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_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

REVISION

 $Id: Project.pm 1131 2009-06-16 10:49:21Z rvos $

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