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lib/Bio/MUST/Core/Ali.pm  view on Meta::CPAN

package Bio::MUST::Core::Ali;
# ABSTRACT: Multiple sequence alignment
# CONTRIBUTOR: Catherine COLSON <ccolson@doct.uliege.be>
# CONTRIBUTOR: Arnaud DI FRANCO <arnaud.difranco@gmail.com>
$Bio::MUST::Core::Ali::VERSION = '0.252040';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

# use Smart::Comments;

use Carp;
use File::Temp;
use List::AllUtils qw(uniq indexes sum0);
use Path::Class qw(file);
use POSIX qw(ceil floor);
use Statistics::Descriptive;
use Tie::IxHash;

use Bio::MUST::Core::Types;
use Bio::MUST::Core::Constants qw(:ncbi :gaps :files);

use aliased 'Bio::MUST::Core::Seq';
use aliased 'Bio::MUST::Core::SeqId';
use aliased 'Bio::MUST::Core::SeqMask';

# TODO: add information about methods available in Ali-like objects

# ATTRIBUTES


has 'seqs' => (
    traits   => ['Array'],
    is       => 'ro',
    isa      => 'ArrayRef[Bio::MUST::Core::Seq]',
    default  => sub { [] },
    writer   => '_set_seqs',
    handles  => {
          add_seq  => 'push',
          get_seq  => 'get',
          set_seq  => 'set',
       delete_seq  => 'delete',
       insert_seq  => 'insert',
        count_seqs => 'count',
          all_seqs => 'elements',
        first_seq  => 'first',
       filter_seqs => 'grep',
    },
);


has 'file' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Types::File',
    default  => 'untitled.ali',
    coerce   => 1,
    handles  => {
        filename => 'stringify',
    },
);


has 'guessing' => (
    traits   => ['Bool'],
    is       => 'ro',