NAME

Bio::Phylo::Forest - Container for tree objects

SYNOPSIS

use Bio::Phylo::Factory;
my $fac = Bio::Phylo::Factory->new;
my $forest = $fac->create_forest;
my $tree = $fac->create_tree;
$forest->insert($tree);
print $forest->to_nexus;

DESCRIPTION

The Bio::Phylo::Forest object models a set of trees. The object subclasses the Bio::Phylo::Listable object, so look there for more methods available to forest objects.

METHODS

CONSTRUCTOR

new()

Forest constructor.

Type    : Constructor
Title   : new
Usage   : my $trees = Bio::Phylo::Forest->new;
Function: Instantiates a Bio::Phylo::Forest object.
Returns : A Bio::Phylo::Forest object.
Args    : None required, though see the superclass
          Bio::Phylo::Listable from which this
          object inherits.

METHODS

insert()

Inserts trees in forest.

Type    : Method
Title   : insert
Usage   : $trees->insert( $tree1, $tree2, ... );
Function: Inserts trees in forest.
Returns : A Bio::Phylo::Forest object.
Args    : Trees
Comment : The last seen tree that is set as default
          becomes the default for the entire forest

get_default_tree()

Gets the default tree in the forest.

Type    : Method
Title   : get_default_tree
Usage   : my $tree = $trees->get_default_tree;
Function: Gets the default tree in the forest.
Returns : A Bio::Phylo::Forest::Tree object.
Args    : None
Comment : If no default tree has been set, 
          returns first tree.

check_taxa()

Validates taxon links of nodes in invocant's trees.

Type    : Method
Title   : check_taxa
Usage   : $trees->check_taxa;
Function: Validates the taxon links of the
          nodes of the trees in $trees
Returns : A validated Bio::Phylo::Forest object.
Args    : None

make_matrix()

Creates an MRP matrix object.

Type    : Method
Title   : make_matrix
Usage   : my $matrix = $obj->make_matrix
Function: Creates an MRP matrix object
Returns : $matrix
Args    : NONE

make_taxa()

Creates a taxa block from the objects contents if none exists yet.

Type    : Method
Title   : make_taxa
Usage   : my $taxa = $obj->make_taxa
Function: Creates a taxa block from the objects contents if none exists yet.
Returns : $taxa
Args    : NONE

to_newick()

Serializes invocant to newick string.

Type    : Stringifier
Title   : to_newick
Usage   : my $string = $forest->to_newick;
Function: Turns the invocant forest object 
          into a newick string, one line per tree
Returns : SCALAR
Args    : The same arguments as 
          Bio::Phylo::Forest::Tree::to_newick

to_nexus()

Serializer to nexus format.

Type    : Format convertor
Title   : to_nexus
Usage   : my $data_block = $matrix->to_nexus;
Function: Converts matrix object into a nexus data block.
Returns : Nexus data block (SCALAR).
Args    : Trees can be formatted using the same arguments as those
          passed to Bio::Phylo::Unparsers::Newick. In addition, you
          can provide: 
          
          # as per mesquite's inter-block linking system (default is false):
          -links => 1 (to create a TITLE token, and a LINK token, if applicable)
          
          # rooting is determined based on basal trichotomy. "token" means 'TREE' or 'UTREE'
          # is used, "comment" means [&R] or [&U] is used, "nhx" means [%unrooted=on] or
          # [%unrooted=off] if used, default is "comment"
          -rooting => one of (token|comment|nhx)
          
          # to map taxon names to indices (default is false)
          -make_translate => 1 (autogenerate translation table, overrides -translate => {})
Comments:

INHERITED METHODS

Bio::Phylo::Forest inherits from one or more superclasses. This means that objects of class Bio::Phylo::Forest 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::Listable

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

add_set()

Type    : Mutator
Title   : add_set
Usage   : $obj->add_set($set)
Function: Associates a Bio::Phylo::Set object with the invocant
Returns : Invocant
Args    : A Bio::Phylo::Set object

add_to_set()

Type    : Mutator
Title   : add_to_set
Usage   : $listable->add_to_set($obj,$set);
Function: Adds first argument to the second argument
Returns : Invocant
Args    : $obj - an object to add to $set
          $set - the Bio::Phylo::Set object to add to
Notes   : this method assumes that $obj is already 
          part of the invocant. If that assumption is
          violated a warning message is printed.

can_contain()

Tests if argument can be inserted in invocant.

