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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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 [email protected]

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