<commit_before>=head1 NAME

AlignedMember - DESCRIPTION of Object

=head1 DESCRIPTION

A subclass of Member which extends it to allow it to be aligned with other
AlignedMember objects.  General enough to allow for global, local, pair-wise and 
multiple alignments.  To be used primarily in NestedSet Tree data-structure.

=head1 CONTACT

Contact <NAME> on module implemetation/design detail: <EMAIL>
Contact <NAME> on EnsEMBL/Compara: <EMAIL>
Contact <NAME> on EnsEMBL in general: <EMAIL>

=cut

=head1 APPENDIX

The rest of the documentation details each of the object methods. 
Internal methods are usually preceded with a _

=cut

package Bio::EnsEMBL::Compara::AlignedMember;

use strict;
use Time::HiRes qw(time gettimeofday tv_interval);
use Bio::EnsEMBL::Utils::Exception;

use Bio::EnsEMBL::Compara::Member;
our @ISA = qw(Bio::EnsEMBL::Compara::Member);


sub cigar_line {
  my $self = shift;
  $self->{'_cigar_line'} = shift if(@_);
  return $self->{'_cigar_line'};
}

sub cigar_start {
  my $self = shift;
  $self->{'_cigar_start'} = shift if(@_);
  return $self->{'_cigar_start'};
}

sub cigar_end {
  my $self = shift;
  $self->{'_cigar_end'} = shift if(@_);
  return $self->{'_cigar_end'};
}


sub perc_cov {
  my $self = shift;
  $self->{'perc_cov'} = shift if(@_);
  return $self->{'perc_cov'};<commit_msg>override the -name method so that it redirects to Member::stable_id if a user process changes the name of an AlignedMember it will also be changing its stable_id<commit_after>=head1 NAME

AlignedMember - DESCRIPTION of Object

=head1 DESCRIPTION

A subclass of Member which extends it to allow it to be aligned with other
AlignedMember objects.  General enough to allow for global, local, pair-wise and 
multiple alignments.  To be used primarily in NestedSet Tree data-structure.

=head1 CONTACT

Contact <NAME> on module implemetation/design detail: <EMAIL>
Contact <NAME> on EnsEMBL/Compara: <EMAIL>
Contact <NAME> on EnsEMBL in general: <EMAIL>

=cut

=head1 APPENDIX

The rest of the documentation details each of the object methods. 
Internal methods are usually preceded with a _

=cut

package Bio::EnsEMBL::Compara::AlignedMember;

use strict;
use Time::HiRes qw(time gettimeofday tv_interval);
use Bio::EnsEMBL::Utils::Exception;

use Bio::EnsEMBL::Compara::Member;
our @ISA = qw(Bio::EnsEMBL::Compara::Member);

sub name {
  my $self = shift;
  return $self->stable_id(@_);
}

sub cigar_line {
  my $self = shift;
  $self->{'_cigar_line'} = shift if(@_);
  return $self->{'_cigar_line'};
}

sub cigar_start {
  my $self = shift;
  $self->{'_cigar_start'} = shift if(@_);
  return $self->{'_cigar_start'};
}

sub cigar_end {
  my $self = shift;
  $self->{'_cigar_end'} = shift if(@_);
  return $self->{'_cigar_end'};
}


sub perc_cov {
  my $self = shift;
  $self->{'perc_cov'} = shift if(@_);
  return $self->{'perc_cov'};
{'fraction_non_alphanumeric': 0.1257883672039243, 'fraction_numerical': 0.002803083391730904, 'mean_word_length': 4.838445807770961, 'pattern_counts': {'":': 0, '<': 15, '<?xml version=': 0, '>': 32, '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': '123705', 'n_tokens_mistral': 1048, 'n_tokens_neox': 984, 'n_words': 318}