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.

prune_taxa()

Removes taxa by name or object

 Type    : Method
 Title   : prune_taxa
 Usage   : $taxa->prune_taxa([$t1, $t2]);
 Function: Prunes taxa from the taxa object           
 Returns : A pruned Bio::Phylo::Taxa object.
 Args    : An array reference of taxa, either by name or as taxon 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:

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>