Bio::Phylo::Listable(3)

NAME
Bio::Phylo::Listable - List of things, super class for many objects

SYNOPSIS
 No direct usage, parent class. Methods documented here
 are available for all objects that inherit from it.

DESCRIPTION
A listable object is an object that contains multiple smaller objects of the same type. For example: a tree contains nodes, so it's a listable object.

This class contains methods that are useful for all listable objects: Matrices (i.e. sets of matrix objects), individual Matrix objects, Datum objects (i.e. character state sequences), Taxa, Forest, Tree and Node objects.

METHODS

  ARRAY METHODS

insert()
    Pushes an object into its container.

     Type    : Mutator
     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 container at argument index.

     Type    : Mutator
     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.

delete()
    Deletes argument from container.

     Type    : Mutator
     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.

clear()
    Empties container object.

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

keep_entities()
    Keeps the container's contents specified by an array reference of indices.

     Type    : Mutator
     Title   : keep_entities
     Usage   : $list->keep_entities([9,7,7,6]);
     Function: Keeps a subset of contents
     Returns : A Bio::Phylo::Listable object.
     Args    : An array reference of indices

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

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

  ITERATOR METHODS

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 container.
     Returns : A Bio::Phylo::* object
     Args    : none.

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 container.
     Returns : A Bio::Phylo::* object
     Args    : none.

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 container.
     Returns : A Bio::Phylo::* object
     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 container.
     Returns : A Bio::Phylo::* object
     Args    : none.

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 container.
     Returns : A Bio::Phylo::* object
     Args    : none.

current_index()
    Returns the current internal index of the container.

     Type    : Accessor
     Title   : current_index
     Usage   : my $last_index = $obj->current_index;
     Function: Returns the current internal
               index of the container or 0
     Returns : An integer
     Args    : none.

last_index()
    Returns the highest valid index of the container.

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

  UTILITY METHODS

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 container) as its first argument.

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:

  SETS MANAGEMENT
Many Bio::Phylo objects are segmented, i.e. they contain one or more subparts of the same type. For example, a matrix contains multiple rows; each row contains multiple cells; a tree contains nodes, and so on. (Segmented objects all inherit from Bio::Phylo::Listable, i.e. the class whose documentation you're reading here.) In many cases it is useful to be able to define subsets of the contents of segmented objects, for example sets of taxon objects inside a taxa block. The Bio::Phylo::Listable object allows this through a number of methods (add_set, remove_set, add_to_set, remove_from_set etc.). Those methods delegate the actual management of the set contents to the Bio::Phylo::Set object. Consult the documentation for Bio::Phylo::Set for a code sample.

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

set_sets()
     Type    : Mutator
     Title   : set_sets
     Usage   : $obj->set_sets([ $s1, $s2, $s3 ])
     Function: Assigns all Bio::Phylo::Set objects to the container
     Returns : Invocant
     Args    : An array ref of Bio::Phylo::Set objects

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

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 $set object is associated with the container,
                  i.e. add_set($set) has been called previously
               ii) the $obj object is part of the container
               If either assumption is violated a warning message
               is printed.

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 container. If that assumption is
               violated a warning message is printed.

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 container. If that assumption is
               violated a warning message is printed.

SEE ALSO
There is a mailing list at <https://groups.google.com/forum/#!forum/bio-phylo> for any user or developer questions and discussions.

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

  Objects inheriting from Bio::Phylo::Listable

Bio::Phylo::Forest
    Iterate over a set of trees.

Bio::Phylo::Forest::Tree
    Iterate over nodes in a tree.

Bio::Phylo::Forest::Node
    Iterate of children of a node.

Bio::Phylo::Matrices
    Iterate over a set of matrices.

Bio::Phylo::Matrices::Matrix
    Iterate over the datum objects in a matrix.

Bio::Phylo::Matrices::Datum
    Iterate over the characters in a datum.

Bio::Phylo::Taxa
    Iterate over a set of taxa.

  Superclasses

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

CITATION
If you use Bio::Phylo in published research, please cite it:

Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. <http://dx.doi.org/10.1186/1471-2105-12-63>