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

is_equal()

Tests whether the invocant and the argument are the same. Normally this is done by comparing object identifiers, but if the argument is not an object but a string then the string is taken to be a name with which to compare, e.g. $taxon->is_equal('Homo sapiens')

Type    : Test
Title   : is_equal
Usage   : if ( $obj->is_equal($other) ) { ... }
Function: Tests whether the invocant and the argument are the same
Returns : BOOLEAN
Args    : Object to compare with, or a string representing a
          name to compare with the invocant's name

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