lib/CXGN/Chromosome/LineGraph.pm

   1
   2 =head1 NAME
   3
   4 CXGN::Cview::Chromosome::LineGraph - a class for displaying numeric quanity information alongside a genetic map
   5
   6 =head1 DESCRIPTION
   7
   8 Inherits from L<CXGN::Cview::Chromosome::Graph>.
   9
  10 =head1 SEE ALSO
  11
  12 See also the documentation in L<CXGN::Cview>.
  13
  14 =head1 AUTHORS
  15
  16 Lukas Mueller (lam87@cornell.edu) and Isaak Tecle (iyt2@cornell.edu)
  17
  18 =head1 FUNCTIONS
  19
  20
  21 =cut
  22
  23 use strict;
  24
  25 use CXGN::Cview::Chromosome;
  26
  27 package CXGN::Cview::Chromosome::LineGraph;
  28
  29 use base qw(CXGN::Cview::Chromosome::Graph);
  30
  31 =head2 function new()
  32
  33   Synopsis:     constructor
  34   Arguments:    none
  35   Returns:      a pointer to the CXGN::Cview::Chromosme::LineGraph object
  36   Side effects:
  37   Description:
  38
  39 =cut
  40
  41 sub new {
  42     my $class = shift;
  43     my $self = $class->SUPER::new(@_);
  44     $self->set_types("LOD");
  45     $self->set_color(100,100,100);
  46     return $self;
  47 }
  48
  49 =head2 function render()
  50
  51   Synopsis:     $lg -> render($image)
  52   Arguments:    a GD::Image object
  53   Returns:
  54   Side effects:
  55   Description:  renders the graph on the image
  56
  57 =cut
  58
  59 sub render {
  60     my $self= shift;
  61     my $image = shift;
  62
  63     $self->_calculate_chromosome_length();
  64     $self->_calculate_scaling_factor();
  65
  66     #print STDERR "rendering physical...\n";
  67
  68     my $color = $image -> colorResolve($self->get_color());
  69
  70     # draw coordinate system lines
  71     #
  72     my $halfwidth = $self->get_width()/2;
  73
  74     if (defined($self->get_maximum())) {
  75         $self->{largest} = $self->get_maximum();
  76     }
  77     else {
  78         $self->{largest} = $self->_get_largest_group();
  79     }
  80
  81     $image -> line($self->get_horizontal_offset()-$halfwidth, $self->get_vertical_offset(), $self->get_horizontal_offset()-$halfwidth, $self->get_vertical_offset()+$self->{height}, $color);
  82
  83     $image -> stringUp($self->{font}, $self->get_horizontal_offset()-$halfwidth-$self->{font}->height()/2, $self->get_vertical_offset()-4, $self->get_caption(), $color);
  84
  85     # draw the 10 line.
  86     #
  87     my $x = $self->get_horizontal_offset()-$halfwidth+10/($self->{largest})*$self->get_width();
  88     $image -> dashedLine ($x, $self->get_vertical_offset(), $x, $self->get_vertical_offset()+$self->{height}, $color);
  89     $image -> stringUp ($self->{font}, $x - $self->{font}->height()/2, $self->get_vertical_offset()-4,"10", $color);
  90
  91     # draw the 2 line.
  92     #
  93     #if ($self->{largest}>100) {
  94     my $red_color = $image->colorResolve(255, 0, 0);
  95     $x = $self->get_horizontal_offset()-$halfwidth+2/($self->{largest}*$self->get_width());
  96     $image -> dashedLine ($x, $self->get_vertical_offset(), $x, $self->get_vertical_offset()+$self->{height}, $red_color);
  97     $image -> stringUp ($self->{font}, $x - $self->{font}->height()/2, $self->get_vertical_offset()-4,"2", $color);
  98     #}
  99     # draw the boxes
 100     #
 101     print STDERR "Largest = $self->{largest} WIDTH= ".$self->get_width()."\n";
 102     #print STDERR "Physical connections: ".@{$self->{offset}}."\n";
 103     foreach my $type ($self->get_types()) {
 104         if (exists($self->{offset}{$type})) {
 105             my $last_position = $self->get_vertical_offset();
 106             my $last_value = $self->get_horizontal_offset() - $halfwidth;
 107             for (my $i=0; $i<(@{$self->{offset}{$type}}); $i++) {
 108                 #print STDERR "offset = $i, $self->{offset}[$i]\n";
 109                 if (exists($self->{offset}{$type}[$i])) {
 110                     my $y = $self->get_vertical_offset()+$self->mapunits2pixels($i);
 111                     #print STDERR "Drawing box...y = $y scaling: $self->{scaling_factor}\n";
 112                     my $x = ($self->get_horizontal_offset()-$halfwidth) + ($self->{offset}{$type}[$i]/($self->{largest})*$self->get_width());
 113                     #if ($box_width<1) { $box_width=2; }
 114
 115                     $image -> line(
 116                                               $last_value,
 117                                               $last_position,
 118                                               $x,
 119                                               $y,
 120                                               $color);
 121
 122                     print STDERR "x $last_value, y $last_position, x $x, y $y\n";
 123
 124                     $last_position = $y;
 125                     $last_value = $x;
 126                 }
 127
 128
 129             }
 130         }
 131     }
 132 }
 133
 134
 135 # sub draw_chromosome {
 136 #     my $self = shift;
 137 #     my $image = shift;
 138 #     $self->render($image);
 139 # }
 140
 141 # sub get_box_rect {
 142 #     my $self = shift;
 143 #     my $offset = shift;
 144 #     my $type = shift;
 145 #     my $y = $self->get_vertical_offset()+$offset;
 146 #     if ($self->{offset}{$type}[$offset] > 0 && $self->{largest}>0) {
 147 #       print STDERR "LARGEST: $self->{largest}\n";
 148 #       print STDERR "WIDTH ". $self->get_width()."\n";
 149 #       my $box_width = log($self->{offset}{$type}[$offset])/log($self->{largest})*$self->get_width();
 150 #       if ($box_width<1) { $box_width=2; }
 151 #       return ($self->get_horizontal_offset() - $self->get_width()/2, $y-$self->{box_height}/2, ($self->get_horizontal_offset()-$self->get_width()/2)+$box_width,  $y + $self->{box_height}/2);
 152 #     }
 153 # }
 154
 155 # sub get_image_map {
 156 #     my $self = shift;
 157 #     my $string = "";
 158 #     my ($x, $y, $a, $b) = $self->get_enclosing_rect();
 159 #     my $url = $self->get_url();
 160 #     $string .= qq{ <area shape="rect" coords="$x, $y, $a, $b" href="$url" alt="" /> };
 161 # #     #print STDERR "get_image_map physical\n";
 162 # #     if ($self->get_url()) {
 163 # #     foreach my $type ($self->get_types()) {
 164 # #         for (my $i; $i<(@{$self->{offset}{$type}}); $i++) {
 165 # #             my ($x, $y, $v, $w) = $self -> get_box_rect($i, $type);
 166 # #             $string .="<area shape=\"rect\" coords=\"$x, $y, ".($self->get_horizontal_offset()+$self->get_width()/2).", $w \" href=\"".$self->get_url()."\" alt=\"\" />";
 167 # #         }
 168 # #     }
 169 # #     }
 170 #     return $string;
 171 # }
 172
 173
 174
 175 return 1;