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Bio-Phylo-0.17_RC9
River stage two • 9 direct dependents • 18 total dependents
/ Bio::Phylo::Annotation

NAME

Bio::Phylo::Annotation - Single key/value annotation, used within dictionary

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>

DESCRIPTION

To comply with the NeXML standard (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 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: XML::DOM, XML::GDOME, XML::Twig, XML::DOM2, XML::DOMBacked, XML::Handler, XML::Element, XML::API, XML::Code or XML::XMLWriter. Alternatively, you can provide a RDF::Core::Model for semantic annotations or a Bio::Phylo::Dictionary to create recursively nested dictionaries.

METHODS

CONSTRUCTOR

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

MUTATORS

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.

ACCESSORS

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

SERIALIZERS

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:

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.

SUPERCLASS Bio::Phylo::Util::XMLWritable

Bio::Phylo::Annotation inherits from superclass Bio::Phylo::Util::XMLWritable. Below are the public methods (if any) from this superclass.

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
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_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.
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_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_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_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
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
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
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_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
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');
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_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)
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

SUPERCLASS Bio::Phylo

Bio::Phylo::Annotation inherits from superclass Bio::Phylo. Below are the public methods (if any) from this superclass.

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.
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';
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
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
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
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
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
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_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
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
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
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.
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( );
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.
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.
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_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

SEE ALSO

Bio::Phylo::Dictionary

Annotation objects are combined into a dictionary.

Bio::Phylo::Util::XMLWritable

This object inherits from Bio::Phylo::Util::XMLWritable, so methods defined there are also applicable here.

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.

REVISION

 $Id: Annotation.pm 844 2009-03-05 00:07:26Z rvos $