lib/CXGN/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
  17
  18 =head2 function new()
  19
  20   Synopsis:
  21   Arguments:    a database handle [ DBI object or CXGN::DB::Connection object]
  22                 the base dir [ file path ]
  23                 the temp_dir [ relative path ]
  24   Returns:      a handle to a view_maps object
  25   Side effects:
  26   Description:  constructor
  27
  28 =cut
  29
  30 sub new {
  31     my $class = shift;
  32     my $dbh = shift;
  33     my $basepath = shift;
  34     my $temp_dir = shift;
  35
  36     my $self = bless {}, $class;
  37     $self->set_dbh($dbh);
  38     # set some defaults...
  39     #
  40     $self->{unzoomedheight} = 20; # how many cM are seen at zoom level 1
  41
  42     # create an set the cache file in the constructor,
  43     # such that we can define the temp dirs before
  44     # we generate the image using generate_image()
  45     #
  46     my $cache = CXGN::Tools::WebImageCache->new();
  47     $self->set_cache($cache);
  48     $cache->set_basedir($basepath);
  49     $cache->set_temp_dir($temp_dir);
  50
  51     return $self;
  52 }
  53
  54 sub adjust_parameters {
  55     my $self = shift;
  56
  57     # adjust input arguments
  58     #
  59
  60
  61 }
  62
  63 =head2 accessors set_maps(), get_maps()
  64
  65   Property:
  66   Setter Args:
  67   Getter Args:
  68   Getter Ret:
  69   Side Effects:
  70   Description:
  71
  72 =cut
  73
  74 sub get_maps {
  75     my $self=shift;
  76     return @{$self->{maps}};
  77 }
  78
  79 sub set_maps {
  80     my $self=shift;
  81     @{$self->{maps}}=@_;
  82 }
  83
  84 =head2 accessors set_cache(), get_cache()
  85
  86   Property:     the CXGN::Tools::WebImageCache object
  87   Args/Ret:     the same
  88   Side Effects: this is the object used to generate the
  89                 cache image.
  90   Description:
  91
  92 =cut
  93
  94 sub get_cache {
  95     my $self=shift;
  96     return $self->{cache};
  97 }
  98
  99 sub set_cache {
 100     my $self=shift;
 101     $self->{cache}=shift;
 102 }
 103
 104
 105
 106
 107 =head2 function generate_page()
 108
 109   Arguments:    none
 110   Returns:      nothing
 111   Side effects: generates the CXGN::Cview::MapImage and stores it
 112                 to the cache if necessary, or reads just reads
 113                 the image cache if it is still valid.
 114
 115 =cut
 116
 117 sub generate_image {
 118     my $self = shift;
 119
 120     # define a key for the cache. lets just use the name of the
 121     # script and the map_version_ids of the maps being displayed
 122     #
 123     $self->get_cache()->set_key("view_maps".(join "-", map { $_->get_id() } ($self->get_maps())));
 124
 125     $self->get_cache()->set_expiration_time(86400);
 126
 127
 128     if (! $self->get_cache()->is_valid()) {
 129         my $map_width = $self->{map_width} = 720;
 130         my $x_distance = $map_width/4; # the number of pixels the different elements are spaced
 131         my $row_count = 0;
 132         my $row_height = 120;    # the height of a row (vertical space for each chromosome image)
 133         my $y_distance = $row_height * (1/3);
 134         my $chr_height = $row_height * (2/3);
 135         my $map_height;
 136
 137         # determine the maximum chromosome count among all maps
 138         # so that we can accommodate it
 139         #
 140         my $max_chr = 0;
 141         foreach my $m ($self->get_maps()) {
 142             my $chr_count = 0;
 143             if ($m) {
 144                 $chr_count = $m->get_chromosome_count();
 145             }
 146             if ($chr_count > $max_chr) { $max_chr=$chr_count; }
 147         }
 148
 149         $map_height = $row_height * $max_chr+2*$y_distance;
 150         # show the ruler if requested
 151         #
 152 #       if ($self->{show_ruler}) {
 153 #           my $r = ruler->new($x_distance-20, $row_height * $row_count + $y_distance, $chr_height, 0, $self->{c}{$track}[$i]->get_chromosome_length());
