NAME
Bio::Phylo::Taxa - Container of taxon objects
SYNOPSIS
use Bio::Phylo::Factory;
my $fac = Bio::Phylo::Factory->new;
# A mesquite-style default
# taxa block for 10 taxa.
my $taxa = $fac->create_taxa;
for my $i ( 1 .. 10 ) {
$taxa->insert( $fac->create_taxon( '-name' => "taxon_${i}" ) );
}
# prints a taxa block in nexus format
print $taxa->to_nexus;
DESCRIPTION
The Bio::Phylo::Taxa object models a set of operational taxonomic units. The object subclasses the Bio::Phylo::Listable object, and so the filtering methods of that class are available.
A taxa object can link to multiple forest and matrix objects.
METHODS
CONSTRUCTOR
- new()
-
Taxa constructor.
Type : Constructor Title : new Usage : my $taxa = Bio::Phylo::Taxa->new; Function: Instantiates a Bio::Phylo::Taxa object. Returns : A Bio::Phylo::Taxa object. Args : none.
MUTATORS
- set_forest()
-
Sets associated Bio::Phylo::Forest object.
Type : Mutator Title : set_forest Usage : $taxa->set_forest( $forest ); Function: Associates forest with the invocant taxa object (i.e. creates reference). Returns : Modified object. Args : A Bio::Phylo::Forest object Comments: A taxa object can link to multiple forest and matrix objects.
- set_matrix()
-
Sets associated Bio::Phylo::Matrices::Matrix object.
Type : Mutator Title : set_matrix Usage : $taxa->set_matrix($matrix); Function: Associates matrix with the invocant taxa object (i.e. creates reference). Returns : Modified object. Args : A Bio::Phylo::Matrices::Matrix object Comments: A taxa object can link to multiple forest and matrix objects.
- unset_forest()
-
Removes association with argument Bio::Phylo::Forest object.
Type : Mutator Title : unset_forest Usage : $taxa->unset_forest($forest); Function: Disassociates forest from the invocant taxa object (i.e. removes reference). Returns : Modified object. Args : A Bio::Phylo::Forest object
- unset_matrix()
-
Removes association with Bio::Phylo::Matrices::Matrix object.
Type : Mutator Title : unset_matrix Usage : $taxa->unset_matrix($matrix); Function: Disassociates matrix from the invocant taxa object (i.e. removes reference). Returns : Modified object. Args : A Bio::Phylo::Matrices::Matrix object
ACCESSORS
- get_forests()
-
Gets all associated Bio::Phylo::Forest objects.
Type : Accessor Title : get_forests Usage : @forests = @{ $taxa->get_forests }; Function: Retrieves forests associated with the current taxa object. Returns : An ARRAY reference of Bio::Phylo::Forest objects. Args : None.
- get_matrices()
-
Gets all associated Bio::Phylo::Matrices::Matrix objects.
Type : Accessor Title : get_matrices Usage : @matrices = @{ $taxa->get_matrices }; Function: Retrieves matrices associated with the current taxa object. Returns : An ARRAY reference of Bio::Phylo::Matrices::Matrix objects. Args : None.
- get_ntax()
-
Gets number of contained Bio::Phylo::Taxa::Taxon objects.
Type : Accessor Title : get_ntax Usage : my $ntax = $taxa->get_ntax; Function: Retrieves the number of taxa for the invocant. Returns : INT Args : None. Comments:
METHODS
- merge_by_name()
-
Merges argument Bio::Phylo::Taxa object with invocant.
Type : Method Title : merge_by_name Usage : $taxa->merge_by_name($other_taxa); Function: Merges two taxa objects such that internally different taxon objects with the same name become a single object with the combined references to datum objects and node objects contained by the two. Returns : A merged Bio::Phylo::Taxa object. Args : A Bio::Phylo::Taxa object.
- to_nexus()
-
Serializes invocant to nexus format.
Type : Format convertor Title : to_nexus Usage : my $block = $taxa->to_nexus; Function: Converts $taxa into a nexus taxa block. Returns : Nexus taxa block (SCALAR). Args : -links => 1 (optional, adds 'TITLE' token) Comments:
SEE ALSO
- Bio::Phylo::Listable
-
The Bio::Phylo::Taxa object inherits from the Bio::Phylo::Listable object. Look there for more methods applicable to the taxa object.
- Bio::Phylo::Manual
-
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.
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
REVISION
$Id: Taxa.pm 1660 2011-04-02 18:29:40Z rvos $