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Bio::Phylo::NeXML::WriUsereContributed Perl DocuBio::Phylo::NeXML::Writable(3)

NAME
       Bio::Phylo::NeXML::Writable - Superclass	for objects that serialize to
       NeXML

SYNOPSIS
	# no direct usage

DESCRIPTION
       This is the superclass for all objects that can be serialized to	NeXML
       (<http://www.nexml.org>).

METHODS
   MUTATORS
       set_namespaces()
	    Type    : Mutator
	    Title   : set_namespaces
	    Usage   : $obj->set_namespaces( 'dwc' => 'http://www.namespaceTBD.org/darwin2' );
	    Function: Adds one or more prefix/namespace	pairs
	    Returns : $self
	    Args    : One or more prefix/namespace pairs, as even-sized	list,
		      or as a hash reference, i.e.:
		      $obj->set_namespaces( 'dwc' => 'http://www.namespaceTBD.org/darwin2' );
		      or
		      $obj->set_namespaces( { 'dwc' => 'http://www.namespaceTBD.org/darwin2' } );
	    Notes   : This is a	global for the XMLWritable class, so that in a recursive
			      to_xml call the outermost	element	contains the namespace definitions.
			      This method can also be called as	a static class method, i.e.
			      Bio::Phylo::NeXML::Writable->set_namespaces(
			      'dwc' => 'http://www.namespaceTBD.org/darwin2');

       set_suppress_ns()
	    Type    : Mutator
	    Title   : set_suppress_ns
	    Usage   : $obj->set_suppress_ns();
	    Function: Tell this	object not to write namespace attributes
	    Returns :
	    Args    : none

       clear_suppress_ns()
	    Type    : Mutator
	    Title   : clear_suppress_ns
	    Usage   : $obj->clear_suppress_ns();
	    Function: Tell this	object to write	namespace attributes
	    Returns :
	    Args    : none

       add_meta()
	    Type    : Mutator
	    Title   : add_meta
	    Usage   : $obj->add_meta($meta);
	    Function: Adds a metadata attachment to the	object
	    Returns : $self
	    Args    : A	Bio::Phylo::NeXML::Meta	object

       remove_all_meta()
	    Type    : Mutator
	    Title   : remove_all_meta
	    Usage   : $obj->remove_all_meta();
	    Function: Removes all metadata attachments from the	object
	    Returns : $self
	    Args    : None

       remove_meta()
	    Type    : Mutator
	    Title   : remove_meta
	    Usage   : $obj->remove_meta($meta);
	    Function: Removes a	metadata attachment from the object
	    Returns : $self
	    Args    : Bio::Phylo::NeXML::Meta

       set_meta_object()
	    Type    : Mutator
	    Title   : set_meta_object
	    Usage   : $obj->set_meta_object($predicate => $object);
	    Function: Attaches a $predicate => $object pair to the invocant
	    Returns : $self
	    Args    : $predicate => (a valid curie of a	known namespace)
			  $object => (an object	value)

       set_meta()
	    Type    : Mutator
	    Title   : set_meta
	    Usage   : $obj->set_meta([ $m1, $m2, $m3 ]);
	    Function: Assigns all metadata objects
	    Returns : $self
	    Args    : An array ref of metadata objects

       set_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). For such objects,	id generation can be
	   explicitly disabled using this method.  Typically, this is done
	   internally -	you will probably never	use this method.

	    Type    : Mutator
	    Title   : set_identifiable
	    Usage   : $obj->set_identifiable(0);
	    Function: Enables/disables id generation
	    Returns : $self
	    Args    : BOOLEAN

       set_tag()
	   This	method is usually only used internally,	to define or alter the
	   name	of the tag into	which the object is serialized.	For example,
	   for a Bio::Phylo::Forest::Node object, this method would be called
	   with	the 'node' argument, so	that the object	is serialized into an
	   xml element structure called	<node/>

	    Type    : Mutator
	    Title   : set_tag
	    Usage   : $obj->set_tag('node');
	    Function: Sets the tag name
	    Returns : $self
	    Args    : A	tag name (must be a valid xml element name)

       set_name()
	   Sets	invocant name.

	    Type    : Mutator
	    Title   : set_name
	    Usage   : $obj->set_name($name);
	    Function: Assigns an object's name.
	    Returns : Modified object.
	    Args    : Argument must be a string. Ensure	that this string is safe to use	for
		      whatever output format you want to use (this differs between xml and
		      nexus, for example).

       set_attributes()
	   Assigns attributes for the element.

	    Type    : Mutator
	    Title   : set_attributes
	    Usage   : $obj->set_attributes( 'foo' => 'bar' )
	    Function: Sets the xml attributes for the object;
	    Returns : $self
	    Args    : key/value	pairs or a hash	ref

       set_xml_id()
	   This	method is usually only used internally,	to store the xml id of
	   an object as	it is parsed out of a nexml file - this	is for the
	   purpose of round-tripping nexml info	sets.

	    Type    : Mutator
	    Title   : set_xml_id
	    Usage   : $obj->set_xml_id('node345');
	    Function: Sets the xml id
	    Returns : $self
	    Args    : An xml id	(must be a valid xml NCName)

       set_base_uri()
	   This	utility	method can be used to set the xml:base attribute, i.e.
	   to specify a	location for the object's XML serialization that
	   potentially differs from the	physical location of the containing
	   document.

	    Type    : Mutator
	    Title   : set_base_uri
	    Usage   : $obj->set_base_uri('http://example.org');
	    Function: Sets the xml:base	attribute
	    Returns : $self
	    Args    : A	URI string

       set_link()
	   This	sets a clickable link, i.e. a url, for the object. This	has no
	   relation to the xml:base attribute, it is solely intended for
	   serializations that allow clickable links, such as SVG or RSS.

