lib/CXGN/IL.pm

   1
   2
   3 =head1 NAME
   4
   5 CXGN::Cview::IL - a class for drawing Isogenic Line (IL) diagrams
   6
   7 =head1 DESCRIPTION
   8
   9 Inherits from L<CXGN::Cview::Chromosome>.
  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 use CXGN::Cview::Chromosome;
  28
  29 package CXGN::Cview::IL;
  30
  31 use base qw( CXGN::Cview::Chromosome );
  32
  33 sub new {
  34     my $class = shift;
  35     my $self = $class->SUPER::new(@_);
  36     $self->{sections}=();
  37     $self->{fragments} =();
  38     return $self;
  39 }
  40
  41 sub add_section {
  42     # sections are the non-overlapping sections of the ILs that have labels of the form 1-A
  43     my $self=shift;
  44     my $section_name = shift;
  45     my $marker1 = shift;
  46     my $offset1 = shift;
  47     my $marker2 = shift;
  48     my $offset2 = shift;
  49
  50
  51     my %section = ();
  52     $section{marker1}=$marker1;
  53     $section{offset1}=$offset1;
  54     $section{marker2}=$marker2;
  55     $section{offset2}=$offset2;
  56     $section{name}=$section_name;
  57     $section{label_position} = 0;
  58     push @{$self->{sections}}, \%section;
  59
  60 }
  61
  62
  63 sub add_fragment {
  64     # fragments are the overlapping sections defining the different IL lines and have lables of the form IL1-1.
  65     my $self=shift;
  66     my $fragment_name=shift;
  67     my $marker1=shift;
  68     my $offset1 = shift;
  69     my $marker2 = shift;
  70     my $offset2 = shift;
  71
  72     my %fragment = ();
  73     $fragment{marker1}=$marker1;
  74     $fragment{offset1}=$offset1;
  75     $fragment{marker2}=$marker2;
  76     $fragment{offset2}=$offset2;
  77     $fragment{name}=$fragment_name;
  78     $fragment{label_position} = 0;
  79     push @{$self->{fragments}}, \%fragment;
  80
  81 }
  82
  83 sub render {
  84     my $self=shift;
  85     my $image = shift;
  86
  87     $self->_calculate_scaling_factor();
  88     $self->_calculate_chromosome_length();
  89     $self-> set_color(100,100,100);
  90     #print STDERR "Rendering ILs...\n";
  91     $self->{font}= GD::Font->Small();
  92     my $section_x = $self->get_horizontal_offset() - $self->get_width()/2;
  93
  94     my $color = $image -> colorResolve($self->{color}[0], $self->{color}[1], $self->{color}[2]);
  95     my $light_color = $image -> colorResolve(200, 200, 200);
  96     #
  97     # render sections
  98     #
  99     my $previous_label_position = 0;
 100     my $line =  1;
 101     my $spacing = 7;
 102
 103
 104     foreach my $s (@{$self->{sections}}) {
 105         my $y_start = $self->get_vertical_offset()+$self->mapunits2pixels($$s{offset1});
 106         my $y_end   = $self->get_vertical_offset()+$self->mapunits2pixels($$s{offset2 });
 107
 108
 109         $image -> line($section_x - 10, $y_start, $section_x + @{$self->{fragments}}*$spacing, $y_start, $light_color);
 110         $image -> line($section_x - 10, $y_end,   $section_x + @{$self->{fragments}}*$spacing, $y_end,  $light_color);
 111         $image -> line($section_x,      $y_start, $section_x, $y_end,   $color);
 112         $image -> string($self->{font}, $section_x - $self->{font}->width()* length($$s{name})-2, ($y_end + $y_start)/2-$self->{font}->height()/2, $$s{name}, $color);
 113
 114     }
 115
 116     # render fragments
 117     #
 118     if (!defined($self->{fragments})) { print STDERR "IL: no fragments to render.\n"; return; }
 119     my $max_fragments = @{$self->{fragments}};
 120
 121     foreach my $f (@{$self->{fragments}}) {
 122         my $y_start = $self->get_vertical_offset()+$self->mapunits2pixels($$f{offset1});
 123         my $y_end   = $self->get_vertical_offset()+$self->mapunits2pixels($$f{offset2 });
 124
 125         my $label_position = ($y_end+$y_start)/2;
 126         if ($label_position < ($previous_label_position+$self->{font}->height())) { $label_position = $previous_label_position + $self->{font}->height(); }
 127
 128         $image -> line($section_x+$line*$spacing, $y_start, $section_x+$line*$spacing, $y_end,$color);
 129         $image -> line($section_x+$line*$spacing+1, $y_start, $section_x+$line*$spacing+1, $y_end,   $color);
 130         $image -> string($self->{font}, $section_x +$max_fragments*$spacing+3, $label_position-$self->{font}->height()/2, $$f{name}, $color);
 131         $image -> line($section_x+$line*$spacing, ($y_end+$y_start)/2, $section_x+$max_fragments*$spacing+3, $label_position, $color);
 132         $line++;
 133         $previous_label_position = $label_position;
 134     }
 135
 136 }
 137
 138