Bio::Phylo::Matrices::Characters - Container of character objects
# No direct usage
Objects of this type hold a list of Bio::Phylo::Matrices::Character objects, i.e. columns in a matrix. By default, a matrix will be initialized to hold one object of this type (which can be retrieved using $matrix->get_characters). Its main function is to facilitate NeXML serialization of matrix objects, though this may expand in the future.
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 : Optional: a hash of code references to
override reflection-based getter/setter copying
my $clone = $object->clone(
'set_forest' => sub {
my ( $self, $clone ) = @_;
for my $forest ( @{ $self->get_forests } ) {
$clone->set_forest( $forest );
}
},
'set_matrix' => sub {
my ( $self, $clone ) = @_;
for my $matrix ( @{ $self->get_matrices } ) {
$clone->set_matrix( $matrix );
}
);
Comments: Cloning is currently experimental, use with caution.
It works on the assumption that the output of get_foo
called on the invocant is to be provided as argument
to set_foo on the clone - such as
$clone->set_name( $self->get_name ). Sometimes this
doesn't work, for example where this symmetry doesn't
exist, or where the return value of get_foo isn't valid
input for set_foo. If such a copy fails, a warning is
emitted. To make sure all relevant attributes are copied
into the clone, additional code references can be
provided, as in the example above. Typically, this is
done by overrides of this method in child classes.
Serializes characters to nexml format.
Type : Format convertor Title : to_xml Usage : my $xml = $characters->to_xml; Function: Converts characters object into a nexml element structure. Returns : Nexml block (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.
This object inherits from Bio::Phylo::Matrices::TypeSafeData, so the methods defined therein are also applicable to characters objects objects.
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.
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
