lib/CXGN/Cview/Marker/Physical.pm

   1
   2 =head1 NAME
   3
   4 CXGN::Cview::Marker::Physical - a class to draw markers representing physical associations to maps, such as BACs or contigs.
   5
   6 =head1 DESCRIPTION
   7
   8 CXGN::Cview::Marker::Physical inherits from L<CXGN::Cview::Marker>.
   9
  10 my $m = CXGN::Cview::Marker::Physical->new();
  11 $m->set_offset(30);
  12
  13 =head1 AUTHOR
  14
  15 Lukas Mueller (lam87@cornell.edu)
  16
  17 =head1 FUNCTIONS
  18
  19 This class implements the following functions:
  20
  21 =cut
  22
  23 use strict;
  24 use CXGN::Cview::Marker;
  25 use CXGN::Cview::Label::Physical;
  26
  27 package CXGN::Cview::Marker::Physical;
  28
  29 use base qw / CXGN::Cview::Marker::RangeMarker /;
  30
  31 =head2 function new()
  32
  33   Constructor.
  34   Arguments:   A CXGN::Cview::Chromosome object (or subclassed object)
  35                to which this marker belongs.
  36
  37 =cut
  38
  39 sub new {
  40     my $class = shift;
  41     my $chromosome = shift;
  42     my $self = $class -> SUPER::new($chromosome);
  43
  44     my $bac_label = CXGN::Cview::Label::Physical->new();
  45     $self->show_label();
  46     $self->set_label($bac_label);
  47     $self->set_label_side("right");
  48     $self->set_hilite_chr_region(0);
  49     $self->set_region_hilite_color(100, 100, 150);
  50     $self->set_north_range(1);
  51     $self->set_south_range(1);
  52     return $self;
  53 }
  54
  55 sub render {
  56     my $self = shift;
  57     my $image = shift;
  58
  59     # calculate the pos in pixels of the northern range limit
  60     #
  61     my $north_pixels = $self->get_chromosome()->mapunits2pixels($self->get_offset()) + $self->get_chromosome()->get_vertical_offset() - $self->get_chromosome()->mapunits2pixels($self->get_north_range());
  62
  63     # determine the pixels of the southern limit
  64     #
  65     my $south_pixels = $self->get_chromosome()->mapunits2pixels($self->get_offset()) + $self->get_chromosome()->get_vertical_offset() + $self->get_chromosome()->mapunits2pixels($self->get_south_range());
  66 #    print STDERR "cM = ".$self->get_north_range().", pixels= $north_pixels\n";
  67 #    print STDERR "cM = ".$self->get_south_range().", pixels= $south_pixels\n";
  68
  69     $self->get_label()->set_north_position($north_pixels);
  70     $self->get_label()->set_south_position($south_pixels);
  71
  72     #if ($self->get_url()) { $self->get_label()->set_url($self->get_url()); }
  73
  74     my $stacking = $self->get_label()->get_stacking_height() * $self->get_label()->get_stacking_level();
  75
  76
  77     if ($self->is_visible()) {
  78         if ($self->get_label_side() eq "right") {
  79             my $x = $self->get_chromosome()->get_horizontal_offset()
  80                 +int($self->get_chromosome()->get_width()/2)
  81                 +$stacking;
  82
  83             my $label_horizontal_position = $x + 50;
  84             if ($stacking > 200) {
  85                 $label_horizontal_position=$x-100;
  86                 $self->get_label()->align_right();
  87             }
  88             $self->get_label()->set_horizontal_offset($label_horizontal_position);
  89             $self->get_label()->set_reference_point($x, int($north_pixels+$south_pixels)/2);
  90
  91         }
  92         elsif ($self->get_label_side() eq "left") {
  93             my $x = $self->get_chromosome()->get_horizontal_offset()-int($self->get_chromosome()->get_width()/2) - $self->get_label()->get_stacking_height()*($self->get_label()->get_stacking_level());
  94
  95             $self->get_label()->set_horizontal_offset($x-50);
  96             $self->get_label()->set_reference_point($x, int($north_pixels+$south_pixels)/2);
  97
  98         }
  99         else {
 100             die "[RangeMarker.pm] label_side can either be right or left. Sorry.";
 101         }
 102         if ($self->is_label_visible()) {
 103             $self->get_label()->render($image);
 104         }
 105
 106         if ($self->get_hilite_chr_region()) {
 107             $self->hilite_chr_region($image);
 108         }
 109         $self->draw_tick($image);
 110     }
 111
 112 }
 113
 114
 115 =head2 accessors set_region_hilite_color(), get_region_hilite_color()
 116
 117   Property:
 118   Setter Args:
 119   Getter Args:
 120   Getter Ret:
 121   Side Effects:
 122   Description:
 123
 124 =cut
 125
 126 sub get_region_hilite_color {
 127     my $self=shift;
 128     return @{$self->{region_hilite_color}};
 129 }
 130
 131 sub set_region_hilite_color {
 132     my $self=shift;
 133     @{$self->{region_hilite_color}}= (shift, shift, shift);
 134 }
 135
 136 =head2 accessors set_hilite_chr_region(), get_hilite_chr_region()
 137
 138   Property:
 139   Setter Args:
 140   Getter Args:
 141   Getter Ret:
 142   Side Effects:
 143   Description:
 144
 145 =cut
 146
 147 sub get_hilite_chr_region {
 148     my $self=shift;
 149     return $self->{hilite_chr_region};
 150 }
 151
 152 sub set_hilite_chr_region {
 153     my $self=shift;
 154     $self->{hilite_chr_region}=shift;
 155 }
 156
 157 sub draw_tick {
 158     my $self = shift;
 159     my $image = shift;
 160     my $color = $image -> colorResolve($self->get_color());
 161
 162     my ($x, $north_y, $y, $south_y) = $self->get_enclosing_rect();
 163
 164     if ($self->get_show_tick()) {
 165         $image -> rectangle($x, $north_y, $y, $south_y, $color);
 166     }
 167 }
 168
 169 sub get_image_map {
 170     my $self = shift;
 171     my $coords = join ",", ($self->get_enclosing_rect());
 172
 173
 174     my $s= '<area shape="rect" coords="'.$coords.'" href="'.$self->get_url().'" alt="'.$self->get_marker_name().'" title="'.$self->get_tooltip().'" />';
 175     #print STDERR "Imagemap = $s\n";
 176     return $s;
 177
 178 }
 179
 180 sub get_enclosing_rect {
 181     my $self = shift;
 182     my $halfwidth = int($self->get_chromosome->get_width/2);
 183     my $north_y = $self->get_chromosome()->get_vertical_offset() + $self->get_chromosome()->mapunits2pixels($self->get_offset()-$self->get_north_range());
 184
 185     my $south_y = $self->get_chromosome()->get_vertical_offset() + $self->get_chromosome()->mapunits2pixels($self->get_offset()+$self->get_south_range());
 186
 187     my $x = $self->get_chromosome()->get_horizontal_offset()+$halfwidth+$self->get_label()->get_stacking_height()*$self->get_label()->get_stacking_level();
 188     return ($x-1, $north_y, $x+1, $south_y);
 189 }
 190
 191 return 1;
 192