Bio::Phylo::Taxa::Taxon - Operational taxonomic unit

NAME

Bio::Phylo::Taxa::Taxon - Operational taxonomic unit

SYNOPSIS

 use Bio::Phylo::IO qw(parse);
 use Bio::Phylo::Factory;
 my $fac = Bio::Phylo::Factory->new;

 # array of names
 my @apes = qw(
     Homo_sapiens
     Pan_paniscus
     Pan_troglodytes
     Gorilla_gorilla
 );

 # newick string
 my $str = '(((Pan_paniscus,Pan_troglodytes),';
 $str   .= 'Homo_sapiens),Gorilla_gorilla);';

 # create tree object
 my $tree = parse(
    -format => 'newick',
    -string => $str
 )->first;

 # instantiate taxa object
 my $taxa = $fac->create_taxa;

 # instantiate taxon objects, insert in taxa object
 foreach( @apes ) {
    my $taxon = $fac->create_taxon(
        -name => $_,
    );
    $taxa->insert($taxon);
 }

 # crossreference tree and taxa
 $tree->crossreference($taxa);

 # iterate over nodes
 while ( my $node = $tree->next ) {

    # check references
    if ( $node->get_taxon ) {

        # prints crossreferenced tips
        print "match: ", $node->get_name, "\n";
            }
         }

DESCRIPTION

The taxon object models a single operational taxonomic unit. It is useful for cross-referencing datum objects and tree nodes.

METHODS

CONSTRUCTOR

new()

Taxon constructor.

 Type    : Constructor
 Title   : new
 Usage   : my $taxon = Bio::Phylo::Taxa::Taxon->new;
 Function: Instantiates a Bio::Phylo::Taxa::Taxon
           object.
 Returns : A Bio::Phylo::Taxa::Taxon object.
 Args    : none.

MUTATORS

set_data()

Associates argument data with invocant.

 Type    : Mutator
 Title   : set_data
 Usage   : $taxon->set_data( $datum );
 Function: Associates data with
           the current taxon.
 Returns : Modified object.
 Args    : Must be an object of type
           Bio::Phylo::Matrices::Datum
set_nodes()

Associates argument node with invocant.

 Type    : Mutator
 Title   : set_nodes
 Usage   : $taxon->set_nodes($node);
 Function: Associates tree nodes
           with the current taxon.
 Returns : Modified object.
 Args    : A Bio::Phylo::Forest::Node object
unset_datum()

Removes association between argument data and invocant.

 Type    : Mutator
 Title   : unset_datum
 Usage   : $taxon->unset_datum($node);
 Function: Disassociates datum from
           the invocant taxon (i.e.
           removes reference).
 Returns : Modified object.
 Args    : A Bio::Phylo::Matrix::Datum object
unset_node()

Removes association between argument node and invocant.

 Type    : Mutator
 Title   : unset_node
 Usage   : $taxon->unset_node($node);
 Function: Disassociates tree node from
           the invocant taxon (i.e.
           removes reference).
 Returns : Modified object.
 Args    : A Bio::Phylo::Forest::Node object

ACCESSORS

get_data()

Retrieves associated datum objects.

 Type    : Accessor
 Title   : get_data
 Usage   : @data = @{ $taxon->get_data };
 Function: Retrieves data associated
           with the current taxon.
 Returns : An ARRAY reference of
           Bio::Phylo::Matrices::Datum
           objects.
 Args    : None.
get_nodes()

Retrieves associated node objects.

 Type    : Accessor
 Title   : get_nodes
 Usage   : @nodes = @{ $taxon->get_nodes };
 Function: Retrieves tree nodes associated
           with the current taxon.
 Returns : An ARRAY reference of
           Bio::Phylo::Trees::Node objects
 Args    : None.

SEE ALSO

the Bio::Phylo manpage

The taxon objects inherits from the the Bio::Phylo manpage object. The methods defined there are also applicable to the taxon object.

the Bio::Phylo::Manual manpage

Also see the manual: the Bio::Phylo::Manual manpage and http://rutgervos.blogspot.com.

REVISION

 $Id: Taxon.pm 844 2009-03-05 00:07:26Z rvos $
 Bio::Phylo::Taxa::Taxon - Operational taxonomic unit