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

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

Index

Code Index:

NAME

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Bio::Phylo::Matrices::Datatype::Protein - 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

FORUM

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CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo

REVISION

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


# podinherit_insert_token


$LOOKUP = {
    'A' => ['A'],
    'B' => [ 'D', 'N' ],
    'C' => ['C'],
    'D' => ['D'],
    'E' => ['E'],
    'F' => ['F'],
    'G' => ['G'],
    'H' => ['H'],
    'I' => ['I'],
    'K' => ['K'],
    'L' => ['L'],
    'M' => ['M'],
    'N' => ['N'],
    'P' => ['P'],
    'Q' => ['Q'],
    'R' => ['R'],
    'S' => ['S'],
    'T' => ['T'],
    'U' => ['U'],
    'V' => ['V'],
    'W' => ['W'],
    'X' => ['X'],
    'Y' => ['Y'],
    'Z' => [ 'E', 'Q' ],
    '*' => ['*'],
};
$MISSING = '?';
$GAP     = '-';
1;