NAME
Bio::Phylo::Taxa - An object-oriented module for managing taxa.
SYNOPSIS
use
Bio::Phylo::Taxa;
# A mesquite-style default
# taxa block for 10 taxa.
my
$taxa
= Bio::Phylo::Taxa->new;
for
my
$i
( 1 .. 10 ) {
my
$taxon
= Bio::Phylo::Taxa::Taxon->new(
'-name'
=>
'taxon_'
.
$i
,
);
$taxa
->insert(
$taxon
);
}
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()
-
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()
-
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()
-
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()
-
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()
-
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()
-
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()
-
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()
-
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()
-
Type : Method
Title : merge_by_name
Usage :
$taxa
->merge_by_name(
$other_taxa
);
Function: Merges two 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 : A Bio::Phylo::Taxa object.
DESTRUCTOR
- DESTROY()
-
Type : Destructor
Title : DESTROY
Usage :
$phylo
->DESTROY
Function: Destroys Phylo object
Alias :
Returns : TRUE
Args : none
Comments: You don't really need this,
it is called automatically
when
the object goes out of scope.
SEE ALSO
- 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.
FORUM
CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo
BUGS
Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org
, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:
$Id: Taxa.pm 1721 2006-07-20 03:43:06Z rvosa $
AUTHOR
Rutger Vos,
- email:
rvosa@sfu.ca
- web page: http://www.sfu.ca/~rvosa/
ACKNOWLEDGEMENTS
The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.
COPYRIGHT & LICENSE
Copyright 2005 Rutger Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.