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)