\" />\n";
2653         }
2654
2655     }
2656
2657     my $disabled;
2658     if ($self->is_enabled()) {
2659         $disabled = "disabled=\"disabled\"";
2660     }
2661     else {
2662         $disabled="";
2663     }
2664     $s .="<input type=\"submit\" value=\"".$self->get_name()."\" $disabled />\n";
2665     $s .="</form>\n";
2666     return $s;
2667 }
2668
2669 sub render {
2670     my $self=shift;
2671     print $self->render_string();
2672 }
2673
2674
2675 # <FORM style="margin-bottom:0" action=/cview/view_chromosome.pl>
2676 #       <INPUT TYPE=hidden NAME=chr_nr VALUE="$self->{chr_nr}" />
2677 #       <INPUT TYPE=hidden NAME=map_id VALUE="$self->{map_id}" />
2678 #       <INPUT TYPE=hidden NAME=zoom VALUE="$self->{zoom}" />
2679 #       <INPUT TYPE=hidden NAME=cM VALUE="$self->{cM}" />
2680 #       <INPUT TYPE=hidden NAME=show_ruler VALUE="$self->{show_ruler}" />
2681 #       <INPUT TYPE=hidden NAME=show_IL VALUE="$self->{IL}" />
2682 #       <INPUT TYPE=hidden NAME=comp_map VALUE="$self->{comp_map}" />
2683 #       <INPUT TYPE=hidden NAME=comp_chr VALUE="$self->{comp_chr}" />
2684 #       <INPUT TYPE=hidden NAME=color_model VALUE="$self->{color_model}" />
2685 #       <INPUT TYPE=hidden NAME=show_zoomed VALUE="$self->{show_zoomed}" />
2686 #       <INPUT TYPE=hidden NAME=show_physical VALUE="$self->{show_physical}" />
2687 #       <INPUT TYPE=hidden NAME=confidence VALUE="$self->{confidence}" />
2688 #       <INPUT TYPE=hidden NAME=size VALUE="$toggle_size" />
2689 #       <INPUT TYPE=hidden NAME=hilite VALUE="$self->{hilite}" />
2690 #       <INPUT TYPE=submit VALUE="$size_button" />
2691 #       </FORM>