Bio::Symbol::AlphabetI - A Symbol Alphabet
# get a Bio::Symbol::AlphabetI object somehow 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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
Title : alphabets Usage : my @alphabets = $alphabet->alphabets(); Function: Get/Set Sub Alphabet list for an alphabet Sub-alphabets. E.g. codons made from DNAxDNAxDNA alphabets Returns : Array of L<Bio::Symbol::AlphabetI> objects Args : (optional) Array of L<Bio::Symbol::AlphabetI> objects
Title : contains Usage : if($alphabet->contains($symbol)) { } Function: Tests of Symbol is contained in this alphabet Returns : Boolean Args : L<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.