 154 #           $self->{map}->add_ruler($r);
 155 #       }
 156         $row_count++;
 157
 158         $self->{map} = CXGN::Cview::MapImage -> new("", $map_width, $map_height);
 159
 160         # get all the chromosomes and add them to the map
 161         #
 162         my $track = 0;
 163         foreach my $map ($self->get_maps()) {
 164             my @chr_names = $map->get_chromosome_names();
 165             for (my $i=0; $i<$map->get_chromosome_count(); $i++) {
 166
 167                 $self->{c}{$track}[$i] = ($self->get_maps())[$track]->get_chromosome($i+1);
 168                 $self->{c}{$track}[$i] -> set_vertical_offset($row_height*$i+$y_distance);
 169                 $self->{c}{$track}[$i] -> set_horizontal_offset($x_distance + $x_distance * ($track));
 170                 $self->{c}{$track}[$i] -> set_height($chr_height);
 171                 $self->{c}{$track}[$i] -> set_caption( $chr_names[$i] );
 172                 $self->{c}{$track}[$i] -> set_width(16);
 173                 $self->{c}{$track}[$i] -> set_url("/cview/view_chromosome.pl?map_version_id=".($self->get_maps())[$track]->get_id()."&amp;chr_nr=$i");
 174
 175                 $self->{c}{$track}[$i] -> set_labels_none();
 176                 $self->{map}->add_chromosome($self->{c}{$track}[$i]);
 177             }
 178             $track++;
 179
 180         }
 181
 182         # get the connections between the chromosomes
 183         #
 184         my %find = ();
 185
 186         for (my $track=0; $track<($self->get_maps()); $track++) {
 187             for (my $i =0; $i< ($self->get_maps())[$track]->get_chromosome_count(); $i++) {
 188                 foreach my $m ($self->{c}{$track}[$i]->get_markers()) {
 189                     $m->hide_label();
 190                     # make entry into the find hash and store corrsponding chromosomes and offset
 191                     # (for drawing connections)
 192                     # if the map is the reference map ($compare_to_map is false).
 193                     #
 194                     $find{$m->get_id()}->{$track}->{chr}=$i;
 195                     $find{$m->get_id()}->{$track}->{offset}=$m->get_offset();
 196
 197                     # set the marker colors
 198                     #
 199                     set_marker_color($m, "marker_types");
 200                 }
 201
 202             }
 203         }
 204         foreach my $f (keys(%find)) {
 205             foreach my $t (keys %{$find{$f}}) {
 206                 my $chr = $find{$f}->{$t}->{chr};
 207                 my $offset = $find{$f}->{$t}->{offset};
 208
 209                 if (exists($find{$f}->{$t-1}) || defined($find{$f}->{$t-1})) {
 210                     my $comp_chr = $find{$f}->{$t-1}->{chr};
 211                     my $comp_offset = $find{$f}->{$t-1}->{offset};
 212                     #print STDERR "Found on track $t: Chr=$chr offset=$offset, links to track ".($t-1)." Chr=$comp_chr offset $comp_offset\n";
 213                     if ($comp_chr) {
 214                         my $link1 = CXGN::Cview::ChrLink->new($self->{c}{$t}[$chr], $offset, $self->{c}{$t-1}[$comp_chr], $comp_offset);
 215                         $self->{map}->add_chr_link($link1);
 216                     }
 217                 }
 218                 if (exists($find{$f}->{$t+1})) {
 219                     my $comp_chr = $find{$f}->{$t+1}->{chr};
 220                     my $comp_offset = $find{$f}->{$t+1}->{offset};
 221                     my $link2 = CXGN::Cview::ChrLink->new($self->{c}{$t}[$chr], $offset, $self->{c}{$t+1}[$comp_chr], $comp_offset);
 222                     $self->{map}->add_chr_link($link2);
 223
 224                 }
 225             }
 226
 227         }
 228
 229         $self->get_cache()->set_map_name("viewmap");
 230         $self->get_cache()->set_image_data($self->{map}->render_png_string());
 231         $self->get_cache()->set_image_map_data($self->{map}->get_image_map("viewmap"));
