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

NAME

       Bio::Symbol::AlphabetI - A Symbol Alphabet

SYNOPSIS

	   # get a Bio::Symbol::AlphabetI object somehow
	   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 _

   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 L<Bio::Symbol::SymbolI> objects
	Args	: (optional) Array of L<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 L<Bio::Symbol::AlphabetI> objects
	Args	: (optional) Array of L<Bio::Symbol::AlphabetI> objects

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

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