Christopher Fields > BioPerl-1.6.901 > Bio::Symbol::Symbol



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Module Version: 1.006901   Source   Latest Release: BioPerl-1.6.924


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 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.


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

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:

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
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