lib/CXGN/Cview/ViewMaps.pm

   1
   2 package CXGN::Cview::ViewMaps;
   3
   4 use CXGN::Page::FormattingHelpers qw | page_title_html |;
   5 use CXGN::Cview::MapFactory;
   6 use CXGN::Cview::Chromosome_viewer;
   7 use CXGN::Cview::ChrLink;
   8 use CXGN::Cview::Utils qw | set_marker_color |;
   9 use CXGN::Cview::MapImage;
  10 use CXGN::Tools::WebImageCache;
  11 use CXGN::Map;
  12 use CXGN::VHost;
  13
  14 use base qw | CXGN::DB::Object |;
  15
  16 1;
  17
  18 =head2 function new()
  19
  20   Synopsis:
  21   Arguments:    none
  22   Returns:      a handle to a view_maps object
  23   Side effects:
  24   Description:  constructor
  25
  26 =cut
  27
  28 sub new {
  29     my $class = shift;
  30     my $dbh = shift;
  31     my $page = CXGN::Page->new();
  32     my $self = bless {}, $class;
  33     $self->set_dbh($dbh);
  34     # set some defaults...
  35     #
  36     $self->{page} = $page;
  37     $self -> {unzoomedheight} = 20; # how many cM are seen at zoom level 1
  38
  39     return $self;
  40 }
  41
  42 sub adjust_parameters {
  43     my $self = shift;
  44
  45     # adjust input arguments
  46     #
  47
  48
  49 }
  50
  51 =head2 accessors set_maps(), get_maps()
  52
  53   Property:
  54   Setter Args:
  55   Getter Args:
  56   Getter Ret:
  57   Side Effects:
  58   Description:
  59
  60 =cut
  61
  62 sub get_maps {
  63     my $self=shift;
  64     return @{$self->{maps}};
  65 }
  66
  67 sub set_maps {
  68     my $self=shift;
  69     @{$self->{maps}}=@_;
  70 }
  71
  72 =head2 accessors set_cache(), get_cache()
  73
  74   Property:     the CXGN::Tools::WebImageCache object
  75   Args/Ret:     the same
  76   Side Effects: this is the object used to generate the
  77                 cache image.
  78   Description:
  79
  80 =cut
  81
  82 sub get_cache {
  83     my $self=shift;
  84     return $self->{cache};
  85 }
  86
  87 sub set_cache {
  88     my $self=shift;
  89     $self->{cache}=shift;
  90 }
  91
  92
  93
  94
  95 =head2 function generate_page()
  96
  97   Arguments:    none
  98   Returns:      nothing
  99   Side effects: generates the CXGN::Cview::MapImage and stores it
 100                 to the cache if necessary, or reads just reads
 101                 the image cache if it is still valid.
 102
 103 =cut
 104
 105 sub generate_page {
 106     my $self = shift;
 107
 108     my $vhost = CXGN::VHost->new();
 109     my $cache = CXGN::Tools::WebImageCache->new();
 110
 111     # define a key for the cache. lets just use the name of the
 112     # script and the map_version_ids of the maps being displayed
 113     #
 114     $cache->set_key("view_maps".(join "-", map { $_->get_id() } ($self->get_maps())));
 115
 116     $cache->set_basedir($vhost->get_conf("basepath"));
 117     $cache->set_temp_dir(File::Spec->catfile($vhost->get_conf("tempfiles_subdir"), "cview"));
 118     $cache->set_expiration_time(86400);
 119
 120     $self->set_cache($cache);
 121
 122     if (! $self->get_cache()->is_valid()) {
 123         my $map_width = $self->{map_width} = 720;
 124         my $x_distance = $map_width/4; # the number of pixels the different elements are spaced
 125         my $row_count = 0;
 126         my $row_height = 120;    # the height of a row (vertical space for each chromosome image)
 127         my $y_distance = $row_height * (1/3);
 128         my $chr_height = $row_height * (2/3);
 129         my $map_height;
 130
 131         # determine the maximum chromosome count among all maps
 132         # so that we can accommodate it
 133         #
 134         my $max_chr = 0;
 135         foreach my $m ($self->get_maps()) {
 136             my $chr_count = 0;
 137             if ($m) {
 138                 $chr_count = $m->get_chromosome_count();
 139             }
 140             if ($chr_count > $max_chr) { $max_chr=$chr_count; }
 141         }
 142
 143         $map_height = $row_height * $max_chr+2*$y_distance;
 144         # show the ruler if requested
 145         #
 146 #       if ($self->{show_ruler}) {
