<commit_before>package Bio::BioVeL::Service::NeXMLExtractor::CharSetWriter::nexus;
use strict;
use warnings;

use List::MoreUtils qw(uniq);

use Bio::BioVeL::Service::NeXMLExtractor::CharSetWriter;
use base 'Bio::BioVeL::Service::NeXMLExtractor::CharSetWriter';

=over

=item write_charsets

Writes character set definitions to a NEXUS string. The syntax is expected to be like what
is used inside C<mrbayes> blocks and inside C<sets> blocks, i.e.:

	charset <name> = <start coordinate>(-<end coordinate>)?(\<offset>)? ...;

That is, the definition starts with the C<charset> token, a name and an equals sign. Then,
one or more coordinate sets. Each coordinate set has a start coordinate, an optional end
coordinate (otherwise it's interpreted as a single site), and an optional offset statement,
e.g. for codon positions. Alternatively, instead of coordinates, names of other character 
sets may be used. The statement ends with a semicolon. 

=back

=cut
<commit_msg>removed unused import<commit_after>package Bio::BioVeL::Service::NeXMLExtractor::CharSetWriter::nexus;
use strict;
use warnings;

use Bio::BioVeL::Service::NeXMLExtractor::CharSetWriter;
use base 'Bio::BioVeL::Service::NeXMLExtractor::CharSetWriter';

=over

=item write_charsets

Writes character set definitions to a NEXUS string. The syntax is expected to be like what
is used inside C<mrbayes> blocks and inside C<sets> blocks, i.e.:

	charset <name> = <start coordinate>(-<end coordinate>)?(\<offset>)? ...;

That is, the definition starts with the C<charset> token, a name and an equals sign. Then,
one or more coordinate sets. Each coordinate set has a start coordinate, an optional end
coordinate (otherwise it's interpreted as a single site), and an optional offset statement,
e.g. for codon positions. Alternatively, instead of coordinates, names of other character 
sets may be used. The statement ends with a semicolon. 

=back

=cut

{'fraction_non_alphanumeric': 0.09660574412532637, 'fraction_numerical': 0.0, 'mean_word_length': 5.629757785467128, 'pattern_counts': {'":': 0, '<': 17, '<?xml version=': 0, '>': 17, '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': '1691535', 'n_tokens_mistral': 578, 'n_tokens_neox': 552, 'n_words': 231}