lib/CXGN/Cview/Map_overviews/Physical.pm

   1
   2
   3 =head1 NAME
   4
   5 CXGN::Cview::Map_overviews::Physical - a class to draw physical map representations.
   6
   7 =head1 SYNOPSYS
   8
   9 see L<CXGN::Cview::Map_overviews>.
  10
  11 =head1 DESCRIPTION
  12
  13
  14 =head1 AUTHOR(S)
  15
  16 Lukas Mueller (lam87@cornell.edu)
  17
  18 =head1 VERSION
  19
  20
  21 =head1 LICENSE
  22
  23
  24 =head1 FUNCTIONS
  25
  26 This class implements/overrides the following functions:
  27
  28 =cut
  29
  30
  31
  32 =head1 CXGN::Cview::Map_overviews::physical_overview
  33
  34 A class to display a genetic map with the overgo results next to it.
  35 Inherits from CXGN::Cview::Map_overviews.
  36
  37 =cut
  38
  39 use strict;
  40
  41 package CXGN::Cview::Map_overviews::Physical;
  42
  43 use base qw( CXGN::Cview::Map_overviews::Generic );
  44
  45 sub hilite_marker {
  46     my $self = shift;
  47     my $marker_name = shift;
  48     push @{$self->{hilite_markers}}, $marker_name;
  49 }
  50
  51 sub render_map {
  52     my $self = shift;
  53
  54     if ($self->has_cache()) { return; }
  55
  56
  57     $self->{map_image}=CXGN::Cview::MapImage->new("", 13*$self->get_horizontal_spacing(), 150);
  58     my @c = ();
  59
  60     my $cM_eq = 0.4; # 1 cM corresponds to 0.4 pixels.
  61     my $max_chr_len_cM = 0;
  62     my $max_chr_len_pixels = 0;
  63
  64     # draw chromosomes
  65     #
  66     for (my $i=1; $i<=@{$self->get_map()->linkage_groups()}; $i++) {
  67         $c[$i]= CXGN::Cview::Chromosome -> new(1, 100, $self->get_horizontal_spacing()*$i, 40);
  68         CXGN::Cview::Cview_data_adapter::fetch_chromosome($self, $c[$i], $self->get_map(), $i);
  69         my @markers = $c[$i]->get_markers();
  70         #$self->set_marker_count($i, scalar(@markers));
  71         my $chr_len = 0;
  72         foreach my $m (@markers) {
  73             $m -> hide_label();
  74             $m -> set_color(200, 100, 100);
  75             if ($m->get_offset() > $chr_len) { $chr_len = $m->get_offset(); }
  76         }
  77         $c[$i]->set_caption($i);
  78         $c[$i]->set_width(12);
  79         #$c[$i]->set_url("/cview/view_chromosome.pl?map_id=$self->{map_id}&amp;chr_nr=$i");
  80         my $chr_len_pixels = $chr_len*$cM_eq;
  81         $c[$i]->set_height($chr_len_pixels);
  82         if ($chr_len > $max_chr_len_cM) {
  83             $max_chr_len_cM = $chr_len;
  84             $max_chr_len_pixels = $chr_len_pixels;
  85         }
  86         $c[$i]->set_length($chr_len);
  87         $c[$i]->layout();
  88         $c[$i]->rasterize(5);
  89         $c[$i]->set_rasterize_link("/cview/view_chromosome.pl?map_version_id=".$self->get_map()->map_version_id()."&amp;chr_nr=$i&amp;show_ruler=1&amp;show_zoomed=1&amp;show_physical=1&amp;cM=");
  90
  91         $self->{map_image}->add_chromosome($c[$i]);
  92     }
  93     my @p; # the physical maps
  94     # draw physical maps
  95     #
  96     for (my $i=1; $i<=@{$self->get_map()->linkage_groups()}; $i++) {
  97         $p[$i]= CXGN::Cview::Physical -> new(1, 100, $self->get_horizontal_spacing()*$i+22, 40);
  98         CXGN::Cview::Cview_data_adapter::fetch_chromosome($self, $p[$i], $self->get_map(), $i);
  99         CXGN::Cview::Cview_data_adapter::fetch_physical($self, $p[$i], $self->get_map(), $i);
 100         $p[$i]->set_box_height(2);
 101         my @markers = $p[$i]->get_markers();
 102 #       $self->{marker_count}[$i] = scalar(@markers);
 103         my $chr_len = 0;
 104         foreach my $m (@markers) {
 105             $m -> hide_label();
 106             if ($m->get_offset() > $chr_len) { $chr_len = $m->get_offset(); }
 107         }
 108
 109         my $chr_len_pixels = $chr_len*$cM_eq;
 110         $p[$i]->set_height($chr_len_pixels);
 111         if ($chr_len > $max_chr_len_cM) {
 112             $max_chr_len_cM = $chr_len;
 113             $max_chr_len_pixels = $chr_len_pixels;
 114         }
 115         #$c[$i]->rasterize(5);
 116         #$c[$i]->set_rasterize_link("/cview/view_chromosome.pl?map_id=$self->{map_id}&amp;chr_nr=$i&amp;show_zoomed=1&amp;cM=");
 117
 118         $self->{map_image}->add_physical($p[$i]);
 119     }
 120 #    print STDERR "mac chr len pixels: $max_chr_len_pixels, max chr len: $max_chr_len_cM\n";
 121     $self->{map_image}->add_ruler(CXGN::Cview::Ruler->new(20, 40, $max_chr_len_pixels, 0, $max_chr_len_cM));
 122
 123     $self->set_image_map( $self->{map_image}->get_image_map("#mapmap") );
 124 }
 125
 126 package CXGN::Cview::Map_overviews::physical_overview;
 127
 128 use base qw | CXGN::Cview::Map_overviews::Physical | ;
 129
 130 sub new {
 131     my $class = shift;
 132     my $self = $class->SUPER::new(@_);
 133     return $self;
 134 }
 135
 136
 137 return 1;