 147 #           my $r = ruler->new($x_distance-20, $row_height * $row_count + $y_distance, $chr_height, 0, $self->{c}{$track}[$i]->get_chromosome_length());
 148 #           $self->{map}->add_ruler($r);
 149 #       }
 150         $row_count++;
 151
 152         $self->{map} = CXGN::Cview::MapImage -> new("", $map_width, $map_height);
 153
 154         # get all the chromosomes and add them to the map
 155         #
 156         my $track = 0;
 157         foreach my $map ($self->get_maps()) {
 158             my @chr_names = $map->get_chromosome_names();
 159             for (my $i=0; $i<$map->get_chromosome_count(); $i++) {
 160
 161                 $self->{c}{$track}[$i] = ($self->get_maps())[$track]->get_chromosome($i+1);
 162                 $self->{c}{$track}[$i] -> set_vertical_offset($row_height*$i+$y_distance);
 163                 $self->{c}{$track}[$i] -> set_horizontal_offset($x_distance + $x_distance * ($track));
 164                 $self->{c}{$track}[$i] -> set_height($chr_height);
 165                 $self->{c}{$track}[$i] -> set_caption( $chr_names[$i] );
 166                 $self->{c}{$track}[$i] -> set_width(16);
 167                 $self->{c}{$track}[$i] -> set_url("/cview/view_chromosome.pl?map_version_id=".($self->get_maps())[$track]->get_id()."&amp;chr_nr=$i");
 168
 169                 $self->{c}{$track}[$i] -> set_labels_none();
 170                 $self->{map}->add_chromosome($self->{c}{$track}[$i]);
 171             }
 172             $track++;
 173
 174         }
 175
 176         # get the connections between the chromosomes
 177         #
 178         my %find = ();
 179
 180         for (my $track=0; $track<($self->get_maps()); $track++) {
 181             for (my $i =0; $i< ($self->get_maps())[$track]->get_chromosome_count(); $i++) {
 182                 foreach my $m ($self->{c}{$track}[$i]->get_markers()) {
 183                     $m->hide_label();
 184                     # make entry into the find hash and store corrsponding chromosomes and offset
 185                     # (for drawing connections)
 186                     # if the map is the reference map ($compare_to_map is false).
 187                     #
 188                     $find{$m->get_id()}->{$track}->{chr}=$i;
 189                     $find{$m->get_id()}->{$track}->{offset}=$m->get_offset();
 190
 191                     # set the marker colors
 192                     #
 193                     set_marker_color($m, "marker_types");
 194                 }
 195
 196             }
 197         }
 198         foreach my $f (keys(%find)) {
 199             foreach my $t (keys %{$find{$f}}) {
 200                 my $chr = $find{$f}->{$t}->{chr};
 201                 my $offset = $find{$f}->{$t}->{offset};
 202
 203                 if (exists($find{$f}->{$t-1}) || defined($find{$f}->{$t-1})) {
 204                     my $comp_chr = $find{$f}->{$t-1}->{chr};
 205                     my $comp_offset = $find{$f}->{$t-1}->{offset};
 206                     #print STDERR "Found on track $t: Chr=$chr offset=$offset, links to track ".($t-1)." Chr=$comp_chr offset $comp_offset\n";
 207                     if ($comp_chr) {
 208                         my $link1 = CXGN::Cview::ChrLink->new($self->{c}{$t}[$chr], $offset, $self->{c}{$t-1}[$comp_chr], $comp_offset);
 209                         $self->{map}->add_chr_link($link1);
 210                     }
 211                 }
 212                 if (exists($find{$f}->{$t+1})) {
 213                     my $comp_chr = $find{$f}->{$t+1}->{chr};
 214                     my $comp_offset = $find{$f}->{$t+1}->{offset};
 215                     my $link2 = CXGN::Cview::ChrLink->new($self->{c}{$t}[$chr], $offset, $self->{c}{$t+1}[$comp_chr], $comp_offset);
 216                     $self->{map}->add_chr_link($link2);
 217
 218                 }
 219             }
 220
 221         }
 222
 223         $self->get_cache()->set_map_name("viewmap");
 224         $self->get_cache()->set_image_data($self->{map}->render_png_string());