 232
 233 #       # show the ruler if requested
 234 #       #
 235 #       if ($self->{show_ruler}) {
 236 #           my $r = ruler->new($x_distance-20, $row_height * $row_count + $y_distance, $chr_height, 0, $self->{c}{$track}[$i]->get_chromosome_length());
 237 #           $self->{map}->add_ruler($r);
 238 #       }
 239     }
 240
 241
 242         # my $filename = "cview".(rand())."_".$$.".png";
 243
 244 #     $self->{image_path} = $vhost_conf->get_conf('basepath').$vhost_conf->get_conf('tempfiles_subdir')."/cview/$filename";
 245 #     $self->{image_url} = $vhost_conf->get_conf('tempfiles_subdir')."/cview/$filename";
 246
 247 #     $self->{map} -> render_png_file($self->{image_path});
 248
 249 #     $self->{imagemap} = $self->{map}->get_image_map("imagemap");
 250
 251
 252 }
 253
 254
 255 sub get_select_toolbar {
 256     my $self = shift;
 257
 258 #    $left_map = $self->get_left_map() || 0;
 259 #    $center_map = $self->get_center_map() || 0;
 260 #    $right_map = $self->get_right_map || 0;
 261     my @names = ("left_map_version_id", "center_map_version_id", "right_map_version_id");
 262     my @selects = ();
 263     for (my $i=0; $i< 3; $i++) {
 264         if ( defined(($self->get_maps())[$i])) {
 265             push @selects,  CXGN::Cview::Utils::get_maps_select($self->get_dbh(), ($self->get_maps())[$i]->get_id(), $names[$i], 1);
 266         }
 267         else {
 268             push @selects, CXGN::Cview::Utils::get_maps_select($self->get_dbh(), undef, $names[$i], 1);
 269         }
 270     }
 271 #    my $center_select = CXGN::Cview::Utils::get_maps_select($self, !$center_map || $center_map->get_id(), "center_map_version_id", 1);
 272 #    my $right_select = CXGN::Cview::Utils::get_maps_select($self, !$right_map || $right_map->get_id(), "right_map_version_id", 1);
 273
 274
 275     return qq {
 276         <form action="#">
 277             <center>
 278             <table summary=""><tr><td>$selects[0]</td><td>$selects[1]</td><td>$selects[2]</td></tr></table>
 279             <input type="submit" value="set" />
 280             </center>
 281         </form>
 282         };
 283 }
 284
 285 # =head2 function display()
 286
 287 #   Synopsis:
 288 #   Arguments:
 289 #   Returns:
 290 #   Side effects:
 291 #   Description:        composes the page and displays it.
 292
 293 # =cut
 294
 295 # sub display {
 296 #     my $self = shift;
 297
 298
 299 #     $self->{page}->header("SGN comparative mapviewer");
 300 #     my $width = int($self->{map_width}/3);
 301
 302 #     my $select = $self->get_select_toolbar();
 303
 304 #     print "$select";
 305
 306 #     if (!$self->get_maps()) {
 307 #       print "<br /><br /><center>Note: No maps are selected. Please select maps from the pull down menus above.</center>\n";
 308 #     }
 309
 310 #     print $self->get_cache()->get_image_html();
 311
 312 # #    print "<img src=\"$self->{image_url}\" usemap=\"#chr_comp_map\" border=\"0\" alt=\"\" />\n";
 313
 314 # #    print $self->{map}->get_image_map("chr_comp_map");
 315
 316 #     $self->{page}->footer();
 317
 318
 319
 320 # }
 321
 322 =head2 function error_message_page()
 323
 324   Synopsis:
 325   Arguments:
 326   Returns:
 327   Side effects:
 328   Description:
 329
 330 =cut
 331
 332 sub error_message_page {
 333     my $self = shift;
 334
 335     my $title = page_title_html("Error: No center map defined");
 336
 337     print <<HTML;
 338
 339     $title
 340         <p>
 341         A center map needs to be defined for this page to work. Please supply
 342         a center_map_version_id as a parameter. If this was the result of a link,
 343         please inform SGN about the error.
 344         </p>
 345         <p>
 346         Contact SGN at <a href="mailto:sgn-feedback\@sgn.cornell.edu">sgn-feedback\@sgn.cornell.edu</a>
 347
 348 HTML
 349
 350     exit();
 351 }
 352
 353
 354 sub clean_up {
 355     my $self = shift;
 356 }
 357
 358
 359 return 1;