# $Id: Taxon.pm 844 2009-03-05 00:07:26Z rvos $ package Bio::Phylo::Taxa::Taxon; use strict; use Bio::Phylo::Util::XMLWritable; use Bio::Phylo::Util::CONSTANT qw(_DATUM_ _NODE_ _TAXON_ _TAXA_ looks_like_object); use Bio::Phylo::Mediators::TaxaMediator; use vars qw(@ISA); # classic @ISA manipulation, not using 'base' @ISA = qw(Bio::Phylo::Util::XMLWritable); { my $TYPE_CONSTANT = _TAXON_; my $CONTAINER_CONSTANT = _TAXA_; my $DATUM_CONSTANT = _DATUM_; my $NODE_CONSTANT = _NODE_; my $logger = __PACKAGE__->get_logger; my $mediator = 'Bio::Phylo::Mediators::TaxaMediator'; =head1 NAME Bio::Phylo::Taxa::Taxon - Operational taxonomic unit =head1 SYNOPSIS use Bio::Phylo::IO qw(parse); use Bio::Phylo::Factory; my $fac = Bio::Phylo::Factory->new; # array of names my @apes = qw( Homo_sapiens Pan_paniscus Pan_troglodytes Gorilla_gorilla ); # newick string my $str = '(((Pan_paniscus,Pan_troglodytes),'; $str .= 'Homo_sapiens),Gorilla_gorilla);'; # create tree object my $tree = parse( -format => 'newick', -string => $str )->first; # instantiate taxa object my $taxa = $fac->create_taxa; # instantiate taxon objects, insert in taxa object foreach( @apes ) { my $taxon = $fac->create_taxon( -name => $_, ); $taxa->insert($taxon); } # crossreference tree and taxa $tree->crossreference($taxa); # iterate over nodes while ( my $node = $tree->next ) { # check references if ( $node->get_taxon ) { # prints crossreferenced tips print "match: ", $node->get_name, "\n"; } } =head1 DESCRIPTION The taxon object models a single operational taxonomic unit. It is useful for cross-referencing datum objects and tree nodes. =head1 METHODS =head2 CONSTRUCTOR =over =item new() Taxon constructor. Type : Constructor Title : new Usage : my $taxon = Bio::Phylo::Taxa::Taxon->new; Function: Instantiates a Bio::Phylo::Taxa::Taxon object. Returns : A Bio::Phylo::Taxa::Taxon object. Args : none. =cut sub new { # could be child class my $class = shift; # notify user $logger->info("constructor called for '$class'"); # go up inheritance tree, eventually get an ID return $class->SUPER::new( '-tag' => 'otu', @_ ); } =back =head2 MUTATORS =over =item set_data() Associates argument data with invocant. Type : Mutator Title : set_data Usage : $taxon->set_data( $datum ); Function: Associates data with the current taxon. Returns : Modified object. Args : Must be an object of type Bio::Phylo::Matrices::Datum =cut sub set_data { my ( $self, $datum ) = @_; if ( looks_like_object $datum, $DATUM_CONSTANT ) { $mediator->set_link( '-one' => $self, '-many' => $datum, ); } return $self; } =item set_nodes() Associates argument node with invocant. Type : Mutator Title : set_nodes Usage : $taxon->set_nodes($node); Function: Associates tree nodes with the current taxon. Returns : Modified object. Args : A Bio::Phylo::Forest::Node object =cut sub set_nodes { my ( $self, $node ) = @_; if ( looks_like_object $node, $NODE_CONSTANT ) { $mediator->set_link( '-one' => $self, '-many' => $node, ); } return $self; } =item unset_datum() Removes association between argument data and invocant. Type : Mutator Title : unset_datum Usage : $taxon->unset_datum($node); Function: Disassociates datum from the invocant taxon (i.e. removes reference). Returns : Modified object. Args : A Bio::Phylo::Matrix::Datum object =cut sub unset_datum { my ( $self, $datum ) = @_; $mediator->remove_link( '-one' => $self, '-many' => $datum, ); return $self; } =item unset_node() Removes association between argument node and invocant. Type : Mutator Title : unset_node Usage : $taxon->unset_node($node); Function: Disassociates tree node from the invocant taxon (i.e. removes reference). Returns : Modified object. Args : A Bio::Phylo::Forest::Node object =cut sub unset_node { my ( $self, $node ) = @_; $mediator->remove_link( '-one' => $self, '-many' => $node, ); return $self; } =back =head2 ACCESSORS =over =item get_data() Retrieves associated datum objects. Type : Accessor Title : get_data Usage : @data = @{ $taxon->get_data }; Function: Retrieves data associated with the current taxon. Returns : An ARRAY reference of Bio::Phylo::Matrices::Datum objects. Args : None. =cut sub get_data { my $self = shift; return $mediator->get_link( '-source' => $self, '-type' => $DATUM_CONSTANT, ); } =item get_nodes() Retrieves associated node objects. Type : Accessor Title : get_nodes Usage : @nodes = @{ $taxon->get_nodes }; Function: Retrieves tree nodes associated with the current taxon. Returns : An ARRAY reference of Bio::Phylo::Trees::Node objects Args : None. =cut sub get_nodes { my $self = shift; return $mediator->get_link( '-source' => $self, '-type' => $NODE_CONSTANT, ); } =begin comment Taxon destructor. Type : Destructor Title : DESTROY Usage : $phylo->DESTROY Function: Destroys Phylo object Alias : Returns : TRUE Args : none Comments: You don't really need this, it is called automatically when the object goes out of scope. =end comment =cut sub DESTROY { my $self = shift; # notify user #$logger->debug("destructor called for '$self'"); # recurse up inheritance tree for cleanup $self->SUPER::DESTROY; } =begin comment Type : Internal method Title : _container Usage : $taxon->_container; Function: Returns : CONSTANT Args : =end comment =cut sub _container { $CONTAINER_CONSTANT } =begin comment Type : Internal method Title : _type Usage : $taxon->_type; Function: Returns : CONSTANT Args : =end comment =cut sub _type { $TYPE_CONSTANT } =back =cut # podinherit_insert_token # podinherit_start_token_do_not_remove # AUTOGENERATED pod created by /Users/rvosa/Applications/podinherit on Wed Mar 4 17:13:57 2009 # DO NOT EDIT the code below, rerun /Users/rvosa/Applications/podinherit instead. =pod =head1 INHERITED METHODS Bio::Phylo::Taxa::Taxon inherits from one or more superclasses. This means that objects of class Bio::Phylo::Taxa::Taxon 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::Taxa::Taxon 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::Taxa::Taxon 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 The taxon objects inherits from the L object. The methods defined there are also applicable to the taxon object. =item L Also see the manual: L and L. =back =head1 REVISION $Id: Taxon.pm 844 2009-03-05 00:07:26Z rvos $ =cut } 1;