lib/CXGN/Cview/Chromosome/PachyteneIdiogram.pm

   1
   2
   3
   4
   5 =head1 NAME
   6
   7 CXGN::Cview::PachyteneIdiogram - a class for drawing a schematic representation of chromosomes in the pachytene phase.
   8
   9 =head1 DESCRIPTION
  10
  11 This object renders a pachytene idiogram, which are currently only defined for each of the 12 tomato chromosomes. It inherits from CXGN::Cview::chromosome. Inherits from L<CXGN::Cview::Chromosome>. The description of the tomato pachytene chromosomes is available in a flat file version, and there is a function in L<CXGN::Cview::Cview_data_adatper> to load it.
  12
  13 =head1 SEE ALSO
  14
  15 See also the documentation in L<CXGN::Cview>.
  16
  17 =head1 AUTHOR(S)
  18
  19 Lukas Mueller (lam87@cornell.edu)
  20
  21 =head1 FUNCTIONS
  22
  23
  24 =cut
  25
  26 use strict;
  27
  28 use CXGN::Cview::Chromosome;
  29 use CXGN::Cview::Ruler::PachyteneRuler;
  30
  31 package CXGN::Cview::Chromosome::PachyteneIdiogram;
  32
  33 use base qw( CXGN::Cview::Chromosome );
  34
  35 =head2 function new()
  36
  37 Constructor. Takes the same parameters as CXGN::Cview::Chromosome::new().
  38
  39 =cut
  40
  41 sub new {
  42     my $class = shift;
  43     my $self = $class->SUPER::new(@_);
  44     $self->set_outline_color(0,0,0);
  45     $self->set_color(255, 255, 255);
  46     $self->set_hilite_color(50, 255, 50);
  47     $self->set_width(10);
  48     $self->set_vertical_offset_top_edge();
  49     $self->{curved_height} = 8;
  50
  51     $self->{feature_color} = {
  52         short_arm => "100 ,100,250",
  53         long_arm => "100,100,250",
  54         heterochromatin => "75,75,250",
  55         telomere => "25,75,200",
  56         satellite => "75,75,250",
  57     };
  58     $self->{feature_width} = {
  59         short_arm => 6,
  60         long_arm => 6,
  61         heterochromatin => 10,
  62         telomere => 8,
  63         satellite => 8,
  64     };
  65
  66     @{$self->{render_order}} = (
  67                                  "short_arm",
  68                                  "long_arm",
  69                                  "heterochromatin",
  70                                  "telomere",
  71                                  "satellite"
  72                                  );
  73
  74     my $r = CXGN::Cview::Ruler::PachyteneRuler->new();
  75     $self->set_ruler($r);
  76     return $self;
  77 }
  78
  79 =head2 function add_feature()
  80
  81 Add a feature to the pachytene idiogram. Allowed feature types are restricted to:
  82 telomere, satellite, long_arm, short_arm etc. This is used to construct the
  83 image representation of the idiogram.
  84
  85 Note: feature types are rendered in a specific order. See new().
  86
  87 =cut
  88
  89 sub add_feature {
  90     my $self = shift;
  91     my $type = shift;
  92     my $start_coord = shift;
  93     my $end_coord = shift;
  94
  95     #print STDERR "Cview::pchytene::add_feature: Adding feature  $type, $start_coord, $end_coord\n";
  96
  97     if (!exists($self->{feature_color}->{$type})) {
  98         print STDERR "Cview.pm [pachytene_idiogram]: Unknown feature type: $type\n";
  99     }
 100     if ($type eq "short_arm") {
 101         $self->set_short_arm_length(abs($end_coord-$start_coord));
 102         #print STDERR  "short arm length: $self->{short_arm_length}\n";
 103     }
 104     if ($type eq "long_arm") {
 105         $self->set_long_arm_length(abs($end_coord-$start_coord));
 106     }
 107
 108     my %h = ( type => $type,
 109               start_coord => $start_coord,
 110               end_coord => $end_coord,
 111               );
 112
 113     push @{$self->{features}}, \%h;
 114 }
 115
 116 #
 117 # Note: _calculate_scaling_factor is overridden to account for the differences in the representation
 118 # of a pachytene chromosome.
