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


       Bio::Symbol::Symbol - A biological symbol


           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;


       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

       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.


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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::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

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

        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

        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

        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

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