Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)


Bio::Symbol::SymbolI - Interface for a Symbol


     # get a Bio::Symbol::SymbolI object somehow
     my ($name,$token) = ($symbol->name, $symbol->token);
     my @symbols       = $symbol->symbols;
     my $matches       = $symbol->matches;


Symbol represents a single token in the sequence. Symbol can have multiple synonyms or matches within the same Alphabet, which makes possible to represent ambiguity codes and gaps.

Symbols can be also composed from ordered list other symbols. For example, codons can be represented by single Symbol using a compound Alphabet made from three DNA Alphabets.

This module was implemented for the purposes of meeting the BSANE/BioCORBA spec 0.3 only.


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AUTHOR - Jason Stajich



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

Bio::Symbol::SymbolI interface methods


  Title   : name
  Usage   : my $name = $symbol->name();
  Function: Get/Set Descriptive name for Symbol
  Returns : string
  Args    : (optional) string


  Title   : token
  Usage   : my $token = $self->token();
  Function: Get/Set token for this symbol
  Example : Letter A,C,G,or T for a DNA alphabet Symbol
  Returns : string
  Args    : (optional) string


  Title   : symbols
  Usage   : my @symbols = $self->symbols();
  Function: Get/Set Symbols this Symbol is composed from
  Example : A codon is composed of 3 DNA symbols
  Returns : Array of Bio::Symbol::SymbolI objects
  Args    : (optional) Array of Bio::Symbol::SymbolI objects


  Title   : matches
  Usage   : my $matchalphabet = $symbol->matches();
  Function: Get/Set (Sub) alphabet of symbols matched by this symbol
            including the symbol itself (i.e. if symbol is DNA
            ambiguity code W then the matches contains symbols for W
            and T)
  Returns : Bio::Symbol::AlphabetI
  Args    : (optional) Bio::Symbol::AlphabetI


  Title   : equals
  Usage   : if( $symbol->equals($symbol2) ) { }
  Function: Tests if a symbol is equal to another 
  Returns : Boolean
  Args    : Bio::Symbol::SymbolI