package Bio::Phylo::Annotation;
use strict;
use Bio::Phylo::Util::XMLWritable;
use Bio::Phylo::Util::CONSTANT qw(_ANNOTATION_ _DICTIONARY_);
use vars '@ISA';
use UNIVERSAL qw'can isa';
use Bio::Phylo::Util::Exceptions 'throw';
@ISA=qw(Bio::Phylo::Util::XMLWritable);
{
my @fields = \( my ( %key, %datatype, %value ) );
my $TYPE_CONSTANT = _ANNOTATION_;
my $CONTAINER_CONSTANT = _DICTIONARY_;
=head1 NAME
Bio::Phylo::Annotation - Single key/value annotation, used within dictionary
=head1 SYNOPSIS
use Bio::Phylo::Factory;
my $fac = Bio::Phylo::Factory->new;
# there are several data types: string, integer, float, uri, any, etc.
# refer to nexml.org for a complete list
my $dic = $fac->create_dictionary( -tag => 'string' );
my $ann = $fac->create_annotation( -value => 'This is a description' );
$dic->insert( $ann );
print $dic->to_xml;
# prints: <dict><string id="string2">This is a description</string></dict>
=head1 DESCRIPTION
To comply with the NeXML standard (L<http://www.nexml.org>), Bio::Phylo implements
dictionary annotations, which consist conceptually of key/value pairs where the
key is an xml id (which is either autogenerated or can be set using the set_xml_id
method) and the value is the containing element (whose name specifies the data
type of its text contents, i.e. string, integer, float and so on).
This class implements a single key/value pair, of which multiples can be inserted
in a dictionary to create a data structure that is serialized to something akin
to a hash. The dictionary can be attached to any of the subclasses of
L<Bio::Phylo::Util::XMLWritable>.
Of note is the fact that annotations can has different xml tag names, where the
name specifies the data type of the annotation text content. For example, if you
set the tag name to 'string' (i.e. $ann->set_tag('string')) then the value is
interpreted to be a string (i.e. $ann->set_value('some kind of string')). Also,
a common tag name is 'any', which means that the value is any kind of xml structure,
which can be provided as a raw string, or as an xml element tree object of one of
the following distributions: L<XML::DOM>, L<XML::GDOME>, L<XML::Twig>, L<XML::DOM2>,
L<XML::DOMBacked>, L<XML::Handler>, L<XML::Element>, L<XML::API>, L<XML::Code> or
L<XML::XMLWriter>. Alternatively, you can provide a L<RDF::Core::Model> for
semantic annotations or a L<Bio::Phylo::Dictionary> to create recursively nested
dictionaries.
=head1 METHODS
=head2 CONSTRUCTOR
=over
=item new()
Type : Constructor
Title : new
Usage : my $anno = Bio::Phylo::Annotation->new;
Function: Initializes a Bio::Phylo::Annotation object.
Returns : A Bio::Phylo::Annotation object.
Args : optional constructor arguments are key/value
pairs where the key corresponds with any of
the methods that starts with set_ (i.e. mutators)
and the value is the permitted argument for such
a method. The method name is changed such that,
in order to access the set_value($val) method
in the constructor, you would pass -value => $val
=cut
sub new {
return shift->SUPER::new( '-tag' => 'string', @_ );
}
=back
=head2 MUTATORS
=over
=item set_value()
Sets the annotation value, e.g. for an annotation with tag 'string',
this would be a free form string, such as a description.
Type : Mutator
Title : set_value
Usage : $anno->set_value('this is a description');
Function: Sets the annotation value
Returns : Modified object.
Args : A valid argument is whatever is valid for the annotation
data type.
=cut
sub set_value {
my ( $self, $value ) = @_;
$value{ $self->get_id } = $value;
return $self;
}
=back
=head2 ACCESSORS
=over
=item get_value()
Gets invocant's value.
Type : Accessor
Title : get_value
Usage : my $val = $anno->get_value;
Function: Gets invocant's value.
Returns : The specified value, whose data type depends on the
xml tag name.
