lib/CXGN/Cview/MapOverviews/Generic.pm

   1
   2 =head1 NAME
   3
   4 CXGN::Cview::MapOverviews::Generic - a class to display generic genetic map overviews.
   5
   6 =head1 SYNOPSYS
   7
   8 see L<CXGN::Cview::MapOverviews> for a definition of the interface.
   9
  10 =head1 DESCRIPTION
  11
  12 This class implements an overview of a genetic map that is stored in the database.
  13
  14 =head1 AUTHOR(S)
  15
  16 Lukas Mueller (lam87@cornell.edu)
  17
  18 =head1 VERSION
  19
  20 1.0
  21
  22 =head1 FUNCTIONS
  23
  24 This class implements the following functions:
  25
  26 =cut
  27
  28 use strict;
  29
  30 package CXGN::Cview::MapOverviews::Generic;
  31
  32 use CXGN::Cview::Map::Tools;
  33 use CXGN::Marker::Tools qw | clean_marker_name |;
  34
  35 use base qw | CXGN::Cview::MapOverviews CXGN::DB::Object |;
  36
  37 =head2 function new()
  38
  39  Synopsis:      my $overview = CXGN::Cview::MapOverviews::generic_map_overview->new(CXGN::Cview::Map::SGN::Genetic->new(9));
  40  Arguments:     The a CXGN::Cview::Map object for the map to be displayed.
  41  Returns:       an overview object (constructor)
  42  Side effects:  sets up the overview object.
  43  Description:
  44
  45 =cut
  46
  47 sub new {
  48     my $class = shift;
  49     my $map = shift;
  50     my $args = shift;
  51
  52     my $self = $class -> SUPER::new($map, $args);
  53
  54 #    if (!$map) { exit(); }
  55
  56     $self->set_dbh($args->{dbh});
  57     $self->set_map($map);
  58     return $self;
  59 }
  60
  61
  62 sub render {
  63     my $self = shift;
  64     my $map_width=$self->get_image_width();
  65     my $image_height = $self->get_image_height();
  66     my $top_margin = 40;
  67     $self->{map_image}= CXGN::Cview::MapImage->new("", $map_width, $image_height);
  68
  69     my @c = ();
  70 #    my $unit_eq = 0.4; # 1 cM corresponds to 0.4 pixels.
  71
  72     # determine the longest chromosome for proper scaling...
  73     #
  74     my @c_len = $self->get_map()->get_chromosome_lengths();
  75     #print STDERR "chromosome lengths: ".(join " ", @c_len)."\n";
  76     my $longest_length = 0; # zero based
  77     my $longest_chr = undef;
  78     if (!$self->get_map()->get_chromosome_count()) {
  79         die "This map does not seem to have any chromosomes...";
  80     }
  81     for (my $i=0; $i<$self->get_map()->get_chromosome_count(); $i++)  {
  82         if ($c_len[$i] >= $longest_length) {
  83             $longest_chr = $i;
  84             $longest_length = $c_len[$i];
  85         }
  86     }
  87
  88
  89     # Prevent division by zero, but does it make sense?
  90     my $unit_eq = $longest_length ? ($image_height-2*$top_margin) / $longest_length : 0;
  91     #print STDERR "unit_eq = $unit_eq\n";
  92
  93     my @clean_markers = ();
  94     foreach my $hm ($self->get_hilite_markers()) {
  95         my($clean, $suffix) = clean_marker_name($hm);
  96         push @clean_markers, $clean;
  97     }
  98
  99     my @map_item_names = map { (split /\s+/, $_)[2] } $self->get_map()->get_map_items();
 100
 101     my $hilite_markers = join (" ", @clean_markers, @map_item_names);
 102     my $hilite_markers_link = $hilite_markers;
 103     $hilite_markers_link =~ s/ /\+/g;
 104 #    my $max_chr_len_units = 0;
 105 #    my $max_chr_len_pixels = 0;
 106     my $chr_count = $self->get_map()->get_chromosome_count();
 107     my @chr_names = $self->get_map()->get_chromosome_names();
 108
 109     #print STDERR "chromosome names: ".(join " ", @chr_names)."\n";
 110     $self->set_horizontal_spacing(int(($map_width-40)/($chr_count)));
 111
 112     #print STDERR "chromosome count is $chr_count\n";
 113     my %marker_found = ();
 114
 115     for (my $i=$chr_count-1; $i>=0; $i--) {
 116
 117         #print STDERR "Instantiating chr $chr_names[$i]... in index $i\n";
 118
 119         $c[$i] = $self->get_map()->get_overview_chromosome($chr_names[$i]);
 120
 121         $c[$i]->set_horizontal_offset($self->get_horizontal_spacing()*($i)+35);
 122         $c[$i]->set_vertical_offset($top_margin);
 123
 124         $c[$i]->set_caption($chr_names[$i]);
 125
 126         my @markers = $c[$i]->get_markers();
 127
 128         my $chr_len = 0;
 129
 130         foreach my $m (@markers) {
 131
 132             #$m -> set_color(200, 100, 100);
 133             if ($m->get_offset() > $chr_len) { $chr_len = $m->get_offset(); }
 134             #print STDERR "Read: ".$m->get_name." offset: ".$m->get_offset()."\n";
 135             my $marker_name_suffix = $m->get_marker_name();
 136             my $marker_name = $m->get_name();
 137             my $marker_id = $m->get_id();
 138             foreach my $label ($marker_name, $marker_name_suffix, $m->get_synonyms()) {
 139                 #if (($hilite_markers =~ /\b($marker_name)\b|\b($marker_name_suffix)\b/i)) {
