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: This is a description =head1 DESCRIPTION To comply with the NeXML standard (L), 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. 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, L, L, L, L, L, L, L, L or L. Alternatively, you can provide a L for semantic annotations or a L 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 . ""; 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. 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 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. 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 Annotation objects are combined into a dictionary. =item L This object inherits from L, so methods defined there are also applicable here. =item L Also see the manual: L and L. =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;