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LEARN ABOUT DEBIAN

bio::symbol::alphabet

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

NAME

       Bio::Symbol::Alphabet - BSANE/BioCORBA compliant symbol list alphabet

SYNOPSIS

	 {
	     my $alphabet = Bio::Symbols::Alphabet->new(-symbols => [ @s ],
						       -subalphabets => [ @alphas ] );

	     my @symbols = $alphabet->symbols;
	     my @subalphas = $alphabet->alphabets;
	     if( $alphabet->contains($symbol) ) {
		 # do something
	     }
	 }

DESCRIPTION

       Alphabet contains set of symbols, which can be concatenated to form symbol lists. Sequence string, for example, is stringified
       representation of the symbol list (tokens of symbols).

       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::Alphabet->new();
	Function: Builds a new Bio::Symbol::Alphabet object
	Returns : Bio::Symbol::Alphabet
	Args	: -symbols  => Array ref of Bio::Symbol::SymbolI objects
		  -subalphas=> Array ref of Bio::Symbol::AlphabetI objects
			       representing sub alphabets

   AlphabetI Interface methods
   symbols
	Title	: symbols
	Usage	: my @symbols = $alphabet->symbols();
	Function: Get/Set Symbol list for an alphabet
		  List of symbols, which make up this alphabet.
	Returns : Array of Bio::Symbol::SymbolI objects
	Args	: (optionalalphabets) Array of Bio::Symbol::SymbolI objects

   alphabets
	Title	: alphabets
	Usage	: my @alphabets = $alphabet->alphabets();
	Function: Get/Set Sub Alphabet list for an alphabet
		  Sub-alphabets. E.g. codons made from DNAxDNAxDNA alphabets
	Returns : Array of Bio::Symbol::AlphabetI objects
	Args	: (optional) Array of Bio::Symbol::AlphabetI objects

   contains
	Title	: contains
	Usage	: if($alphabet->contains($symbol)) { }
	Function: Tests of Symbol is contained in this alphabet
	Returns : Boolean
	Args	: Bio::Symbol::SymbolI

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