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Man Pages


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

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NAME

Bio::Phylo::Taxa::TaxaLinker - Superclass for objects that link to taxa objects

CONTENTS

SYNOPSIS



 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 );
 }



DESCRIPTION

This module is a superclass for objects that link to Bio::Phylo::Taxa objects.

METHODS

    MUTATORS

set_taxa() 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.



unset_taxa() 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



    ACCESSORS

get_taxa() 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.



check_taxa() 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



make_taxa() 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



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::Matrices::Matrix The matrix object subclasses Bio::Phylo::Taxa::TaxaLinker.
Bio::Phylo::Forest The forest object subclasses Bio::Phylo::Taxa::TaxaLinker.
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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perl v5.20.3 BIO::PHYLO::TAXA::TAXALINKER (3) 2014-02-08

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