 119 #
 120 sub _calculate_scaling_factor {
 121     my $self = shift;
 122     $self->{scaling_factor} = ($self->get_height()/($self->get_short_arm_length()+$self->get_long_arm_length()));
 123     #print STDERR "pachytene_idiogram: _calculate_scaling_factor::scaling factor: $self->{scaling_factor}\n";
 124 }
 125
 126 =head2 function mapunits2pixels()
 127
 128 Override the chromosome mapunits2pixels to reflect the different unit and representation of this map.
 129
 130 =cut
 131
 132 sub mapunits2pixels {
 133     my $self = shift;
 134     my $percent = shift;
 135     my $pixels = 0;
 136     # note: give the pixels from the vertical_offset (centromere) to the percent marker positioin
 137     my $shortarmratio = $self->get_short_arm_length()/($self->get_short_arm_length()+$self->get_long_arm_length());
 138     my $longarmratio = 1-$shortarmratio;
 139     if ($percent < 0) {
 140         $pixels = $self->get_height() * $shortarmratio * $percent / 100;
 141         # the result is a negative number, always measured from the centromere
 142     }
 143     else {
 144         $pixels = $self->get_height()* $longarmratio * $percent / 100;
 145     }
 146     return $pixels;
 147 }
 148
 149 =head2 function get_short_arm_length()
 150
 151  Synopsis:
 152  Arguments:     None
 153  Returns:       the length of the short arm in arbitrary units.
 154  Side effects:
 155  Description:
 156
 157 =cut
 158
 159 sub get_short_arm_length {
 160     my $self=shift;
 161     return $self->{short_arm_length};
 162 }
 163
 164 =head2 function set_short_arm_length()
 165
 166  Synopsis:
 167  Arguments:
 168  Returns:
 169  Side effects:
 170  Description:
 171
 172 =cut
 173
 174 sub set_short_arm_length {
 175     my $self=shift;
 176     $self->{short_arm_length}=shift;
 177 }
 178
 179 =head2 function get_long_arm_length()
 180
 181  Synopsis:
 182  Arguments:
 183  Returns:       The short arm length in arbitrary units.
 184  Side effects:
 185  Description:
 186
 187 =cut
 188
 189 sub get_long_arm_length  {
 190     my $self=shift;
 191     return $self->{long_arm_length};
 192 }
 193
 194 =head2 function set_long_arm_length()
 195
 196  Synopsis:
 197  Arguments:
 198  Returns:
 199  Side effects:
 200  Description:
 201
 202 =cut
 203
 204 sub set_long_arm_length  {
 205     my $self=shift;
 206     $self->{long_arm_length}=shift;
 207 }
 208
 209
 210
 211 sub draw_chromosome {
 212     my $self  =shift;
 213    #print STDERR "Rendering the PACHYTENE business...\n";
 214     my $image = shift;
 215     $self->_calculate_scaling_factor();
 216
 217     # calculate ruler properties...
 218     #
 219     $self->get_ruler()->set_height($self->get_height());
 220     $self->get_ruler()->set_short_arm_ruler_pixels($self->get_short_arm_length()*$self->get_scaling_factor());
 221     $self->get_ruler()->set_long_arm_ruler_pixels($self->get_long_arm_length()*$self->get_scaling_factor());
 222
 223     #$image -> line(0, $self->get_vertical_offset(), 100, $self->get_vertical_offset(), $image->colorResolve(0, 0, 0));
 224
 225
 226     # features have to be rendered in the correct order -- first the arms and then the rest.
 227     foreach my $type (@{$self->{render_order}}) {
 228         foreach my $f (@{$self->{features}}) {
 229             if ($f->{type} eq $type) {
 230                 #print STDERR "Rendering feature $f->{type}, $f->{start_coord}, $f->{end_coord} | Color: $self->{feature_color}->{$f->{type}}\n";
 231                 if (!exists($self->{feature_color}->{$f->{type}})) { print STDERR "$f->{type} HAS NO ASSOCIATED FEATURE COLOR!\n";}
 232                 my ($red, $green, $blue) = split /\,/, $self->{feature_color}->{$f->{type}};
 233                 my $color = $image-> colorResolve($red, $green,$blue);
 234
 235                 my $x = $self->get_horizontal_offset() - $self->{feature_width}->{$f->{type}}/2;
 236                 my $y = $self->get_vertical_offset()+$f->{start_coord}*$self->get_scaling_factor();
 237                 my $lx = $self->get_horizontal_offset()+ $self->{feature_width}->{$f->{type}}/2;
 238                 my $ly = $self->get_vertical_offset()+$f->{end_coord}*$self->get_scaling_factor();
 239
 240                 #print STDERR "Featurescreencoords: $f->{type}, $x, $y, $lx, $ly, $color\n";
 241                 # gd can't draw a filled rectangle with $y > $ly, so swap if that's the case.
