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Manual Reference Pages  -  BIO::PHYLO::TAXA::TAXON (3)

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NAME

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

CONTENTS

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
 $tree->cross_reference($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

    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

There is a mailing list at <https://groups.google.com/forum/#!forum/bio-phylo> for any user or developer questions and discussions.
Bio::Phylo::NeXML::Writable The taxon objects inherits from the Bio::Phylo::NeXML::Writable 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

If you use Bio::Phylo in published research, please cite it:

<B>Rutger A VosB>, <B>Jason CaravasB>, <B>Klaas HartmannB>, <B>Mark A JensenB> and <B>Chase MillerB>, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics <B>12B>:63. <http://dx.doi.org/10.1186/1471-2105-12-63>

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