Bio::Phylo::Set(3)

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

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

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 Bio::Phylo::Listable. 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 "SETS MANAGEMENT" in Bio::Phylo::Listable for more information on how to use this feature.

METHODS

  CONSTRUCTOR

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

  TESTS

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

SEE ALSO
There is a mailing list at <https://groups.google.com/forum/#!forum/bio-phylo> for any user or developer questions and discussions.

Also see the manual: Bio::Phylo::Manual and <http://rutgervos.blogspot.com>.

Consult the documentation for "SETS MANAGEMENT" in Bio::Phylo::Listable for more info on how to define subsets of the contents of segmented objects.

  Superclasses

Bio::Phylo::Listable
    This object inherits from Bio::Phylo::Listable, so methods defined there are also applicable here.

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

Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. <http://dx.doi.org/10.1186/1471-2105-12-63>