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