 242                 if ($y > $ly)  { my $z=$y; $y=$ly; $ly=$z; }
 243                 $image -> filledRectangle(
 244                                           $x,
 245                                           $y,
 246                                           $lx,
 247                                           $ly,
 248                                           $color);
 249             }
 250         }
 251     }
 252
 253     $self->draw_centromere($image);
 254
 255     $self->draw_caption($image);
 256 }
 257
 258 sub render_markers {
 259     my $self = shift;
 260     my $image = shift;
 261
 262     my @m = $self->get_markers();
 263     foreach my $m (@m) {
 264         #print STDERR "Drawing marker ".$self->get_name()."\n";
 265         $m -> render($image);
 266     }
 267
 268 }
 269
 270 =head2 draw_centromere
 271
 272  Usage:
 273  Desc:
 274  Ret:
 275  Args:
 276  Side Effects:
 277  Example:
 278
 279 =cut
 280
 281 sub draw_centromere {
 282     my $self = shift;
 283     my $image = shift;
 284     my $centromere_color = $image->colorResolve(80, 80, 150);
 285     $image->filledArc($self->get_X(),$self->get_Y(),10,10,0,360, $centromere_color);
 286 }
 287
 288
 289
 290 =head2 function set_vertical_offset_centromere()
 291
 292 This function sets the vertical offset to the centromere (default).
 293
 294 =cut
 295
 296 sub set_vertical_offset_centromere {
 297     my $self = shift;
 298     $self->{vertical_offset_type} = "centromere";
 299 }
 300
 301 sub set_vertical_offset_top_edge {
 302     my $self = shift;
 303     $self->{vertical_offset_type} = "top_edge";
 304 }
 305
 306
 307 # sub get_vertical_offset {
 308 #     my $self = shift;
 309 #     if ($self->{vertical_offset_type} eq "top_edge") {
 310 #       return $self->SUPER::get_vertical_offset()+100;
 311 #     }
 312 # }
 313
 314 # The following method is overridden because the caption is rendered
 315 # at a slightly different location (the vertical offset defines the
 316 # centromere and not the top edge)
 317 #
 318 sub draw_caption {
 319     my $self = shift;
 320     my $image = shift;
 321
 322     my $outline_color = $image -> colorResolve(
 323                                                $self->{outline_color}[0],
 324                                                $self->{outline_color}[1],
 325                                                $self->{outline_color}[2]
 326                                                );
 327     my $bigfont = GD::Font->Large();
 328     $image -> string(
 329                      $bigfont,
 330                      $self->get_horizontal_offset()- $bigfont->width() * length($self->get_caption())/2,
 331                      $self->get_vertical_offset()-$self->{scaling_factor}*$self->{short_arm_length}-$bigfont->height(),
 332                      $self->get_caption(), $outline_color );
 333
 334     #$image->string($bigfont, 50, 50, "HELLO", $outline_color);
 335 }
 336
 337 sub layout {
 338     my $self=shift;
 339
 340     print STDERR "EXECUTING layout() in PachyteneIdiogram...\n";
 341     # determine the offset type
 342     if ($self->{vertical_offset_type} eq "top_edge") {
 343         my $new_offset = $self->get_vertical_offset()-$self->mapunits2pixels(-100);
 344         #print STDERR "Setting the vertical offset to $new_offset..\n";
 345         $self->set_vertical_offset($new_offset);
 346     }
 347
 348     $self->_calculate_scaling_factor();
 349     $self->distribute_labels();
 350
 351
 352 }
 353
 354 sub get_enclosing_rect {
 355     my $self = shift;
 356     if ($self->{vertical_offset_type} eq "top_edge") {
 357         $self->set_vertical_offset($self->get_vertical_offset()-$self->mapunits2pixels(-100));
 358     }
 359     return ($self->get_horizontal_offset()-int($self->get_width()/2),
 360             $self->get_vertical_offset()+$self->mapunits2pixels(-100),
 361             $self->get_horizontal_offset()+int($self->get_width()/2),
 362             $self->get_vertical_offset()+$self->mapunits2pixels(100)
 363             );
 364
 365 }
 366
 367 return 1;