Type    : Test
Title   : can_contain
Usage   : &do_something if $listable->can_contain( $obj );
Function: Tests if $obj can be inserted in $listable
Returns : BOOL
Args    : An $obj to test

clear()

Empties container object.

Type    : Object method
Title   : clear
Usage   : $obj->clear();
Function: Clears the container.
Returns : A Bio::Phylo::Listable object.
Args    : Note.
Note    :

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.

contains()

Tests whether the invocant object contains the argument object.

Type    : Test
Title   : contains
Usage   : if ( $obj->contains( $other_obj ) ) {
              # do something
          }
Function: Tests whether the invocant object 
          contains the argument object
Returns : BOOLEAN
Args    : A Bio::Phylo::* object

cross_reference()

The cross_reference method links node and datum objects to the taxa they apply to. After crossreferencing a matrix with a taxa object, every datum object has a reference to a taxon object stored in its $datum->get_taxon field, and every taxon object has a list of references to datum objects stored in its $taxon->get_data field.

Type    : Generic method
Title   : cross_reference
Usage   : $obj->cross_reference($taxa);
Function: Crossreferences the entities 
          in the invocant with names 
          in $taxa
Returns : string
Args    : A Bio::Phylo::Taxa object
Comments:

current()

Returns the current focal element of the listable object.

Type    : Iterator
Title   : current
Usage   : my $current_obj = $obj->current;
Function: Retrieves the current focal 
          entity in the invocant.
Returns : A Bio::Phylo::* object
Args    : none.

current_index()

Returns the current internal index of the invocant.

Type    : Generic query
Title   : current_index
Usage   : my $last_index = $obj->current_index;
Function: Returns the current internal 
          index of the invocant.
Returns : An integer
Args    : none.

delete()

Deletes argument from invocant object.

Type    : Object method
Title   : delete
Usage   : $obj->delete($other_obj);
Function: Deletes an object from its container.
Returns : A Bio::Phylo::Listable object.
Args    : A Bio::Phylo::* object.
Note    : Be careful with this method: deleting 
          a node from a tree like this will 
          result in undefined references in its 
          neighbouring nodes. Its children will 
          have their parent reference become 
          undef (instead of pointing to their 
          grandparent, as collapsing a node would 
          do). The same is true for taxon objects 
          that reference datum objects: if the 
          datum object is deleted from a matrix 
          (say), the taxon will now hold undefined 
          references.

first()

Jumps to the first element contained by the listable object.

Type    : Iterator
Title   : first
Usage   : my $first_obj = $obj->first;
Function: Retrieves the first 
          entity in the invocant.
Returns : A Bio::Phylo::* object
Args    : none.

get_by_index()

Gets element defined by argument index from invocant container.

Type    : Query
Title   : get_by_index
Usage   : my $contained_obj = $obj->get_by_index($i);
Function: Retrieves the i'th entity 
          from a listable object.
Returns : An entity stored by a listable 
          object (or array ref for slices).
Args    : An index or range. This works 
          the way you dereference any perl
          array including through slices, 
          i.e. $obj->get_by_index(0 .. 10)>
          $obj->get_by_index(0, -1) 
          and so on.
Comments: Throws if out-of-bounds

get_by_name()

Gets first element that has argument name

Type    : Visitor predicate
Title   : get_by_name
Usage   : my $found = $obj->get_by_name('foo');
Function: Retrieves the first contained object
          in the current Bio::Phylo::Listable 
          object whose name is 'foo'
Returns : A Bio::Phylo::* object.
Args    : A name (string)

get_by_regular_expression()

Gets elements that match regular expression from invocant container.

