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Bio::Phylo::NeXML::MetUser Contributed Perl DocumentBio::Phylo::NeXML::Meta(3)

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>

perl v5.24.1			  2014-02-08	    Bio::Phylo::NeXML::Meta(3)

NAME | SYNOPSIS | DESCRIPTION | METHODS | SEE ALSO | CITATION

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