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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email [email protected]

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