<commit_before>#
# Ensembl module for Bio::EnsEMBL::Funcgen::DBSQL::FeatureTypeAdaptor
#

=head1 LICENSE

  Copyright (c) 1999-2012 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <<EMAIL>>.

  Questions may also be sent to the Ensembl help desk at
  <<EMAIL>>.


=head1 NAME

Bio::EnsEMBL::Funcgen::DBSQL::FeatureTypeAdaptor - Adaptor for fetching and
storing FeatureType objects.

=head1 SYNOPSIS

my $ft_adaptor = $db->get_FeatureTypeAdaptor;

my $feature_type = $ft_adaptor->fetch_by_name("H3K4me3");


=head1 DESCRIPTION

The FeatureTypeAdaptor is a database adaptor for storing and retrieving
Funcgen FeatureType objects.

=head1 SEE ALSO

Bio::EnsEMBL::Funcgen::FeatureType
Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor

=cut

package Bio::EnsEMBL::Funcgen::DBSQL::FeatureTypeAdaptor;

use strict;
use warnings;
use Bio::EnsEMBL::Utils::Exception qw( warning throw deprecate );
use Bio::EnsEMBL::Funcgen::FeatureType;
use Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor;

use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor);

#Query extension stuff
use constant TRUE_TABLES => [['feature_type', 'ft']];
use constant TABLES      => [['feature_type', 'ft']];

#Regulatory evidence information

my %regulatory_evidence_info = 
  (
   core => 
   {
    name      => 'Open chromatin & TFBS',
    long_name => 'Open chromatin & Transcription factor binding sites',
    label     => 'DNase1 & TFBS',
    classes   => ['Transcription Factor', 
                  'Transcription Factor Complex',   
                  'Open Chromatin'],
   },
   
   non_core => 
   {
    name      => 'Histones & polymerases',
    long_name => 'Histone modifications & RNA polymerases',
    label     => 'Hists & Pols',
    classes   => ['Polymerase',  'Histone'],
   }
  );<commit_msg>license update and reorder tf class config<commit_after>#
# Ensembl module for Bio::EnsEMBL::Funcgen::DBSQL::FeatureTypeAdaptor
#

=head1 LICENSE

  Copyright (c) 1999-2013 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <<EMAIL>>.

  Questions may also be sent to the Ensembl help desk at
  <<EMAIL>>.


=head1 NAME

Bio::EnsEMBL::Funcgen::DBSQL::FeatureTypeAdaptor - Adaptor for fetching and
storing FeatureType objects.

=head1 SYNOPSIS

my $ft_adaptor = $db->get_FeatureTypeAdaptor;

my $feature_type = $ft_adaptor->fetch_by_name("H3K4me3");


=head1 DESCRIPTION

The FeatureTypeAdaptor is a database adaptor for storing and retrieving
Funcgen FeatureType objects.

=head1 SEE ALSO

Bio::EnsEMBL::Funcgen::FeatureType
Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor

=cut

package Bio::EnsEMBL::Funcgen::DBSQL::FeatureTypeAdaptor;

use strict;
use warnings;
use Bio::EnsEMBL::Utils::Exception qw( warning throw deprecate );
use Bio::EnsEMBL::Funcgen::FeatureType;
use Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor;

use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor);

#Query extension stuff
use constant TRUE_TABLES => [['feature_type', 'ft']];
use constant TABLES      => [['feature_type', 'ft']];

#Regulatory evidence information

my %regulatory_evidence_info = 
  (
   core => 
   {
    name      => 'Open chromatin & TFBS',
    long_name => 'Open chromatin & Transcription factor binding sites',
    label     => 'DNase1 & TFBS',
    classes   => ['Open Chromatin',
                  'Transcription Factor', 
                  'Transcription Factor Complex'],
   },
   
   non_core => 
   {
    name      => 'Histones & polymerases',
    long_name => 'Histone modifications & RNA polymerases',
    label     => 'Hists & Pols',
    classes   => ['Polymerase',  'Histone'],
   }
  );
{'fraction_non_alphanumeric': 0.11510791366906475, 'fraction_numerical': 0.008633093525179856, 'mean_word_length': 4.136699507389163, 'pattern_counts': {'":': 0, '<': 11, '<?xml version=': 0, '>': 39, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, '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': '2648640', 'n_tokens_mistral': 1447, 'n_tokens_neox': 1344, 'n_words': 364}