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

merge()

Project constructor.

 Type    : Constructor
 Title   : merge
 Usage   : my $project = Bio::Phylo::Project->merge( @projects )
 Function: Populates a Bio::Phylo::Project object from a list of projects
 Returns : A Bio::Phylo::Project object.
 Args    : A list of Bio::Phylo::Project objects to be merged

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

reset_xml_ids()

Resets all xml ids to default values

 Type    : Mutator
 Title   : reset_xml_ids
 Usage   : $project->reset_xml_ids
 Function: Resets all xml ids to default values
 Returns : A Bio::Phylo::Project object.
 Args    : None

ACCESSORS

get_taxa()

Getter for taxa objects

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

get_items()

Gets all items of the specified type, recursively. This method can be used to get things like all the trees in all the forest objects as one flat list (or, indeed, all nodes, all taxon objects, etc.)

 Type    : Accessor
 Title   : get_items
 Usage   : my @nodes = @{ $proj->get_items(_NODE_) };
 Function: Getter for items of specified type
 Returns : An array reference of objects
 Args    : A type constant as defined in Bio::Phylo::Util::CONSTANT

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

There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.

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