File Coverage

blib/lib/Bio/Phylo/Set.pm

Criterion	Covered	Total	%
statement	14	16	87.5
branch	1	2	50.0
condition			n/a
subroutine	5	7	71.4
pod	1	1	100.0
total	21	26	80.7

package Bio::Phylo::Set;
use strict;
use base 'Bio::Phylo::Listable';
use Bio::Phylo::Util::CONSTANT qw'_NONE_ _SET_';

=head1 NAME

Bio::Phylo::Set - Subset of the parts inside a container

=head1 SYNOPSIS

 use Bio::Phylo::Factory;
 my $fac = Bio::Phylo::Factory->new;

 my $forest = $fac->create_forest;
 my $tree = $fac->create_tree;
 $forest->insert($tree);

 my $set = $fac->create_set( -name => 'TreeSet1' );
 $forest->add_set($set);
 $forest->add_to_set($tree,$set); # $tree is now part of TreeSet1

=head1 DESCRIPTION

Many Bio::Phylo objects are segmented: they contain one or more subparts
of the same type. For example, a matrix contains multiple rows; each row
contains multiple cells; a tree contains nodes, and so on. Segmented objects
all inherit from L. In many cases it is useful to be
able to define subsets of the contents of segmented objects, for example
sets of taxon objects inside a taxa block. The Bio::Phylo::Listable object
allows this through a number of methods (add_set, remove_set, add_to_set,
remove_from_set and so on). Those methods delegate the actual management of the set
contents to the Bio::Phylo::Set object, the class whose documentation you're
reading now. Consult the documentation for L
for more information on how to use this feature.

=head1 METHODS

=head2 CONSTRUCTOR

=over

=item new()

 Type    : Constructor
 Title   : new
 Usage   : my $anno = Bio::Phylo::Set->new;
 Function: Initializes a Bio::Phylo::Set object.
 Returns : A Bio::Phylo::Set object.
 Args    : optional constructor arguments are key/value
 		   pairs where the key corresponds with any of
 		   the methods that starts with set_ (i.e. mutators)
 		   and the value is the permitted argument for such
 		   a method. The method name is changed such that,
 		   in order to access the set_value($val) method
 		   in the constructor, you would pass -value => $val

=cut

{
    my $NONE = _NONE_;
    my $TYPE = _SET_;

    #     sub new {
    #         return shift->SUPER::new( '-tag' => 'class', @_ );
    #     }

=back

=head2 TESTS

=over

=item can_contain()

Tests if argument can be inserted in invocant.

 Type    : Test
 Title   : can_contain
 Usage   : &do_something if $listable->can_contain( $obj );
 Function: Tests if $obj can be inserted in $listable
 Returns : BOOL
 Args    : An $obj to test

=cut

    sub can_contain {
        my ( $self, @obj ) = @_;
        for my $obj (@obj) {
            return 0 if ref $obj;
        }
        return 1;
    }
    sub _container { $NONE }
    sub _type      { $TYPE }
    sub _tag       { 'set' }
}

=back

=cut

# podinherit_insert_token

=head1 SEE ALSO

There is a mailing list at L
for any user or developer questions and discussions.

Also see the manual: L and L.

Consult the documentation for L for more info
on how to define subsets of the contents of segmented objects.

=head2 Superclasses

=over

=item L

This object inherits from L, so methods
defined there are also applicable here.

=back

=head1 CITATION

If you use Bio::Phylo in published research, please cite it:

B, B, B, B
and B, 2011. Bio::Phylo - phyloinformatic analysis using Perl.
I B<12>:63.
L

=cut

1;