<commit_before>package Bio::EnsEMBL::GlyphSet::cnv_probes;

use strict;

use base qw(Bio::EnsEMBL::GlyphSet_simple);

sub my_label { return 'Copy Number Variant Probes'; }

sub features {
  my $self   = shift; 
  my $slice  = $self->{'container'};
  my $source = $self->my_config('source');

  my $var_features;
  
  if ($source =~ /^\w/) {
    $var_features = $slice->get_all_CopyNumberVariantProbes($source);
  } else {
    $var_features = $slice->get_all_CopyNumberVariantProbes;
  }
  
  return $var_features;  
}


sub colour_key  {
  my ($self, $f) = @_;
  return $f->source;
}

sub tag {
  my ($self, $f) = @_;
  
  return ({
    style  => 'fg_ends',
    colour => $self->my_colour($f->source),
		start  => $f->start,
    end    => $f->end
  });
} 

sub href {
  my ($self, $f) = @_;
  <commit_msg>Updated the calls from the StructuralVariation object<commit_after>package Bio::EnsEMBL::GlyphSet::cnv_probes;

use strict;

use base qw(Bio::EnsEMBL::GlyphSet_simple);

sub my_label { return 'Copy Number Variant Probes'; }

sub features {
  my $self   = shift; 
  my $slice  = $self->{'container'};
  my $source = $self->my_config('source');

  my $var_features;
  
  if ($source =~ /^\w/) {
    $var_features = $slice->get_all_CopyNumberVariantProbeFeatures($source);
  } else {
    $var_features = $slice->get_all_CopyNumberVariantProbeFeatures;
  }
  
  return $var_features;  
}


sub colour_key  {
  my ($self, $f) = @_;
  return $f->source;
}

sub tag {
  my ($self, $f) = @_;
  
  return ({
    style  => 'fg_ends',
    colour => $self->my_colour($f->source),
		start  => $f->start,
    end    => $f->end
  });
} 

sub href {
  my ($self, $f) = @_;
  
{'fraction_non_alphanumeric': 0.17427884615384615, 'fraction_numerical': 0.0, 'mean_word_length': 3.324675324675325, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 29, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3301776', 'n_tokens_mistral': 664, 'n_tokens_neox': 644, 'n_words': 132}