NAME

Bio::Phylo::ListableRole - Extra functionality for things that are lists

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

prune_entities()

Prunes the container's contents specified by an array reference of indices.

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

get_index_of()

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

Type    : Accessor
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_by_index()

Gets element at index from container.

Type    : Accessor
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_regular_expression()

Gets elements that match regular expression from container.

Type    : Accessor
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 container.

Type    : Accessor
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_name()

Gets first element that has argument name

Type    : Accessor
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)

VISITOR METHODS

visit()

Iterates over objects contained by container, 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 container, possibly modified.
Args    : a CODE reference.

TESTS

contains()

Tests whether the container object contains the argument object.

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

can_contain()

Tests if argument can be inserted in container.

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

UTILITY METHODS

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 container with names 
          in $taxa
Returns : string
Args    : A Bio::Phylo::Taxa object
Comments:

alphabetize()

Sorts the contents alphabetically by their name.

Type    : Generic method
Title   : alphabetize
Usage   : $obj->alphabetize;
Function: Sorts the contents alphabetically by their name.
Returns : $self
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.

sets_to_xml()

Returns string representation of sets

Type    : Accessor
Title   : sets_to_xml
Usage   : my $str = $obj->sets_to_xml;
Function: Gets xml string
Returns : Scalar
Args    : None

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