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

package Bio::MUST::Core::Tree::Forest;
# ABSTRACT: Collection of (bootstrap) trees
$Bio::MUST::Core::Tree::Forest::VERSION = '0.252040';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Bio::Phylo::IO qw(parse);

use Bio::MUST::Core::Types;
use aliased 'Bio::MUST::Core::Tree';


# public array
has 'trees' => (
    traits   => ['Array'],
    is       => 'ro',
    isa      => 'ArrayRef[Bio::MUST::Core::Tree]',
    default  => sub { [] },
    handles  => {
        count_trees => 'count',
          all_trees => 'elements',
          add_tree  => 'push',
          get_tree  => 'get',
    },
);



sub restore_ids {
    my $self   = shift;
    my $mapper = shift;

    $_->restore_ids($mapper) for $self->all_trees;

    return;
}


sub load {
    my $class  = shift;
    my $infile = shift;

    my @trees;

    # build Bio::MUST::Core::Tree object from each Bio::Phylo::Forest::Tree
    my $forest = parse(-format => 'newick', -file => $infile);
    while (my $tree = $forest->next) {
        push @trees, Tree->new( tree => $tree );
    }

    return $class->new( trees => \@trees );
}


sub store {
    my $self    = shift;
    my $outfile = shift;

    open my $out, '>', $outfile;

    say {$out} join "\n", map {
        $_->tree->to_newick( -nodelabels => 0 )     # This might be an issue!