lib/CXGN/Cview/Chromosome/Scaffold.pm

   1
   2 use strict;
   3
   4 package CXGN::Cview::Chromosome::Scaffold;
   5
   6 use base "CXGN::Cview::Chromosome";
   7
   8 our $INTER_SCAFFOLD_DISTANCE = 100_000;
   9
  10 sub new {
  11     my $class = shift;
  12     my $file = shift;
  13     my $chr_nr = shift;
  14     my $marker_link = shift;
  15
  16     my $self = $class-> SUPER::new($chr_nr);
  17
  18     $self->{marker_link} = $marker_link;
  19
  20     open (my $F, "<", $file) || die "Can't open file $file: $!";
  21
  22     my $current_offset = 0;
  23
  24     while (<$F>) {
  25         chomp;
  26
  27         my ($scaffold, $length, $c, $cM) = split /\t/;
  28
  29         if ($c != $chr_nr) { next(); }
  30
  31         my $m = CXGN::Cview::Marker::RangeMarker->new($self);
  32
  33         $current_offset += $INTER_SCAFFOLD_DISTANCE;
  34
  35         $m->get_label()->set_name($scaffold);
  36         $m->set_marker_name($scaffold);
  37         $m->get_label()->set_url(&{$self->{marker_link}}($scaffold));
  38         $m->set_offset($current_offset + ($length/2));
  39         $m->set_north_range($length/2);
  40         $m->set_south_range($length/2);
  41         $self->add_marker($m);
  42         $current_offset += $length;
  43     }
  44     close($F);
  45
  46     $self->sort_markers();
  47     $self->set_length($current_offset);
  48     #$chr->set_url($self->{url});
  49     $self->distribute_labels();
  50     $self->distribute_label_stacking();
  51     $self->set_ruler(CXGN::Cview::Ruler::ScaffoldRuler->new());
  52     $self->set_units('bp');
  53     return $self;
  54 }
  55
  56 return 1;