lib/CXGN/Cview/Chromosome/Glyph.pm

   1
   2 =head1 NAME
   3
   4 CXGN::Cview::Chromosome::Glyph - a class for drawing chromosome glyphs.
   5
   6 =head1 DESCRIPTION
   7
   8 The chromosomes are represented as small glyphs that can be partially filled with a color to represent the state of a chromosome sequencing project, for example. This class inherits from L<CXGN::Cview::Chromosome>.
   9
  10 =head1 SEE ALSO
  11
  12 See also the documentation in L<CXGN::Cview>.
  13
  14 =head1 AUTHOR(S)
  15
  16 Lukas Mueller (lam87@cornell.edu)
  17
  18 =head1 FUNCTIONS
  19
  20
  21 =cut
  22
  23 1;
  24
  25 use strict;
  26 use CXGN::Cview::Chromosome;
  27
  28
  29 package CXGN::Cview::Chromosome::Glyph;
  30
  31 use base qw |  CXGN::Cview::Chromosome |;
  32
  33 =head2 function new()
  34
  35   Synopsis:     constructor
  36   Arguments:    see L<CXGN::Cview::Chromosome>
  37
  38 =cut
  39
  40 sub new {
  41     my $class = shift;
  42     my $self = $class->SUPER::new(@_);
  43     $self->set_outline_color(0,0,0);
  44     $self->set_color(255, 255, 255);
  45     $self->set_hilite_color(50, 255, 50);
  46     $self->set_width(10);
  47     $self->{curved_height} = 8;
  48     $self->set_track_colors( [  0, 255,   0],
  49                              [200, 255, 200],
  50
  51                              [200, 200, 200],
  52                              [100, 150, 100], );
  53     return $self;
  54
  55 }
  56
  57 =head2 function set_fill_level()
  58
  59   Synopsis:
  60   Arguments:    the track number and the fill level of the chromosome in %
  61                 (eg, 50, not 0.5, to represent 50%).
  62                 tracks: 0 for available and htgs3
  63                         1 for available and < htgs3
  64                         2 for complete, not submitted
  65                         3 for in progress
  66   Returns:      nothing
  67   Side effects: the chromosome will be displayed with % filled in.
  68                 For fill levels specified above 100, the fill level value
  69                 will be capped at 100. (Yay! nice problem to have!).
  70   Description:
  71
  72 =cut
  73
  74 sub set_fill_level {
  75     #
  76     # set the percentage level to be displayed as finished in the chromosome. 50% would be 50, not 0.5
  77     #
  78     my $self=shift;
  79     my $track = shift;
  80     my $level = shift;
  81
  82     if ($level>100) { $level = 100; }
  83     if (!defined($track)) { die "set_fill_level: Need a track"; }
  84     $self->{fill_level}->[$track] = $level;
  85 }
  86
  87 sub get_fill_level {
  88     my $self = shift;
  89     my $track = shift;
  90     return $self->{fill_level}->[$track];
  91 }
  92
  93 =head2 function set_bac_count()
  94
  95   Synopsis:
  96   Arguments:    an integer reflecting the BACs sequenced.
  97                 is displayed below the glyph.
  98   Returns:
  99   Side effects:
 100   Description:
 101
 102 =cut
 103
 104
 105 sub set_bac_count {
 106     #
 107     # set the number of bacs sequenced for that chromosome
 108     #
 109     my $self=shift;
 110     $self->{bac_count} = shift;
 111 }
 112
 113 =head2 accessors get_track_colors(), set_track_colors()
 114
 115  Usage:        $glyph->set_track_colors([255,255,0], [0,0,255]);
 116  Desc:
 117  Ret:
 118  Args:
 119  Side Effects:
 120  Example:
 121
 122 =cut
 123
 124 sub get_track_colors {
 125   my $self=shift;
 126   return @{$self->{track_colors}};
 127
 128 }
 129
 130 sub set_track_colors {
 131   my $self=shift;
 132   @{$self->{track_colors}}=@_;
 133 }
 134
 135 =head2 get_track_color
 136
 137  Usage:        my ($r, $g, $b) = $glyph->get_track_color($track1)
 138  Desc:
 139  Ret:
 140  Args:
 141  Side Effects:
 142  Example:
 143
 144 =cut
 145
 146 sub get_track_color {
 147     my $self = shift;
 148     my $track = shift;
 149     return $self->{track_colors}->[$track];
 150 }
 151
 152 =head2 function render()
