NAME

       Bio::Symbol::Symbol - A biological symbol

SYNOPSIS

           use Bio::Symbol::Symbol;
           my $thymine = Bio::Symbol::Symbol->new(-name => 'Thy',
                                                 -token=> 'T');
           my $a = Bio::Symbol::Symbol->new(-token => 'A' );
           my $u = Bio::Symbol::Symbol->new(-token => 'U' );
           my $g = Bio::Symbol::Symbol->new(-token => 'G' );

           my $M = Bio::Symbol::Symbol->new(-name  => 'Met',
                                           -token => 'M',
                                           -symbols => [ $a, $u, $g ]);

           my ($name,$token) = ($a->name, $a->token);
           my @symbols       = $a->symbols;
           my $matches       = $a->matches;

DESCRIPTION

       Symbol represents a single token in the sequence. Symbol can have multiple synonyms or
       matches within the same Alphabet, which makes possible to represent ambiguity codes and
       gaps.

       Symbols can be also composed from ordered list other symbols. For example, codons can be
       represented by single Symbol using a compound Alphabet made from three DNA Alphabets.

       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://github.com/bioperl/bioperl-live/issues

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::Symbol->new();
        Function: Builds a new Bio::Symbol::Symbol object
        Returns : Bio::Symbol::Symbol
        Args    : -name    => descriptive name (string) [e.g. Met]
                  -token   => Shorthand token (string)  [e.g. M]
                  -symbols => Symbols that make up this symbol (array) [e.g. AUG]
                  -matches => Alphabet in the event symbol is an ambiguity
                              code.

   name
        Title   : name
        Usage   : my $name = $symbol->name();
        Function: Get/Set Descriptive name for Symbol
        Returns : string
        Args    : (optional) string

   token
        Title   : token
        Usage   : my $token = $self->token();
        Function: Get/Set token for this symbol
        Example : Letter A,C,G,or T for a DNA alphabet Symbol
        Returns : string
        Args    : (optional) string

   symbols
        Title   : symbols
        Usage   : my @symbols = $self->symbols();
        Function: Get/Set Symbols this Symbol is composed from
        Example : Ambiguity symbols are made up > 1 base symbol
        Returns : Array of Bio::Symbol::SymbolI objects
        Args    : (optional) Array of Bio::Symbol::SymbolI objects

   matches
        Title   : matches
        Usage   : my $matchalphabet = $symbol->matches();
        Function: Get/Set (Sub) alphabet of symbols matched by this symbol
                  including the symbol itself (i.e. if symbol is DNA
                  ambiguity code W then the matches contains symbols for W
                  and T)
        Returns : Bio::Symbol::AlphabetI
        Args    : (optional) Bio::Symbol::AlphabetI

   equals
        Title   : equals
        Usage   : if( $symbol->equals($symbol2) ) { }
        Function: Tests if a symbol is equal to another
        Returns : Boolean
        Args    : Bio::Symbol::SymbolI