Bio::Phylo::Matrices::Characters - Container of character objects

Bio-Phylo documentation Contained in the Bio-Phylo distribution.

Index

Code Index:

NAME

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Bio::Phylo::Matrices::Characters - Container of character objects

SYNOPSIS

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 # No direct usage

DESCRIPTION

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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.

METHODS

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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

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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

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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

REVISION

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 $Id: Characters.pm 1660 2011-04-02 18:29:40Z rvos $
Bio-Phylo documentation Contained in the Bio-Phylo distribution. 
package Bio::Phylo::Matrices::Characters;
use strict;
use base 'Bio::Phylo::Matrices::TypeSafeData';
use Bio::Phylo::Util::CONSTANT qw'_CHARACTERS_ _NONE_';
use Bio::Phylo::Factory;


sub to_xml {
    my $self = shift;
    my $xml = '';
    for my $ent ( @{ $self->get_entities } ) {
        $xml .= $ent->to_xml;
    }
    $xml .= $self->sets_to_xml;
    return $xml;
}
sub _validate  { 1 }
sub _container { _NONE_ }
sub _type      { _CHARACTERS_ }
sub _tag       { undef }


# podinherit_insert_token


1;