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Summary

Bio::Symbol::AlphabetI - A Symbol Alphabet

Package variables

Included modules

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.

Methods

Methods description

 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

 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    : (optional) Array of Bio::Symbol::SymbolI objects

Methods code

sub alphabets {

    my ($self,@args) = @_;
    $self->throw_not_implemented();

}

sub contains {

   my ($self,@args) = @_;
   $self->throw_not_implemented();
}

# Other methods from BSANE - not sure if we will implement here or only in
# BioCORBA implementation

# Resolve symbols from the token string.
#    SymbolList to_symbol(in string tokens) raises ( IllegalSymbolException) ;

# Convinience method, which returns gap symbol that do not
# match with any other symbols in the alphabet.
#   Symbol get_gap_symbol() raises ( DoesNotExist) ;


# Returns a ambiguity symbol, which represent list of
# symbols. All symbols in a list must be members of
# this alphabet otherwise IllegalSymbolException is
# thrown.
# Symbol get_ambiguity( in SymbolList symbols) raises( IllegalSymbolException);


#  Returns a Symbol, which represents ordered list of symbols
#  given as a parameter. Each symbol in the list must be member of
#  different sub-alphabet in the order defined by the alphabets
#  attribute. For example, codons can be represented by a compound
#  Alphabet of three DNA Alphabets, in which case the get_symbol(
#  SymbolList[ a,g,t]) method of the Alphabet returns Symbol for
#  the codon agt.<p>

#  IllegalSymbolException is raised if members of symbols
#  are not Symbols over the alphabet defined by
#  get_alphabets()-method
#  Symbol get_symbol(in SymbolList symbols) raises(IllegalSymbolException) ;

1;

}

sub symbols {

   my ($self,@args) = @_;
   $self->throw_not_implemented();

}

General documentation

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