NAME

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

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:

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