Rutger Vos > Bio-Phylo-0.55 > Bio::Phylo::Matrices::Character

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Source   Latest Release: Bio-Phylo-0.58

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

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