Bio::Symbol::Alphabet - DESCRIPTION of Object
{ my $alphabet = new Bio::Symbols::Alphabet(-symbols => [ @s ], -subalphabets => [ @alphas ] ); my @symbols = $alphabet->symbols; my @subalphas = $alphabet->alphabets; if( $alphabet->contains($symbol) ) { # do something } }
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.
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/MailList.shtml - About the mailing lists
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 email or the web:
bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/
Email jason@bioperl.org
Describe contact details here
Additional contributors names and emails here
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = new Bio::Symbol::Alphabet(); 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
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
Title : alphabets Usage : my @alphabets = $alphabet->alphabets(); Function: Get/Set Sub Alphabet list for an alphabet Sub-alphabets. E.g. codons made from DNAxDNAxDNA alphabets Returns : Array of Bio::Symbol::AlphabetI objects Args : (optional) Array of Bio::Symbol::AlphabetI objects
Title : contains Usage : if($alphabet->contains($symbol)) { } Function: Tests of Symbol is contained in this alphabet Returns : Boolean Args : Bio::Symbol::SymbolI
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.