Provided by: libbio-perl-perl_1.7.2-3_all bug


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


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

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


       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.


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AUTHOR - Jason Stajich



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

        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
        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

        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

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