Bio::Phylo::Matrices::Datatype::Rna - Validator subclass,

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

Index

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NAME

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Bio::Phylo::Matrices::Datatype::Rna - Validator subclass, no serviceable parts inside

DESCRIPTION

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The Bio::Phylo::Matrices::Datatype::* classes are used to validate data contained by Bio::Phylo::Matrices::Matrix and Bio::Phylo::Matrices::Datum objects.

SEE ALSO

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Bio::Phylo::Matrices::Datatype

This class subclasses Bio::Phylo::Matrices::Datatype.

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: Rna.pm 1660 2011-04-02 18:29:40Z rvos $
Bio-Phylo documentation Contained in the Bio-Phylo distribution. 
# $Id: Rna.pm 1660 2011-04-02 18:29:40Z rvos $
package Bio::Phylo::Matrices::Datatype::Rna;
use strict;
use base 'Bio::Phylo::Matrices::Datatype';
our ( $LOOKUP, $MISSING, $GAP );


# podinherit_insert_token


$LOOKUP = {
    'A' => ['A'],
    'C' => ['C'],
    'G' => ['G'],
    'U' => ['U'],
    'M' => [ 'A', 'C' ],
    'R' => [ 'A', 'G' ],
    'W' => [ 'A', 'U' ],
    'S' => [ 'C', 'G' ],
    'Y' => [ 'C', 'U' ],
    'K' => [ 'G', 'U' ],
    'V' => [ 'A', 'C', 'G' ],
    'H' => [ 'A', 'C', 'U' ],
    'D' => [ 'A', 'G', 'U' ],
    'B' => [ 'C', 'G', 'U' ],
    'X' => [ 'G', 'A', 'U', 'C' ],
    'N' => [ 'G', 'A', 'U', 'C' ],
};
$MISSING = '?';
$GAP     = '-';
1;