Args : NONE
=cut
sub get_value {
my $self = shift;
return $value{ $self->get_id };
}
=back
=head2 SERIALIZERS
=over
=item to_xml()
Serializes object to an xml string
Type : Serializer
Title : to_xml()
Usage : print $ann->to_xml();
Function: Serializes object to xml string
Returns : String
Args : None
Comments:
=cut
sub to_xml {
my $self = shift;
my $key = $self->get_xml_id;
my $xml = '';
my $value = $self->get_value;
if ( ref($value) ) {
# for RDF::Core::Model objects
if ( isa($value, 'RDF::Core::Model') ) {
eval {
require RDF::Core::Model::Serializer;
my $serialized_model = '';
my $serializer = RDF::Core::Model::Serializer->new(
'Model' => $value,
'Output' => \$serialized_model,
# BaseURI => 'URI://BASE/',
);
$value = $serialized_model;
};
if ( $@ ) {
throw 'API' => $@;
}
}
# for XML::XMLWriter object
elsif ( isa($value, 'XML::XMLWriter') ) {
$value = $value->get;
}
else {
my $concatenated = '';
my ( @values, @raw_values );
if ( ref($value) eq 'ARRAY' ) {
@values = @{ $value };
}
else {
push @values, $value;
}
for my $v ( @values ) {
# duck-typing
# Bio::Phylo => to_xml, XML::DOM,XML::GDOME => toString, XML::Twig => sprint
# XML::DOM2 => xmlify, XML::DOMBacked => as_xml,
# XML::Handler => dump_tree, XML::Element => as_XML
# XML::API => _as_string, XML::Code => code
if ( ref($v) ) {
my @methods = qw(to_xml toString sprint _as_string code xmlify as_xml dump_tree as_XML);
SERIALIZER: for my $method ( @methods ) {
if ( can($v,$method) ) {
$concatenated .= $v->$method;
last SERIALIZER;
}
}
}
else {
push @raw_values, $v;
}
}
$value = scalar(@raw_values) ? join(' ',@raw_values) : $concatenated;
}
}
my $type = $self->get_tag;
$xml .= "<${type} id=\"${key}\">" . $value . "</${type}>";
return $xml;
}
=back
=cut
# podinherit_insert_token
# podinherit_start_token_do_not_remove
# AUTOGENERATED pod created by /Users/rvosa/Applications/podinherit on Wed Mar 4 17:13:19 2009
# DO NOT EDIT the code below, rerun /Users/rvosa/Applications/podinherit instead.
=pod
=head1 INHERITED METHODS
Bio::Phylo::Annotation inherits from one or more superclasses. This means that objects of
class Bio::Phylo::Annotation also "do" the methods from the superclasses in addition to the
ones implemented in this class. Below is the documentation for those additional
methods, organized by superclass.
=head2 SUPERCLASS Bio::Phylo::Util::XMLWritable
Bio::Phylo::Annotation inherits from superclass L<Bio::Phylo::Util::XMLWritable>.
Below are the public methods (if any) from this superclass.
=over
=item add_dictionary()
Type : Mutator
Title : add_dictionary
Usage : $obj->add_dictionary($dict);
Function: Adds a dictionary attachment to the object
Returns : $self
Args : Bio::Phylo::Dictionary
=item 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
=item get_dictionaries()
Retrieves the dictionaries for the element.
Type : Accessor
Title : get_dictionaries
Usage : my @dicts = @{ $obj->get_dictionaries };
Function: Retrieves the dictionaries for the element.
Returns : An array ref of Bio::Phylo::Dictionary objects
Args : None.
=item 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
=item 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.
=item 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.
=item 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
=item 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
=item remove_dictionary()
Type : Mutator
Title : remove_dictionary
Usage : $obj->remove_dictionary($dict);
Function: Removes a dictionary attachment from the object
Returns : $self
Args : Bio::Phylo::Dictionary
=item 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
=item 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_tag(0);
Function: Enables/disables id generation
Returns : $self
Args : BOOLEAN
=item 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::Util::XMLWritable->set_namespaces(
'dwc' => 'http://www.namespaceTBD.org/darwin2');
=item 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)
=item 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)
=item 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
=back
=head2 SUPERCLASS Bio::Phylo
Bio::Phylo::Annotation inherits from superclass L<Bio::Phylo>.
Below are the public methods (if any) from this superclass.
=over
=item clone()
Clones invocant.
Type : Utility method
Title : clone
Usage : my $clone = $object->clone;
Function: Creates a copy of the invocant object.
Returns : A copy of the invocant.
Args : None.
Comments: Cloning is currently experimental, use with caution.
=item get()
Attempts to execute argument string as method on invocant.
Type : Accessor
Title : get
Usage : my $treename = $tree->get('get_name');
Function: Alternative syntax for safely accessing
any of the object data; useful for
interpolating runtime $vars.
Returns : (context dependent)
Args : a SCALAR variable, e.g. $var = 'get_name';
=item get_desc()
Gets invocant description.
Type : Accessor
Title : get_desc
Usage : my $desc = $obj->get_desc;
Function: Returns the object's description (if any).
Returns : A string
Args : None
=item get_generic()
Gets generic hashref or hash value(s).
