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

Bio-Phylo documentation Contained in the Bio-Phylo distribution.

Index

Code Index:

NAME

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

SYNOPSIS

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 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

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

METHODS

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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

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Bio::Phylo

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

Bio::Phylo::Manual

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

CITATION

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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

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 $Id: Taxon.pm 1660 2011-04-02 18:29:40Z rvos $
Bio-Phylo documentation Contained in the Bio-Phylo distribution. 
# $Id: Taxon.pm 1660 2011-04-02 18:29:40Z rvos $
package Bio::Phylo::Taxa::Taxon;
use strict;
use base 'Bio::Phylo::NeXML::Writable';
use Bio::Phylo::Util::CONSTANT qw':objecttypes looks_like_object';
use Bio::Phylo::Mediators::TaxaMediator;
{
    my $TYPE_CONSTANT      = _TAXON_;
    my $CONTAINER_CONSTANT = _TAXA_;
    my $DATUM_CONSTANT     = _DATUM_;
    my $NODE_CONSTANT      = _NODE_;
    my $logger             = __PACKAGE__->get_logger;
    my $mediator           = 'Bio::Phylo::Mediators::TaxaMediator';


    #     sub new {
    #         # could be child class
    #         my $class = shift;
    #
    #         # notify user
    #         $logger->info("constructor called for '$class'");
    #
    #         # go up inheritance tree, eventually get an ID
    #         return $class->SUPER::new( '-tag' => __PACKAGE__->_tag, @_ );
    #     }


    sub set_data {
        my ( $self, $datum ) = @_;
        if ( looks_like_object $datum, $DATUM_CONSTANT ) {
            $mediator->set_link(
                '-one'  => $self,
                '-many' => $datum,
            );
        }
        return $self;
    }


    sub set_nodes {
        my ( $self, $node ) = @_;
        if ( looks_like_object $node, $NODE_CONSTANT ) {
            $mediator->set_link(
                '-one'  => $self,
                '-many' => $node,
            );
        }
        return $self;
    }


    sub unset_datum {
        my ( $self, $datum ) = @_;
        $mediator->remove_link(
            '-one'  => $self,
            '-many' => $datum,
        );
        return $self;
    }


    sub unset_node {
        my ( $self, $node ) = @_;
        $mediator->remove_link(
            '-one'  => $self,
            '-many' => $node,
        );
        return $self;
    }


    sub get_data {
        my $self = shift;
        return $mediator->get_link(
            '-source' => $self,
            '-type'   => $DATUM_CONSTANT,
        );
    }


    sub get_nodes {
        my $self = shift;
        return $mediator->get_link(
            '-source' => $self,
            '-type'   => $NODE_CONSTANT,
        );
    }


    sub DESTROY {
        my $self = shift;

        # notify user
        #$logger->debug("destructor called for '$self'");
        # recurse up inheritance tree for cleanup
        $self->SUPER::DESTROY;
    }


    sub _container { $CONTAINER_CONSTANT }


    sub _type { $TYPE_CONSTANT }
    sub _tag  { 'otu' }


    # podinherit_insert_token


}
1;