lib/CXGN/Cview/ViewMaps.pm

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