 140                 if ($hilite_markers =~ /\b($label)\b/) {
 141                     my $match = $1;
 142                     #print STDERR "MATCH:$match\n";
 143                     $marker_found{$match}=1;
 144                     $m->set_label_spacer(15);
 145                     #$m->set_url("/search/markers/markerinfo.pl?marker_id=$marker_id");
 146                     $m->show_label();
 147                     $m->get_label()->set_label_text($label);
 148                     $m->hilite();
 149                 }
 150             }
 151         }
 152
 153         #print STDERR "$i, $c_len[$i], $unit_eq\n";
 154         #print STDERR "(".join(", ", @c_len).")\n";
 155         $c[$i]->set_height($c_len[$i]*$unit_eq);
 156         $c[$i]->set_length($c_len[$i]);
 157         $c[$i]->layout();
 158         if ($self->get_map()->can_zoom()) {
 159             my $lg_name = $chr_names[$i];
 160             $c[$i]->rasterize(5);
 161             $c[$i]->set_rasterize_link("/cview/view_chromosome.pl?map_version_id=".$self->get_map()->get_id()."&amp;chr_nr=$lg_name&amp;show_offsets=1&amp;show_zoomed=1&amp;show_ruler=1&amp;hilite=$hilite_markers_link&amp;clicked=1&amp;cM=");
 162
 163         }
 164         else {
 165             $c[$i]->set_url("/cview/view_chromosome.pl?map_version_id=".($self->get_map()->get_id())."&amp;chr_nr=$chr_names[$i]");
 166         }
 167         if ($c[$i]->get_scaling_factor() == 0) {
 168             print STDERR join (", ", map { $_->get_offset } $c[$i]->get_markers())."\n";
 169             print STDERR "LENGTH = ".$c[$i]->get_length()."\n";
 170             print STDERR "HEIGHT = ".$c[$i]->get_height()."\n";
 171             die "Scaling factor is 0 for chromosome $i. How did this happen?";
 172         }
 173         $self->{map_image}->add_chromosome($c[$i]);
 174     }
 175 #    if (!$self->is_fish_map()) {
 176 #       my $ruler = CXGN::Cview::Ruler->new(20, $top_margin, $longest_length * $unit_eq, 0, $longest_length, $self->get_map()->get_units());
 177 #       $ruler ->set_units( $self->get_map()->get_units() );
 178 #       $self->{map_image}->add_ruler($ruler);
 179
 180 #}
 181     # get the ruler and add it to the image
 182     #
 183     #print STDERR "Setting up the ruler... longest chr is $longest_chr\n";
 184     my $ruler = $c[$longest_chr]->get_ruler();
 185     $ruler->set_vertical_offset($top_margin);
 186     $ruler->set_horizontal_offset(20);
 187     $ruler->set_units($self->get_map()->get_units());
 188     $ruler->set_start_value(0);
 189     $ruler->set_end_value( $c[$longest_chr]->get_length() );
 190     $ruler->set_height( $c[$longest_chr]->get_height() );
 191
 192
 193     $self->{map_image}->add_ruler($ruler);
 194
 195     #print STDERR "done.\n";
 196
 197     # hilite markers that were requested...
 198     #
 199     foreach my $hm (@clean_markers) {
 200         chomp($hm);
 201         if (!exists($marker_found{$hm})) {
 202             #print STDERR "Adding $hm to the list...\n";
 203             $self->add_marker_not_found($hm);
 204         }
 205     }
 206
 207     # add a legend if the map is F2-2000.
 208     #
 209     if (CXGN::Cview::Map::Tools::find_map_id_with_version($self->get_dbh(), $self->get_map()->get_id()) == CXGN::Cview::Map::Tools::current_tomato_map_id()) {
 210
 211         #   $image->string($font,$x,$y,$string,$color)
 212         my $legend = CXGN::Cview::Label->new();
 213         $legend->set_name('Note: Positions of fully sequenced BACs are shown in yellow');
 214         $legend->set_vertical_offset($image_height-12);
 215         $legend->set_horizontal_offset(30);
 216         $legend->set_reference_point(30, $image_height-15);
 217
 218         $self->{map_image}->add_image_object($legend);
 219     }
 220     $self->set_chromosomes(\@c);
 221 }
 222
 223
 224
 225 sub render_map {
 226     my $self = shift;
 227
 228     # set up the cache
 229     $self->get_cache()->set_key($self->get_map()->get_id()."-".($self->get_image_height())."-".join (".", $self->get_map()->get_map_items())."-".(join "-", ($self->get_hilite_markers())).__PACKAGE__ );
 230     $self->get_cache()->set_map_name("mapmap");
 231
 232     if ($self->get_cache()->is_valid())  {
 233         return;
 234     }
 235
 236     #print STDERR "Regenerating the map ".$self->get_map()->get_id()."\n";
 237     $self->render();
 238
 239     $self->get_cache()->set_image_data( $self->{map_image}->render_png_string());
 240     $self->get_cache()->set_image_map_data( $self->{map_image}->get_image_map("mapmap") );
 241
 242
 243 }
 244
 245 sub is_fish_map {
 246     my $self = shift;
 247     if ($self->get_map()->get_type() =~/fish/i) { return 1;    }
 248     else {
 249         return 0;
 250     }
 251 }
 252
 253
 254
 255 1;