Bio::Phylo::Matrices::Character - A character (column) in a matrix
# No direct usage
Objects of this type represent a single character in a matrix. By default, a matrix will adjust the number of such objects it requires automatically as its contents grow or shrink. The main function, at present, for objects of this type is to facilitate NeXML serialization of characters and their annotations.
Type : Mutator Title : set_weight Usage : $character->set_weight(2); Function: Sets character weight Returns : $self Args : A number
Type : Mutator Title : set_codonpos Usage : $character->set_codonpos(2); Function: Sets codon position for the column Returns : $self Args : A number
Type : Accessor Title : get_weight Usage : my $weight = $character->get_weight(); Function: Gets character weight Returns : A number (default is 1) Args : NONE
Type : Mutator Title : get_codonpos Usage : my $pos = $character->get_codonpos; Function: Gets codon position for the column Returns : 1, 2, 3 or undef Args : None
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
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.