Bio::Symbol::Alphabet - DESCRIPTION of Object { my $alphabet = new Bio::Symbols::Alphabet(-symbols => [ @s ], -subalphabets => [ @alphas ] ); my @symbols = $alphabet->symbols; my @subalphas = $alphabet->alphabets; if( $alphabet->contains($symbol) ) { # do something } } 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.

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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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email jason@bioperl.org Describe contact details here Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::Symbol::Alphabet(); 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