Type    : Visitor predicate
Title   : get_by_regular_expression
Usage   : my @objects = @{ 
              $obj->get_by_regular_expression(
                   -value => $method,
                   -match => $re
           ) };
Function: Retrieves the data in the 
          current Bio::Phylo::Listable 
          object whose $method output 
          matches $re
Returns : A list of Bio::Phylo::* objects.
Args    : -value => any of the string 
                    datum props (e.g. 'get_type')
          -match => a compiled regular 
                    expression (e.g. qr/^[D|R]NA$/)

get_by_value()

Gets elements that meet numerical rule from invocant container.

Type    : Visitor predicate
Title   : get_by_value
Usage   : my @objects = @{ $obj->get_by_value(
             -value => $method,
             -ge    => $number
          ) };
Function: Iterates through all objects 
          contained by $obj and returns 
          those for which the output of 
          $method (e.g. get_tree_length) 
          is less than (-lt), less than 
          or equal to (-le), equal to 
          (-eq), greater than or equal to 
          (-ge), or greater than (-gt) $number.
Returns : A reference to an array of objects
Args    : -value => any of the numerical 
                    obj data (e.g. tree length)
          -lt    => less than
          -le    => less than or equals
          -eq    => equals
          -ge    => greater than or equals
          -gt    => greater than

get_entities()

Returns a reference to an array of objects contained by the listable object.

Type    : Generic query
Title   : get_entities
Usage   : my @entities = @{ $obj->get_entities };
Function: Retrieves all entities in the invocant.
Returns : A reference to a list of Bio::Phylo::* 
          objects.
Args    : none.

get_index_of()

Returns the index of the argument in the list, or undef if the list doesn't contain the argument

Type    : Generic query
Title   : get_index_of
Usage   : my $i = $listable->get_index_of($obj)
Function: Returns the index of the argument in the list,
          or undef if the list doesn't contain the argument
Returns : An index or undef
Args    : A contained object

get_sets()

Type    : Accessor
Title   : get_sets
Usage   : my @sets = @{ $obj->get_sets() };
Function: Retrieves all associated Bio::Phylo::Set objects
Returns : Invocant
Args    : None

insert()

Pushes an object into its container.

Type    : Object method
Title   : insert
Usage   : $obj->insert($other_obj);
Function: Pushes an object into its container.
Returns : A Bio::Phylo::Listable object.
Args    : A Bio::Phylo::* object.

insert_at_index()

Inserts argument object in invocant container at argument index.

Type    : Object method
Title   : insert_at_index
Usage   : $obj->insert_at_index($other_obj, $i);
Function: Inserts $other_obj at index $i in container $obj
Returns : A Bio::Phylo::Listable object.
Args    : A Bio::Phylo::* object.

is_in_set()

Type    : Test
Title   : is_in_set
Usage   : @do_something if $listable->is_in_set($obj,$set);
Function: Returns whether or not the first argument is listed in the second argument
Returns : Boolean
Args    : $obj - an object that may, or may not be in $set
          $set - the Bio::Phylo::Set object to query
Notes   : This method makes two assumptions:
          i) the $set object is associated with the invocant,
             i.e. add_set($set) has been called previously
          ii) the $obj object is part of the invocant
          If either assumption is violated a warning message
          is printed.

last()

Jumps to the last element contained by the listable object.

Type    : Iterator
Title   : last
Usage   : my $last_obj = $obj->last;
Function: Retrieves the last 
          entity in the invocant.
Returns : A Bio::Phylo::* object
Args    : none.

last_index()

Returns the highest valid index of the invocant.

Type    : Generic query
Title   : last_index
Usage   : my $last_index = $obj->last_index;
Function: Returns the highest valid 
          index of the invocant.
Returns : An integer
Args    : none.

next()

Returns the next focal element of the listable object.

Type    : Iterator
Title   : next
Usage   : my $next_obj = $obj->next;
Function: Retrieves the next focal 
          entity in the invocant.
Returns : A Bio::Phylo::* object
Args    : none.

notify_listeners()

Notifies listeners of changed contents.

Type    : Utility method
Title   : notify_listeners
Usage   : $object->notify_listeners;
Function: Notifies listeners of changed contents.
Returns : Invocant.
Args    : NONE.
Comments:

previous()

Returns the previous element of the listable object.