 225         $self->get_cache()->set_image_map_data($self->{map}->get_image_map("viewmap"));
 226
 227 #       # show the ruler if requested
 228 #       #
 229 #       if ($self->{show_ruler}) {
 230 #           my $r = ruler->new($x_distance-20, $row_height * $row_count + $y_distance, $chr_height, 0, $self->{c}{$track}[$i]->get_chromosome_length());
 231 #           $self->{map}->add_ruler($r);
 232 #       }
 233     }
 234
 235
 236         # my $filename = "cview".(rand())."_".$$.".png";
 237
 238 #     $self->{image_path} = $vhost_conf->get_conf('basepath').$vhost_conf->get_conf('tempfiles_subdir')."/cview/$filename";
 239 #     $self->{image_url} = $vhost_conf->get_conf('tempfiles_subdir')."/cview/$filename";
 240
 241 #     $self->{map} -> render_png_file($self->{image_path});
 242
 243 #     $self->{imagemap} = $self->{map}->get_image_map("imagemap");
 244
 245
 246 }
 247
 248
 249 sub get_select_toolbar {
 250     my $self = shift;
 251
 252 #    $left_map = $self->get_left_map() || 0;
 253 #    $center_map = $self->get_center_map() || 0;
 254 #    $right_map = $self->get_right_map || 0;
 255     my @names = ("left_map_version_id", "center_map_version_id", "right_map_version_id");
 256     my @selects = ();
 257     for (my $i=0; $i< 3; $i++) {
 258         if ( defined(($self->get_maps())[$i])) {
 259             push @selects,  CXGN::Cview::Utils::get_maps_select($self->get_dbh(), ($self->get_maps())[$i]->get_id(), $names[$i], 1);
 260         }
 261         else {
 262             push @selects, CXGN::Cview::Utils::get_maps_select($self->get_dbh(), undef, $names[$i], 1);
 263         }
 264     }
 265 #    my $center_select = CXGN::Cview::Utils::get_maps_select($self, !$center_map || $center_map->get_id(), "center_map_version_id", 1);
 266 #    my $right_select = CXGN::Cview::Utils::get_maps_select($self, !$right_map || $right_map->get_id(), "right_map_version_id", 1);
 267
 268
 269     return qq {
 270         <form action="#">
 271             <center>
 272             <table summary=""><tr><td>$selects[0]</td><td>$selects[1]</td><td>$selects[2]</td></tr></table>
 273             <input type="submit" value="set" />
 274             </center>
 275         </form>
 276         };
 277 }
 278
 279 =head2 function display()
 280
 281   Synopsis:
 282   Arguments:
 283   Returns:
 284   Side effects:
 285   Description:  composes the page and displays it.
 286
 287 =cut
 288
 289 sub display {
 290     my $self = shift;
 291
 292
 293     $self->{page}->header("SGN comparative mapviewer");
 294     my $width = int($self->{map_width}/3);
 295
 296     my $select = $self->get_select_toolbar();
 297
 298     print "$select";
 299
 300     if (!$self->get_maps()) {
 301         print "<br /><br /><center>Note: No maps are selected. Please select maps from the pull down menus above.</center>\n";
 302     }
 303
 304     print $self->get_cache()->get_image_html();
 305
 306 #    print "<img src=\"$self->{image_url}\" usemap=\"#chr_comp_map\" border=\"0\" alt=\"\" />\n";
 307
 308 #    print $self->{map}->get_image_map("chr_comp_map");
 309
 310     $self->{page}->footer();
 311
 312
 313
 314 }
 315
 316 =head2 function error_message_page()
 317
 318   Synopsis:
 319   Arguments:
 320   Returns:
 321   Side effects:
 322   Description:
 323
 324 =cut
 325
 326 sub error_message_page {
 327     my $self = shift;
 328     my $page = CXGN::Page->new();
 329     $page->header();
 330
 331     my $title = page_title_html("Error: No center map defined");
 332
 333     print <<HTML;
 334
 335     $title
 336         <p>
 337         A center map needs to be defined for this page to work. Please supply
 338         a center_map_version_id as a parameter. If this was the result of a link,
 339         please inform SGN about the error.
 340         </p>
 341         <p>
 342         Contact SGN at <a href="mailto:sgn-feedback\@sgn.cornell.edu">sgn-feedback\@sgn.cornell.edu</a>
 343
 344 HTML
 345
 346      $page->footer();
 347
 348     exit();
 349 }
 350
 351
 352 sub clean_up {
 353     my $self = shift;
 354 }
 355