Bio::Phylo::Taxa::TaxaLinker - Superclass for objects that link to taxa objects
use Bio::Phylo::Factory; my $fac = Bio::Phylo::Factory->new; my $matrix = $fac->create_matrix; my $taxa = $fac->create_taxa; if ( $matrix->isa('Bio::Phylo::Taxa::TaxaLinker') ) { $matrix->set_taxa( $taxa ); }
This module is a superclass for objects that link to Bio::Phylo::Taxa objects.
Associates invocant with Bio::Phylo::Taxa argument.
Type : Mutator Title : set_taxa Usage : $obj->set_taxa( $taxa ); Function: Links the invocant object to a taxa object. Returns : Modified $obj Args : A Bio::Phylo::Taxa object.
Removes association between invocant and Bio::Phylo::Taxa object.
Type : Mutator Title : unset_taxa Usage : $obj->unset_taxa(); Function: Removes the link between invocant object and taxa Returns : Modified $obj Args : NONE
Retrieves association between invocant and Bio::Phylo::Taxa object.
Type : Accessor Title : get_taxa Usage : my $taxa = $obj->get_taxa; Function: Retrieves the Bio::Phylo::Taxa object linked to the invocant. Returns : Bio::Phylo::Taxa Args : NONE Comments: This method returns the Bio::Phylo::Taxa object to which the invocant is linked. The returned object can therefore contain *more* taxa than are actually in the matrix.
Performs sanity check on taxon relationships.
Type : Interface method Title : check_taxa Usage : $obj->check_taxa Function: Performs sanity check on taxon relationships Returns : $obj Args : NONE
Creates a taxa block from the objects contents if none exists yet.
Type : Decorated interface method Title : make_taxa Usage : my $taxa = $obj->make_taxa Function: Creates a taxa block from the objects contents if none exists yet. Returns : $taxa Args : NONE
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
The matrix object subclasses Bio::Phylo::Taxa::TaxaLinker.
The forest object subclasses Bio::Phylo::Taxa::TaxaLinker.
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.
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
To install Bio::Phylo, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Phylo
CPAN shell
perl -MCPAN -e shell install Bio::Phylo
For more information on module installation, please visit the detailed CPAN module installation guide.