/ 
Bio-Phylo-0.24
River stage two • 9 direct dependents • 18 total dependents
8 ++
/ Bio::Phylo::Project

NAME

Bio::Phylo::Project - Container for related data

SYNOPSIS

 use Bio::Phylo::Factory;
 my $fac  = Bio::Phylo::Factory->new;
 my $proj = $fac->create_project;
 my $taxa = $fac->create_taxa;
 $proj->insert($taxa);
 $proj->insert($fac->create_matrix->set_taxa($taxa));
 $proj->insert($fac->create_forest->set_taxa($taxa));
 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.
get_document()
 Type    : Serializer
 Title   : doc
 Usage   : $proj->get_document()
 Function: Creates a DOM Document object, containing the 
           present state of the project by default
 Returns : a Document object
 Args    : a DOM factory object
           Optional: pass 1 to obtain a document node without 
           content

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
to_dom()
 Type    : Serializer
 Title   : to_dom
 Usage   : $node->to_dom
 Function: Generates a DOM subtree from the invocant
           and its contained objects
 Returns : an XML::LibXML::Element object
 Args    : a DOM factory object

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: Project.pm 1302 2010-06-11 15:33:11Z rvos $