Bio::Phylo::ListableRole - Extra functionality for things that are lists
No direct usage, parent class. Methods documented here are available for all objects that inherit from it.
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.
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
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
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
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 $re Returns : A list of Bio::Phylo::* objects. Args : -value => any of the string datum props (e.g. 'get_type') -match => a compiled regular expression (e.g. qr/^[D|R]NA$/)
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
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)
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 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
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
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.
$datum->get_taxon
$taxon->get_data
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:
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:
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.
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
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.
Iterate over a set of trees.
Iterate over nodes in a tree.
Iterate of children of a node.
Iterate over a set of matrices.
Iterate over the datum objects in a matrix.
Iterate over the characters in a datum.
Iterate over a set of taxa.
This object inherits from Bio::Phylo::NeXML::Writable, so methods defined there are also applicable here.
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
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.