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

MUTATORS

set_datasource()

Project constructor.

Type    : Constructor
Title   : set_datasource
Usage   : $project->set_datasource( -file => $file, -format => 'nexus' )
Function: Populates a Bio::Phylo::Project object from a data source
Returns : A Bio::Phylo::Project object.
Args    : Arguments as must be passed to Bio::Phylo::IO::parse

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

get_attributes()

Retrieves attributes for the element.

Type    : Accessor
Title   : get_attributes
Usage   : my %attrs = %{ $obj->get_attributes };
Function: Gets the xml attributes for the object;
Returns : A hash reference
Args    : None.
Comments: throws ObjectMismatch if no linked taxa object 
          can be found

is_identifiable()

By default, all XMLWritable objects are identifiable when serialized, i.e. they have a unique id attribute. However, in some cases a serialized object may not have an id attribute (governed by the nexml schema). This method indicates whether that is the case.

Type    : Test
Title   : is_identifiable
Usage   : if ( $obj->is_identifiable ) { ... }
Function: Indicates whether IDs are generated
Returns : BOOLEAN
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

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.

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

REVISION

$Id: Project.pm 1660 2011-04-02 18:29:40Z rvos $