Bio::Phylo::Set - Subset of the parts inside a container
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
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.
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 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
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
Consult the documentation for "SETS MANAGEMENT" in Bio::Phylo::Listable for more info on how to define subsets of the contents of segmented objects.
This object inherits from Bio::Phylo::Listable, so methods defined there are also applicable here.
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