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

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AUTHOR - Jason Stajich

Email jason@bioperl.org

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

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>