lib/CXGN/Cview/Marker/AGPRegion.pm

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