 153
 154   Synopsis:
 155   Arguments:    a GD image object.
 156   Returns:
 157   Side effects: generates the image representing the glyph
 158   Description:
 159
 160 =cut
 161
 162 sub render {
 163     #
 164     # draw the chromosome
 165     #
 166     my $self= shift;
 167
 168     $self->_calculate_scaling_factor();
 169
 170     my $image = shift;
 171
 172     # allocate colors
 173     #
 174     my $outline_color = $image -> colorResolve($self->{outline_color}->[0], $self->{outline_color}->[1], $self->{outline_color}->[2]);
 175     my $hilite_color = $image -> colorResolve($self->{hilite_color}->[0], $self->{hilite_color}->[1], $self->{hilite_color}->[2]);
 176     my $color = $image -> colorResolve($self->{color}->[0], $self->{color}->[1], $self->{color}->[2]);
 177
 178     my $halfwidth = $self ->{width}/2;
 179
 180     $image -> line($self->get_horizontal_offset() - $halfwidth, $self->get_vertical_offset() , $self->get_horizontal_offset()-$halfwidth, $self->get_vertical_offset()+$self->{height}, $outline_color);
 181     $image -> line($self->get_horizontal_offset() + $halfwidth, $self->get_vertical_offset() , $self->get_horizontal_offset()+$halfwidth, $self->get_vertical_offset()+$self->{height}, $outline_color);
 182     $image -> arc ($self->get_horizontal_offset(), $self->get_vertical_offset(), $self->{width}, $self->{curved_height}, 180, 0, $outline_color);
 183     $image -> arc ($self->get_horizontal_offset(), $self->get_vertical_offset()+$self->{height}, $self->{width}, $self->{curved_height}, 0, 180, $outline_color);
 184     $image -> fill ($self->get_horizontal_offset(), $self->get_vertical_offset(), $color);
 185
 186     my @track_color = ();
 187     foreach my $track (0..(scalar($self->get_track_colors())-1)) {
 188
 189         #if ($track ==4) { die "TRACK=$track!!!!!"; }
 190         my $colorRef = $self->get_track_color($track);
 191         #print STDERR "TRACK COLOR: $colorRef->[0], $colorRef->[1], $colorRef->[2]\n";
 192         $track_color[$track] = $image->colorResolve($colorRef->[0], $colorRef->[1], $colorRef->[2]);
 193     }
 194
 195     my $start_level = $self->get_vertical_offset() + $self->mapunits2pixels(0);
 196     foreach my $track (0..(scalar($self->get_track_colors())-1)) {
 197         my $level = $self->get_vertical_offset() + $self->mapunits2pixels($self->get_fill_level($track));
 198         #print STDERR "LEVEL: $level\n";
 199
 200         $image ->filledRectangle($self->get_horizontal_offset()-$halfwidth+1, $level,
 201                                  $self->get_horizontal_offset()+$halfwidth-1, $start_level,
 202                                  $track_color[$track]);
 203
 204         if ($self->get_fill_level($track) >= 99) {
 205             $image->fill($self->get_horizontal_offset(), $self->get_vertical_offset()-2, $track_color[$track]);
 206         }
 207         $start_level = $level;
 208     }
 209
 210     $image->fill($self->get_horizontal_offset(), $self->get_vertical_offset()+$self->mapunits2pixels(0)+1, $track_color[0]);
 211
 212     if ($self->{caption}) {
 213         my $bigfont = GD::Font->Large();
 214         $image -> string($bigfont, $self->get_horizontal_offset()- $bigfont->width() * length($self->{caption})/2, $self->get_vertical_offset()-$bigfont->height()-$self->{curved_height}/2, "$self->{caption}", $outline_color);
 215     }
 216     my $percent_finished =  $self->get_fill_level(2);
 217 #    my $percent_finished_caption = (sprintf "%3d", $self->get_fill_level(0)."\%"); #+$self->get_fill_level(1))."\%";
 218     my $percent_finished_caption = (sprintf "%3d", $percent_finished)."\%";
 219     $image -> string($self->{font}, $self->get_horizontal_offset()- $self->{font}->width() * length($percent_finished_caption)/2, $self->get_vertical_offset() + $self->get_height()+$self->{curved_height}, "$percent_finished_caption", $outline_color);
 220
 221
 222 }
 223
 224 sub draw_chromosome {
 225     my $self = shift;
 226     my $image = shift;
 227     $self->render($image);
 228 }
 229
 230 sub mapunits2pixels {
 231     my $self = shift;
 232     my $mapunits = shift;
 233
 234     my $pixels = $self->get_height() * (100-$mapunits)/100;
 235     #print STDERR "Mapunits2pixels: $mapunits are $pixels pixels\n";
 236     return $pixels;
 237 }