/ 
Bio-Phylo-0.17_RC8
/ Bio::Phylo::Project

NAME

Bio::Phylo::Project - Container object to collect related data

SYNOPSIS

use Bio::Phylo::Project;
use Bio::Phylo::Factory;
my $fac = Bio::Phylo::Factory->new;
my $proj = Bio::Phylo::Project->new;
$proj->insert($fac->create_taxa);
$proj->insert($fac->create_matrix);
$proj->insert($fac->create_forest)
print $proj->to_xml;

DESCRIPTION

The project module is used to collect taxa blocks, tree blocks and matrices.

METHODS

CONSTRUCTOR

new()

Project constructor.

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

ACCESSORS

get_taxa()

Getter for taxa objects

Type    : Constructor
Title   : get_taxa
Usage   : my $taxa = $proj->get_taxa;
Function: Getter for taxa objects
Returns : An array reference of taxa objects
Args    : NONE.
get_forests()

Getter for forest objects

Type    : Constructor
Title   : get_forests
Usage   : my $forest = $proj->get_forests;
Function: Getter for forest objects
Returns : An array reference of forest objects
Args    : NONE.
get_matrices()

Getter for matrix objects

Type    : Constructor
Title   : get_matrices
Usage   : my $matrix = $proj->get_matrices;
Function: Getter for matrix objects
Returns : An array reference of matrix objects
Args    : NONE.

SERIALIZERS

to_xml()

Serializes invocant to XML.

Type    : XML serializer
Title   : to_xml
Usage   : my $xml = $obj->to_xml;
Function: Serializes $obj to xml
Returns : An xml string
Args    : Same arguments as can be passed to individual contained objects
to_nexus()

Serializes invocant to NEXUS.

Type    : NEXUS serializer
Title   : to_nexus
Usage   : my $nexus = $obj->to_nexus;
Function: Serializes $obj to nexus
Returns : An nexus string
Args    : Same arguments as can be passed to individual contained objects

SEE ALSO

Bio::Phylo::Listable

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

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.

REVISION

$Id: Taxa.pm 604 2008-09-05 17:32:28Z rvos $