Bio::Symbol::Symbol(3pm)				User Contributed Perl Documentation				  Bio::Symbol::Symbol(3pm)

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://redmine.open-bio.org/projects/bioperl/

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

perl v5.14.2							    2012-03-02						  Bio::Symbol::Symbol(3pm)