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