lib/CXGN/ChrLink.pm

   1
   2
   3 =head1 NAME
   4
   5 CXGN::Cview::ChrLink - an class for drawing chromosome relationships.
   6
   7 =head1 DESCRIPTION
   8
   9 Inherits from L<CXGN::Cview::ImageObject>.
  10
  11 =head1 SEE ALSO
  12
  13 See also the documentation in L<CXGN::Cview>.
  14
  15 =head1 AUTHOR(S)
  16
  17 Lukas Mueller (lam87@cornell.edu)
  18
  19 =head1 FUNCTIONS
  20
  21
  22 =cut
  23
  24 1;
  25
  26 use strict;
  27
  28 use CXGN::Cview::ImageObject;
  29
  30 package CXGN::Cview::ChrLink;
  31
  32 use base qw/CXGN::Cview::ImageObject/;
  33
  34 use GD;
  35
  36 sub new {
  37     my $class = shift;
  38     my $args = {};
  39     my $self = bless $args, $class;
  40
  41     $self->{chr1}=shift;
  42     $self->{cM1} = shift;
  43     $self->{chr2}=shift;
  44     $self->{cM2} = shift;
  45     $self->{marker_name}=shift;
  46
  47     # define default color
  48     $self -> set_color(100, 100, 100);
  49     return $self;
  50 }
  51
  52 sub set_color {
  53     my $self = shift;
  54     $self->{color}[0]=shift;
  55     $self->{color}[1]=shift;
  56     $self->{color}[2]=shift;
  57 }
  58
  59 sub render {
  60     my $self = shift;
  61     my $image = shift;
  62
  63     # draw only of both markers are visible...
  64     if ($self->{chr1}->is_visible($self->{cM1}) && $self->{chr2}->is_visible($self->{cM2})) {
  65         my $sign = (($self->{chr2}->get_horizontal_offset()) <=> ($self->{chr1}->get_horizontal_offset()));
  66         my $x1 = $self->{chr1}->get_horizontal_offset() + $sign*($self->{chr1}->get_width()/2);
  67         my $y1 = $self->{chr1}->mapunits2pixels($self->{cM1});
  68         my $x2 = $self->{chr2}->get_horizontal_offset() - $sign*($self->{chr2}-> get_width()/2);
  69         my $y2 = $self->{chr2}->mapunits2pixels($self->{cM2});
  70
  71         #print STDERR "link color: $self->{color}[0], $self->{color}[1], $self->{color}[2]\n";
  72         my $color = $image -> colorResolve($self->{color}[0], $self->{color}[1], $self->{color}[2]);
  73         $image->setAntiAliased($color);
  74         $image -> line($x1, $self->{chr1}->get_vertical_offset()+$y1, $x2, $self->{chr2}->get_vertical_offset()+$y2, gdAntiAliased);
  75     }
  76     else {
  77         #print STDERR "Not rendering link because not visible. chr1 cM: $self->{cM1} chr2 cM: $self->{cM2}\n";
  78     }
  79
  80 }
  81
  82 =head2 get_marker_name(), set_marker_name()
  83
  84  Usage:
  85  Desc:
  86  Ret:
  87  Args:
  88  Side Effects:
  89  Example:
  90
  91 =cut
  92
  93 sub get_marker_name {
  94   my $self=shift;
  95   return $self->{marker_name};
  96
  97 }
  98
  99 sub set_marker_name {
 100     my $self=shift;
 101     $self->{marker_name}=shift;
 102 }
 103