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

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NAME

Bio::Phylo::Taxa - Container of taxon objects

CONTENTS

SYNOPSIS



 use Bio::Phylo::Factory;
 my $fac = Bio::Phylo::Factory->new;

 # A mesquite-style default
 # taxa block for 10 taxa.
 my $taxa  = $fac->create_taxa;
 for my $i ( 1 .. 10 ) {
     $taxa->insert( $fac->create_taxon( -name => "taxon_${i}" ) );
 }

 # prints a taxa block in nexus format
 print $taxa->to_nexus;



DESCRIPTION

The Bio::Phylo::Taxa object models a set of operational taxonomic units. The object subclasses the Bio::Phylo::Listable object, and so the filtering methods of that class are available.

A taxa object can link to multiple forest and matrix objects.

METHODS

    CONSTRUCTOR

new() Taxa constructor.



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



    MUTATORS

set_forest() Sets associated Bio::Phylo::Forest object.



 Type    : Mutator
 Title   : set_forest
 Usage   : $taxa->set_forest( $forest );
 Function: Associates forest with the
           invocant taxa object (i.e.
           creates reference).
 Returns : Modified object.
 Args    : A Bio::Phylo::Forest object
 Comments: A taxa object can link to multiple
           forest and matrix objects.



set_matrix() Sets associated Bio::Phylo::Matrices::Matrix object.



 Type    : Mutator
 Title   : set_matrix
 Usage   : $taxa->set_matrix($matrix);
 Function: Associates matrix with the
           invocant taxa object (i.e.
           creates reference).
 Returns : Modified object.
 Args    : A Bio::Phylo::Matrices::Matrix object
 Comments: A taxa object can link to multiple
           forest and matrix objects.



unset_forest() Removes association with argument Bio::Phylo::Forest object.



 Type    : Mutator
 Title   : unset_forest
 Usage   : $taxa->unset_forest($forest);
 Function: Disassociates forest from the
           invocant taxa object (i.e.
           removes reference).
 Returns : Modified object.
 Args    : A Bio::Phylo::Forest object



unset_matrix() Removes association with Bio::Phylo::Matrices::Matrix object.



 Type    : Mutator
 Title   : unset_matrix
 Usage   : $taxa->unset_matrix($matrix);
 Function: Disassociates matrix from the
           invocant taxa object (i.e.
           removes reference).
 Returns : Modified object.
 Args    : A Bio::Phylo::Matrices::Matrix object



    ACCESSORS

get_forests() Gets all associated Bio::Phylo::Forest objects.



 Type    : Accessor
 Title   : get_forests
 Usage   : @forests = @{ $taxa->get_forests };
 Function: Retrieves forests associated
           with the current taxa object.
 Returns : An ARRAY reference of
           Bio::Phylo::Forest objects.
 Args    : None.



get_matrices() Gets all associated Bio::Phylo::Matrices::Matrix objects.



 Type    : Accessor
 Title   : get_matrices
 Usage   : @matrices = @{ $taxa->get_matrices };
 Function: Retrieves matrices associated
           with the current taxa object.
 Returns : An ARRAY reference of
           Bio::Phylo::Matrices::Matrix objects.
 Args    : None.



get_ntax() Gets number of contained Bio::Phylo::Taxa::Taxon objects.



 Type    : Accessor
 Title   : get_ntax
 Usage   : my $ntax = $taxa->get_ntax;
 Function: Retrieves the number of taxa for the invocant.
 Returns : INT
 Args    : None.
 Comments:



    METHODS

merge_by_name() Merges argument Bio::Phylo::Taxa object with invocant.



 Type    : Method
 Title   : merge_by_name
 Usage   : $merged = $taxa->merge_by_name($other_taxa);
 Function: Merges two or more taxa objects such that
           internally different taxon objects
           with the same name become a single
           object with the combined references
           to datum objects and node objects
           contained by the two.          
 Returns : A merged Bio::Phylo::Taxa object.
 Args    : Bio::Phylo::Taxa objects.



merge_by_meta() Merges argument Bio::Phylo::Taxa object with invocant.



 Type    : Method
 Title   : merge_by_meta
 Usage   : $taxa->merge_by_name(dc:identifier,$other_taxa);
 Function: Merges two taxa objects such that
           internally different taxon objects
           with the same annotation value become
           a single object with the combined references
           to datum objects, node objects and
           metadata annotations contained by
           the two.          
 Returns : A merged Bio::Phylo::Taxa object.
 Args    : a CURIE predicate and Bio::Phylo::Taxa objects.



to_nexus() Serializes invocant to nexus format.



 Type    : Format convertor
 Title   : to_nexus
 Usage   : my $block = $taxa->to_nexus;
 Function: Converts $taxa into a nexus taxa block.
 Returns : Nexus taxa block (SCALAR).
 Args    : -links => 1 (optional, adds TITLE token)
 Comments:



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::Listable The Bio::Phylo::Taxa object inherits from the Bio::Phylo::Listable object. Look there for more methods applicable to the taxa 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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