Type    : Iterator
Title   : previous
Usage   : my $previous_obj = $obj->previous;
Function: Retrieves the previous 
          focal entity in the invocant.
Returns : A Bio::Phylo::* object
Args    : none.

remove_from_set()

Type    : Mutator
Title   : remove_from_set
Usage   : $listable->remove_from_set($obj,$set);
Function: Removes first argument from the second argument
Returns : Invocant
Args    : $obj - an object to remove from $set
          $set - the Bio::Phylo::Set object to remove from
Notes   : this method assumes that $obj is already 
          part of the invocant. If that assumption is
          violated a warning message is printed.

remove_set()

Type    : Mutator
Title   : remove_set
Usage   : $obj->remove_set($set)
Function: Removes association between a Bio::Phylo::Set object and the invocant
Returns : Invocant
Args    : A Bio::Phylo::Set object

set_listener()

Attaches a listener (code ref) which is executed when contents change.

Type    : Utility method
Title   : set_listener
Usage   : $object->set_listener( sub { my $object = shift; } );
Function: Attaches a listener (code ref) which is executed when contents change.
Returns : Invocant.
Args    : A code reference.
Comments: When executed, the code reference will receive $object
          (the invocant) as its first argument.

visit()

Iterates over objects contained by invocant, executes argument code reference on each.

Type    : Visitor predicate
Title   : visit
Usage   : $obj->visit( 
              sub{ print $_[0]->get_name, "\n" } 
          );
Function: Implements visitor pattern 
          using code reference.
Returns : The invocant, possibly modified.
Args    : a CODE reference.

SUPERCLASS Bio::Phylo::Util::XMLWritable

Bio::Phylo::Forest 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()

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::Forest 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

SUPERCLASS Bio::Phylo::Taxa::TaxaLinker

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

check_taxa()

Performs sanity check on taxon relationships.

Type    : Interface method
Title   : check_taxa
Usage   : $obj->check_taxa
Function: Performs sanity check on taxon relationships
Returns : $obj
Args    : NONE

get_taxa()

Retrieves association between invocant and Bio::Phylo::Taxa object.

Type    : Accessor
Title   : get_taxa
Usage   : my $taxa = $obj->get_taxa;
Function: Retrieves the Bio::Phylo::Taxa
          object linked to the invocant.
Returns : Bio::Phylo::Taxa
Args    : NONE
Comments: This method returns the Bio::Phylo::Taxa
          object to which the invocant is linked.
          The returned object can therefore contain
          *more* taxa than are actually in the matrix.

make_taxa()

Creates a taxa block from the objects contents if none exists yet.

Type    : Decorated interface method
Title   : make_taxa
Usage   : my $taxa = $obj->make_taxa
Function: Creates a taxa block from the objects contents if none exists yet.
Returns : $taxa
Args    : NONE

set_taxa()

Associates invocant with Bio::Phylo::Taxa argument.

Type    : Mutator
Title   : set_taxa
Usage   : $obj->set_taxa( $taxa );
Function: Links the invocant object
          to a taxa object.
Returns : Modified $obj
Args    : A Bio::Phylo::Taxa object.

unset_taxa()

Removes association between invocant and Bio::Phylo::Taxa object.

Type    : Mutator
Title   : unset_taxa
Usage   : $obj->unset_taxa();
Function: Removes the link between invocant object and taxa
Returns : Modified $obj
Args    : NONE

REVISION

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

To install Bio::Phylo, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Bio::Phylo

CPAN shell

perl -MCPAN -e shell
install Bio::Phylo

For more information on module installation, please visit the detailed CPAN module installation guide.

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NAME

SYNOPSIS

DESCRIPTION

METHODS

CONSTRUCTOR

METHODS

INHERITED METHODS

SUPERCLASS Bio::Phylo::Listable

SUPERCLASS Bio::Phylo::Util::XMLWritable

SUPERCLASS Bio::Phylo

SUPERCLASS Bio::Phylo::Taxa::TaxaLinker

SEE ALSO

REVISION

Module Install Instructions