	    Type    : Mutator
	    Title   : set_link
	    Usage   : $node->set_link($url);
	    Function: Sets clickable link
	    Returns : $self
	    Args    : url

       unset_attribute()
	   Removes specified attribute

	    Type    : Mutator
	    Title   : unset_attribute
	    Usage   : $obj->unset_attribute( 'foo' )
	    Function: Removes the specified xml	attribute for the object
	    Returns : $self
	    Args    : an attribute name

   ACCESSORS
       get_namespaces()
	    Type    : Accessor
	    Title   : get_namespaces
	    Usage   : my %ns = %{ $obj->get_namespaces };
	    Function: Retrieves	the known namespaces
	    Returns : A	hash of	prefix/namespace key/value pairs, or
		      a	single namespace if a single, optional
		      prefix was provided as argument
	    Args    : Optional - a namespace prefix

       get_prefix_for_namespace()
	    Type    : Accessor
	    Title   : get_prefix_for_namespace
	    Usage   : my $prefix = $obj->get_prefix_for_namespace('http://example.org/')
	    Function: Retrieves	the prefix for the argument namespace
	    Returns : A	prefix string
	    Args    : A	namespace URI

       get_meta()
	   Retrieves the metadata for the element.

	    Type    : Accessor
	    Title   : get_meta
	    Usage   : my @meta = @{ $obj->get_meta };
	    Function: Retrieves	the metadata for the element.
	    Returns : An array ref of Bio::Phylo::NeXML::Meta objects
	    Args    : Optional:	a list of CURIE	predicates, in which case
		      the returned objects will	be those matching these
		      predicates

       get_meta_object()
	   Retrieves the metadata annotation object for	the provided predicate

	    Type    : Accessor
	    Title   : get_meta_object
	    Usage   : my $title	= $obj->get_meta_object('dc:title');
	    Function: Retrieves	the metadata annotation	value for the object.
	    Returns : An annotation value, i.e.	the object of a	triple
	    Args    : Required:	a CURIE	predicate for which the	annotation
		      value is returned
	    Note    : This method returns the object for the first annotation
		      with the provided	predicate. Keep	this in	mind when dealing
		      with an object that has multiple annotations with	the same
		      predicate.

       get_tag()
	   Retrieves tag name for the element.

	    Type    : Accessor
	    Title   : get_tag
	    Usage   : my $tag =	$obj->get_tag;
	    Function: Gets the xml tag name for	the object;
	    Returns : A	tag name
	    Args    : None.

       get_name()
	   Gets	invocant's name.

	    Type    : Accessor
	    Title   : get_name
	    Usage   : my $name = $obj->get_name;
	    Function: Returns the object's name.
	    Returns : A	string
	    Args    : None

       get_xml_tag()
	   Retrieves tag string

	    Type    : Accessor
	    Title   : get_xml_tag
	    Usage   : my $str =	$obj->get_xml_tag;
	    Function: Gets the xml tag for the object;
	    Returns : A	tag, i.e. pointy brackets
	    Args    : Optional:	a true value, to close an empty	tag

       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

       get_xml_id()
	   Retrieves xml id for	the element.

	    Type    : Accessor
	    Title   : get_xml_id
	    Usage   : my $id = $obj->get_xml_id;
	    Function: Gets the xml id for the object;
	    Returns : An xml id
	    Args    : None.

       get_base_uri()
	   This	utility	method can be used to get the xml:base attribute,
	   which specifies a location for the object's XML serialization that
	   potentially differs from the	physical location of the containing
	   document.

	   If no xml:base attribute has	been defined on	the focal object, this
	   method moves	on, recursively, to containing objects (e.g. from node
	   to tree to forest) until such time that a base URI has been found.

	    Type    : Mutator
	    Title   : get_base_uri
	    Usage   : my $base = $obj->get_base_uri;
	    Function: Gets the xml:base	attribute
	    Returns : A	URI string
	    Args    : None

       get_link()
	   This	returns	a clickable link for the object. This has no relation
	   to the xml:base attribute, it is solely intended for	serializations
	   that	allow clickable	links, such as SVG or RSS.

	    Type    : Accessor
	    Title   : get_link
	    Usage   : my $link = $obj->get_link();
	    Function: Returns a	clickable link
	    Returns : url
	    Args    : NONE

       get_dom_elt()
	    Type    : Serializer
	    Title   : get_dom_elt
	    Usage   : $obj->get_dom_elt
	    Function: Generates	a DOM element from the invocant
	    Returns : a	DOM element object (default XML::Twig)
	    Args    : DOM factory object

   TESTS
       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

       is_ns_suppressed()
	    Type    : Test
	    Title   : is_ns_suppressed
	    Usage   : if ( $obj->is_ns_suppressed ) { ... }
	    Function: Indicates	whether	namespace attributes should not
		      be written on XML	serialization
	    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    : None

       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.

       to_json()
	   Serializes object to	JSON string

	    Type    : Serializer
	    Title   : to_json()
	    Usage   : print $obj->to_json();
	    Function: Serializes object	to JSON	string
	    Returns : String
	    Args    : None
	    Comments:

       to_cdao()
	   Serializes object to	CDAO RDF/XML string

	    Type    : Serializer
	    Title   : to_cdao()
	    Usage   : print $obj->to_cdao();
	    Function: Serializes object	to CDAO	RDF/XML	string
	    Returns : String
	    Args    : None
	    Comments:

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

       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::Writable(3)

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

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