NAME

Bio::Phylo::NeXML::Meta - Single predicate/object annotation, attached to an xml-writable subject

SYNOPSIS

 use Bio::Phylo::Factory;
 use Bio::Phylo::Util::CONSTANT ':namespaces';
 my $fac = Bio::Phylo::Factory->new;
 my $url = 'http://purl.org/phylo/treebase/phylows/study/TB2:S1787';
 my $proj = $fac->create_project->add_meta(
     $fac->create_meta(
         '-namespaces' => { 'cdao' => _NS_CDAO_ },
         '-triple'     => { 
             'cdao:hasMeta' => $fac->create_meta(
                 '-namespaces' => { 'cdao' => _NS_CDAO_ },
                 '-triple'     => { 'cdao:has_External_Reference' => $url }
             )
         }
     )
 );

DESCRIPTION

To comply with the NeXML standard (http://www.nexml.org), Bio::Phylo implements metadata annotations which consist conceptually of RDF triples where the subject is a container object that subclasses Bio::Phylo::NeXML::Writable, and the predicate and object are defined in this class.

The objects of the triples provided by this class can be of any simple type (string, number) or one of XML::DOM, XML::GDOME, XML::LibXML, XML::Twig, XML::DOM2, XML::DOMBacked, XML::Handler, XML::Element, XML::API, XML::Code or XML::XMLWriter or RDF::Core::Model.

When serialized, the Bio::Phylo::NeXML::Meta object in NeXML is typically written out as an element called 'meta', with RDFa compliant attributes.

METHODS

CONSTRUCTOR

new()

 Type    : Constructor
 Title   : new
 Usage   : my $anno = Bio::Phylo::NeXML::Meta->new;
 Function: Initializes a Bio::Phylo::NeXML::Meta object.
 Returns : A Bio::Phylo::NeXML::Meta object.
 Args    : optional constructor arguments are key/value
                   pairs where the key corresponds with any of
                   the methods that starts with set_ (i.e. mutators) 
                   and the value is the permitted argument for such 
                   a method. The method name is changed such that,
                   in order to access the set_value($val) method
                   in the constructor, you would pass -value => $val

MUTATORS

set_triple()

Populates the triple, assuming that the invocant is attached to a subject.

 Type    : Mutator
 Title   : set_triple
 Usage   : $meta->set_triple( $predicate, $object );
 Function: Populates the triple.
 Returns : Modified object.
 Args    : $predicate - a CURIE whose namespace prefix must 
                        have been bound previously using 
                        $meta->set_namespaces( $prefix, $uri );
           $object    - any of the valid object types: a number,
                        a string, a url, a nested annotation
                        or anything that can be adapted by
                        Bio::Phylo::NeXML::Meta::XMLLiteral 

ACCESSORS

get_triple ()

Returns predicate and object for the triple

 Type    : Accessor
 Title   : get_triple
 Usage   : my ( $predicate, $object ) = $anno->get_triple;
 Function: Returns triple
 Returns : Predicate and object of a triple
 Args    : NONE

get_object()

Returns triple object

 Type    : Accessor
 Title   : get_object
 Usage   : my $val = $anno->get_object;
 Function: Returns triple object
 Returns : A triple object
 Args    : NONE

get_predicate()

Returns triple predicate

 Type    : Accessor
 Title   : get_predicate
 Usage   : my $val = $anno->get_predicate;
 Function: Returns triple predicate
 Returns : A triple predicate
 Args    : NONE

get_predicate_namespace()

Returns predicate namespace

 Type    : Accessor
 Title   : get_predicate_namespace
 Usage   : my $val = $anno->get_predicate_namespace;
 Function: Returns predicate namespace
 Returns : A namespace
 Args    : NONE

get_predicate_local()

Returns predicate without prefix

 Type    : Accessor
 Title   : get_predicate_local
 Usage   : my $val = $anno->get_predicate_local;
 Function: Returns predicate without prefix
 Returns : A predicate
 Args    : NONE

get_object_type()

Returns data type of object

 Type    : Accessor
 Title   : get_object_type
 Usage   : my $val = $anno->get_object_type;
 Function: Returns data type of object
 Returns : A local predicate, e.g. 'boolean'
 Args    : NONE

TESTS

is_resource()

Returns whether the object is a resource (e.g. an href or a nested XMLLiteral)

 Type    : Accessor
 Title   : is_resource
 Usage   : my $val = $anno->is_resource;
 Function: Returns whether object is a resource
 Returns : Boolean
 Args    : NONE

is_xml_literal()

Returns whether the object is a nested XMLLiteral

 Type    : Accessor
 Title   : is_xml_literal
 Usage   : my $val = $anno->is_xml_literal;
 Function: Returns whether object is a nested XMLLiteral
 Returns : Boolean
 Args    : NONE

SERIALIZERS

to_dom()

 Type    : Serializer
 Title   : to_dom
 Usage   : $obj->to_dom
 Function: Generates a DOM subtree from the invocant and
           its contained objects
 Returns : a DOM element object (default: XML::Twig flavor)
 Args    : DOM factory object
 Note    : This is the generic function. It is redefined in the 
           classes below.

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::Dictionary

Annotation objects are combined into a dictionary.

Bio::Phylo::NeXML::Writable

This object inherits from Bio::Phylo::NeXML::Writable, so methods defined there are also applicable here.

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