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)