Type : Accessor
Title : get_generic
Usage : my $value = $obj->get_generic($key);
or
my %hash = %{ $obj->get_generic() };
Function: Returns the object's generic data. If an
argument is used, it is considered a key
for which the associated value is returned.
Without arguments, a reference to the whole
hash is returned.
Returns : A string or hash reference.
Args : None
=item get_id()
Gets invocant's UID.
Type : Accessor
Title : get_id
Usage : my $id = $obj->get_id;
Function: Returns the object's unique ID
Returns : INT
Args : None
=item get_internal_name()
Gets invocant's 'fallback' name (possibly autogenerated).
Type : Accessor
Title : get_internal_name
Usage : my $name = $obj->get_internal_name;
Function: Returns the object's name (if none was set, the name
is a combination of the $obj's class and its UID).
Returns : A string
Args : None
=item get_logger()
Gets a logger object.
Type : Accessor
Title : get_logger
Usage : my $logger = $obj->get_logger;
Function: Returns a Bio::Phylo::Util::Logger object
Returns : Bio::Phylo::Util::Logger
Args : None
=item 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
=item get_obj_by_id()
Attempts to fetch an in-memory object by its UID
Type : Accessor
Title : get_obj_by_id
Usage : my $obj = Bio::Phylo->get_obj_by_id($uid);
Function: Fetches an object from the IDPool cache
Returns : A Bio::Phylo object
Args : A unique id
=item get_score()
Gets invocant's score.
Type : Accessor
Title : get_score
Usage : my $score = $obj->get_score;
Function: Returns the object's numerical score (if any).
Returns : A number
Args : None
=item new()
The Bio::Phylo root constructor, is rarely used directly. Rather, many other
objects in Bio::Phylo internally go up the inheritance tree to this constructor.
The arguments shown here can therefore also be passed to any of the child
classes' constructors, which will pass them on up the inheritance tree. Generally,
constructors in Bio::Phylo subclasses can process as arguments all methods that
have set_* in their names. The arguments are named for the methods, but "set_"
has been replaced with a dash "-", e.g. the method "set_name" becomes the
argument "-name" in the constructor.
Type : Constructor
Title : new
Usage : my $phylo = Bio::Phylo->new;
Function: Instantiates Bio::Phylo object
Returns : a Bio::Phylo object
Args : Optional, any number of setters. For example,
Bio::Phylo->new( -name => $name )
will call set_name( $name ) internally
=item set_desc()
Sets invocant description.
Type : Mutator
Title : set_desc
Usage : $obj->set_desc($desc);
Function: Assigns an object's description.
Returns : Modified object.
Args : Argument must be a string.
=item set_generic()
Sets generic key/value pair(s).
Type : Mutator
Title : set_generic
Usage : $obj->set_generic( %generic );
Function: Assigns generic key/value pairs to the invocant.
Returns : Modified object.
Args : Valid arguments constitute:
* key/value pairs, for example:
$obj->set_generic( '-lnl' => 0.87565 );
* or a hash ref, for example:
$obj->set_generic( { '-lnl' => 0.87565 } );
* or nothing, to reset the stored hash, e.g.
$obj->set_generic( );
=item 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, will be single
quoted if it contains [;|,|:\(|\)]
or spaces. Preceding and trailing spaces
will be removed.
=item set_score()
Sets invocant score.
Type : Mutator
Title : set_score
Usage : $obj->set_score($score);
Function: Assigns an object's numerical score.
Returns : Modified object.
Args : Argument must be any of
perl's number formats, or undefined
to reset score.
=item 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:
=item to_string()
Serializes object to general purpose string
Type : Serializer
Title : to_string()
Usage : print $obj->to_string();
Function: Serializes object to general purpose string
Returns : String
Args : None
Comments: This is YAML
=back
=cut
# podinherit_stop_token_do_not_remove
=head1 SEE ALSO
=over
=item L<Bio::Phylo::Dictionary>
Annotation objects are combined into a dictionary.
=item L<Bio::Phylo::Util::XMLWritable>
This object inherits from L<Bio::Phylo::Util::XMLWritable>, so methods
defined there are also applicable here.
=item L<Bio::Phylo::Manual>
Also see the manual: L<Bio::Phylo::Manual> and L<http://rutgervos.blogspot.com>.
=back
=head1 REVISION
$Id: Annotation.pm 844 2009-03-05 00:07:26Z rvos $
=cut
sub _type { $TYPE_CONSTANT }
sub _container { $CONTAINER_CONSTANT }
sub _cleanup {
my $self = shift;
my $id = $self->get_id;
for my $field ( @fields ) {
delete $field->{$id};
}
}
}
1;