lib/CXGN/Cview/Marker/AGP.pm

   1
   2 =head1 NAME
   3
   4 CXGN::Cview::Marker::AGP - a class to draw markers that represent regions as defined in an AGP file
   5
   6 =head1 DESCRIPTION
   7
   8 CXGN::Cview::Marker::AGP inherits from L<CXGN::Cview::Marker>.
   9
  10 my $m = CXGN::Cview::Marker::AGP->new();
  11 $m->set_offset(30);
  12 $m->set_north_range(10);
  13 $m->set_south_range(10);
  14
  15 =head1 AUTHOR
  16
  17 Lukas Mueller (lam87@cornell.edu)
  18
  19 =head1 FUNCTIONS
  20
  21 This class implements the following functions:
  22
  23 =cut
  24
  25 use strict;
  26
  27 package CXGN::Cview::Marker::AGP;
  28
  29 use CXGN::Cview::Marker;
  30 use CXGN::Cview::Marker::Physical;
  31
  32 use base qw / CXGN::Cview::Marker::Physical /;
  33
  34 =head2 function new
  35
  36   Synopsis:
  37   Arguments:
  38   Returns:
  39   Side effects:
  40   Description:
  41
  42 =cut
  43
  44 sub new {
  45     my $class = shift;
  46     my $chromosome = shift;
  47     my $self = $class -> SUPER::new($chromosome);
  48
  49 #     my $range_label = CXGN::Cview::Label::RangeLabel->new();
  50 #     $range_label->set_horizontal_offset($self->get_label()->get_horizontal_offset());
  51 #     $range_label->set_vertical_offset($self->get_label()->get_vertical_offset());
  52 #     $range_label->set_name($self->get_label()->get_name());
  53 #     $range_label->set_reference_point($self->get_label()->get_reference_point());
  54 #     $range_label->set_enclosing_rect($self->get_label()->get_enclosing_rect());
  55 #     $self->set_label($range_label);
  56
  57     $self->get_label()->set_stacking_level(1);
  58     $self->set_label_side("right");
  59     $self->set_hilite_chr_region(1);
  60     $self->set_region_hilite_color(100, 100, 150);
  61     return $self;
  62 }
  63
  64 # =head2 functions get_north_range(), set_north_range()
  65
  66 #   Synopsis:   $m->get_north_range()
  67 #   Arguments:  setter: the north range of the range marker
  68 #                         in the units of the map
  69 #   Returns:    getter: the north range
  70 #   Side effects:       the markers range drawn on the northern side
  71 #                 reflects this value
  72 #   Description:
  73
  74 # =cut
  75
  76 # sub get_north_range {
  77 #     my $self=shift;
  78 #     return $self->{north_range};
  79 # }
  80
  81
  82 # sub set_north_range {
  83 #     my $self=shift;
  84 #     my $cM = shift;
  85 #     $self->{north_range}=$cM;
  86
  87 # }
  88
  89 # =head2 functions get_south_range(), set_south_range()
  90
  91 #   Synopsis:   see north range
  92 #   Arguments:
  93 #   Returns:
  94 #   Side effects:
  95 #   Description:
  96
  97 # =cut
  98
  99 # sub get_south_range {
 100 #     my $self=shift;
 101
 102 #     return $self->{south_range};
 103 # }
 104
 105 # sub set_south_range {
 106 #     my $self=shift;
 107 #     my $cM = shift;
 108 #     $self->{south_range}=$cM;
 109
 110
 111 # }
 112
 113
 114 sub render {
 115     my $self = shift;
 116     my $image = shift;
 117
 118     # calculate the pos in pixels of the northern range limit
 119     #
 120     my $north_pixels = $self->get_chromosome()->mapunits2pixels($self->get_offset()) + $self->get_chromosome()->get_vertical_offset() - $self->get_chromosome()->mapunits2pixels($self->get_north_range());
 121
 122     # determine the pixels of the southern limit
 123     #
 124     my $south_pixels = $self->get_chromosome()->mapunits2pixels($self->get_offset()) + $self->get_chromosome()->get_vertical_offset() + $self->get_chromosome()->mapunits2pixels($self->get_south_range());
 125 #    print STDERR "cM = ".$self->get_north_range().", pixels= $north_pixels\n";
 126 #    print STDERR "cM = ".$self->get_south_range().", pixels= $south_pixels\n";
