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.
- 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
- 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
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.
- Bio::Phylo::Listable
- 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>