Bio::Phylo::Matrices::Character(3)

NAME
Bio::Phylo::Matrices::Character - A character (column) in a matrix

SYNOPSIS
 # No direct usage

DESCRIPTION
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.

METHODS

  MUTATORS

set_weight()
     Type    : Mutator
     Title   : set_weight
     Usage   : $character->set_weight(2);
     Function: Sets character weight
     Returns : $self
     Args    : A number

set_codonpos()
     Type    : Mutator
     Title   : set_codonpos
     Usage   : $character->set_codonpos(2);
     Function: Sets codon position for the column
     Returns : $self
     Args    : A number

  ACCESSORS

get_weight()
     Type    : Accessor
     Title   : get_weight
     Usage   : my $weight = $character->get_weight();
     Function: Gets character weight
     Returns : A number (default is 1)
     Args    : NONE

get_codonpos()
     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

  SERIALIZERS

to_xml()
    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

SEE ALSO
There is a mailing list at <https://groups.google.com/forum/#!forum/bio-phylo> for any user or developer questions and discussions.

Bio::Phylo::Matrices::TypeSafeData
    This object inherits from Bio::Phylo::Matrices::TypeSafeData, so the methods defined therein are also applicable to characters objects objects.

Bio::Phylo::Manual
    Also see the manual: Bio::Phylo::Manual and <http://rutgervos.blogspot.com>.

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>