/ 
Bio-Phylo-0.10
River stage two • 9 direct dependents • 18 total dependents
/ Bio::Phylo::Listable

NAME

Bio::Phylo::Listable - Parent class for listable/iterator 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, Matrix objects, Alignment objects, Taxa, Forest, Tree objects.

METHODS

CONSTRUCTOR

new()
Type    : Constructor
Title   : new
Usage   : my $obj = Bio::Phylo::Listable->new;
Function: Instantiates a Bio::Phylo::Listable object
Returns : A Bio::Phylo::Listable object.
Args    : none

ARRAY METHODS

insert()
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.
delete()
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.
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:
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.
contains()
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

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 invocant.
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 invocant.
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 invocant.
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 invocant.
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 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.
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.
get_by_index()

The get_by_index method is used to retrieve the i'th entity contained by a listable object.

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. C<$obj-E<gt>get_by_index(0 .. 10)>
          C<$obj-E<gt>get_by_index(0, -1)> 
          and so on.
Comments: Throws if out-of-bounds

VISITOR METHODS

get_by_value()

The get_by_value method can be used to filter out objects contained by the listable object that meet a numerical condition.

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_by_regular_expression()

The get_by_regular_expression method can be used to filter out objects contained by the listable object that match a regular expression.

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 $re
Returns : A list of Bio::Phylo::* objects.
Args    : -value => any of the string 
                    datum props (e.g. 'get_type')
          -match => a compiled regular 
                    expression (e.g. qr/^[D|R]NA$/)
visit()

The visit method can be used to iterate over all objects in the Listable object. At every iteration, the CODE reference in the argument is applied to the focal object. The object enters the CODE reference as $_[0]. The objects are visited in the order in which they were inserted in the Listable object.

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.

DESTRUCTOR

DESTROY()
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.

SEE ALSO

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::Matrices

Iterate over a set of matrices.

Bio::Phylo::Matrices::Matrix

Iterate over the datum objects in a matrix.

Bio::Phylo::Matrices::Alignment

Iterate over the sequences in an alignment.

Bio::Phylo::Taxa

Iterate over a set of taxa.

Superclass

Bio::Phylo

The listable class inherits from Bio::Phylo, so look there for more methods applicable to Bio::Phylo::Listable objects and subclasses.

Also see the manual: Bio::Phylo::Manual.

FORUM

CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo

BUGS

Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:

$Id: Listable.pm,v 1.31 2006/04/12 22:38:22 rvosa Exp $

AUTHOR

Rutger Vos,

email: rvosa@sfu.ca
web page: http://www.sfu.ca/~rvosa/

ACKNOWLEDGEMENTS

The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.

COPYRIGHT & LICENSE

Copyright 2005 Rutger Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.