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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:

   http://bugzilla.open-bio.org/
 
 

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>