NAME

       Bio::Symbol::Alphabet - BSANE/BioCORBA compliant symbol list alphabet

SYNOPSIS

         {
             my $alphabet = Bio::Symbols::Alphabet->new(-symbols => [ @s ],
                                                       -subalphabets => [ @alphas ] );

             my @symbols = $alphabet->symbols;
             my @subalphas = $alphabet->alphabets;
             if( $alphabet->contains($symbol) ) {
                 # do something
             }
         }

DESCRIPTION

       Alphabet contains set of symbols, which can be concatenated to form symbol lists. Sequence
       string, for example, is stringified representation of the symbol list (tokens of symbols).

       This module was implemented for the purposes of meeting the BSANE/BioCORBA spec 0.3 only.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich

       Email jason@bioperl.org

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   new
        Title   : new
        Usage   : my $obj = Bio::Symbol::Alphabet->new();
        Function: Builds a new Bio::Symbol::Alphabet object
        Returns : Bio::Symbol::Alphabet
        Args    : -symbols  => Array ref of Bio::Symbol::SymbolI objects
                  -subalphas=> Array ref of Bio::Symbol::AlphabetI objects
                               representing sub alphabets

   AlphabetI Interface methods
   symbols
        Title   : symbols
        Usage   : my @symbols = $alphabet->symbols();
        Function: Get/Set Symbol list for an alphabet
                  List of symbols, which make up this alphabet.
        Returns : Array of Bio::Symbol::SymbolI objects
        Args    : (optionalalphabets) Array of Bio::Symbol::SymbolI objects

   alphabets
        Title   : alphabets
        Usage   : my @alphabets = $alphabet->alphabets();
        Function: Get/Set Sub Alphabet list for an alphabet
                  Sub-alphabets. E.g. codons made from DNAxDNAxDNA alphabets
        Returns : Array of Bio::Symbol::AlphabetI objects
        Args    : (optional) Array of Bio::Symbol::AlphabetI objects

   contains
        Title   : contains
        Usage   : if($alphabet->contains($symbol)) { }
        Function: Tests of Symbol is contained in this alphabet
        Returns : Boolean
        Args    : Bio::Symbol::SymbolI