 127
 128     $self->get_label()->set_north_position($north_pixels);
 129     $self->get_label()->set_south_position($south_pixels);
 130
 131     if ($self->get_label_side() eq "right") {
 132         $self->get_label()->set_reference_point($self->get_chromosome()->get_horizontal_offset()+int($self->get_chromosome()->get_width()/2)+$self->get_label()->get_stacking_height()*($self->get_label()->get_stacking_level()), int($north_pixels+$south_pixels)/2);
 133     }
 134     elsif ($self->get_label_side() eq "left") {
 135         $self->get_label()->set_reference_point($self->get_chromosome()->get_horizontal_offset()-int($self->get_chromosome()->get_width()/2)-$self->get_label()->get_stacking_height()*$self->get_label()->get_stacking_level(), int($north_pixels+$south_pixels)/2);
 136     }
 137     else {
 138         die "[RangeMarker.pm] label_side can either be right or left. Sorry.";
 139     }
 140     if ($self->get_hilite_chr_region()) {
 141         $self->hilite_chr_region($image);
 142     }
 143
 144     $self->SUPER::render($image);
 145 }
 146
 147
 148 =head2 accessors set_region_hilite_color, get_region_hilite_color
 149
 150   Property:
 151   Setter Args:
 152   Getter Args:
 153   Getter Ret:
 154   Side Effects:
 155   Description:
 156
 157 =cut
 158
 159 sub get_region_hilite_color {
 160     my $self=shift;
 161     return @{$self->{region_hilite_color}};
 162 }
 163
 164 sub set_region_hilite_color {
 165     my $self=shift;
 166     @{$self->{region_hilite_color}}= (shift, shift, shift);
 167 }
 168
 169
 170
 171 =head2 accessors set_hilite_chr_region(), get_hilite_chr_region()
 172
 173   Property:
 174   Setter Args:
 175   Getter Args:
 176   Getter Ret:
 177   Side Effects:
 178   Description:
 179
 180 =cut
 181
 182 sub get_hilite_chr_region {
 183     my $self=shift;
 184     return $self->{hilite_chr_region};
 185 }
 186
 187 sub set_hilite_chr_region {
 188     my $self=shift;
 189     $self->{hilite_chr_region}=shift;
 190 }
 191
 192
 193
 194 sub hilite_chr_region {
 195     my $self = shift;
 196     my $image = shift;
 197
 198     my $north_pixels = $self->get_label()->get_north_position();
 199     my $south_pixels = $self->get_label()->get_south_position();
 200
 201     my $left_pixels =  $self->get_chromosome()->get_horizontal_offset()-$self->get_chromosome()->get_width()/2+1;
 202     my $right_pixels = $self->get_chromosome()->get_horizontal_offset()+$self->get_chromosome()->get_width()/2-1;
 203
 204     #print STDERR  "North: $north_pixels South: $south_pixels. left: $left_pixels. Right: $right_pixels\n";
 205
 206     $image->filledRectangle($left_pixels, $north_pixels, $right_pixels, $south_pixels, $image->colorAllocate($self->get_region_hilite_color()));
 207 }
 208
 209 sub draw_tick {
 210     my $self = shift;
 211     my $image = shift;
 212     my $color = $image -> colorResolve($self->get_color());
 213     my $halfwidth = int($self->get_chromosome->get_width/2);
 214     my $north_y = $self->get_chromosome()->get_vertical_offset() + $self->get_chromosome()->mapunits2pixels($self->get_offset()-$self->get_north_range());
 215
 216     my $south_y = $self->get_chromosome()->get_vertical_offset() + $self->get_chromosome()->mapunits2pixels($self->get_offset()+$self->get_south_range());
 217
 218     if ($self->get_show_tick()) {
 219         $image -> line($self->get_chromosome()->get_horizontal_offset() - $halfwidth +1, $north_y, $self->get_chromosome()->get_horizontal_offset()+$halfwidth-1, $north_y, $color);
 220         $image -> line($self->get_chromosome()->get_horizontal_offset() - $halfwidth +1, $south_y, $self->get_chromosome()->get_horizontal_offset()+$halfwidth-1, $south_y, $color);
 221     }
 222 }
 223
 224
 225 return 1;
 226