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>