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Christopher Fields > BioPerl > Bio::Symbol::AlphabetI



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Module Version: 1.007002   Source  


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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Please direct usage questions or support issues to the mailing list:

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.

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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:

AUTHOR - Jason Stajich ^



The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

AlphabetI Interface methods


 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>
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